keyword
MENU ▼
Read by QxMD icon Read
search

dN/dS

keyword
https://www.readbyqxmd.com/read/29167739/measuring-evolutionary-rates-of-proteins-in-a-structural-context
#1
Dariya K Sydykova, Benjamin R Jack, Stephanie J Spielman, Claus O Wilke
We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as dN/dS. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses...
2017: F1000Research
https://www.readbyqxmd.com/read/29162445/the-neuromorphological-caudate-putaminal-clustering-of-neostriate-interneurons-kohonen-self-organizing-maps-and-supervised-artificial-neural-networks-with-multivariate-analysis
#2
Ivan Grbatinić, Nebojša Milošević, Bojana Krstonošić
AIMS: The objective of this study is to investigate the possibility of the neuromorphotopological clustering of neostriate interneurons (NSIN) and their consequent classification into caudate (CIN) and putaminal neuron type (PIN), according to the nuclear localization of the neurons. It tends to discover whether these two topological neuron types are morphologically different. MATERIAL AND METHODS: The binary images of adult human NSIN are used for the purposes of the analysis...
November 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29128519/genetic-structure-of-two-erythrocyte-binding-antigens-of-plasmodium-falciparum-reveals-a-contrasting-pattern-of-selection
#3
Pramita Chowdhury, Srikanta Sen, Sumana Datta Kanjilal, Sanghamitra Sengupta
Erythrocyte binding antigens 175 (EBA-175) and 140 (EBA-140) play key roles in erythrocyte invasion by binding to glycophorin A (GPA) and C (GPC) respectively in human malaria. Since antigenic variation in malaria endemic region is a major barrier to development of effective vaccine, we explore the nature and pattern of sequence diversity of these two vaccine candidates in Kolkata, India. Population genetic parameters based on parasite sequences representing region II of Pfeba-175 and Pfeba-140 genes were estimated using DnaSP V...
November 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29126243/faster-evolving-primate-genes-are-more-likely-to-duplicate
#4
Áine N O'Toole, Laurence D Hurst, Aoife McLysaght
An attractive and long-standing hypothesis regarding the evolution of genes after duplication posits that the duplication event creates new evolutionary possibilities by releasing a copy of the gene from constraint. Apparent support was found in numerous analyses, particularly the observation of higher rates of evolution in duplicated as compared to singleton genes. Could it, instead, be that more duplicable genes (owing to mutation, fixation or retention biases) are intrinsically faster evolving? To uncouple the measurement of rates of evolution from the determination of duplicate or singleton status, we measure the rates of evolution in singleton genes in outgroup primate lineages but classify these genes as to whether they have duplicated or not in a crown group of great apes...
November 7, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29109707/genomic-comparisons-reveal-microevolutionary-differences-in-mycobacterium-abscessus-subspecies
#5
Joon L Tan, Kee P Ng, Chia S Ong, Yun F Ngeow
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29096703/regulatory-and-evolutionary-signatures-of-sex-biased-genes-on-both-the-x-chromosome-and-the-autosomes
#6
Jiangshan J Shen, Ting-You Wang, Wanling Yang
BACKGROUND: Sex is an important but understudied factor in the genetics of human diseases. Analyses using a combination of gene expression data, ENCODE data, and evolutionary data of sex-biased gene expression in human tissues can give insight into the regulatory and evolutionary forces acting on sex-biased genes. METHODS: In this study, we analyzed the differentially expressed genes between males and females. On the X chromosome, we used a novel method and investigated the status of genes that escape X-chromosome inactivation (escape genes), taking into account the clonality of lymphoblastoid cell lines (LCLs)...
November 2, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/29044435/impact-of-clinical-parameters-in-the-intrahost-evolution-of-hiv-1-subtype-b-in-pediatric-patients-a-machine-learning-approach
#7
Patricia Rojas Sánchez, Alberto Cobos, Marisa Navaro, José Tomas Ramos, Israel Pagán, África Holguín
Determining the factors modulating the genetic diversity of HIV-1 populations is essential to understand viral evolution. This study analyzes the relative importance of clinical factors in the intrahost HIV-1 subtype B (HIV-1B) evolution and in the fixation of drug resistance mutations (DRM) during longitudinal pediatric HIV-1 infection. We recovered 162 partial HIV-1B pol sequences (from 3 to 24 per patient) from 24 perinatally infected patients from the Madrid Cohort of HIV-1 infected children and adolescents in a time interval ranging from 2...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036352/environmental-plasticity-in-the-intersexual-correlation-and-sex-bias-of-gene-expression
#8
Changde Cheng, Mark Kirkpatrick, Melissa Wilson Sayres
Intersexual genetic correlations are expected to constrain the evolution of sexual dimorphic traits, including the degree of sex-biased gene expression. Consistent with that expectation, studies in fruit flies and birds have reported that genes whose expression has a strong intersexual genetic correlation (rMF) show a lower level of sex-biased expression (SBE). However, it is known that both rMF and SBE can be affected by the environment. It is therefore unclear whether there is a consistent relationship between these 2 quantities across multiple environments...
