1. AUTOMATED BIBLIOGRAPHY: Pangenome
Although the enforced stability of genomic content is ubiquitous among multi-cellular eukaryotes, the opposite is proving to be the case among prokaryotes, which exhibit remarkable and adaptive plasticity of genomic content. Early bacterial whole-genome sequencing efforts discovered that whenever a particular "species" was re-sequenced, new genes were found that had not been detected earlier — entirely new genes, not merely new alleles. This led to the concepts of the bacterial core-genome, the set of genes found in all members of a particular "species", and the flex-genome, the set of genes found in some, but not all members of the "species". Together these make up the species' pan-genome.
2. /recommended/literature//paleo-seq/
3. AUTOMATED BIBLIOGRAPHY: Paleonotology Meets Genomics — Sequencing Ancient DNA
The ideas behind Jurassic Park have become real, kinda sorta. It is now possible to retrieve and sequence DNA from ancient specimens. Although these sequences arebased on poor quality DNA and thus have many inferential steps (i,e, the resultingsequence is not likely to be a perfect replica of the living DNA), the insights tobe gained from paleosequentcing are nonetheless great. For example, paleo-sequencinghas shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.
4. AUTOMATED BIBLIOGRAPHY: Symbiosis
Symbiosis refers to an interaction between two or moredifferent organisms living in close physical association, typically tothe advantage of both. Symbiotic relationships were once thought to beexceptional situations. Recent studies, however, have shown thatevery multicellular eukaryote exists in a tight symbioticrelationship with billions of microbes. The associated microbial ecosystemsare referred to as microbiome and the combination of a multicellular organism and its microbiota has been described as a holobiont. It seems "we are all lichens now."
5. AUTOMATED BIBLIOGRAPHY: Archaea
In 1977, Carl Woese and George Fox applied molecular techniques to biodiversity and discovered that life on Earth consisted of three, not two (prokaryotes and eukaryotes), major lineages, tracing back nearly to the very origin of life on Earth. The third lineagehas come to be known as the Archaea. Organisms now considered Archaea were originally thought to be a kind of prokaryote, but Woese and Fox showed that they were as different from prokaryotes as they were from eukaryotes. To understand life on Earthone must also understand the Archaea.
6. AUTOMATED BIBLIOGRAPHY: Neanderthals
Wikipedia: Neanderthals or Neandertals — named for the Neandertal region in Germany — were a species or subspecies of archaic human, in the genus Homo. Neanderthals became extinct around 40,000 years ago. They were closely related to modern humans, sharing 99.7% of DNA. Remains left by Neanderthals include bone and stone tools, which are found in Eurasia, from Western Europe to Central and Northern Asia. Neanderthals are generally classified by paleontologists as the species Homo neanderthalensis, having separated from the Homo sapiens lineage 600,000 years ago, but a minority consider them to be a subspecies of Homo sapiens (Homo sapiens neanderthalensis). Several cultural assemblages have been linked to the Neanderthals in Europe. The earliest, the Mousterian stone tool culture, dates to about 160,000 years ago. Late Mousterian artifacts were found in Gorham's Cave on the south-facing coast of Gibraltar.Compared to Homo sapiens, Neanderthals had a lower surface-to-volume ratio, with shorter legs and a bigger body, in conformance with Bergmann's rule, as an energy-loss reduction adaptation to life in a high-latitude (i.e. seasonally cold) climate. Their average cranial capacity was notably larger than typical for modern humans: 1600 cm3 vs. 1250-1400 cm3. The Neanderthal genome project published papers in 2010 and 2014 stating that Neanderthals contributed to the DNA of modern humans, including most humans outside sub-Saharan Africa, as well as a few populations in sub-Saharan Africa, through interbreeding, likely between 50,000 and 60,000 years ago.
7. /recommended/literature//aa-bd-pangenome/
8. AUTOMATED BIBLIOGRAPHY: Metagenomics
While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.
9. AUTOMATED BIBLIOGRAPHY: 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.
10. AUTOMATED BIBLIOGRAPHY: CRISPR-Cas
Clustered regularly interspaced short palindromic repeats (CRISPR, pronounced crisper) are segments of prokaryotic DNA containing short repetitions of base sequences. Each repetition is followed by short segments of "spacer DNA" from previous exposures to foreign DNA (e.g a virus or plasmid).The CRISPR/Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages, and provides a form of acquired immunity. CRISPR associated proteins (Cas) use the CRISPR spacers to recognize and cut these exogenous genetic elements in a manner analogous to RNA interference in eukaryotic organisms. CRISPRs are found in approximately 40% of sequenced bacterial genomes and 90% of sequenced archaea.By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added. The Cas9-gRNA complex corresponds with the CAS III crRNA complex in the above diagram. CRISPR/Cas genome editing techniques have many potential applications, including altering the germline of humans, animals, and food crops. The use of CRISPR Cas9-gRNA complex for genome editing was the AAAS's choice for breakthrough of the year in 2015.
