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https://www.readbyqxmd.com/read/28732357/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#1
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732175/genome-wide-identification-functional-prediction-and-evolutionary-analysis-of-r2r3-myb-superfamily-in-brassica-napus
#2
Ali Hajiebrahimi, Hajar Owji, Shiva Hemmati
R2R3-MYBs are important transcription factors (TFs) in planta, involved in development and various stress conditions. Phylogenetic analysis showed the presence of 249 R2R3-MYB TFs in Brassica napus called BnaR2R3-MYBs, clustered into 38 clades. BnaR2R3-MYBs were distributed on 19 chromosomes of B. napus. Sixteen gene clusters were identified. BnaR2R3-MYBs were characterized by motif prediction, gene structure analysis and gene ontology. Evolutionary analysis revealed that BnaR2R3-MYBs are mainly formed as a result of whole genome duplication...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28731826/convergently-evolved-toxic-secondary-metabolites-in-plants-drive-the-parallel-molecular-evolution-of-insect-resistance
#3
Georg Petschenka, Vera Wagschal, Michael von Tschirnhaus, Alexander Donath, Susanne Dobler
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae)...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#4
Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K Lowe, C Titus Brown, Billie J Swalla, Lionel Christiaen, Alberto Stolfi, Filomena Ristoratore
BACKGROUND: Analyzing close species with diverse developmental modes is instrumental for investigating the evolutionary significance of physiological, anatomical and behavioral features at a molecular level. Many examples of trait loss are known in metazoan populations living in dark environments. Tunicates are the closest living relatives of vertebrates and typically present a lifecycle with distinct motile larval and sessile adult stages. The nervous system of the motile larva contains melanized cells associated with geotactic and light-sensing organs...
2017: EvoDevo
https://www.readbyqxmd.com/read/28729868/the-c4-model-grass-setaria-is-a-short-day-plant-with-secondary-long-day-genetic-regulation
#5
Andrew N Doust, Margarita Mauro-Herrera, John G Hodge, Jessica Stromski
The effect of photoperiod (day:night ratio) on flowering time was investigated in the wild species, Setaria viridis, and in a set of recombinant inbred lines (RILs) derived from a cross between foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis). Photoperiods totaled 24 h, with three trials of 8:16, 12:12 and 16:8 light:dark hour regimes for the RIL population, and these plus 10:14 and 14:10 for the experiments with S. viridis alone. The response of S. viridis to light intensity as well as photoperiod was assessed by duplicating photoperiods at two light intensities (300 and 600 μmol...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729204/characterization-of-clinical-isolates-oxacillin-susceptible-meca-positive-staphylococcus-aureus-os-mrsa-in-china-from-2009-2014
#6
Yunjia Song, Lanqing Cui, Yuan Lv, Yun Li, Feng Xue
OBJECTIVE: The study aimed to investigate the prevalence and molecular characteristics of clinical oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) isolates in China from July 2009 to June 2014. METHODS: A total of 2,068 non-duplicated Staphylococcus aureus isolates were collected from 21 hospitals and the susceptibility test were performed by agar dilution method. All the OS-MRSA strains were screened for the presence of the mecA, mecC and nuc gene as well as Panton-Valentine leucocidin gene(PVL)...
July 17, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28728564/comparison-of-the-protein-coding-genomes-of-three-deep-sea-sulfur-oxidising-bacteria-candidatus-ruthia-magnifica-candidatus-vesicomyosocius-okutanii-and-thiomicrospira-crunogena
#7
Susan E McGill, Daniel Barker
OBJECTIVE: " Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, "Candidatus R. magnifica" and "Candidatus V. okutanii", may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities...
