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https://www.readbyqxmd.com/read/28934485/detecting-gene-subnetworks-under-selection-in-biological-pathways
#1
Alexandre Gouy, Joséphine T Daub, Laurent Excoffier
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934377/the-environmental-acinetobacter-baumannii-isolate-dsm30011-reveals-clues-into-the-preantibiotic-era-genome-diversity-virulence-potential-and-niche-range-of-a-predominant-nosocomial-pathogen
#2
Guillermo D Repizo, Alejandro M Viale, Vítor Borges, María M Cameranesi, Najwa Taib, Martín Espariz, Céline Brochier-Armanet, João Paulo Gomes, Suzana P Salcedo
Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28934256/transcriptome-analysis-of-sex-related-genes-in-the-blood-clam-tegillarca-granosa
#3
Heng Chen, Guoqiang Xiao, Xueliang Chai, Xingguan Lin, Jun Fang, Shuangshuang Teng
BACKGROUND: Blood clams (Tegillarca granosa) are one of the most commercial shellfish in China and South Asia with wide distribution in Indo-Pacific tropical to temperate estuaries. However, recent data indicate a decline in the germplasm of this species. Furthermore, the molecular mechanisms underpinning reproductive regulation remain unclear and information regarding genetic diversity is limited. Understanding the reproductive biology of shellfish is important in interpreting their embryology development, reproduction and population structure...
2017: PloS One
https://www.readbyqxmd.com/read/28934237/identification-of-low-overpressure-interval-and-its-implication-to-hydrocarbon-migration-case-study-in-the-yanan-sag-of-the-qiongdongnan-basin-south-china-sea
#4
Qinghai Xu, Wanzhong Shi, Yuhong Xie, Zhenfeng Wang, Xusheng Li, Chuanxin Tong
The Qiongdongnan Basin is a strongly overpressured basin with the maximum pressure coefficient (the ratio of the actual pore pressure versus hydrostatic pressure at the same depth) over 2.27. However, there exists a widespread low-overpressure interval between the strong overpressure intervals in the Yanan Sag of western basin. The mechanisms of the low-overpressure interval are not well understood. Three main approaches, pore pressure test data and well-log analysis, pressure prediction based on the relationship between the deviation of the velocity and the pressure coefficients, and numerical modeling, were employed to illustrate the distribution and evolution of the low-overpressure interval...
2017: PloS One
https://www.readbyqxmd.com/read/28933138/assessment-of-treatment-effects-on-digital-ulcer-and-blood-perfusion-by-laser-speckle-contrast-analysis-in-a-patient-affected-by-systemic-sclerosis
#5
B Ruaro, S Paolino, C Pizzorni, M Cutolo, A Sulli
Laser speckle contrast analysis (LASCA) is a good tool to evaluate the variation in peripheral blood perfusion during long-term follow-up and is able to safely monitor digital ulcer evolution in scleroderma patients. It evaluates blood perfusion in different areas within the skin lesions and surrounding them during standard treatment.
