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https://www.readbyqxmd.com/read/28822772/differentiation-of-candida-albicans-candida-glabrata-and-candida-krusei-by-ft-ir-and-chemometrics-by-chromagar%C3%A2-candida
#1
Denise Wohlmeister, Débora Renz Barreto Vianna, Virginia Etges Helfer, Luciane Noal Calil, Andréia Buffon, Alexandre Meneghello Fuentefria, Valeriano Antonio Corbellini, Diogo André Pilger
Pathogenic Candida species are detected in clinical infections. CHROMagar™ is a phenotypical method used to identify Candida species, although it has limitations, which indicates the need for more sensitive and specific techniques. Infrared Spectroscopy (FT-IR) is an analytical vibrational technique used to identify patterns of metabolic fingerprint of biological matrixes, particularly whole microbial cell systems as Candida sp. in association of classificatory chemometrics algorithms. On the other hand, Soft Independent Modeling by Class Analogy (SIMCA) is one of the typical algorithms still little employed in microbiological classification...
August 16, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28821716/transcriptome-analysis-reveals-long-intergenic-non-coding-rnas-involved-in-skeletal-muscle-growth-and-development-in-pig
#2
Cheng Zou, Jingxuan Li, Wenzhe Luo, Long Li, An Hu, Yuhua Fu, Ye Hou, Changchun Li
Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28820904/parametric-studies-of-metabolic-cooperativity-in-escherichia-coli-colonies-strain-and-geometric-confinement-effects
#3
Joseph R Peterson, John A Cole, Zaida Luthey-Schulten
Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise due to the subtle interplay between microenvironmental conditions and the cells' regulatory machinery, often involving cascades of intra- and extracellular signalling molecules. In the simplest of cases, as demonstrated in a recent study of the model organism Escherichia coli, metabolic cross-feeding can arise in monoclonal colonies of bacteria driven merely by spatial heterogeneity in the availability of growth substrates; namely, acetate, glucose and oxygen...
2017: PloS One
https://www.readbyqxmd.com/read/28820204/droplet-microfluidics-for-synthetic-biology
#4
REVIEW
Philip C Gach, Kosuke Iwai, Peter W Kim, Nathan J Hillson, Anup K Singh
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility...
August 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28819044/the-parkinson-s-disease-associated-protein-dj-1-plays-a-positive-nonmitochondrial-role-in-endocytosis-in-dictyostelium-cells
#5
Suwei Chen, Sarah J Annesley, Rasha A F Jasim, Vanessa J Musco, Oana Sanislav, Paul R Fisher
The loss of function of DJ-1 caused by mutations of DJ-1 causes a form of familial Parkinson's Disease (PD). However, the role of DJ-1 in healthy and in PD cells is poorly understood. Even its subcellular localization in mammalian cells is uncertain, both cytosolic and mitochondrial locations having been reported. We show here that DJ-1 is normally located in the cytoplasm in healthy Dictyostelium discoideum cells. With its unique life cycle, straightforward genotype-phenotype relationships, experimental accesibility and genetic tractability, Dictyostelium discoideum offers an attractive model to investigate the roles of PD-associated genes...
August 17, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28818640/the-influence-of-physical-activity-in-the-anti-tumor-immune-response-in-experimental-breast-tumor
#6
Thiago M Bianco, Douglas R Abdalla, Chamberttan S Desidério, Sofie Thys, Cindy Simoens, John-Paul Bogers, Eddie F C Murta, Márcia A Michelin
This study aimed to investigate the influence of physical activity in innate immunity to conduce to an effective antitumoral immune response analyzing the phenotype and activation status of infiltrating cells. We analyzed the intracellular cytokines and the transcription factors of tumor infiltrating lymphocytes (TILS) and spleen leukocytes. The Nos2 gene expression was evaluated in spleen cells and futhermore the ROS production was measured and spleen cells; another cell evaluated was dendritic cells (TIDCs), their cytokines expression and membrane molecules; finally to understood the results obtained, we analysed the dendritic cells obtained from bone marrow...
August 14, 2017: Immunology Letters
https://www.readbyqxmd.com/read/28818371/assessment-of-molecular-and-epigenetic-changes-in-the-albinism-of-agave-angustifolia-haw
#7
Rosa Us-Camas, Eduardo Castillo-Castro, Margarita Aguilar-Espinosa, Verónica Limones-Briones, Renata Rivera-Madrid, Manuel L Robert-Díaz, Clelia De-la-Peña
Albinism in plants is a rare phenomenon that occurs in nature and is characterized by the total or partial loss of photosynthetic pigments. Although progress has been made in understanding the nature of this phenomenon, the precise causes and biological basis are still unexplored. Here, we study the genetic and epigenetic differences between green (G), variegated (V) and albino (A) A. angustifolia Haw. plantlets obtained by in vitro propagation in order to present new insights into albinism from a plant system that offers a unique set of biological phenotypic characteristics...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28817722/nicotinamide-alone-accelerates-the-conversion-of-mouse-embryonic-stem-cells-into-mature-neuronal-populations
#8
Síle M Griffin, Mark R Pickard, Rowan P Orme, Clive P Hawkins, Adrian C Williams, Rosemary A Fricker
INTRODUCTION: Vitamin B3 has been shown to play an important role during embryogenesis. Specifically, there is growing evidence that nicotinamide, the biologically active form of vitamin B3, plays a critical role as a morphogen in the differentiation of stem cells to mature cell phenotypes, including those of the central nervous system (CNS). Detailed knowledge of the action of small molecules during neuronal differentiation is not only critical for uncovering mechanisms underlying lineage-specification, but also to establish more effective differentiation protocols to obtain clinically relevant cells for regenerative therapies for neurodegenerative conditions such as Huntington's disease (HD)...