July 20, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28728153/genetic-variants-of-cytochrome-cyp2d6-in-two-mixed-chilean-populations
#8
Mónica Acuña, Eric Pinto, Paulina Olivares, Carolina Ríos
OBJECTIVES: It is known that the interindividual and interethnic variability of the genetic polymorphisms of CYP2D6 plays an important role in the presentation of adverse drug reactions and concerning lack of therapeutic effects in humans. However, there are few data available from mixed populations of Latin America, including the Chilean. The aim of this study was therefore to estimate the frequencies of CYP2D6 variants in two samples of hospitals from the northern (Hospital San José, HSJ) and eastern (Clínica Las Condes, CLC) parts of Santiago, Chile, with different degrees of Amerindian admixture (HSJ: 34...
July 21, 2017: Human Heredity
https://www.readbyqxmd.com/read/28727761/genome-wide-identification-of-the-potato-wrky-transcription-factor-family
#9
Chao Zhang, Dongdong Wang, Chenghui Yang, Nana Kong, Zheng Shi, Peng Zhao, Yunyou Nan, Tengkun Nie, Ruoqiu Wang, Haoli Ma, Qin Chen
WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes...
2017: PloS One
https://www.readbyqxmd.com/read/28727266/next-generation-sequencing-of-cytologic-preparations-an-analysis-of-quality-metrics
#10
David H Hwang, Elizabeth P Garcia, Matthew D Ducar, Edmund S Cibas, Lynette M Sholl
BACKGROUND: Next-generation sequencing (NGS) fails for many small biopsies (BXs) because of a low overall DNA concentration or tumor percentage. Cytology smears and liquid-based preparations (LBPs), or smears/LBPs, often contain abundant tumor cells and may provide adequate material for molecular testing when other materials are insufficient. This study examined the performance of smears/LBPs on a clinical NGS assay. METHODS: This study retrospectively reviewed quality metrics from consecutive smear/LBP, core BX, and cell block (CB) cases run on a hybrid-capture NGS assay interrogating 309 cancer-related genes...
July 20, 2017: Cancer
https://www.readbyqxmd.com/read/28724605/heterozygous-loss-of-function-mutation-in-odd-skipped-related-1-osr1-is-associated-with-vesico-ureteric-reflux-duplex-systems-and-hydronephrosis
#11
Marie-Lyne Fillion, Jasmine El Andalousi, Fatima Tokhmafshan, Vasikar Murugapoopathy, Christine L Watt, Inga J Murawski, John-Paul Capolicchio, Mohamed El-Sherbiny, Roman Jednak, Indra Rani Gupta
Osr1 is a transcriptional repressor that plays critical roles in maintaining the mesenchymal stem cell population within the developing kidney. Here, we report that newborn pups with a heterozygous null mutation in Osr1 exhibit a 21% incidence of vesico-ureteric reflux and have hydronephrosis and urinary tract duplications. Newborn pups have a short intravesical ureter resulting in a less competent uretero-vesical junction which arises from a delay in urinary tract development. We describe a new domain of Osr1 expression in the ureteral mesenchyme and within the developing bladder in the mouse...
July 19, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28722801/primary-familial-brain-calcification-with-a-novel-slc20a2-mutation-analysis-of-pit-2-expression-and-localization
#12
Ilaria Taglia, Patrizia Formichi, Carla Battisti, Giulia Peppoloni, Melissa Barghigiani, Alessandra Tessa, Antonio Federico
Primary Familial Brain Calcification (PFBC) is an autosomal dominant rare disorder characterized by bilateral and symmetric brain calcifications and neuropsychiatric manifestations. Four genes have been linked to PFBC: SLC20A2, PDGFRB, PDGFB and XPR1. In this study, we report molecular and clinical data of a PFBC patient carrying a novel SLC20A2 mutation and we investigate the impact of the mutation on PiT-2 expression and function. Sanger sequencing of SLC20A2, PDGFRB, PDGFB, XPR1 led to the identification of a novel duplication of twelve nucleotides (c...
