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https://www.readbyqxmd.com/read/28535585/good-laboratory-standards-for-clinical-next-generation-sequencing-cancer-panel-tests
#1
REVIEW
Jihun Kim, Woong-Yang Park, Nayoung K D Kim, Se Jin Jang, Sung-Min Chun, Chang-Ohk Sung, Jene Choi, Young-Hyeh Ko, Yoon-La Choi, Hyo Sup Shim, Jae-Kyung Won
Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS...
May 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/28535172/invited-commentary-the-framingham-offspring-study-a-pioneering-investigation-into-familial-aggregation-of-cardiovascular-risk
#2
JoAnn E Manson, Shari S Bassuk
Launched in 1948, the Framingham Heart Study was a seminal prospective cohort study of 5,209 adult residents of Framingham, Massachusetts, that was designed to uncover the determinants and natural history of coronary heart disease. Data from this original cohort established the cardiac threat posed by high blood pressure, high cholesterol, smoking, obesity, physical inactivity, diabetes, and other factors. In the late 1960s, investigators conceived the innovative idea of assembling a second cohort that comprised the adult children of the original study population (and these children's spouses)...
May 23, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28535149/quantitative-computational-models-of-molecular-self-assembly-in-systems-biology
#3
Marcus Thomas, Russell Schwartz
Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems...
May 23, 2017: Physical Biology
https://www.readbyqxmd.com/read/28533782/towards-an-integrative-understanding-of-diet-host-gut-microbiome-interactions
#4
Mark N Read, Andrew J Holmes
Over the last 20 years, a sizeable body of research has linked the microbiome and host diet to a remarkable diversity of diseases. Yet, unifying principles of microbiome assembly or function, at levels required to rationally manipulate a specific individual's microbiome to their benefit, have not emerged. A key driver of both community composition and activity is the host diet, but diet-microbiome interactions cannot be characterized without consideration of host-diet interactions such as appetite and digestion...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28533768/novel-large-sulfur-bacteria-in-the-metagenomes-of-groundwater-fed-chemosynthetic-microbial-mats-in-the-lake-huron-basin
#5
Allison M Sharrar, Beverly E Flood, Jake V Bailey, Daniel S Jones, Bopaiah A Biddanda, Steven A Ruberg, Daniel N Marcus, Gregory J Dick
Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28530167/biofilm-community-succession-a-neutral-perspective
#6
Stephen Woodcock, William T Sloan
Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested...
May 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28529720/recent-advances-in-metacommunities-and-meta-ecosystem-theories
#7
REVIEW
Frédéric Guichard
Metacommunity theory has provided many insights into the general problem of local versus regional control of species diversity and relative abundance. The metacommunity framework has been extended from competitive interactions to whole food webs that can be described as spatial networks of interaction networks. Trophic metacommunity theory greatly contributed to resolving the community complexity-stability debate by predicting its dependence on the regional spatial context. The meta-ecosystem framework has since been suggested as a useful simplification of complex ecosystems to apply this spatial context to spatial flows of both individuals and matter...
2017: F1000Research
https://www.readbyqxmd.com/read/28529408/wind-dispersal-results-in-a-gradient-of-dispersal-limitation-and-environmental-match-among-discrete-aquatic-habitats
#8
Zsófia Horváth, Csaba F Vad, Robert Ptacnik
Directional dispersal by wind and other dispersal agents may generate spatial patterns in passively dispersing metacommunities which cannot be detected by classical eigenvector methods based on Euclidean distances. We analysed zooplankton communities (Rotifera, Cladocera, Copepoda) in a cluster of soda pans distributed over a short spatial scale of 18 km and tested explicitly for directional signals in their spatial configuration. The study area is exposed to a prevailing northwestern wind direction. By applying asymmetric eigenvector maps (AEM), we were able to identify corresponding directionality in the spatial structure of communities...
