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https://www.readbyqxmd.com/read/29222702/molecular-insights-into-the-non-recombining-nature-of-the-spinach-male-determining-region
#1
Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe, Atsushi Toyoda, Hideki Hirakawa, Yutaka Suzuki, Nobuko Ohmido, Yasuyuki Onodera
Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars...
December 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29222504/rnastructuromedb-a-genome-wide-database-for-rna-structural-inference
#2
Ryan J Andrews, Levi Baber, Walter N Moss
RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database ( https://structurome.bb.iastate.edu ), a comprehensive repository of RNA secondary structural information that spans the entire human genome...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29212206/line-1-methylation-in-peripheral-blood-leukocytes-and-clinical-characteristics-and-prognosis-of-prostate-cancer-patients
#3
Yuyan Han, Junfeng Xu, Jeri Kim, Xifeng Wu, Jian Gu
Global DNA methylation of long interspersed nucleotide elements (LINE-1) in leukocytes has been suggested to be a risk factor for a few cancers. There has been no report of LINE-1 methylation in leukocytes as a risk factor for aggressive prostate cancer at diagnosis and prognosis after treatments. In this study, we measured the leukocyte DNA methylation of LINE-1 in 795 PCa patients and compared the methylation levels across different clinical subgroups. We then determined the association of LINE-1 methylation in leukocytes with clinicopathological variables at diagnosis using logistic regression analysis and biochemical recurrence in patients receiving active treatments (prostatectomy and radiotherapy) using Cox proportional hazard model after adjusting for age, BMI, smoking status, pack year, D'Amico risk groups, and treatments...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29211049/living-organisms-author-their-read-write-genomes-in-evolution
#4
REVIEW
James A Shapiro
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life...
December 6, 2017: Biology
https://www.readbyqxmd.com/read/29209748/monitoring-cytochrome-p450-activity-in-living-hepatocytes-by-chromogenic-substrates-in-response-to-drug-treatment-or-during-cell-maturation
#5
Jannick Theobald, Xinlai Cheng, Ali Ghanem, Haristi Gaitantzi, Guangqi Song, Edda Klipp, Judith Wodke, Holger Becker, Ralf Mrowka, Katja Breitkopf-Heinlein, Steven Dooley, Stefan Wölfl
The metabolic activity of hepatocytes is a central prerequisite for drug activity and a key element in drug-drug interaction. This central role in metabolism largely depends on the activity of the cytochrome P450 (CYP450) enzyme family, which is not only dependent on liver cell maturation but is also controlled in response to drug and chemical exposure. Here, we report the use of VividDye fluorogenic CYP450 substrates to directly measure and continuously monitor metabolic activity in living hepatocytes. We observed time- and dose-dependent correlation in response to established and putative CYP450 inducers acting through the aryl hydrocarbon receptor and drug combinations...
December 5, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/29209557/line-1-in-response-to-exposure-to-ionizing-radiation
#6
COMMENT
Igor Koturbash
It is becoming increasingly recognized that Long Interspersed Nuclear Element, 1 (LINE-1), the most ubiquitous repetitive element in the mammalian genomes, plays an important role in the pathogenesis of disease and in the response to exposure to environmental stressors. Ionizing radiation is a known genotoxic stressor, but it is capable of targeting the cellular epigenome as well. Radiation-induced alterations in LINE-1 DNA methylation are the most frequently observed epigenetic effects of exposure. The extent of this aberrant DNA methylation, however, strongly depends on a number of factors, including the type and dose of radiation...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/29202418/prenatal-urinary-polycyclic-aromatic-hydrocarbon-metabolites-global-dna-methylation-in-cord-blood-and-birth-outcomes-a-cohort-study-in-china
#7
Pan Yang, Ya-Jie Gong, Wen-Cheng Cao, Rui-Xin Wang, Yi-Xin Wang, Chong Liu, Ying-Jun Chen, Li-Li Huang, Song-Hua Ai, Wen-Qing Lu, Qiang Zeng
BACKGROUND: Prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) is a potential risk factor for adverse birth outcomes. Epigenetic mechanisms may play a key role in which PAHs exert its effects. OBJECTIVE: Our study aimed to examine whether prenatal PAH exposure was associated with adverse birth outcomes and altered DNA methylation and to explore potential mediating roles of DNA methylation. METHODS: Ten urinary PAH metabolites were measured from 106 pregnant women during late pregnancy in a Chinese cohort study...
