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Evolutionary Bioinformatics Online

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https://read.qxmd.com/read/30733626/modelling-animal-interactive-rhythms-in-communication
#1
Andrea Ravignani, Koen de Reus
Time is one crucial dimension conveying information in animal communication. Evolution has shaped animals' nervous systems to produce signals with temporal properties fitting their socio-ecological niches. Many quantitative models of mechanisms underlying rhythmic behaviour exist, spanning insects, crustaceans, birds, amphibians, and mammals. However, these computational and mathematical models are often presented in isolation. Here, we provide an overview of the main mathematical models employed in the study of animal rhythmic communication among conspecifics...
2019: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30733625/salibase-a-database-of-simulated-protein-alignments
#2
REVIEW
Muhammad Tariq Pervez, Hayat Ali Shah, Masroor Ellahi Babar, Nasir Naveed, Muhammad Shoaib
Simulated alignments are alternatives to manually constructed multiple sequence alignments for evaluating performance of multiple sequence alignment tools. The importance of simulated sequences is recognized because their true evolutionary history is known, which is very helpful for reconstructing accurate phylogenetic trees and alignments. However, generating simulated alignments require expertise to use bioinformatics tools and consume several hours for reconstructing even a few hundreds of simulated sequences...
2019: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30718942/exploring-the-structure-of-haplotype-blocks-and-genetic-diversity-in-chinese-indigenous-pig-populations-for-conservation-purpose
#3
Qing-Bo Zhao, Hao Sun, Zhe Zhang, Zhong Xu, Babatunde Shittu Olasege, Pei-Pei Ma, Xiang-Zhe Zhang, Qi-Shan Wang, Yu-Chun Pan
Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data...
2019: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30692845/feature-learning-of-virus-genome-evolution-with-the-nucleotide-skip-gram-neural-network
#4
Hyunjin Shim
Recent studies reveal that even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce multiple time-point whole-genome data, which enable potential interactions between these alleles to be investigated empirically. To investigate these interactions, we represent alleles as distributed vectors that encode for relationships with other alleles in the course of evolution and apply artificial neural networks to time-sampled whole-genome datasets for feature learning...
2019: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30626996/nommpred-prediction-of-mitochondrial-and-mitochondrion-related-organelle-proteins-of-nonmodel-organisms
#5
Keitaro Kume, Toshiyuki Amagasa, Tetsuo Hashimoto, Hiroyuki Kitagawa
To estimate the functions of mitochondria of diverse eukaryotic nonmodel organisms in which the mitochondrial proteomes are not available, it is necessary to predict the protein sequence features of the mitochondrial proteins computationally. Various prediction methods that are trained using the proteins of model organisms belonging particularly to animals, plants, and fungi exist. However, such methods may not be suitable for predicting the proteins derived from nonmodel organisms because the sequence features of the mitochondrial proteins of diversified nonmodel organisms can differ from those of model organisms that are present only in restricted parts of the tree of eukaryotes...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30559593/putative-interaction-proteins-of-the-ubiquitin-ligase-hrd1-in-magnaporthe-oryzae
#6
Haolang Jiang, Lianyu Lin, Wei Tang, Xuehang Chen, Qiaojia Zheng, Jun Huang, Tao Yang, Li Su, Yanhan Dong, Baohua Wang, Zonghua Wang
The endoplasmic reticulum (ER) is the entry portal of the conventional secretory pathway where the newly synthesized polypeptides fold, modify, and assemble. The ER responses to the unfolded proteins in its lumen (ER stress) by triggering intracellular signal transduction pathways include the ER-associated degradation (ERAD) pathway and the unfolded protein response (UPR) pathway. In yeast and mammals, the ubiquitin ligase Hrd1 is indispensable for the ERAD pathway, and also Hrd1-mediated ERAD pathway plays a crucial role in maintaining homeostasis and metabolism of human beings...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30546255/why-we-do-not-evolve-software-analysis-of-evolutionary-algorithms
#7
Roman V Yampolskiy
In this article, we review the state-of-the-art results in evolutionary computation and observe that we do not evolve nontrivial software from scratch and with no human intervention. A number of possible explanations are considered, but we conclude that computational complexity of the problem prevents it from being solved as currently attempted. A detailed analysis of necessary and available computational resources is provided to support our findings.
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30546254/prediction-of-horizontally-and-widely-transferred-genes-in-prokaryotes
#8
Yoji Nakamura
Horizontal gene transfer (HGT) is the process whereby an organism acquires exogenous genes (horizontally transferred genes or HT genes) that are not inherited from the parent, but are derived from another organism. In prokaryotes, HGT has been considered as one of the important driving forces of evolution. Previously, genome-wide analyses have been conducted for estimating the proportion of HT genes in prokaryotic genomes, but the number of species examined at the time was limited, and gene annotation was relatively poor...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30364489/how-to-reveal-magnitude-of-gene-signals-hierarchical-hypergeometric-complementary-cumulative-distribution-function
#9
Bongsong Kim
This article introduces a new method for genome-wide association study (GWAS), hierarchical hypergeometric complementary cumulative distribution function (HH-CCDF). Existing GWAS methods, e.g. the linear model and hierarchical association coefficient algorithm , calculate the association between a marker variable and a phenotypic variable. The ideal GWAS practice is to calculate the association between a marker variable and a gene-signal variable. If the gene-signal variable and phenotypic variable are imperfectly proportional, the existing methods do not properly reveal the magnitude of the association between the gene-signal variable and marker variable...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30364468/rooting-phylogenies-and-the-tree-of-life-while-minimizing-ad-hoc-and-auxiliary-assumptions
#10
REVIEW
Gustavo Caetano-Anollés, Arshan Nasir, Kyung Mo Kim, Derek Caetano-Anollés
Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30245567/s-plot2-rapid-visual-and-statistical-analysis-of-genomic-sequences
#11
Laurynas Kalesinskas, Evan Cudone, Yuriy Fofanov, Catherine Putonti
With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30210232/systematic-identification-and-classification-of-%C3%AE-lactamases-based-on-sequence-similarity-criteria-%C3%AE-lactamase-annotation
#12
Melise Chaves Silveira, Rangeline Azevedo da Silva, Fábio Faria da Mota, Marcos Catanho, Rodrigo Jardim, Ana Carolina R Guimarães, Antonio B de Miranda
β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are widespread among prokaryotic genera. However, current β-lactamase classification schemes do not represent their present diversity. Here, we propose a workflow to identify and classify β-lactamases. Initially, a set of curated sequences was used as a model for the construction of profiles Hidden Markov Models (HMM), specific for each β-lactamase class. An extensive, nonredundant set of β-lactamase sequences was constructed from 7 different resistance proteins databases to test the methodology...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30116102/a-novel-approach-for-identifying-relevant-genes-for-breast-cancer-survivability-on-specific-therapies
#13
REVIEW
Ashraf Abou Tabl, Abedalrhman Alkhateeb, Huy Quang Pham, Luis Rueda, Waguih ElMaraghy, Alioune Ngom
Analyzing the genetic activity of breast cancer survival for a specific type of therapy provides a better understanding of the body response to the treatment and helps select the best course of action and while leading to the design of drugs based on gene activity. In this work, we use supervised and nonsupervised machine learning methods to deal with a multiclass classification problem in which we label the samples based on the combination of the 5-year survivability and treatment; we focus on hormone therapy, radiotherapy, and surgery...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30083050/transcriptome-analysis-and-microsatellite-markers-development-of-a-traditional-chinese-medicinal-herb-halenia-elliptica-d-don-gentianaceae
#14
Mingliu Yang, Nanyu Han, Heng Li, Lihua Meng
Halenia elliptica is a popular Chinese medicinal herb that is used to treat jaundice disease and virus hepatitis, and its wild populations have been reduced significantly due to overharvesting recently. However, effective conservation could not be implemented because of the lack of genomic information and genetic markers. In this study, a de novo transcriptome of H elliptica was sequenced using the NGS Illumina, and 132 695 unigenes with the length >200 bp (base pairs) were obtained. Among them, a total of 32 109 unigenes were scanned to develop simple sequence repeats (SSRs)...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30083049/comparative-genome-analysis-of-2-mycobacterium-tuberculosis-strains-from-pakistan-insights-globally-into-drug-resistance-virulence-and-niche-adaptation
#15
Asma Muhammad Yar, Ghanva Zaman, Annam Hussain, Yan Changhui, Azhar Rasul, Abrar Hussain, Zhu Bo, Habib Bokhari, Muhammad Ibrahim
Multidrug-resistant Mycobacterium tuberculosis is a global threat particularly in developing countries like Pakistan. In this study, we identified 2 M tuberculosis strains, mnpk and swlpk, by 16S RNA genes, sequenced their draft genome, and compared the 2 genomes with reference strain H37Rv and gene expression analysis of selected virulent genes. Phylogenetic analysis of M tuberculosis strains, mnpk and swlpk, using 16S RNA genes revealed that the strains are closely related with reference strain H37Rv. The draft genome sequence of mnpk and swlpk contains 4305 and 4295 protein-coding genes, respectively, having 99...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30046236/-bhlh13-regulates-jasmonate-mediated-defense-responses-and-growth
#16
Huang Huang, Hua Gao, Bei Liu, Meng Fan, Jiaojiao Wang, Cuili Wang, Haixia Tian, Lanxiang Wang, Chengyuan Xie, Dewei Wu, Liangyu Liu, Jianbin Yan, Tiancong Qi, Susheng Song
Jasmonates (JAs) regulate plant growth and defense responses. On perception of bioactive JAs, the JA receptor CORONATINE INSENSITIVE1 (COI1) recruits JA ZIM-domain (JAZ) proteins for degradation, and JAZ-targeted transcription factors are released to regulate JA responses. The subgroup IIId bHLH transcriptional factors, including bHLH17, bHLH13, bHLH3, and bHLH14, interact with JAZs and repress JA responses. In this study, we show that IIId bHLH factors form dimers via the C-terminus in yeast. N-terminus of bHLH13 is essential for its transcriptional repression function...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30038485/distinguishing-species-using-gc-contents-in-mixed-dna-or-rna-sequences
#17
REVIEW
Kamran Karimi, Daniel M Wuitchik, Matthew J Oldach, Peter D Vize
With the advent of whole transcriptome and genome analysis methods, classifying samples containing multiple origins has become a significant task. Nucleotide sequences can be allocated to a genome or transcriptome by aligning sequences to multiple target sequence sets, but this approach requires extensive computational resources and also depends on target sequence sets lacking contaminants, which is often not the case. Here, we demonstrate that raw sequences can be rapidly sorted into groups, in practice corresponding to genera, by exploiting differences in nucleotide GC content...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30038484/lateral-gene-transfer-between-protozoa-related-giant-viruses-of-family-mimiviridae-and-chlamydiae
#18
Takanori Watanabe, Sumire Yamazaki, Chinatsu Maita, Mizue Matushita, Junji Matsuo, Torahiko Okubo, Hiroyuki Yamaguchi
Obligate intracellular chlamydiae diverged into pathogenic and environmental chlamydiae 0.7-1.4 billion years ago. While pathogenic chlamydiae have adapted to a wide range of vertebrates, environmental chlamydiae inhabit unicellular amoebae, the free-living Acanthamoeba . However, how and why this divergence occurred remains unclear. Meanwhile, giant viruses consisting of protozoa-related and protozoa-unrelated viruses have been discovered, with the former group being suggested to have more influenced environmental chlamydiae during their evolution while cohabiting host amoebae...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30034216/homology-inference-based-on-a-reconciliation-approach-for-the-comparative-genomics-of-protozoa
#19
Darueck A Campos, Elisa C Pereira, Rodrigo Jardim, Rafael Rc Cuadrat, Juliana S Bernardes, Alberto Mr Dávila
Protozoa parasites are responsible for several diseases in tropical countries, such as malaria, sleeping sickness, Chagas disease, leishmaniasis, amebiasis, and giardiasis, which together threaten millions of people around the world. In addition, most of the classic parasitic diseases due to protozoa are zoonotic. Understanding the biology of these organisms plays a relevant role in combating these diseases. Using homology inference and comparative genomics, this study targeted 3 protozoan species from different Phyla: Cryptosporidium muris (Apicomplexa), Entamoeba invadens (Amoebozoa), and Trypanosoma grayi (Euglenozoa)...
2018: Evolutionary Bioinformatics Online
https://read.qxmd.com/read/30022808/atypical-evolution-of-the-f-1-f-o-adenosine-triphosphate-synthase-regulatory-atp6-subunit-in-glacier-ice-worms-annelida-clitellata-mesenchytraeus
#20
Shirley A Lang, Daniel H Shain
The glacier ice worm, Mesenchytraeus solifugus , is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction...
2018: Evolutionary Bioinformatics Online
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