Biology Direct is an online open access scientific journal that publishes original, peer-reviewed research papers, reviews, hypotheses, comments and discovery notes in biology. The journal is published by BioMed Central.
The journal follows a peer review system which is different from the traditional peer review system, which aims to give more responsibility to authors, and reduce sources of bias. Published articles include signed reviewer reports, and responses to the reports from the authors, to provide readers with an additional guide to the article.
Based on the information presented on their website: "Biology Direct's key aim is to provide authors and readers with an alternative to the traditional model of peer review. This includes making the author responsible for selecting potentially suitable reviewers for their manuscript, from the journal's Editorial Board; making the peer review process open rather than anonymous; and making the reviewers' reports public, thus increasing the responsibility of the referees and eliminating sources of abuse in the refereeing process."
|Edited by||Eugene Koonin, Laura Landweber, David J. Lipman|
A bikont ("two flagella") is any of the eukaryotic organisms classified in the group Bikonta. Many single-celled members of the group, and the presumed ancestor, have two flagella.Biogenesis
For the origin of life, see Abiogenesis.Biogenesis is the production of new living organisms or organelles. Conceptually, biogenesis is primarily attributed to Louis Pasteur and encompasses the belief that complex living things come only from other living things, by means of reproduction. That is, life does not spontaneously arise from non-living material, which was the position held by spontaneous generation. This is summarized in the phrase Omne vivum ex vivo, Latin for "all life [is] from life." A related statement is Omnis cellula e cellula, "all cells [are] from cells;" this conclusion is one of the central statements of cell theory.CRISPR
CRISPR () (clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found within the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments from viruses that have previously infected the prokaryote and are used to detect and destroy DNA from similar viruses during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes.Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and cleave specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within organisms. This editing process has a wide variety of applications including basic biological research, development of biotechnology products, and treatment of diseases.
The CRISPR-Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity. RNA harboring the spacer sequence helps Cas (CRISPR-associated) proteins recognize and cut foreign pathogenic DNA. Other RNA-guided Cas proteins cut foreign RNA. CRISPR are found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.Central dogma of molecular biology
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA makes protein," although this is not its original meaning. It was first stated by Francis Crick in 1957, then published in 1958:
and re-stated in a Nature paper published in 1970:
A second version of the central dogma is popular but incorrect. This is the simplistic DNA → RNA → protein pathway published by James Watson in the first edition of The Molecular Biology of the Gene (1965). Watson's version differs from Crick's because Watson describes the two-step (DNA → RNA and RNA → protein) pathway as the central dogma. While the dogma, as originally stated by Crick, remains valid today, Watson's version does not.
The dogma is a framework for understanding the transfer of sequence information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3=9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: three general transfers (believed to occur normally in most cells), three special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and three unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation). The special transfers describe: RNA being copied from RNA (RNA replication), DNA being synthesised using an RNA template (reverse transcription), and proteins being synthesised directly from a DNA template without the use of mRNA. The unknown transfers describe: a protein being copied from a protein, synthesis of RNA using the primary structure of a protein as a template, and DNA synthesis using the primary structure of a protein as a template - these are not thought to naturally occur.Common descent
Common descent describes how, in evolutionary biology, a group of organisms share a most recent common ancestor. There is "massive" evidence of common descent of all life on Earth from the last universal common ancestor (LUCA). In July 2016, scientists reported identifying a set of 355 genes from the LUCA, by comparing the genomes of the three domains of life, archaea, bacteria, and eukaryotes.Common ancestry between organisms of different species arises during speciation, in which new species are established from a single ancestral population. Organisms which share a more-recent common ancestor are more closely related. The most recent common ancestor of all currently living organisms is the last universal ancestor, which lived about 3.9 billion years ago. The two earliest evidences for life on Earth are graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in western Greenland and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia. All currently living organisms on Earth share a common genetic heritage, though the suggestion of substantial horizontal gene transfer during early evolution has led to questions about the monophyly (single ancestry) of life. 6,331 groups of genes common to all living animals have been identified; these may have arisen from a single common ancestor that lived 650 million years ago in the Precambrian.Universal common descent through an evolutionary process was first proposed by the British naturalist Charles Darwin in the concluding sentence of his 1859 book On the Origin of Species:
There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.Enzyme Commission number
The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze.
As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme.
