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1
Belaganahalli, M., S. Maan, and P. P. C. Mertens. "Caractérisation génétique des virus Tilligerry et Mitchell River." Revue d’élevage et de médecine vétérinaire des pays tropicaux 62, no. 2-4 (February 1, 2009): 151. http://dx.doi.org/10.19182/remvt.10060.
Повний текст джерелаАнотація:
Viruses that are normally safely contained within their host species can emerge due to intense livestock farming, trade, travel, climate change and encroachment of human activities into new environments. The unexpected emergence of bluetongue virus (BTV), the prototype species of the genus Orbivirus, in economically important livestock species (sheep and cattle) across the whole of Europe (since 1998), indicates that other orbiviruses represent a potential further threat to animal and human populations in Europe and elsewhere. The genus Orbivirus is the largest within the family Reoviridae, containing 22 virus species, as well as 14 unclassified orbiviruses, some of which may represent additional or novel species. The orbiviruses are transmitted primarily by arthropod vectors (e.g. Culicoides, mosquitoes or ticks). Viral genome sequence data provide a basis for virus taxonomy and diagnostic test development, and make it possible to address fundamental questions concerning virus biology, pathogenesis, virulence and evolution, that can be further explored in mutation and reverse genetics studies. Genome sequences also provide criteria for the classification of novel isolates within individual Orbivirus species, as well as the identification of different serotypes, topotypes, reassortants and even closely related but distinct virus lineages. Full-length genome characterization of Tilligerry virus (TILV), a member of the Eubenangee virus species, and Mitchell River virus (MRV), a member of the Warrego virus species, have revealed highly conserved 5’ and 3’ terminal hexanucleotide sequences. Phylogenetic analyses of orbivirus T2 ‘sub-core-shell’ protein sequences reinforce the hypothesis that this protein is an important evolutionary marker for these viruses. The T2 protein shows high levels of amino acid (AA) sequence identity (> 91%) within a single Orbivirus species / serogroup, which can be used for species identification. The T2-protein gene has therefore been given priority in sequencing studies. The T2 protein of TILV is closely related to that of Eubenangee virus (~91% identity), confirming that they are both members of the same Eubenangee virus species. Although TILV is reported to be related to BTV in serological assays, the TILV T2 protein shows only 68-70% AA identity to BTV. This supports its current classification within a different serogroup (Eubenangee). Warrego virus and MRV are currently classified as two distinct members (different serotypes) within the Warrego virus species. However, they show only about 79% AA identity in their T2 protein (based on partial sequences). It is therefore considered likely that they could be reclassified as members of distinct Orbivirus species. The taxonomic classification of MRV will be reviewed after generating full length sequences for the entire genomes of both viruses. The taxonomic status of each of these viruses will also be tested further by co-infections and attempts to create reassortants between them (only viruses belonging to the same species can reassort their genome segments). TILV and MRV are the first viruses from their respective serogroups / virus species to be genetically fully characterized, and will provide a basis for the further characterization / identification of additional viruses within each group / species. These data will assist in the development of specific diagnostic assays and potentially in control of emerging diseases. The sequences generated will also help to evaluate current diagnostic [reverse transcriptase - polymerase chain reaction (RT-PCR)] tests for BTV, African horse sickness virus, epizootic haemorrhagic disease virus, etc., in silico, by identifying any possibility of cross reactivity.
2
Giovannelli, Donato, and Costantino Vetriani. "From extreme environments to human pathogens: an evolutionary journey." Biochemist 39, no. 6 (December 1, 2017): 4–9. http://dx.doi.org/10.1042/bio03906004.
Повний текст джерелаАнотація:
The history of our planet is underpinned by roughly 4 billion years of microbial evolution. From its emergence in a (probably) hot and anoxic environment, microbial life has evolved to colonize every available niche on our planet, including the inside and outside of other organisms. Yet, the emergence and evolution of microbial metabolism remains a major unsolved problem. How have microbes adapted to colonize every available environmental niche, including other organisms? How did they evolve to colonize mammals and our human ancestors? Answers to these questions will allow us to understand the emergence and evolution of life on our planet, inform the search for life elsewhere and, in the making, reveal important insight that will help us fight infections.
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Meyer, Stephen C. "Do Christians Need to Reconcile Evolutionary Theory and Doctrines of Divine Providence and Creation?" Philosophia Christi 22, no. 1 (2020): 63–74. http://dx.doi.org/10.5840/pc20202215.
Повний текст джерелаАнотація:
Many Christian scholars have argued that standard versions of evolutionary theory and orthodox theological commitments can be reconciled. Some theistic evolutionists or “evolutionary creationists” have argued that evolutionary mechanisms such as random mutation and natural selection are nothing less than God’s way of creating. Though I dispute the logical coherence of these attempted reconciliations elsewhere, I argue here that there is little reason for Christians to attempt them, since an accumulating body of evidence from multiple subdisciplines of biology casts doubt on the creative power of the main evolutionary mechanisms. Thus, rather than addressing the question, “Can a meaningful doctrine of divine providence or creation be reconciled with mainstream evolutionary theory?” this essay will address the question of whether Christians should, or need to, attempt such a reconciliation at all.
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Rothschild, Lynn J. "The evolution of photosynthesis…again?" Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1504 (May 16, 2008): 2787–801. http://dx.doi.org/10.1098/rstb.2008.0056.
Повний текст джерелаАнотація:
‘Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.
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Chela-Flores, J. "Testing the universality of biology: a review." International Journal of Astrobiology 6, no. 3 (June 11, 2007): 241–48. http://dx.doi.org/10.1017/s1473550407003795.
Повний текст джерелаАнотація:
AbstractWe discuss whether it is possible to test the universality of biology, a quest that is of paramount relevance for one of its most recent branches, namely astrobiology. We review this topic in terms of the relative roles played on the Earth biota by contingency and evolutionary convergence. Following the seminal contribution of Darwin, it is reasonable to assume that all forms of life known to us so far are not only terrestrial, but are descendants of a common ancestor that evolved on this planet at the end of a process of chemical evolution. We also raise the related question of whether the molecular events that were precursors to the origin of life on Earth are bound to occur elsewhere in the Universe, wherever the environmental conditions are similar to the terrestrial ones. We refer to ‘cosmic convergence’ as the possible occurrence elsewhere in the Universe of Earth-like environmental conditions. We argue that cosmic convergence is already suggested by observational data. The set of hypotheses for addressing the question of the universality of biology can be tested by future experiments that are feasible with current technology. We focus on landing on Europa and the broader implications of selecting the specific example of the right landing location. We have previously discussed the corresponding miniaturized equipment that is already in existence. The significance of these crucial points needs to be put into a wider scientific perspective, which is one of the main objectives of this review.
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Wu, Tao, Lu Xiong, Fuli Wang, Xiaozhen Xu, Jiao Wang, Feng Lin, Chunhua Li, Ling Lu, and Yuanping Zhou. "A Unique Pattern of HCV Genotype Distribution on Hainan Island in China Revealed by Evolutionary Analysis." Cellular Physiology and Biochemistry 39, no. 1 (2016): 316–30. http://dx.doi.org/10.1159/000445626.
