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https://www.readbyqxmd.com/read/27901429/no-panacea-next-gen-sequencing-will-not-mitigate-adoptees-lack-of-genetic-family-health-history
#1
Stephanie M Fullerton
No abstract text is available yet for this article.
December 2016: American Journal of Bioethics: AJOB
https://www.readbyqxmd.com/read/27785359/pygeno-a-python-package-for-precision-medicine-and-proteogenomics
#2
Tariq Daouda, Claude Perreault, Sébastien Lemieux
pyGeno is a python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of python, a general programming language...
2016: F1000Research
https://www.readbyqxmd.com/read/27745839/structural-chromosomal-rearrangements-require-nucleotide-level-resolution-lessons-from-next-generation-sequencing-in-prenatal-diagnosis
#3
Zehra Ordulu, Tammy Kammin, Harrison Brand, Vamsee Pillalamarri, Claire E Redin, Ryan L Collins, Ian Blumenthal, Carrie Hanscom, Shahrin Pereira, India Bradley, Barbara F Crandall, Pamela Gerrol, Mark A Hayden, Naveed Hussain, Bibi Kanengisser-Pines, Sibel Kantarci, Brynn Levy, Michael J Macera, Fabiola Quintero-Rivera, Erica Spiegel, Blair Stevens, Janet E Ulm, Dorothy Warburton, Louise E Wilkins-Haug, Naomi Yachelevich, James F Gusella, Michael E Talkowski, Cynthia C Morton
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27706155/alignerboost-a-generalized-software-toolkit-for-boosting-next-gen-sequencing-mapping-accuracy-using-a-bayesian-based-mapping-quality-framework
#4
Qi Zheng, Elizabeth A Grice
Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27624755/proposal-of-coetzeea-brasiliensis-gen-nov-sp-nov-isolated-from-larvae-of-anopheles-darlingi
#5
Peter Kämpfer, Stefanie P Glaeser, Osvaldo Marinotti, Lionel Guy, Sebastian Håkansson, Wanderli P Tadei, Hans-Jürgen Busse, Olle Terenius
A Gram-negative, rod-shaped strain, Braz8T, isolated from larvae of Anopheles darlingi was investigated using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene showed that strain Braz8T was closest related to species of the genus Thorsellia with 95.6%, 96.5% and 96.6% 16S rRNA gene sequence similarity to the type strains of T. anophelis, T. kandunguensis, and T. kenyensis, respectively, and formed a separate branch in the phylogenetic tree next to the monophyletic cluster of the genus Thorsellia...
September 12, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27489207/genome-wide-analysis-of-polyadenylation-events-in-schmidtea-mediterranea
#6
Vairavan Lakshmanan, Dhiru Bansal, Jahnavi Kulkarni, Deepak Poduval, Srikar Krishna, Vidyanand Sasidharan, Praveen Anand, Aswin Seshasayee, Dasaradhi Palakodeti
In eukaryotes, 3' untranslated regions (UTRs) play important roles in regulating posttranscriptional gene expression. The 3'UTR is defined by regulated cleavage/polyadenylation of the pre-mRNA. The advent of next-generation sequencing technology has now enabled us to identify these events on a genome-wide scale. In this study, we used poly(A)-position profiling by sequencing (3P-Seq) to capture all poly(A) sites across the genome of the freshwater planarian, Schmidtea mediterranea, an ideal model system for exploring the process of regeneration and stem cell function...
October 13, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27488298/clinical-decision-making-integrating-advances-in-the-molecular-understanding-of-spine-tumors
#7
C Rory Goodwin, Nancy Abu-Bonsrah, Mark H Bilsky, Jeremy J Reynolds, Laurence D Rhines, Ilya Laufer, Alexander C Disch, Arpad Bozsodi, Shreyaskumar R Patel, Ziya L Gokaslan, Daniel M Sciubba, Chetan Bettegowda
STUDY DESIGN: Literature review. OBJECTIVE: To describe advancements in molecular techniques, biomarkers, technology, and targeted therapeutics and the potential these modalities hold to predict treatment paradigms, clinical outcomes, and/or survival in patients diagnosed with primary spinal column tumors. SUMMARY OF BACKGROUND DATA: Advances in molecular technologies and techniques have influenced the prevention, diagnosis, and overall management of patients diagnosed with cancer...