Strictly speaking, EC numbers do not specify enzymes, but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. Furthermore, through convergent evolution, completely different protein folds can catalyze an identical reaction and therefore would be assigned an identical EC number (these are called non-homologous isofunctional enzymes, or NISE). By contrast, UniProt identifiers uniquely specify a protein by its amino acid sequence.Eugene Koonin
Eugene Viktorovich Koonin (Russian: Евге́ний Ви́кторович Ку́нин) (born October 26, 1956) is a Russian-American biologist and Senior Investigator at the National Center for Biotechnology Information (NCBI). He is a recognised expert in the field of evolutionary and computational biology.Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. The word intron is derived from the term intragenic region, i.e. a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.Last universal common ancestor
The last universal common ancestor (LUCA), also called the last universal ancestor (LUA), cenancestor, or (incorrectly) progenote, is the most recent population of organisms from which all organisms now living on Earth have a common descent. LUCA is the most recent common ancestor of all current life on Earth. LUCA is not thought to be the first living organism on Earth, but only one of many early organisms, whereas the others became extinct.
While there is no specific fossil evidence of LUCA, it can be studied by comparing the genomes of its descendants, all organisms known to be living today. By this means, a 2016 study identified a set of 355 genes inferred to have been present in LUCA. This would imply it was already a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information between DNA, RNA, and proteins. However, some of those genes could have developed later and spread universally by horizontal gene transfer between archaea and bacteria.LUCA is estimated to have lived some 3.5 to 3.8 billion years ago in the Paleoarchean era, a few hundred million years after the earliest evidence of life on Earth, for which there are several candidates. Microbial mat fossils have been found in 3.48 billion-year-old sandstone from Western Australia, while biogenic graphite has been found in 3.7 billion-year-old metamorphized sedimentary rocks from Western Greenland. Recent studies have tentatively proposed evidence of life as early as 4.28 billion years ago.Charles Darwin proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859, saying, "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." Later biologists have separated the problem of the origin of life from that of the LUCA.Metamorphosis
Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Metamorphosis is iodothyronine-induced and an ancestral feature of all chordates. Some insects, fishes, amphibians, mollusks, crustaceans, cnidarians, echinoderms, and tunicates undergo metamorphosis, which is often accompanied by a change of nutrition source or behavior. Animals that go through metamorphosis are called metamorphoses. Animals can be divided into species that undergo complete metamorphosis ("holometaboly"), incomplete metamorphosis ("hemimetaboly"), or no metamorphosis ("ametaboly").
Scientific usage of the term is technically precise, and it is not applied to general aspects of cell growth, including rapid growth spurts. References to "metamorphosis" in mammals are imprecise and only colloquial, but historically idealist ideas of transformation and monadology, as in Goethe's Metamorphosis of Plants, have influenced the development of ideas of evolution.Narayanaswamy Srinivasan
Narayanaswamy Srinivasan (born 1962) is an Indian molecular biophysicist and a professor and the head of Proteins: Structure, Function and Evolutionary Group (N. S. Group) at the Molecular Biophysics Unit of the Indian Institute of Science. He is known for his researches in the fields of computational genomics and protein structure analysis. An elected fellow of the Indian Academy of Sciences and the National Academy of Sciences, India, he is a J. C. Bose National fellow of the Department of Biotechnology and a recipient of the National Bioscience Award for Career Development of the Department of Science and Technology. The Council of Scientific and Industrial Research, the apex agency of the Government of India for scientific research, awarded him the Shanti Swarup Bhatnagar Prize for Science and Technology, one of the highest Indian science awards, in 2007, for his contributions to biological sciences.Organism
In biology, an organism (from Greek: ὀργανισμός, organismos) is any individual entity that exhibits the properties of life. It is a synonym for "life form".
Organisms are classified by taxonomy into specified groups such as the multicellular animals, plants, and fungi; or unicellular microorganisms such as a protists, bacteria, and archaea. All types of organisms are capable of reproduction, growth and development, maintenance, and some degree of response to stimuli. Humans are multicellular animals composed of many trillions of cells which differentiate during development into specialized tissues and organs.
An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains – bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles (such as mitochondria in animals and plants and plastids in plants and algae, all generally considered to be derived from endosymbiotic bacteria). Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes.