Повний текст джерелаАнотація:
Background/Aims: Different genotypes of HCV may differ in both disease progression and response to antiviral therapies. Hainan Island has been inhabited by the “Li” aboriginal minority for centuries. We aimed to provide a better understanding of HCV infection on Hainan Island, so that the information would help improve strategies for HCV prevention and control on the island and in the wider country. Methods: Using RT-PCR and DNA sequencing, we determined HCV sequences from 100 patients living on Hainan Island. Results: Phylogenetic analysis classified these sequences into six subtypes: 6a (n=35), 1b (n=31), 3b (n=16), 2a (n=8), 3a (n=6), and 1a (n=4). By including reference sequences reported from elsewhere in China, phylogeographic trees were reconstructed to indicate their migration patterns. While the predominant 6a isolates were estimated to have origins in Guangdong and Guangxi provinces, the increase in 3b strains must have resulted from IDU network transmission from the southwest. A Bayesian Skyline Plot for subtype 1a, which is rare in China, showed a rapid population growth since 1998. Although slowed in rate around 2005, this growth continued to the present. Not found for any other HCV lineage. Conclusions: Overall, a delayed growth pattern may indicate the unique history of 1a dissemination in China and its recently increasing prevalence, despite measures taken to improve HCV prevention.
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Anjard, Christophe, and William F. Loomis. "Evolutionary Analyses of ABC Transporters of Dictyostelium discoideum." Eukaryotic Cell 1, no. 4 (August 2002): 643–52. http://dx.doi.org/10.1128/ec.1.4.643-652.2002.
Повний текст джерелаАнотація:
ABSTRACT The ABC superfamily of genes is one of the largest in the genomes of both bacteria and eukaryotes. The proteins encoded by these genes all carry a characteristic 200- to 250-amino-acid ATP-binding cassette that gives them their family name. In bacteria they are mostly involved in nutrient import, while in eukaryotes many are involved in export. Seven different families have been defined in eukaryotes based on sequence homology, domain topology, and function. While only 6 ABC genes in Dictyostelium discoideum have been studied in detail previously, sequences from the well-advanced Dictyostelium genome project have allowed us to recognize 68 members of this superfamily. They have been classified and compared to animal, plant, and fungal orthologs in order to gain some insight into the evolution of this superfamily. It appears that many of the genes inferred to have been present in the ancestor of the crown organisms duplicated extensively in some but not all phyla, while others were lost in one lineage or the other.
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Shaw, John. "Geomorphic Evidence of Postglacial Terrestrial Environments on Atlantic Canadian Continental Shelves." Géographie physique et Quaternaire 59, no. 2-3 (April 4, 2007): 141–54. http://dx.doi.org/10.7202/014752ar.
Повний текст джерелаАнотація:
Abstract Changes in the geography of Atlantic Canada since the last glacial maximum (LGM) are grouped into three phases. The first phase (LGM – ca. 13 ka BP) commences with glaciers at the edge of the continental shelves, and ends with the glaciers having retreated to near modern coasts. In the second phase (ca. 13 ka BP‑10 ka BP), glaciers were mainly on land; on the continental shelves there were scattered small ice caps and an outer-shelf archipelago. Early in phase three, beginning ca. 10 ka BP, glaciers were largely absent, and the archipelago was gradually submerging; elsewhere, falling relative sea levels caused emergence. Multibeam sonar mapping has revealed the geomorphic evidence of submerged terrestrial environments of phases II and III, including fluvial, deltaic, and coastal systems. The best-preserved fluvial systems are in Northumberland Strait and the Bras d’Or Lakes. Elsewhere, multibeam bathymetric data allow discrimination between fluvial and non-fluvial channels. Deltas were mainly preserved in the special circumstances of Newfoundland fjords. Submerged coastal systems are common in the Bras d’Or Lakes, but rare elsewhere. Landscape preservation is ascribed to special circumstances. Paleogeographic reconstructions have applications in the field of evolutionary biology and archaeology.
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Channon, Alastair. "Maximum Individual Complexity is Indefinitely Scalable in Geb." Artificial Life 25, no. 2 (May 2019): 134–44. http://dx.doi.org/10.1162/artl_a_00285.
Повний текст джерелаАнотація:
Geb was the first artificial life system to be classified as exhibiting open-ended evolutionary dynamics according to Bedau and Packard's evolutionary activity measures and is the only one to have been classified as such according to the enhanced version of that classification scheme. Its evolution is driven by biotic selection, that is (approximately), by natural selection rather than artificial selection. Whether or not Geb can generate an indefinite increase in maximum individual complexity is evaluated here by scaling two parameters: world length (which bounds population size) and the maximum number of neurons per individual. Maximum individual complexity is found to be asymptotically bounded when scaling either parameter alone. However, maximum individual complexity is found to be indefinitely scalable, to the extent evaluated so far (with run times in years and billions of reproductions per run), when scaling both world length and the maximum number of neurons per individual together. Further, maximum individual complexity is shown to scale logarithmically with (the lower of) maximum population size and maximum number of neurons per individual. This raises interesting questions and lines of thought about the feasibility of achieving complex results within open-ended evolutionary systems and how to improve on this order of complexity growth.
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Lane, Nick, William F. Martin, John A. Raven, and John F. Allen. "Energy, genes and evolution: introduction to an evolutionary synthesis." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1622 (July 19, 2013): 20120253. http://dx.doi.org/10.1098/rstb.2012.0253.
Повний текст джерелаАнотація:
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. No energy, no evolution. The ‘modern synthesis’ of the past century explained evolution in terms of genes, but this is only part of the story. While the mechanisms of natural selection are correct, and increasingly well understood, they do little to explain the actual trajectories taken by life on Earth. From a cosmic perspective—what is the probability of life elsewhere in the Universe, and what are its probable traits?—a gene-based view of evolution says almost nothing. Irresistible geological and environmental changes affected eukaryotes and prokaryotes in very different ways, ones that do not relate to specific genes or niches. Questions such as the early emergence of life, the morphological and genomic constraints on prokaryotes, the singular origin of eukaryotes, and the unique and perplexing traits shared by all eukaryotes but not found in any prokaryote, are instead illuminated by bioenergetics. If nothing in biology makes sense except in the light of evolution, nothing in evolution makes sense except in the light of energetics. This Special Issue of Philosophical Transactions examines the interplay between energy transduction and genome function in the major transitions of evolution, with implications ranging from planetary habitability to human health. We hope that these papers will contribute to a new evolutionary synthesis of energetics and genetics.
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Culberson, Joseph C. "On the Futility of Blind Search: An Algorithmic View of “No Free Lunch”." Evolutionary Computation 6, no. 2 (June 1998): 109–27. http://dx.doi.org/10.1162/evco.1998.6.2.109.
Повний текст джерелаАнотація:
The paper is in three parts. First, we use simple adversary arguments to redevelop and explore some of the no-free-lunch (NFL) theorems and perhaps extend them a little. Second, we clarify the relationship of NFL theorems to algorithm theory and complexity classes such as NP. We claim that NFL is weaker in the sense that the constraints implied by the conjectures of traditional algorithm theory on what an evolutionary algorithm may be expected to accomplish are far more severe than those implied by NFL. Third, we take a brief look at how natural evolution relates to computation and optimization. We suggest that the evolution of complex systems exhibiting high degrees of orderliness is not equivalent in difficulty to optimizing hard (in the complexity sense) problems, and that the optimism in genetic algorithms (GAs) as universal optimizers is not justified by natural evolution. This is an informal tutorial paper—most of the information presented is not formally proven, and is either “common knowledge” or formally proven elsewhere. Some of the claims are intuitions based on experience with algorithms, and in a more formal setting should be classified as conjectures.
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VilÀ, Montserrat, Alison M. Dunn, Franz Essl, Elena GÓmez-DÍaz, Philip E. Hulme, Jonathan M. Jeschke, MartÍn A. NÚÑez, et al. "Viewing Emerging Human Infectious Epidemics through the Lens of Invasion Biology." BioScience 71, no. 7 (May 19, 2021): 722–40. http://dx.doi.org/10.1093/biosci/biab047.
