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https://www.readbyqxmd.com/read/29786765/analysis-of-streptomyces-ghanaensis-atcc14672-gene-ssfg_07725-for-putative-%C3%AE-butyrolactone-synthase
#1
Yuriy Kuzhyk, Halyna Mutenko, Victor Fedorenko, Bohdan Ostash
Low molecular weight signaling compounds (LMWC) are important players in regulating various aspects of Streptomyces biology. Their exact roles in certain strain will ultimately depend on overall configuration of regulatory network and thus cannot be predicted on basis of in silico studies. Here, we explored S. ghanaensis gene SSFG_07725 (afsA gh ) presumably involved in initial steps of formation of γ-butyrolactone LMWC. Disruption of afsA gh impaired aerial mycelium formation and increased the transcription of pleiotropic regulatory gene adpA gh , whereas level of moenomycin production remained virtually unaffected...
May 21, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29786556/assessment-of-stem-cell-differentiation-based-on-genome-wide-expression-profiles
#2
REVIEW
Patricio Godoy, Wolfgang Schmidt-Heck, Birte Hellwig, Patrick Nell, David Feuerborn, Jörg Rahnenführer, Kathrin Kattler, Jörn Walter, Nils Blüthgen, Jan G Hengstler
In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences from the intended target cells or tissues. The pipeline requires RNA-Seq or gene array data of the stem cell starting population, derived 'mature' cells and primary target cells or tissue...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29785401/rheumatoid-arthritis-and-mirnas-a-critical-review-through-a-functional-view
#3
REVIEW
Maria Cristina Moran-Moguel, Stefania Petarra-Del Rio, Evangelina E Mayorquin-Galvan, Maria G Zavala-Cerna
Rheumatoid arthritis (RA) is a systemic autoimmune disease with severe joint inflammation and destruction associated with an inflammatory environment. The etiology behind RA remains to be elucidated; most updated concepts include the participation of environmental, proteomic, epigenetic, and genetic factors. Epigenetic is considered the missing link to explain genetic diversification among RA patients. Within epigenetic factors participating in RA, miRNAs are defined as small noncoding molecules with a length of approximately 22 nucleotides, capable of gene expression modulation, either negatively through inhibition of translation and degradation of the mRNA or positively through increasing the translation rate...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29785339/identification-of-potential-crucial-genes-and-pathways-associated-with-vein-graft-restenosis-based-on-gene-expression-analysis-in-experimental-rabbits
#4
Qiang Liu, Xiujie Yin, Mingzhu Li, Li Wan, Liqiao Liu, Xiang Zhong, Zhuoqi Liu, Qun Wang
Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the most prevalently performed treatment for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, the clinical efficacy of bypass graft surgery is highly affected by the long-term potency rates of vein grafts, and no optimal treatments are available for the prevention of vein graft restenosis (VGR) at present. Hence, there is an urgent need to improve our understanding of the molecular mechanisms involved in mediating VGR...
2018: PeerJ
https://www.readbyqxmd.com/read/29785139/blockage-of-store-operated-ca-2-entry-antagonizes-epstein-barr-virus-promoted-angiogenesis-by-inhibiting-ca-2-signaling-regulated-vegf-production-in-nasopharyngeal-carcinoma
#5
Jiaxiang Ye, Junqi Huang, Qian He, Weilin Zhao, Xiaoying Zhou, Zhe Zhang, Yongqiang Li, Jiazhang Wei, Jinyan Zhang
Background: Epstein-Barr virus (EBV) actively contributes to the pathological process of nasopharyngeal carcinoma (NPC) by enabling NPC cells to acquire various capacities required for their malignant biological actions. Our earlier works demonstrated that EBV-encoded latent membrane protein 1 (LMP1) enhanced vascular endothelial growth factor (VEGF)-mediated angiogenesis by boosting store-operated Ca2+ entry (SOCE) upon extracellular epidermal growth factor (EGF) stimulation. However, the antagonistic effects of SOCE blockage on EBV-promoted angiogenesis must be appropriately evaluated in vivo, and the global effect of EBV infection on the EGF-elicited cytosolic Ca2+ signaling, which regulates VEGF-mediated angiogenesis remains to be further clarified...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29785073/scale-free-networks-in-metabolomics
#6
Hema Sekhar Reddy Rajula, Matteo Mauri, Vassilios Fanos
Metabolomics is an expanding discipline in biology. It is the process of portraying the phenotype of a cell, tissue or species organism using a comprehensive set of metabolites. Therefore, it is of interest to understand complex systems such as metabolomics using a scale-free topology. Genetic networks and the World Wide Web (WWW) are described as networks with complex topology. Several large networks have vertex connectivity that goes beyond a scale-free power-law distribution. It is observed that (a) networks expand constantly by the addition of recent vertices, and (b) recent vertices attach preferentially to sites that are already well connected...