August 2016: Ecography
https://www.readbyqxmd.com/read/28529346/wartime-scars-or-reservoirs-of-biodiversity-the-value-of-bomb-crater-ponds-in-aquatic-conservation
#9
Csaba F Vad, Attila L Péntek, Nastasia J Cozma, Angéla Földi, Adrienn Tóth, Bence Tóth, NóraA Böde, Arnold Móra, Robert Ptacnik, Éva Ács, Katalin Zsuga, Zsófia Horváth
Considering the ongoing loss of aquatic habitats, anthropogenic ponds are gaining importance as substitute habitats. It is therefore important to assess their functioning in comparison to their natural precursors. Here we assess the biodiversity value of sodic bomb crater ponds by comparing their gamma diversity to that of natural reference habitats, astatic soda pans, and assess their importance on the landscape level by studying alpha and beta diversity. We studied aquatic organisms ranging from algae to vertebrates in a dense cluster of 54 sodic bomb crater ponds in Central Europe...
May 2017: Biological Conservation
https://www.readbyqxmd.com/read/28523397/the-heterogeneity-of-composition-and-assembly-processes-of-the-microbial-community-between-different-nutrient-loading-lake-zones-in-taihu-lake
#10
Dayong Zhao, Xinyi Cao, Rui Huang, Jin Zeng, Feng Shen, Huimin Xu, Sichen Wang, Xiaowei He, Zhongbo Yu
To investigate the differences in the microbial community composition and assembly process in two lake zones (Meiliang Bay (MLB) and Xukou Bay (XKB) in Taihu Lake, China) with different nutrient loadings, water samples were collected. Both the 16S ribosomal RNA (rRNA) gene for the bacterial community and the 18S rRNA gene for the microeukaryote community were investigated using the Illumina second-generation sequencing platform (2 × 250 paired-end). The results indicated that both the bacterioplankton and microeukaryote community composition derived from the two lake zones were significantly different...
May 18, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28522975/hypoxia-and-inactivity-related-physiological-changes-constipation-inflammation-are-not-reflected-at-the-level-of-gut-metabolites-and-butyrate-producing-microbial-community-the-planhab-study
#11
Robert Šket, Nicole Treichel, Tadej Debevec, Ola Eiken, Igor Mekjavic, Michael Schloter, Marius Vital, Jenna Chandler, James M Tiedje, Boštjan Murovec, Zala Prevoršek, Blaž Stres
We explored the assembly of intestinal microbiota in healthy male participants during the run-in (5 day) and experimental phases [21-day normoxic bed rest (NBR), hypoxic bedrest (HBR)], and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, balanced fluid, and dietary intakes, controlled circadian rhythm, microbial ambiental burden, and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28521776/solid-medical-waste-a-cross-sectional-study-of-household-disposal-practices-and-reported-harm-in-southern-ghana
#12
Emilia Asuquo Udofia, Gabriel Gulis, Julius Fobil
BACKGROUND: Solid medical waste (SMW) in households is perceived to pose minimal risks to the public compared to SMW generated from healthcare facilities. While waste from healthcare facilities is subject to recommended safety measures to minimize risks to human health and the environment, similar waste in households is often untreated and co-mingled with household waste which ends up in landfills and open dumps in many African countries. In Ghana, the management of this potentially hazardous waste stream at household and community level has not been widely reported...
May 18, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28514442/architecture-of-the-human-interactome-defines-protein-communities-and-disease-networks
#13
Edward L Huttlin, Raphael J Bruckner, Joao A Paulo, Joe R Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P Gygi, Hannah Parzen, John Szpyt, Stanley Tam, Gabriela Zarraga, Laura Pontano-Vaites, Sharan Swarup, Anne E White, Devin K Schweppe, Ramin Rad, Brian K Erickson, Robert A Obar, K G Guruharsha, Kejie Li, Spyros Artavanis-Tsakonas, Steven P Gygi, J Wade Harper
The physiology of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is critical to elucidating how genome variation contributes to disease...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28514052/shift-in-community-structure-in-an-early-successional-mediterranean-shrubland-driven-by-long-term-experimental-warming-and-drought-and-natural-extreme-droughts
#14
Daijun Liu, Marc Estiarte, Romà Ogaya, Xiaohong Yang, Josep Peñuelas
Global warming and recurring drought are expected to accelerate water limitation for plant communities in semiarid Mediterranean ecosystems and produce directional shifts in structure and composition that are not easily detected, and supporting evidence is scarce. We conducted a long-term (17 years) nocturnal-warming (+0.6 °C) and drought (-40% rainfall) experiment in an early-successional Mediterranean shrubland to study the changes in community structure and composition, contrasting functional groups and dominant species, and the superimposed effects of natural extreme drought...
