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https://www.readbyqxmd.com/read/29228298/seedstor-a-germplasm-information-management-system-and-public-database
#1
R S P Horler, A Turner, P Fretter, M Ambrose
SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Inness Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates' germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives as well as precise genetic stocks, near-isogenic lines and mapping populations...
December 8, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29226804/systems-pharmacology-dissection-of-cholesterol-regulation-reveals-determinants-of-large-pharmacodynamic-variability-between-cell-lines
#2
Peter Blattmann, David Henriques, Michael Zimmermann, Fabian Frommelt, Uwe Sauer, Julio Saez-Rodriguez, Ruedi Aebersold
In individuals, heterogeneous drug-response phenotypes result from a complex interplay of dose, drug specificity, genetic background, and environmental factors, thus challenging our understanding of the underlying processes and optimal use of drugs in the clinical setting. Here, we use mass-spectrometry-based quantification of molecular response phenotypes and logic modeling to explain drug-response differences in a panel of cell lines. We apply this approach to cellular cholesterol regulation, a biological process with high clinical relevance...
November 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/29226564/-lowe-syndrome-a-particularly-severe-phenotype-without-clinical-kidney-involvement
#3
Abdalla Etesam, El-Beheiry Ahmed, Dieterich Klaus, Thevenon Julien, Fauré Julien, Rendu John
Lowe syndrome (LS) is a very rare disorder of phosphatidylinositol metabolism, which manifests with a complex phenotype comprising a clinical triad encompassing major abnormalities of the eyes, the kidneys, and the central nervous system. We are reporting a 23-year-old Egyptian male with a severe phenotype of LS with a minimal kidney disease. Direct sequencing of the OCRL gene detected a p.His375Arg mutation in the catalytic domain of the protein. The patient suffered from bilateral congenital cataracts and glaucoma, striking growth deficiency, severe psychomotor disability, a severe osteopathy, and seizures, but only minimal renal dysfunction...
December 11, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29225960/utility-of-amorphous-calcium-phosphate-based-scaffolds-in-dental-biomedical-applications
#4
Diane R Bienek, Drago Skrtic
Calcium phosphate (CaP) materials are important inorganic constituents in biological hard tissue. CaPs, including amorphous calcium phosphate (ACP) have been widely applied in dental and biomedical applications, such as tissue engineering. Scaffold constructs are commonly used as templates to create a biomimetic environment. This review considers ACP scaffold fabrication techniques, including tissue-engineered constructs with intrinsic incorporation of ACP as well as scaffolds formed via precipitation of mineralized solutions on a substrate...
2017: Biointerface Research in Applied Chemistry
https://www.readbyqxmd.com/read/29224246/circadian-peak-dopaminergic-activity-response-at-the-biological-clock-pacemaker-suprachiasmatic-nucleus-area-mediates-the-metabolic-responsiveness-to-a-high-fat-diet
#5
Shuqin Luo, Yahong Zhang, Michael Ezrokhi, Yang Li, Tsung-Huang Tsai, Anthony H Cincotta
Among vertebrate species of the major vertebrate classes in the wild, a seasonal rhythm of whole body fuel metabolism, oscillating from lean to obese condition, is a common biological phenomenon. This annual cycle is driven in part by annual changes in the circadian dopaminergic signaling at the suprachiasmatic nuclei (SCN), with diminution of circadian peak dopaminergic activity at the SCN facilitating development of the seasonal obese insulin resistant condition. The present study investigated whether such an ancient circadian dopamine-SCN activity system for expression of the seasonal obese, insulin resistant phenotype may be operative in animals made obese, insulin resistant by high fat feeding and if so whether reinstatement of the circadian dopaminergic peak at the SCN would be sufficient to reverse the adverse metabolic impact of the high fat diet without alteration of caloric intake...
