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https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#1
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820456/deciphering-single-nucleotide-polymorphisms-and-evolutionary-trends-in-isolates-of-the-cydia-pomonella-granulovirus
#2
Jörg T Wennmann, Pit Radtke, Karolin E Eberle, Gianpiero Gueli Alletti, Johannes A Jehle
Six complete genome sequences of Cydia pomonella granulovirus (CpGV) isolates from Mexico (CpGV-M and CpGV-M1), England (CpGV-E2), Iran (CpGV-I07 and CpGV-I12), and Canada (CpGV-S) were aligned and analyzed for genetic diversity and evolutionary processes. The selected CpGV isolates represented recently identified phylogenetic lineages of CpGV, namely, the genome groups A to E. The genomes ranged from 120,816 bp to 124,269 bp. Several common differences between CpGV-M, -E2, -I07, -I12 and -S to CpGV-M1, the first sequenced and published CpGV isolate, were highlighted...
August 18, 2017: Viruses
https://www.readbyqxmd.com/read/28820334/evolutionary-analysis-of-a-novel-zinc-ribbon-in-the-n-terminal-region-of-threonine-synthase
#3
Gurmeet Kaur, Srikrishna Subramanian
Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28820115/six-key-traits-of-fungi-their-evolutionary-origins-and-genetic-bases
#4
László G Nagy, Renáta Tóth, Enikő Kiss, Jason Slot, Attila Gácser, Gábor M Kovács
The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28819981/highly-efficient-guiding-of-motile-microtubules-on-non-topographical-motor-patterns
#5
Cordula Reuther, Matthäus Mittasch, Sundar Naganathan, Stephan Grill, Stefan Diez
Molecular motors, highly-efficient biological nano-machines, hold the potential to be employed for a wide range of nanotechnological applications. Towards this end, kinesin, dynein or myosin motor proteins are commonly surface-immobilized within engineered environments in order to transport cargo attached to cytoskeletal filaments. Being able to flexibly control the direction of filament motion - in particular on planar, non-topographical surfaces - has, however, remained challenging. Here, we demonstrate the applicability of a UV-laser-based ablation technique to programmably generate highly-localized patterns of functional kinesin-1 motors with different shapes and sizes on PLL-g-PEG-coated polystyrene surfaces...
August 18, 2017: Nano Letters
https://www.readbyqxmd.com/read/28819830/identification-and-characterization-of-tyrosine-kinases-in-anole-lizard-indicate-the-conserved-tyrosine-kinase-repertoire-in-vertebrates
#6
Ake Liu, Funan He, Xun Gu
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified...
August 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28819749/time-dependent-asymmetric-linear-parsimonious-ancestral-state-reconstruction
#7
Gilles Didier
The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter...
August 17, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28819320/genome-wide-identification-and-expression-analysis-of-e2-ubiquitin-conjugating-enzymes-in-tomato
#8
Bhaskar Sharma, Tarun Kumar Bhatt
The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819154/rpos-independent-evolution-reveals-the-importance-of-attenuated-camp-crp-regulation-in-high-hydrostatic-pressure-resistance-acquisition-in-e-coli
#9
Elisa Gayán, Alexander Cambré, Chris W Michiels, Abram Aertsen
High hydrostatic pressure (HHP) processing is an attractive non-thermal alternative to food pasteurization. Nevertheless, the large inter- and intra-species variations in HHP resistance among foodborne pathogens and the ease by which they can acquire extreme resistance are an issue of increasing concern. Since RpoS activity has been considered as a central determinant in the HHP resistance of E. coli and its pathovars, this study probed for the potential of an E. coli MG1655 ΔrpoS mutant to acquire HHP resistance by directed evolution...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818949/in-situ-architecture-function-and-evolution-of-a-contractile-injection-system
#10
Désirée Böck, João M Medeiros, Han-Fei Tsao, Thomas Penz, Gregor L Weiss, Karin Aistleitner, Matthias Horn, Martin Pilhofer
Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by intracellular localization and attachment to the cytoplasmic membrane. Here we used cryo-focused ion beam milling, electron cryotomography, and functional assays to study a T6SS in Amoebophilus asiaticus The in situ architecture revealed three modules, including a contractile sheath-tube, a baseplate, and an anchor...
August 18, 2017: Science
https://www.readbyqxmd.com/read/28818669/notch-and-fgf-signaling-during-electrosensory-versus-mechanosensory-lateral-line-organ-development-in-a-non-teleost-ray-finned-fish
#11
Melinda S Modrell, Olivia R A Tidswell, Clare V H Baker
The lateral line system is a useful model for studying the embryonic and evolutionary diversification of different organs and cell types. In jawed vertebrates, this ancestrally comprises lines of mechanosensory neuromasts over the head and trunk, flanked on the head by fields of electrosensory ampullary organs, all innervated by lateral line neurons in cranial lateral line ganglia. Both types of sense organs, and their afferent neurons, develop from cranial lateral line placodes. Current research primarily focuses on the posterior lateral line primordium in zebrafish, which migrates as a cell collective along the trunk; epithelial rosettes form in the trailing zone and are deposited as a line of neuromasts, within which hair cells and supporting cells differentiate...
