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https://www.readbyqxmd.com/read/29661449/genetic-mechanisms-involved-in-the-generation-of-hla-alleles-in-brazilians-description-and-comparison-of-hla-alleles
#1
R A Fabreti-Oliveira, M F Lasmar, C K F Oliveira, E M G Vale, E Nascimento
BACKGROUND: The HLA genes show high levels of diversity as indicated by the number of HLA alleles. There are almost 11,000 classical HLA-A, -B, -DRB1 alleles in populations around the world, making the search for compatible donors difficult. HLA diversity is generated by different genetic mechanisms, such as point mutations, which result in single nucleotide polymorphisms, insertion and deletion, and recombination. The aim of this study was to describe genetic mechanisms involved in the generation of HLA alleles in Brazilians...
April 2018: Transplantation Proceedings
https://www.readbyqxmd.com/read/29659490/a-comparative-genomic-survey-provides-novel-insights-into-molecular-evolution-of-l-aromatic-amino-acid-decarboxylase-in-vertebrates
#2
Yanping Li, Yunyun Lv, Chao Bian, Xinxin You, Li Deng, Qiong Shi
Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD) is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad -like gene, which formed a novel AAAD family...
April 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29611801/a-naturally-occurring-feline-apobec3-variant-that-loses-anti-lentiviral-activity-by-lacking-two-amino-acid-residues
#3
Yoriyuki Konno, Shumpei Nagaoka, Izumi Kimura, Mahoko Takahashi Ueda, Ryuichi Kumata, Jumpei Ito, So Nakagawa, Tomoko Kobayashi, Yoshio Koyanagi, Kei Sato
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) is a mammalian protein that restricts lentiviral replication. Various polymorphisms of mammalian APOBEC3 genes have been observed in humans, Old World monkeys and domestic cats; however, the genetic diversity of APOBEC3 genes in other mammals remains unaddressed. Here we identify a novel haplotype of the feline APOBEC3Z3 gene, an APOBEC3 gene that restricts feline immunodeficiency virus (FIV) replication, in a Eurasian lynx (Lynx lynx)...
April 3, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29610199/absence-of-azole-or-echinocandin-resistance-in-candida-glabrata-isolates-in-india-despite-background-prevalence-of-strains-with-defects-in-dna-mismatch-repair-pathway
#4
Ashutosh Singh, Kelley R Healey, Priyanka Yadav, Gargi Upadhyaya, Neelam Sachdeva, Smita Sarma, Anil Kumar, Bansidhar Tarai, David S Perlin, Anuradha Chowdhary
Candida glabrata infections are increasing world-wide and exhibit greater rates of antifungal resistance than other species. DNA mismatch repair (MMR) gene deletions, such as msh2Δ , in C. glabrata resulting in a mutator phenotype has recently been reported to facilitate rapid acquisition of antifungal resistance. This study determined the antifungal susceptibility profile of 210 C. glabrata isolates, in 10 hospitals in India and investigated the impact of novel MSH 2 polymorphisms on mutation potential. No echinocandin or azole resistant strains were detected among C...
April 2, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29574604/evolution-of-melanoma-antigen-a11-magea11-during-primate-phylogeny
#5
Christopher S Willett, Elizabeth M Wilson
Melanoma antigen-A11 (MAGE-A11) is an X-linked and primate-specific steroid hormone receptor transcriptional coregulator and proto-oncogenic protein whose increased expression promotes the growth of prostate cancer. The MAGEA11 gene is expressed at low levels in normal human testis, ovary, and endometrium, and at highest levels in castration-resistant prostate cancer. Annotated genome predictions throughout the surviving primate lineage show that MAGEA11 acquired three 5' coding exons unique within the MAGEA subfamily during the evolution of New World monkeys (NWM), Old World monkeys (OWM), and apes...
March 24, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29532931/a-novel-chloroplast-gene-reported-for-flagellate-plants
#6
Michael Song, Li-Yaung Kuo, Layne Huiet, Kathleen M Pryer, Carl J Rothfels, Fay-Wei Li
PREMISE OF THE STUDY: Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS: We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction...
January 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29529038/the-complete-chloroplast-genome-sequence-of-epipremnum-aureum-and-its-comparative-analysis-among-eight-araceae-species
#7
Na Tian, Limin Han, Chen Chen, Zhezhi Wang
Epipremnum aureum is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of E. aureum by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes...
