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Bibliography on: The Denisovans, Another Human Ancestor

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The Denisovans, Another Human Ancestor

Wikipedia: The Denisovans are an extinct species or subspecies of human in the genus Homo. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. Two teeth belonging to different members of the same population have since been reported. In November 2015, a tooth fossil containing DNA was reported to have been found and studied. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known. Analysis of the mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from the mtDNAs of Neanderthals and modern humans. Subsequent study of the nuclear genome from this specimen suggests that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans. A comparison with the genome of a Neanderthal from the same cave revealed significant local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, while evidence was also detected of interbreeding with an as yet unidentified ancient human lineage.

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Citations The Papers (from PubMed®)


RevDate: 2021-08-27

Deņisova A, Pilmane M, Eņģelis A, et al (2021)

Gallbladder Interleukins in Children with Calculous Cholecystitis.

Pediatric reports, 13(3):470-482 pii:pediatric13030054.

Calculous cholecystitis connects to inflammation and various complications. It is a common disease in the paediatric population, yet it is still uncertain how inflammation factors are involved in its morphopathogenesis. Twenty calculous cholecystitis surgery tissue samples were obtained from 20 children. As a control, seven unaffected gallbladders were used. Tissues were immunohistochemically stained for IL-1α, IL-4, IL-6, IL-7, IL-8, IL-10, and IL-17A, and the slides were inspected by light microscopy. To evaluate statistical differences and correlations between interleukins, Mann-Whitney U and Spearman's tests were used. Statistically significant difference between patient and control gallbladder epithelium was for IL-1α and IL-17A, but connective tissue-IL-1α, IL-4, IL-6, IL-7, IL-8, and IL-17A positive structures. A strong positive correlation in patients was detected between epithelial IL-1α and IL-1α in connective tissue, epithelial IL-6 and IL-7, IL-6 and IL-17A, IL-7 and IL-10, IL-7 and IL-17A, as well as between IL-6 and IL-7, IL-7 and IL-10 in connective tissue. The increase of IL-1α, IL-4, IL-6, IL-7, IL-8 and IL-17A positive structures suggests their role in the morphopathogenesis of calculous cholecystitis. The correlations between interleukins in epithelium and in connective tissues prove that the epithelial barrier function and inflammatory response in deeper layers are sustained through intercellular signalling pathways.

RevDate: 2021-08-27

Sobolev V, Nesterova A, Soboleva A, et al (2021)

Analysis of PPARγ Signaling Activity in Psoriasis.

International journal of molecular sciences, 22(16): pii:ijms22168603.

In our previous work, we built the model of PPARγ dependent pathways involved in the development of the psoriatic lesions. Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor and transcription factor which regulates the expression of many proinflammatory genes. We tested the hypothesis that low levels of PPARγ expression promote the development of psoriatic lesions triggering the IL17-related signaling cascade. Skin samples of normally looking and lesional skin donated by psoriasis patients and psoriatic CD3+ Tcells samples (n = 23) and samples of healthy CD3+ T cells donated by volunteers (n = 10) were analyzed by real-time PCR, ELISA and immunohistochemistry analysis. We found that the expression of PPARγ is downregulated in human psoriatic skin and laser treatment restores the expression. The expression of IL17, STAT3, FOXP3, and RORC in psoriatic skin before and after laser treatment were correlated with PPARγ expression according to the reconstructed model of PPARγ pathway in psoriasis.In conclusion, we report that PPARγ weakens the expression of genes that contribute in the development of psoriatic lesion. Our data show that transcriptional regulation of PPARγ expression by FOSL1 and by STAT3/FOSL1 feedback loop may be central in the psoriatic skin and T-cells.

RevDate: 2021-08-26

Carlhoff S, Duli A, Nägele K, et al (2021)

Genome of a middle Holocene hunter-gatherer from Wallacea.

Nature, 596(7873):543-547.

Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

RevDate: 2021-08-13

Larena M, McKenna J, Sanchez-Quinto F, et al (2021)

Philippine Ayta possess the highest level of Denisovan ancestry in the world.

Current biology : CB pii:S0960-9822(21)00977-5 [Epub ahead of print].

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world-∼30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

RevDate: 2021-08-02

Brown S, Wang N, Oertle A, et al (2021)

Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave.

Scientific reports, 11(1):15457.

Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.

RevDate: 2021-08-01

Condemi S, Mazières S, Faux P, et al (2021)

Blood groups of Neandertals and Denisova decrypted.

PloS one, 16(7):e0254175.

Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual's entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.

RevDate: 2021-08-03

Schaefer NK, Shapiro B, RE Green (2021)

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.

Science advances, 7(29):.

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.

RevDate: 2021-07-04

Bezverbnaya K, Moogk D, Cummings D, et al (2021)

Development of a B-cell maturation antigen-specific T-cell antigen coupler receptor for multiple myeloma.

Cytotherapy pii:S1465-3249(21)00687-3 [Epub ahead of print].

BACKGROUND AIMS: T cells engineered with synthetic receptors have delivered powerful therapeutic results for patients with relapsed/refractory hematologic malignancies. The authors have recently described the T-cell antigen coupler (TAC) receptor, which co-opts the endogenous T-cell receptor (TCR) and activates engineered T cells in an HLA-independent manner. Here the authors describe the evolution of a next-generation TAC receptor with a focus on developing a TAC-engineered T cell for multiple myeloma.

METHODS: To optimize the TAC scaffold, the authors employed a bona fide antigen-binding domain derived from the B-cell maturation antigen-specific monoclonal antibody C11D5.3, which has been used successfully in the clinic. The authors first tested humanized versions of the UCHT1 domain, which is used by the TAC to co-opt the TCR. The authors further discovered that the signal peptide affected surface expression of the TAC receptor. Higher density of the TAC receptor enhanced target binding in vitro, which translated into higher levels of Lck at the immunological synapse and stronger proliferation when only receptor-ligand interactions were present.

RESULTS: The authors observed that the humanized UCHT1 improved surface expression and in vivo efficacy. Using TAC T cells derived from both healthy donors and multiple myeloma patients, the authors determined that despite the influence of receptor density on early activation events and effector function, receptor density did not impact late effector functions in vitro, nor did the receptor density affect in vivo efficacy.

CONCLUSIONS: The modifications to the TAC scaffold described herein represent an important step in the evolution of this technology, which tolerates a range of expression levels without impacting therapeutic efficacy.

RevDate: 2021-07-07
CmpDate: 2021-07-07

Gibbons A (2021)

'Dragon Man' may be an elusive Denisovan.

Science (New York, N.Y.), 373(6550):11-12.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Sudarkina OY, Filippenkov IB, Stavchansky VV, et al (2021)

Brain Protein Expression Profile Confirms the Protective Effect of the ACTH(4-7)PGP Peptide (Semax) in a Rat Model of Cerebral Ischemia-Reperfusion.

International journal of molecular sciences, 22(12):.

The Semax (Met-Glu-His-Phe-Pro-Gly-Pro) peptide is a synthetic melanocortin derivative that is used in the treatment of ischemic stroke. Previously, studies of the molecular mechanisms underlying the actions of Semax using models of cerebral ischemia in rats showed that the peptide enhanced the transcription of neurotrophins and their receptors and modulated the expression of genes involved in the immune response. A genome-wide RNA-Seq analysis revealed that, in the rat transient middle cerebral artery occlusion (tMCAO) model, Semax suppressed the expression of inflammatory genes and activated the expression of neurotransmitter genes. Here, we aimed to evaluate the effect of Semax in this model via the brain expression profiling of key proteins involved in inflammation and cell death processes (MMP-9, c-Fos, and JNK), as well as neuroprotection and recovery (CREB) in stroke. At 24 h after tMCAO, we observed the upregulation of active CREB in subcortical structures, including the focus of the ischemic damage; downregulation of MMP-9 and c-Fos in the adjacent frontoparietal cortex; and downregulation of active JNK in both tissues under the action of Semax. Moreover, a regulatory network was constructed. In conclusion, the suppression of inflammatory and cell death processes and the activation of recovery may contribute to the neuroprotective action of Semax at both the transcriptome and protein levels.

RevDate: 2021-06-29

Graham F (2021)

Daily briefing: DNA in Denisova Cave soil records several human species.

RevDate: 2021-07-27

Zavala EI, Jacobs Z, Vernot B, et al (2021)

Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.

Nature, 595(7867):399-403.

Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1-4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8-11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.

RevDate: 2021-06-22

Amos W (2021)

Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.

Royal Society open science, 8(6):201229.

Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/'hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar 'double' trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32, 2665-2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two 'out of Africa' events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.

RevDate: 2021-06-09
CmpDate: 2021-06-09

Dergunova LV, Dmitrieva VG, Filippenkov IB, et al (2021)

[The Peptide Drug ACTH(4-7)PGP (Semax) Suppresses mRNA Transcripts Encoding Proinflammatory Mediators Induced by Reversible Ischemia of the Rat Brain].

Molekuliarnaia biologiia, 55(3):402-411.

Due to its nootropic, neuroprotective, and immunomodulatory effects, the peptide Semax is utilized in the treatment of ischemic stroke. Our earlier RNA-Seq analysis of the transcriptome in an ischemic model of transient occlusion of the middle cerebral artery showed an increase in the mRNA levels of many proinflammatory genes, and the suppression of their induction by Semax. However, for many relevant genes, including Il1a, Il1b, Il6 and Tnfa, the levels of their expression were too low for detailed quantitative evaluation. Here we utilize qRT-PCR to analyze the effects of the Semax peptide on the expression of weakly expressed mRNAs encoding several proinflammatory mediators, and show that exposure to Semax leads to a statistically significant decrease in the Il1a, Il1b, Il6, Ccl3, and Cxcl2 mRNAs, which compensates for the increase in the transcription of these genes induced by ischemia-reperfusion. We conclude that the observed protective effect of Semax in the model of stroke may be due to its anti-inflammatory effects. We also discuss the limitations of the RNA-Seq when applied to quantifying less abundant transcripts as compared to the real-time RT-PCR method.

RevDate: 2021-06-08

Zhou Y, SR Browning (2021)

Protocol for detecting introgressed archaic variants with SPrime.

STAR protocols, 2(2):100550.

The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).

RevDate: 2021-06-11

Shtratnikova V, Naumov V, Bezuglov V, et al (2021)

Optimization of small RNA extraction and comparative study of NGS library preparation from low count sperm samples.

Systems biology in reproductive medicine, 67(3):230-243.

Recent studies demonstrate that sperm epigenome is a vehicle that conveys paternal experiences to offspring phenotype. That evidence triggers interest of both experimental and epidemiological studies of epigenetic markers in sperm. Since samples are often unique in epidemiological studies, a careful and efficient use of the material is a critical requirement. The goal of this study was to provide optimization of methods for the isolation of small RNAs from spermatozoa and library preparation for sequencing. A total 67 fractionated sperm samples from the Russian Children's Study biobank prospectively collected at 18-20 years of age were used to isolate small RNAs with median (IQR) input total sperm count 17.0 (7.4-35.9) million. Twenty-four pairs of libraries were prepared using the NEBNext and NEXTFlex kits, 19 libraries using NEBNext and 6 using NEXTFlex. All libraries were sequenced on NextSeq 500, and the results were evaluated as a function of the number of small non-coding RNA (sncRNA) detected, quality parameters of sequencing libraries, as well as technical features of sample preparation. Although the same amount of miRNA input was used for NEBNext and NEXTFlex libraries, the concentration of DNA in NEBNext libraries was significantly higher in comparison with NEXTFlex libraries. In high input (sperm count >28 million and more than 25 ng miRNA in library) NEXTFlex Small RNA-Seq kit detected more microRNAs. In low input, the NEBNext proved more effective. The tricks and traps to protocol optimization are presented, including an efficient and effector gel-based system for the removal of sequencing library adaptors.