August 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28818621/codon-usage-bias-in-the-n-gene-of-rabies-virus
#12
Wanting He, Hongyu Zhang, Yuchen Zhang, Ruyi Wang, Sijia Lu, Yanjie Ji, Chang Liu, Pengkun Yuan, Shuo Su
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure...
August 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28818616/molecular-insights-of-two-stat1-variants-from-rock-bream-oplegnathus-fasciatus-and-their-transcriptional-regulation-in-response-to-pathogenic-stress-interleukin-10-and-tissue-injury
#13
S D N K Bathige, Navaneethaiyer Umasuthan, G I Godahewa, William Shanthakumar Thulasitha, J D H E Jayasinghe, Qiang Wan, Jehee Lee
Signal transducers and activators of transcription 1 (STAT1) is critically involved in mediating cytokine-driven signaling, and triggers the transcription of target genes to activate cellular functions. Although the structural and functional aspects of STAT members have been well described in mammals, only limited information is available for the STAT genes in teleost fishes. In the present study, two variants of STAT1 genes (RbSTAT1 and RbSTAT1L) were identified from rock bream and characterized at the cDNA and genomic sequence levels...
August 14, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28818614/the-transcription-of-atypical-protein-kinase-c-in-hemocytes-of-the-giant-freshwater-prawn-macrobrachium-rosenbergii-during-the-molt-stage-and-injection-of-pathogen-associated-compounds
#14
Yi-Chun Yeh, Chin-Chyuan Chang, Pai-Po Lee, Winton Cheng
Protein kinase C (PKC), which is involved in cell signaling pathways, comprises a family of serine/threonine kinases ubiquitously present in animals and its members are grouped on the basis of structural and activation characteristics into novel, classical, and atypical PKC forms. In this study, an atypical PKC of Macrobrachium rosenbergii, designated MraPKC, was successfully cloned, and its protein comprised structural domains similar to those of atypical PKC homologues, including the Phox and Bem1 (PB1) domain, a zinc finger phorbol-ester/DAG-type signature, protein kinase signatures, and a cAMP-dependent, cGMP-dependent, and PKC (AGC) kinase C-terminal domain...
August 14, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28818345/mobile-group-ii-introns-as-ancestral-eukaryotic-elements
#15
REVIEW
Olga Novikova, Marlene Belfort
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes...
August 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28818331/molecular-epidemiology-of-epizootic-haematopoietic-necrosis-virus-ehnv
#16
Paul M Hick, Kuttichantran Subramaniam, Patrick M Thompson, Thomas B Waltzek, Joy A Becker, Richard J Whittington
Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3...
August 14, 2017: Virology
https://www.readbyqxmd.com/read/28817588/phylogeography-of-the-reticulated-python-malayopython-reticulatus-ssp-conservation-implications-for-the-worlds-most-traded-snake-species
#17
Gillian Murray-Dickson, Muhammad Ghazali, Rob Ogden, Rafe Brown, Mark Auliya
As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas...
2017: PloS One
https://www.readbyqxmd.com/read/28817247/assessing-predictions-of-fitness-effects-of-missense-mutations-in-sumo-conjugating-enzyme-ube2i
#18
Jing Zhang, Lisa N Kinch, Qian Cong, Jochen Weile, Song Sun, Atina G Cote, Frederick P Roth, Nick V Grishin
The exponential growth of genomic variants uncovered by next-generation sequencing necessitates efficient and accurate computational analyses to predict their functional effects. A number of computational methods have been developed for the task, but few unbiased comparisons of their performance are available. To fill the gap, The Critical Assessment of Genome Interpretation (CAGI) comprehensively assesses phenotypic predictions on newly collected experimental datasets. Here, we present the results of the SUMO conjugase challenge where participants were predicting functional effects of missense mutations in human SUMO-conjugating enzyme UBE2I...
September 2017: Human Mutation
https://www.readbyqxmd.com/read/28816684/a-multiobjective-evolutionary-algorithm-based-on-structural-and-attribute-similarities-for-community-detection-in-attributed-networks
#19
Zhangtao Li, Jing Liu, Kai Wu
Most of the existing community detection algorithms are based on vertex connectivity. While in many real networks, each vertex usually has one or more attributes describing its properties which are often homogeneous in a cluster. Such networks can be modeled as attributed graphs, whose attributes sometimes are equally important to topological structure in graph clustering. One important challenge is to detect communities considering both topological structure and vertex properties simultaneously. To this propose, a multiobjective evolutionary algorithm based on structural and attribute similarities (MOEA-SA) is first proposed to solve the attributed graph clustering problems in this paper...
August 16, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28815929/aggregation-of-population-based-genetic-variation-over-protein-domain-homologues-and-its-potential-use-in-genetic-diagnostics
#20
Laurens Wiel, Hanka Venselaar, Joris A Veltman, Gerrit Vriend, Christian Gilissen
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population-based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease-causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 "meta-domains"...
August 16, 2017: Human Mutation
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