Повний текст джерелаАнотація:
Abstract Invasion biology examines species originated elsewhere and moved with the help of humans, and those species’ impacts on biodiversity, ecosystem services, and human well-being. In a globalized world, the emergence and spread of many human infectious pathogens are quintessential biological invasion events. Some macroscopic invasive species themselves contribute to the emergence and transmission of human infectious agents. We review conceptual parallels and differences between human epidemics and biological invasions by animals and plants. Fundamental concepts in invasion biology regarding the interplay of propagule pressure, species traits, biotic interactions, eco-evolutionary experience, and ecosystem disturbances can help to explain transitions between stages of epidemic spread. As a result, many forecasting and management tools used to address epidemics could be applied to biological invasions and vice versa. Therefore, we advocate for increasing cross-fertilization between the two disciplines to improve prediction, prevention, treatment, and mitigation of invasive species and infectious disease outbreaks, including pandemics.
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Harris, Paul L. "Children's understanding of death: from biology to religion." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1754 (July 16, 2018): 20170266. http://dx.doi.org/10.1098/rstb.2017.0266.
Повний текст джерелаАнотація:
Young children construct a biological conception of death, recognizing that death terminates mental and bodily processes. Despite this recognition, many children are receptive to an alternative conception of death, which affirms that the deceased has an afterlife elsewhere. A plausible interpretation of children's receptivity to this alternative conception is that human beings, including young children, are naturally disposed to remember and keep in mind individuals to whom they are attached even when those individuals leave and are absent for extended periods. This disposition is reflected in the pervasive tendency to talk about death as a departure rather than a terminus. It also enables the living to sustain their ties to the dead, even if, in the case of death, the departure is permanent rather than temporary. Linguistic and developmental evidence for these claims is reviewed. Possible biological origins and implications for archaeological research are also discussed. This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
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Evseev, Peter, Daria Gutnik, Mikhail Shneider, and Konstantin Miroshnikov. "Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of Duplodnaviria Viruses." Biomolecules 13, no. 1 (January 5, 2023): 110. http://dx.doi.org/10.3390/biom13010110.
Повний текст джерелаАнотація:
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm Duplodnaviria, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified Duplodnaviria families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal Duplodnaviria groups, and problems relating to the taxonomic classification of Duplodnaviria have been discussed.
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Brooks, Robert. "“Asia's Missing Women” as a Problem in Applied Evolutionary Psychology?" Evolutionary Psychology 10, no. 5 (December 1, 2012): 147470491201000. http://dx.doi.org/10.1177/147470491201000512.
Повний текст джерелаАнотація:
In many parts of Asia, the Middle East and North Africa, women and children are so undervalued, neglected, abused, and so often killed, that sex ratios are now strongly male biased. In recent decades, sex-biased abortion has exacerbated the problem. In this article I highlight several important insights from evolutionary biology into both the origin and the severe societal consequences of “Asia's missing women”, paying particular attention to interactions between evolution, economics and culture. Son preferences and associated cultural practices like patrilineal inheritance, patrilocality and the Indian Hindu dowry system arise among the wealthy and powerful elites for reasons consistent with models of sex-biased parental investment. Those practices then spread via imitation as technology gets cheaper and economic development allows the middle class to grow rapidly. I will consider evidence from India, China and elsewhere that grossly male-biased sex ratios lead to increased crime, violence, local warfare, political instability, drug abuse, prostitution and trafficking of women. The problem of Asia's missing women presents a challenge for applied evolutionary psychology to help us understand and ameliorate sex ratio biases and their most severe consequences.
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Igloi, Gabor L. "The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms." Journal of Molecular Evolution 89, no. 7 (July 12, 2021): 484–93. http://dx.doi.org/10.1007/s00239-021-10019-z.
Повний текст джерелаАнотація:
AbstractDuring the endosymbiotic evolution of mitochondria, the genes for aminoacyl-tRNA synthetases were transferred to the ancestral nucleus. A further reduction of mitochondrial function resulted in mitochondrion-related organisms (MRO) with a loss of the organelle genome. The fate of the now redundant ancestral mitochondrial aminoacyl-tRNA synthetase genes is uncertain. The derived protein sequence for arginyl-tRNA synthetase from thirty mitosomal organisms have been classified as originating from the ancestral nuclear or mitochondrial gene and compared to the identity element at position 20 of the cognate tRNA that distinguishes the two enzyme forms. The evolutionary choice between loss and retention of the ancestral mitochondrial gene for arginyl-tRNA synthetase reflects the coevolution of arginyl-tRNA synthetase and tRNA identity elements.
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Shen, Libing, Chao Chen, Hongxiang Zheng, and Li Jin. "The Evolutionary Relationship between Microbial Rhodopsins and Metazoan Rhodopsins." Scientific World Journal 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/435651.
Повний текст джерелаАнотація:
Rhodopsins are photoreceptive proteins with seven-transmembrane alpha-helices and a covalently bound retinal. Based on their protein sequences, rhodopsins can be classified into microbial rhodopsins and metazoan rhodopsins. Because there is no clearly detectable sequence identity between these two groups, their evolutionary relationship was difficult to decide. Through ancestral state inference, we found that microbial rhodopsins and metazoan rhodopsins are divergently related in their seven-transmembrane domains. Our result proposes that they are homologous proteins and metazoan rhodopsins originated from microbial rhodopsins. Structure alignment shows that microbial rhodopsins and metazoan rhodopsins share a remarkable structural homology while the position of retinal-binding lysine is different between them. It suggests that the function of photoreception was once lost during the evolution of rhodopsin genes. This result explains why there is no clearly detectable sequence similarity between the two rhodopsin groups: after losing the photoreception function, rhodopsin gene was freed from the functional constraint and the process of divergence could quickly change its original sequence beyond recognition.
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Gati, Noble Selasi, Ozan Altan Altinok, Sriram Kumar, Verónica A. Ferrando, Joachim Kurtz, Michael Quante, Stephan Ludwig, and Alexander Mellmann. "Integrating evolutionary aspects into dual-use discussion: the cases of influenza virus and enterohemorrhagic Escherichia coli." Evolution, Medicine, and Public Health 9, no. 1 (January 1, 2021): 383–92. http://dx.doi.org/10.1093/emph/eoab034.
Повний текст джерелаАнотація:
Abstract Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential.
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Bygraves, J. A., R. Urwin, A. J. Fox, S. J. Gray, J. E. Russell, I. M. Feavers, and M. C. J. Maiden. "Population Genetic and Evolutionary Approaches to Analysis ofNeisseria meningitidis Isolates Belonging to the ET-5 Complex." Journal of Bacteriology 181, no. 18 (September 15, 1999): 5551–56. http://dx.doi.org/10.1128/jb.181.18.5551-5556.1999.
Повний текст джерелаАнотація:
ABSTRACT Periodically, new disease-associated variants of the human pathogenNeisseria meningitidis arise. These meningococci diversify during spread, and related isolates recovered from different parts of the world have different genetic and antigenic characteristics. An example is the ET-5 complex, members of which were isolated globally from the mid-1970s onwards. Isolates from a hyperendemic outbreak of meningococcal disease in Worcester, England, during the late 1980s were characterized by multilocus sequence typing and sequence determination of antigen genes. These data established that the Worcester outbreak was caused by ET-5 complex meningococci which were not closely related to the ET-5 complex bacteria responsible for a hyperendemic outbreak in the nearby town of Stroud during the years preceding the Worcester outbreak. A comparison with other ET-5 complex meningococci established that there were at least three distinct globally distributed subpopulations within the ET-5 complex, characterized by particular housekeeping and antigen gene alleles. The Worcester isolates belonged to one of these subpopulations, the Stroud isolates belonged to another, and at least one representative of the third subpopulation identified in this work was isolated elsewhere in the United Kingdom. The sequence data demonstrated that ET-5 variants have arisen by multiple complex pathways involving the recombination of antigen and housekeeping genes and de novo mutation of antigen genes. The data further suggest that either the ET-5 complex has been in existence for many years, evolving and spreading relatively slowly until its disease-causing potential was recognized, or it has evolved and spread rapidly since its first identification in the 1970s, with each of the subpopulations attaining a distribution spanning several continents.
