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https://www.readbyqxmd.com/read/29346589/urban-evolutionary-ecology-and-the-potential-benefits-of-implementing-genomics
#1
Christopher J Schell
Urban habitats are quickly becoming exceptional models to address adaptation under rapid environmental change, given the expansive temporal and spatial scales with which anthropogenic landscape conversion occurs. Urban ecologists in the last 10-15 years have done an extraordinary job of highlighting phenotypic patterns that correspond with urban living, as well as delineating urban population structure using traditional genetic markers. The underpinning genetic mechanisms that govern those phenotypic patterns, however, are less well established...
January 13, 2018: Journal of Heredity
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#2
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346425/hippocampal-corticotropin-releasing-hormone-neurons-support-recognition-memory-and-modulate-hippocampal-excitability
#3
Andrew Hooper, Patrick M Fuller, Jamie Maguire
Corticotropin-releasing hormone (CRH) signaling in the hippocampus has been established to be important for mediating the effects of stress on learning and memory. Given our laboratory's recent characterization of a subset of hippocampal CRH neurons as a novel class of GABAergic interneurons, we hypothesized that these local GABAergic hippocampal CRH neurons may influence hippocampal function. Here we applied an array of molecular tools to selectively label and manipulate hippocampal CRH neurons in mice, in order to assess this interneuron population's impact on hippocampus-dependent behaviors and hippocampal network excitability...
2018: PloS One
https://www.readbyqxmd.com/read/29346413/genetic-diversity-and-potential-routes-of-transmission-of-mycobacterium-bovis-in-mozambique
#4
Adelina Machado, Teresa Rito, Solomon Ghebremichael, Nuelma Muhate, Gabriel Maxhuza, Custodia Macuamule, Ivania Moiane, Baltazar Macucule, Angelica Suzana Marranangumbe, Jorge Baptista, Joaquim Manguele, Tuija Koivula, Elizabeth Maria Streicher, Robin Mark Warren, Gunilla Kallenius, Paul van Helden, Margarida Correia-Neves
Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa, with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products. In order to understand and quantify this risk and design intervention strategies, good epidemiological studies are needed. Such studies can include molecular typing of M. bovis isolates. The aim of this study was to apply these tools to provide novel information concerning the distribution of bovine tuberculosis in cattle in Mozambique and thereby provide relevant information to guide policy development and strategies to contain the disease in livestock, and reduce the risk associated with transmission to humans...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29346368/mechanical-feedback-coordinates-cell-wall-expansion-and-assembly-in-yeast-mating-morphogenesis
#5
Samhita P Banavar, Carlos Gomez, Michael Trogdon, Linda R Petzold, Tau-Mu Yi, Otger Campàs
The shaping of individual cells requires a tight coordination of cell mechanics and growth. However, it is unclear how information about the mechanical state of the wall is relayed to the molecular processes building it, thereby enabling the coordination of cell wall expansion and assembly during morphogenesis. Combining theoretical and experimental approaches, we show that a mechanical feedback coordinating cell wall assembly and expansion is essential to sustain mating projection growth in budding yeast (Saccharomyces cerevisiae)...
January 18, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29346217/pathological-and-molecular-aspects-to-improve-endoscopic-ultrasonography-guided-fine-needle-aspiration-from-solid-pancreatic-lesions
#6
Hiroyuki Matsubayashi, Keiko Sasaki, Sachiyo Ono, Masato Abe, Hirotoshi Ishiwatari, Akira Fukutomi, Katsuhiko Uesaka, Hiroyuki Ono
Endoscopic ultrasonography-guided fine-needle aspiration (EUS-FNA) has been applied to pancreatic lesions since the 1990s, and its use is now widespread. Improvements in endoscopic devices and sampling techniques have resulted in excellent diagnostic ability for solid pancreatic lesions. However, clinical improvements alone are not responsible for it; pathological aspects have also played important roles. Rapid on-site evaluation minimizes endoscopic procedures, although its value at improving the diagnostic ratio is still debated...
February 2018: Pancreas
https://www.readbyqxmd.com/read/29345968/mature-gastric-chief-cells-are-not-required-for-the-development-of-metaplasia
#7
Hiroto Kinoshita, Yoku Hayakawa, Zhengchuan Niu, Mitsuru Konishi, Masahiro Hata, Mayo Tsuboi, Yuki Hayata, Yohko Hikiba, Sozaburo Ihara, Hayato Nakagawa, Yoshihiro Hirata, Timothy C Wang, K Koike
During human gastric carcinogenesis, intestinal metaplasia (IM) is frequently seen in the atrophic stomach. In mice, a distinct type of metaplasia known as spasmolytic polypeptide-expressing metaplasia (SPEM) is found in several inflammatory and genetically engineered models. Given the diversity of long- and short-term models of mouse SPEM, it remains unclear whether all models have a shared or distinct molecular mechanism. The origin of SPEM in mice is currently under debate. It is postulated that stem or progenitor cells acquire genetic alterations that then supply metaplastic cell clones, while the possibility of transdifferentiation or dedifferentiation from mature gastric chief cells has also been suggested...