December 1, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29198400/osteochondritis-dissecans-of-skeletal-elements-of-the-foot-in-a-19th-century-rural-farming-community-from-the-netherlands
#8
Irene Vikatou, Menno L P Hoogland, Andrea L Waters-Rist
Osteochondritis Dissecans (OD) is a pathological condition of the subchondral bone and surrounding cartilage of synovial joints, associated with strenuous activity and/or trauma. Reports of OD in archaeological skeletal remains are few and the majority demonstrate low OD prevalence (<1%). A predominantly 19th century skeletal sample from Middenbeemster, the Netherlands, was assessed for OD. The sample included adult individuals of both sexes. There were no definitive OD lesions in non-pedal elements, yet 12...
December 2017: International Journal of Paleopathology
https://www.readbyqxmd.com/read/29194997/piecing-together-cis-regulatory-networks-insights-from-epigenomics-studies-in-plants
#9
REVIEW
Shao-Shan Huang, Joseph Ecker
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell...
November 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29173213/evaluation-of-reference-genes-for-reverse-transcription-quantitative-pcr-assays-in-organs-of-zebrafish-exposed-to-glyphosate-based-herbicide-roundup
#10
M L Jaramillo, A G Pereira, C E Davico, L Nezzi, D Ammar, Y M R Müller, E M Nazari
Roundup is a glyphosate-based herbicide (GBH) widely used in agriculture and may cause toxic effects in non-target organisms. Model organisms, as zebrafish, and analysis of gene expression by reverse transcription-quantitative PCR (RT-qPCR) could be used to better understand the Roundup toxicity. A prerequisite for RT-qPCR is the availability of appropriate reference genes; however, they have not been described for Roundup-exposed fish. The aim of this study was to evaluate the expression stability of six reference genes (rpl8, β-act, gapdh, b2m, ef1α, hprt1) and one expressed repetitive element (hatn10) in organs of males (brain, gill, testis) and females (ovary) of zebrafish exposed to Roundup WG at three concentrations (0...
November 27, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29166857/genome-analysis-of-the-foxtail-millet-pathogen-sclerospora-graminicola-reveals-the-complex-effector-repertoire-of-graminicolous-downy-mildews
#11
Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
BACKGROUND: Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches' broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S...
November 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29164044/characterization-of-clostridium-difficile-strains-isolated-from-patients-with-c-difficile-associated-disease-in-korea
#12
Seung-Hak Cho, Jung-Whan Chon, Kun-Ho Seo, Young Kwon Kim, Jung-Beom Kim, Young-Seok Bak, Woon-Won Jung, Cheorl-Ho Kim, Jong Tae Choi
Objectives: Studies on Clostridium difficile are rare in Korea. We investigated the epidemiological characteristics of C. difficile isolates from patients with C. difficile-associated disease (CDAD) in Korea. Methods: Multiplex polymerase chain reaction was performed to detect the presence of tcdA and tcdB toxin genes. Antimicrobial susceptibility test was carried out by the disk-dilution method. C. difficile strains were subtyped by automated repetitive-element palindromic PCR (rep-PCR)...
October 2017: Osong Public Health and Research Perspectives
https://www.readbyqxmd.com/read/29153322/bats-use-path-integration-rather-than-acoustic-flow-to-assess-flight-distance-along-flyways
#13
Gal Aharon, Meshi Sadot, Yossi Yovel
Navigation can be achieved using different strategies from simple beaconing to complex map-based movement [1-4]. Bats display remarkable navigation capabilities, ranging from nightly commutes of several kilometers and up to seasonal migrations over thousands of kilometers [5]. Many bats have been suggested to fly along fixed routes termed "flyways," when flying from their roost to their foraging sites [6]. Flyways commonly stretch along linear landscape elements such as tree lines, hedges, or rivers [7]. When flying along a flyway, bats must estimate the distance they have traveled in order to determine when to turn...