September 21, 2017: Reumatismo
https://www.readbyqxmd.com/read/28933129/-analysis-of-color-regulation-of-fluoritum-in-chinese-pharmacopoeia-based-on-the-coloration-mechanism-of-fluorite
#6
Ting Han, Zhe Jia, Hui Zhang, Huan Liu, Yan Gao, Ying Zhang, Qing-Hua Lin, Shu-Ya Xu, Xin-Fang Xu, Xiang-Ri Li
The fluoritum is used for gynecology frequently and it's for those diseases: kidney yang deficiency, Gong cold sterility, palpitation due to fright, insomnia and dreaminess and cold cough. It's ruled in Chinese Pharmacopoeia (1985 edition) that the fluoritum originates from fluorite which belongs to fluoride minerals. Its main content is CaF2. The colors are of differents grades with purple or green. In the market, there are large differences in quality and it has various colors. Besides of the ruled color of purple and green, white and yellow are also common colors...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932414/hox-gene-cluster-of-the-ascidian-halocynthia-roretzi-reveals-multiple-ancient-steps-of-cluster-disintegration-during-ascidian-evolution
#7
Yuka Sekigami, Takuya Kobayashi, Ai Omi, Koki Nishitsuji, Tetsuro Ikuta, Asao Fujiyama, Noriyuki Satoh, Hidetoshi Saiga
BACKGROUND: Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28932346/insights-from-the-draft-genome-into-the-pathogenicity-of-a-clinical-isolate-of-elizabethkingia-meningoseptica-em3
#8
Shicheng Chen, Marty Soehnlen, Frances P Downes, Edward D Walker
Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28932212/comparative-genomics-of-burkholderia-singularis-sp-nov-a-low-g-c-content-free-living-bacterium-that-defies-taxonomic-dissection-of-the-genus-burkholderia
#9
Peter Vandamme, Charlotte Peeters, Birgit De Smet, Erin P Price, Derek S Sarovich, Deborah A Henry, Trevor J Hird, James E A Zlosnik, Mark Mayo, Jeffrey Warner, Anthony Baker, Bart J Currie, Aurélien Carlier
Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154(T) (=CCUG 65685(T)). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154(T) was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28932209/the-mobilome-a-major-contributor-to-escherichia-coli-stx2-positive-o26-h11-strains-intra-serotype-diversity
#10
Sabine Delannoy, Patricia Mariani-Kurkdjian, Hattie E Webb, Stephane Bonacorsi, Patrick Fach
Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28931954/structure-of-the-solar-photosphere-studied-from-the-radiation-hydrodynamics-code-antares
#11
P Leitner, B Lemmerer, A Hanslmeier, T Zaqarashvili, A Veronig, H Grimm-Strele, H J Muthsam
The ANTARES radiation hydrodynamics code is capable of simulating the solar granulation in detail unequaled by direct observation. We introduce a state-of-the-art numerical tool to the solar physics community and demonstrate its applicability to model the solar granulation. The code is based on the weighted essentially non-oscillatory finite volume method and by its implementation of local mesh refinement is also capable of simulating turbulent fluids. While the ANTARES code already provides promising insights into small-scale dynamical processes occurring in the quiet-Sun photosphere, it will soon be capable of modeling the latter in the scope of radiation magnetohydrodynamics...
2017: Astrophysics and Space Science
https://www.readbyqxmd.com/read/28931879/longitudinal-analysis-of-colon-crypt-stem-cell-dynamics-in-sulindac-treated-familial-adenomatous-polyposis-patients
#12
Huiying Ma, Lodewijk A A Brosens, Sjoerd G Elias, Folkert H M Morsink, Isaac J Nijman, Linda M Hylind, Elizabeth A Montgomery, G Johan A Offerhaus, Francis M Giardiello, Wendy W J de Leng
The non-steroidal anti-inflammatory drug sulindac decreases size and number of adenomas after 4-6 months of treatment for familial adenomatous polyposis (FAP) patients. However, the underlying mechanism remains unknown. As stem cells are thought to be the tumor precursor cells, visualizing their behavior is crucial for monitoring tumor progression. Increased tag diversity in inactive genes is indicative of a protracted clonal evolution and consequently, increased risk for tumor formation. Therefore, the effect of sulindac on stem cell dynamics was studied...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28929282/anoperineal-lesions-in-crohn-s-disease-french-recommendations-for-clinical-practice
#13
REVIEW
D Bouchard, L Abramowitz, G Bouguen, C Brochard, A Dabadie, V de Parades, M Eléouet-Kaplan, N Fathallah, J-L Faucheron, L Maggiori, Y Panis, F Pigot, P Rouméguère, A Sénéjoux, L Siproudhis, G Staumont, J-M Suduca, B Vinson-Bonnet, J-D Zeitoun
BACKGROUND: Anoperineal lesion (APL) occurrence is a significant event in the evolution of Crohn's disease (CD). Management should involve a multidisciplinary approach combining the knowledge of the gastroenterologist, the colorectal surgeon and the radiologist who have appropriate experience in this area. Given the low level of evidence of available medical and surgical strategies, the aim of this work was to establish a French expert consensus on management of anal Crohn's disease. These recommendations were led under the aegis of the Société Nationale Française de Colo-Proctologie (SNFCP)...
