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https://www.readbyqxmd.com/read/29933404/complete-chloroplast-genome-of-tetragonia-tetragonioides-molecular-phylogenetic-relationships-and-evolution-in-caryophyllales
#1
Kyoung Su Choi, Myounghai Kwak, Byoungyoon Lee, SeonJoo Park
The chloroplast genome of Tetragonia tetragonioides (Aizoaceae; Caryophyllales) was sequenced to provide information for studies on phylogeny and evolution within Caryophyllales. The chloroplast genome of Tetragonia tetragonioides is 149,506 bp in length and includes a pair of inverted repeats (IRs) of 24,769 bp that separate a large single copy (LSC) region of 82,780 bp and a small single copy (SSC) region of 17,188 bp. Comparative analysis of the chloroplast genome showed that Caryphyllales species have lost many genes...
2018: PloS One
https://www.readbyqxmd.com/read/29926005/analysis-of-all-34-exons-of-the-spink5-gene-in-japanese-atopic-dermatitis-patients
#2
Shin Morizane, Mamoru Ouchida, Ko Sunagawa, Saeko Sugimoto, Mina Kobashi, Satoru Sugihara, Hayato Nomura, Kazuhide Tsuji, Atsushi Sato, Yoshihiro Miura, Hiroaki Hattori, Kotaro Tada, Wook-Kang Huh, Akemi Seno, Keiji Iwatsuki
Lympho-epithelial Kazal-type-related inhibitor (LEKTI) is a large multidomain serine protease inhibitor that is expressed in epidermal keratinocytes. Nonsense mutations of the SPINK5 gene, which codes for LEKTI, cause Netherton syndrome, which is characterized by hair abnormality, ichthyosis, and atopy. A single nucleotide polymorphism (SNP) of SPINK5, p.K420E, is reported to be associated with the pathogenesis of atopic dermatitis (AD). We studied all 34 exons of the SPINK5 gene in Japanese 57 AD patients and 50 normal healthy controls...
June 2018: Acta Medica Okayama
https://www.readbyqxmd.com/read/29910209/positive-selection-in-f-box-domain-lpp0233-encoded-in-legionella-pneumophila-strains
#3
Takehiko Kenzaka, Madoka Yasui, Takashi Baba, Masao Nasu, Katsuji Tani
 Recent studies have shown that the genome of Legionella pneumophila is characterized by many foreign genes from a variety of eukaryotes. The eukaryotic like proteins are known to play a role in its multiplication within host cells; however, their evolutionary genetics of L. pneumophila in environments is unknown. In this study, we examined the nonsynonymous/synonymous substitution rate of eukaryotic like domain encoding genes among L. pneumophila strains. In silico analysis revealed that the nonsynonymous/synonymous substitution rate in F-box domain gene (lpp0233) was higher than those in other eukaryotic like domain and protein encoding genes and housekeeping genes...
2018: Biocontrol Science
https://www.readbyqxmd.com/read/29909015/is-there-a-mutation-gradient-along-vertebrate-mitochondrial-genome-mediated-by-genome-replication
#4
Xuhua Xia
There is a long-held belief that a mutation gradient exists along vertebrate mtDNA, mediated by mitochondrial replication that leaves different parts of the H-strand exposed in single-stranded state for different durations (DssH ). However, the predicted mutation gradient and its tests suffer from both conceptual and empirical problems. I assembled representative mammalian, avian and crocodilian mtDNA to test this prediction. I measured substitution rates at codon positions 1 and 2 (S12 ) and at codon position 3 (S3 ), as well as synonymous and nonsynonymous substitution rates, and checked their change along the hypothetical gradient...
June 14, 2018: Mitochondrion
https://www.readbyqxmd.com/read/29875816/unintentional-exposure-to-terrestrial-pesticides-drives-widespread-and-predictable-evolution-of-resistance-in-freshwater-crustaceans
#5
Kaley M Major, Donald P Weston, Michael J Lydy, Gary A Wellborn, Helen C Poynton
Pesticide runoff from terrestrial environments into waterways is often lethal to freshwater organisms, but exposure may also drive evolution of pesticide resistance. We analyzed the degree of resistance and molecular genetic changes underlying resistance in Hyalella azteca , a species complex of freshwater crustaceans inadvertently exposed to pesticide pollution via runoff. We surveyed 16 waterways encompassing most major watersheds throughout California and found that land use patterns are predictive of both pyrethroid presence in aquatic sediments and pyrethroid resistance in H...