October 30, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29030254/complete-structure-and-variation-of-the-chloroplast-genome-of-agropyron-cristatum-l-gaertn
#9
Ning Chen, Li-Na Sha, Zhen-Zhen Dong, Chao Tang, Yi Wang, Hou-Yang Kang, Hai-Qin Zhang, Xue-Bin Yan, Yong-Hong Zhou, Xing Fan
Agropyron cristatum (L.) Gaertner, a perennial grass in the tribe Triticeae (Poaceae), is a wild relative of cereal crops that is suitable for genetic improvement. In this study, we first sequenced the complete chloroplast (cp) genome of Ag. cristatum using Hiseq4000 PE150. The Ag. cristatum chloroplast genome is 135,554bp in length, has a typical quadripartite structure and contains 76 protein-coding genes, 29 tRNA genes and four rRNA genes. The cp genome of Ag. cristatum was used for comparison with other seven Triticeae species...
January 15, 2018: Gene
https://www.readbyqxmd.com/read/28985307/sequence-based-analysis-of-thermal-adaptation-and-protein-energy-landscapes-in-an-invasive-blue-mussel-mytilus-galloprovincialis
#10
Norah P Saarman, Kord M Kober, W Brian Simison, Grant H Pogson
Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985306/plastome-evolution-in-the-sole-hemiparasitic-genus-laurel-dodder-cassytha-and-insights-into-the-plastid-phylogenomics-of-lauraceae
#11
Chung-Shien Wu, Ting-Jen Wang, Chia-Wen Wu, Ya-Nan Wang, Shu-Miaw Chaw
To date, little is known about the evolution of plastid genomes (plastomes) in Lauraceae. As one of the top five largest families in tropical forests, the Lauraceae contain many species that are important ecologically and economically. Lauraceous species also provide wonderful materials to study the evolutionary trajectory in response to parasitism because they contain both non-parasitic and parasitic species. This study compared the plastomes of nine Lauraceous species, including the sole hemiparasitic and herbaceous genus Cassytha (laurel dodder; here represented by Cas...
September 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28947714/analysis-of-polymorphisms-and-selective-pressures-on-ama1-gene-in-plasmodium-knowlesi-isolates-from-sabah-malaysia
#12
Chuen Yang Chua, Ping Chin Lee, Tiek Ying Lau
The apical membrane antigen-1 (AMA-1) of Plasmodium spp. is a merozoite surface antigen that is essential for the recognition and invasion of erythrocytes. Polymorphisms occurring in this surface antigen will cause major obstacles in developing effective malaria vaccines based on AMA-1. The objective of this study was to characterize ama1 gene in Plasmodium knowlesi isolates from Sabah. DNA was extracted from blood samples collected from Keningau, Kota Kinabalu and Kudat. The Pkama1 gene was amplified using nested PCR and subjected to bidirectional sequencing...
September 2017: Journal of Genetics
https://www.readbyqxmd.com/read/28874229/molecular-evolution-and-phylogeography-of-infectious-hematopoietic-necrosis-virus-with-a-focus-on-its-presence-in-france-over-the-last-30-years
#13
Laure Bellec, Lénaïg Louboutin, Joëlle Cabon, Jeanne Castric, Joëlle Cozien, Richard Thiéry, Thierry Morin
Infectious hematopoietic necrosis virus (IHNV) is among the most important pathogens affecting the salmonid industry. Here, we investigated the molecular evolution and circulation of isolates from 11 countries or regions all over the world, with a special focus on the epidemiological situation in France. The phylogeography, time to the most recent common ancestor (TMRCA) and nucleotide substitution rate were studied using 118 full-length glycoprotein gene sequences isolated from 9 countries (5 genogroups) over a period of 47 years...