December 10, 2017: Journal of Neuroendocrinology
https://www.readbyqxmd.com/read/29222764/optimization-of-multi-omic-genome-scale-models-methodologies-hands-on-tutorial-and-perspectives
#6
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222759/techniques-for-large-scale-bacterial-genome-manipulation-and-characterization-of-the-mutants-with-respect-to-in-silico-metabolic-reconstructions
#7
George C diCenzo, Turlough M Finan
The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222755/integrated-host-pathogen-metabolic-reconstructions
#8
Anu Raghunathan, Neema Jamshidi
The science and art of Genome scale metabolic network reconstructions have been explicitly documented in the literature for organisms across all the three kingdoms of life. Constraints-based models derived from such reconstructions have been used to assess metabolic phenotypes of their complex connections to genotype accurately. The problem of infectious disease is complex due to the multifactorial response of the host to the pathogen. Systems biology approaches and modeling allow one to study, understand, and predict emergent properties of such complex responses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222753/integration-of-comparative-genomics-with-genome-scale-metabolic-modeling-to-investigate-strain-specific-phenotypical-differences
#9
Jonathan Monk, Emanuele Bosi
Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29220613/fully-automated-pipetting-sorting-system-for-different-morphological-phenotypes-of-zebrafish-embryos
#10
Helmut Breitwieser, Thomas Dickmeis, Marcel Vogt, Marco Ferg, Christian Pylatiuk
Systems biology methods, such as transcriptomics and metabolomics, require large numbers of small model organisms, such as zebrafish embryos. Manual separation of mutant embryos from wild-type embryos is a tedious and time-consuming task that is prone to errors, especially if there are variable phenotypes of a mutant. Here we describe a zebrafish embryo sorting system with two cameras and image processing based on template-matching algorithms. In order to evaluate the system, zebrafish rx3 mutants that lack eyes due to a patterning defect in brain development were separated from their wild-type siblings...
December 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/29216271/genomic-and-phenotypic-characteristics-of-swedish-c-jejuni-water-isolates
#11
Anna Nilsson, Cecilia Johansson, Astrid Skarp, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens...
2017: PloS One
https://www.readbyqxmd.com/read/29216180/the-ink4a-arf-locus-operates-as-a-regulator-of-the-circadian-clock-modulating-ras-activity
#12
Rukeia El-Athman, Nikolai N Genov, Jeannine Mazuch, Kaiyang Zhang, Yong Yu, Luise Fuhr, Mónica Abreu, Yin Li, Thomas Wallach, Achim Kramer, Clemens A Schmitt, Angela Relógio
The mammalian circadian clock and the cell cycle are two major biological oscillators whose coupling influences cell fate decisions. In the present study, we use a model-driven experimental approach to investigate the interplay between clock and cell cycle components and the dysregulatory effects of RAS on this coupled system. In particular, we focus on the Ink4a/Arf locus as one of the bridging clock-cell cycle elements. Upon perturbations by the rat sarcoma viral oncogene (RAS), differential effects on the circadian phenotype were observed in wild-type and Ink4a/Arf knock-out mouse embryonic fibroblasts (MEFs), which could be reproduced by our modelling simulations and correlated with opposing cell cycle fate decisions...
December 2017: PLoS Biology
https://www.readbyqxmd.com/read/29209560/pd-l1-and-epithelial-mesenchymal-transition-in-circulating-tumor-cells-from-non-small-cell-lung-cancer-patients-a-molecular-shield-to-evade-immune-system
#13
Cristina Raimondi, Guido Carpino, Chiara Nicolazzo, Angela Gradilone, Walter Gianni, Alain Gelibter, Eugenio Gaudio, Enrico Cortesi, Paola Gazzaniga
The programmed cell death 1 (PD-1)/PD-1 ligand 1 (PD-L1) pathway has emerged as a critical inhibitory pathway regulating T-cell response in non-small-cell lung cancer (NSCLC), and the development of PD-1/PD-L1 inhibitors has changed the landscape of NSCLC therapy. Nevertheless, the high degree of non-responders demonstrates that we are still far from completely understanding the events underlying tumor immune resistance. Although the expression of PD-L1 in tumor tissue has been correlated with clinical response to anti PD-1 inhibitors, the ability of this marker to discriminate the subgroup of patients who derive benefit from immunotherapy is suboptimal...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29206329/cardiac-tissue-regeneration-a-preliminary-study-on-carbon-based-nanotubes-gelatin-scaffold
#14
Manuela Cabiati, Federico Vozzi, Federica Gemma, Francesca Montemurro, Carmelo De Maria, Giovanni Vozzi, Claudio Domenici, Silvia Del Ry
The aim of this study was set-up and test of gelatin and carbon nanotubes scaffolds. Gelatin-based (5%) genipin cross-linked (0.2%) scaffolds embedding single-walled carbon nanotubes (SWCNTs, 0.3, 0.5, 0.7, 0.9, and 1.3% w/w) were prepared and mechanically/electrically characterized. For biological evaluation, H9c2 cell line was cultured for 10 days. Cytotoxicity, cell growth and differentiation, immunohistochemistry, and real-time PCR analysis were performed. Myoblast and cardiac differentiation were obtained by serum reduction to 1% (C1% ) and stimulation with 50 nM all trans-retinoic acid (CRA ), respectively...