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Amore, Giusi, Luigi Bertolotti, Gabriel L. Hamer, Uriel D. Kitron, Edward D. Walker, Marilyn O. Ruiz, Jeffrey D. Brawn, and Tony L. Goldberg. "Multi-year evolutionary dynamics of West Nile virus in suburban Chicago, USA, 2005–2007." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1548 (June 27, 2010): 1871–78. http://dx.doi.org/10.1098/rstb.2010.0054.
Повний текст джерелаАнотація:
West Nile virus has evolved in concert with its expansion across North America, but little is known about the evolutionary dynamics of the virus on local scales. We analysed viral nucleotide sequences from mosquitoes collected in 2005, 2006, and 2007 from a known transmission ‘hot spot’ in suburban Chicago, USA. Within this approximately 11 × 14 km area, the viral envelope gene has increased approximately 0.1% yr −1 in nucleotide-level genetic diversity. In each year, viral diversity was higher in ‘residential’ sites characterized by dense housing than in more open ‘urban green space’ sites such as cemeteries and parks. Phylodynamic analyses showed an increase in incidence around 2005, consistent with a higher-than-average peak in mosquito and human infection rates that year. Analyses of times to most recent common ancestor suggest that WNV in 2005 and 2006 may have arisen predominantly from viruses present during 2004 and 2005, respectively, but that WNV in 2007 had an older common ancestor, perhaps indicating a predominantly mixed or exogenous origin. These results show that the population of WNV in suburban Chicago is an admixture of viruses that are both locally derived and introduced from elsewhere, containing evolutionary information aggregated across a breadth of spatial and temporal scales.
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van Berkum, Peter, Zewdu Terefework, Lars Paulin, Sini Suomalainen, Kristina Lindström, and Bertrand D. Eardly. "Discordant Phylogenies within the rrn Loci of Rhizobia." Journal of Bacteriology 185, no. 10 (May 15, 2003): 2988–98. http://dx.doi.org/10.1128/jb.185.10.2988-2998.2003.
Повний текст джерелаАнотація:
ABSTRACT It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of α-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.
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Li, Jia, Litian Zhang, Rania G. Elbaiomy, Lilan Chen, Zhenrong Wang, Jie Jiao, Jiliang Zhu, et al. "Evolution analysis of FRIZZY PANICLE (FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae)." PeerJ 10 (March 11, 2022): e12880. http://dx.doi.org/10.7717/peerj.12880.
Повний текст джерелаАнотація:
FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family’s evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene’s functions should take note of the possible presence of various roles in other grass species.
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Wang, Pauline W., Linda Chu, and David S. Guttman. "Complete Sequence and Evolutionary Genomic Analysis of the Pseudomonas aeruginosa Transposable Bacteriophage D3112." Journal of Bacteriology 186, no. 2 (January 15, 2004): 400–410. http://dx.doi.org/10.1128/jb.186.2.400-410.2004.
Повний текст джерелаАнотація:
ABSTRACT Bacteriophage D3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. To further our understanding of transposable phage in P. aeruginosa, we have sequenced the complete genome of D3112. The genome is 37,611 bp, with an overall G+C content of 65%. We have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes A and B) that have been previously characterized and sequenced. The organization of the putative coding regions corresponds to published genetic and transcriptional maps and is very similar to that of enterobacteriophage Mu. In contrast, the International Committee on Taxonomy of Viruses has classified D3112 as a λ-like phage on the basis of its morphology. Similarity-based analyses identified 27 open reading frames with significant matches to proteins in the NCBI databases. Forty-eight percent of these were similar to Mu-like phage and prophage sequences, including proteins responsible for transposition, transcriptional regulation, virion morphogenesis, and capsid formation. The tail proteins were highly similar to prophage sequences in Escherichia coli and phage Phi12 from Staphylococcus aureus, while proteins at the right end were highly similar to proteins in Xylella fastidiosa. We performed phylogenetic analyses to understand the evolutionary relationships of D3112 with respect to Mu-like versus λ-like bacteriophages. Different results were obtained from similarity-based versus phylogenetic analyses in some instances. Overall, our findings reveal a highly mosaic structure and suggest that extensive horizontal exchange of genetic material played an important role in the evolution of D3112.
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Keller, G. A., S. Krisans, S. J. Gould, J. M. Sommer, C. C. Wang, W. Schliebs, W. Kunau, S. Brody, and S. Subramani. "Evolutionary conservation of a microbody targeting signal that targets proteins to peroxisomes, glyoxysomes, and glycosomes." Journal of Cell Biology 114, no. 5 (September 1, 1991): 893–904. http://dx.doi.org/10.1083/jcb.114.5.893.
Повний текст джерелаАнотація:
Peroxisomes, glyoxysomes, glycosomes, and hydrogenosomes have each been classified as microbodies, i.e., subcellular organelles with an electron-dense matrix that is bound by a single membrane. We investigated whether these organelles might share a common evolutionary origin by asking if targeting signals used for translocation of proteins into these microbodies are related. A peroxisomal targeting signal (PTS) consisting of the COOH-terminal tripeptide serine-lysine-leucine-COOH has been identified in a number of peroxisomal proteins (Gould, S.J., G.-A. Keller, N. Hosken, J. Wilkinson, and S. Subramani. 1989. J. Cell Biol. 108:1657-1664). Antibodies raised to a peptide ending in this sequence (SKL-COOH) recognize a number of peroxisomal proteins. Immunocryoelectron microscopy experiments using this anti-SKL antibody revealed the presence of proteins containing the PTS within glyoxysomes of cells from Pichia pastoris, germinating castor bean seeds, and Neurospora crassa, as well as within the glycosomes of Trypanosoma brucei. Western blot analysis of purified organelle fractions revealed the presence of many proteins containing this PTS in both glyoxysomes and glycosomes. These results indicate that at least one of the signals, and therefore the mechanism, for protein translocation into peroxisomes, glyoxysomes, and glycosomes has been conserved, lending support to a common evolutionary origin for these microbodies. Hydrogenosomes, the fourth type of microbody, did not contain proteins that cross-reacted with the anti-PTS antibody, suggesting that this organelle is unrelated to microbodies.
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Arcas, Aida, David G. Wilkinson, and M. Ángela Nieto. "The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms." Molecular Biology and Evolution 37, no. 2 (October 7, 2019): 379–94. http://dx.doi.org/10.1093/molbev/msz222.
Повний текст джерелаАнотація:
Abstract Eph receptor (Eph) and ephrin signaling regulate fundamental developmental processes through both forward and reverse signaling triggered upon cell–cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that 1) premetazoan choanoflagellates may already have rudimental Eph/ephrin signaling as they have an Eph-/ephrin-like pair and homologs of downstream-signaling genes; 2) both forward- and reverse-downstream signaling might already occur in Porifera since sponges have most genes involved in these types of signaling; 3) the nonvertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane-anchoring structure, glycosylphosphatidylinositol, or transmembrane; 4) Eph/ephrin cross-class binding is specific to Gnathostomata; and 5) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signaling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream-signaling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell–cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.
