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https://www.readbyqxmd.com/read/29775563/anolis-carolinensis-as-a-model-to-understand-molecular-and-cellular-basis-of-foveal-development
#1
Naif S Sannan, Xianghong Shan, Kevin Gregory-Evans, Kenro Kusumi, Cheryl Y Gregory-Evans
The fovea is an anatomical specialization of the central retina containing closely packed cone-photoreceptors providing an area of high acuity vision in humans and primates. Despite its key role in the clarity of vision, little is known about the molecular and cellular basis of foveal development, due to the absence of a foveal structure in commonly used laboratory animal models. Of the amniotes the retina in birds of prey and some reptiles do exhibit a typical foveal structure, but they have not been studied in the context of foveal development due to lack of availability of embryonic tissue, lack of captive breeding programs, and limited genomic information...
May 15, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29773674/deep-sequencing-of-complex-proteoglycans-a-novel-strategy-for-high-coverage-and-site-specific-identification-of-glycosaminoglycan-linked-peptides
#2
Joshua A Klein, Le Meng, Joseph Zaia
Proteoglycans are distributed in all animal tissues and play critical, multifaceted, physiological roles.  Expressed in a spatially- and temporally-regulated manner, these molecules regulate interactions among growth factors and cell surface receptors and play key roles in basement membranes and other extracellular matrices.  Due to the high degree of glycosylation by glycosaminoglycan (GAG), N-glycan and mucin-type O-glycan classes, the peptide sequence coverage of complex proteoglycans is revealed poorly by standard mass spectrometry-based proteomics methods...
May 17, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29767357/a-guide-for-designing-and-analyzing-rna-seq-data
#3
Aniruddha Chatterjee, Antonio Ahn, Euan J Rodger, Peter A Stockwell, Michael R Eccles
The identity of a cell or an organism is at least in part defined by its gene expression and therefore analyzing gene expression remains one of the most frequently performed experimental techniques in molecular biology. The development of the RNA-Sequencing (RNA-Seq) method allows an unprecedented opportunity to analyze expression of protein-coding, noncoding RNA and also de novo transcript assembly of a new species or organism. However, the planning and design of RNA-Seq experiments has important implications for addressing the desired biological question and maximizing the value of the data obtained...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765282/next-generation-sequencing-approach-for-the-diagnosis-of-human-diseases-open-challenges-and-new-opportunities
#4
Chiara Di Resta, Silvia Galbiati, Paola Carrera, Maurizio Ferrari
The rapid evolution and widespread use of next generation sequencing (NGS) in clinical laboratories has allowed an incredible progress in the genetic diagnostics of several inherited disorders. However, the new technologies have brought new challenges. In this review we consider the important issue of NGS data analysis, as well as the interpretation of unknown genetic variants and the management of the incidental findings. Moreover, we focus the attention on the new professional figure of bioinformatics and the new role of medical geneticists in clinical management of patients...
April 2018: EJIFCC
https://www.readbyqxmd.com/read/29752561/searching-whole-genome-sequences-for-biochemical-identification-features-of-emerging-and-reemerging-pathogenic-corynebacterium-species
#5
André S Santos, Rommel T Ramos, Artur Silva, Raphael Hirata, Ana L Mattos-Guaraldi, Roberto Meyer, Vasco Azevedo, Liza Felicori, Luis G C Pacheco
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis...
May 11, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29746690/retrospective-analysis-reproducibility-of-interblastomere-differences-of-mrna-expression-in-2-cell-stage-mouse-embryos-is-remarkably-poor-due-to-combinatorial-mechanisms-of-blastomere-diversification
#6
E Casser, S Israel, S Schlatt, V Nordhoff, M Boiani
STUDY QUESTION: What is the prevalence, reproducibility and biological significance of transcriptomic differences between sister blastomeres of the mouse 2-cell embryo? SUMMARY ANSWER: Sister 2-cell stage blastomeres are distinguishable from each other by mRNA analysis, attesting to the fact that differentiation starts mostly early in the mouse embryo; however, the interblastomere differences are poorly reproducible and invoke the combinatorial effects of known and new mechanisms of blastomere diversification...
May 9, 2018: Molecular Human Reproduction
https://www.readbyqxmd.com/read/29746620/grouper-graph-based-clustering-and-annotation-for-improved-de-novo-transcriptome-analysis
#7
Laraib Malik, Fatemeh Almodaresi, Rob Patro
Motivation: De novo transcriptome analysis using RNA-seq offers a promising means to study gene expression in non-model organisms. Yet, the difficulty of transcriptome assembly means that the contigs provided by the assembler often represent a fractured and incomplete view of the transcriptome, complicating downstream analysis. We introduce Grouper, a new method for clustering contigs from de novo assemblies that are likely to belong to the same transcripts and genes; these groups can subsequently be analyzed more robustly...