September 19, 2017: Techniques in Coloproctology
https://www.readbyqxmd.com/read/28929112/imaging-diagnosis-of-right-ventricle-involvement-in-chagas-cardiomyopathy
#14
REVIEW
Minna M D Romano, Henrique T Moreira, André Schmidt, Benedito Carlos Maciel, José Antônio Marin-Neto
Right ventricle (RV) is considered a neglected chamber in cardiology and knowledge about its role in cardiac function was mostly focused on ventricular interdependence. However, progress on the understanding of myocardium diseases primarily involving the RV led to a better comprehension of its role in health and disease. In Chagas disease (CD), there is direct evidence from both basic and clinical research of profound structural RV abnormalities. However, clinical detection of these abnormalities is hindered by technical limitations of imaging diagnostic tools...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28928936/exploring-differential-evolution-for-inverse-qsar-analysis
#15
Tomoyuki Miyao, Kimito Funatsu, Jürgen Bajorath
Inverse quantitative structure-activity relationship (QSAR) modeling encompasses the generation of compound structures from values of descriptors corresponding to high activity predicted with a given QSAR model. Structure generation proceeds from descriptor coordinates optimized for activity prediction. Herein, we concentrate on the first phase of the inverse QSAR process and introduce a new methodology for coordinate optimization, termed differential evolution (DE), that originated from computer science and engineering...
2017: F1000Research
https://www.readbyqxmd.com/read/28928764/exploring-and-harnessing-haplotype-diversity-to-improve-yield-stability-in-crops
#16
REVIEW
Lunwen Qian, Lee T Hickey, Andreas Stahl, Christian R Werner, Ben Hayes, Rod J Snowdon, Kai P Voss-Fels
In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928723/analysis-of-the-sequences-structures-and-functions-of-product-releasing-enzyme-domains-in-fungal-polyketide-synthases
#17
Lu Liu, Zheng Zhang, Chang-Lun Shao, Chang-Yun Wang
Product-releasing enzyme (PRE) domains in fungal non-reducing polyketide synthases (NR-PKSs) play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I-VIII). It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE), reductase (R), and metallo-β-lactamase-type TE (MβL-TE)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28928424/genome-characterization-of-two-bile-isolated-vibrio-fluvialis-strains-an-insight-into-pathogenicity-and-bile-salt-adaption
#18
Beiwen Zheng, Xiawei Jiang, Hong Cheng, Lihua Guo, Jing Zhang, Hao Xu, Xiao Yu, Chen Huang, Jinru Ji, Chaoqun Ying, Youjun Feng, Yonghong Xiao, Lanjuan Li
Vibrio fluvialis is recognized as an emerging pathogen. However, not much is known about the mechanism of its pathogenesis, and its adaptation to a special niche such as the gall bladder. Here we describe two V. fluvialis strains that cause acute cholecystitis. It is noteworthy that both strains were susceptible to all antibiotics tested, which is in contrast to previous studies, suggesting substantial genetic diversity among V. fluvialis isolates. In agreement with their survival and growth in the gall bladder, the genomes of strains 12605 and 3663 contain a considerable number of genes that confer resistance to bile, including toxR, omp U, tolC, cmeABC, rlpB, yrbK, rpoS, damX and gltK...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928341/the-pursuit-of-healthier-communities-through-a-community-health-medical-education-program
#19
Francisco Lamus-Lemus, Camilo Correal-Muñoz, Erwin Hernandez-Rincon, Natalia Serrano-Espinosa, Clara Jaimes-deTriviño, Diana Diaz-Quijano, Juan Gabriel García-Manrique
BACKGROUND: Distinct periods in the community health undergraduate medical program at the University of La Sabana (Colombia) were identified in its evolution from 1999 to 2013. We describe each period and explain the succesion of changes toward improvement. METHODS: An ordered review of the community health program was constructed based on the retrospective recollection, classification, and analysis of information from document archives and interviews with participants...
May 2017: Education for Health: Change in Training & Practice
https://www.readbyqxmd.com/read/28928209/combining-comprehensive-analysis-of-off-site-lambda-phage-integration-with-a-crispr-based-means-of-characterizing-downstream-physiology
#20
Yu Tanouchi, Markus W Covert
During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance...
September 19, 2017: MBio
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