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Hyma, Katie E., David W. Lacher, Adam M. Nelson, Alyssa C. Bumbaugh, J. Michael Janda, Nancy A. Strockbine, Vincent B. Young, and Thomas S. Whittam. "Evolutionary Genetics of a New Pathogenic Escherichia Species: Escherichiaalbertii and Related Shigellaboydii Strains." Journal of Bacteriology 187, no. 2 (January 15, 2005): 619–28. http://dx.doi.org/10.1128/jb.187.2.619-628.2005.
Повний текст джерелаАнотація:
ABSTRACT A bacterium originally described as Hafnia alvei induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic Escherichia coli. Subsequent studies identified similar H. alvei-like strains that are positive for an intimin gene (eae) probe and, based on DNA relatedness, are classified as a distinct Escherichia species, Escherichia albertii. We determined sequences for multiple housekeeping genes in five E. albertii strains and compared these sequences to those of strains representing the major groups of pathogenic E. coli and Shigella. A comparison of 2,484 codon positions in 14 genes revealed that E. albertii strains differ, on average, at ∼7.4% of the nucleotide sites from pathogenic E. coli strains and at 15.7% from Salmonella enterica serotype Typhimurium. Interestingly, E. albertii strains were found to be closely related to strains of Shigella boydii serotype 13 (Shigella B13), a distant relative of E. coli representing a divergent lineage in the genus Escherichia. Analysis of homologues of intimin (eae) revealed that the central conserved domains are similar in E. albertii and Shigella B13 and distinct from those of eae variants found in pathogenic E. coli. Sequence analysis of the cytolethal distending toxin gene cluster (cdt) also disclosed three allelic groups corresponding to E. albertii, Shigella B13, and a nontypeable isolate serologically related to S. boydii serotype 7. Based on the synonymous substitution rate, the E. albertii-Shigella B13 lineage is estimated to have split from an E. coli-like ancestor ∼28 million years ago and formed a distinct evolutionary branch of enteric pathogens that has radiated into groups with distinct virulence properties.
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Bae, Soyeon, Vladimir Li, Juyong Hong, Jin Nam Kim, and Heebal Kim. "Phylogenetic and evolutionary analysis of foot-and-mouth disease virus A/ASIA/Sea-97 lineage." Virus Genes 57, no. 5 (July 14, 2021): 443–47. http://dx.doi.org/10.1007/s11262-021-01848-7.
Повний текст джерелаАнотація:
AbstractFoot-and-mouth disease virus (FMDV) A/ASIA/Sea-97 is a predominant lineage in Southeast Asia and East Asia. However, Sea-97 lineage has not been well studied since its first outbreak in Thailand in 1997. Thus, we conducted phylogenetic and evolutionary analysis of Sea-97 using 224 VP1 sequences of FMDV A/ASIA during 1960 and 2018. Phylogenetic analysis revealed that Sea-97 lineage can be classified into five groups (G1–G5). After the emergence of G2 from G1, the genetic diversity of Sea-97 increased sharply, causing divergence into G3, G4 and G5. During this evolutionary process, Sea-97 lineage, which was initially found only in some countries in Southeast Asia, gradually spread to East Asia. The evolution rate of this lineage was estimated to be 1.2 × 10–2 substitutions/site/year and there were many differences in amino acid residues compared to vaccine strain. Substitutions at antigenically important sites may affect the efficacy of the vaccine, suggesting the need for appropriate vaccine strains. Our results could provide meaningful information to understand comprehensive characteristic of Sea-97 lineage.
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Zerbini, F. Murilo, and Elliot W. Kitajima. "From Contagium vivum fluidum to Riboviria: A Tobacco Mosaic Virus-Centric History of Virus Taxonomy." Biomolecules 12, no. 10 (September 24, 2022): 1363. http://dx.doi.org/10.3390/biom12101363.
Повний текст джерелаАнотація:
Viruses were discovered as agents of disease in the late 19th century, but it was not until the 1930s that the nature of these agents was elucidated. Nevertheless, as soon as viral diseases started to be recognized and cataloged, there were attempts to classify and name viruses. Although these early attempts failed to be adopted by the nascent virology community, they are evidence of the human compulsion to try to organize the natural world into well-defined categories. Different classification schemes were proposed during the 20th century, but again none were widely embraced by virologists. In 1966, with the creation of the International Committee on Nomenclature of Viruses (eventually renamed as the International Committee on Taxonomy of Viruses), a more organized effort led to an official taxonomy in which viruses were classified into families and genera. At present, a much better understanding of the evolutionary relationships among viruses has led to the establishment of a 15-rank taxonomy based primarily on these evolutionary relationships. This review of virus taxonomy will be centered on the tobacco mosaic virus (TMV), the agent of the disease studied by Dmitry Ivanovsky and the first virus to be recognized as such, which was often historically at the center of major advancements in virology during the 20th century.
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Bowen, Brian W., Zac H. Forsman, Jonathan L. Whitney, Anuschka Faucci, Mykle Hoban, Sean J. Canfield, Erika C. Johnston, et al. "Species Radiations in the Sea: What the Flock?" Journal of Heredity 111, no. 1 (January 2020): 70–83. http://dx.doi.org/10.1093/jhered/esz075.
Повний текст джерелаАнотація:
Abstract Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawaiʻi is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a “terrestrial” mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.
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Woods, Roseina, Ian Barnes, Selina Brace, and Samuel T. Turvey. "Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents." Molecular Biology and Evolution 38, no. 1 (October 9, 2020): 84–95. http://dx.doi.org/10.1093/molbev/msaa189.
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Abstract Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.
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Metrovic, Nevenka, Brankica Mravinac, Carlos Juan, Ðurdica Ugarkovic, and Miroslav Plohl. "Comparative study of satellite sequences and phylogeny of five species from the genus Palorus (Insecta, Coleoptera)." Genome 43, no. 5 (October 1, 2000): 776–85. http://dx.doi.org/10.1139/g00-035.
Повний текст джерелаАнотація:
Major satellite sequences are analysed in the three tenebrionid beetles Palorus cerylonoides, P. genalis, and P. ficicola, and compared with the ones from P. ratzeburgii and P. subdepressus reported elsewhere. All of them are A+T rich, pericentromerically located, and with lengths of about 150 bp, either in the form of monomers or formed by more complex repeating units. A preliminary phylogenetic analysis of Palorus species using the 3' end of the mitochondrial Cytochrome Oxidase I gene shows that the five Palorus species have been diverging for a considerable amount of evolutionary time, with the pair P. ratzeburgii and P. genalis being the most closely related. Only these two taxa showed some similarity between their respective high-copy-number satellite sequences, while other satellites are mutually unrelated and might have originated independently. However, all the satellites have in common tertiary structure induced by intrinsic DNA curvature, a characteristic which is conserved within the genus. Palorus major satellites were previously detected in the genomes of congeneric species as low-copy-number clusters (Metrovic et al., Mol. Biol. Evol. 15: 1062-1068. 1998). Given the divergences between the analysed species, the substitution rate deduced from high- and low-copy-number repeats is unexpectedly low. The presence of sequence-induced DNA curvature in all Palorus satellites and similar satellite DNAs in the species pair P. ratzeburgii and P. genalis suggest (i) that constraints are at the tertiary structure; and (ii) that the satellite DNA evolutionary turnover can be dependant on the history of the taxa under study, resulting in retention of similar satellites in related taxa.Key words: satellite DNA, evolution, mitochondrial cytochrome oxidase I, DNA curvature.
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Sudha, Govindarajan, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, and Arne Elofsson. "The evolutionary history of topological variations in the CPA/AT transporters." PLOS Computational Biology 17, no. 8 (August 17, 2021): e1009278. http://dx.doi.org/10.1371/journal.pcbi.1009278.