RevDate: 2021-06-15

Denisova YI, Shandryuk GA, Arinina MP, et al (2021)

Multiblock Copolymers of Norbornene and Cyclododecene: Chain Structure and Properties.

Polymers, 13(11):.

We investigate the structure-property relations of the multiblock copolymers of norbornene with cyclododecene synthesized via the macromolecular cross-metathesis reaction between amorphous polynorbornene and semicrystalline polydodecenamer in the presence of the first-generation Grubbs catalyst. By adjusting the reaction time, catalyst amount, and composition of the initial system, we obtain a set of statistical multiblock copolymers that differ in the composition and average length of norbornene and dodecenylene unit sequences. Structural, thermal, and mechanical characterization of the copolymers with NMR, XRD, DSC (including thermal fractionation by successive self-nucleation and annealing), and rotational rheology allows us to relate the reaction conditions to the average length of crystallizable unit sequences, thicknesses of corresponding lamellas, and temperatures of their melting. We demonstrate that isolated dodecenylene units can be incorporated into crystalline lamellas so that even nearly random copolymers should retain crystallinity. Weak high-temperature endotherms observed in the multiblock copolymers of norbornene with cyclododecene and other cycloolefins could indicate that the corresponding systems are microphase-separated in the melt state.

RevDate: 2021-06-18

Zhang X, Witt KE, Bañuelos MM, et al (2021)

The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans.

Proceedings of the National Academy of Sciences of the United States of America, 118(22):.

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

RevDate: 2021-05-28

Denisova E, Westphal D, Surowy HM, et al (2021)

Whole-exome sequencing in eccrine porocarcinoma indicates promising therapeutic strategies.

Cancer gene therapy [Epub ahead of print].

Malignant sweat gland tumours are rare, with the most common form being Eccrine porocarcinoma (EP). To investigate the mutational landscape of EP, we performed whole-exome sequencing (WES) on 14 formalin-fixed paraffin-embedded samples of matched primary EP and healthy surrounding tissue. Mutational profiling revealed a high overall median mutation rate. This was attributed to signatures of mutational processes related to ultraviolet (UV) exposure, APOBEC enzyme dysregulation, and defective homologous double-strand break repair. All of these processes cause genomic instability and are implicated in carcinogenesis. Recurrent driving somatic alterations were detected in the EP candidate drivers TP53, FAT2, CACNA1S, and KMT2D. The analyses also identified copy number alterations and recurrent gains and losses in several chromosomal regions including that containing BRCA2, as well as deleterious alterations in multiple HRR components. In accordance with this reduced or even a complete loss of BRCA2 protein expression was detected in 50% of the investigated EP tumours. Our results implicate crucial oncogenic driver pathways and suggest that defective homologous double-strand break repair and the p53 pathway are involved in EP aetiology. Targeting of the p53 axis and PARP inhibition, and/or immunotherapy may represent promising treatment strategies.

RevDate: 2021-08-02

Ahlquist KD, Bañuelos MM, Funk A, et al (2021)

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.

Genome biology and evolution, 13(7):.

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.

RevDate: 2021-07-22

Mualim K, Theunert C, M Slatkin (2021)

Estimation of coalescence probabilities and population divergence times from SNP data.

Heredity, 127(1):1-9.

We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

RevDate: 2021-07-31

Villanea FA, Huerta-Sanchez E, K Fox (2021)

ABO Genetic Variation in Neanderthals and Denisovans.

Molecular biology and evolution, 38(8):3373-3382.

Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two variants of the O1 allele, functionally similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared with portions of the genome evolving neutrally.

RevDate: 2021-06-25

Weiss CV, Harshman L, Inoue F, et al (2021)

The cis-regulatory effects of modern human-specific variants.

eLife, 10:.

The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.

RevDate: 2021-04-22

Anonymous (2020)

Podcast: Denisovan DNA in modern Europeans, and the birth of an unusual celestial object.

RevDate: 2021-04-21

Denisova K (2021)

Genetic vulnerability of exposures to antenatal maternal treatments in 1- to 2-month-old infants.

Infancy : the official journal of the International Society on Infant Studies, 26(3):515-532.

The growth and maturation of the nervous system are vulnerable during pregnancy. The impact of antenatal exposures to maternal treatments, in the context of genetic vulnerability of the fetus, on sensorimotor functioning in early infancy remains unexplored. Statistical features of head movements obtained from resting-state sleep fMRI scans are examined in 1- to 2-month-old infants, both those at high risk (HR) for autism spectrum disorder (ASD) due to a biological sibling with ASD and at low risk (LR) (N = 56). In utero exposures include maternal prescription medications (psychotropic Rx: N = 3HR ; N = 5LR vs. non-psychotropic Rx: N = 11HR ; N = 9LR vs. none: N = 11HR ; N = 16LR), psychiatric diagnoses (two or more Dx2 : N = 5HR ; N = 1LR ; one Dx1 : N = 4HR ; N = 5LR ; no Dx: N = 12HR ; N = 19LR), infections requiring antibiotics (infection: N = 5HR ; N = 8LR ; no infection: N = 20HR ; N = 22LR), or high fever (fever: N = 2HR ; N = 2LR ; no fever: N = 23HR ; N = 27LR). Movements with significantly higher variability are detected in infants exposed to psychotropics (e.g., opioid analgesics) and those whose mothers had fever, and this effect is significantly worse for infants at HR for ASD. Movements are significantly less variable in HR infants with non-psychotropic exposures (e.g., antibiotics). Heightened number of psychiatric or mental health conditions is associated with noisier movements in both risk groups. Genetic vulnerability due to in utero exposure to maternal treatments is an important future approach to be advanced in the field of early mind and brain development.

RevDate: 2021-04-22

Choin J, Mendoza-Revilla J, Arauna LR, et al (2021)

Genomic insights into population history and biological adaptation in Oceania.

Nature, 592(7855):583-589.

The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes1. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2-4. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.

RevDate: 2021-04-09
CmpDate: 2021-04-09

Gulaĭ IS, Snegirev AI, Denisova NP, et al (2021)

[Chronic spinal stimulation in treatment of lower limb critical ischaemia syndrome].

Angiologiia i sosudistaia khirurgiia = Angiology and vascular surgery, 27(1):128-135.

Obliterating peripheral artery disease is a commonly occurring pathological condition, most often resulting from an atherosclerotic lesion of vessels with progressive narrowing of their lumens. The consequences of decompensation of chronic arterial insufficiency such as ischaemic pain, claudication, and trophic impairments are in some instances difficult to treat, despite using multicomponent medicamentous therapy and/or performing revascularizing interventions. This article describes a clinical case report regarding the use of spinal stimulation in a patient presenting with stage IV chronic lower limb ischaemia according to the Fontaine classification. This is accompanied and followed by depicting the dynamics of the laboratory, instrumental, and clinical parameters over a two-year follow-up period. In order to explain the choice of the intervention and the causes of the described picture, discussed are the existing theories of the mechanisms of action of spinal stimulation. To this is added a literature review of using this method in treatment of lower limb critical ischaemia when performing reconstructive angiosurgical treatment is unavailable. Mention is also made of the incidence and types of probable complications, as well as possibilities and limitations of the method.

RevDate: 2021-05-10

Shunatova N, Denisova S, S Shchenkov (2021)

Ultrastructure of rhizoids in the marine bryozoan Dendrobeania fruticosa (Gymnolaemata: Cheilostomata).

Journal of morphology, 282(6):847-862.

Bryozoans form colonies of iterated modules, termed zooids, and display varying degrees of polymorphism. Polymorphic colonies comprise autozooids (or feeding zooids) and heteromorphic zooids, among which the most common types are avicularia and kenozooids. Kenozooids differ in shape, size, and presumed function. Among this diversity, there are rhizoids, which serve to attach colonies to the substrate or to lift them above it. To date, only general data on anatomy of kenozooids at light microscopy level are available. Here, we present the first description of the ultrastructure of the holdfast-like rhizoids of the cheilostome bryozoan Dendrobeania fruticosa. The rhizoid wall is composed of a single-layered epidermis, which produces the ectocyst. The voluminous cavity is acoelomate: it has no special cellular lining, nor any signs of an extracellular matrix toward the epidermis. It is traversed by delicate branching funicular strands that originate from the pore plate. The only cells in contact with the epidermis are the cells of the funicular system and the storage cells. The pore plate between the rhizoid and autozooid includes a variable number of communication pores. Each pore is plugged with a rosette complex, which includes a cincture cell and four special cells extending through the pore. The limiting cells are absent, and the special cells are in direct contact with the funicular strands. Cell contacts between special cells are absent; moreover, there are spaces between their proximal lobes filled with a heterogeneous matrix similar to that in the lumen of the funicular strands. Such matrix is also found outside of the extracellular matrix surrounding the special cells. These findings allow us to suggest that nutrient transport most likely occurs between, rather than through, the special cells. However, further studies are needed to understand how the rosette complex functions.

RevDate: 2021-07-31
CmpDate: 2021-05-19

Teixeira JC, Jacobs GS, Stringer C, et al (2021)

Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture.

Nature ecology & evolution, 5(5):616-624.

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

RevDate: 2021-05-27
CmpDate: 2021-05-27

Denisova K, A Barmettler (2021)

Evaluating the Thyroid Eye Disease Patient.

International ophthalmology clinics, 61(2):33-52.

RevDate: 2021-03-17
CmpDate: 2021-03-17

Soldatsky YL, Denisova OA, Vitkovskaya IP, et al (2021)

[Modern causes of tracheostomy in children].

Vestnik otorinolaringologii, 86(1):36-40.

The purpose of work is to analyze the causes of tracheostomy in children hospitalized in a large multidisciplinary pediatric hospital.

MATERIAL AND METHODS: Retrospective analysis of case of children treated in a multidisciplinary urgent hospital - GBUZ «Morozovskaya CCCH of MDH», which in the period from 01.01.16 to 31.12.18 was made operation «tracheostomy» was conducted.

RESULTS: Tracheostomy was performed in 138 (0.064%) among 216 469 hospitalized children. Age at the time of tracheostomy ranged from 2 weeks to 17.5 years (on average 67.9±59.84 months, Me=47.5 months), and 36.2% of children had tracheostomy was done on the 1st year of life. 126 (91.3%) patients required prolonged tracheal intubation prior to tracheostomy placement; the duration of intubation ranged from 1 to 95 days (on average 19.9±13.42 days, Me=14 days). The main reasons of tracheostomy were the need for long-term mechanical ventilation/respiratory support; the need for constant sanitation of the lower respiratory tract with bulbar/pseudobulbar disorders; upper respiratory paths obstruction. The diseases that led to this condition can be grouped into 4 categories: CNS pathology - 76 (55.1%) patients; brain / spinal cord tumors - 36 (26.1%); neurodystrophy and stenosis of the upper respiratory tract of various etiology - 13 (9.4% each) patients. 68.1% of patients were found incurable and required palliative care. Mortality among patients with a known catamnesis was 39.1%, mainly due to progression of the underlying disease; the lethality associated with tracheal cannulation was 1.4%.