October 15, 2016: Spine
https://www.readbyqxmd.com/read/27470940/herbihabitans-rhizosphaerae-gen-nov-sp-nov-a-member-of-the-family-pseudonocardiaceae-isolated-from-rhizosphere-soil-of-the-herb-limonium-sinense-girard
#8
Chang-Feng Zhang, Meng-Jie Ai, Ju-Xian Wang, Shao-Wei Liu, Li-Li Zhao, Jing Su, Cheng-Hang Sun, Li-Yan Yu, Yu-Qin Zhang
The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides...
October 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27446181/-omics-tools-for-better-understanding-the-plant-endophyte-interactions
#9
REVIEW
Sanjana Kaul, Tanwi Sharma, Manoj K Dhar
Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27390188/tartrate-resistant-acid-phosphatase-deficiency-in-the-predisposition-to-systemic-lupus-erythematosus
#10
Jie An, Tracy A Briggs, Audrey Dumax-Vorzet, Marta E Alarcón-Riquelme, Alexandre Belot, Michael Beresford, Ian N Bruce, Claudia Carvalho, Laurence Chaperot, Johan Frostegård, Joel Plumas, Gillian I Rice, Timothy J Vyse, Alice Wiedeman, Yanick J Crow, Keith B Elkon
OBJECTIVE: Mutations in the ACP5 gene, which encodes tartrate-resistant acid phosphatase (TRAP), cause the immuno-osseous disorder spondyloenchondrodysplasia, which includes as disease features systemic lupus erythematosus (SLE) and a type I interferon (IFN) signature. Our aims were to identify TRAP substrates, determine the consequences of TRAP deficiency in immune cells, and assess whether ACP5 mutations are enriched in sporadic cases of SLE. METHODS: Interaction between TRAP and its binding partners was tested by a yeast 2-hybrid screening, confocal microscopy, and immunoprecipitation/Western blotting...
July 7, 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27388436/next-generation-sequencing-of-an-88-year-old-specimen-of-the-poorly-known-species-liagora-japonica-nemaliales-rhodophyta-supports-the-recognition-of-otohimella-gen-nov
#11
Masahiro Suzuki, Takahiro Segawa, Hiroshi Mori, Ayumi Akiyoshi, Ryo Ootsuki, Akira Kurihara, Hidetoshi Sakayama, Taiju Kitayama, Tsuyoshi Abe, Kazuhiro Kogame, Hiroshi Kawai, Hisayoshi Nozaki
Liagora japonica is a red algal species distributed in temperate regions of Japan. This species has not been collected from its type locality on the Pacific coast of Japan since 1927 and seems to have become extinct in this area. For molecular characterization of L. japonica, we extracted DNA from the topotype material of L. japonica collected in 1927, analyzed seven genes using Illumina next-generation sequencing, and compared these data with sequences from modern samples of similar red algae collected from the Japan Sea coast of Japan...
2016: PloS One
https://www.readbyqxmd.com/read/27376026/editorial-hereditary-cancer-risk-assessment-new-perspectives-and-challenges-for-the-next-gen-sequencing-era
#12
Israel Gomy
No abstract text is available yet for this article.
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27318200/genome-puzzle-master-gpm-an-integrated-pipeline-for-building-and-editing-pseudomolecules-from-fragmented-sequences
#13
Jianwei Zhang, Dave Kudrna, Ting Mu, Weiming Li, Dario Copetti, Yeisoo Yu, Jose Luis Goicoechea, Yang Lei, Rod A Wing
MOTIVATION: Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative data sets (e.g. physical, optical & genetic maps). To address this problem, we developed a semi-automated software tool - Genome Puzzle Master (GPM) - that enables the integration of additional genomic signposts to edit and build "new-gen-assemblies" that result in high-quality "annotation-ready" pseudomolecules...
June 17, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27225403/rapid-drug-susceptibility-testing-of-drug-resistant-mycobacterium-tuberculosis-isolates-directly-from-clinical-samples-by-use-of-amplicon-sequencing-a-proof-of-concept-study
#14
Rebecca E Colman, Julia Anderson, Darrin Lemmer, Erik Lehmkuhl, Sophia B Georghiou, Hannah Heaton, Kristin Wiggins, John D Gillece, James M Schupp, Donald G Catanzaro, Valeriu Crudu, Ted Cohen, Timothy C Rodwell, David M Engelthaler
Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results...