January 18, 2018: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/29345901/playing-with-the-molecules-of-life
#8
Douglas D Young, Peter G Schultz
Our understanding of the complex molecular processes of living organisms is growing exponentially. This knowledge, togeth-er with a powerful arsenal of tools for manipulating the structures of biological macromolecules, is allowing chemists to begin to harness and reprogram the remarkable machinery of life. Here we review one such example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins in ways previously unimaginable...
January 18, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29345728/analytical-performance-of-the-thyroseq-v3-genomic-classifier-for-cancer-diagnosis-in-thyroid-nodules
#9
Marina N Nikiforova, Stephanie Mercurio, Abigail I Wald, Michelle Barbi de Moura, Keith Callenberg, Lucas Santana-Santos, William E Gooding, Linwah Yip, Robert L Ferris, Yuri E Nikiforov
BACKGROUND: Molecular tests have clinical utility for thyroid nodules with indeterminate fine-needle aspiration (FNA) cytology, although their performance requires further improvement. This study evaluated the analytical performance of the newly created ThyroSeq v3 test. METHODS: ThyroSeq v3 is a DNA- and RNA-based next-generation sequencing assay that analyzes 112 genes for a variety of genetic alterations, including point mutations, insertions/deletions, gene fusions, copy number alterations, and abnormal gene expression, and it uses a genomic classifier (GC) to separate malignant lesions from benign lesions...
January 18, 2018: Cancer
https://www.readbyqxmd.com/read/29345414/molecular-characterization-of-a-series-of-990-index-patients-with-albinism
#10
E Lasseaux, C Plaisant, V Michaud, P Pennamen, A Trimouille, L Gaston, S Monfermé, D Lacombe, C Rooryck, F Morice-Picard, B Arveiler
Albinism is a clinically and genetically heterogeneous disease characterized by variable degrees of hypopigmentation and by nystagmus, foveal hypoplasia, and chiasmatic misrouting of the optic nerves. The wide phenotypic heterogeneity impedes the establishment of phenotype-genotype correlations. In order to obtain a precise diagnosis we screened the 19 known albinism genes in 990 index patients using targeted next generation sequencing (NGS) and high resolution comparative genomic hybridization. A molecular diagnosis was obtained in 72...
January 18, 2018: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/29345394/viruses-as-key-modulators-of-the-tgf-%C3%AE-pathway-a-double-edged-sword-involved-in-cancer
#11
REVIEW
Habibollah Mirzaei, Ebrahim Faghihloo
Transforming growth factor-β (TGF-β) signaling pathway is a key network in cell signaling that controls vital processes such as proliferation, differentiation, apoptosis, epithelial-mesenchymal transition, and migration, thus acting as a double-edged sword in normal development and diseases, in particular organ fibrosis, vascular disorders, and cancer. Early in tumorigenesis, the pathway exerts anti-tumor effects through suppressing cell cycle and inducing apoptosis, while during late stages, it functions as a tumor promoter by enhancing tumor invasiveness and metastasis...
January 18, 2018: Reviews in Medical Virology
https://www.readbyqxmd.com/read/29345341/novel-insights-into-fas-defects-underlying-autoimmune-lymphoproliferative-syndrome-revealed-by-studies-in-consanguineous-patients
#12
REVIEW
Imen Ben-Mustapha, Nourhen Agrebi, Mohamed-Ridha Barbouche
Autoimmune lymphoproliferative syndrome (ALPS) is a primary immunodeficiency disease due to impaired Fas-Fas ligand apoptotic pathway. It is characterized by chronic nonmalignant, noninfectious lymphadenopathy and/or splenomegaly associated with autoimmune manifestations primarily directed against blood cells. Herein, we review the heterogeneous ALPS molecular bases and discuss recent findings revealed by the study of consanguineous patients. Indeed, this peculiar genetic background favored the identification of a novel form of AR ALPS-FAS associated with normal or residual protein expression, expanding the spectrum of ALPS types...
December 27, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29345036/application-of-molecular-tools-to-elucidate-the-microbiota-of-seafood
#13
Paloma de Almeida Rodrigues, Rafaela Gomes Ferrari, Carlos Adam Conte Junior
The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages, and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result...
