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https://www.readbyqxmd.com/read/29786908/opposing-patterns-of-intraspecific-and-interspecific-differentiation-in-sex-chromosomes-and-autosomes
#1
Peter A Moran, Sonia Pascoal, Timothee Cezard, Judith E Risse, Michael G Ritchie, Nathan W Bailey
Linking intraspecific and interspecific divergence is an important challenge in speciation research. X chromosomes are expected to evolve faster than autosomes and disproportionately contribute to reproductive barriers, and comparing genetic variation on X and autosomal markers within and between species can elucidate evolutionary processes that shape genome variation. We performed RADseq on a 16-population transect of two closely-related Australian cricket species, Teleogryllus commodus and T. oceanicus, covering allopatry and sympatry...
May 22, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29786815/role-of-circulating-micrornas-in-acute-appendicitis
#2
Avni Uygar Seyhan, Elif Funda Şener, Oğuzhan Bol, Serpil Taheri, Tugba Topaloglu, Esra Tufan, Reyhan Tahtasakal, Nahide Ekici Günay, Hatice Karabulut, Nurullah Günay
BACKGROUND: Acute appendicitis (AA) is a momentous, emergency, surgical pathology that has still been investigated for both etiopathogenetic unknowns and challenges in diagnosis. Presently, there is little information about the role of microRNAs (miRNAs), which have basic biological functions in the cell, can be a marker, and are associated with various pathologies, in patients with AA. The aim of this study was to investigate the expressions of some miRNAs in AA. METHODS: Overall, 41 miRNAs were screened in 48 individuals comprising 24 patients with AA and 24 healthy controls at Erciyes University Genome and Stem Cell Center (GENKOK)...
May 2018: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29786699/the-draft-genome-sequence-of-cork-oak
#3
António Marcos Ramos, Ana Usié, Pedro Barbosa, Pedro M Barros, Tiago Capote, Inês Chaves, Fernanda Simões, Isabl Abreu, Isabel Carrasquinho, Carlos Faro, Joana B Guimarães, Diogo Mendonça, Filomena Nóbrega, Leandra Rodrigues, Nelson J M Saibo, Maria Carolina Varela, Conceição Egas, José Matos, Célia M Miguel, M Margarida Oliveira, Cândido P Ricardo, Sónia Gonçalves
Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size...
May 22, 2018: Scientific Data
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#4
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29785946/-crispr-cas-systems-in-genome-engineering-of-bacteriophages
#5
Cai Jiao Liang, Fan Mei Meng, Yun Can Ai
Researches on CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) systems, that are adaptive immunity systems encoded by prokaryotes, have promoted the development of new genome-editing tools. Bacteriophages are not only the driving elements for the evolution of prokaryotes' CRISPR arrays, but also the targets of the CRISPR/Cas systems. Studies on functional genomics of bacteriophages have been lagging behind the discovery of new phage strains and the sequencing of their genomes...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29785944/-overview-of-the-genetic-control-of-horse-coat-color-patterns
#6
Ruo Yang Zhao, Yi Ping Zhao, Bei Li, Gerelchimeg Bou, Xin Zhuang Zhang, Togtokh Mongke, Tugeqin Bao, Shurenchimeg Gereliin, Tsimbai Gereltuuin, Chao Li, Dong Yi Bai, Mang Lai Dugarjaviin
Mammalian coat color is one of the first phenotypic changes resulting from positive selection by humans, and it serves important roles in genetic and evolutionary processes. Among them, horses show a broad variety of coat color patterns, based on which it is difficult to distinguish the real phenotypes, resulting in confused records in horse breed registration. Thus, research in the genetic mechanisms on the development of coat color patterns is significant in horse reproduction and breeding. With the recent establishment of genomics and sequencing technologies, there are significant advances in research in the genetics of horse coat colors, which demonstrate that special coat colors could be associated with certain diseases...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29785615/molecular-characterization-of-proton-beam-induced-mutations-in-soybean-using-genotyping-by-sequencing
#7
Woon Ji Kim, Jaihyunk Ryu, Juhyun Im, Sang Hun Kim, Si-Yong Kang, Jeong-Hee Lee, Sung-Hwan Jo, Bo-Keun Ha
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS)...