CONCLUSION: Currently, pediatric tracheostomy is moving into the category of predominantly planned surgical interventions. More than 2/3 of children requiring tracheostomy are patients in need of palliative care with severe pathology of the central nervous system; in which the main indications for surgery are the need for respiration support and regular tracheobronchial care..

RevDate: 2021-03-04

Makarova EN, Yakovleva TV, Balyibina NY, et al (2020)

Pharmacological effects of fibroblast growth factor 21 are sex-specific in mice with the lethal yellow (Ay) mutation.

Vavilovskii zhurnal genetiki i selektsii, 24(2):200-208.

Hypothalamic melanocortin 4 receptors (MC4R) regulate energy balance. Mutations in the MC4R gene are the most common cause of monogenic obesity in humans. Fibroblast growth factor 21 (FGF21) is a promising antiobesity agent, but its effects on melanocortin obesity are unknown. Sex is an important biological variable that must be considered when conducting preclinical studies; however, in laboratory animal models, the pharmacological effects of FGF21 are well documented only for male mice. We aimed at investigating whether FGF21 affects metabolism in male and female mice with the lethal yellow (Ay) mutation, which results in MC4R blockage and obesity development. Obese C57Bl-Ay male and female mice were administered subcutaneously for 10 days with vehicle or FGF21 (1 mg per 1 kg). Food intake (FI), body weight (BW), blood parameters, and gene expression in the liver, muscles, brown adipose tissue, subcutaneous and visceral white adipose tissues, and hypothalamus were measured. FGF21 action strongly depended on the sex of the animals. In the males, FGF21 decreased BW and insulin blood levels without affecting FI. In the females, FGF21 increased FI and liver weight, but did not affect BW. In control Ay-mice, expression of genes involved in lipid and glucose metabolism (Ppargc1a, Cpt1, Pck1, G6p, Slc2a2) in the liver and genes involved in lipogenesis (Pparg, Lpl, Slc2a4) in visceral adipose tissue was higher in females than in males, and FGF21 administration inhibited the expression of these genes in females. FGF21 administration decreased hypothalamic POMC mRNA only in males. Thus, the pharmacological effect of FGF21 were significantly different in male and female Ay-mice; unlike males, females were resistant to catabolic effects of FGF21.

RevDate: 2021-02-16
CmpDate: 2021-02-16

Gusev EI, Blokhin VE, Vartanov SA, et al (2021)

[Development of early diagnosis of Parkinson's disease and comprehensive economic analysis of the effect of its implementation].

Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova, 121(1):9-20.

The paper summarizes the literature and author's data on the development of early (preclinical) diagnosis of Parkinson's disease (PD). Implementation of this diagnosis will promote the use of preventive therapy and change investments in diagnosis and treatment of patients. The paper declares that at present the only approach to early diagnosis of PD is positron-emission tomography of the nigrostriatal dopaminergic system, but it cannot be used for preventive examination due to its high cost. The authors consider that a less specific, but more promising approach to the development of early diagnosis of PD is the search for markers in body fluids, mainly in the blood, in patients at the prodromal stage of PD. Indeed, a number of markers as changes in the level of metabolites of monoamines, sphingolipids, urates, and indicators of oxidative stress were found in patients selected for the risk group of the prodromal stage of PD, according to characteristic premotor symptoms. In addition, it is assumed that the search for blood markers at an earlier - pre-prodromal stage is possible only in animal models of PD at the early preclinical stage. This approach can also be used to verify blood markers identified in patients at the clinical stage of PD. It is also evident that the complex socio-economic factors influencing the incidence of PD is different in developed versus developing countries. The societal and medical costs of Parkinson's are huge and efforts to improve early preclinical diagnosis of PD will lead to considerable economical and societal benefits. For instance this will allow efficient selection of patients for preclinical diagnostic tests. To assess the effectiveness of this strategy considering the uncertainty of socio-economic issues, a modification of the «cost-utility» analysis is proposed. For the first time, a Markov model of PD including preclinical diagnostic tests and possible neuroprotective therapy was developed and studied. Analytical outcomes of this process suggest that the idea of developing a new multimodal strategy is promising from a socio-economic point of view.

RevDate: 2021-05-21
CmpDate: 2021-02-26

Trujillo CA, Rice ES, Schaefer NK, et al (2021)

Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.

Science (New York, N.Y.), 371(6530):.

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.

RevDate: 2021-07-27

Reinscheid RK, Mafessoni F, Lüttjohann A, et al (2021)

Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality.

Peptides, 138:170506.

The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.

RevDate: 2021-04-13

Bonfante B, Faux P, Navarro N, et al (2021)

A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.

Science advances, 7(6):.

To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

RevDate: 2021-01-20
CmpDate: 2021-01-20

Kondratieva EA, Kondratev SA, Denisova AA, et al (2020)

[Results of treatment with intravenous amantadine sulfate (PK-Merz) patients with chronic disorders of consciousness].

Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova, 120(12):102-108.

The article presents literature review of the recent publications devoted to the drugs with dopaminergic, antiglutamatergic and GABA-ergic effects in the treatment of patients with vegetative state/areactive wakefulness syndrome (VS/AWS). The authors analyzed their own results of the effects of intravenous form of amantadine sulfate (PK Merz) in 142 VS/AWS patients caused by different etiological factors. Depending on the dominant neurological symptoms, patients were divided into three main groups: areactive type of course (group 1 - 61 patients), predominance of primitive limbic reactions (group 2 - 35 patients) and predominance of extrapyramidal symptoms (group 3 - 46 patients). Therapy results were evaluated one month later by CRS-R scale, which showed that the most distinct positive dynamics was observed in group 3.

RevDate: 2021-05-28
CmpDate: 2021-05-28

Greer C, Bhakta H, Ghanem L, et al (2021)

Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.

Human reproduction (Oxford, England), 36(3):734-755.

STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?

SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.

WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average ∼2%) present in non-African extant humans.

STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.

Ancient DNA from six Neanderthals and two Denisovans dated between ∼82 000 and 43 000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.

Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage ≥20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.

While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.

This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.

This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.


RevDate: 2021-01-11

Alexeeva E, Horneff G, Dvoryakovskaya T, et al (2021)

Early combination therapy with etanercept and methotrexate in JIA patients shortens the time to reach an inactive disease state and remission: results of a double-blind placebo-controlled trial.

Pediatric rheumatology online journal, 19(1):5.

BACKGROUND: Remission is the primary objective of treating juvenile idiopathic arthritis (JIA). It is still debatable whether early intensive treatment is superior in terms of earlier achievement of remission. The aim of this study was to evaluate the effectiveness of early etanercept+methotrexate (ETA+MTX) combination therapy versus step-up MTX monotherapy with ETA added in refractory disease.

METHODS: A multi-centre, double-blind, randomized study in active polyarticular JIA patients treated with either ETA+MTX (n = 35) or placebo+MTX (n = 33) for up to 24 weeks, followed by a 24-week open-label phase. The efficacy endpoints included pedACR30 criteria improvement at week 12, inactive disease at week 24, and remission at week 48. Patients who failed to achieve the endpoints at week 12 or at week 24 escaped to open-label ETA+MTX. Safety was assessed at each visit.

RESULTS: By intention-to-treat analysis, more patients in the ETA+MTX group reached the pedACR30 response at week 12 (33 (94.3%)) than in the placebo+MTX group (20 (60.6%); p = 0.001). At week 24, comparable percentages of patients reached inactive disease (11 (31.4%) vs 11 (33.3%)). At week 48, 11 (31.4%) and eight (24.2%) patients achieved remission. The median (+/-IQR) times to achieve an inactive disease state in the ETA+MTX and placebo+MTX groups were 24 (14-32) and 32 (24-40) weeks, respectively. Forty-four (74/100 patient-years) adverse events (AEs) were reported, leading to treatment discontinuation in 6 patients.

CONCLUSIONS: Early combination therapy with ETA+MTX proved to be highly effective compared to the standard step-up regimen. Compared to those treated with the standard regimen, more patients treated with a combination of ETA+MTX reached the pedACR30 response and achieved inactive disease and remission more rapidly.

RevDate: 2021-03-12

Bentzon AK, Panteleev A, Mitsura V, et al (2021)

Healthcare delivery for HIV-positive people with tuberculosis in Europe.

HIV medicine, 22(4):283-293.

BACKGROUND: In a 2013 survey, we reported distinct discrepancies in delivery of tuberculosis (TB) and HIV services in eastern Europe (EE) vs. western Europe (WE).

OBJECTIVES: To verify the differences in TB and HIV services in EE vs. WE.

METHODS: Twenty-three sites completed a survey in 2018 (EE, 14; WE, nine; 88% response rate). Results were compared across as well as within the two regions. When possible, results were compared with the 2013 survey.

RESULTS: Delivery of healthcare was significantly less integrated in EE: provision of TB and HIV services at one site (36% in EE vs. 89% in WE; P = 0.034), and continued TB follow-up in one location (42% vs. 100%; P = 0.007). Although access to TB diagnostics, standard TB and HIV drugs was generally good, fewer sites in EE reported unlimited access to rifabutin/multi-drug-resistant TB (MDR-TB) drugs, HIV integrase inhibitors and opioid substitution therapy (OST). Compared with 2013, routine usage of GeneXpert was more common in EE in 2018 (54% vs. 92%; P = 0.073), as was access to moxifloxacin (46% vs. 91%; P = 0.033), linezolid (31% vs. 64%; P = 0.217), and bedaquiline (0% vs. 25%; P = 0.217). Integration of TB and HIV services (46% vs. 39%; P = 1.000) and provision of OST to patients with opioid dependency (54% vs. 46%; P = 0.695) remained unchanged.

CONCLUSION: Delivery of TB and HIV healthcare, including integration of TB and HIV care and access to MDR-TB drugs, still differs between WE and EE, as well as between individual EE sites.

RevDate: 2021-02-10
CmpDate: 2021-02-10

Cook S, Kudryavtsev AV, Bobrova N, et al (2020)

Prevalence of symptoms, ever having received a diagnosis and treatment of depression and anxiety, and associations with health service use amongst the general population in two Russian cities.

BMC psychiatry, 20(1):537.

BACKGROUND: Little is known about the burden of common mental disorders in Russia despite high levels of suicide and alcohol-related mortality. Here we investigated levels of symptoms, self-reports of ever having received a diagnosis and treatment of anxiety and depression in two Russian cities.

METHODS: The study population was men and women aged 35-69 years old participating in cross-sectional population-based studies in the cities of Arkhangelsk and Novosibirsk (2015-18). Participants completed an interview which included the PHQ-9 and GAD-7 scales, questions on whether participants had ever received a diagnosis of depression or anxiety, and health service use in the past year. Participants also reported current medication use and medications were coded in line with the WHO anatomical therapeutic classification (ATC). Depression was defined as PHQ-9 ≥ 10 and Anxiety as GAD-7 ≥ 10.

RESULTS: Age-standardised prevalence of PHQ-9 ≥ 10 was 10.7% in women and 5.4% in men (GAD-7 ≥ 10 6.2% in women; 3.0% in men). Among those with PHQ-9 ≥ 10 17% reported ever having been diagnosed with depression (equivalent finding for anxiety 29%). Only 1.5% of those with PHQ-9 ≥ 10 reported using anti-depressants and 0.6% of those with GAD-7 ≥ 10 reported using anxiolytics. No men with PHQ-9 ≥ 10 and/or GAD-7 ≥ 10 reported use of anti-depressants or anxiolytics. Use of health services increased with increasing severity of both depression and anxiety.

