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https://www.readbyqxmd.com/read/28651352/circular-rna-profiling-reveals-that-circular-rnas-from-anxa2-can-be-used-as-new-biomarkers-for-multiple-sclerosis
#1
Iparraguirre Leire, Muñoz-Culla Maider, Prada Iñigo, Castillo-Triviño Tamara, Olascoaga Javier, Otaegui David
Multiple Sclerosis is an autoimmune disease, with higher prevalence in women, in whom the immune system is dysregulated. This dysregulation has been shown to correlate with changes in transcriptome expression as well as in gene-expression regulators, such as non-coding RNAs (e.g. microRNAs). Indeed, some of these have been suggested as biomarkers for multiple sclerosis even though few biomarkers have reached the clinical practice.Recently, a novel family of non-coding RNAs, circular RNAs, has emerged as a new player in the complex network of gene-expression regulation...
June 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28651222/assessing-habitat-quality-in-relation-to-the-spatial-distribution-of-protected-areas-in-italy
#2
Lorenzo Sallustio, Andrea De Toni, Andrea Strollo, Mirko Di Febbraro, Elena Gissi, Laura Casella, Davide Geneletti, Michele Munafò, Matteo Vizzarri, Marco Marchetti
The conservation of species and habitats is increasingly threatened by anthropogenic impacts, particularly land use change, from local to global scales. Although many efforts have been carried out so far to halt or at least reduce the biodiversity loss (e.g., the establishment of protected areas' networks), there are still both knowledge and policy gaps slowing the conservation of species and habitats in complex environments, such as the Mediterranean region. In particular, the human-driven impacts and threats on biodiversity need more careful analysis...
June 23, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28651183/investigating-the-effect-of-different-transducer-stiffness-values-on-the-contactin-complex-detachment-by-steered-molecular-dynamics
#3
Parnian Kianfar, Nabiollah Abolfathi, Navid Zarif Karimi
This study investigated the adhesion behavior of Contactin4 (CNTN4), a member of Immunoglobulin Super Family (Ig-SF) of cell adhesion molecules. Contactin4 plays a crucial role in the formation, maintenance, and plasticity of neuronal networks. Contactin in its complex configuration with protein tyrosine phosphatase gamma (PTPRG) was selected for simulation. By utilizing Steered Molecular Dynamics (SMD), the uniaxial force was applied to induce unbinding of the complex, and the force-induced detachment of complex components was probed...
June 2, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28650998/functional-annotation-of-alzheimer-s-disease-associated-loci-revealed-by-gwass
#4
Zengpeng Han, Han Huang, Yue Gao, Qingyang Huang
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28650678/an-integrative-approach-for-identifying-network-biomarkers-of-breast-cancer-subtypes-using-genomic-interactomic-and-transcriptomic-data
#5
Forough Firoozbakht, Iman Rezaeian, Michele D'agnillo, Lisa Porter, Luis Rueda, Alioune Ngom
Breast cancer is a complex disease that can be classified into at least 10 different molecular subtypes. Appropriate diagnosis of specific subtypes is critical for ensuring the best possible patient treatment and response to therapy. Current computational methods for determining the subtypes are based on identifying differentially expressed genes (i.e., biomarkers) that can best discriminate the subtypes. Such approaches, however, are known to be unreliable since they yield different biomarker sets when applied to data sets from different studies...
June 26, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28650651/tuning-selectivity-of-co2-hydrogenation-reactions-at-the-metal-oxide-interface
#6
Shyam Kattel, Ping Liu, Jingguang G Chen
The chemical transformation of CO2 not only mitigates the anthropogenic CO2 emission into the earth's atmosphere but also produces carbon compounds that can be used as precursors for the production of chemicals and fuels. The activation and conversion of CO2 can be achieved on multifunctional catalytic sites available at the metal/oxide interface by taking advantage of the synergy between the metal nanoparticles and oxide support. Herein, we reviewed the recent progress in mechanistic studies of CO2 hydrogenation to C1 (CO, CH3OH and CH4) compounds on metal/oxide catalysts...