11. AUTOMATED BIBLIOGRAPHY: Climate Change
The world is warming up, with 2023 being by far the hottest year since record keeping began and 2024 shaping up to be hotter yet. But these changes only involve one or two degrees. What's the big deal?
The amount of energy required to raise the temperature of one liter of water by one degree is one kilocalorie (kcal). Scaling up, the amount of energy required for a one-degree increase in the water temperature of the Gulf of Mexico is 2,434,000,000,000,000,000 kcals. That's 25 million times more energy than released by the WW-II atomic bomb that destroyed the city of Hiroshima and killed more than 100,000 people.
So, for every one degree increase in water temperature, the Gulf of Mexico takes on 25-million atomic bombs worth of new energy, which is then available to fuel hurricanes and other storms. Maybe a one-degree rise in temperature is a big deal.
12. /recommended/literature//crispr/
13. AUTOMATED BIBLIOGRAPHY: Fecal Transplantation
Fecal Transplantion is a procedure in which fecal matter is collected from a tested donor, mixed with a saline or other solution, strained, and placed in a patient, by colonoscopy, endoscopy, sigmoidoscopy, or enema.The theory behind the procedure is that a normal gut microbial ecosystem is required for good health and that sometimes a benefucuial ecosystem can be destroyed, perhaps by antibiotics,allowing other bacteria, specifically Clostridium difficile to over-populate the colon, causing debilitating, sometimes fatal diarrhea.C. diff. is on the rise throughout the world. The CDC reports that approximately 347,000 people in the U.S. alone were diagnosed with this infection in 2012. Of those, at least 14,000 died.Fecal transplant has also had promising results with many other digestive or auto-immune diseases, including Irritable Bowel Syndrome, Crohn's Disease, and Ulcerative Colitis. It has also been used around the world to treat other conditions, although more research in other areas is needed.Fecal transplant was first documented in 4th century China, where the treatment wasknown as yellow soup.
14. AUTOMATED BIBLIOGRAPHY: Brain-Computer Interface
Wikipedia: A brainG€“computer interface (BCI), sometimes called a neural control interface (NCI), mindG€“machine interface (MMI), direct neural interface (DNI), or brainG€“machine interface (BMI), is a direct communication pathway between an enhanced or wired brain and an external device. BCIs are often directed at researching, mapping, assisting, augmenting, or repairing human cognitive or sensory-motor functions.Research on BCIs began in the 1970s at the University of California, Los Angeles (UCLA) under a grant from the National Science Foundation, followed by a contract from DARPA. The papers published after this research also mark the first appearance of the expression brainG€“computer interface in scientific literature.BCI-effected sensory input: Due to the cortical plasticity of the brain, signals from implanted prostheses can, after adaptation, be handled by the brain like natural sensor or effector channels. Following years of animal experimentation, the first neuroprosthetic devices implanted in humans appeared in the mid-1990s.BCI-effected motor output: When artificial intelligence is used to decode neural activity, then send that decoded information to some kind of effector device, BCIs have the potential to restore communication to people who have lost the ability to move or speak. To date, the focus has largely been on motor skills such as reaching or grasping. However, in May of 2021 a study showed that an AI/BCI system could be use to translate thoughts about handwriting into the output of legible characters at a usable rate (90 characters per minute with 94% accuracy).
16. AUTOMATED BIBLIOGRAPHY: Topologically Associating Domains
"Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the mechanisms of their formation and how they exert their regulatory effect on embedded genes. Further, similar domains have been detected in other organisms, including flies, worms, fungi and bacteria. Although in all these cases these domains appear similar as detected by 3C-based methods, their biology appears to be quite distinct with differences in the protein complexes involved in their formation and differences in their internal organization."QUOTE FROM: Dekker Job and Heard Edith (2015), Structural and functional diversity of Topologically Associating Domains, FEBS Letters, 589, doi: 10.1016/j.febslet.2015.08.044
17. AUTOMATED BIBLIOGRAPHY: Microbiome
It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.