May 21, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29785409/-de-novo-genome-and-transcriptome-resources-of-the-adzuki-bean-borer-ostrinia-scapulalis-lepidoptera-crambidae
#8
B Gschloessl, F Dorkeld, P Audiot, A Bretaudeau, C Kerdelhué, R Streiff
We present a draft genome assembly with a de novo prediction and automated functional annotation of coding genes, and a reference transcriptome of the Adzuki bean borer, Ostrinia scapulalis , based on RNA sequencing of various tissues and developmental stages. The genome assembly spans 419 Mb, has a GC content of 37.4% and includes 26,120 predicted coding genes. The reference transcriptome holds 33,080 unigenes and contains a high proportion of a set of genes conserved in eukaryotes and arthropods, used as quality assessment of the reconstructed transcripts...
April 2018: Data in Brief
https://www.readbyqxmd.com/read/29785398/marker-assisted-introgression-of-saltol-qtl-enhances-seedling-stage-salt-tolerance-in-the-rice-variety-pusa-basmati-1
#9
Vivek Kumar Singh, Brahma Deo Singh, Amit Kumar, Sadhna Maurya, Subbaiyan Gopala Krishnan, Kunnummal Kurungara Vinod, Madan Pal Singh, Ranjith Kumar Ellur, Prolay Kumar Bhowmick, Ashok Kumar Singh
Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol . A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29785177/characterization-of-new-microsatellite-markers-based-on-the-transcriptome-sequencing-of-clematis-finetiana
#10
Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye, Yongbao Shen
Background: Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the "Queen of the Vines". However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C...
2018: Hereditas
https://www.readbyqxmd.com/read/29784926/clinical-utility-of-circulating-non-coding-rnas-an-update
#11
REVIEW
Simone Anfossi, Anna Babayan, Klaus Pantel, George A Calin
Over the past decade, the amount of research and the number of publications on associations between circulating small and long non-coding RNAs (ncRNAs) and cancer have grown exponentially. Particular focus has been placed on the development of diagnostic and prognostic biomarkers to enable efficient patient management - from early detection of cancer to monitoring for disease recurrence or progression after treatment. Owing to their high abundance and stability, circulating ncRNAs have potential utility as non-invasive, blood-based biomarkers that can provide information on tumour biology and the effects of treatments, such as targeted therapies and immunotherapies...
May 21, 2018: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/29784861/genome-variation-and-molecular-epidemiology-of-salmonella-typhimurium-pathovariants
#12
Priscilla Branchu, Matt Bawn, Robert A Kingsley
Salmonella enterica serovar Typhimurium ( S Typhimurium) is one of approximately 2500 distinct serovars of the genus Salmonella , but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of non-typhoid Salmonella (NTS) infections, accounting for a quarter of infections, second only to S Enteritidis in incidence. S Typhimurium was once considered the archetypal broad host range Salmonella serovar due to its wide distribution in livestock and wild animals and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, ATCC14028)...
May 21, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29784672/genetic-screening-and-multipotency-in-rhesus-monkey-haploid-neural-progenitor-cells
#13
Haisong Wang, Wenhao Zhang, Jian Yu, Congyu Wu, Qian Gao, Xu Li, Yanni Li, Jinxin Zhang, Yaru Tian, Tao Tan, Weizhi Ji, Luyuan Li, Yang Yu, Ling Shuai
Haploid embryonic stem cells (haESCs) have been extensively applied in forward and reverse genetic screening. However, the mammalian haploid somatic cell line is difficult to achieve because of spontaneous diploidization in differentiation. As a non-human primate species, monkeys are widely used in basic and pre-clinical research in which haploid cells are restricted to ESCs. Here, we report that rhesus monkey haESCs in an optimized culture medium showed naïve-state pluripotency and stable haploidy. This model facilitated the derivation of haploid neural progenitor cells (haNPCs), which maintained haploidy and differentiation potential into neurons and glia for a long period in vitro High-throughput trapping mutations can be efficiently introduced into haNPCs via piggyBac transposons...
