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https://www.readbyqxmd.com/read/28717152/effects-of-population-bottleneck-and-balancing-selection-on-the-chinese-alligator-are-revealed-by-locus-specific-characterization-of-mhc-genes
#1
Teng Zhai, Hai-Qiong Yang, Rui-Can Zhang, Li-Ming Fang, Guo-Heng Zhong, Sheng-Guo Fang
Chinese alligator (Alligator sinensis) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28711373/comparative-genomic-and-phylogenetic-analysis-of-a-toxigenic-clinical-isolate-of-corynebacterium-diphtheriae-strain-b-d-16-78-from-malaysia
#2
Kar-Wai Hong, A W Asmah Hani, C A Nurul Aina Murni, R R Pusparani, Chee Kheong Chong, Khebir Verasahib, Wan Noraini W Yusoff, Noorliza M Noordin, Kok Keng Tee, Wai-Fong Yin, Choo Yee Yu, Geik Yong Ang, Kok-Gan Chan
In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile...
July 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#3
Áki Jarl Láruson
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28671612/mutations-in-cancer-cause-gain-of-cysteine-histidine-and-tryptophan-at-the-expense-of-a-net-loss-of-arginine-on-the-proteome-level
#4
Viktoriia Tsuber, Yunus Kadamov, Lars Brautigam, Ulrika Warpman Berglund, Thomas Helleday
Accumulation of somatic mutations is critical for the transition of a normal cell to become cancerous. Mutations cause amino acid substitutions that change properties of proteins. However, it has not been studied as to what extent the composition and accordingly chemical properties of the cell proteome is altered as a result of the increased mutation load in cancer. Here, we analyzed data on amino acid substitutions caused by mutations in about 2000 protein coding genes from the Cancer Cell Line Encyclopedia that contains information on nucleotide and amino acid alterations in 782 cancer cell lines, and validated the analysis with information on amino acid substitutions for the same set of proteins in the Catalogue of Somatic Mutations in Cancer (COSMIC; v78) in circa 18,000 tumor samples...
July 3, 2017: Biomolecules
https://www.readbyqxmd.com/read/28665990/molecular-evolutionary-analysis-of-a-gender-limited-mid-ortholog-from-the-homothallic-species-volvox-africanus-with-male-and-monoecious-spheroids
#5
Kayoko Yamamoto, Hiroko Kawai-Toyooka, Takashi Hamaji, Yuki Tsuchikane, Toshiyuki Mori, Fumio Takahashi, Hiroyuki Sekimoto, Patrick J Ferris, Hisayoshi Nozaki
Volvox is a very interesting oogamous organism that exhibits various types of sexuality and/or sexual spheroids depending upon species or strains. However, molecular bases of such sexual reproduction characteristics have not been studied in this genus. In the model species V. carteri, an ortholog of the minus mating type-determining or minus dominance gene (MID) of isogamous Chlamydomonas reinhardtii is male-specific and determines the sperm formation. Male and female genders are genetically determined (heterothallism) in V...
2017: PloS One
https://www.readbyqxmd.com/read/28654758/looking-into-a-whale-s-heart-investigating-a-genetic-basis-for-cardiomyopathy-in-a-non-model-species
#6
Amelia Viricel, Patricia E Rosel
Understanding the pathogenesis of complex diseases can benefit from multi-species comparative studies. Yet these studies rarely include natural populations of non-model species. Here, we focused on the cause of a heart muscle disease, cardiomyopathy (CM), affecting multiple mammalian species including humans, cats, dogs, and certain species of whales. Mutations in genes coding for sarcomeric proteins have been identified as a leading cause for CM in humans, and some were also revealed to be responsible for CM in cats...
June 27, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28642160/a-novel-missense-variant-gln220arg-of-gnb4-encoding-guanine-nucleotide-binding-protein-subunit-beta-4-in-a-japanese-family-with-autosomal-dominant-motor-and-sensory-neuropathy
#7
Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kazuhito Noda, Kengo Kosaka, Takayuki Taniwaki, Hiroki Shibata
Dominant intermediate Charcot-Marie-Tooth disease F (CMTDIF) is an autosomal dominant hereditary form of Charcot-Marie-Tooth disease (CMT) caused by variations in the guanine nucleotide-binding protein, subunit beta-4 gene (GNB4). We examined two Japanese familial cases with CMT. Case 1 was a 49-year-old male whose chief complaint was slowly progressive gait disturbance and limb dysesthesia that appeared at the age of 47. On neurological examination, he showed hyporeflexia or areflexia, distal limb muscle weakness, and distal sensory impairment with lower dominancy...
June 19, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28630112/rapid-evolution-of-ovarian-biased-genes-in-the-yellow-fever-mosquito-aedes-aegypti
#8
Carrie A Whittle, Cassandra G Extavour
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2,927, 2,013 and 4,449 coding-sequences (CDS) with ovary-biased, testis-biased and unbiased expression respectively in the yellow-fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28616179/prediction-of-harmful-variants-on-mitochondrial-genes-test-of-habitat-dependent-and-demographic-effects-in-a-euryhaline-fish
#9
Anti Vasemägi, Janne Sulku, Matthieu Bruneaux, Olaf Thalmann, Hannu Mäkinen, Mikhail Ozerov
Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of Pungitius pungitius collected from brackish and freshwater habitats...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28604700/excess-of-non-conservative-amino-acid-changes-in-marine-bacterioplankton-lineages-with-reduced-genomes
#10
Haiwei Luo, Yongjie Huang, Ramunas Stepanauskas, Jijun Tang
Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed...
