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https://www.readbyqxmd.com/read/29458158/toll-like-receptor-tlr-9-promotor-polymorphisms-and-gene-expression-are-associated-with-persistent-staphylococcus-aureus-nasal-carriage
#1
Dennis Nurjadi, Klaus Heeg, Alexander N R Weber, Philipp Zanger
OBJECTIVES: Toll-like receptor (TLR) -9 could have importance in human S. aureus immunity, but population level evidence for this hypothesis is missing. METHODS: We phenotyped 603 volunteers for S. aureus nasal carriage using four consecutive swabs, genotyped TLR9 promotor variants in 106 persistent carriers and 219 non-carriers, measured TLR9-mRNA expression in whole blood after stimulation with viable S. aureus, and studied mutual associations of carriage, transcriptional activity, and single nucleotide polymorphisms while accounting for sex and hormonal contraceptive use (HCU+/- )...
February 16, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29455315/mitogenomes-of-two-neotropical-bird-species-and-the-multiple-independent-origin-of-mitochondrial-gene-orders-in-passeriformes
#2
Renato Caparroz, Amanda V Rocha, Gustavo S Cabanne, Pablo Tubaro, Alexandre Aleixo, Emily M Lemmon, Alan R Lemmon
At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined...
February 17, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29455143/the-birth-and-death-of-effectors-in-rapidly-evolving-filamentous-pathogen-genomes
#3
REVIEW
Simone Fouché, Clémence Plissonneau, Daniel Croll
Plant pathogenic fungi and oomycetes are major risks to food security due to their evolutionary success in overcoming plant defences. Pathogens produce effectors to interfere with host defences and metabolism. These effectors are often encoded in rapidly evolving compartments of the genome. We review how effector genes emerged and were lost in pathogen genomes drawing on the links between effector evolution and chromosomal rearrangements. Some new effectors entered pathogen genomes via horizontal transfer or introgression...
February 15, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29454308/the-unique-evolutionary-pattern-of-the-hydroxyproline-rich-glycoproteins-superfamily-in-chinese-white-pear-pyrus-bretschneideri
#4
Huijun Jiao, Xing Liu, Shuguang Sun, Peng Wang, Xin Qiao, Jiaming Li, Chao Tang, Juyou Wu, Shaoling Zhang, Shutian Tao
BACKGROUND: The hydroxyproline-rich glycoprotein (HRGP) superfamily, comprising three families (arabinogalactan-proteins, AGPs; extensins, EXTs; proline-rich proteins, PRPs), is a class of proline-rich proteins that exhibit high diversity and are involved in many aspects of plant biology. RESULTS: In this study, 838 HRGPs were identified from Chinese white pear (Pyrus bretschneideri) by searching for biased amino acid composition and conserved motifs. 405 HRGPs were derived from whole genome duplication (WGD) events which is suggested to be the major force of driving HRGPs expansion and the recent WGD event shared by apple and pear generated most duplicated HRGPs in pear...
February 17, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29453999/evolutionary-and-expression-analyses-reveal-a-pattern-of-ancient-duplications-and-functional-specializations-in-the-diversification-of-the-downstream-of-kinase-dok-genes
#5
Geoffrey Guittard, Pierre Pontarotti, Samuel Granjeaud, Magda Rodrigues, Laurent Abi-Rached, Jacques A Nunès
Downstream of Kinase (DOK) proteins represent a multigenic family of adaptors that includes negative regulators of immune cell signaling. Using phylogenetics and intron/exon structure data, we show here that the seven human DOK genes (DOK1 to DOK7) form three highly divergent groups that emerged before the protostome-deuterostome split: DOK1/2/3, DOK4/5/6, and DOK7. For two of these three groups (DOK1/2/3 and DOK4/5/6), further gene duplications occurred in vertebrates and so while chordates only have three DOK genes, vertebrates have seven DOK genes over the three groups...
February 14, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29452566/near-tetraploid-cancer-cells-show-chromosome-instability-triggered-by-replication-stress-and-exhibit-enhanced-invasiveness
#6
Darawalee Wangsa, Isabel Quintanilla, Keyvan Torabi, Maria Vila-Casadesús, Amaia Ercilla, Gregory Klus, Zeynep Yuce, Claudia Galofré, Miriam Cuatrecasas, Juan José Lozano, Neus Agell, Daniela Cimini, Antoni Castells, Thomas Ried, Jordi Camps
A considerable proportion of tumors exhibit aneuploid karyotypes, likely resulting from the progressive loss of chromosomes after whole-genome duplication. Here, by using isogenic diploid and near-tetraploid (4N) single-cell-derived clones from the same parental cell lines, we aimed at exploring how polyploidization affects cellular functions and how tetraploidy generates chromosome instability. Gene expression profiling in 4N clones revealed a significant enrichment of transcripts involved in cell cycle and DNA replication...
