The WikiJournal of Science is an open access, free-to-publish Wikipedia-integrated journal devoted to science in its broadest sense. It is part of the larger WikiJournal publishing group. Its function is to put articles through academic peer review for stable, citable versions, whose content can potentially benefit Wikipedia and other Wikimedia projects.
VOLUME 3 (2020)
Authors: Deepesh Nagarajan , Neha Nanajkar
Proteins are biological polymers composed of linear chains of 20 different amino acids. The sequence of amino acids for every protein is unique, and guides its folding into intricate 3-dimensional shapes, known as protein folds. The TIM barrel is one such fold, and is characterized by an interior 8-stranded β-barrel, surrounded and enclosed by 8 α-helices. TIM barrels are named after triose phosphate isomerase (TIM), an enzyme first structurally characterized in 1975, which lends its name to the fold. TIM barrels are prevalent in all forms of life, and across diverse metabolic pathways, with over 10% of all enzymes adopting this fold. The majority of TIM barrels are thought to have evolved from a common ancestor through gene duplication and domain fusion processes. TIM barrels have been created by protein engineers using preexisting half-barrel templates and de novo, without an existing template. This review will discuss the topological, structural, evolutionary, and design characteristics of TIM barrels in detail.
Author: Bryan Ericksen , et al.
Virtual colony count (VCC) is a kinetic, 96-well microbiological assay originally developed to measure the activity of defensins. It has since been applied to other antimicrobial peptides including LL-37. It utilizes a method of enumerating bacteria called quantitative growth kinetics, which compares the time taken for a bacterial batch culture to reach a threshold optical density with that of a series of calibration curves. The name VCC has also been used to describe the application of quantitative growth kinetics to enumerate bacteria in cell culture infection models. Antimicrobial susceptibility testing (AST) can be done on 96-well plates by diluting the antimicrobial agent at varying concentrations in broth inoculated with bacteria and measuring the minimum inhibitory concentration that results in no growth. However, these methods cannot be used to study some membrane-active antimicrobial peptides, which are inhibited by the broth itself. The virtual colony count procedure takes advantage of this fact by first exposing bacterial cells to the active antimicrobial agent in a low-salt buffer for two hours, then simultaneously inhibiting antimicrobial activity and inducing exponential growth by adding broth. The growth kinetics of surviving cells can then be monitored using a temperature-controlled plate reader. The time taken for each growth curve to reach a threshold change in optical density is then converted into virtual survival values, which serve as a measure of antimicrobial activity.
Authors: Tyler Rushton , Sebastian Dworkin
The Grainyhead-like genes are a family of highly conserved transcription factors that are functionally and structurally homologous across a large number of vertebrate and invertebrate species. For an estimated 100 million years or more, this genetic family has been evolving alongside life to fine tune the regulation of epithelial barrier integrity during development, fine-tuning epithelial barrier establishment, maintenance and subsequent homeostasis. The three main orthologues, Grainyhead-like 1, 2 and 3, regulate numerous genetic pathways within different organisms and perform analogous roles between them, ranging from neural tube closure, wound healing, establishment of the craniofacial skeleton and repair of the epithelium. When Grainyhead-like genes are impaired, due to genetic mutations in embryogenesis, it will cause the organism to present with developmental defects that largely affect ectodermal (and sometimes also endodermal) tissues in which they are expressed. These subsequent congenital disorders, including cleft lip and exencephaly, vary greatly in their severity and impact on the quality of life for the affected individual. There is so much more to learn about the function of these genes and the more complex roles of Grainyhead-like genes are yet to be discovered.
Author: Iain Reid , et al.
Paranthodon is a genus of extinct stegosaurian dinosaur that lived in South Africa during the Early Cretaceous, between 139 and 131 million years ago. Discovered in 1845, it was one of the first stegosaurians found. Its only remains, a partial skull and isolated teeth, were found in the Kirkwood Formation. British paleontologist Richard Owen initially identified the fragments as those of the pareiasaur Anthodon. After remaining untouched for years in the British Museum of Natural History, the partial skull was identified by South African paleontologist Robert Broom as belonging to a different genus; he named the specimen Palaeoscincus africanus. Several years later, Hungarian paleontologist Franz Nopcsa, unaware of Broom's new name, similarly concluded that it represented a new taxon, and named it Paranthodon owenii. Since Nopcsa's species name was assigned after Broom's, and Broom did not assign a new genus, both names are now synonyms of the current binomial, Paranthodon africanus. The genus name combines the Ancient Greek para (near) with the genus name Anthodon, to represent the initial referral of the remains.