2018: Bioinformation
https://www.readbyqxmd.com/read/29785028/the-reference-epigenome-and-regulatory-chromatin-landscape-of-chronic-lymphocytic-leukemia
#7
Renée Beekman, Vicente Chapaprieta, Núria Russiñol, Roser Vilarrasa-Blasi, Núria Verdaguer-Dot, Joost H A Martens, Martí Duran-Ferrer, Marta Kulis, François Serra, Biola M Javierre, Steven W Wingett, Guillem Clot, Ana C Queirós, Giancarlo Castellano, Julie Blanc, Marta Gut, Angelika Merkel, Simon Heath, Anna Vlasova, Sebastian Ullrich, Emilio Palumbo, Anna Enjuanes, David Martín-García, Sílvia Beà, Magda Pinyol, Marta Aymerich, Romina Royo, Montserrat Puiggros, David Torrents, Avik Datta, Ernesto Lowy, Myrto Kostadima, Maša Roller, Laura Clarke, Paul Flicek, Xabier Agirre, Felipe Prosper, Tycho Baumann, Julio Delgado, Armando López-Guillermo, Peter Fraser, Marie-Laure Yaspo, Roderic Guigó, Reiner Siebert, Marc A Martí-Renom, Xose S Puente, Carlos López-Otín, Ivo Gut, Hendrik G Stunnenberg, Elias Campo, Jose I Martin-Subero
Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29784986/a-workflow-for-the-integrative-transcriptomic-description-of-molecular-pathology-and-the-suggestion-of-normalizing-compounds-exemplified-by-parkinson-s-disease
#8
Mohamed Hamed, Yvonne Gladbach, Steffen Möller, Sarah Fischer, Mathias Ernst, Stephan Struckmann, Alexander Storch, Georg Fuellen
The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784782/riboswitches-for-the-alarmone-ppgpp-expand-the-collection-of-rna-based-signaling-systems
#9
Madeline E Sherlock, Narasimhan Sudarsan, Ronald R Breaker
Riboswitches are noncoding portions of certain mRNAs that bind metabolite, coenzyme, signaling molecule, or inorganic ion ligands and regulate gene expression. Most known riboswitches sense derivatives of RNA monomers. This bias in ligand chemical composition is consistent with the hypothesis that widespread riboswitch classes first emerged during the RNA World, which is proposed to have existed before proteins were present. Here we report the discovery and biochemical validation of a natural riboswitch class that selectively binds guanosine tetraphosphate (ppGpp), a widespread signaling molecule and bacterial "alarmone" derived from the ribonucleotide GTP...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784759/of-what-use-is-connectomics-a-personal-perspective-on-the-drosophila-connectome
#10
REVIEW
Ian A Meinertzhagen
The brain is a network of neurons and its biological output is behaviour. This is an exciting age, with a growing acknowledgement that the comprehensive compilation of synaptic circuits densely reconstructed in the brains of model species is now both technologically feasible and a scientifically enabling possibility in neurobiology, much as 30 years ago genomics was in molecular biology and genetics. Implemented by huge advances in electron microscope technology, especially focused ion beam-scanning electron microscope (FIB-SEM) milling (see Glossary), image capture and alignment, and computer-aided reconstruction of neuron morphologies, enormous progress has been made in the last decade in the detailed knowledge of the actual synaptic circuits formed by real neurons, in various brain regions of the fly Drosophila It is useful to distinguish synaptic pathways that are major, with 100 or more presynaptic contacts, from those that are minor, with fewer than about 10; most neurites are both presynaptic and postsynaptic, and all synaptic sites have multiple postsynaptic dendrites...