May 21, 2018: Development
https://www.readbyqxmd.com/read/29784537/artificial-intelligence-a-joint-narrative-on-potential-use-in-pediatric-stem-and-immune-cell-therapies-and-regenerative-medicine
#14
REVIEW
Irena Sniecinski, Jerard Seghatchian
Artificial Intelligence (AI) reflects the intelligence exhibited by machines and software. It is a highly desirable academic field of many current fields of studies. Leading AI researchers describe the field as "the study and design of intelligent agents". McCarthy invented this term in 1955 and defined it as "the science and engineering of making intelligent machines". The central goals of AI research are reasoning, knowledge, planning, learning, natural language processing (communication), perception and the ability to move and manipulate objects...
May 9, 2018: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/29782705/wild-gwas-association-mapping-in-natural-populations
#15
Anna W Santure, Dany Garant
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such 'gene mapping' studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment...
May 21, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29782620/genomic-big-data-hitting-the-storage-bottleneck
#16
Louis Papageorgiou, Picasi Eleni, Sofia Raftopoulou, Meropi Mantaiou, Vasileios Megalooikonomou, Dimitrios Vlachakis
During the last decades, there is a vast data explosion in bioinformatics. Big data centres are trying to face this data crisis, reaching high storage capacity levels. Although several scientific giants examine how to handle the enormous pile of information in their cupboards, the problem remains unsolved. On a daily basis, there is a massive quantity of permanent loss of extensive information due to infrastructure and storage space problems. The motivation for sequencing has fallen behind. Sometimes, the time that is spent to solve storage space problems is longer than the one dedicated to collect and analyse data...
2018: EMBnet.journal
https://www.readbyqxmd.com/read/29782159/reduced-zebrafish-transcriptome-atlas-toward-understanding-the-environmental-neurotoxicants
#17
Kun Zhang, Yanbin Zhao
Transcriptomic approaches monitoring gene responses at genome-scale are increasingly used in toxicological research and help to clarify the molecular mechanisms of adverse effects caused by environmental toxicants. However, their applications for chemical assessment are hampered due to high expenses required and more importantly the lack of in-depth data mining and mechanistic perspectives. Here, we described a Reduced Transcriptome Atlas (RTA) approach which integrates transcriptomic datasets and a comprehensive panel of genes generated to represent neurogenesis and the early neuronal development of zebrafish, to determine the potential neurodevelopmental toxicities of environmental chemicals...
May 21, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29782003/collection-and-extraction-of-occupational-air-samples-for-analysis-of-fungal-dna
#18
Angela R Lemons, William G Lindsley, Brett J Green
Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several limitations that have resulted in the exclusion of many species. Advances in the field over the last two decades have led occupational health researchers to turn to molecular-based approaches for identifying fungal hazards. These methods have resulted in the detection of many species within indoor and occupational environments that have not been detected using traditional methods...
May 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781996/replication-of-the-ordered-nonredundant-library-of-pseudomonas-aeruginosa-strain-pa14-transposon-insertion-mutants
#19
Eliana Drenkard, Rhianna M Hibbler, D Alina Gutu, Alexander D Eaton, Amy L Silverio, Frederick M Ausubel, Bryan P Hurley, Lael M Yonker
Pseudomonas aeruginosa is a phenotypically and genotypically diverse and adaptable Gram-negative bacterium ubiquitous in human environments. P. aeruginosa is able to form biofilms, develop antibiotic resistance, produce virulence factors, and rapidly evolve in the course of a chronic infection. Thus P. aeruginosa can cause both acute and chronic, difficult to treat infections, resulting in significant morbidity in certain patient populations. P. aeruginosa strain PA14 is a human clinical isolate with a conserved genome structure that infects a variety of mammalian and nonvertebrate hosts making PA14 an attractive strain for studying this pathogen...
May 4, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781033/microarray-analysis-of-circular-rna-expression-profiles-associated-with-gemcitabine-resistance-in-pancreatic-cancer-cells
#20
Chao Xu, Yue Yu, Fei Ding
Pancreatic cancer (PC) is one of the most malignant tumors of the digestive system due to its rapid progression, metastasis and resistance to chemotherapy. Gemcitabine (GEM) chemotherapy is the first‑choice treatment for advanced PC. However, the effect of GEM‑based chemotherapy on PC is limited due to the development of chemoresistance, and the molecular mechanisms underlying this resistance have yet to be investigated. Circular RNAs (circRNAs), which can function as microRNA sponges, have been found to be involved in the development of several types of cancer...
May 17, 2018: Oncology Reports
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