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https://www.readbyqxmd.com/read/29677478/unfinished-business-evolution-of-the-mhc-and-the-adaptive-immune-system-of-jawed-vertebrates
#1
Jim Kaufman
The major histocompatibility complex (MHC) is a large genetic region with many genes, including the highly polymorphic classical class I and II genes that play crucial roles in adaptive as well as innate immune responses. The organization of the MHC varies enormously among jawed vertebrates, but class I and II genes have not been found in other animals. How did the MHC arise, and are there underlying principles that can help us to understand the evolution of the MHC? This review considers what it means to be an MHC and the potential importance of genome-wide duplication, gene linkage, and gene coevolution for the emergence and evolution of an adaptive immune system...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29675811/systematic-analysis-and-comparison-of-the-phd-finger-gene-family-in-chinese-pear-pyrus-bretschneideri-and-its-role-in-fruit-development
#2
Yunpeng Cao, Yahui Han, Dandan Meng, Muhammad Abdullah, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes...
April 20, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29675612/complement-receptor-1-gene-cr1-intragenic-duplication-and-risk-of-alzheimer-s-disease
#3
Ezgi Kucukkilic, Keeley Brookes, Imelda Barber, Tamar Guetta-Baranes, Kevin Morgan, Edward J Hollox
Single nucleotide variants (SNVs) within and surrounding the complement receptor 1 (CR1) gene show some of the strongest genome-wide association signals with late-onset Alzheimer's disease. Some studies have suggested that this association signal is due to a duplication allele (CR1-B) of a low copy repeat (LCR) within the CR1 gene, which increases the number of complement C3b/C4b-binding sites in the mature receptor. In this study, we develop a triplex paralogue ratio test assay for CR1 LCR copy number allowing large numbers of samples to be typed with a limited amount of DNA...
April 19, 2018: Human Genetics
https://www.readbyqxmd.com/read/29674453/multiple-large-scale-gene-and-genome-duplications-during-the-evolution-of-hexapods
#4
Zheng Li, George P Tiley, Sally R Galuska, Chris R Reardon, Thomas I Kidder, Rebecca J Rundell, Michael S Barker
Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals...
April 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29674435/phylogenetic-and-phylogenomic-definition-of-rhizopus-species
#5
Andrii P Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M Anishchenko, Kerstin Voigt, G Sybren de Hoog, Matthew E Smith, Joseph Heitman, Rytas Vilgalys, Jason E Stajich
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R...
April 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29673984/bioinformatics-analysis-and-epitope-screening-of-a-potential-vaccine-antigen-tolb-from-acinetobacter-baumannii-outer-membrane-protein
#6
Xiaojie Song, Hua Zhang, Dongsheng Zhang, Weifeng Xie, Guanghui Zhao
The clinical isolation rate of multidrug-resistant or pan-resistant Acinetobacter baumannii (A. baumannii) is increasing, resulting that optional antibiotics are very limited in clinical practice. To deal with such a dilemma in treatment, the development of effective vaccines serves as a good strategy. Outer membrane proteins (Omp) often contain potential excellent vaccine antigens, and NCBI has published >300 Omp sequences of A. baumannii (including the duplicates). To accurately screen out the potential excellent antigen molecules from a large number of sequences, and avoid repetitive experimental processes is of great significance...
April 16, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29673731/duplication-of-sox9-associated-with-46-xx-ovotesticular-disorder-of-sex-development
#7
Berenice López-Hernández, Juan Pablo Méndez, Ramón Mauricio Coral-Vázquez, Jesús Benítez-Granados, Juan Carlos Zenteno, Vanessa Villegas-Ruiz, Raúl Calzada-León, Daniela Soderlund, Patricia Canto
RESEARCH QUESTION: The purpose of the present study was to investigate whether ten unrelated SRY-negative individuals with this sex differentiation disorder presented a double dose of SOX9 as the cause of their disease. DESIGN: Ten unrelated SRY-negative 46,XX ovotesticular disorder of sexual development (DSD) subjects were molecularly studied. Multiplex-ligation dependent probe amplification (MLPA) and quantitative real-time PCR analysis (qRT-PCR) for SOX9 were performed...