CONCLUSION: There was a large gap between symptoms and reporting of past diagnosis and treatment of common mental disorders in two Russian cities. Interventions aimed at improving mental health literacy and reducing stigma could be of benefit in closing this substantial treatment gap.

RevDate: 2021-01-10

Aston S, Denisova K, Hurlbert A, et al (2020)

Exploring the Determinants of Color Perception Using #Thedress and Its Variants: The Role of Spatio-Chromatic Context, Chromatic Illumination, and Material-Light Interaction.

Perception, 49(11):1235-1251.

The colors that people see depend not only on the surface properties of objects but also on how these properties interact with light as well as on how light reflected from objects interacts with an individual's visual system. Because individual visual systems vary, the same visual stimulus may elicit different perceptions from different individuals. #thedress phenomenon drove home this point: different individuals viewed the same image and reported it to be widely different colors: blue and black versus white and gold. This phenomenon inspired a collection of demonstrations presented at the Vision Sciences Society 2015 Meeting which showed how spatial and temporal manipulations of light spectra affect people's perceptions of material colors and illustrated the variability in individual color perception. The demonstrations also explored the effects of temporal alterations in metameric lights, including Maxwell's Spot, an entoptic phenomenon. Crucially, the demonstrations established that #thedress phenomenon occurs not only for images of the dress but also for the real dress under real light sources of different spectral composition and spatial configurations.

RevDate: 2021-01-08
CmpDate: 2021-01-08

Vorobieva NV, Makunin AI, Druzhkova AS, et al (2020)

High genetic diversity of ancient horses from the Ukok Plateau.

PloS one, 15(11):e0241997.

A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.

RevDate: 2021-07-13
CmpDate: 2021-07-13

Nesterenko MA, Starunov VV, Shchenkov SV, et al (2020)

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae).

Parasites & vectors, 13(1):559.

BACKGROUND: Parasitic flatworms (Trematoda: Digenea) represent one of the most remarkable examples of drastic morphological diversity among the stages within a life cycle. Which genes are responsible for extreme differences in anatomy, physiology, behavior, and ecology among the stages? Here we report a comparative transcriptomic analysis of parthenogenetic and amphimictic generations in two evolutionary informative species of Digenea belonging to the family Psilostomatidae.

METHODS: In this study the transcriptomes of rediae, cercariae and adult worm stages of Psilotrema simillimum and Sphaeridiotrema pseudoglobulus, were sequenced and analyzed. High-quality transcriptomes were generated, and the reference sets of protein-coding genes were used for differential expression analysis in order to identify stage-specific genes. Comparative analysis of gene sets, their expression dynamics and Gene Ontology enrichment analysis were performed for three life stages within each species and between the two species.

RESULTS: Reference transcriptomes for P. simillimum and S. pseudoglobulus include 21,433 and 46,424 sequences, respectively. Among 14,051 orthologous groups (OGs), 1354 are common and specific for two analyzed psilostomatid species, whereas 13 and 43 OGs were unique for P. simillimum and S. pseudoglobulus, respectively. In contrast to P. simillimum, where more than 60% of analyzed genes were active in the redia, cercaria and adult worm stages, in S. pseudoglobulus less than 40% of genes had such a ubiquitous expression pattern. In general, 7805 (36.41%) and 30,622 (65.96%) of genes were preferentially expressed in one of the analyzed stages of P. simillimum and S. pseudoglobulus, respectively. In both species 12 clusters of co-expressed genes were identified, and more than a half of the genes belonging to the reference sets were included into these clusters. Functional specialization of the life cycle stages was clearly supported by Gene Ontology enrichment analysis.

CONCLUSIONS: During the life cycles of the two species studied, most of the genes change their expression levels considerably, consequently the molecular signature of a stage is not only a unique set of expressed genes, but also the specific levels of their expression. Our results indicate unexpectedly high level of plasticity in gene regulation between closely related species. Transcriptomes of P. simillimum and S. pseudoglobulus provide high quality reference resource for future evolutionary studies and comparative analyses.

RevDate: 2020-11-06

Mahesh S, Denisova T, Gerasimova L, et al (2020)

Multimorbidity After Surgical Menopause Treated with Individualized Classical Homeopathy: A Case Report.

Clinical medicine insights. Case reports, 13:1179547620965560.

Classical homeopathy was shown to be beneficial in climacteric syndrome in many studies, but the clinical effect is unclear. To inspect if individualized classical homeopathy has a role in treating complaints after surgical menopause through real world case, we present a case of a 54-year-old Russian woman treated with individualized classical homeopathy for multimorbid conditions after surgical menopause examined for changes from homeopathic treatment. We assessed changes in climacteric symptoms, changes in comorbidities, and the general well-being of the patient. The woman had severe climacteric syndrome, pelvic inflammatory disease, dyslipidemia, obesity, hepatic steatosis, pancreatic lipomatosis, gall bladder disease, and mild subclinical hypothyroidism to begin with. She was treated with individualized classical homeopathy and followed up for 31 months. She was relieved of the vasomotor symptoms and psychological disturbances of climacteric syndrome, her weight reduced, the ultrasound scan showed absence of lipomatosis/gall bladder disease/hepatic steatosis. Blood tests showed reduction of thyroid stimulating hormone and a balance in the lipid status. Individualized classical homeopathy may have a role in the climacteric syndrome and comorbidities after surgical menopause. The efficacy of homeopathic therapy in climacteric problems must be scientifically investigated further.

RevDate: 2020-11-03

Chernyshev VM, Denisova EA, Eremin DB, et al (2020)

The key role of R-NHC coupling (R = C, H, heteroatom) and M-NHC bond cleavage in the evolution of M/NHC complexes and formation of catalytically active species.

Chemical science, 11(27):6957-6977.

Complexes of metals with N-heterocyclic carbene ligands (M/NHC) are typically considered the systems of choice in homogeneous catalysis due to their stable metal-ligand framework. However, it becomes obvious that even metal species with a strong M-NHC bond can undergo evolution in catalytic systems, and processes of M-NHC bond cleavage are common for different metals and NHC ligands. This review is focused on the main types of the M-NHC bond cleavage reactions and their impact on activity and stability of M/NHC catalytic systems. For the first time, we consider these processes in terms of NHC-connected and NHC-disconnected active species derived from M/NHC precatalysts and classify them as fundamentally different types of catalysts. Problems of rational catalyst design and sustainability issues are discussed in the context of the two different types of M/NHC catalysis mechanisms.

RevDate: 2020-12-21
CmpDate: 2020-12-21

Zhang D, Xia H, Chen F, et al (2020)

Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau.

Science (New York, N.Y.), 370(6516):584-587.

A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau.

RevDate: 2020-12-21
CmpDate: 2020-12-21

Massilani D, Skov L, Hajdinjak M, et al (2020)

Denisovan ancestry and population history of early East Asians.

Science (New York, N.Y.), 370(6516):579-583.

We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

RevDate: 2020-12-21
CmpDate: 2020-12-21

Gibbons A (2020)

Denisovan DNA found in cave on Tibetan Plateau.

Science (New York, N.Y.), 370(6516):512-513.

RevDate: 2020-10-20

Pan L, Dumoncel J, Mazurier A, et al (2020)

Hominin diversity in East Asia during the Middle Pleistocene: A premolar endostructural perspective.

Journal of human evolution, 148:102888 pii:S0047-2484(20)30149-4 [Epub ahead of print].

Following the recent studies of East Asian mid-Middle to early Late Pleistocene hominin material, a large spectrum of morphological diversity has been recognized and the coexistence of archaic ('Homo erectus-like') and derived ('modern-like') dental morphological patterns has been highlighted. In fact, for most of these Chinese fossils, generally categorized as 'archaic Homo sapiens' or 'post-H. erectus Homo', the taxonomic attribution is a matter of contention. With the help of μCT techniques and a deformation-based 3D geometric morphometric approach, we focused on the morphological variation in the enamel-dentine junction (EDJ) of 18 upper and lower premolars from Chinese Middle Pleistocene hominins. We then compared our results with a number of fossil and modern human groups, including Early Pleistocene H. erectus from Sangiran; late Early Pleistocene hominins from Tighenif, Algeria; classic Neanderthals; and modern humans. Our results highlight an evolutionary/chronological trend of crown base reduction, elevation of EDJ topography, and EDJ surface simplification in the hominin groups studied here. Moreover, this study brings insights to the taxonomy/phylogeny of 6 late Middle Pleistocene specimens whose evolutionary placement has been debated for decades. Among these specimens, Changyang premolars show features that can be aligned with the Asian H. erectus hypodigm, whereas Panxian Dadong and Tongzi premolars are more similar to Late Pleistocene Homo. Compared with early to mid-Middle Pleistocene hominins in East Asia, late Middle Pleistocene hominins evince an enlarged morphological variation. A persistence of archaic morphotypes and possible admixture among populations during the late Middle Pleistocene are discussed.

RevDate: 2020-12-14
CmpDate: 2020-12-04

Petr M, Hajdinjak M, Fu Q, et al (2020)

The evolutionary history of Neanderthal and Denisovan Y chromosomes.

Science (New York, N.Y.), 369(6511):1653-1656.

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

RevDate: 2020-09-28

Merisaari J, Denisova OV, Doroszko M, et al (2020)

Monotherapy efficacy of blood-brain barrier permeable small molecule reactivators of protein phosphatase 2A in glioblastoma.

Brain communications, 2(1):fcaa002.

Glioblastoma is a fatal disease in which most targeted therapies have clinically failed. However, pharmacological reactivation of tumour suppressors has not been thoroughly studied as yet as a glioblastoma therapeutic strategy. Tumour suppressor protein phosphatase 2A is inhibited by non-genetic mechanisms in glioblastoma, and thus, it would be potentially amendable for therapeutic reactivation. Here, we demonstrate that small molecule activators of protein phosphatase 2A, NZ-8-061 and DBK-1154, effectively cross the in vitro model of blood-brain barrier, and in vivo partition to mouse brain tissue after oral dosing. In vitro, small molecule activators of protein phosphatase 2A exhibit robust cell-killing activity against five established glioblastoma cell lines, and nine patient-derived primary glioma cell lines. Collectively, these cell lines have heterogeneous genetic background, kinase inhibitor resistance profile and stemness properties; and they represent different clinical glioblastoma subtypes. Moreover, small molecule activators of protein phosphatase 2A were found to be superior to a range of kinase inhibitors in their capacity to kill patient-derived primary glioma cells. Oral dosing of either of the small molecule activators of protein phosphatase 2A significantly reduced growth of infiltrative intracranial glioblastoma tumours. DBK-1154, with both higher degree of brain/blood distribution, and more potent in vitro activity against all tested glioblastoma cell lines, also significantly increased survival of mice bearing orthotopic glioblastoma xenografts. In summary, this report presents a proof-of-principle data for blood-brain barrier-permeable tumour suppressor reactivation therapy for glioblastoma cells of heterogenous molecular background. These results also provide the first indications that protein phosphatase 2A reactivation might be able to challenge the current paradigm in glioblastoma therapies which has been strongly focused on targeting specific genetically altered cancer drivers with highly specific inhibitors. Based on demonstrated role for protein phosphatase 2A inhibition in glioblastoma cell drug resistance, small molecule activators of protein phosphatase 2A may prove to be beneficial in future glioblastoma combination therapies.

RevDate: 2020-12-07

Eremin DB, Boiko DA, Kostyukovich AY, et al (2020)

Mechanistic Study of Pd/NHC-Catalyzed Sonogashira Reaction: Discovery of NHC-Ethynyl Coupling Process.