July 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28720579/recruitment-of-histone-modifications-to-assist-mrna-dosage-maintenance-after-degeneration-of-cytosine-dna-methylation-during-animal-evolution
#13
Andrew Yf Chang, Ben-Yang Liao
Following gene duplication, mRNA expression of the duplicated gene is reduced to maintain mRNA dosage. In mammals, this process is achieved with increased cytosine DNA methylation of the promoters of duplicated genes to suppress transcriptional initiation. However, not all animal species possess a full apparatus for cytosine DNA methylation. For such species such as roundworm (Caenorhabditis elegans, "worm" hereafter) or fruit fly (Drosophila melanogaster, "fly" hereafter), it is unclear how reduced expression of duplicated genes has been achieved evolutionarily...
July 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28720553/response-to-growth-hormone-treatment-in-a-patient-with-insulin-like-growth-factor-1-receptor-igf1r-deletion
#14
Ranim Mahmoud, Ajanta Naidu, Hiba Risheg, Virginia Kimonis
We report a six year-old boy who presented with short stature, microcephaly, dysmorphic features and developmental delay, who was identified with a terminal deletion of 15q26.2q26.3 containing the insulin like growth factor receptor (IGF1R) gene, in addition to a terminal duplication of the 4q35.1q35.2 region. We compare our case with other reports of deletions and mutations affecting the IGF1R gene associated with pre-and postnatal growth restriction. We report the dramatic response to growth hormone therapy in this patient which highlights the importance of identifying patients with IGF1R deletion and treating them early...
July 17, 2017: Journal of Clinical Research in Pediatric Endocrinology
https://www.readbyqxmd.com/read/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#15
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717047/annotated-draft-genome-assemblies-for-the-northern-bobwhite-colinus-virginianus-and-the-scaled-quail-callipepla-squamata-reveal-disparate-estimates-of-modern-genome-diversity-and-historic-effective-population-size
#16
David L Oldeschulte, Yvette A Halley, Miranda L Wilson, Eric K Bhattarai, Wesley Brashear, Joshua Hill, Richard P Metz, Charles D Johnson, Dale Rollins, Markus J Peterson, Derek M Bickhart, Jared E Decker, John F Sewell, Christopher M Seabury
Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their U.S. ranges. Illumina-based first- (v1.0) and second-generation (v2.0) draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 Mb and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥ 90% of the assembled genomes were captured within 1,313 and 8,990 scaffolds, respectively...
July 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28715335/evolutionary-model-for-the-statistical-divergence-of-paralogous-and-orthologous-gene-pairs-generated-by-whole-genome-duplication-and-speciation
#17
Yue Zhang, Chunfang Zheng, David Sankoff
We outline a principled approach to the analysis of duplicate gene similarity distributions, based on a model integrating sequence divergence and the process of fractionation of duplicate genes resulting from whole genome duplication (WGD). This model allows us predict duplicate gene similarity distributions for series of two or three WGD, for whole genome triplication followed by a WGD, and for triplication, followed by speciation, followed by WGD. We calculate the probabilities of all possible fates of a gene pair as its two members proliferate or are lost, predicting the number of surviving pairs from each event...
July 14, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28714247/-molecular-cytogenetics-to-characterize-mechanisms-of-gene-duplication-in-pesticide-resistance
#18
REVIEW
Mithila Jugulam, Bikram S Gill
Recent advances in molecular cytogenetics empower construction of physical maps to illustrate the precise position of genetic loci on the chromosomes. Such maps provide visible information about the position of DNA sequences, including the distribution of repetitive sequences on the chromosomes. This will be an important step forward toward unraveling the genetic mechanisms implicated in chromosomal aberrations (e.g., gene duplication). In response to stress, such as pesticide selection, the duplicated genes provide an immediate adaptive advantage to organisms that overcome unfavorable conditions...
July 17, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28713421/analyses-of-genomic-trna-reveal-presence-of-novel-trnas-in-oryza-sativa
#19
Tapan K Mohanta, Hanhong Bae
Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNA(Ser) found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713414/divergent-evolutionary-patterns-of-nac-transcription-factors-are-associated-with-diversification-and-gene-duplications-in-angiosperm
#20
Xiaoli Jin, Jing Ren, Eviatar Nevo, Xuegui Yin, Dongfa Sun, Junhua Peng
NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages...
2017: Frontiers in Plant Science
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