WikiJournal of Science
WikiJournal of Science
Open access • Publication charge free • Public peer review • Wikipedia-integrated
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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 4 (2021)
ISSUE 1
Current issue
Authors: Felix Richter, et al.
RNA-Seq, named as an abbreviation of "RNA sequencing" and sometimes spelled RNA-seq, RNAseq, or RNASeq, uses next-generation sequencing (NGS) to reveal the presence and quantity of ribonucleic acid (RNA) in a biological sample at a given moment. RNA-Seq is used to analyze the continuously changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/single nucleotide polymorphisms (SNPs) and changes in gene expression over time, or differences in gene expression in different groups or treatments. In addition to messenger RNA (mRNA) transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as microRNA (miRNA), transfer RNA (tRNA), and ribosomal profiling. RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. Recent advances in RNA-Seq include single cell sequencing, in situ sequencing of fixed tissue, and native RNA molecule sequencing with single-molecule real-time sequencing. Prior to RNA-Seq, gene expression studies were done with hybridization-based microarrays. Issues with microarrays include cross-hybridization artifacts, poor quantification of lowly and highly expressed genes, and needing to know the sequence a priori. Because of these technical issues, transcriptomics transitioned to sequencing-based methods. These progressed from Sanger sequencing of Expressed Sequence Tag libraries, to chemical tag-based methods (e.g., serial analysis of gene expression), and finally to the current technology, next-gen sequencing of complementary DNA (cDNA), notably RNA-Seq. doi: 10.15347/WJS/2021.004
Author: Joel Brewster Lewis
The affine symmetric group is a mathematical structure that describes the symmetries of the number line and the regular triangular tesselation of the plane, as well as related higher dimensional objects. It is an infinite extension of the symmetric group, which consists of all permutations (rearrangements) of a finite set. In addition to its geometric description, the affine symmetric group may be defined as the collection of permutations of the integers (..., −2, −1, 0, 1, 2, ...) that are periodic in a certain sense, or in purely algebraic terms as a group with certain generators and relations. These different definitions allow for the extension of many important properties of the finite symmetric group to the infinite setting, and are studied as part of the fields of combinatorics and representation theory. doi: 10.15347/WJS/2021.003
Authors: Yingxuan Ma, Kim Johnson
Arabinogalactan-proteins (AGPs) are highly glycosylated proteins (glycoproteins) found in the cell walls of plants. AGPs account for only a small portion of the cell wall, usually no more than 1% of dry mass of the primary wall. AGPs are members of the hydroxyproline-rich glycoprotein (HRGP) superfamily that represent a large and diverse group of glycosylated wall proteins. AGPs have attracted considerable attention due to their highly complex structures and potential roles in signalling. In addition, they have industrial and health applications due to their chemical/physical properties (water-holding, adhesion and emulsification). Glycosylation can account for more than 90% of the total mass. AGPs have been reported in a wide range of higher plants in seeds, roots, stems, leaves and inflorescences. They have also been reported in secretions of cell culture medium of root, leaf, endosperm and embryo tissues, and some exudate producing cell types such as stylar canal cells are capable of producing lavish amounts of AGPs. doi: 10.15347/WJS/2021.002
Authors: Rebecca Chastain, Daniel Taub
Female body shape has an apparent influence on mate value as perceived by males. Some researchers have suggested that human male mate preference has evolved to universally favor a specific body shape which can be quantified with a particular value for Waist-Hip Ratio and/or Body Mass Index. Other research has presented evidence that populations of males exhibit differentiated preferences for female body shape. The research literature largely supports the hypothesis that male mate preference for female body shape is variable and dependent upon local resource availability. These conclusions provide insight into the evolutionary processes that have acted to produce adaptive flexibility in human male mate preferences in accordance with the environment. doi: 10.15347/WJS/2021.001
VOLUME 3 (2020)
ISSUE 1
Previous issue
Author: Boris Tsirelson
Contrary to popular misconception, the question in the title is far from simple. It involves sets of numbers on the first level, sets of sets of numbers on the second level, and so on, endlessly. The infinite hierarchy of the levels involved distinguishes the concept of "definable number" from such notions as "natural number", "rational number", "algebraic number", "computable number" etc. doi: 10.15347/WJS/2020.008
Authors: Subir Sarker, Jade Forwood, Shane Raidal