April 4, 2018: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/29673170/cysteine-proteinase-c1a-paralog-profiles-correspond-with-phylogenetic-lineages-of-pathogenic-piroplasmids
#8
Mariano E Ascencio, Monica Florin-Christensen, Choukri B Mamoun, William Weir, Brian Shiels, Leonhard Schnittger
Piroplasmid parasites comprising of Babesia , Theileria , and Cytauxzoon are transmitted by ticks to farm and pet animals and have a significant impact on livestock industries and animal health in tropical and subtropical regions worldwide. In addition, diverse Babesia spp. infect humans as opportunistic hosts. Molecular phylogeny has demonstrated at least six piroplasmid lineages exemplified by B. microti , B. duncani , C. felis , T. equi , Theileria sensu stricto ( T. annulata , T. parva , and T. orientalis ) and Babesia sensu stricto ( B...
April 17, 2018: Veterinary Sciences
https://www.readbyqxmd.com/read/29672665/evolutionary-and-functional-potential-of-ploidy-increase-within-individual-plants-somatic-ploidy-mapping-of-the-complex-labellum-of-sexually-deceptive-bee-orchids
#9
Richard M Bateman, Jessica J Guy, Paula J Rudall, Ilia J Leitch, Jaume Pellicer, Andrew R Leitch
Background and Aims: Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function. Methods: We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination...
April 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29670636/positive-selection-driving-cytoplasmic-genome-evolution-of-the-medicinally-important-ginseng-plant-genus-panax
#10
Peng Jiang, Feng-Xue Shi, Ming-Rui Li, Bao Liu, Jun Wen, Hong-Xing Xiao, Lin-Feng Li
Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29669830/evolution-guided-structural-and-functional-analyses-of-the-herc-family-reveals-an-ancient-marine-origin-and-determinants-of-antiviral-activity
#11
Ermela Paparisto, Matthew W Woods, Macon D Coleman, Seyed A Moghadasi, Divjyot S Kochar, Sean K Tom, Hinissan P Kohio, Richard M Gibson, Taryn J Rohringer, Nina R Hunt, Eric J Di Gravio, Jonathan Y Zhang, Meijuan Tian, Yong Gao, Eric J Arts, Stephen D Barr
In humans, 'homologous to the E6-AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing protein 5' (HERC5) is an interferon-induced protein that inhibits replication of evolutionarily diverse viruses including human immunodeficiency virus type 1 (HIV-1). To better understand the origin, evolution and function of HERC5, we performed phylogenetic, structural and functional analyses of the entire human small HERC family, which includes HERC3, HERC4, HERC5 and HERC6...
April 18, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29669130/distinct-patterns-of-selection-in-selenium-dependent-genes-between-land-and-aquatic-vertebrates
#12
Gaurab K Sarangi, Frédéric Romagné, Sergi Castellano
Selenium (Se), a sparse element on earth, is an essential micronutrient in the vertebrate diet and its intake depends on its content in soils and waters worldwide. Selenium is required due to its function in selenoproteins, which contain selenocysteine (Sec), the 21st amino acid in the genetic code, as one of their constituent residues. Selenocysteine is analogous to the amino acid cysteine (Cys), which uses the abounding element sulfur instead. Despite the irregular distribution of Se worldwide, its distinct biochemical properties have made the substitution of Sec for Cys rare in vertebrate proteins...
April 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29668722/a-family-of-long-intergenic-non-coding-rna-genes-in-human-chromosomal-region-22q11-2-carry-a-dna-translocation-breakpoint-at-rich-sequence
#13
Nicholas Delihas
FAM230C, a long intergenic non-coding RNA (lincRNA) gene in human chromosome 13 (chr13) is a member of lincRNA genes termed family with sequence similarity 230. An analysis using bioinformatics search tools and alignment programs was undertaken to determine properties of FAM230C and its related genes. Results reveal that the DNA translocation element, the Translocation Breakpoint Type A (TBTA) sequence, which consists of satellite DNA, Alu elements, and AT-rich sequences is embedded in the FAM230C gene. Eight lincRNA genes related to FAM230C also carry the TBTA sequences...
2018: PloS One
https://www.readbyqxmd.com/read/29667925/massive-over-representation-of-solute-binding-proteins-sbps-from-the-tripartite-tricarboxylate-transporter-ttt-family-in-the-genome-of-the-%C3%AE-proteobacterium-rhodoplanes-sp-z2-yc6860
#14
Leonardo T Rosa, Vicki Springthorpe, Matheus E Bianconi, Gavin H Thomas, David J Kelly
Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower...