May 17, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28511936/biotechnologies-for-marine-oil-spill-cleanup-indissoluble-ties-with-microorganisms
#15
REVIEW
Francesca Mapelli, Alberto Scoma, Grégoire Michoud, Federico Aulenta, Nico Boon, Sara Borin, Nicolas Kalogerakis, Daniele Daffonchio
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies...
May 13, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28510261/constraints-on-trait-combinations-explain-climatic-drivers-of-biodiversity-the-importance-of-trait-covariance-in-community-assembly
#16
John M Dwyer, Daniel C Laughlin
Trade-offs maintain diversity and structure communities along environmental gradients. Theory indicates that if covariance among functional traits sets a limit on the number of viable trait combinations in a given environment, then communities with strong multidimensional trait constraints should exhibit low species diversity. We tested this prediction in winter annual plant assemblages along an aridity gradient using multilevel structural equation modelling. Univariate and multivariate functional diversity measures were poorly explained by aridity, and were surprisingly poor predictors of community richness...
May 16, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28507540/microbial-population-dynamics-and-ecosystem-functions-of-anoxic-aerobic-granular-sludge-in-sequencing-batch-reactors-operated-at-different-organic-loading-rates
#17
Enikö Szabó, Raquel Liébana, Malte Hermansson, Oskar Modin, Frank Persson, Britt-Marie Wilén
The granular sludge process is an effective, low-footprint alternative to conventional activated sludge wastewater treatment. The architecture of the microbial granules allows the co-existence of different functional groups, e.g., nitrifying and denitrifying communities, which permits compact reactor design. However, little is known about the factors influencing community assembly in granular sludge, such as the effects of reactor operation strategies and influent wastewater composition. Here, we analyze the development of the microbiomes in parallel laboratory-scale anoxic/aerobic granular sludge reactors operated at low (0...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28505745/ecological-communities-with-lotka-volterra-dynamics
#18
Guy Bunin
Ecological communities in heterogeneous environments assemble through the combined effect of species interaction and migration. Understanding the effect of these processes on the community properties is central to ecology. Here we study these processes for a single community subject to migration from a pool of species, with population dynamics described by the generalized Lotka-Volterra equations. We derive exact results for the phase diagram describing the dynamical behaviors, and for the diversity and species abundance distributions...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28505366/bacterioplankton-assemblages-in-coastal-ponds-reflect-the-influence-of-hydrology-and-geomorphological-setting
#19
Megan J Huggett, Christopher R J Kavazos, Rachele Bernasconi, Robert Czarnik, Pierre Horwitz
The factors that shape microbial community assembly in aquatic ecosystems have been widely studied yet it is still unclear how distinct communities within a connected landscape influence one another. Coastal lakes are recipients of, and thus are connected to, both marine and terrestrial environments. Thus they may host microbial assemblages that reflect the relative degree of influence by, and connectivity to, either system. In order to address this idea we interrogated microbial community diversity at 49 sites in seven ponds in two seasons in the Lake MacLeod basin, a system fed by seawater flowing inland through underground karst...
May 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28503311/a-community-resource-for-exploring-and-utilizing-genetic-diversity-in-the-usda-pea-single-plant-plus-collection
#20
William L Holdsworth, Elodie Gazave, Peng Cheng, James R Myers, Michael A Gore, Clarice J Coyne, Rebecca J McGee, Michael Mazourek
Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs...
2017: Horticulture Research
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