November 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29149170/vibrio-parahaemolyticus-vtra-is-a-membrane-bound-regulator-and-is-activated-via-oligomerization
#14
Ryu Okada, Shigeaki Matsuda, Tetsuya Iida
Vibrio parahaemolyticus is a Gram-negative pathogen that causes food-borne gastroenteritis. A major virulence determinant of the organism is a type III secretion system (T3SS2) encoded on a pathogenicity island, Vp-PAI. Vp-PAI gene expression is regulated by two transcriptional regulators, VtrA and VtrB, whose N-terminal regions share homology with an OmpR-family DNA-binding domain. VtrA activates the gene expression of VtrB, which in turn activates Vp-PAI gene expression; however, the mechanism of this transcriptional activation by VtrA is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/29148768/the-cyanopivaloyl-ester-in-the-automated-solid-phase-synthesis-of-oligorhamnans
#15
Anne Geert Volbeda, Jeanine van Mechelen, Nico Meeuwenoord, Herman S Overkleeft, Gijsbert A van der Marel, Jeroen D C Codée
The development of effective protecting group chemistry is an important driving force behind the progress in the synthesis of complex oligosaccharides. Automated solid phase oligosaccharide synthesis is an attractive technique for the rapid assembly of oligosaccharides build up of repetitive elements. The fact that (harsh) reagents are used in excess in multiple reaction cycles make this technique extra demanding on the protecting groups used. Here, the synthesis of a set of oligorhamnan fragments is reported using the cyanopivaloyl (PivCN) ester, to ensure effective neighboring group participation during the glycosylation events...
November 17, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29145975/in-cancer-a-to-i-rna-editing-can-be-the-driver-the-passenger-or-the-mechanic
#16
Nabeel S Ganem, Noa Ben-Asher, Ayelet T Lamm
In recent years, A-to-I RNA modifications performed by the Adenosine Deaminase Acting on RNA (ADAR) protein family were found to be expressed at altered levels in multiple human malignancies. A-to-I RNA editing changes adenosine to inosine on double stranded RNA, thereby changing transcript sequence and structure. Although A-to-I RNA editing have the potential to change essential mRNA transcripts, affecting their corresponding protein structures, most of the human editing sites identified to date reside in non-coding repetitive transcripts such as Alu elements...
May 2017: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/29145825/assembling-large-genomes-analysis-of-the-stick-insect-clitarchus-hookeri-genome-reveals-a-high-repeat-content-and-sex-biased-genes-associated-with-reproduction
#17
Chen Wu, Victoria G Twort, Ross N Crowhurst, Richard D Newcomb, Thomas R Buckley
BACKGROUND: Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145801/comparative-genomics-of-coniophora-olivacea-reveals-different-patterns-of-genome-expansion-in-boletales
#18
Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V Grigoriev, Antonio G Pisabarro, Lucía Ramírez
BACKGROUND: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. RESULTS: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143604/fine-organization-of-genomic-regions-tagged-to-the-5s-rdna-locus-of-the-bread-wheat-5b-chromosome
#19
Ekaterina M Sergeeva, Andrey B Shcherban, Irina G Adonina, Michail A Nesterov, Alexey V Beletsky, Andrey L Rakitin, Andrey V Mardanov, Nikolai V Ravin, Elena A Salina
BACKGROUND: The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29138611/volunteer-patients-and-small-groups-contribute-to-abdominal-examination-s-success
#20
Helen M Shields, Nielsen Q Fernandez-Becker, Sarah N Flier, Byron P Vaughn, Melissa H Tukey, Stephen R Pelletier, Douglas A Horst
Background: Prior to 2007, we taught the abdominal examination in a hospital based group to 40 students, at one hospital. We used volunteer patients, small groups, repetition, and required faculty development sessions. In 2007, our medical school changed its "Introduction to Physical Examination" session so that the entire class was to be taught in a geographically central session. Our hospital was selected to lead the abdominal examination portion of the session. Aim: Our aim was to answer three questions...
2017: Advances in Medical Education and Practice
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