January 18, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29344953/established-emerging-and-elusive-molecular-targets-in-the-treatment-of-lung-cancer
#14
REVIEW
Jean-Nicolas Gallant, Christine M Lovly
Although histological subtype still underlies tumor classification and treatment, the recognition that lung cancer is, largely, a genetic disease has prompted a push to reconfigure cancer taxonomies according to molecular criteria. In this review, we discuss established (e.g. EGFR, ALK, ROS1, PD-1/PD-L1), emerging (e.g. MET, RET, NTRK), and elusive (e.g. TP53, KRAS, MYC) molecular targets in the treatment of lung cancer. We synthesize a large and rapidly growing body of literature regarding the discovery and therapeutic inhibition of these targets in lung cancer...
January 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344886/identifying-genetic-dependencies-in-cancer-by-analyzing-sirna-screens-in-tumor-cell-line-panels
#15
James Campbell, Colm J Ryan, Christopher J Lord
Loss-of-function screening using RNA interference or CRISPR approaches can be used to identify genes that specific tumor cell lines depend upon for survival. By integrating the results from screens in multiple cell lines with molecular profiling data, it is possible to associate the dependence upon specific genes with particular molecular features (e.g., the mutation of a cancer driver gene, or transcriptional or proteomic signature). Here, using a panel of kinome-wide siRNA screens in osteosarcoma cell lines as an example, we describe a computational protocol for analyzing loss-of-function screens to identify genetic dependencies associated with particular molecular features...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344858/laser-capture-microdissection-as-a-tool-to-study-the-mucosal-immune-response-in-celiac-disease
#16
Giuseppe Iacomino, Vera Rotondi Aufiero, Pasquale Marena, Antonella Venezia, Riccardo Troncone, Salvatore Auricchio, Giuseppe Mazzarella
Laser capture microdissection (LCM) is a powerful tool for selection and isolation of single cells or compartments from complex primary tissues to perform molecular analyses. Celiac disease is a genetic autoimmune disorder where the ingestion of gluten leads to damage in the small intestine. Increased intraepithelial lymphocytes and the presence of the lamina propria inflammatory infiltrate of the duodenal mucosa is a common part of the disease. These cells promote inflammatory processes through the release of cytokines...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344856/next-generation-sequencing-analysis-of-laser-microdissected-formalin-fixed-and-paraffin-embedded-ffpe-tissue-specimens
#17
Lavinia Mägel, Stephan Bartels, Ulrich Lehmann
In recent years, next-generation sequencing (NGS) became widely used in molecular pathology. Comprehensive mutational profiling improved diagnosis and prognosis, as well as the identification of therapeutically relevant genetic alterations. However, the vast majority of studies analyzing tissue samples use DNA extracted from bulk tissue or only manually microdissected specimens. Laser-assisted microdissection offers the possibility of isolating morphologically defined small tissue compartments (like individual glands) or even of single cells for further molecular analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344848/current-status-and-future-possibilities-of-molecular-genetics-techniques-in-brassica-napus
#18
REVIEW
Muhammad Afzal, Salem Safer Alghamdi, Muhammad Habib Ur Rahman, Awais Ahmad, Tahir Farooq, Mukhtar Alam, Imtiaz Ali Khan, Hidayat Ullah, Wajid Nasim, Shah Fahad
As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29344835/genetic-evidence-for-the-role-of-a-rice-vacuolar-invertase-as-a-molecular-sink-strength-determinant
#19
Shamitha Rao Morey, Tatsuro Hirose, Yoichi Hashida, Akio Miyao, Hirohiko Hirochika, Ryu Ohsugi, Junko Yamagishi, Naohiro Aoki
BACKGROUND: Rice is a major crop feeding the majority of the global population, and increasing its sink strength is one of the modes to alleviate the declining availability of food for the rapidly growing world population. We demonstrate a role for an important rice vacuolar invertase isoform, OsINV3, in sink strength determination. RESULTS: OsINV3 mutants showed shorter panicles with lighter and smaller grains, owing to a smaller cell size on the outer and inner surfaces of the palea and lemma as observed by scanning electron microscopy...
January 17, 2018: Rice
https://www.readbyqxmd.com/read/29344693/triplet-based-codon-organization-optimizes-the-impact-of-synonymous-mutation-on-nucleic-acid-molecular-dynamics
#20
Gregory A Babbitt, Erin E Coppola, Jamie S Mortensen, Patrick X Ekeren, Cosmo Viola, Dallan Goldblatt, André O Hudson
Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties...
January 17, 2018: Journal of Molecular Evolution
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