Chemistry (Weinheim an der Bergstrasse, Germany), 26(67):15672-15681.

The product of a revealed transformation-NHC-ethynyl coupling-was observed as a catalyst transformation pathway in the Sonogashira cross-coupling, catalyzed by Pd/NHC complexes. The 2-ethynylated azolium salt was isolated in individual form and fully characterized, including X-ray analysis. A number of possible intermediates of this transformation with common formulae (NHC)n Pd(C2 Ph) (n=1,2) were observed and subjected to collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments to elucidate their structure. Measured bond dissociation energies (BDEs) and IRMPD spectra were in an excellent agreement with quantum calculations for coupling product π-complexes with Pd0 . Molecular dynamics simulations confirmed the observed multiple CID fragmentation pathways. An unconventional methodology to study catalyst evolution suggests the reported transformation to be considered in the development of new catalytic systems for alkyne functionalization reactions.

RevDate: 2021-07-20
CmpDate: 2020-12-17

Telis N, Aguilar R, K Harris (2020)

Selection against archaic hominin genetic variation in regulatory regions.

Nature ecology & evolution, 4(11):1558-1566.

Traces of Neandertal and Denisovan DNA persist in the modern human gene pool, but have been systematically purged by natural selection from genes and other functionally important regions. This implies that many archaic alleles harmed the fitness of hybrid individuals, but the nature of this harm is poorly understood. Here, we show that enhancers contain less Neandertal and Denisovan variation than expected given the background selection they experience, suggesting that selection acted to purge these regions of archaic alleles that disrupted their gene regulatory functions. We infer that selection acted mainly on young archaic variation that arose in Neandertals or Denisovans shortly before their contact with humans; enhancers are not depleted of older variants found in both archaic species. Some types of enhancer appear to have tolerated introgression better than others; compared with tissue-specific enhancers, pleiotropic enhancers show stronger depletion of archaic single-nucleotide polymorphisms. To some extent, evolutionary constraint is predictive of introgression depletion, but certain tissues' enhancers are more depleted of Neandertal and Denisovan alleles than expected given their comparative tolerance to new mutations. Foetal brain and muscle are the tissues whose enhancers show the strongest depletion of archaic alleles, but only brain enhancers show evidence of unusually stringent purifying selection. We conclude that epistatic incompatibilities between human and archaic alleles are needed to explain the degree of archaic variant depletion from foetal muscle enhancers, perhaps due to divergent selection for higher muscle mass in archaic hominins compared with humans.

RevDate: 2021-03-05
CmpDate: 2021-03-01

Quartier P, Alexeeva E, Constantin T, et al (2021)

Tapering Canakinumab Monotherapy in Patients With Systemic Juvenile Idiopathic Arthritis in Clinical Remission: Results From a Phase IIIb/IV Open-Label, Randomized Study.

Arthritis & rheumatology (Hoboken, N.J.), 73(2):336-346.

OBJECTIVE: To evaluate the efficacy and safety of 2 canakinumab monotherapy tapering regimens in order to maintain complete clinical remission in children with systemic juvenile idiopathic arthritis (JIA).

METHODS: The study was designed as a 2-part phase IIIb/IV open-label, randomized trial. In the first part, patients received 4 mg/kg of canakinumab subcutaneously every 4 weeks and discontinued glucocorticoids and/or methotrexate as appropriate. Patients in whom clinical remission was achieved (inactive disease for at least 24 weeks) with canakinumab monotherapy were entered into the second part of the trial, in which they were randomized 1:1 into 1 of 2 treatment arms. In arm 1, the dose of canakinumab was reduced from 4 mg/kg to 2 mg/kg and then to 1 mg/kg, followed by discontinuation. In arm 2, the 4 mg/kg dose interval was prolonged from every 4 weeks, to every 8 weeks, and then to every 12 weeks, followed by discontinuation. In both arms, canakinumab exposure could be reduced provided systemic JIA remained in clinical remission for 24 weeks with each step. The primary objective was to assess whether >40% of randomized patients in either arm maintained clinical remission of systemic JIA for 24 weeks in the first part of the study.

RESULTS: In part 1 of the study, 182 patients were enrolled, with 75 of those patients randomized before entering part 2 of the trial. Among the 75 randomized patients, clinical remission was maintained for 24 weeks in 27 (71%) of 38 patients in arm 1 (2 mg/kg every 4 weeks) and 31 (84%) of 37 patients in arm 2 (4 mg/kg every 8 weeks) (P ≤ 0.0001 for arm 1 versus arm 2 among those meeting the 40% threshold). Overall, 25 (33%) of 75 patients discontinued canakinumab, and clinical remission was maintained for at least 24 weeks in all 25 of these patients. No new safety signals were identified.

CONCLUSION: Reduction of canakinumab exposure may be feasible in patients who have achieved clinical remission of systemic JIA, but consistent interleukin-1 inhibition appears necessary to maintain this response.

RevDate: 2020-09-23
CmpDate: 2020-09-23

Hubisz MJ, Williams AL, A Siepel (2020)

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.

PLoS genetics, 16(8):e1008895.

The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these "super-archaic" regions-comprising at least about 4Mb-were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.

RevDate: 2021-03-04
CmpDate: 2020-10-16

Course MM, Gudsnuk K, Smukowski SN, et al (2020)

Evolution of a Human-Specific Tandem Repeat Associated with ALS.

American journal of human genetics, 107(3):445-460.

Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.

RevDate: 2020-09-23
CmpDate: 2020-09-23

Örd T, Puurand T, Örd D, et al (2020)

A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.

PLoS genetics, 16(8):e1008981.

Tribbles homolog 3 (TRIB3) is pseudokinase involved in intracellular regulatory processes and has been implicated in several diseases. In this article, we report that human TRIB3 promoter contains a 33-bp variable number tandem repeat (VNTR) and characterize the heterogeneity and function of this genetic element. Analysis of human populations around the world uncovered the existence of alleles ranging from 1 to 5 copies of the repeat, with 2-, 3- and 5-copy alleles being the most common but displaying considerable geographical differences in frequency. The repeated sequence overlaps a C/EBP-ATF transcriptional regulatory element and is highly conserved, but not repeated, in various mammalian species, including great apes. The repeat is however evident in Neanderthal and Denisovan genomes. Reporter plasmid experiments in human cell culture reveal that an increased copy number of the TRIB3 promoter 33-bp repeat results in increased transcriptional activity. In line with this, analysis of whole genome sequencing and RNA-Seq data from human cohorts demonstrates that the copy number of TRIB3 promoter 33-bp repeats is positively correlated with TRIB3 mRNA expression level in many tissues throughout the body. Moreover, the copy number of the TRIB3 33-bp repeat appears to be linked to known TRIB3 eQTL SNPs as well as TRIB3 SNPs reported in genetic association studies. Taken together, the results indicate that the promoter 33-bp VNTR constitutes a causal variant for TRIB3 expression variation between individuals and could underlie the results of SNP-based genetic studies.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Agrawal R, Testi I, Bodaghi B, et al (2021)

Collaborative Ocular Tuberculosis Study Consensus Guidelines on the Management of Tubercular Uveitis-Report 2: Guidelines for Initiating Antitubercular Therapy in Anterior Uveitis, Intermediate Uveitis, Panuveitis, and Retinal Vasculitis.

Ophthalmology, 128(2):277-287.

TOPIC: The Collaborative Ocular Tuberculosis Study (COTS), supported by the International Ocular Inflammation Society, International Uveitis Study Group, and Foster Ocular Immunological Society, set up an international, expert-led consensus project to develop evidence- and experience-based guidelines for the management of tubercular uveitis (TBU).

CLINICAL RELEVANCE: The absence of international agreement on the use of antitubercular therapy (ATT) in patients with TBU contributes to a significant heterogeneity in the approach to the management of this condition.

METHODS: Consensus statements for the initiation of ATT in TBU were generated using a 2-step modified Delphi technique. In Delphi step 1, a smart web-based survey based on background evidence from published literature was prepared to collect the opinion of 81 international experts on the use of ATT in different clinical scenarios. The survey included 324 questions related to tubercular anterior uveitis (TAU), tubercular intermediate uveitis (TIU), tubercular panuveitis (TPU), and tubercular retinal vasculitis (TRV) administered by the experts, after which the COTS group met in November 2019 for a systematic and critical discussion of the statements in accordance with the second round of the modified Delphi process.

RESULTS: Forty-four consensus statements on the initiation of ATT in TAU, TIU, TPU, and TRV were obtained, based on ocular phenotypes suggestive of TBU and corroborative evidence of tuberculosis, provided by several combinations of immunologic and radiologic test results. Experts agreed on initiating ATT in recurrent TAU, TIU, TPU, and active TRV depending on the TB endemicity. In the presence of positive results for any 1 of the immunologic tests along with radiologic features suggestive of past evidence of tuberculosis infection. In patients with a first episode of TAU, consensus to initiate ATT was reached only if both immunologic and radiologic test results were positive.

DISCUSSION: The COTS consensus guidelines were generated based on the evidence from published literature, specialists' opinions, and logic construction to address the initiation of ATT in TBU. The guidelines also should inform public policy by adding specific types of TBU to the list of conditions that should be treated as tuberculosis.

RevDate: 2021-03-18
CmpDate: 2021-03-18

Filippenkov IB, Stavchansky VV, Denisova AE, et al (2020)

Novel Insights into the Protective Properties of ACTH(4-7)PGP (Semax) Peptide at the Transcriptome Level Following Cerebral Ischaemia-Reperfusion in Rats.

Genes, 11(6):.

Cerebral ischaemia is the most common cause of impaired brain function. Biologically active peptides represent potential drugs for reducing the damage that occurs after ischaemia. The synthetic melanocortin derivative, ACTH(4-7)PGP (Semax), has been used successfully in the treatment of patients with severe impairment of cerebral blood circulation. However, its molecular mechanisms of action within the brain are not yet fully understood. Previously, we used the transient middle cerebral artery occlusion (tMCAO) model to study the damaging effects of ischaemia-reperfusion on the brain transcriptome in rats. Here, using RNA-Seq analysis, we investigated the protective properties of the Semax peptide at the transcriptome level under tMCAO conditions. We have identified 394 differentially expressed genes (DEGs) (>1.5-fold change) in the brains of rats at 24 h after tMCAO treated with Semax relative to saline. Following tMCAO, we found that Semax suppressed the expression of genes related to inflammatory processes and activated the expression of genes related to neurotransmission. In contrast, ischaemia-reperfusion alone activated the expression of inflammation-related genes and suppressed the expression of neurotransmission-related genes. Therefore, the neuroprotective action of Semax may be associated with a compensation of mRNA expression patterns that are disrupted during ischaemia-reperfusion conditions.

RevDate: 2021-07-02
CmpDate: 2021-07-02

Mathov Y, Batyrev D, Meshorer E, et al (2020)

Harnessing epigenetics to study human evolution.

Current opinion in genetics & development, 62:23-29.

Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.

RevDate: 2020-09-21
CmpDate: 2020-09-21

Kim J, Perkins GB, PT Coates (2020)

Evolutionary immunology: how your ancestry can affect your kidney transplant.

Kidney international, 98(1):45-47.

RevDate: 2021-07-12
CmpDate: 2021-07-12

Khan N, de Manuel M, Peyregne S, et al (2020)

Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins.

Genome biology and evolution, 12(7):1040-1050.

Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2-3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a "hotspot" in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human-Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal-human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.

RevDate: 2020-09-01
CmpDate: 2020-09-01

Mafessoni F, Grote S, de Filippo C, et al (2020)

A high-coverage Neandertal genome from Chagyrskaya Cave.

Proceedings of the National Academy of Sciences of the United States of America, 117(26):15132-15136.

We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.

RevDate: 2021-01-21
CmpDate: 2021-01-21

Almarri MA, Bergström A, Prado-Martinez J, et al (2020)

Population Structure, Stratification, and Introgression of Human Structural Variation.

Cell, 182(1):189-199.e15.

Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.

RevDate: 2021-04-08
CmpDate: 2020-06-24

Skov L, Coll Macià M, Sveinbjörnsson G, et al (2020)

The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes.

Nature, 582(7810):78-83.

Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.

RevDate: 2021-02-05
CmpDate: 2020-07-03

Denisova K, A Barmettler (2020)

Oculoplastic considerations for refractive procedures.

Current opinion in ophthalmology, 31(4):241-246.

PURPOSE OF REVIEW: Refractive surgery is one of the most popular elective procedures performed in the world. Given that dry eye is a common complaint following keratorefractive surgery, evaluation, and treatment of periocular conditions that further predispose the patient to dry eye symptoms is an important part of the presurgical assessment. Periocular conditions and surgeries can also affect the ocular surface and keratometry, and should be addressed. For example, ptosis, orbital fat herniation, ectropion, and eyelid masses have been shown to induce corneal topography changes and astigmatism. The oculoplastic considerations for refractive surgery include both the contribution of eyelid position on dry eye, ocular surface damage, refractive error, and outcomes, as well as the timing of oculoplastic surgery in relation to the refractive surgery. In this review, the recently published literature on eyelid and orbital surgery in relation to keratorefractive surgery is reviewed to elucidate the relationship of periocular factors with refractive surgery outcomes and complications. To improve keratorefractive surgery outcomes, a literature review is presented, discussing evaluation, management, and timing of management of oculoplastics conditions.

RECENT FINDINGS: Dry eye syndrome is a well known complication of keratorefractive procedures. This is exacerbated with concurrent eyelid or orbital disorders, such as ectropion, lagophthalmos, and thyroid eye disease. In addition to impacting dry eye and ocular surface damage, eyelid surgeries can also affect corneal topography and refraction. Studies have found that patients with ptosis have topographic corneal aberrations from the eyelid exerting pressure on the cornea, while ptosis repair and blepharoplasty patients may undergo an astigmatic change postoperatively. Finally, the corneal flap created in laser-assisted in situ keratomileusis may be at risk for displacement or damage postoperatively with this risk changing, depending on method of flap creation, and time elapsed since keratorefractive surgery.

SUMMARY: Eyelid and orbital conditions that predispose to dry eye syndrome and refractive changes should be evaluated and optimized prior to keratorefractive surgery. Patients electing to have oculoplastic surgery, like ptosis repair, should be fully healed prior to any refractive surgery to allow both refractive changes and eyelid positions to stabilize prior to the refractive surgery.

RevDate: 2020-07-20
CmpDate: 2020-07-20

Larina VN, Akhmatova FD, Arakelov SE, et al (2020)

[Modern strategies for cardiac rehabilitation after myocardial infarction and percutaneous coronary intervention].

Kardiologiia, 60(3):111-118.

Modern cardiac rehabilitation represents a structured, multicomponent program, which includes physical activity, education of the patient, modification of the health behavior, and psychological and social support. In EU countries, only 44.8% of patients with ischemic heart disease receive a recommendation to participate in any form of rehabilitation, and only 36.5% of all patients presently have an access to any rehabilitation program. Systematic analysis of programs for prevention of cardiovascular diseases and for rehabilitation in patients with myocardial infarction (MI) and percutaneous coronary intervention showed that complex programs can still reduce all-cause and cardiovascular mortality and frequency of recurrent MI and stroke. These programs include key components of cardiac rehabilitation, reduction of six or more risk factors, and effective control by drug therapy.

RevDate: 2020-12-14
CmpDate: 2020-12-10

Denisova SA, SV Shchenkov (2020)

Fine structure of the nervous system of Cercaria parvicaudata Stunkard & Shaw, 1931 (Digenea, Renicolidae).

Journal of morphology, 281(7):765-777.

The biology of free-living and parasitic Platyhelminthes is diverse. Taking into account the widespread prevalence of parasitic flatworms, Digenea is the least studied group regarding the fine structure of nervous system especially of the cercarial life stage. Here, we present a description of the fine structure of central nervous system (CNS) and two types of uniciliate sensory papillae of xiphidiocercaria Cercaria parvicaudata (Microphalloidea, Renicolidae). The present study documents that C. parvicaudata has a complex nervous system that includes a well-developed ganglion with a cortex of perikarya and glia-like sheaths, myelin-like structures within one of the dorsal nerve cords and four types of polarized synapses between neurites. Different types of neurons in the CNS could not be distinguished on ultrastructural level due to high similarity in their fine structure. Shared polarized synapses with high electron density of presynaptic components are numerous in the neuropile and nerve cords of this larva. Within the larval body, we detected specialized "support" processes that relate to different tissues. Some "support" processes are also closely related to the nervous system of C. parvicaudata, where they are considered as glia-like structures. In this case, the fine structure of glia-like "support" cells of C. parvicaudata differs from those described as glia-like cells in adult flatworms. We suggest a wide prevalence of glia-like cells among cercariae, as well as the fact that glia-like structures in digenean nervous systems can develop from various nonneuronal tissues.

RevDate: 2020-09-28

Hammill JA, Kwiecien JM, Dvorkin-Gheva A, et al (2020)

A Cross-Reactive Small Protein Binding Domain Provides a Model to Study Off-Tumor CAR-T Cell Toxicity.

Molecular therapy oncolytics, 17:278-292.

Tumor-targeted chimeric antigen receptor (CAR)-engineered T lymphocytes (CAR-T cells) have demonstrated striking clinical success, but their use has been associated with a constellation of toxicities. A better understanding of the pathogenesis of these toxicities is required to improve the safety profile of CAR-T cells. Herein, we describe a xenograft model of off-tumor CAR-T cell-associated toxicity. Human CAR-T cells targeted against HER2 using a small-protein binding domain induced acute, dose-dependent toxicities in mice. The inclusion of a CD28 or 4-1BB co-stimulatory domain in the CAR was required to produce toxicity; however, co-stimulation through CD28 was most toxic on a per-cell basis. CAR-T cell activation in the lungs and heart was associated with a systemic cytokine storm. The severity of observed toxicities was dependent upon the peripheral blood mononuclear cell (PBMC) donor used as a T cell source and paralleled the CD4+-to-CD8+ T cell ratio in the adoptive transfer product. CD4+ CAR-T cells were determined to be the primary contributors to CAR-T cell-associated toxicity. However, donor-specific differences persisted after infusion of a purified CD4+ CAR-T cell product, indicating a role for additional variables. This work highlights the contributions of CAR-T cell-intrinsic variables to the pathogenesis of off-tumor toxicity.

RevDate: 2021-04-16
CmpDate: 2021-04-16

Lodewijk GA, Fernandes DP, Vretzakis I, et al (2020)

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels.

Molecular biology and evolution, 37(9):2531-2548.

Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.

RevDate: 2021-06-15
CmpDate: 2021-06-15

Kurmukov A, Mussabaeva A, Denisova Y, et al (2020)

Optimizing Connectivity-Driven Brain Parcellation Using Ensemble Clustering.

Brain connectivity, 10(4):183-194.

This work addresses the problem of constructing a unified, topologically optimal connectivity-based brain atlas. The proposed approach aggregates an ensemble partition from individual parcellations without label agreement, providing a balance between sufficiently flexible individual parcellations and intuitive representation of the average topological structure of the connectome. The methods exploit a previously proposed dense connectivity representation, first performing graph-based hierarchical parcellation of individual brains, and subsequently aggregating the individual parcellations into a consensus parcellation. The search for consensus-based on the hard ensemble (HE) algorithm-approximately minimizes the sum of cluster membership distances, effectively estimating a pseudo-Karcher mean of individual parcellations. Computational stability, graph structure preservation, and biological relevance of the simplified representation resulting from the proposed parcellation are assessed on the Human Connectome Project data set. These aspects are assessed using (1) edge weight distribution divergence with respect to the dense connectome representation, (2) interhemispheric symmetry, (3) network characteristics' stability and agreement with respect to individually and anatomically parcellated networks, and (4) performance of the simplified connectome in a biological sex classification task. Ensemble parcellation was found to be highly stable with respect to subject sampling, outperforming anatomical atlases and other connectome-based parcellations in classification as well as preserving global connectome properties. The HE-based parcellation also showed a degree of symmetry comparable with anatomical atlases and a high degree of spatial contiguity without using explicit priors.

RevDate: 2020-04-06

Agrawal R, Testi I, Mahajan S, et al (2020)

The Collaborative Ocular Tuberculosis Study (COTS) Consensus (CON) Group Meeting Proceedings.

Ocular immunology and inflammation [Epub ahead of print].

An international, expert led consensus initiative was set up by the Collaborative Ocular Tuberculosis Study (COTS) group to develop systematic, evidence, and experience-based recommendations for the treatment of ocular TB using a modified Delphi technique process. In the first round of Delphi, the group identified clinical scenarios pertinent to ocular TB based on five clinical phenotypes (anterior uveitis, intermediate uveitis, choroiditis, retinal vasculitis, and panuveitis). Using an interactive online questionnaires, guided by background knowledge from published literature, 486 consensus statements for initiating ATT were generated and deliberated amongst 81 global uveitis experts. The median score of five was considered reaching consensus for initiating ATT. The median score of four was tabled for deliberation through Delphi round 2 in a face-to-face meeting. This report describes the methodology adopted and followed through the consensus process, which help elucidate the guidelines for initiating ATT in patients with choroidal TB.

RevDate: 2020-09-28

Mitoudi Vagourdi E, Zhang W, Denisova K, et al (2020)

Synthesis and Characterization of Two New Second Harmonic Generation Active Iodates: K3Sc(IO3)6 and KSc(IO3)3Cl.

ACS omega, 5(10):5235-5240.

Transparent single crystals of two new iodates K3Sc(IO3)6 and KSc(IO3)3Cl have been synthesized hydrothermally. Single-crystal X-ray diffraction was used to determine their crystal structures. Both compounds crystallize in non-centrosymmetric space groups. The compound K3Sc(IO3)6 crystallizes in the orthorhombic space group Fdd2. The crystal structure is made up of [ScO6] octahedra, [IO3] trigonal pyramids, and [KO8] distorted cubes. The compound KSc(IO3)3Cl crystallizes in the trigonal space group R3. The building blocks are [ScO6] octahedra, [KO12] polyhedra, and [IO3] trigonal pyramids. The Cl- ions act as counter ions and reside in tunnels in the crystal structure. The second harmonic generation (SHG) measurements at room temperature, using 1064 nm radiation, on polycrystalline samples show that the SHG intensities of K3Sc(IO3)6 and KSc(IO3)3Cl are around 2.8 and 2.5 times that of KH2PO4 (KDP), respectively. In addition, K3Sc(IO3)6 and KSc(IO3)3Cl are phase-matchable at the fundamental wavelength of 1064 nm. The large anharmonicity in the optical response of both compounds is further supported by an anomalous temperature dependence of optical phonon frequencies as well as their enlarged intensities in Raman scattering. The latter corresponds to a very large electronic polarizability.