Повний текст джерелаАнотація:
CPA/AT transporters are made up of scaffold and a core domain. The core domain contains two non-canonical helices (broken or reentrant) that mediate the transport of ions, amino acids or other charged compounds. During evolution, these transporters have undergone substantial changes in structure, topology and function. To shed light on these structural transitions, we create models for all families using an integrated topology annotation method. We find that the CPA/AT transporters can be classified into four fold-types based on their structure; (1) the CPA-broken fold-type, (2) the CPA-reentrant fold-type, (3) the BART fold-type, and (4) a previously not described fold-type, the Reentrant-Helix-Reentrant fold-type. Several topological transitions are identified, including the transition between a broken and reentrant helix, one transition between a loop and a reentrant helix, complete changes of orientation, and changes in the number of scaffold helices. These transitions are mainly caused by gene duplication and shuffling events. Structural models, topology information and other details are presented in a searchable database, CPAfold (cpafold.bioinfo.se).
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Kwon, Annie, Steven Scott, Rahil Taujale, Wayland Yeung, Krys J. Kochut, Patrick A. Eyers, and Natarajan Kannan. "Tracing the origin and evolution of pseudokinases across the tree of life." Science Signaling 12, no. 578 (April 23, 2019): eaav3810. http://dx.doi.org/10.1126/scisignal.aav3810.
Повний текст джерелаАнотація:
Protein phosphorylation by eukaryotic protein kinases (ePKs) is a fundamental mechanism of cell signaling in all organisms. In model vertebrates, ~10% of ePKs are classified as pseudokinases, which have amino acid changes within the catalytic machinery of the kinase domain that distinguish them from their canonical kinase counterparts. However, pseudokinases still regulate various signaling pathways, usually doing so in the absence of their own catalytic output. To investigate the prevalence, evolutionary relationships, and biological diversity of these pseudoenzymes, we performed a comprehensive analysis of putative pseudokinase sequences in available eukaryotic, bacterial, and archaeal proteomes. We found that pseudokinases are present across all domains of life, and we classified nearly 30,000 eukaryotic, 1500 bacterial, and 20 archaeal pseudokinase sequences into 86 pseudokinase families, including ~30 families that were previously unknown. We uncovered a rich variety of pseudokinases with notable expansions not only in animals but also in plants, fungi, and bacteria, where pseudokinases have previously received cursory attention. These expansions are accompanied by domain shuffling, which suggests roles for pseudokinases in plant innate immunity, plant-fungal interactions, and bacterial signaling. Mechanistically, the ancestral kinase fold has diverged in many distinct ways through the enrichment of unique sequence motifs to generate new families of pseudokinases in which the kinase domain is repurposed for noncanonical nucleotide binding or to stabilize unique, inactive kinase conformations. We further provide a collection of annotated pseudokinase sequences in the Protein Kinase Ontology (ProKinO) as a new mineable resource for the signaling community.
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Smail, Harem othman. "Evolution of human diseases." International Journal of Applied Biology 4, no. 1 (June 29, 2020): 52–67. http://dx.doi.org/10.20956/ijab.v4i1.9914.
Повний текст джерелаАнотація:
The main aims of this review were to understand the roles of evolutionary process in human disease. The suffering of human from disease may be millions years ago and until now are continuing and the human disease can be classified into many types based on their sources such as bacterial, Genetics and viral. For the past sixty years the scientist carried out high number of experiment to understand and the decision of the evolutionary process impact of the human disease. the main example of effect of evolution on the human health are using overuse of antibiotics against bacterial infection and the results to the speedy evolution of bacteria that are resistant to multiple antibiotics such that even vancomycin. The process of natural selection which is proposed by Charles Darwin play vital roles in Biological and medical process and also helps to predict and find the relationship between natural selection process of evolution and phenotypical traits. Understanding the developmental and genetic underpinnings of unique evolutionary changes have been hindered by way of insufficient databases of evolutionary anatomy and through the lack of a computational method to become aware of underlying candidate genes and regulators to the developing o the process of the evolution with helps of other branches of modern sciences such as genetics, Bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry.
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Chen, Shi-Yi, Cao Li, Xianbo Jia, and Song-Jia Lai. "Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes." International Journal of Molecular Sciences 20, no. 15 (August 6, 2019): 3834. http://dx.doi.org/10.3390/ijms20153834.
Повний текст джерелаАнотація:
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
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Gregory, Richard L. "The Medawar Lecture 2001 Knowledge for vision: vision for knowledge." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1458 (June 29, 2005): 1231–51. http://dx.doi.org/10.1098/rstb.2005.1662.
Повний текст джерелаАнотація:
An evolutionary development of perception is suggested—from passive reception to active perception to explicit conception —earlier stages being largely retained and incorporated in later species. A key is innate and then individually learned knowledge, giving meaning to sensory signals. Inappropriate or misapplied knowledge produces rich cognitive phenomena of illusions, revealing normally hidden processes of vision, tentatively classified here in a ‘peeriodic table’. Phenomena of physiology are distinguished from phenomena of general rules and specific object knowledge. It is concluded that vision uses implicit knowledge, and provides knowledge for intelligent behaviour and for explicit conceptual understanding including science.
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Moosavian, Naser, and Barbara Lence. "Testing evolutionary algorithms for optimization of water distribution networks." Canadian Journal of Civil Engineering 46, no. 5 (May 2019): 391–402. http://dx.doi.org/10.1139/cjce-2018-0137.
Повний текст джерелаАнотація:
Water distribution networks (WDNs) are one of the most important elements of urban infrastructure and require large investment for construction. Design of WDNs is classified as a large combinatorial discrete nonlinear optimization problem. The main concerns associated with the optimization of such networks are the nonlinearity of the discharge-head loss relationships for pipes and the discrete nature of pipe sizes. Due to these issues, this problem is widely considered to be a benchmark problem for testing and evaluating the performance of nonlinear and heuristic optimization algorithms. This paper compares different techniques, all based on evolutionary algorithms (EAs), which yield optimal solutions for least-cost design of WDNs. All of these algorithms search for the global optimum starting from populations of solutions, rather than from a single solution, as in Newton-based search methods. They use different operators to improve the performance of many solutions over repeated iterations. Ten EAs, four of them for the first time, are applied to the design of three networks and their performance in terms of the least cost, under different stopping criteria, are evaluated. Statistical information for 20 executions of the ten algorithms is summarized, and Friedman tests are conducted. Results show that, for the two-loop benchmark network, the particle swarm optimization gravitational search and biology and bioinformatics global optimization algorithms efficiently converge to the global optimum, but perform poorly for large networks. In contrast, given a sufficient number of function evaluations, the covariance matrix adaptation evolution strategy and soccer league competition algorithm consistently converge to the global optimum, for large networks.
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Vosberg, Sebastian, Luise Hartmann, Klaus H. Metzeler, Daniela Schumacher, Friederike Pastore, Kathrin Bräundl, Evelyn Zellmeier, et al. "Evolutionary Patterns of Cytogenetically Normal Acute Myeloid Leukemia Correlate with Time to Relapse." Blood 128, no. 22 (December 2, 2016): 288. http://dx.doi.org/10.1182/blood.v128.22.288.288.