December 5, 2017: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
https://www.readbyqxmd.com/read/29203707/extracellular-cell-stress-heat-shock-proteins-immune-responses-and-disease-an-overview
#15
REVIEW
A Graham Pockley, Brian Henderson
Extracellular cell stress proteins are highly conserved phylogenetically and have been shown to act as powerful signalling agonists and receptors for selected ligands in several different settings. They also act as immunostimulatory 'danger signals' for the innate and adaptive immune systems. Other studies have shown that cell stress proteins and the induction of immune reactivity to self-cell stress proteins can attenuate disease processes. Some proteins (e.g. Hsp60, Hsp70, gp96) exhibit both inflammatory and anti-inflammatory properties, depending on the context in which they encounter responding immune cells...
January 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29201428/effect-of-aging-on-the-female-reproductive-function
#16
REVIEW
Koumei Shirasuna, Hisataka Iwata
Aging is a complex biological process that involves the accrual of bodily changes over a long life span. In humans, advanced maternal age is associated with infertility and adverse pregnancy complications. Cellular and organic senescence is hypothesized to contribute to the age-related decline in reproductive function. Accumulating evidence suggests that immune cells play pivotal roles in physiological reproductive function and pregnancy. The concept of "inflammaging" has recently emerged- an age-dependent, low-grade, chronic, and systemic inflammatory state induced by the senescence-associated secretory phenotype (SASP), which is produced by the innate immune, parenchymal, and nonparenchymal cells within the organs...
2017: Contraception and Reproductive Medicine
https://www.readbyqxmd.com/read/29200109/2016-world-health-organization-classification-of-central-nervous-system-tumors
#17
Patrick Y Wen, Jason T Huse
PURPOSE OF REVIEW: Since 1979, the World Health Organization (WHO) has periodically published a consensus classification and grading of tumors of the central nervous system (CNS) to ensure uniform histopathologic diagnostic criteria worldwide. In 2016, the WHO published an update of the fourth edition of the classification of CNS tumors. This article summarizes the major changes in the update and discusses their impact on clinical practice. RECENT FINDINGS: For the first time, the 2016 revision of the WHO classification uses molecular parameters in addition to traditional histology to diagnose many CNS tumors, resulting in major restructuring of the classification of many tumors, especially gliomas, ependymomas, and medulloblastomas...
December 2017: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/29199104/reverse-engineering-the-cancer-metabolic-network-using-flux-analysis-to-understand-drivers-of-human-disease
#18
REVIEW
Mehmet G Badur, Christian M Metallo
Metabolic dysfunction has reemerged as an essential hallmark of tumorigenesis, and metabolic phenotypes are increasingly being integrated into pre-clinical models of disease. The complexity of these metabolic networks requires systems-level interrogation, and metabolic flux analysis (MFA) with stable isotope tracing present a suitable conceptual framework for such systems. Here we review efforts to elucidate mechanisms through which metabolism influences tumor growth and survival, with an emphasis on applications using stable isotope tracing and MFA...
November 30, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29199093/evolutionary-epistemology-reviewing-and-reviving-with-new-data-the-research-programme-for-distributed-biological-intelligence
#19
REVIEW
Predrag Slijepcevic
Numerous studies in microbiology, eukaryotic cell biology, plant biology, biomimetics, synthetic biology, and philosophy of science appear to support the principles of the epistemological theory inspired by evolution, also known as "Evolutionary Epistemology", or EE. However, that none of the studies acknowledged EE suggests that its principles have not been formulated with sufficient clarity and depth to resonate with the interests of the empirical research community. In this paper I review evidence in favor of EE, and also reformulate EE principles to better inform future research...
November 30, 2017: Bio Systems
https://www.readbyqxmd.com/read/29198564/linking-stem-cell-function-and-growth-pattern-of-intestinal-organoids
#20
Torsten Thalheim, Marianne Quaas, Maria Herberg, Ulf-Dietrich Braumann, Christiane Kerner, Markus Loeffler, Gabriela Aust, Joerg Galle
Intestinal stem cells (ISCs) require well-defined signals from their environment in order to carry out their specific functions. Most of these signals are provided by neighboring cells that form a stem cell niche, whose shape and cellular composition self-organize. Major features of this self-organization can be studied in ISC-derived organoid culture. In this system, manipulation of essential pathways of stem cell maintenance and differentiation results in well-described growth phenotypes. We here provide an individual cell-based model of intestinal organoids that enables a mechanistic explanation of the observed growth phenotypes...
October 31, 2017: Developmental Biology
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