2017: PloS One
https://www.readbyqxmd.com/read/28816643/pharmacometabolomics-informs-quantitative-radiomics-for-glioblastoma-diagnostic-innovation
#9
Theodora Katsila, Minos-Timotheos Matsoukas, George P Patrinos, Dimitrios Kardamakis
Applications of omics systems biology technologies have enormous promise for radiology and diagnostics in surgical fields. In this context, the emerging fields of radiomics (a systems scale approach to radiology using a host of technologies, including omics) and pharmacometabolomics (use of metabolomics for patient and disease stratification and guiding precision medicine) offer much synergy for diagnostic innovation in surgery, particularly in neurosurgery. This synthesis of omics fields and applications is timely because diagnostic accuracy in central nervous system tumors still challenges decision-making...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28815872/a-multimethod-computational-simulation-approach-for-investigating-mitochondrial-dynamics-and-dysfunction-in-degenerative-aging
#10
Timothy E Hoffman, Katherine J Barnett, Lyle Wallis, William H Hanneman
Research in biogerontology has largely focused on the complex relationship between mitochondrial dysfunction and biological aging. In particular, the mitochondrial free radical theory of aging (MFRTA) has been well accepted. However, this theory has been challenged by recent studies showing minimal increases in reactive oxygen species (ROS) as not entirely deleterious in nature, and even beneficial under the appropriate cellular circumstances. To assess these significant and nonintuitive observations in the context of a functional system, we have taken an in silico approach to expand the focus of the MFRTA by including other key mitochondrial stress response pathways, as they have been observed in the nematode Caenorhabditis elegans...
August 16, 2017: Aging Cell
https://www.readbyqxmd.com/read/28814445/meeting-report-on-experimental-approaches-to-evolution-and-ecology-using-yeast-and-other-model-systems
#11
Daniel Jarosz, Aimée M Dudley
The fourth EMBO-sponsored conference on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems (https://www.embl.de/training/events/2016/EAE16-01/), was held at the EMBL in Heidelberg, Germany, October 19-23, 2016. The conference was organized by Judith Berman (Tel Aviv University), Maitreya Dunham (University of Washington), Jun-Yi Leu (Academia Sinica), and Lars Steinmetz (EMBL Heidelberg and Stanford University). The meeting attracted ~120 researchers from 28 countries and covered a wide range of topics in the fields of genetics, evolutionary biology, and ecology with a unifying focus on yeast as a model system...
August 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28814270/transcriptional-analysis-of-abdominal-fat-in-chickens-divergently-selected-on-bodyweight-at-two-ages-reveals-novel-mechanisms-controlling-adiposity-validating-visceral-adipose-tissue-as-a-dynamic-endocrine-and-metabolic-organ
#12
C W Resnyk, W Carré, X Wang, T E Porter, J Simon, E Le Bihan-Duval, M J Duclos, S E Aggrey, L A Cogburn
BACKGROUND: Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28813705/the-lncrna-tug1-ezh2-axis-promotes-pancreatic-cancer-cell-proliferation-migration-and-emt-phenotype-formation-through-sponging-mir-382
#13
Liang Zhao, Hongwei Sun, Hongru Kong, Zongjing Chen, Bicheng Chen, Mengtao Zhou
BACKGROUND/AIMS: Pancreatic carcinoma (PC) is the one of the most common and malignant cancers worldwide. LncRNA taurine upregulated gene 1 (TUG1) was initially identified as a transcript upregulated by taurine, and the abnormal expression of TUG1 has been reported in many cancers. However, the biological role and molecular mechanism of TUG1 in PC still needs further investigation. METHODS: Quantitative real-time PCR (qRT-PCR) was performed to measure the expression of TUG1 in PC cell lines and tissues...
August 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28812721/predicting-evolution
#14
Michael Lässig, Ville Mustonen, Aleksandra M Walczak
The face of evolutionary biology is changing: from reconstructing and analysing the past to predicting future evolutionary processes. Recent developments include prediction of reproducible patterns in parallel evolution experiments, forecasting the future of individual populations using data from their past, and controlled manipulation of evolutionary dynamics. Here we undertake a synthesis of central concepts for evolutionary predictions, based on examples of microbial and viral systems, cancer cell populations, and immune receptor repertoires...