The beak and feather disease virus (BFDV) causes psittacine beak and feather disease, an often chronic and fatal disease in psittacine birds. The virus most commonly infects psittacine birds, but is also capable of infecting non-psittacine bird species in Australasia. The virus induces an immunosuppressive condition with chronic symmetrical irreversible loss of feather, as well as beak and claw deformities eventually leading to death. No specific treatment is currently commercially available for infected birds; however, a combination of quarantine and hygiene control, diagnostic testing and enhancing flock adaptive immunity is recommended to provide the most effective and sustainable control. Recent structural determination of BFDV capsid protein provides insights into the different assemblies that can be formed from one of the smallest known DNA viruses. doi: 10.15347/WJS/2020.007
Author: Keshab Magar
E-extension is an approach to agricultural knowledge extension through electronic technologies where online platforms such as web sites, mobile applications and social media are used. Low cost and high effectiveness suggest substantial future possibilities. Nepal's rapid increase in internet usage provides the potential to employ e-extension as a valuable mechanism in the prevailing system of agriculture extension, providing direct advantages to Nepalese farmers. Access to e-extension enables timely updates to newer technologies, information and e-news, with better chances of broad discourse in Nepalese agriculture. This paper aims to document recent initiatives in current e-extension developments in Nepal. Constraints may arise from issues of user-friendliness, affordability and reliability. If promoted with innovation and considerations of actual access, e-extension can have multiple positive impacts on Nepalese agriculture in the near future. doi: 10.15347/WJS/2020.006
Authors: Jan Kameníček, et al.
On 13 October 1990, meteoroid EN131090, with an estimated mass of 44 kg, entered the Earth's atmosphere above Czechoslovakia and Poland and, after a few seconds, returned to space. Observations of such events are quite rare; this was the second recorded using scientific astronomical instruments (after the 1972 Great Daylight Fireball) and the first recorded from two distant positions, which enabled the calculation of several of its orbital characteristics. The encounter with Earth significantly changed its orbit and, to a smaller extent, some of its physical properties (mass and structure of its outer layer). doi: 10.15347/WJS/2020.005
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. doi: 10.15347/WJS/2020.004
Authors: 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. This article presents a brief review of published VCC experiments, followed by the presentation of an example VCC experiment investigating the effect of varying the inoculum of Escherichia coli cells when assayed against the defensin HNP1. A Microsoft Excel file containing the macro used for the calculation of threshold times and data analysis is also presented. The experiment demonstrated a pronounced inoculum effect at high inocula. The results of five similar experiments are also reported, showing variation among replicate data. doi: 10.15347/WJS/2020.003
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. doi: 10.15347/WJS/2020.002
Authors: Iain Reid, et al.
Paranthodon (/pəˈrænθədɒn/) 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. In identifying the remains as those of Palaeoscincus, Broom initially classified Paranthodon as an ankylosaurian, a statement backed by the research of Coombs in the 1970s. However, in 1929, Nopcsa identified the taxon as a stegosaurid, with which most modern studies agree. In 1981, the genus was reviewed with modern taxonomy, and found to be a valid genus of stegosaurid. However, a 2018 review of Paranthodon could only identify one distinguishing feature, and while that study still referred it to Stegosauria based on similarity and multiple phylogenetic analyses, no diagnostic features of the group could be identified in Paranthodon. doi: 10.15347/WJS/2020.001
VOLUME 2 (2019)
ISSUE 1
Previous issue
Authors: 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. doi: 10.15347/WJS/2019.007
Authors: Ignacio Lopez de Blas, 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. doi: 10.15347/WJS/2019.006
Authors: 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. Binary search runs in logarithmic time in the worst case, making comparisons, where is the number of elements in the array, the is Big O notation, and is the logarithm. Binary search is faster than linear search except for small arrays. However, the array must be sorted first to be able to apply binary search. There are specialized data structures designed for fast searching, such as hash tables, that can be searched more efficiently than binary search. However, binary search can be used to solve a wider range of problems, such as finding the next-smallest or next-largest element in the array relative to the target even if it is absent from the array. There are numerous variations of binary search. In particular, fractional cascading speeds up binary searches for the same value in multiple arrays. Fractional cascading efficiently solves a number of search problems in computational geometry and in numerous other fields. Exponential search extends binary search to unbounded lists. The binary search tree and B-tree data structures are based on binary search. doi: 10.15347/WJS/2019.005
Authors: Michael J Stear, David Piedrafita, Caitlin J Jenvey, Sarah Sloan, Dalal Alenizi, Callum Cairns
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. doi: 10.15347/WJS/2019.004
Authors: Michael Bech, et al.