RevDate: 2021-01-10
CmpDate: 2020-03-24

Bergström A, McCarthy SA, Hui R, et al (2020)

Insights into human genetic variation and population history from 929 diverse genomes.

Science (New York, N.Y.), 367(6484):.

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

RevDate: 2021-04-05
CmpDate: 2021-04-05

Stark MS, Denisova E, Kays TA, et al (2020)

Mutation Signatures in Melanocytic Nevi Reveal Characteristics of Defective DNA Repair.

The Journal of investigative dermatology, 140(10):2093-2096.e2.

RevDate: 2020-11-10
CmpDate: 2020-11-10

Rogers AR, Harris NS, AA Achenbach (2020)

Neanderthal-Denisovan ancestors interbred with a distantly related hominin.

Science advances, 6(8):eaay5483.

Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.

RevDate: 2020-03-09
CmpDate: 2020-03-09

Denisova OA, Gudina TV, Bukina IA, et al (2020)

[The medical pedagogical prevention of deviant behavior in adolescents from disadvantaged family in conditions of rural school].

Problemy sotsial'noi gigieny, zdravookhraneniia i istorii meditsiny, 28(1):74-82.

The article considers medical and pedagogical prevention of deviant behavior of adolescents from dysfunctional families in conditions of rural school, related to the need of strengthening targeted joint interaction of medical and pedagogical institutions. The description and results of testing of diagnostic tools used to establish severity of deviant behavior of children in a selected group is discussed. The interaction of medical and educational institutions in preventing deviant behavior of adolescents from dysfunctional families in rural school is of key importance for combating prevalence of drug addiction, tobacco smoking, alcohol abuse and psychoactive substances consumption, and contributing to physical and mental health promotion of younger generation, development of healthy lifestyle. The study was organized to cover cognitive, behavioral, affective and value-motivational components. The qualitative characteristics of levels of severity of deviant behavior of adolescents from dysfunctional families were developed and proposed for practice application.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Agrawal R, Testi I, Mahajan S, et al (2021)

Collaborative Ocular Tuberculosis Study Consensus Guidelines on the Management of Tubercular Uveitis-Report 1: Guidelines for Initiating Antitubercular Therapy in Tubercular Choroiditis.

Ophthalmology, 128(2):266-276.

TOPIC: An international, expert-led consensus initiative organized by the Collaborative Ocular Tuberculosis Study (COTS), along with the International Ocular Inflammation Society and the International Uveitis Study Group, systematically developed evidence- and experience-based recommendations for the treatment of tubercular choroiditis.

CLINICAL RELEVANCE: The diagnosis and management of tubercular uveitis (TBU) pose a significant challenge. Current guidelines and literature are insufficient to guide physicians regarding the initiation of antitubercular therapy (ATT) in patients with TBU.

METHODS: An international expert steering subcommittee of the COTS group identified clinical questions and conducted a systematic review of the published literature on the use of ATT for tubercular choroiditis. Using an interactive online questionnaire, guided by background knowledge from published literature, 81 global experts (including ophthalmologists, pulmonologists, and infectious disease physicians) generated preliminary consensus statements for initiating ATT in tubercular choroiditis, using Oxford levels of medical evidence. In total, 162 statements were identified regarding when to initiate ATT in patients with tubercular serpiginous-like choroiditis, tuberculoma, and tubercular focal or multifocal choroiditis. The COTS group members met in November 2018 to refine these statements by a 2-step modified Delphi process.

RESULTS: Seventy consensus statements addressed the initiation of ATT in the 3 subtypes of tubercular choroiditis, and in addition, 10 consensus statements were developed regarding the use of adjunctive therapy in tubercular choroiditis. Experts agreed on initiating ATT in tubercular choroiditis in the presence of positive results for any 1 of the positive immunologic tests along with radiologic features suggestive of tuberculosis. For tubercular serpiginous-like choroiditis and tuberculoma, positive results from even 1 positive immunologic test were considered sufficient to recommend ATT, even if there were no radiologic features suggestive of tuberculosis.

DISCUSSION: Consensus guidelines were developed to guide the initiation of ATT in patients with tubercular choroiditis, based on the published literature, expert opinion, and practical experience, to bridge the gap between clinical need and available medical evidence.

RevDate: 2020-03-03

Shlyakhtina AV, Avdeev M, Lyskov NV, et al (2020)

Structure, conductivity and magnetism of orthorhombic and fluorite polymorphs in MoO3-Ln2O3 (Ln = Gd, Dy, Ho) systems.

Dalton transactions (Cambridge, England : 2003), 49(9):2833-2842.

Phase-pure orthorhombic compositions at a Ln/Mo ratio ∼ 5.2-5.7 (Ln = Gd, Dy, Ho) have been obtained for the first time by prolonged (40-160 h) heat treatment of mechanically activated 5Ln2O3 + 2MoO3 (Ln = Gd, Dy, Ho) oxide mixtures at 1200 °C. Although the starting Ln : Mo ratio was 5 : 1 (Ln10Mo2O21 (Ln = Dy, Ho)), it changed slightly in the final product due to the volatility of molybdenum oxide at 1200 °C (40-160 h) (ICP-MS analysis). Brief high-temperature firing (1600 °C, 3 h) of 5Ln2O3 + 2MoO3 (Ln = Gd, Dy, Ho) oxide mixtures leads to the formation of phase-pure fluorites with compositions close to Ln10Mo2O21 (Ln = Gd, Dy, Ho). Gd10Mo2O21 molybdate seems to undergo an order-disorder (orthorhombic-fluorite) phase transition in the range of 1200-1600 °C. For the first time, using the neutron diffraction method, it was shown that low-temperature phases with a Ln/Mo ratio ∼ 5.2-5.7 (Ln = Gd, Dy, Ho) have an orthorhombic structure rather than a tetragonal structure. Proton contribution to the total conductivity of Ln10Mo2O21 (Ln = Gd, Dy, Ho) fluorites and gadolinium and dysprosium orthorhombic phases in a wet atmosphere was observed for the first time. In both orthorhombic and fluorite phases, the total conductivity in wet air decreases with decreasing lanthanide ionic radii. In a wide temperature range, the compounds under study exhibit paramagnetic behaviour. However, the orthorhombic phases of Dy and Ho compounds reach the antiferromagnetic state at 2.4 K and 2.6 K, respectively.

RevDate: 2020-02-11

Gokhman D, Mishol N, de Manuel M, et al (2020)

Reconstructing Denisovan Anatomy Using DNA Methylation Maps.

Cell, 180(3):601.

RevDate: 2021-07-12
CmpDate: 2021-07-12

Rudnev S, Burns JS, Williams PL, et al (2020)

Comparison of bioimpedance body composition in young adults in the Russian Children's Study.

Clinical nutrition ESPEN, 35:153-161.

BACKGROUND & AIMS: Body mass index is a simple anthropometric measure (kg/m2) used as an indirect estimate of body fat in individuals, and in assessments of population health and comparisons between populations. Bioelectrical impedance analysis (BIA) is often used to provide additional information on body fat and fat-free mass, and has been used to generate body composition reference data in national health surveys. However, BIA measurements are known to be device-specific and there are few published studies comparing results from different BIA instruments. Therefore, we compared the performance of two BIA instruments in the Russian Children's Study (RCS) of male growth, pubertal development and maturation.

METHODS: Paired BIA measurements were obtained using the Tanita BC-418MA (Tanita Corp., Tokyo, Japan) and ABC-01 'Medas' (Medas Ltd, Moscow, Russia) BIA instruments. Cross-sectional data on 236 RCS subjects aged 18-22 years were used for the BIA comparison and the development of a conversion formula between measured resistances; follow-up data (n = 96) were used for validation of the conversion formula.

RESULTS: Whole-body resistances were highly correlated (Spearman rho = 0.95), but fat mass (FM) estimates were significantly higher with the Medas than the Tanita device (median difference 3.3 kg, 95% CI: 2.9, 3.6 kg) with large limits of agreement (LoA) for the FM difference (-2.0, 8.6 kg). A conversion formula between the resistances (Res) was obtained: Medas Res = 0.882 × Tanita Res+26.2 (r2 = 0.91, SEE = 17.6 Ohm). After applying the conversion formula to Tanita data and application of the Medas assessment algorithm, the 'converted' Tanita FM estimates closely matched the Medas original estimates (median difference -0.1 kg, 95% CI: -0.3, 0.2 kg), with relatively small LoA for the FM difference (-2.3 to 2.1 kg), suggesting potential interchangeability of the ABC-01 'Medas' and Tanita BC-418MA data at the group level.

CONCLUSIONS: Our results support the importance of cross-calibration of BIA instruments for population comparisons and proper data interpretation in clinical and epidemiological studies.

RevDate: 2021-03-22
CmpDate: 2021-03-22

Gouy A, L Excoffier (2020)

Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens.

Molecular biology and evolution, 37(5):1420-1433.

Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.

RevDate: 2020-04-20
CmpDate: 2020-04-20

Bücking R, Cox MP, Hudjashov G, et al (2019)

Archaic mitochondrial DNA inserts in modern day nuclear genomes.

BMC genomics, 20(1):1017.

BACKGROUND: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs).

RESULTS: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male.

CONCLUSIONS: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

RevDate: 2020-06-17
CmpDate: 2020-04-06

Scott GR, Irish JD, M Martinón-Torres (2020)

A more comprehensive view of the Denisovan 3-rooted lower second molar from Xiahe.

Proceedings of the National Academy of Sciences of the United States of America, 117(1):37-38.

RevDate: 2021-01-10

Agrawal R, Agarwal A, Jabs DA, et al (2019)

Standardization of Nomenclature for Ocular Tuberculosis - Results of Collaborative Ocular Tuberculosis Study (COTS) Workshop.

Ocular immunology and inflammation [Epub ahead of print].

Purpose: To standardize a nomenclature system for defining clinical phenotypes, and outcome measures for reporting clinical and research data in patients with ocular tuberculosis (OTB).Methods: Uveitis experts initially administered and further deliberated the survey in an open meeting to determine and propose the preferred nomenclature for terms related to the OTB, terms describing the clinical phenotypes and treatment and reporting outcomes.Results: The group of experts reached a consensus on terming uveitis attributable to tuberculosis (TB) as tubercular uveitis. The working group introduced a SUN-compatible nomenclature that also defines disease "remission" and "cure", both of which are relevant for reporting treatment outcomes.Conclusion: A consensus nomenclature system has been adopted by a large group of international uveitis experts for OTB. The working group recommends the use of standardized nomenclature to prevent ambiguity in communication and to achieve the goal of spreading awareness of this blinding uveitis entity.

RevDate: 2020-08-24
CmpDate: 2020-04-02

Wall JD, Ratan A, Stawiski E, et al (2019)

Identification of African-Specific Admixture between Modern and Archaic Humans.

American journal of human genetics, 105(6):1254-1261.

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

RevDate: 2020-01-08
CmpDate: 2019-12-18

Buzlukov AL, Arapova IY, Baklanova YV, et al (2019)

Coexistence of three types of sodium motion in double molybdate Na9Sc(MoO4)6: 23Na and 45Sc NMR data and ab initio calculations.

Physical chemistry chemical physics : PCCP, 22(1):144-154.