June 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29842914/genetic-diversity-of-the-human-adenovirus-species-c-dna-polymerase
#6
Linda Feghoul, Séverine Mercier-Delarue, Maud Salmona, Nora Ntsiba, Jean-Hugues Dalle, André Baruchel, Bernard Klonjkowski, Jennifer Richardson, François Simon, Jérôme LeGoff
BACKGROUND: Human Adenovirus (HAdV) are responsible for severe infections in hematopoietic stem cells transplant (HSCT) recipient, species C viruses being the most commonly observed in this population. There is no approved antiviral treatment yet. Cidofovir (CDV), a cytidine analog, is the most frequently used and its lipophilic conjugate, brincidofovir (BCV), is under clinical development. These drugs target the viral DNA polymerase (DNA pol). Little is known about the natural polymorphism of HAdV DNA pol in clinical strains...
May 26, 2018: Antiviral Research
https://www.readbyqxmd.com/read/29739321/comparison-of-the-chinese-bamboo-partridge-and-red-junglefowl-genome-sequences-highlights-the-importance-of-demography-in-genome-evolution
#7
G P Tiley, R T Kimball, E L Braun, J G Burleigh
BACKGROUND: Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29736014/resequencing-of-243-diploid-cotton-accessions-based-on-an-updated-a-genome-identifies-the-genetic-basis-of-key-agronomic-traits
#8
Xiongming Du, Gai Huang, Shoupu He, Zhaoen Yang, Gaofei Sun, Xiongfeng Ma, Nan Li, Xueyan Zhang, Junling Sun, Min Liu, Yinhua Jia, Zhaoe Pan, Wenfang Gong, Zhaohui Liu, Heqin Zhu, Lei Ma, Fuyan Liu, Daigang Yang, Fan Wang, Wei Fan, Qian Gong, Zhen Peng, Liru Wang, Xiaoyang Wang, Shuangjiao Xu, Haihong Shang, Cairui Lu, Hongkun Zheng, Sanwen Huang, Tao Lin, Yuxian Zhu, Fuguang Li
The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243 G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions...
May 7, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29720106/gc-bias-lead-to-increased-small-amino-acids-and-random-coils-of-proteins-in-cold-water-fishes
#9
Dongsheng Zhang, Peng Hu, Taigang Liu, Jian Wang, Shouwen Jiang, Qianghua Xu, Liangbiao Chen
BACKGROUND: Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their biological molecules, which enables their functioning in extreme cold. To study nucleotide and amino acid preference in cold-water fishes, we investigated the substitution asymmetry of codons and amino acids in protein-coding DNA sequences between cold-water fishes and tropical fishes...
May 2, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29702214/comparative-transcriptomics-and-genomic-patterns-of-discordance-in-capsiceae-solanaceae
#10
Daniel Spalink, Kevin Stoffel, Genevieve K Walden, Amanda M Hulse-Kemp, Theresa A Hill, Allen Van Deynze, Lynn Bohs
The integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lycianthes and Capsicum (peppers). In combining the annotated genomes of Capsicum with newly sequenced transcriptomes of four species of Lycianthes and Capsicum, we develop phylogenies for 6747 genes, and construct a backbone species tree using both concordance and explicit phylogenetic network approaches...
September 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29693617/complete-chloroplast-genome-of-cercis-chuniana-fabaceae-with-structural-and-genetic-comparison-to-six-species-in-caesalpinioideae
#11
Wanzhen Liu, Hanghui Kong, Juan Zhou, Peter W Fritsch, Gang Hao, Wei Gong
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana , endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted...
April 25, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29688540/selection-and-neutral-mutations-drive-pervasive-mutability-losses-in-long-lived-anti-hiv-b-cell-lineages
#12
Marcos C Vieira, Daniel Zinder, Sarah Cobey
High-affinity antibodies arise within weeks of infection from the evolution of B-cell receptors under selection to improve antigen recognition. This rapid adaptation is enabled by the distribution of highly mutable "hotspot" motifs in B-cell receptor genes. High mutability in antigen-binding regions (complementarity determining regions [CDRs]) creates variation in binding affinity, whereas low mutability in structurally important regions (framework regions [FRs]) may reduce the frequency of destabilizing mutations...
May 1, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29661449/genetic-mechanisms-involved-in-the-generation-of-hla-alleles-in-brazilians-description-and-comparison-of-hla-alleles
#13
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
#14
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
#15
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-the-dna-mismatch-repair-pathway
#16
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 worldwide and exhibit greater rates of antifungal resistance than those with other species. DNA mismatch repair (MMR) gene deletions, such as msh2Δ , in C. glabrata resulting in a mutator phenotype have recently been reported to facilitate rapid acquisition of antifungal resistance. This study determined the antifungal susceptibility profiles of 210 C. glabrata isolates in 10 hospitals in India and investigated the impact of novel MSH2 polymorphisms on mutation potential...
June 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29574604/evolution-of-melanoma-antigen-a11-magea11-during-primate-phylogeny
#17
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...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29532931/a-novel-chloroplast-gene-reported-for-flagellate-plants
#18
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
#19
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
#20
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...
April 2, 2018: Journal of Clinical Investigation
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