Estimates on the number of Earth's current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to over five billion species, that ever lived are estimated to be extinct. In 2016, a set of 355 genes from the last universal common ancestor (LUCA) of all organisms was identified.Saltation (biology)
In biology, saltation (from Latin, saltus, "leap") is a sudden and large mutational change from one generation to the next, potentially causing single-step speciation. This was historically offered as an alternative to Darwinism. Some forms of mutationism were effectively saltationist, implying large discontinuous jumps.
Speciation, such as by polyploidy in plants, can sometimes be achieved in a single and in evolutionary terms sudden step. Evidence is accumulating for various forms of saltation in a variety of organisms.Temple F. Smith
Temple Ferris Smith (born March 7, 1939) is a emeritus professor in biomedical engineering who helped to develop the Smith-Waterman algorithm with Michael Waterman in 1981. The Smith-Waterman algorithm serves as the basis for multi sequence comparisons, identifying the segment with the maximum local sequence similarity, see sequence alignment. This algorithm is used for identifying similar DNA, RNA and protein segments. He was director of the BioMolecular Engineering Research Center at Boston University for twenty years and is now professor emeritus.Theodor Otto Diener
Theodor Otto Diener (born February 28, 1921) is the Swiss-American plant pathologist who, in 1971, discovered that the causative agent of the potato spindle tuber disease is not a virus, but a novel agent, which consists solely of a short strand of single-stranded RNA without a protein capsid, eighty times smaller than the smallest viruses. He proposed to name it and similar agents to be discovered viroids.
Viroids displace viruses as the smallest infectious agents known.Thermoproteales
In taxonomy, the Thermoproteales are an order of the Thermoprotei. They are the only organisms known to lack the SSB proteins, instead possessing the protein ThermoDBP that has displaced them.
The rRNA genes of these organisms contain multiple introns, which can be homing endonuclease encoding genes, and their presence can impact the binding of "universal" 16S rRNA primers often used in environmental sequencing surveys.Troponin I
Troponin I is a cardiac and skeletal muscle protein useful in the laboratory diagnosis of heart attack. It occurs in different plasma concentration but the same circumstances as troponin T - either test can be performed for confirmation of cardiac muscle damage and laboratories usually offer one test or the other.Troponin I is a part of the troponin protein complex, where it binds to actin in thin myofilaments to hold the actin-tropomyosin complex in place. Because of it, myosin cannot bind actin in relaxed muscle. When calcium binds to the troponin C it causes conformational changes which lead to dislocation of troponin I and finally tropomyosin leaves the binding site for myosin on actin leading to contraction of muscle. The letter I is given due to its inhibitory character.
The tissue specific subtypes are:
Slow-twitch skeletal muscle isoform troponin I, TNNI1 (1q31.3, 191042)
Fast-twitch skeletal muscle isoform troponin I, TNNI2 (11p15.5, 191043)
Cardiac troponin I, TNNI3 (19q13.4, 191044)Virus
A virus is a small infectious agent that replicates only inside the living cells of an organism. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants, and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, about 5,000 virus species have been described in detail, although there are millions of types. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. The study of viruses is known as virology, a sub-speciality of microbiology.
While not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles. These viral particles, also known as virions, consist of: (i) the genetic material made from either DNA or RNA, long molecules that carry genetic information; (ii) a protein coat, called the capsid, which surrounds and protects the genetic material; and in some cases (iii) an envelope of lipids that surrounds the protein coat. The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the size of the average bacterium.
The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity. Viruses are considered by some to be a life form, because they carry genetic material, reproduce, and evolve through natural selection, but lack key characteristics (such as cell structure) that are generally considered necessary to count as life. Because they possess some but not all such qualities, viruses have been described as "organisms at the edge of life", and as replicators.Viruses spread in many ways; viruses in plants are often transmitted from plant to plant by insects that feed on plant sap, such as aphids; viruses in animals can be carried by blood-sucking insects. These disease-bearing organisms are known as vectors. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route and are passed from person to person by contact, entering the body in food or water. HIV is one of several viruses transmitted through sexual contact and by exposure to infected blood. The variety of host cells that a virus can infect is called its "host range". This can be narrow, meaning a virus is capable of infecting few species, or broad, meaning it is capable of infecting many.Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection. Some viruses, including those that cause AIDS and viral hepatitis, evade these immune responses and result in chronic infections. Several antiviral drugs have been developed.