February 21, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812673/craniofacial-diversification-in-the-domestic-pigeon-and-the-evolution-of-the-avian-skull
#15
Nathan M Young, Marta Linde-Medina, John W Fondon, Benedikt Hallgrímsson, Ralph S Marcucio
A central question in evolutionary developmental biology is how highly conserved developmental systems can generate the remarkable phenotypic diversity observed among distantly related species. In part, this paradox reflects our limited knowledge about the potential for species to both respond to selection and generate novel variation. Consequently, the developmental links between small-scale microevolutionary variations within populations to larger macroevolutionary patterns among species remain unbridged...
March 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812179/a-hybrid-co-culture-model-with-endothelial-cells-designed-for-the-hepatic-tissue-engineering
#16
Xiaoning Yang, Xin Wang, Xiaobo Huang, Ruiqiang Hang, Xiangyu Zhang, Bin Tang
The cultured hepatic cells in vitro are prone to losing their characteristic morphologies and biological functions. To avoid this problem, a hybrid co-culture system was proposed to elucidate the effect of cellular communication on the phenotype of hepatic cells. A monolayer of endothelial cells (ECs) was co-cultured on the surface of a three-dimensional (3D) scaffold embedded with HepG2 cells. In this hybrid co-culture system, the growth of encapsulated hepatic cells is barely influenced by the co-cultured ECs...
August 10, 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/28809418/native-extracellular-matrix-derived-semipermeable-optically-transparent-and-inexpensive-membrane-inserts-for-microfluidic-cell-culture
#17
Mark J Mondrinos, Yoon-Suk Yi, Nan-Kun Wu, Xueting Ding, Dongeun Huh
Semipermeable cell culture membranes are commonly used in multilayered microfluidic devices to mimic the basement membrane in vivo and to create compartmentalized microenvironments for physiological cell growth and differentiation. However, existing membranes are predominantly made up of synthetic polymers, providing limited capacity to replicate cellular interactions with native extracellular matrices that play a crucial role in the induction of physiological phenotypes. Here we describe a new type of cell culture membranes engineered from native extracellular matrix (ECM) materials that are thin, semipermeable, optically transparent, and amenable to integration into microfluidic cell culture devices...
August 15, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28808057/a-kidney-specific-genetic-control-module-in-mice-governs-endocrine-regulation-of-the-cytochrome-p450-gene-cyp27b1-essential-for-vitamin-d3-activation
#18
Mark B Meyer, Nancy A Benkusky, Martin Kaufmann, Seong Min Lee, Melda Onal, Glenville Jones, J Wesley Pike
The vitamin D endocrine system regulates mineral homeostasis through its activities in the intestine, kidney, and bone. Terminal activation of vitamin D3 to its hormonal form, 1,25(OH)2D3, occurs in the kidney via the cytochrome P450 enzyme CYP27B1. Despite its importance in vitamin D metabolism, the molecular mechanisms underlying the regulation of the gene for this enzyme, Cyp27b1, are unknown. Here, we identified a kidney-specific control module governed by a renal cell-specific chromatin structure located distal to Cyp27b1 that mediates unique basal and parathyroid hormone (PTH)-, fibroblast growth factor 23 (FGF23)-, and 1,25(OH)2D3-mediated regulation of Cyp27b1 expression...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28807931/identification-of-novel-growth-regulators-in-plant-populations-expressing-random-peptides
#19
Zhilong Bao, Maureen A Clancy, Raquel F Carvalho, Kiona Elliott, Kevin M Folta
The use of chemical genomics approaches allows the identification of small molecules that integrate into biological systems, thereby changing discrete processes that influence growth, development or metabolism. Libraries of chemicals are applied to living systems, and changes in phenotype are observed, potentially leading to the identification of new growth regulators. This work describes an approach that is the nexus of chemical-genomics and synthetic biology. Here each plant in an extensive population synthesizes a unique small peptide arising from a transgene composed of a randomized nucleic acid sequence core, flanked by translational start, stop, and cysteine-encoding (for disulfide cyclization) sequences...
August 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28805927/the-relationship-between-different-measures-of-feed-efficiency-and-feeding-behavior-traits-in-duroc-pigs
#20
D Lu, S Jiao, F Tiezzi, M Knauer, Y Huang, K A Gray, C Maltecca
Utilization of feed in livestock species consists of a wide range of biological processes, and therefore, its efficiency can be expressed in various ways, including direct measurement, such as daily feed intake, as well as indicator measures, such as feeding behavior. Measuring feed efficiency is important to the swine industry, and its accuracy can be enhanced by using automated feeding systems, which record feed intake and associated feeding behavior of individual animals. Each automated feeder space is often shared among several pigs and therefore raises concerns about social interactions among pen mates with regard to feeding behavior...
August 2017: Journal of Animal Science
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