The rechargeable Na-ion batteries attract much attention as an alternative to the widely used but expensive Li-ion batteries. The search for materials with high sodium diffusion is important for the development of solid state electrolytes. We present the results of experimental and ab initio studies of the Na-ion diffusion mechanism in Na9Sc(MoO4)6. The ion conductivity reaches the value of 3.6 × 10-2 S cm-1 at T ∼ 850 K. The 23Na and 45Sc NMR data reveal the coexistence of three different types of Na-ion motion in the temperature range from 300 to 750 K. They are activated at different temperatures and are characterized by substantially different dynamics parameters. These features are confirmed by ab initio calculations of activation barriers for sodium diffusion along various paths.

RevDate: 2020-01-10
CmpDate: 2020-01-10

Bulynko SA, Denisova OA, Kovalets ES, et al (2019)

[Two cases of bilateral lymphangiomatous palatine tonsil polyps in children].

Vestnik otorinolaringologii, 84(5):73-75.

Lymphangiomatous polyps of palatine tonsils are a rare condition, which is diagnosed with patomorphological study. About cases in total are reported in the literature, mostly with one-sided lesions. We managed to find only two reports of lymphangiomatous polyps of palatine tonsils in the available literature. The patients were children in both cases. We report our two cases of children with lymphangiomatous polyps of palatine tonsils.

RevDate: 2020-01-13
CmpDate: 2020-01-13

Evseeva NV, Tkachenko OV, Denisova AY, et al (2019)

Functioning of plant-bacterial associations under osmotic stress in vitro.

World journal of microbiology & biotechnology, 35(12):195.

The search for effective plant-growth-promoting strains of rhizospheric bacteria that would ensure the resistance of plant-microbial associations to environmental stressors is essential for the design of environmentally friendly agrobiotechnologies. We investigated the interaction of potato (cv. Nevsky) microplants with the plant-growth-promoting bacteria Azospirillum brasilense Sp245 and Ochrobactrum cytisi IPA7.2 under osmotic stress in vitro. The bacteria improved the physiological and biochemical variables of the microplants, significantly increasing shoot length and root number (1.3-fold, on average). Inoculation also led a more effective recovery of the plants after stress. During repair, inoculation contributed to a decreased leaf content of malonic dialdehyde. With A. brasilense Sp245, the decrease was 1.75-fold; with O. cytisi IPA7.2, it was 1.4-fold. During repair, the shoot length, node number, and root number of the inoculated plants were greater than the control values by an average of 1.3-fold with A. brasilense Sp245 and by an average of 1.6-fold with O. cytisi IPA7.2. O. cytisi IPA7.2, previously isolated from the potato rhizosphere, protected the physiological and biochemical processes in the plants under stress and repair better than did A. brasilense Sp245. Specifically, root weight increased fivefold during repair, as compared to the noninoculated plants, while chlorophyll a content remained at the level found in the nonstressed controls. The results indicate that these bacteria can be used as components of biofertilizers. A. brasilense Sp245 has favorable prospects for use in temperate latitudes, whereas O. cytisi IPA7.2 can be successfully used in saline and drought-stressed environments.

RevDate: 2020-09-09
CmpDate: 2020-09-09

Bazhan N, Jakovleva T, Feofanova N, et al (2019)

Sex Differences in Liver, Adipose Tissue, and Muscle Transcriptional Response to Fasting and Refeeding in Mice.

Cells, 8(12):.

Fasting is often used for obesity correction but the "refeeding syndrome" limits its efficiency, and molecular mechanisms underlying metabolic response to different food availability are under investigation. Sex was shown to affect hormonal and metabolic reactions to fasting/refeeding. The aim of this study was to evaluate hormonal and transcriptional responses to fasting and refeeding in male and female C57Bl/6J mice. Sex asymmetry was observed both at the hormonal and transcriptional levels. Fasting (24 h) induced increase in hepatic Fgf21 gene expression, which was associated with elevation of plasma FGF21 and adiponectin levels, and the upregulation of expression of hepatic (Pparα, Cpt1α) and muscle (Cpt1β, Ucp3) genes involved in fatty acid oxidation. These changes were more pronounced in females. Refeeding (6 h) evoked hyperinsulinemia and increased hepatic expression of gene related to lipogenesis (Fasn) only in males and hyperleptinemia and increase in Fgf21 gene expression in muscles and adipose tissues only in females. The results suggest that in mice, one of the molecular mechanisms underlying sex asymmetry in hepatic Pparα, Cpt1α, muscle Cpt1β, and Ucp3 expression during fasting is hepatic Fgf21 expression, and the reason for sex asymmetry in hepatic Fasn expression during refeeding is male-specific hyperinsulinemia.

RevDate: 2019-11-14

Eremin DB, Denisova EA, Yu Kostyukovich A, et al (2019)

Ionic Pd/NHC Catalytic System Enables Recoverable Homogeneous Catalysis: Mechanistic Study and Application in the Mizoroki-Heck Reaction.

Chemistry (Weinheim an der Bergstrasse, Germany) [Epub ahead of print].

Invited for the cover of this issue is Valentine P. Ananikkov and co-workers. The image depicts the dynamic behaviour of a Pd/NHC catalytic system with easy transition from molecular to ionic complex. Read the full text of the article at 10.1002/chem.201903221.

RevDate: 2021-01-04
CmpDate: 2021-01-04

Denisova EI, Kozhevnikova VV, Bazhan NM, et al (2020)

Sex-specific effects of leptin administration to pregnant mice on the placentae and the metabolic phenotypes of offspring.

FEBS open bio, 10(1):96-106.

Obesity during pregnancy has been shown to increase the risk of metabolic diseases in the offspring. However, the factors within the maternal milieu which affect offspring phenotypes and the underlying mechanisms remain unknown. The adipocyte hormone leptin plays a key role in regulating energy homeostasis and is known to participate in sex-specific developmental programming. To examine the action of leptin on fetal growth, placental gene expression and postnatal offspring metabolism, we injected C57BL mice with leptin or saline on gestational day 12 and then measured body weights (BWs) of offspring fed on a standard or obesogenic diet, as well as mRNA expression levels of insulin-like growth factors and glucose and amino acid transporters. Male and female offspring born to leptin-treated mothers exhibited growth retardation before and a growth surge after weaning. Mature male offspring, but not female offspring, exhibited increased BWs on a standard diet. Leptin administration prevented the development of hyperglycaemia in the obese offspring of both sexes. The placentas of the male and female foetuses differed in size and gene expression, and leptin injection decreased the fetal weights of both sexes, the placental weights of the male foetuses and placental gene expression of the GLUT1 glucose transporter in female foetuses. The data suggest that mid-pregnancy is an ontogenetic window for the sex-specific programming effects of leptin, and these effects may be exerted via fetal sex-specific placental responses to leptin administration.

RevDate: 2020-12-17
CmpDate: 2020-12-17

Gokcumen O (2020)

Archaic hominin introgression into modern human genomes.

American journal of physical anthropology, 171 Suppl 70:60-73.

Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?

RevDate: 2021-03-15
CmpDate: 2021-03-15

Denisova O, Chernogoryuk G, Baranovskaya N, et al (2020)

Trace Elements in the Lung Tissue Affected by Sarcoidosis.

Biological trace element research, 196(1):66-73.

In the lungs of 76 patients with verified sarcoidosis, 28 chemical elements were identified with neutron activation analysis. High levels of Ca, Fe, Cr, Co, Cs, Eu, Lu, Th, Hf, Au, and U and low level of Na compared to the control samples were determined in sarcoidosis. There were no significant differences in the content of Zn, Rb, La, Sm, Sr, Nd, As, Br, Ag, Tb, Sc, Ta, Sb, Ba, and Yb. Spearman correlation analysis shows multiple positive associations, with the maximum being in pairs as follows: Fe-Cr, Eu-La, Ce-Lu, Hf-Cr, Sc-Zn, Fe-Hf, Ce-Co, and Sb-Cr. These studies support the hypothesis that sarcoidosis is a response of the organism in the form of granulomatous inflammation when exposed to heavy metals and rare earth elements in the environment. We assume that the role of calcium and iron is to separate granulomas from the tissues of the body.

RevDate: 2021-01-10
CmpDate: 2019-12-16

Colbran LL, Gamazon ER, Zhou D, et al (2019)

Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.

Nature ecology & evolution, 3(11):1598-1606.

Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes' regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.

RevDate: 2020-01-31
CmpDate: 2020-01-31

Shchenkov SV, Denisova SA, Kremnev GA, et al (2019)

Five new morphological types of virgulate and microcotylous xiphidiocercariae based on morphological and molecular phylogenetic analyses.

Journal of helminthology, 94:e94 pii:S0022149X19000853.

The phylogenetic position of most xiphidiocercariae from subgroups Cercariae virgulae and Cercariae microcotylae remains unknown or unclear, even at the family level. In this paper, we studied the morphology and molecular phylogeny of 15 microcotylous and virgulate cercariae (11 new and four previously described ones). Based on morphological and molecular data, we suggested five distinct morphological types of xiphidiocercariae, which are a practical alternative to Cercariae virgulae and Cercariae microcotylae subgroups. Four of these types correspond to actual digenean taxa (Microphallidae, Lecithodendriidae, Pleurogenidae and Prosthogonimidae), while the fifth is represented by Cercaria nigrospora Wergun, 1957, which we classified on the basis of molecular data for the first time. We reassessed the relative importance of morphological characters used for the classification of virgulate and microcotylous cercariae, and discussed the main evolutionary trends within xiphidiocercariae. Now stylet cercariae can be reliably placed into several sub-taxa of Microphalloidea on the basis of their morphological features.

RevDate: 2020-06-23
CmpDate: 2020-06-23

Mata X, Renaud G, C Mollereau (2019)

The repertoire of family A-peptide GPCRs in archaic hominins.

Peptides, 122:170154.

Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. We then searched in the literature the functional changes, phenotypes and risk of disease possibly associated with the detected variants. Our survey suggests that Neanderthal and Denisovan hominins were likely prone to lower risk of obesity, to enhanced platelet aggregation in response to thrombin, to better response to infection, to less anxiety and aggressiveness and to favorable sociability. While some archaic variants were likely advantageous in the past, they might be responsible for maladaptive disorders today in the context of modern life and/or specific regional distribution. For example, an archaic haplotype in the neuromedin receptor 2 is susceptible to confer risk of diabetic nephropathy in type 1 diabetes in present-day Europeans. Paying attention to the pharmacological properties of some of the archaic variants described in this study may be helpful to understand the variability of therapeutic efficacy between individuals or ethnic groups.

RevDate: 2021-01-10
CmpDate: 2020-10-26

Morley MW, Goldberg P, Uliyanov VA, et al (2019)

Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).

Scientific reports, 9(1):13785.

Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.

RevDate: 2020-06-08
CmpDate: 2020-06-08

Gokhman D, Mishol N, de Manuel M, et al (2019)

Reconstructing Denisovan Anatomy Using DNA Methylation Maps.

Cell, 179(1):180-192.e10.

Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.


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One of the most intriguing, and philosophically suggestive, recent scientific findings has been the discovery that the human lineage included several branches at the species level in which each species had developed culture (tool making, mastery of fire, burial of the dead). Before the Chicxulub impact that ended the realm of the dinosaurs, sentience and culture had not occurred in any lineage, despite several hundred million years of evolution. However, in the mammalian radiation that occurred afterwards, several primate lineages occurred. In just the last few million years, one of those lineages diverged into several sentient, culture-developing species. This book explores how only one of those species (ours) survived, while the others went extinct. Recommended. R. Robbins

Electronic Scholarly Publishing
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Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )