ESP Library: Bibliographies 20 Dec 2024 Updated: 

Selected Bibliographies

(with links to sources)

Keeping up with the literature can be challenging. Here we offer several automatically-created bibliographies on selected topics, with links out to the original document (via the publisher's DOI), to PubMed, to Google Scholar, etc.

The bibliographies are updated regularly and are sorted to show the most recent at the top. For long bibliographies the link is to a page containing only the most recent 100 entries, with a Bibliography Options menu allowing access to a page with the remaining entries. These additional pages can be very large and slow to load, but they can be valuable if you are interested in a comprehensive listing. The options menu also allows you to download the entire bibliography in bibtex format, for easy loading into reference-management software. The topics are chosen because they seemed likely to be of interest to the ESP community. We would be happy to consider adding additional topics. Contact ESP to suggest additional topics.

Current Health Issues

covid-19 updated: 20 Dec 2024 at 01:43
48343 citations

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, or SARS-CoV-2), a virus closely related to the SARS virus. The disease was discovered and named during the 2019-20 coronavirus outbreak. Those affected may develop a fever, dry cough, fatigue, and shortness of breath. A sore throat, runny nose or sneezing is less common. While the majority of cases result in mild symptoms, some can progress to pneumonia and multi-organ failure. The infection is spread from one person to others via respiratory droplets produced from the airways, often during coughing or sneezing. Time from exposure to onset of symptoms is generally between 2 and 14 days, with an average of 5 days. The standard method of diagnosis is by reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab or sputum sample, with results within a few hours to 2 days. Antibody assays can also be used, using a blood serum sample, with results within a few days. The infection can also be diagnosed from a combination of symptoms, risk factors and a chest CT scan showing features of pneumonia. Correct handwashing technique, maintaining distance from people who are coughing and not touching one's face with unwashed hands are measures recommended to prevent the disease. It is also recommended to cover one's nose and mouth with a tissue or a bent elbow when coughing. Those who suspect they carry the virus are recommended to wear a surgical face mask and seek medical advice by calling a doctor rather than visiting a clinic in person. Masks are also recommended for those who are taking care of someone with a suspected infection but not for the general public. There is no vaccine or specific antiviral treatment, with management involving treatment of symptoms, supportive care and experimental measures. The case fatality rate is estimated at between 1% and 3%. The World Health Organization (WHO) has declared the 2019-20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC). As of 29 February 2020, China, Hong Kong, Iran, Italy, Japan, Singapore, South Korea and the United States are areas having evidence of community transmission of the disease.

PUBMED QUERY: ( SARS-CoV-2 OR COVID-19 OR (wuhan AND coronavirus) AND review[SB] ) NOT pmcbook NOT ispreviousversion

Classical Genetics

Classical Genetics updated: 20 Dec 2024 at 01:41
1727 citations

Wikipedia: Classical genetics is often referred to as the oldest form of genetics, and began with Gregor Mendel's experiments that formulated and defined a fundamental biological concept known as Mendelian Inheritance. Mendelian Inheritance is the process in which genes and traits are passed from a set of parents to their offspring. These inherited traits are passed down mechanistically with one gene from one parent and the second gene from another parent in sexually reproducing organisms. This creates the pair of genes in diploid organisms. Gregor Mendel started his experimentation and study of inheritance with phenotypes of garden peas and continued the experiments with plants. He focused on the patterns of the traits that were being passed down from one generation to the next generation. This was assessed by test-crossing two peas of different colors and observing the resulting phenotypes. After determining how the traits were likely inherited, he began to expand the amount of traits observed and tested and eventually expanded his experimentation by increasing the number of different organisms he tested.

PUBMED QUERY: 1890:1938[PDAT] AND (genetic OR gene OR genes OR genetics OR heredity OR inheritance OR mutation OR chromosome OR mendel) NOT pmcbook NOT ispreviousversion

Classical Genetics: Drosophila updated: 20 Dec 2024 at 01:41
943 citations

Wikipedia: Drosophila is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit. One species of Drosophila in particular, D. melanogaster, has been heavily used in research in genetics and is a common model organism in developmental biology. The terms "fruit fly" and "Drosophila" are often used synonymously with D. melanogaster in modern biological literature. The entire genus, however, contains more than 1,500 species and is very diverse in appearance, behavior, and breeding habitat. D. melanogaster is a popular experimental animal because it is easily cultured en masse out of the wild, has a short generation time, and mutant animals are readily obtainable. In 1906, Thomas Hunt Morgan began his work on D. melanogaster and reported his first finding of a 'white' (eyed) mutant in 1910 to the academic community. He was in search of a model organism to study genetic heredity and required a species that could randomly acquire genetic mutation that would visibly manifest as morphological changes in the adult animal. His work on Drosophila earned him the 1933 Nobel Prize in Medicine for identifying chromosomes as the vector of inheritance for genes.

PUBMED QUERY: 1890:1953[PDAT] AND drosophila NOT pmcbook NOT ispreviousversion

Classical Genetics: Mutation updated: 20 Dec 2024 at 01:41
1529 citations

Wikipedia: We now know that, in biology, a mutation is the process that produces heritable change via the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements. Mutations result from errors during DNA replication or other types of damage to DNA (such as may be caused by exposure to radiation or carcinogens), which then may undergo error-prone repair, or cause an error during other forms of repair, or else may cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements. Mutations may or may not produce discernible changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer, and the development of the immune system, including junctional diversity. In the early days of classical genetics, work to characterize, model, and understand the phenomenology of mutation were critically important for developing the foundations of modern molecular genetics.

PUBMED QUERY: 1859:1953[PDAT] AND (mutation OR mutant OR mutagen) NOT pmcbook NOT ispreviousversion

Classical Genetics: Sex Determination updated: 20 Dec 2024 at 01:41
273 citations

Scitable: In humans and many other animal species, sex is determined by specific chromosomes. The first inkling that sex chromosomes were unique from all other chromosomes came from experiments conducted by German biologist Hermann Henking in 1891. While studying sperm formation in wasps, Henking saw that some wasp sperm cells had 12 chromosomes, while others had only 11. Moreover, while observing the stages of meiosis that formed these sperm cells, Henking noticed that the mysterious twelfth chromosome looked different from all the others. He thus named this chromosome the "X element," to represent its unknown nature. nce that supported this hypothesis. About 10 years after Henking's studies, American zoologist C. E. McClung began extensive research into the idea that the X element must have something to do with sex determination. First, McClung asserted that this strange chromosome be called the "accessory chromosome," because it appeared to have a separate purpose compared to the other chromosomes. Next, he decided to undertake a wide comparative study of spermatogenesis not just in insects but in many different organisms, including spiders and mice. While observing sperm generation in grasshoppers, McClung noted that the accessory chromosome did not behave as the other chromosomes did during the first meiotic division. Specifically, this "twelfth chromosome" was not distributed equally to the four sperm cells that arose from one grasshopper spermatogonium; instead, it was present in only half of them. This consistent pattern of segregation in the spermatogenesis of many different organisms caused McClung to speculate that there must be some fundamental reason for the generation of two types of sperm cells. McClung thought about the consequences of this 50/50 distribution of the accessory chromosome, and he pondered how this distribution probably resulted in two different kinds of zygotes. He also noted that there was really only one characteristic that varied among zygotes of many different species in 50/50 proportions, and that characteristic was sex.

PUBMED QUERY: 1890:1953[PDAT] AND ("sex-determination" OR "sex determination" OR "sex chromosome" OR "X chromosome" OR "Y chromosome") NOT pmcbook NOT ispreviousversion

Drosophila: The Fly Room updated: 20 Dec 2024 at 01:49
61 citations

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.

PUBMED QUERY: ( 1890:1932[PDAT] AND (drosophila OR gene OR genetic OR map OR chromosome OR mutant OR mutation) AND ( "morgan th"[author] OR "morgan lv"[author] OR "sturtevant AH"[author] OR "bridges CB"[author] OR "muller HJ"[author] ) ) NOT pmcbook NOT ispreviousversion

History of Genetics updated: 20 Dec 2024 at 01:49
1015 citations

PUBMED QUERY: genetics (classical OR mendelian) genetics history[mesh] NOT pmcbook NOT ispreviousversion

Gregor Mendel updated: 20 Dec 2024 at 01:49
165 citations

In 1865, Gregor Mendel reported the results of his experiments with peas and in so doing laid the foundations of what has become the modern science of genetics. There are few examples of entire fields having been so clearly founded upon the works of one man.

PUBMED QUERY: mendel[title] AND (gregor OR brno OR versuche OR darwin OR "father of genetics") NOT "James Ross" NOT Antarctic NOT pmcbook NOT ispreviousversion

Did Mendel Cheat? updated: 20 Dec 2024 at 01:52
37 citations

In 1936, R. A. Fisher noted that Mendel's results seem to come too close to the expected value too often, leading him to conclude "the general level of agreement between Mendel's expectations and his reported results shows that it is closer than would be expected in the best of several thousand repetitions. The data have evidently been sophisticated systematically..." That is, Mendel's data had been fiddled with. A small industry has grown up, with various authors taking sides on the controversy.

PUBMED QUERY: (mendel[TITLE] OR mendelian[TITLE]) AND (cheat OR "too good"[TITLE] OR fisher OR controversy OR controversies) NOT (Humans[MESH] OR rats[MESH] OR Software[MESH] OR "Mendelian randomization") NOT pmcbook NOT ispreviousversion

Did Mendel Cheat? (related papers) updated:
citations

PUBMED QUERY:

Paleontological Miscellany

Paleonotology Meets Genomics — Sequencing Ancient DNA updated: 20 Dec 2024 at 01:56
3212 citations

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 are based on poor quality DNA and thus have many inferential steps (i,e, the resulting sequence is not likely to be a perfect replica of the living DNA), the insights to be gained from paleosequentcing are nonetheless great. For example, paleo-sequencing has shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.

PUBMED QUERY: ( "ancient DNA"[TIAB] OR "ancient genome"[TIAB] OR paleogenetic OR paleogenetics OR paleogenomics OR "DNA,ancient"[MESH]) NOT pmcbook NOT ispreviousversion

Neanderthals updated: 20 Dec 2024 at 01:56
1563 citations

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.

PUBMED QUERY: ( Neanderthal[TIAB] OR Neandertal[TIAB] ) NOT pmcbook NOT ispreviousversion

The Denisovans, Another Human Ancestor updated: 20 Dec 2024 at 01:56
275 citations

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.

PUBMED QUERY: ( denisovan[TIAB] OR denisova[TIAB] ) NOT pmcbook NOT ispreviousversion

Homo floresiensis, The Hobbit updated: 20 Dec 2024 at 01:56
123 citations

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.

PUBMED QUERY: ( "Homo floresiensis"[TIAB] ) NOT pmcbook NOT ispreviousversion

Feathered Dinosaurs updated: 20 Dec 2024 at 01:46
245 citations

"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

PUBMED QUERY: ( (dinosaur[TIAB] OR dinosaurs[TIAB]) AND (feather OR feathers OR feathered OR plumage OR pigmentation OR pigment OR countershading) ) NOT pmcbook NOT ispreviousversion

The New Biodiversity

Archaea updated: 20 Dec 2024 at 01:30
3452 citations

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 lineage has 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 Earth one must also understand the Archaea .

PUBMED QUERY: ( archaea[TITLE] OR archaebacteria[TITLE] ) NOT pmcbook NOT ispreviousversion

Biodiversity and Metagenomics updated: 20 Dec 2024 at 01:30
14334 citations

If evolution is the only light in which biology makes sense, and if variation is the raw material upon which selection works, then variety is not merely the spice of life, it is the essence of life — the sine qua non without which life could not exist. To understand biology, one must understand its diversity. Historically, studies of biodiversity were directed primarily at the realm of multicellular eukaryotes, since few tools existed to allow the study of non-eukaryotes. Because metagenomics allows the study of intact microbial communities, without requiring individual cultures, it provides a tool for understanding this huge, hitherto invisible pool of biodiversity, whether it occurs in free-living communities or in commensal microbiomes associated with larger organisms.

PUBMED QUERY: biodiversity metagenomics NOT pmcbook NOT ispreviousversion

Microbial Ecology updated: 20 Dec 2024 at 01:52
16683 citations

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×10³⁰ cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

PUBMED QUERY: ( "microbial ecology" ) NOT pmcbook NOT ispreviousversion

Biofilms updated: 20 Dec 2024 at 01:40
25701 citations

Wikipedia: Biofilm A biofilm is any group of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPS). The EPS components are produced by the cells within the biofilm and are typically a polymeric conglomeration of extracellular DNA, proteins, and polysaccharides. Because they have three-dimensional structure and represent a community lifestyle for microorganisms, biofilms are frequently described metaphorically as cities for microbes. Biofilms may form on living or non-living surfaces and can be prevalent in natural, industrial and hospital settings. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single-cells that may float or swim in a liquid medium. Biofilms can be present on the teeth of most animals as dental plaque, where they may cause tooth decay and gum disease. Microbes form a biofilm in response to many factors, which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, or in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of antibiotics. When a cell switches to the biofilm mode of growth, it undergoes a phenotypic shift in behavior in which large suites of genes are differentially regulated.

PUBMED QUERY: ( biofilm[title] NOT 28392838[PMID] NOT 31293528[PMID] NOT 29372251[PMID] ) NOT pmcbook NOT ispreviousversion

Horizontal Gene Transfer updated: 20 Dec 2024 at 01:31
14370 citations

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.

PUBMED QUERY: ( "horizontal gene transfer" OR "lateral gene transfer") NOT pmcbook NOT ispreviousversion

Holobiont updated: 20 Dec 2024 at 01:31
2063 citations

Holobionts are assemblages of different species that form ecological units. Lynn Margulis proposed that any physical association between individuals of different species for significant portions of their life history is a symbiosis. All participants in the symbiosis are bionts, and therefore the resulting assemblage was first coined a holobiont by Lynn Margulis in 1991 in the book Symbiosis as a Source of Evolutionary Innovation. Holo is derived from the Ancient Greek word ὅλος (hólos) for “whole”. The entire assemblage of genomes in the holobiont is termed a hologenome.

PUBMED QUERY: ( holobiont OR hologenome OR holospecies ) NOT pmcbook NOT ispreviousversion

Metagenomics updated: 20 Dec 2024 at 01:32
41673 citations

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.

PUBMED QUERY: ( metagenomic OR metagenomics OR metagenome ) NOT pmcbook NOT ispreviousversion

Pangenome updated: 20 Dec 2024 at 01:33
3965 citations

Although the enforced stability of genomic content is ubiquitous among MCEs, 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.

PUBMED QUERY: ( pangenome OR "pan-genome" OR "pan genome" ) NOT pmcbook NOT ispreviousversion

Reynolds Number updated: 20 Dec 2024 at 01:34
4098 citations

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.

PUBMED QUERY: ( "reynolds number" ) NOT pmcbook NOT ispreviousversion

Symbiosis is Ubiquitous

Symbiosis updated: 20 Dec 2024 at 01:57
31680 citations

Symbiosis refers to an interaction between two or more different organisms living in close physical association, typically to the advantage of both. Symbiotic relationships were once thought to be exceptional situations. Recent studies, however, have shown that every multicellular eukaryote exists in a tight symbiotic relationship with billions of microbes. The associated microbial ecosystems are 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."

PUBMED QUERY: ( symbiosis[tiab] OR symbiotic[tiab] ) NOT pmcbook NOT ispreviousversion

Endosymbiosis updated: 20 Dec 2024 at 01:57
6127 citations

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 organelles are believed to have originated from a form of endosymbiosis. The endosymbiotic origin of eukaryotes seems to have been a biological singularity — that is, it happened once, and only once, in the history of life on Earth.

PUBMED QUERY: endosymbiont NOT pmcbook NOT ispreviousversion

Wolbachia updated: 20 Dec 2024 at 02:01
4408 citations

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.

PUBMED QUERY: wolbachia NOT pmcbook NOT ispreviousversion

Microbiome Project(s) updated: 20 Dec 2024 at 01:53
683 citations

For many multicellular organisms, a microscopic study shows that microbial cells outnumber host cells by perhaps ten to one. Until recently, these abundant communities of host-associated microbes were largely unstudied, often for lack of analytical tools or conceptual frameworks. The advent of new tools is rendering visible this previously ignored biosphere and the results have been startling. Many facets of host biology have proven to be profoundly affected by the associated microbiomes. As a result, several large-scale projects — such as the Human Microbiome Project — have been undertaken to jump start an understanding of this critical component of the biosphere.

PUBMED QUERY: "microbiome project" NOT pmcbook NOT ispreviousversion

Microbiome updated: 20 Dec 2024 at 01:53
72134 citations

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.

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Human Microbiome updated: 20 Dec 2024 at 01:52
4380 citations

The human microbiome is the set of all microbes that live on or in humans. Together, a human body and its associated microbiomes constitute a human holobiont. Although a human holobiont is mostly mammal by weight, by cell count it is mostly microbial. The number of microbial genes in the associated microbiomes far outnumber the number of human genes in the human genome. Just as humans (and other multicellular eukaryotes) evolved in the constant presence of gravity, so they also evolved in the constant presence of microbes. Consequently, nearly every aspect of human biology has evolved to deal with, and to take advantage of, the existence of associated microbiota. In some cases, the absence of a "normal microbiome" can cause disease, which can be treated by the transplant of a correct microbiome from a healthy donor. For example, fecal transplants are an effective treatment for chronic diarrhea from over abundant Clostridium difficile bacteria in the gut.

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Squid-Vibrio Symbiosis updated: 20 Dec 2024 at 01:57
457 citations

The small bobtail squid (Euprymna scolopes) has a mutually beneficial relationship with bacteria called Vibrio fischeri that live on the squid's underside. The bacteria allow the squid to produce light, which then allows the squid to escape from things that might want to eat it. "The squid emit ventral luminescence that is often very, very close to the quality of light coming from the moon and stars at night," explains Margaret McFall-Ngai, Margaret McFall-Ngai, professor of medical microbiology and immunology at the University of Wisconsin-Madison. For fish looking up from below for something to eat, the squid are camouflaged against the moon or the starlight because they don't cast a shadow. "It's like a 'Klingon' cloaking device," she notes. But the Vibrio fischeri don't stay in the squid continuously. Every day, in response to the light cue of dawn, the squid vents 90 percent of the bacteria back into the seawater. "And then, while it's sitting quiescent in the sand, the bacteria grow up in the crypt so that when [the squid] comes out in the evening, it will have a full complement of luminous Vibrio fischeri," says McFall-Ngai.

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Multicellular Eukaryotes — The Atypical Biosphere

Origin of Eukaryotes updated: 20 Dec 2024 at 01:47
631 citations

The evolutionary origin of eukaryotes is a critically important, yet poorly understood event in the history of life on earth. The endosymbiotic origin of mitochondria allowed cells to become sufficiently large that they could begin to interact mechanically with their surrounding environment, thereby allowing evolution to create the visible biosphere of multicellular eukaryotes.

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Evolution of Multicelluarity updated: 20 Dec 2024 at 01:48
5108 citations

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Origin of Multicellular Eukaryotes updated: 20 Dec 2024 at 01:51
4136 citations

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Mitochondrial Evolution updated: 20 Dec 2024 at 01:56
9202 citations

The endosymbiotic hypothesis for the origin of mitochondria (and chloroplasts) suggests that mitochondria are descended from specialized bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm.

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Energetics and Mitochondrial Evolution updated: 20 Dec 2024 at 01:55
509 citations

Mitochondria are the energy-producing "engines" that provide the power to drive eukaryotic cells. The energy output of hundreds, or thousands, of mitochondria allowed eukaryotic cells to increase in size 1000-fold, or more, over the size of prokaryotics cells. This increase in size allowed an escape from the constraints of low Reynolds numbers and, for the first time, life could function in a way where mechanism, and thus morphology, mattered. Evolution began to shape morphology, allowing the emergence of the multicellular eukaryotic biosphere — the visible living world.