June 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28547737/08sg2-osbak1-regulates-grain-size-and-number-and-functions-differently-in-indica-and-japonica-backgrounds-in-rice
#11
Hua Yuan, Shijun Fan, Juan Huang, Shijie Zhan, Shifu Wang, Peng Gao, Weilan Chen, Bin Tu, Bingtian Ma, Yuping Wang, Peng Qin, Shigui Li
BACKGROUND: Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying them remains ambiguous. RESULTS: We identified a rice small grain (sg2) mutant in an EMS mutant library generated from an indica variety, Shuhui498. Using the MutMap gene mapping strategy, we identified two linkage regions on chromosome 7 and 8, respectively, consistent with the segregation ratios in the F2 population...
December 2017: Rice
https://www.readbyqxmd.com/read/28537708/nonsynonymous-polymorphisms-in-the-human-as3mt-arsenic-methylation-gene-implications-for-arsenic-toxicity
#12
Jiaojiao Li, Charles Packianathan, Toby G Rossman, Barry P Rosen
Arsenic methylation, the primary biotransformation in the human body, is catalyzed by the enzyme As(III) S-adenosylmethionine (SAM) methyltransferases (hAS3MT). This process is thought to be protective from acute high-level arsenic exposure. However, with long-term low-level exposure, hAS3MT produces intracellular methylarsenite (MAs(III)) and dimethylarsenite (DMAs(III)), which are considerably more toxic than inorganic As(III) and may contribute to arsenic-related diseases. Several single nucleotide polymorphisms (SNPs) in putative regulatory elements of the hAS3MT gene have been shown to be protective...
June 19, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28537236/-allelic-variants-of-immune-response-genes-in-children-with-infectious-complications-during-the-treatment-of-acute-leukemia
#13
M A Avdonina, I S Abramov, Y I Ammour, T V Nasedkina
Infectious complications that arise during the treatment of children with acute leukemia with chemotherapeutic agents at high doses represent a serious problem in oncohematology. To find genetic conditions that may lead to the development of postchemotherapy infections, the genomes of 12 children with acute leukemia who had severe infectious complications during therapy were examined. At the same time, the coding regions of 17 genes involved in the regulation of the immune response were determined by massive parallel sequencing...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28500993/nonsynonymous-changes-of-equine-lentivirus-receptor-1-elr1-gene-in-amino-acids-involved-in-the-interaction-with-equine-infectious-anemia-virus-eiav
#14
C M Corbi-Botto, S A Sadaba, M E Zappa, P Peral-García, S Díaz
Equine lentivirus receptor-1 (ELR1) has been characterized as the specific functional receptor that mediates equine infectious anemia virus (EIAV) entrance to horse macrophages. This receptor is tumor necrosis factor receptor superfamily member 14 (TNFRSF14). The aim of this study was to investigate the occurrence of allelic variants in the coding sequence of equine TNFRSF14 gene by screening for single-nucleotide polymorphisms (SNPs) in different equine populations. Forty seven horse samples were randomly selected from a reservoir of EIAV-seropositive and seronegative samples collected from different outbreaks and regions of Argentina...
May 2, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#15
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28413183/a-slc24a2-gene-variant-uncovered-in-pancreatic-ductal-adenocarcinoma-by-whole-exome-sequencing
#16
Lei Wang, Zhuo Shao, Shiyue Chen, Lu Shi, Zhaoshen Li
Pancreatic ductal adenocarcinoma (PDAC) presents as an aggressive malignancy caused by environmental and genetic factors. In order to identify causal genes for PDAC, we performed whole exome sequencing (WES) to detect gene mutations in seven pairs of PDAC tissue and adjacent non-tumor tissue samples. Finally, we found a new nonsynonymous single nucleotide variant (nsSNV) in solute carrier 24 family member 2 (SLC24A2) gene resulting in the substitution of native glutamic acid (E) into aspartic acid (D) at position of 287 amino acid (E287D) in SLC24A2 protein, and confirmed this variant by Sanger gene sequencing...
April 2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28400484/amino-acid-polymorphisms-in-the-fibronectin-binding-repeats-of-fibronectin-binding-protein-a-affect-bond-strength-and-fibronectin-conformation
#17
Nadia N Casillas-Ituarte, Carlos H B Cruz, Roberto D Lins, Alex C DiBartola, Jessica Howard, Xiaowen Liang, Magnus Höök, Isabelle F T Viana, M Roxana Sierra-Hernández, Steven K Lower
The Staphylococcus aureus cell surface contains cell wall-anchored proteins such as fibronectin-binding protein A (FnBPA) that bind to host ligands (e.g. fibronectin; Fn) present in the extracellular matrix of tissue or coatings on cardiac implants. Recent clinical studies have found a correlation between cardiovascular infections caused by S. aureus and nonsynonymous SNPs in FnBPA. Atomic force microscopy (AFM), surface plasmon resonance (SPR), and molecular simulations were used to investigate interactions between Fn and each of eight 20-mer peptide variants containing amino acids Ala, Asn, Gln, His, Ile, and Lys at positions equivalent to 782 and/or 786 in Fn-binding repeat-9 of FnBPA...
May 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#18
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28393414/role-of-seed-germination-in-adaptation-and-reproductive-isolation-in-arabidopsis-lyrata
#19
Tuomas Hämälä, Tiina M Mattila, Päivi H Leinonen, Helmi Kuittinen, Outi Savolainen
Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci...
April 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28369607/the-influence-of-hiv-on-the-evolution-of-mycobacterium-tuberculosis
#20
Anastasia S Koch, Daniela Brites, David Stucki, Joanna C Evans, Ronnett Seldon, Alexa Heekes, Nicola Mulder, Mark Nicol, Tolu Oni, Valerie Mizrahi, Digby F Warner, Julian Parkhill, Sebastien Gagneux, Darren P Martin, Robert J Wilkinson
HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals...
July 1, 2017: Molecular Biology and Evolution
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