February 8, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29449854/genome-wide-characterization-of-bhlh-genes-in-grape-and-analysis-of-their-potential-relevance-to-abiotic-stress-tolerance-and-secondary-metabolite-biosynthesis
#7
Pengfei Wang, Ling Su, Huanhuan Gao, Xilong Jiang, Xinying Wu, Yi Li, Qianqian Zhang, Yongmei Wang, Fengshan Ren
Basic helix-loop-helix (bHLH) transcription factors are involved in many abiotic stress responses as well as flavonol and anthocyanin biosynthesis. In grapes ( Vitis vinifera L.), flavonols including anthocyanins and condensed tannins are most abundant in the skins of the berries. Flavonols are important phytochemicals for viticulture and enology, but grape bHLH genes have rarely been examined. We identified 94 grape bHLH genes in a genome-wide analysis and performed Nr and GO function analyses for these genes...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29448158/despacito-the-slow-evolutionary-changes-in-plant-micrornas
#8
REVIEW
Patricia Baldrich, Aleksandra Beric, Blake C Meyers
MicroRNAs (miRNAs) are key regulators of gene expression. A handful of miRNAs are broadly conserved in land plants, while the majority are lineage specific; this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution...
February 12, 2018: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29445421/evidence-for-a-pre-malignant-cell-line-in-a-skin-biopsy-from-a-patient-with-nijmegen-breakage-syndrome
#9
Raneem Habib, Heidemarie Neitzel, Aurelie Ernst, John K L Wong, Bozenna Goryluk-Kozakiewicz, Antje Gerlach, Ilja Demuth, Karl Sperling, Krystyna Chrzanowska
Background: Nijmegen breakage syndrome is an autosomal recessive disorder characterized by microcephaly, immunodeficiency, hypersensitivity to X-irradiation, and a high predisposition to cancer. Nibrin, the product of the NBN gene, is part of the MRE11/RAD50 (MRN) complex that is involved in the repair of DNA double strand breaks (DSBs), and plays a critical role in the processing of DSBs in immune gene rearrangements, telomere maintenance, and meiotic recombination. NBS skin fibroblasts grow slowly in culture and enter early into senescence...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29445326/structure-function-studies-of-the-%C3%AE-4-subunit-reveal-evolutionary-loss-of-a-glyr-subtype-involved-in-startle-and-escape-responses
#10
Sophie Leacock, Parnayan Syed, Victoria M James, Anna Bode, Koichi Kawakami, Angelo Keramidas, Maximiliano Suster, Joseph W Lynch, Robert J Harvey
Inhibitory glycine receptors (GlyRs) are pentameric ligand-gated anion channels with major roles in startle disease/hyperekplexia (GlyR α1), cortical neuronal migration/autism spectrum disorder (GlyR α2), and inflammatory pain sensitization/rhythmic breathing (GlyR α3). However, the role of the GlyR α4 subunit has remained enigmatic, because the corresponding human gene ( GLRA4 ) is thought to be a pseudogene due to an in-frame stop codon at position 390 within the fourth membrane-spanning domain (M4). Despite this, a recent genetic study has implicated GLRA4 in intellectual disability, behavioral problems and craniofacial anomalies...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29445025/strong-conservation-of-inbred-mouse-strain-microrna-loci-but-broad-variation-in-brain-micrornas-due-to-rna-editing-and-isomir-expression
#11
Kalevi Trontti, Juho Väänänen, Tessa Sipilä, Dario Greco, Iiris Hovatta
Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by 1) identifying miRNA SNPs in whole genome sequence data from 36 strains, and 2) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of 6 strains, to facilitate the study of miRNAs in neurobehavioral phenotypes...
February 14, 2018: RNA
https://www.readbyqxmd.com/read/29445022/whole-genome-duplication-and-transposable-element-proliferation-drive-genome-expansion-in-corydoradinae-catfishes
#12
Sarah Marburger, Markos A Alexandrou, John B Taggart, Simon Creer, Gary Carvalho, Claudio Oliveira, Martin I Taylor
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size-0...
February 14, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29444111/genome-wide-identification-and-role-of-mkk-and-mpk-gene-families-in-clubroot-resistance-of-brassica-rapa
#13
Yinglan Piao, Kaining Jin, Ying He, Jiaxiu Liu, Shuang Liu, Xiaonan Li, Zhongyun Piao
Mitogen-activated protein kinase (MAPK or MPK) cascades play key roles in responses to various biotic stresses, as well as in plant growth and development. However, the responses of MPK and MPK kinase (MKK) in Chinese cabbage (Brassica rapa ssp. pekinensis) to Plasmodiophora brassicae, a causal agent of clubroot disease in Brassica crops, are still not clear. In the present study, a total of 11 B. rapa MKK (BraMKK) and 30 BraMPK genes were identified and unevenly distributed in 6 and 10 chromosomes, respectively...