VOLUME 2 (2019)
Author: Collin Knopp-Schwyn , et al.
Widgiemoolthalite is a rare hydrated nickel(II) carbonate mineral with the chemical formula (Ni,Mg)5(CO3)4(OH)2·5H2O. Usually bluish-green in color, it is a brittle mineral formed during the weathering of nickel sulfide. Present on gaspéite surfaces, widgiemoolthalite has a Mohs scale hardness of 3.5 and an unknown though likely disordered crystal structure. Widgiemoolthalite was first discovered in 1992 in Widgiemooltha, Western Australia, which was its only known source as of 2016. It was named in 1993 by the three researchers who first reported its existence, Ernest H. Nickel, Bruce W. Robinson, and William G. Mumme.
Author: Ignacio L. B. Munguira , et al.
Lysenin is a pore-forming toxin present in the coelomic fluid of the earthworm Eisenia fetida. Pore-forming toxins (PFTs) are proteinaceous virulence factors produced by many pathogenic bacteria. Following the general mechanism of action of PFTs, lysenin is secreted as a soluble monomer that binds specifically to the membrane receptor sphingomyelin. After attachment, lysenin forms a 9-copy oligomer (nonamer) prepore on the lipid bilayer before membrane insertion. The biological role of lysenin is still unclear, however the most plausible theory is that it is part of an immune-avoiding mechanism. There are many proposed technological applications proposed for lysenin, and understanding its molecular role in bacterial infection could help in developing different antibiotic strategies to solve the problem of multiple drug resistance in bacteria.
Author: Anthony Lin , et al.
In computer science, binary search, also known as half-interval search, logarithmic search, or binary chop, is a search algorithm that finds a position of a target value within a sorted array. Binary search compares the target value to an element in the middle of the array. If they are not equal, the half in which the target cannot lie is eliminated and the search continues on the remaining half, again taking the middle element to compare to the target value, and repeating this until the target value is found. If the search ends with the remaining half being empty, the target is not in the array.
Authors: Michael A. Stear , David Piedrafita , Sarah Sloan , Dalal Alenizi
One of the most important parasites of sheep and goats is the nematode Teladorsagia circumcincta. This is common in cool, temperate areas. There is considerable variation among lambs and kids in susceptibility to infection. Much of the variation is genetic and influences the immune response. The parasite induces a type I hypersensitivy response which is responsible for the relative protein deficiency which is characteristic of severely infected animals. There are mechanistic mathematical models which can predict the course of infection. There are a variety of ways to control the infection and a combination of control measures is likely to provide the most effective and sustainable control.
Author: Michael Bech , et al.
Baryonyx () is a genus of theropod dinosaur which lived in the Barremian stage of the Early Cretaceous Period, about 130–125 million years ago. The first skeleton was discovered in 1983 in the Weald Clay Formation of Surrey, England, and became the holotype specimen of B. walkeri, named by palaeontologists Alan J. Charig and Angela C. Milner in 1986. The generic name, Baryonyx, means "heavy claw" and alludes to the animal's very large claw on the first finger; the specific name, walkeri, refers to its discoverer, amateur fossil collector William J. Walker. The holotype specimen is one of the most complete theropod skeletons from the UK (and remains the most complete spinosaurid), and its discovery attracted media attention. Specimens later discovered in other parts of the United Kingdom and Iberia have also been assigned to the genus.
Author: Mike Christie , et al.
Ice drilling allows scientists studying glaciers and ice sheets to gain access to what is beneath the ice, to take measurements along the interior of the ice, and to retrieve samples. Instruments can be placed in the drilled holes to record temperature, pressure, speed, direction of movement, and for other scientific research, such as neutrino detection.
Author: Natalie A. Borg
RIG-I (retinoic-acid inducible gene I, also known as DDX58) is the best characterized receptor within the RIG-I like receptor (RLR) family. Together with MDA5 (melanoma differentiation-associated 5) and LGP2 (laboratory of genetics and physiology 2), this family of cytoplasmic pattern recognition receptors (PRRs) are sentinels for intracellular viral RNA that is a product of viral infection. The RLR receptors provide frontline defence against viral infections in most tissues.
VOLUME 1 (2018)
Authors: Andrew Z. Colvin , et al.