May 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29739334/exploring-gene-expression-biomarker-candidates-for-neurobehavioral-impairment-from-total-sleep-deprivation
#8
Hilary A Uyhelji, Doris M Kupfer, Vicky L White, Melinda L Jackson, Hans P A Van Dongen, Dennis M Burian
BACKGROUND: Although sleep deprivation is associated with neurobehavioral impairment that may underlie significant risks to performance and safety, there is no reliable biomarker test to detect dangerous levels of impairment from sleep loss in humans. This study employs microarrays and bioinformatics analyses to explore candidate gene expression biomarkers associated with total sleep deprivation (TSD), and more specifically, the phenotype of neurobehavioral impairment from TSD. Healthy adult volunteers were recruited to a sleep laboratory for seven consecutive days (six nights)...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29737976/uniform-resolution-of-compact-identifiers-for-biomedical-data
#9
Sarala M Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A McMurry, Niall Beard, Rafael Jimenez, Jeffrey S Grethe, Henning Hermjakob, Maryann E Martone, Tim Clark
Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such "compact identifiers" have been widely used in biomedical informatics to support global resource identification with local identifier assignment...
May 8, 2018: Scientific Data
https://www.readbyqxmd.com/read/29726899/sorting-cancer-karyotypes-using-double-cut-and-joins-duplications-and-deletions
#10
Ron Zeira, Ron Shamir
Motivation: Problems of genome rearrangement are central in both evolution and cancer research. Most genome rearrangement models assume that the genome contains a single copy of each gene and the only changes in the genome are structural, i.e., reordering of segments. In contrast, tumor genomes also undergo numerical changes such as deletions and duplications, and thus the number of copies of genes varies. Dealing with unequal gene content is a very challenging task, addressed by few algorithms to date...
May 3, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29718215/large-inserts-for-big-data-artificial-chromosomes-in-the-genomic-era
#11
Arianna Tocchetti, Stefano Donadio, Margherita Sosio
The exponential increase in available microbial genome sequences coupled with predictive bioinformatic tools is underscoring the genetic capacity of bacteria to produce an unexpected large number of specialized bioactive compounds. Since most of the biosynthetic gene clusters (BGCs) present in microbial genomes are cryptic, i.e. not expressed under laboratory conditions, a variety of cloning systems and vectors have been devised to harbor DNA fragments large enough to carry entire BGCs and to allow their transfer in suitable heterologous hosts...
May 1, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29713460/sensing-the-cilium-digital-capture-of-ciliary-data-for-comparative-genomics-investigations
#12
Karen R Christie, Judith A Blake
Background: Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work...
2018: Cilia
https://www.readbyqxmd.com/read/29702223/an-integrative-approach-to-investigate-the-association-among-high-sensitive-c-reactive-protein-body-fat-mass-distribution-and-other-cardiometabolic-risk-factors-in-young-healthy-women
#13
Bin Wu, Jingshan Huang, Lihua Zhang, Mohan Vamsi Kasukurthi, Fangwan Huang, Jiang Bian, Keisuke Fukuo, Tsutomu Kazumi
Prior research has indicated that as an important biomarker of chronic low-grade inflammation, high-sensitivity C-reactive protein (hs-CRP) can play important roles on the onset of metabolic syndrome and cardiovascular diseases (CVD). We conducted an integrative approach, which combines biological wet-lab experiments, statistical analysis, and semantics-oriented bioinformatics & computational analysis, to investigate the association among hs-CRP, body fat mass (FM) distribution, and other cardiometabolic risk factors in young healthy women...
April 24, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29698444/formalin-fixation-increases-deamination-mutation-signature-but-should-not-lead-to-false-positive-mutations-in-clinical-practice
#14
Leah M Prentice, Ruth R Miller, Jeff Knaggs, Alborz Mazloomian, Rosalia Aguirre Hernandez, Patrick Franchini, Kourosh Parsa, Basile Tessier-Cloutier, Anna Lapuk, David Huntsman, David F Schaeffer, Brandon S Sheffield
Genomic analysis of cancer tissues is an essential aspect of personalized oncology treatment. Though it has been suggested that formalin fixation of patient tissues may be suboptimal for molecular studies, this tissue processing approach remains the industry standard. Therefore clinical molecular laboratories must be able to work with formalin fixed, paraffin embedded (FFPE) material. This study examines the effects of pre-analytic variables introduced by routine pathology processing on specimens used for clinical reports produced by next-generation sequencing technology...