September 6, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28855525/mitogenome-sequencing-in-the-genus-camelus-reveals-evidence-for-purifying-selection-and-long-term-divergence-between-wild-and-domestic-bactrian-camels
#14
Elmira Mohandesan, Robert R Fitak, Jukka Corander, Adiya Yadamsuren, Battsetseg Chuluunbat, Omer Abdelhadi, Abdul Raziq, Peter Nagy, Gabrielle Stalder, Chris Walzer, Bernard Faye, Pamela A Burger
The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and high-altitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28854633/contrasting-patterns-of-nucleotide-substitution-rates-provide-insight-into-dynamic-evolution-of-plastid-and-mitochondrial-genomes-of-geranium
#15
Seongjun Park, Tracey A Ruhlman, Mao-Lun Weng, Nahid H Hajrah, Jamal S M Sabir, Robert K Jansen
Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28814302/ompa-protein-sequence-based-typing-and-virulence-associated-gene-profiles-of-pasteurella-multocida-isolates-associated-with-bovine-haemorrhagic-septicaemia-and-porcine-pneumonic-pasteurellosis-in-thailand
#16
Teerasak E-Kobon, Ratiporn Leeanan, Saengtian Pannoi, Pornchai Anuntasomboon, Pacharee Thongkamkoon, Arinthip Thamchaipenet
BACKGROUND: Pasteurella multocida is a Gram-negative bacterium that causes economically significant infections of a broad range of animal species. Pneumonic and septicaemic pasteurellosis caused by this bacterium remain important problems in pigs, cattle, and water buffaloes in Thailand. The aim of this study was to characterise the virulence-associated gene profiles and to develop an OmpA molecular typing scheme for classifying 191 bovine and porcine isolates of P. multocida collected between 1989 and 2012 in Thailand using polymerase chain reactions (PCRs), nucleotide sequencing, and sequence and structural bioinformatics analyses...
August 16, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28807856/low-levels-of-genetic-diversity-associated-with-evidence-of-negative-selection-on-the-babesia-bovis-apical-membrane-antigen-1-from-parasite-populations-in-thailand
#17
Amarin Rittipornlertrak, Boondarika Nambooppha, Pacharathon Simking, Veerasak Punyapornwithaya, Saruda Tiwananthagorn, Sathaporn Jittapalapong, Yang-Tsung Chung, Nattawooti Sthitmatee
Babesia bovis, a parasite infecting cattle and buffalo, continues to spread throughout the developing world. The babesial vaccine was developed to be a sustainable alternative treatment to control the parasite. However, genetic diversity is a major obstacle for designing and developing a safe and effective vaccine. The apical membrane antigen 1 (AMA-1) is considered to be a potential vaccine candidate antigen among immunogenic genes of B. bovis. To gain a more comprehensive understanding of B. bovis AMA-1 (BbAMA-1), three B...
August 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28805451/genetic-characterisation-and-analysis-of-infectious-bronchitis-virus-isolated-from-brazilian-flocks-between-2010-and-2015
#18
Claudia Carranza, Claudete S Astolfi-Ferreira, Silvana H Santander Parra, Luis F N Nuñez, Zoltan Penzes, Jorge L Chacón, Luiz Sesti, Ruy D Chacón, Antonio J Piantino Ferreira
1. Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. 2. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. 3. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i...
December 2017: British Poultry Science
https://www.readbyqxmd.com/read/28798740/smrt-sequencing-revealed-mitogenome-characteristics-and-mitogenome-wide-dna-modification-pattern-in-ophiocordyceps-sinensis
#19
Xincong Kang, Liqin Hu, Pengyuan Shen, Rui Li, Dongbo Liu
Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28797243/polymorphism-and-structure-of-style-specific-arabinogalactan-proteins-as-determinants-of-pollen-tube-growth-in-nicotiana
#20
Andrzej K Noyszewski, Yi-Cheng Liu, Koichiro Tamura, Alan G Smith
BACKGROUND: Pollen tube growth and fertilization are key processes in angiosperm sexual reproduction. The transmitting tract (TT) of Nicotiana tabacum controls pollen tube growth in part by secreting pistil extensin-like protein III (PELPIII), transmitting-tract-specific (TTS) protein and 120 kDa glycoprotein (120 K) into the stylar extracellular matrix. The three arabinogalactan proteins (AGP) are referred to as stylar AGPs and are the focus of this research. The transmitting tract regulates pollen tube growth, promoting fertilization or rejecting pollen tubes...
August 10, 2017: BMC Evolutionary Biology
keyword
keyword
106772
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"