June 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28649677/outcome-prediction-for-patient-with-high-grade-gliomas-from-brain-functional-and-structural-networks
#7
Luyan Liu, Han Zhang, Islem Rekik, Xiaobo Chen, Qian Wang, Dinggang Shen
High-grade glioma (HGG) is a lethal cancer, which is characterized by very poor prognosis. To help optimize treatment strategy, accurate preoperative prediction of HGG patient's outcome (i.e., survival time) is of great clinical value. However, there are huge individual variability of HGG, which produces a large variation in survival time, thus making prognostic prediction more challenging. Previous brain imaging-based outcome prediction studies relied only on the imaging intensity inside or slightly around the tumor, while ignoring any information that is located far away from the lesion (i...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28649614/integrated-molecular-landscape-of-parkinson-s-disease
#8
C J H M Klemann, G J M Martens, M Sharma, M B Martens, O Isacson, T Gasser, J E Visser, G Poelmans
Parkinson's disease is caused by a complex interplay of genetic and environmental factors. Although a number of independent molecular pathways and processes have been associated with familial Parkinson's disease, a common mechanism underlying especially sporadic Parkinson's disease is still largely unknown. In order to gain further insight into the etiology of Parkinson's disease, we here conducted genetic network and literature analyses to integrate the top-ranked findings from thirteen published genome-wide association studies of Parkinson's disease (involving 13...
2017: NPJ Parkinson's Disease
https://www.readbyqxmd.com/read/28649443/a-multiscale-model-of-early-cell-lineage-specification-including-cell-division
#9
Alen Tosenberger, Didier Gonze, Sylvain Bessonnard, Michel Cohen-Tannoudji, Claire Chazaud, Geneviève Dupont
Embryonic development is a self-organised process during which cells divide, interact, change fate according to a complex gene regulatory network and organise themselves in a three-dimensional space. Here, we model this complex dynamic phenomenon in the context of the acquisition of epiblast and primitive endoderm identities within the inner cell mass of the preimplantation embryo in the mouse. The multiscale model describes cell division and interactions between cells, as well as biochemical reactions inside each individual cell and in the extracellular matrix...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649440/cross-species-gene-modules-emerge-from-a-systems-biology-approach-to-osteoarthritis
#10
Alan James Mueller, Elizabeth G Canty-Laird, Peter D Clegg, Simon R Tew
Complexities in degenerative disorders, such as osteoarthritis, arise from multiscale biological, environmental, and temporal perturbations. Animal models serve to provide controlled representations of the natural history of degenerative disorders, but in themselves represent an additional layer of complexity. Comparing transcriptomic networks arising from gene co-expression data across species can facilitate an understanding of the preservation of functional gene modules and establish associations with disease phenotypes...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649439/mechanisms-of-action-of-sacubitril-valsartan-on-cardiac-remodeling-a-systems-biology-approach
#11
Oriol Iborra-Egea, Carolina Gálvez-Montón, Santiago Roura, Isaac Perea-Gil, Cristina Prat-Vidal, Carolina Soler-Botija, Antoni Bayes-Genis
Sacubitril/Valsartan, proved superiority over other conventional heart failure management treatments, but its mechanisms of action remains obscure. In this study, we sought to explore the mechanistic details for Sacubitril/Valsartan in heart failure and post-myocardial infarction remodeling, using an in silico, systems biology approach. Myocardial transcriptome obtained in response to myocardial infarction in swine was analyzed to address post-infarction ventricular remodeling. Swine transcriptome hits were mapped to their human equivalents using Reciprocal Best (blast) Hits, Gene Name Correspondence, and InParanoid database...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#12
Michael V Lombardo, Eric Courchesne, Nathan E Lewis, Tiziano Pramparo
BACKGROUND: Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28649257/mati-a-novel-protein-involved-in-the-regulation-of-herbivore-associated-signaling-pathways
#13
M Estrella Santamaría, Manuel Martinez, Ana Arnaiz, Félix Ortego, Vojislava Grbic, Isabel Diaz
The defense response of the plants against herbivores relies on a complex network of interconnected signaling pathways. In this work, we characterized a new key player in the response of Arabidopsis against the two-spotted spider mite Tetranychus urticae, the MATI (Mite Attack Triggered Immunity) gene. This gene was differentially induced in resistant Bla-2 strain relative to susceptible Kon Arabidopsis accessions after mite attack, suggesting a potential role in the control of spider mites. To study the MATI gene function, it has been performed a deep molecular characterization of the gene combined with feeding bioassays using modified Arabidopsis lines and phytophagous arthropods...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28649256/evolutionary-insights-based-on-snp-haplotypes-of-red-pericarp-grain-size-and-starch-synthase-genes-in-wild-and-cultivated-rice