Peripatric speciation is a mode of speciation in which a new species is formed from an isolated peripheral population. Since peripatric speciation resembles allopatric speciation, in that populations are isolated and prevented from exchanging genes, it can often be difficult to distinguish between them. Nevertheless, the primary characteristic of peripatric speciation proposes that one of the populations is much smaller than the other. The terms peripatric and peripatry are often used in biogeography, referring to organisms whose ranges are closely adjacent but do not overlap, being separated where these organisms do not occur—for example on an oceanic island compared to the mainland. Such organisms are usually closely related (e.g. sister species); their distribution being the result of peripatric speciation.
Authors: Mikhail Boldyrev , et al.
Lead is a chemical element with the atomic number 82 and the symbol Pb (from the Latin plumbum). It is a heavy metal that is denser than most common materials. Lead is soft and malleable, and has a relatively low melting point. When freshly cut, lead is silvery with a hint of blue; it tarnishes to a dull gray color when exposed to air. Lead has the highest atomic number of any stable element and concludes three major decay chains of heavier elements.
VOLUME 1 (2018)
Author: Mike Christie , et al.
Radiocarbon dating (also referred to as carbon dating or carbon-14 dating) is a method for determining the age of an object containing organic material by using the properties of radiocarbon, a radioactive isotope of carbon. It transformed the practice of archaeology.
Authors: Guy Vandegrift , Joshua Stomel
In 1964 John Stewart Bell made an observation about the behavior of particles separated by macroscopic distances that had puzzled physicists for at least 29 years, when Einstein, Podolsky and Rosen put forth the famous EPR paradox. Bell made certain assumptions leading to an inequality that entangled are routinely observed to violate in what are now called Bell test experiments. As an alternative showing students this "proof" of Bell's inequality, we introduce a card game that is impossible to win. The solitaire version is so simple it can be used to introduce binomial statistics without mentioning physics or Bell's theorem. Things get interesting in the partners' version of the game because Alice and Bob can win, but only if they cheat. We have identified three cheats, and each corresponds to a Bell's theorem "loophole". This gives the instructor an excuse to discuss detector error, causality, and why there is a maximum speed at which information can travel.
Authors: Cody J. Hall , Tatiana P. Soares da Costa
Amino acids are an essential building block of all life and are commonly incorporated into extending polypeptide chains to produce proteins. Lysine is one such amino acid and is classified as basic and positively charged at physiological pH due to the presence of an additional amino chemical group on the side chain. Lysine has two main biosynthetic pathways, namely the diaminopimelate and α-aminoadipate pathways, which employ different enzymes and substrates and are found in different organisms. Lysine catabolism occurs through one of several pathways, the most common of which is the saccharopine pathway. Lysine plays several roles in humans, most importantly proteinogenesis, but also in the crosslinking of collagen polypeptides, uptake of essential mineral nutrients, and in the production of carnitine, which is key in fatty acid metabolism. Furthermore, lysine is often involved in histone modifications, and thus, impacts the epigenome. Due to the importance of lysine in several biological processes, a lack of lysine can lead to several disease states including; defective connective tissues, impaired fatty acid metabolism, anaemia, and systemic protein-energy deficiency. In juxtaposition to this, an overabundance of lysine, caused by ineffective catabolism, can cause severe neurological issues.
Authors: Shih Chieh Chang , Saumya Bajaj , K. George Chandy
Stichodactyla toxin (ShK) is a 35-residue basic peptide from the sea anemone Stichodactyla helianthus that blocks a number of potassium channels. An analogue of ShK called ShK-186 or Dalazatide is in human trials as a therapeutic for autoimmune diseases.
Author: Boris Tsirelson , et al.
While modern mathematics use many types of spaces, such as Euclidean spaces, linear spaces, topological spaces, Hilbert spaces, or probability spaces, it does not define the notion of "space" itself.
A space consists of selected mathematical objects that are treated as points, and selected relationships between these points. The nature of the points can vary widely: for example, the points can be elements of a set, functions on another space, or subspaces of another space. It is the relationships that define the nature of the space. More precisely, isomorphic spaces are considered identical, wherean isomorphism between two spaces is a one-to-one correspondence between their points that preserves the relationships. For example, the relationships between the points of a three-dimensional Euclidean space are uniquely determined by Euclid's axioms, and all three-dimensional Euclidean spaces are considered identical.
Authors: Thomas Shafee and the WikiJSci Editorial Board
WikiJournal of Science is a open access, peer reviewed journal, free of publication charges for its authors. It has Wikipedia-integration as a key feature and aims to encourage and recognise contributions to Wikipedia by academics. It is a sister journal to the established WikiJournal of Medicine, and covers science, technology, engineering and mathematics. This editorial will discuss the current aims and future scope of the journal, as well as the WikiJournal format in general.