Повний текст джерелаАнотація:
Abstract Even though two-thirds of acute myeloid leukemia (AML) patients respond to induction chemotherapy and achieve complete remission (CR), the majority of these patients will eventually relapse. The time from CR to relapse is an important clinical indicator of disease aggressiveness, as patients relapsing within the first 6 months after initial diagnosis have a poorer prognosis in terms of response to salvage therapy and overall survival compared to patients with a later relapse. To learn about the evolution during the course of disease, we analyzed the somatic mutation patterns from initial diagnosis to relapse in 50 cytogenetically normal (CN) AML patients. Based on the ELN classification, 38% of the patients (n=19) were assigned as "favorable" at diagnosis, all other patients were classified as "intermediate-I". ELN classification was associated with time to relapse as "intermediate-I" patients relapsed earlier than "favorable" patients (median 9.3 months vs. 16.1 months, p=0.008, log-rank test). Somatic alterations were detected by exome sequencing and confirmed by targeted amplicon sequencing of matched diagnostic, remission and relapse samples. FLT3-ITD and NPM1 mutation status were obtained from routine diagnostic tests as the reliable detection of these markers by NGS remains challenging. The vast majority of somatic alterations were present both at diagnosis and at relapse, hereafter referred to as stable mutations (70%, Fig. 1A). All patients in our cohort had ≥1 stable mutation with DNMT3A being the most stably altered gene. In 47 out of 50 patients (94%), we observed mutations that were only found at diagnosis or only at relapse. Based on the mutation patterns, four distinct 'evolutionary' subgroups of patients were defined (Fig. 1B): (I) patients with an identical mutation profile at diagnosis and at relapse ("stable", n=3, 6%), (II) patients who gained mutations at relapse ("stable + gain", n=24, 48%), (III) patients that lost mutations at relapse ("stable + loss", n=8, 16%), and (IV) patients with both loss and gain of mutations at relapse ("mixed", n=15, 30%). Mutations that were lost during the course of the disease were detected in e.g. PTPN11 or NRAS. Relapse-specific mutations were identified in e.g. IDH1/2, WT1, KPNB1 or KDM6A. Evolutionary subgroups showed differences in time to relapse (Fig. 1C). Patients with "stable + loss" relapsed earlier (median 4.1 months) than patients with gain of mutation at relapse (groups "stable + gain" and "mixed", median 12.2 months). All patients in the category "stable + loss" developed relapse within the first year after complete remission. The "stable" group of 3 patients showed an intermediate time to relapse (median 9.6 months), but was too small for a statistically valid comparison. Ultimately, the genetic evolution of CN-AML patients without gain of new mutations at relapse (categories "stable" and "stable + loss") was associated with significantly earlier relapse compared to patients that gained mutations at relapse (categories "stable + gain" and "mixed", Fig. 1D, p=0.001, log-rank test). Distinct predominant patterns of clonal evolution were observed in the ELN genetic groups, as only one patient of the "stable + loss" group was initially classified as "favorable". Interestingly, applying the ELN classification on relapse samples revealed a switch from "favorable" to "intermediate-I" in six patients, all with gain of mutations at relapse. This points towards more aggressive genetic profiles at relapse in these patients. The acquisition of mutations and/or the outgrowth of a resistant clone during/after chemotherapy might require a longer time or is per se associated with a longer time to relapse and a more favorable prognosis. Loss of mutations at relapse suggest the presence of two clones at diagnosis, with a chemotherapy resistant clone expanding after the eradication of a chemotherapy sensitive clone. As both clones share mutations and only the sensitive clone contains specific alterations, the resistant clone might be an ancestor of the sensitive clone. Taken together, in some patients the AML cells may require additional genetic alterations to become chemotherapy resistant, whereas in other patients the selective eradication of a sensitive clone is a potential mechanism underlying disease progression. Understanding the evolution of AML under selective pressure of chemotherapy is essential to cure or prevent AML relapse. Disclosures Hiddemann: Roche: Other: Grants; Genentech: Other: Grants; Roche: Membership on an entity's Board of Directors or advisory committees.
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Ma, Baiquan, Yangyang Yuan, Meng Gao, Tonghui Qi, Mingjun Li, and Fengwang Ma. "Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples." International Journal of Molecular Sciences 19, no. 9 (September 18, 2018): 2807. http://dx.doi.org/10.3390/ijms19092807.
Повний текст джерелаАнотація:
Aluminum-activated malate transporters (ALMTs) play an important role in aluminum tolerance, stomatal opening, and fruit acidity in plants. However, the evolutionary pattern of the ALMT gene family in apples remains relatively unknown. In this study, a total of 25 MdALMT genes were identified from the apple reference genome of the “Golden Delicious” doubled-haploid tree (GDDH13). The physiological and biochemical properties, gene structure, and conserved motifs of MdALMT genes were examined. Chromosome location and gene-duplication analysis indicated that whole-genome duplication/segmental duplication played an important role in the expansion of the MdALMT gene family. The Ka/Ks ratio of duplicated MdALMT genes showed that members of this family have undergone strong purifying selection. Through exploration of the phylogenetic relationships, seven subgroups were classified, and higher old gene duplication frequency and significantly different evolutionary rates of the ALMT gene families were detected. In addition, the functional divergence of ALMT genes occurred during the evolutionary process of Rosaceae species. Furthermore, the functional divergence of MdALMT genes was confirmed by expression discrepancy and different subcellular localizations. This study provides the foundation to better understand the molecular evolution of MdALMT genes and further facilitate functional analysis to unravel their exact role in apples.
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Evseev, Peter, Anna Lukianova, Rashit Tarakanov, Anna Tokmakova, Mikhail Shneider, Alexander Ignatov, and Konstantin Miroshnikov. "Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny, Genomics-Based Taxonomy, Pathogenicity, and Diagnostics." Current Issues in Molecular Biology 44, no. 2 (February 11, 2022): 889–927. http://dx.doi.org/10.3390/cimb44020060.
Повний текст джерелаАнотація:
The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.
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Gómez-Márquez, Jaime. "What is life?" Molecular Biology Reports 48, no. 8 (July 27, 2021): 6223–30. http://dx.doi.org/10.1007/s11033-021-06594-5.
Повний текст джерелаАнотація:
Abstract Background Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings. Results and Conclusions Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.
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Nealson, Kenneth H., and Pamela G. Conrad. "Life: past, present and future." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1392 (December 29, 1999): 1923–39. http://dx.doi.org/10.1098/rstb.1999.0532.
Повний текст джерелаАнотація:
Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote–centric (five–kingdoms) view of the planet to one that is peculiarly prokarote–centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen–using, carbon–eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such ‘metabolic extremophily’ forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.
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Feng, Chen, Shuaiyu Zou, Puxin Gao, and Zupeng Wang. "In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit." PeerJ 9 (October 28, 2021): e12348. http://dx.doi.org/10.7717/peerj.12348.
Повний текст джерелаАнотація:
The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.
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Xie, Gary, Shannon L. Johnson, Karen W. Davenport, Mathumathi Rajavel, Torsten Waldminghaus, John C. Detter, Patrick S. Chain, and Shanmuga Sozhamannan. "Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome." International Journal of Genomics 2017 (2017): 1–14. http://dx.doi.org/10.1155/2017/8724304.
Повний текст джерелаАнотація:
The genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as are recA and mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.
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Adamowicz, Sarah J., Peter M. Hollingsworth, Sujeevan Ratnasingham, and Michelle van der Bank. "International Barcode of Life: Focus on big biodiversity in South Africa." Genome 60, no. 11 (November 2017): 875–79. http://dx.doi.org/10.1139/gen-2017-0210.
Повний текст джерелаАнотація:
Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20–24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale.
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Muthusamy, Muthusamy, Jin-A. Kim, and Soo-In Lee. "Phylogenomics-Based Reconstruction and Molecular Evolutionary Histories of Brassica Photoreceptor Gene Families." International Journal of Molecular Sciences 23, no. 15 (August 4, 2022): 8695. http://dx.doi.org/10.3390/ijms23158695.