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Telomeres updated: 20 Dec 2024 at 01:58
12588 citations

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 (τέλος) "end" and merοs (μέρος, root: μερ-) "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,[3] with 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.

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New Science

CRISPR-Cas updated: 20 Dec 2024 at 01:45
25156 citations

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.

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Fecal Transplantation updated: 20 Dec 2024 at 01:48
10231 citations

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 was known as yellow soup.

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Topologically Associating Domains updated: 20 Dec 2024 at 01:58
923 citations

"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

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Brain-Computer Interface updated: 20 Dec 2024 at 01:39
13807 citations

Wikipedia: A brain–computer interface (BCI), sometimes called a neural control interface (NCI), mind–machine interface (MMI), direct neural interface (DNI), or brain–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 brain–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).

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Closing Miscellany

Climate Change updated: 20 Dec 2024 at 01:59
18600 citations

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.

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Invasive Species updated: 20 Dec 2024 at 01:50
16323 citations

Standard Definition: Invasive species are plants, animals, or pathogens that are non-native (or alien) to the ecosystem under consideration and whose introduction causes or is likely to cause harm. Although that definition allows a logical possibility that some species might be non-native and harmless, most of time it seems that invasive species and really bad critter (or weed) that should be eradicated are seen as equivalent phrases. But, there is a big conceptual problem with that notion: every species in every ecosystem started out in that ecosystem as an invader. If there were no invasive species, all of Hawaii would be nothing but bare volcanic rock. Without an invasion of species onto land, there would be no terrestrial ecosystems at all. For the entire history of life on Earth, the biosphere has responded to perturbation and to opportunity with evolutionary innovation and with physical movement. While one may raise economic or aesthetic arguments against invasive species, it is impossible to make such an argument on scientific grounds. Species movement — the occurrence of invasive species — is the way the biosphere responds to perturbation. One might even argue that species movement is the primary, short-term "healing" mechanism employed by the biosphere to respond to perturbation — to "damage." As with any healing process, the short-term effect may be aesthetically unappealing (who thinks scabs are appealing?), but the long-term effects can be glorious.

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Sociobiology updated: 20 Dec 2024 at 01:57
1076 citations

Sociobiology is a field of scientific study that is based on the hypothesis that social behavior has resulted from evolution and attempts to examine and explain social behavior within that context. Sociobiology investigates social behaviors, such as mating patterns, territorial fights, pack hunting, and the hive society of social insects. It argues that just as selection pressure led to animals evolving useful ways of interacting with the natural environment, it led to the genetic evolution of advantageous social behavior. While the term "sociobiology" can be traced to the 1940s, the concept did not gain major recognition until the publication of Edward O. Wilson's book Sociobiology: The New Synthesis in 1975.

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Kin Selection updated: 20 Dec 2024 at 01:51
1770 citations

Wikipedia: Kin selection is the evolutionary strategy that favours the reproductive success of an organism's relatives, even at a cost to the organism's own survival and reproduction. Kin altruism is altruistic behaviour whose evolution is driven by kin selection. Kin selection is an instance of inclusive fitness, which combines the number of offspring produced with the number an individual can produce by supporting others, such as siblings. Charles Darwin discussed the concept of kin selection in his 1859 book, The Origin of Species, where he reflected on the puzzle of sterile social insects, such as honey bees, which leave reproduction to their mothers, arguing that a selection benefit to related organisms (the same "stock") would allow the evolution of a trait that confers the benefit but destroys an individual at the same time. R.A. Fisher in 1930 and J.B.S. Haldane in 1932 set out the mathematics of kin selection, with Haldane famously joking that he would willingly die for two brothers or eight cousins. In 1964, W.D. Hamilton popularised the concept and the major advance in the mathematical treatment of the phenomenon by George R. Price which has become known as "Hamilton's rule". In the same year John Maynard Smith used the actual term kin selection for the first time. According to Hamilton's rule, kin selection causes genes to increase in frequency when the genetic relatedness of a recipient to an actor multiplied by the benefit to the recipient is greater than the reproductive cost to the actor.

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