2018: PloS One
https://www.readbyqxmd.com/read/29528338/lilrb1-polymorphisms-influence-posttransplant-hcmv-susceptibility-and-ligand-interactions
#8
Kang Yu, Chelsea L Davidson, Agnieszka Wójtowicz, Luiz Lisboa, Ting Wang, Adriana M Airo, Jean Villard, Jeremie Buratto, Tatyana Sandalova, Adnane Achour, Atul Humar, Katia Boggian, Alexia Cusini, Christian van Delden, Adrian Egli, Oriol Manuel, Nicolas Mueller, Pierre-Yves Bochud, Deborah N Burshtyn
UL18 is a human CMV (HCMV) MHC class I (MHCI) homolog that efficiently inhibits leukocyte immunoglobulin-like receptor subfamily B member 1 (LILRB1)+ NK cells. We found an association of LILRB1 polymorphisms in the regulatory regions and ligand-binding domains with control of HCMV in transplant patients. Naturally occurring LILRB1 variants expressed in model NK cells showed functional differences with UL18 and classical MHCI, but not with HLA-G. The altered functional recognition was recapitulated in binding assays with the binding domains of LILRB1...
March 12, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29521145/extensive-sharing-of-mitochondrial-coi-and-cyb-haplotypes-among-reef-building-staghorn-corals-acropora-spp-in-sabah-north-borneo
#9
Rolando Robert, Kenneth Francis Rodrigues, Zarinah Waheed, Subbiah Vijay Kumar
This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts /Tv ), synonymous-to-nonsynonymous rate ratio (dN /dS ), and substitution patterns at the three codon positions...
March 9, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29510674/evolutionary-analysis-of-mitochondrially-encoded-proteins-of-toad-headed-lizards-phrynocephalus-along-an-altitudinal-gradient
#10
Yuanting Jin, Yubin Wo, Haojie Tong, Sen Song, Lixun Zhang, Richard P Brown
BACKGROUND: Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time)...
March 6, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29481587/functional-divergence-of-duplicate-genes-several-million-years-after-gene-duplication-in-arabidopsis
#11
Kousuke Hanada, Ayumi Tezuka, Masafumi Nozawa, Yutaka Suzuki, Sumio Sugano, Atsushi J Nagano, Motomi Ito, Shin-Ichi Morinaga
Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae...
February 21, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29474815/complete-mitochondrial-genome-of-the-tea-looper-caterpillar-ectropis-obliqua-lepidoptera-geometridae-with-a-phylogenetic-analysis-of-geometridae
#12
Li Qian, Wang Xiaoxi, Chen Xuexin, Han Baoyu
The complete mitochondrial genome (mitogenome) of the Ectropis obliqua (Lepidoptera: Geometridae) was sequenced and compared with other species of Geometridae. The mitochondrial genome of E. obliqua is 15,475 bp long and contains 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region. Gene cluster trnI-trnQ-trnM rearranged to trnM-trnI-trnQ comparing with the ancestral mitogenome of insects. All tRNA genes have typical cloverleaf secondary structure except for trnS (AGN)...
February 20, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29468429/comparative-genomic-analysis-of-the-lipase3-gene-family-in-five-plant-species-reveals-distinct-evolutionary-origins
#13
Dan Wang, Lin Zhang, JunFeng Hu, Dianshuai Gao, Xin Liu, Yan Sha
Lipases are physiologically important and ubiquitous enzymes that share a conserved domain and are classified into eight different families based on their amino acid sequences and fundamental biological properties. The Lipase3 family of lipases was reported to possess a canonical fold typical of α/β hydrolases and a typical catalytic triad, suggesting a distinct evolutionary origin for this family. Genes in the Lipase3 family do not have the same functions, but maintain the conserved Lipase3 domain. There have been extensive studies of Lipase3 structures and functions, but little is known about their evolutionary histories...
February 22, 2018: Genetica
https://www.readbyqxmd.com/read/29432191/divergent-and-parallel-routes-of-biochemical-adaptation-in-high-altitude-passerine-birds-from-the-qinghai-tibet-plateau
#14
Xiaojia Zhu, Yuyan Guan, Anthony V Signore, Chandrasekhar Natarajan, Shane G DuBay, Yalin Cheng, Naijian Han, Gang Song, Yanhua Qu, Hideaki Moriyama, Federico G Hoffmann, Angela Fago, Fumin Lei, Jay F Storz
When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau, and we examine whether convergent increases in Hb-O2 affinity have a similar molecular basis in different species. We documented that high-altitude parid and aegithalid species from the Qinghai-Tibet Plateau have evolved derived increases in Hb-O2 affinity in comparison with their closest lowland relatives in East Asia...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29421854/allopolyploidization-in-cucumis-contributes-to-delayed-leaf-maturation-with-repression-of-redundant-homoeologous-genes
#15
Xiaqing Yu, Xixi Wang, Benita Hyldgaard, Zaobing Zhu, Rong Zhou, Katrine Heinsvig Kjaer, Theoharis Ouzounis, Qunfeng Lou, Ji Li, Qingsheng Cai, Eva Rosenqvist, Carl-Otto Ottosen, Jinfeng Chen
The important role of polyploidy in plant evolution is widely recognized. However, many questions remain to be explored to address how polyploidy affects the phenotype of the plant. To shed light on the phenotypic and molecular impacts of allopolyploidy, we investigated the leaf development of a synthesized allotetraploid (Cucumis ×hytivus), with an emphasis on chlorophyll development. Delayed leaf maturation was identified in C. ×hytivus, based on delayed leaf expansion, initial chlorophyll deficiency in the leaves and disordered sink-source transition...
February 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29413881/evolution-of-methicillin-resistant-staphylococcus-aureus-evidence-of-positive-selection-in-a-penicillin-binding-protein-pbp-2a-coding-gene-meca
#16
Xiao-Yong Zhan, Qing-Yi Zhu
Methicillin-resistant Staphylococcus aureus (S. aureus) (MRSA) represents more and more S. aureus infections. MecA, the novel coding gene of penicillin-binding protein (PBP) 2a of MRSA, is the key resistance factor of β-lactam, but little is known about the evolution of this gene. Given the crucial role of mecA in S. aureus physiology and β-lactam resistance, the selective forces may contribute to adaptation of the bacteria to the special environments such as its host or antibiotics. To understand the evolution of this gene, we screened GenBank database and analyzed mecA of 249 S...
January 27, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29408286/mitochondrial-phylogeny-divergence-history-and-high-altitude-adaptation-of-grassland-caterpillars-lepidoptera-lymantriinae-gynaephora-inhabiting-the-tibetan-plateau
#17
Ming-Long Yuan, Qi-Lin Zhang, Li Zhang, Cheng-Lin Jia, Xiao-Peng Li, Xing-Zhuo Yang, Run-Qiu Feng
Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae)...
February 2, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29368655/deleterious-genetic-variants-in-ciliopathy-genes-increase-risk-of-ritodrine-induced-cardiac-and-pulmonary-side-effects
#18
Heewon Seo, Eun Jin Kwon, Young-Ah You, Yoomi Park, Byung Joo Min, Kyunghun Yoo, Han-Sung Hwang, Ju Han Kim, Young Ju Kim
BACKGROUND: Ritodrine is a commonly used tocolytic to prevent preterm labour. However, it can cause unexpected serious adverse reactions, such as pulmonary oedema, pulmonary congestion, and tachycardia. It is unknown whether such adverse reactions are associated with pharmacogenomic variants in patients. METHODS: Whole-exome sequencing of 13 subjects with serious ritodrine-induced cardiac and pulmonary side-effects was performed to identify causal genes and variants...
January 24, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29356095/familial-congenital-methemoglobinemia-in-pomeranian-dogs-caused-by-a-missense-variant-in-the-nadh-cytochrome-b5-reductase-gene
#19
H Shino, Y Otsuka-Yamasaki, T Sato, K Ooi, O Inanami, R Sato, M Yamasaki
BACKGROUND: In veterinary medicine, congenital methemoglobinemia associated with nicotinamide adenine dinucleotide (NADH)-cytochrome b5 reductase (b5R) deficiency is rare. It has been reported in several breeds of dogs, but little information is available about its etiology. OBJECTIVES: To analyze the NADH-cytochrome b5 reductase gene, CYB5R3, in a Pomeranian dog family with methemoglobinemia suspected to be caused by congenital b5R deficiency. ANIMALS: Three Pomeranian dogs from a family with methemoglobinemia were analyzed...
January 2018: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29351740/population-size-may-shape-the-accumulation-of-functional-mutations-following-domestication
#20
Jianhai Chen, Pan Ni, Xinyun Li, Jianlin Han, Ivan Jakovlić, Chengjun Zhang, Shuhong Zhao
BACKGROUND: Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS: Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives...
January 19, 2018: BMC Evolutionary Biology
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