Baryonyx (/ˌbæriˈɒnɪks/) 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. doi: 10.15347/WJS/2019.003
Authors: 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. Many different methods have been used since 1840, when the first scientific ice drilling expedition attempted to drill through the Unteraargletscher in the Alps. Two early methods were percussion, in which the ice is fractured and pulverized, and rotary drilling, a method often used in mineral exploration for rock drilling. In the 1940s, thermal drills began to be used; these drills melt the ice by heating the drill. Drills that use jets of hot water or steam to bore through ice soon followed. A growing interest in ice cores, used for palaeoclimatological research, led to ice coring drills being developed in the 1950s and 1960s, and there are now many different coring drills in use. For obtaining ice cores from deep holes, most investigators use cable-suspended electromechanical drills, which use an armoured cable to carry electrical power to a mechanical drill at the bottom of the borehole. In 1966, a US team successfully drilled through the Greenland ice sheet at Camp Century, at a depth of 1,387 metres (4,551 ft). Since then many other groups have succeeded in reaching bedrock through the two largest ice sheets, in Greenland and Antarctica. Recent projects have focused on finding drilling locations that will give scientists access to very old undisturbed ice at the bottom of the borehole, since an undisturbed stratigraphic sequence is required to accurately date the information obtained from the ice. doi: 10.15347/WJS/2019.002
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. doi: 10.15347/WJS/2019.001
VOLUME 1 (2018)
ISSUE 2
Previous issue
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. doi: 10.15347/WJS/2018.008
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. Lead is a relatively unreactive post-transition metal. Its weak metallic character is illustrated by its amphoteric nature; lead and its oxides react with acids and bases, and it tends to form covalent bonds. Compounds of lead are usually found in the +2 oxidation state rather than the +4 state common with lighter members of the carbon group. Exceptions are mostly limited to organolead compounds. Like the lighter members of the group, lead tends to bond with itself; it can form chains, rings and polyhedral structures. doi: 10.15347/WJS/2018.007
VOLUME 1 (2018)
ISSUE 1
Previous issue
Authors: 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. The method was developed in the late 1940s by Willard Libby, who received the Nobel Prize in Chemistry for his work in 1960. It is based on the fact that radiocarbon (14 doi: 10.15347/WJS/2018.006
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 particles are routinely observed to violate in what are now called Bell test experiments. As an alternative to showing students a "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. doi: 10.15347/WJS/2018.005
Authors: Tatiana P. Soares da Costa, Cody J. Hall
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. doi: 10.15347/WJS/2018.004
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. doi: 10.15347/WJS/2018.003
Authors: 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, where an 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. Topological notions such as continuity have natural definitions in every Euclidean space. However, topology does not distinguish straight lines from curved lines, and the relation between Euclidean and topological spaces is thus "forgetful". Relations of this kind are sketched in Figure 1, and treated in more detail in the Section "Types of spaces". It is not always clear whether a given mathematical object should be considered as a geometric "space", or an algebraic "structure". A general definition of "structure", proposed by Bourbaki, embraces all common types of spaces, provides a general definition of isomorphism, and justifies the transfer of properties between isomorphic structures. doi: 10.15347/WJS/2018.002 Editorial | The aims and scope of WikiJournal of Science
Author: Thomas Shafee, WikiJournal of Science editorial board
WikiJournal of Science is an 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. doi: 10.15347/WJS/2018.001
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