August 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27208355/hiding-in-plain-sight-koshicola-spirodelophila-gen-et-sp-nov-chaetopeltidales-chlorophyceae-a-novel-green-alga-associated-with-the-aquatic-angiosperm-spirodela-polyrhiza
#15
Shin Watanabe, Karolina Fučíková, Louise A Lewis, Paul O Lewis
PREMISE OF THE STUDY: Discovery and morphological characterization of a novel epiphytic aquatic green alga increases our understanding of Chaetopeltidales, a poorly known order in Chlorophyceae. Chloroplast genomic data from this taxon reveals an unusual architecture previously unknown in green algae. METHODS: Using light and electron microscopy, we characterized the morphology and ultrastructure of a novel taxon of green algae. Bayesian phylogenetic analyses of nuclear and plastid genes were used to test the hypothesized membership of this taxon in order Chaetopeltidales...
May 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27170755/complete-unique-genome-sequence-expression-profile-and-salivary-gland-tissue-tropism-of-the-herpesvirus-7-homolog-in-pigtailed-macaques
#16
Jeannette P Staheli, Michael R Dyen, Gail H Deutsch, Ryan S Basom, Matthew P Fitzgibbon, Patrick Lewis, Serge Barcy
UNLABELLED: Human herpesvirus 6A (HHV-6A), HHV-6B, and HHV-7 are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. While the pathogenic potential of HHV-7 is unclear, it can reactivate HHV-6 from latency and thus contributes to severe pathological conditions associated with HHV-6. Because of the ubiquitous nature of roseoloviruses, their roles in such interactions and the resulting pathological consequences have been difficult to study...
August 1, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27109582/transcriptome-analysis-of-genes-responding-to-nnv-infection-in-asian-seabass-epithelial-cells
#17
Peng Liu, Le Wang, Jimmy Kwang, Gen Hua Yue, Sek-Man Wong
Asian seabass is an important food fish in Southeast Asia. Viral nervous necrosis (VNN) disease, triggered by nervous necrosis virus (NNV) infection, has caused mass mortality of Asian seabass larvae, resulting in enormous economic losses in the Asian seabass industry. In order to better understand the complex molecular interaction between Asian seabass and NNV, we investigated the transcriptome profiles of Asian seabass epithelial cells, which play an essential role in immune regulation, after NNV infection...
July 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27066573/genetic-profile-for-suspected-dysferlinopathy-identified-by-targeted-next-generation-sequencing
#18
Rumiko Izumi, Tetsuya Niihori, Toshiaki Takahashi, Naoki Suzuki, Maki Tateyama, Chigusa Watanabe, Kazuma Sugie, Hirotaka Nakanishi, Gen Sobue, Masaaki Kato, Hitoshi Warita, Yoko Aoki, Masashi Aoki
OBJECTIVE: To investigate the genetic causes of suspected dysferlinopathy and to reveal the genetic profile for myopathies with dysferlin deficiency. METHODS: Using next-generation sequencing, we analyzed 42 myopathy-associated genes, including DYSF, in 64 patients who were clinically or pathologically suspected of having dysferlinopathy. Putative pathogenic mutations were confirmed by Sanger sequencing. In addition, copy-number variations in DYSF were investigated using multiplex ligation-dependent probe amplification...
December 2015: Neurology. Genetics
https://www.readbyqxmd.com/read/26965265/ribo-proteomics-approach-to-profile-rna-protein-and-protein-protein-interaction-networks
#19
Hsin-Sung Yeh, Jae-Woong Chang, Jeongsik Yong
Characterizing protein-protein and protein-RNA interaction networks is a fundamental step to understanding the function of an RNA-binding protein. In many cases, these interactions are transient and highly dynamic. Therefore, capturing stable as well as transient interactions in living cells for the identification of protein-binding partners and the mapping of RNA-binding sequences is key to a successful establishment of the molecular interaction network. In this chapter, we will describe a method for capturing the molecular interactions in living cells using formaldehyde as a crosslinker and enriching a specific RNA-protein complex from cell extracts followed by mass spectrometry and Next-Gen sequencing analyses...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26959814/mevalonate-farnesal-biosynthesis-in-ticks-comparative-synganglion-transcriptomics-and-a-new-perspective
#20
COMPARATIVE STUDY
Jiwei Zhu, Sayed M Khalil, Robert D Mitchell, Brooke W Bissinger, Noble Egekwu, Daniel E Sonenshine, R Michael Roe
Juvenile hormone (JH) controls the growth, development, metamorphosis, and reproduction of insects. For many years, the general assumption has been that JH regulates tick and other acarine development and reproduction the same as in insects. Although researchers have not been able to find the common insect JHs in hard and soft tick species and JH applications appear to have no effect on tick development, it is difficult to prove the negative or to determine whether precursors to JH are made in ticks. The tick synganglion contains regions which are homologous to the corpora allata, the biosynthetic source for JH in insects...
2016: PloS One
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