April 18, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29666611/genome-sequence-assembly-and-characterization-of-two-metschnikowia-fructicola-strains-used-as-biocontrol-agents-of-postharvest-diseases
#15
Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, Maria L Gullino, Marc W Allard, Elena Levin, Davide Spadaro, Samir Droby
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29666342/unusual-structure-and-splicing-pattern-of-the-vertebrate-mitochondrial-solute-carrier-slc25a3-gene
#16
Rosa Calvello, Antonia Cianciulli, Maria A Panaro
The DNA sequence corresponding to the second exon of the SLC25A3 gene is duplicated in vertebrates. The second exon codes for the first transmembrane segment and parts of the immediately adjoining intermembrane and mitochondrial matrix segments. The two genomic exon 2 sequences are 84% similar in zebrafish (slc25a3b gene), 70% in chicken, 66% in mouse and 67% in human. The amino acid identity is 86% in zebrafish, 77% in chicken and 70% in mouse and human. The two copies of exon 2 are separated by an intronic interval...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666331/isolation-and-characterization-of-the-major-histocompatibility-complex-dqa1-and-dqa2-genes-in-gayal-bos-frontalis
#17
Sameeullah Memon, Liping Wang, Guozhi Li, Xiangying Liu, Weidong Deng, Dongmei Xi
The species origin of Yunnan gayal has been controversial since many years. However, few recent genetic studies have suggested that it has perhaps originated from the hybridization between male Bos frontalis and female B. taurus or B. indicus. Being an important semi-wild bovid species, this has also been listed under the red list of International Union of Conservation of Nature and Natural Resources. However, there is limited information available about the immunogenicity of this precarious species of Bos...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666322/genetic-control-of-yellow-vein-mosaic-virus-disease-tolerance-in-abelmoschus-esculentus-l-moench
#18
Pushparani Senjam, Bijoy Kumar Senapati, Arup Chattopadhyay, Subrata Dutta
Okra's (Abelmoschus esculentus (L.) Moench) commercial cultivation is threatened in the tropics due to high incidence of yellow vein mosaic virus (YVMV) disease. Okra geneticists across the world tried to understand the inheritance pattern of YVMV disease tolerance without much success. Therefore, the inheritance pattern of YVMV disease in okra was revisited by employing sixgenerations (P₁, P₂, F₁, F₂, BC₁ and BC₂) of four selected crosses (one tolerant × tolerant, two tolerant × susceptible and one susceptible × susceptible) using two tolerant (BCO-1 and Lal Bhendi) and two susceptible (Japanese Jhar Bhendi and PAN 2127) genotypes...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666269/worldwide-distribution-of-the-dcdc2-read1-regulatory-element-and-its-relationship-with-phoneme-variation-across-languages
#19
Mellissa M C DeMille, Kevin Tang, Chintan M Mehta, Christopher Geissler, Jeffrey G Malins, Natalie R Powers, Beatrice M Bowen, Andrew K Adams, Dongnhu T Truong, Jan C Frijters, Jeffrey R Gruen
DCDC2 is a gene strongly associated with components of the phonological processing system in animal models and in multiple independent studies of populations and languages. We propose that it may also influence population-level variation in language component usage. To test this hypothesis, we investigated the evolution and worldwide distribution of the READ1 regulatory element within DCDC2 , and compared its distribution with variation in different language properties. The mutational history of READ1 was estimated by examining primate and archaic hominin sequences...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29665898/-clinical-characteristics-and-prognosis-of-acute-myeloid-leukemia-with-flt3-itd-mutation
#20
Yan Liu, Xiao-Yan Ke, Jing Wang, Ji-Jun Wang, Hong-Mei Jing, Fei Dong
OBJECTIVE: To investigate the clinical characteristics of acute myeloid leukemia(AML) patients with FLT3-ITD(Fms-like tyrosine kinase3, intenal tandem duplication) mutation and their response to treatment. METHODS: Retrospective analysis of 128 newly diagnosed AML (except type M3) patients was performed between January 2014 and July 2017. Patients were divided into FLT3-ITD mutated group and non-mutated group. Mutation detection was carried out by using polymerase chain reaction(PCR) and gene sequencing analysis...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
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