May 20, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29784056/biomarker-micrornas-for-prostate-cancer-metastasis-screened-with-a-network-vulnerability-analysis-model
#11
Yuxin Lin, Feifei Chen, Li Shen, Xiaoyu Tang, Cui Du, Zhandong Sun, Huijie Ding, Jiajia Chen, Bairong Shen
BACKGROUND: Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. METHODS: In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis...
May 21, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29783016/systematic-investigation-of-the-erigeron-breviscapus-mechanism-for-treating-cerebrovascular-disease
#12
Jiangmei Wang, Yangyang Chen, Baoshi Liu, Qian Wang, Lulu Zhang, Zhenzhong Wang, Jun Zhou, Wei Xiao, Chunli Zheng, Yonghua Wang
ETHNOPHARMACOLOGICAL RELEVANCE: Cerebrovascular diseases (CBVDs), characterized by striking morbidity and mortality, have become the most common life-threatening diseases. The existing drugs of CBVDs target one or a few of pathogenic factors, the efficacy of which is limited because of the complexity of CBVDs. Traditional Chinese medicine (TCM), featured by multi-component and multi-target endows the great effectiveness in CBVDs treatment. For instance, Erigeron breviscapus (vant.) Hand...
May 18, 2018: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29782994/structural-covariance-of-brain-region-volumes-is-associated-with-both-structural-connectivity-and-transcriptomic-similarity
#13
Yohan Yee, Darren J Fernandes, Leon French, Jacob Ellegood, Lindsay S Cahill, Dulcie A Vousden, Leigh Spencer Noakes, Jan Scholz, Matthijs C van Eede, Brian J Nieman, John G Sled, Jason P Lerch
An organizational pattern seen in the brain, termed structural covariance, is the statistical association of pairs of brain regions in their anatomical properties. These associations, measured across a population as covariances or correlations usually in cortical thickness or volume, are thought to reflect genetic and environmental underpinnings. Here, we examine the biological basis of structural volume covariance in the mouse brain. We first examined large scale associations between brain region volumes using an atlas-based approach that parcellated the entire mouse brain into 318 regions over which correlations in volume were assessed, for volumes obtained from 153 mouse brain images via high-resolution MRI...
May 18, 2018: NeuroImage
https://www.readbyqxmd.com/read/29782831/mapping-cellular-polarity-networks-using-mass-spectrometry-based-strategies
#14
REVIEW
Avais M Daulat, Tania M Puvirajesinghe, Luc Camoin, Jean-Paul Borg
Cell polarity is a vital biological process involved in the building, maintenance and normal functioning of tissues in invertebrates and vertebrates. Unsurprisingly, molecular defects affecting polarity organization and functions have a strong impact on tissue homeostasis, embryonic development and adult life, and may directly or indirectly lead to diseases. Genetic studies have demonstrated the causative effect of several polarity genes in diseases, however much remains to be clarified before a comprehensive view of the molecular organization and regulation of the protein networks associated with polarity proteins is obtained...
May 18, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29782506/assessment-of-the-national-park-network-of-mainland-spain-by-the-insecurity-index-of-vertebrate-species
#15
Alba Estrada, Raimundo Real
The evaluation of protected area networks on their capacity to preserve species distributions is a key topic in conservation biology. There are different types of protected areas, with National Parks those with highest level of protection. National Parks can be declared attending to many ecological features that include the presence of certain animal species. Here, we selected 37 vertebrate species that were highlighted as having relevant natural value for at least one of the 10 National Parks of mainland Spain...