18. AUTOMATED BIBLIOGRAPHY: Feathered Dinosaurs
"A feathered dinosaur is any species of dinosaur possessing feathers. For over 150 years, since scientific research began on dinosaurs in the early 1800s, dinosaurs were generally believed to be related to the reptile family; the word "dinosaur", coined in 1842 by paleontologist Richard Owen, comes from the Greek for "formidable lizard". This view began to shift during the so-called dinosaur renaissance in scientific research in the late 1960s, and by the mid-1990s significant evidence had emerged that dinosaurs are much more closely related to birds. In fact, birds are now believed to have descended directly from the theropod group of dinosaurs, and are thus classified as dinosaurs themselves, meaning that any modern bird can be considered a feathered dinosaur, since all modern birds possess feathers (with the exception of a few artificially selected chickens).Among extinct dinosaurs, feathers or feather-like integument have been discovered on dozens of genera via both direct and indirect fossil evidence. The vast majority of feather discoveries have been for coelurosaurian theropods. However, integument has also been discovered on at least three ornithischians, raising the likelihood that proto-feathers were also present in earlier dinosaurs." QUOTE FROM: Wikipedia
19. AUTOMATED BIBLIOGRAPHY: Homo floresiensis, The Hobbit
Wikipedia:Homo floresiensis ("Flores Man"; nicknamed "hobbit" for its small stature) is an extinct species in the genus Homo.The remains of an individual that would have stood about 3.5 feet (1.1 m) in height were discovered in 2003 at Liang Bua on the island of Flores in Indonesia. Partial skeletons of nine individuals have been recovered, including one complete skull, referred to as "LB1".These remains have been the subject of intense research to determine whether they represent a species distinct from modern humans. This hominin had originally been considered to be remarkable for its survival until relatively recent times, only 12,000 years ago. However, more extensive stratigraphic and chronological work has pushed the dating of the most recent evidence of their existence back to 50,000 years ago. Their skeletal material is now dated to from 100,000 to 60,000 years ago; stone tools recovered alongside the skeletal remains were from archaeological horizons ranging from 190,000 to 50,000 years ago.Fossil teeth and a partial jaw from hominins believed ancestral to H. floresiensis were discovered in 2014 and described in 2016. These remains are from a site on Flores called Mata Menge, about 74 km from Liang Bua. They date to about 700,000 years ago and are even smaller than the later fossils. The form of the fossils has been interpreted as suggesting that they are derived from a population of H. erectus that arrived on Flores about a million years ago (as indicated by the oldest artifacts excavated on the island) and rapidly became dwarfed.The discoverers (archaeologist Mike Morwood and colleagues) proposed that a variety of features, both primitive and derived, identify these individuals as belonging to a new species, H. floresiensis, within the taxonomic tribe of Hominini, which includes all species that are more closely related to humans than to chimpanzees. Based on previous date estimates, the discoverers also proposed that H. floresiensis lived contemporaneously with modern humans on Flores.Two orthopedic researches published in 2007 reported evidence to support species status for H. floresiensis. A study of three tokens of carpal (wrist) bones concluded there were differences from the carpal bones of modern humans and similarities to those of a chimpanzee or an early hominin such as Australopithecus. A study of the bones and joints of the arm, shoulder, and lower limbs also concluded that H. floresiensis was more similar to early humans and other apes than modern humans. In 2009, the publication of a cladistic analysis and a study of comparative body measurements provided further support for the hypothesis that H. floresiensis and Homo sapiens are separate species.
20. AUTOMATED BIBLIOGRAPHY: Biofilm
It is well known that relative size greatly affects how organisms interact with the world. Less well known, at least among biologists, is that at sufficiently small sizes, mechanical interaction with the environment becomes difficult and then virtually impossible. In fluid dynamics, an important dimensionless parameter is the Reynolds Number (abbreviated Re), which is the ratio of inertial to viscous forces affecting the movement of objects in a fluid medium (or the movement of a fluid in a pipe). Since Re is determined mainly by the size of the object (pipe) and the properties (density and viscosity) of the fluid, organisms of different sizes exhibit significantly different Re values when moving through air or water. A fish, swimming at a high ratio of inertial to viscous forces, gives a flick of its tail and then glides for several body lengths. A bacterium, "swimming" in an environment dominated by viscosity, possesses virtually no inertia. When the bacterium stops moving its flagellum, the bacterium "coasts" for about a half of a microsecond, coming to a stop in a distance less than a tenth the diameter of a hydrogen atom. Similarly, the movement of molecules (nutrients toward, wastes away) in the vicinity of a bacterium is dominated by diffusion. Effective stirring — the generation of bulk flow through mechanical means — is impossible at very low Re. An understanding of the constraints imposed by life at low Reynolds numbers is essentially for understanding the prokaryotic biosphere.