2018: PloS One
https://www.readbyqxmd.com/read/29444109/population-structure-of-the-npgs-senegalese-sorghum-collection-and-its-evaluation-to-identify-new-disease-resistant-genes
#14
Hugo E Cuevas, Louis K Prom, Giseiry Rosa-Valentin
Sorghum germplasm from West and Central Africa is cultivated in rainy and high humidity regions and is an important source of resistance genes to fungal diseases. Mold and anthracnose are two important biotic constraints to sorghum production in wet areas worldwide. Here, 158 National Plant Germplasm System (NPGS) accessions from Senegal were evaluated for agronomic traits, anthracnose, and grain mold resistance at two locations, and genetically characterized according to 20 simple sequence repeat markers. A total of 221 alleles were amplified with an average of 11 alleles per locus...
2018: PloS One
https://www.readbyqxmd.com/read/29442321/zic-genes-in-teleosts-their-roles-in-dorsoventral-patterning-in-the-somite
#15
Kota Abe, Toru Kawanishi, Hiroyuki Takeda
The medaka contains seven zic genes, two of which, zic1 and zic4, have been studied extensively. The analyses are mainly based on the double anal fin (Da) mutant, which was isolated from the wild. Da is an enhancer mutant of zic1/zic4, and the expression of zic1/zic4 is specifically lost in the dorsal half of the somites, which leads to a mirror-image duplication of the ventral half across the lateral midline from larva to adult. The studies of medaka Da give us important insights into the function of zic1/zic4 in mesodermal tissues and also the mechanism of dorsoventral patterning in the vertebrate trunk region occurring during late development, which is a long-standing mystery in developmental biology...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29442314/comparative-genomics-of-the-zic-family-genes
#16
Jun Aruga, Minoru Hatayama
Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29441698/familial-aortic-disease-and-a-large-duplication-in-chromosome-16p13-1
#17
Philipp Erhart, Tobias Brandt, Beate K Straub, Ingrid Hausser, Sabine Hentze, Dittmar Böckler, Caspar Grond-Ginsbach
BACKGROUND AND PURPOSE: A recurrent duplication of chromosome 16p13.1 was associated with aortic dissection as well as with cervical artery dissection. We explore the segregation of this duplication in a family with familial aortic disease. METHODS: Whole exome sequencing (WES) analysis was performed in a patient with a family history of aortic diseases and ischemic stroke due to an aortic dissection extending into both carotid arteries. RESULTS: The index patient, his affected father, and an affected sister of his father carried a large duplication of region 16p13...
February 14, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29440283/evolution-of-neuropeptide-signalling-systems
#18
REVIEW
Maurice R Elphick, Olivier Mirabeau, Dan Larhammar
Neuropeptides are a diverse class of neuronal signalling molecules that regulate physiological processes and behaviour in animals. However, determining the relationships and evolutionary origins of the heterogeneous assemblage of neuropeptides identified in a range of phyla has presented a huge challenge for comparative physiologists. Here, we review revolutionary insights into the evolution of neuropeptide signalling that have been obtained recently through comparative analysis of genome/transcriptome sequence data and by 'deorphanisation' of neuropeptide receptors...
February 9, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29439348/evolvability-of-amyloidogenic-proteins-in-human-brain
#19
Makoto Hashimoto, Gilbert Ho, Shuei Sugama, Yoshiki Takamatsu, Yuka Shimizu, Takato Takenouchi, Masaaki Waragai, Eliezer Masliah
 Currently, the physiological roles of amyloidogenic proteins (APs) in human brain, such as amyloid-β and α-synuclein, are elusive. Given that many APs arose by gene duplication and have been resistant against the pressures of natural selection, APs may be associated with some functions that are advantageous for survival of offspring. Nonetheless, evolvability is the sole physiological quality of APs that has been characterized in microorganisms such as yeast. Since yeast and human brain may share similar strategies in coping with diverse range of critical environmental stresses, the objective of this paper was to discuss the potential role of evolvability of APs in aging-associated neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease...
2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29438956/the-long-and-short-of-doubling-down-polyploidy-epigenetics-and-the-temporal-dynamics-of-genome-fractionation
#20
REVIEW
Jonathan F Wendel, Damon Lisch, Guanjing Hu, Annaliese S Mason
We consider the rapidly advancing discipline of plant evolutionary genomics, with a focus on the evolution of polyploid genomes. In many lineages, polyploidy is followed by 'biased fractionation', the unequal loss of genes from ancestral progenitor genomes. Mechanistically, it has been proposed that biased fractionation results from changes in the epigenetic landscape near genes, likely mediated by transposable elements. These epigenetic changes result in unequal gene expression between duplicates, establishing differential fitness that leads to biased gene loss with respect to ancestral genomes...
February 10, 2018: Current Opinion in Genetics & Development
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