2018: PloS One
https://www.readbyqxmd.com/read/29782142/projection-based-3d-printing-of-cell-patterning-scaffolds-with-multi-scale-channels
#16
Dai Xue, Yancheng Wang, Jiaxin Zhang, Deqing Mei, Yue Wang, Shaochen Chen
To fully actualize artificial, cell-laden biological models in tissue engineering, such as 3D organoids and organs-on-a-chip systems, cells need to be patterned such that they can precisely mimic natural microenvironments in vitro. Despite increasing interest in this area, patterning cells at multiscales (~10 μm - 10 mm) remains a significant challenge in bioengineering. Here we report a projection-based 3D printing system that achieves rapid and high-resolution fabrication of hydrogel scaffolds featuring intricate channels for multi-scale cell patterning...
May 21, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29780857/multi-omic-network-based-interrogation-of-rat-liver-metabolism-following-gastric-bypass-surgery-featuring-swath-proteomics
#17
Gautham Vivek Sridharan, Matthew D'Alessandro, Shyam Sundhar Bale, Vicky Bhagat, Hugo Gagnon, John M Asara, Korkut Uygun, Martin L Yarmush, Nima Saeidi
Morbidly obese patients often elect for Roux-en-Y gastric bypass (RYGB), a form of bariatric surgery that triggers a remarkable 30% reduction in excess body weight and reversal of insulin resistance for those who are type II diabetic. A more complete understanding of the underlying molecular mechanisms that drive the complex metabolic reprogramming post-RYGB could lead to innovative non-invasive therapeutics that mimic the beneficial effects of the surgery, namely weight loss, achievement of glycemic control, or reversal of non-alcoholic steatohepatitis (NASH)...
September 2017: Technology
https://www.readbyqxmd.com/read/29780405/quercetin-induced-lifespan-extension-in-podospora-anserina-requires-methylation-of-the-flavonoid-by-the-o-methyltransferase-pamth1
#18
Verena Warnsmann, Saskia Hainbuch, Heinz D Osiewacz
Quercetin is a flavonoid that is ubiquitously found in vegetables and fruits. Like other flavonoids, it is active in balancing cellular reactive oxygen species (ROS) levels and has a cyto-protective function. Previously, a link between ROS balancing, aging, and the activity of O -methyltransferases was reported in different organisms including the aging model Podospora anserina. Here we describe a role of the S -adenosylmethionine-dependent O -methyltransferase PaMTH1 in quercetin-induced lifespan extension...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29779865/gmf-as-an-actin-network-remodeling-factor
#19
REVIEW
Bruce L Goode, Meredith O Sweeney, Julian A Eskin
Glia maturation factor (GMF) has recently been established as a regulator of the actin cytoskeleton with a unique role in remodeling actin network architecture. Conserved from yeast to mammals, GMF is one of five members of the ADF-H family of actin regulatory proteins, which includes ADF/cofilin, Abp1/Drebrin, Twinfilin, and Coactosin. GMF does not bind actin, but instead binds the Arp2/3 complex with high affinity. Through this association, GMF catalyzes the debranching of actin filament networks and inhibits actin nucleation by Arp2/3 complex...
May 18, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29779095/crispr-cas13a-targeting-of-rna-virus-in-plants
#20
Kulbhushan Chaudhary
This approach is quite promising to control plant viral diseases and create synthetic networks to better understand the structure/function relationship in RNA and proteins. Plant viruses are obligate intracellular parasites which causes enormous losses in crop yield worldwide. These viruses replicate into infected cells by highjacking host cellular machinery. Over the last two decades, diverse approaches such as conventional breeding, transgenic approach and gene silencing strategies have been used to control RNA viruses, but escaped due to high rate of mutation...
May 19, 2018: Plant Cell Reports
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