21. AUTOMATED BIBLIOGRAPHY: Drosophila: The Fly Room
In the small "Fly Room" at Columbia University, T. H. Morgan and his students, A. H. Sturtevant, C. B. Bridges, H. J. Muller, carried out the work that laid the foundations of modern, chromosomal genetics. The excitement of those times, when the whole field of genetics was being created, is captured in this book, written by one of those present at the beginning. In a time when genomics and genetics maps are discussed almost daily in the popular press, it is worth remembering that the world's first genetic map was created in 1913 by A. H. Sturtevant, then a sophomore in college. In 1933, Morgan received the Nobel Prize in medicine, for his "discoveries concerning the role played by the chro- mosome in heredity." In the 67 years since, genetics has continued to advance, leaving behind a fascinating history. The year 2000 was the 100th anniversary of the founding of modern genetics with the rediscovery of Mendel' work and it is the year in which the full DNA sequence of the Drosophila genome was obtained. The fruit fly is still at the center of genetic research, just as it was in 1910 when work first began in Morgan's fly room.
22. AUTOMATED BIBLIOGRAPHY: Horizontal Gene Transfer
The pathology-inducing genes of O157:H7 appear to have been acquired, likely via prophage, by a nonpathogenic E. coli ancestor, perhaps 20,000 years ago. That is, horizontal gene transfer (HGT) can lead to the profound phenotypic change from benign commensal to lethal pathogen. "Horizontal" in this context refers to the lateral or "sideways" movement of genes between microbes via mechanisms not directly associated with reproduction. HGT among prokaryotes can occur between members of the same "species" as well as between microbes separated by vast taxonomic distances. As such, much prokaryotic genetic diversity is both created and sustained by high levels of HGT. Although HGT can occur for genes in the core-genome component of a pan-genome, it occurs much more frequently among genes in the optional, flex-genome component. In some cases, HGT has become so common that it is possible to think of some "floating" genes more as attributes of the environment in which they are useful rather than as attributes of any individual bacterium or strain or "species" that happens to carry them. For example, bacterial plasmids that occur in hospitals are capable of conferring pathogenicity on any bacterium that successfully takes them up. This kind of genetic exchange can occur between widely unrelated taxa.
23. AUTOMATED BIBLIOGRAPHY: Endosymbiosis
A symbiotic relationship in which one of the partners lives within the other, especially if it lives within the cells of the other, is known as endosymbiosis.Mitochondria, chloroplasts, and perhaps other cellular organellesare believed to have originated from a form of endosymbiosis. The endosymbioticorigin of eukaryotes seems to have been a biological singularity — that is,it happened once, and only once, in the history of life on Earth.
24. AUTOMATED BIBLIOGRAPHY: Telomeres
n++Wikipedia:A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and meros "part". For vertebrates, the sequence of nucleotides in telomeres is TTAGGG, with the complementary DNA strand being AATCCC, with a single-stranded TTAGGG overhang. This sequence of TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kilobases at birth to less than 4 kilobases in old age, with the average rate of decline being greater in men than in women.During chromosome replication, the enzymes that duplicate DNA cannot continue their duplication all the way to the end of a chromosome, so in each duplication the end of the chromosome is shortened (this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand). The telomeres are disposable buffers at the ends of chromosomes which are truncated during cell division; their presence protects the genes before them on the chromosome from being truncated instead. The telomeres themselves are protected by a complex of shelterin proteins, as well as by the RNA that telomeric DNA encodes.
25. AUTOMATED BIBLIOGRAPHY: Wolbachia (ALL)
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WIKIPEDIA: Wolbachia is a genus of bacteria which "infects" (usually as intracellular symbionts) arthropod species, including a high proportion of insects, as well as some nematodes. It is one of the world's most common parasitic microbes and is possibly the most common reproductive parasite in the biosphere. Its interactions with its hosts are often complex, and in some cases have evolved to be mutualistic rather than parasitic. Some host species cannot reproduce, or even survive, without Wolbachia infection. One study concluded that more than 16% of neotropical insect species carry bacteria of this genus, and as many as 25 to 70 percent of all insect species are estimated to be potential hosts. Wolbachia also harbor a temperate bacteriophage called WO. Comparative sequence analyses of bacteriophage WO offer some of the most compelling examples of large-scale horizontal gene transfer between Wolbachia coinfections in the same host. It is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that were previously considered highly stable or prone to loss of genes overtime. Outside of insects, Wolbachia infects a variety of isopod species, spiders, mites, and many species of filarial nematodes (a type of parasitic worm), including those causing onchocerciasis ("River Blindness") and elephantiasis in humans as well as heartworms in dogs. Not only are these disease-causing filarial worms infected with Wolbachia, but Wolbachia seem to play an inordinate role in these diseases. A large part of the pathogenicity of filarial nematodes is due to host immune response toward their Wolbachia. Elimination of Wolbachia from filarial nematodes generally results in either death or sterility of the nematode.