Повний текст джерелаАнотація:
Photosensory proteins known as photoreceptors (PHRs) are crucial for delineating light environments in synchronization with other environmental cues and regulating their physiological variables in plants. However, this has not been well studied in the Brassica genus, which includes several important agricultural and horticultural crops. Herein, we identified five major PHR gene families—phytochrome (PHY), cryptochrome (CRY), phototropin (PHOT), F-box containing flavin binding proteins (ZTL/FKF1/LKP2), and UV RESISTANCE LOCUS 8 (UVR8)—genomic scales and classified them into subfamilies based on their phylogenetic clustering with Arabidopsis homologues. The molecular evolution characteristics of Brassica PHR members indicated indirect expansion and lost one to six gene copies at subfamily levels. The segmental duplication was possibly the driving force of the evolution and amplification of Brassica PHRs. Gene replication retention and gene loss events of CRY, PHY, and PHOT members found in diploid progenitors were highly conserved in their tetraploid hybrids. However, hybridization events were attributed to quantitative changes in UVR8 and ZTL/FKF1/LKP2 members. All PHR members underwent purifying selection. In addition, the transcript expression profiles of PHR genes in different tissue and in response to exogenous ABA, and abiotic stress conditions suggested their multiple biological significance. This study is helpful in understanding the molecular evolution characteristics of Brassica PHRs and lays the foundation for their functional characterization.
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Brendza, Robert P., Kathy B. Sheehan, F. R. Turner, and William M. Saxton. "Clonal Tests of Conventional Kinesin Function during Cell Proliferation and Differentiation." Molecular Biology of the Cell 11, no. 4 (April 2000): 1329–43. http://dx.doi.org/10.1091/mbc.11.4.1329.
Повний текст джерелаАнотація:
Null mutations in the Drosophila Kinesin heavy chain gene (Khc), which are lethal during the second larval instar, have shown that conventional kinesin is critical for fast axonal transport in neurons, but its functions elsewhere are uncertain. To test other tissues, single imaginal cells in young larvae were rendered null for Khc by mitotic recombination. Surprisingly, the null cells produced large clones of adult tissue. The rates of cell proliferation were not reduced, indicating that conventional kinesin is not essential for cell growth or division. This suggests that in undifferentiated cells vesicle transport from the Golgi to either the endoplasmic reticulum or the plasma membrane can proceed at normal rates without conventional kinesin. In adult eye clones produced by null founder cells, there were some defects in differentiation that caused mild ultrastructural changes, but they were not consistent with serious problems in the positioning or transport of endoplasmic reticulum, mitochondria, or vesicles. In contrast, defective cuticle deposition by highly elongated Khc null bristle shafts suggests that conventional kinesin is critical for proper secretory vesicle transport in some cell types, particularly ones that must build and maintain long cytoplasmic extensions. The ubiquity and evolutionary conservation of kinesin heavy chain argue for functions in all cells. We suggest interphase organelle movements away from the cell center are driven by multilayered transport mechanisms; that is, individual organelles can use kinesin-related proteins and myosins, as well as conventional kinesin, to move toward the cell periphery. In this case, other motors can compensate for the loss of conventional kinesin except in cells that have extremely long transport tracks.
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Fang, Z., C. Doig, D. T. Kenna, N. Smittipat, P. Palittapongarnpim, B. Watt, and K. J. Forbes. "IS6110-Mediated Deletions of Wild-Type Chromosomes of Mycobacterium tuberculosis." Journal of Bacteriology 181, no. 3 (February 1, 1999): 1014–20. http://dx.doi.org/10.1128/jb.181.3.1014-1020.1999.
Повний текст джерелаАнотація:
ABSTRACT The ipl locus is a site for the preferential insertion of IS6110 and has been identified as an insertion sequence, IS1547, in its own right. Various deletions around theipl locus of clinical isolates of Mycobacterium tuberculosis were identified, and these deletions ranged in length from several hundred base pairs up to several kilobase pairs. The most obvious feature shared by these deletions was the presence of an IS6110 copy at the deletion sites, which suggested two possible mechanisms for their occurrence, IS6110transposition and homologous recombination. To clarify the mechanism, an investigation was conducted; the results suggest that although deletion transpositionally mediated by IS6110 was a possibility, homologous recombination was a more likely one. The implications of such chromosomal rearrangements for the evolution ofM. tuberculosis, for IS6110-mediated mutagenesis, and for the development of genetic tools are discussed. The deletion of genomic DNA in isolates of M. tuberculosishas previously been noted at only a few sites. This study examined the deletional loss of genetic material at a new site and suggests that such losses may occur elsewhere too and may be more prevalent than was previously thought. Distinct from the study of laboratory-induced mutations, the detailed analysis of clinical isolates, in combination with knowledge of their evolutionary relationships to each other, gives us the opportunity to study mutational diversity in isolates that have survived in the human host and therefore offers a different perspective on the importance of particular genetic markers in pathogenesis.
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Lautenschlager, Stephan, Borja Figueirido, Daniel D. Cashmore, Eva-Maria Bendel, and Thomas L. Stubbs. "Morphological convergence obscures functional diversity in sabre-toothed carnivores." Proceedings of the Royal Society B: Biological Sciences 287, no. 1935 (September 30, 2020): 20201818. http://dx.doi.org/10.1098/rspb.2020.1818.
Повний текст джерелаАнотація:
The acquisition of elongated, sabre-like canines in multiple vertebrate clades during the last 265 Myr represents a remarkable example for convergent evolution. Due to striking superficial similarities in the cranial skeleton, the same or similar skull and jaw functions have been inferred for sabre-toothed species and interpreted as an adaptation to subdue large-bodied prey. However, although some sabre-tooth lineages have been classified into different ecomorphs (dirk-tooths and scimitar-tooths) the functional diversity within and between groups and the evolutionary paths leading to these specializations are unknown. Here, we use a suite of biomechanical simulations to analyse key functional parameters (mandibular gape angle, bending strength, bite force) to compare the functional performance of different groups and to quantify evolutionary rates across sabre-tooth vertebrates. Our results demonstrate a remarkably high functional diversity between sabre-tooth lineages and that different cranial function and prey killing strategies evolved within clades. Moreover, different biomechanical adaptations in coexisting sabre-tooth species further suggest that this functional diversity was at least partially driven by niche partitioning.
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Prabhakar, Sunil Kumar, Semin Ryu, In cheol Jeong, and Dong-Ok Won. "A Dual Level Analysis with Evolutionary Computing and Swarm Models for Classification of Leukemia." BioMed Research International 2022 (May 26, 2022): 1–16. http://dx.doi.org/10.1155/2022/2052061.
Повний текст джерелаАнотація:
One of the major reasons of mortality in human beings is cancer, and there is an absolute necessity for doctors to identify and treat a person suffering from it. Leukemia is a group of blood cancers that usually originates in the bone marrow and results in very high number of abnormal cells. For the diagnosis of cancer, microarray data serves as an important clinical application and serves as a great aid to the entire medical community. The dimensionality of the microarray data is too high, and so selection of suitable genes is quite an important step for the improvement of data classification. Therefore, for the prediction and diagnosis of cancer, there is an utmost necessity to select the most informative genes. In this work, Minimum Redundancy Maximum Relevance (MRMR), Signal to Noise Ratio (SNR), Multivariate Error Weight Uncorrelated Shrunken Centroid (EWUSC), and multivariate correlation-based feature selection (CFS) are chosen as initial feature selection techniques. Then, to select the most informative genes, five different kinds of evolutionary optimization techniques too are incorporated here such as African Buffalo Optimization (ABO), Artificial Bee Colony Optimization (ABCO), Cockroach Swarm Optimization (CSO), Imperialist Competitive Optimization (ICO), and Social Spider Optimization (SSO). Finally, the optimized values are fed through classification process and the best results are obtained when multivariate CFS with SSO is utilized and classified with Probabilistic Neural Network (PNN), and a high classification accuracy of 95.70% is obtained.