2018: PloS One
https://www.readbyqxmd.com/read/29695524/evaluation-of-targeted-next-generation-sequencing-for-detection-of-bovine-pathogens-in-clinical-samples
#15
Eman Anis, Ian K Hawkins, Marcia R S Ilha, Moges W Woldemeskel, Jeremiah T Saliki, Rebecca P Wilkes
The laboratory diagnosis of infectious diseases, especially those caused by mixed infections, is challenging. Routinely, this requires submission of multiple samples to separate laboratories. Advances in next-generation sequencing (NGS) have provided the opportunity for development of a comprehensive method to identify infectious agents. This study describes the use of target-specific primers for PCR-mediated amplification with the NGS technology, in which pathogen genomic regions of interest are enriched and selectively sequenced from clinical samples...
April 25, 2018: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29692621/h3africa-current-perspectives
#16
REVIEW
Nicola Mulder, Alash'le Abimiku, Sally N Adebamowo, Jantina de Vries, Alice Matimba, Paul Olowoyo, Michele Ramsay, Michelle Skelton, Dan J Stein
Precision medicine is being enabled in high-income countries by the growing availability of health data, increasing knowledge of the genetic determinants of disease and variation in response to treatment (pharmacogenomics), and the decreasing costs of data generation, which promote routine application of genomic technologies in the health sector. However, there is uncertainty about the feasibility of applying precision medicine approaches in low- and middle-income countries, due to the lack of population-specific knowledge, skills, and resources...
2018: Pharmacogenomics and Personalized Medicine
https://www.readbyqxmd.com/read/29688313/automatic-selection-of-verification-tools-for-efficient-analysis-of-biochemical-models
#17
Mehmet Emin Bakir, Savas Konur, Marian Gheorghe, Natalio Krasnogor, Mike Stannett
Motivation: Formal verification is a computational approach that checks system correctness (in relation to a desired functionality). It has been widely used in engineering applications to verify that systems work correctly. Model checking, an algorithmic approach to verification, looks at whether a system model satisfies its requirements specification. This approach has been applied to a large number of models in systems and synthetic biology as well as in systems medicine. Model checking is, however, computationally very expensive, and is not scalable to large models and systems...
April 24, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29677173/what-does-this-mutation-mean-the-tools-and-pitfalls-of-variant-interpretation-in-lymphoid-malignancies
#18
REVIEW
Yann Guillermin, Jonathan Lopez, Kaddour Chabane, Sandrine Hayette, Claire Bardel, Gilles Salles, Pierre Sujobert, Sarah Huet
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS...
April 20, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29676637/epigenomic-alterations-and-gene-expression-profiles-in-human-respiratory-epithelial-cells-mediated-by-hookah-and-cigarette-smoke
#19
Yin Xiong, Sichuan Xi, Jigui Shan, Elvin Hekimoglu, Shih-Hsin Hsiao, Mary Zhang, Julie A Hong, Chris Tao, Haobin Chen, R Taylor Ripley, Chuong D Hoang, David S Schrump
RATIONALE: The effects of hookah smoke on respiratory epithelia have not been well characterized. OBJECTIVES: To characterize and compare the effects of hookah tobacco smoke and conventional cigarette smoke on the epigenome and transcriptome of human respiratory epithelia. METHODS: Normal human small airway epithelial cells and cyclin-dependent kinase 4/human telomerase reverse transcriptase-immortalized human bronchial epithelial cells were cultured for 5 days in normal media in the presence or absence of water pipe condensates or cigarette smoke condensates under relevant exposure conditions...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29668842/garfield-ngs-genomic-variants-filtering-by-deep-learning-models-in-ngs
#20
Viola Ravasio, Marco Ritelli, Andrea Legati, Edoardo Giacopuzzi
Summary: Exome sequencing approach is extensively used in research and diagnostic laboratories to discover pathological variants and study genetic architecture of human diseases. However, a significant proportion of identified genetic variants are actually false positive calls, and this pose serious challenges for variants interpretation. Here, we propose a new tool named GARFIELD-NGS (Genomic vARiants FIltering by dEep Learning moDels in NGS), which rely on deep learning models to dissect false and true variants in exome sequencing experiments performed with Illumina or ION platforms...
April 14, 2018: Bioinformatics
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