#14
Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Sidhu, Ashok K Singh, Nagendra K Singh
The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28649202/neuronal-chemosensation-and-osmotic-stress-response-converge-in-the-regulation-of-aqp-8-in-c-elegans
#15
Carla Igual Gil, Mirko Jarius, Jens P von Kries, Anne-Katrin Rohlfing
Aquaporins occupy an essential role in sustaining the salt/water balance in various cells types and tissues. Here, we present new insights into aqp-8 expression and regulation in Caenorhabditis elegans. We show, that upon exposure to osmotic stress, aqp-8 exhibits a distinct expression pattern within the excretory cell compared to other C. elegans aquaporins expressed. This expression is correlated to the osmolarity of the surrounding medium and can be activated physiologically by osmotic stress or genetically in mutants with constitutively active osmotic stress response...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28648582/molecular-mechanism-of-phosphate-signaling-in-plants
#16
REVIEW
Fei Wang, Meiju Deng, Jiming Xu, Xinlu Zhu, Chuanzao Mao
Phosphorus (P) is one of the indispensable macronutrients for plant growth and development. To adapt to low phosphate (Pi) environment, plants have evolved complex responsive and adaptive mechanisms for acquisition and remobilization of phosphate to maintain P homeostasis, which are regulated by complex gene regulation networks through the functions of Pi transporters (PTs) and other Pi starvation induced (PSI) genes. This review summarizes the recent progresses on the molecular regulation mechanism of phosphate transporters and phosphate signal transduction pathway (also called phosphate signaling) in dicot model plant Arabidopsis (Arabidopsis thaliana) and monocot model plant rice (Oryza sativa L...
June 22, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28648571/the-neuro-cognitive-representations-of-symbols-the-case-of-concrete-words
#17
Valentina Borghesani, Manuela Piazza
We live our lives surrounded by symbols (e.g., road signs, logos, but especially words and numbers), and throughout our life we use them to evoke, communicate and reflect upon ideas and things that are not currently present to our senses. Symbols are represented in our brains at different levels of complexity: at the first and most simple level, as physical entities, in the corresponding primary and secondary sensory cortices. The crucial property of symbols, however, is that, despite the simplicity of their surface forms, they have the power of evoking higher order multifaceted representations that are implemented in distributed neural networks spanning a large portion of the cortex...
June 22, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28647368/identification-and-characterization-of-the-leaf-specific-networks-of-inner-and-rosette-leaves-in-brassica-rapa
#18
Man-Sun Kim, Seongmin Hong, Devaraj Sangeeth Prasath, Subin Im, Jeong-Rae Kim, Yong Pyo Lim
Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone...
June 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28647089/reverse-phase-protein-arrays-elucidate-mechanisms-of-action-and-phenotypic-response-in-2d-and-3d-models
#19
REVIEW
Michael Pawlak, Neil O Carragher
The development of new 2D and 3D phenotypic screening assays combined with high-throughput genomic and proteomic technologies are well placed to advance a new era of molecular pathway informed Phenotypic Drug Discovery. We describe the application of Reverse Phase Protein Array (RPPA) technology to elucidate the mechanism-of-action of small molecules at the post-translational pathway level. We propose that profiling of phenotypic hits and lead molecules in increasingly more complex 3D in vitro and ex vivo models at the post-translational pathway network level represents an effective strategy to both triage and progress the preclinical development of phenotypic screening hits...
March 2017: Drug Discovery Today. Technologies
https://www.readbyqxmd.com/read/28646692/specific-subcortical-structures-are-activated-during-seizure-induced-death-in-a-model-of-sudden-unexpected-death-in-epilepsy-sudep-a-manganese-enhanced-magnetic-resonance-imaging-study
#20
Srinivasa P Kommajosyula, Marcus E Randall, Thomas J Brozoski, Boris M Odintsov, Carl L Faingold
Sudden unexpected death in epilepsy (SUDEP) is a major concern for patients with epilepsy. In most witnessed cases of SUDEP generalized seizures and respiratory failure preceded death, and pre-mortem neuroimaging studies in SUDEP patients observed changes in specific subcortical structures. Our study examined the role of subcortical structures in the DBA/1 mouse model of SUDEP using manganese-enhanced magnetic resonance imaging (MEMRI). These mice exhibit acoustically-evoked generalized seizures leading to seizure-induced respiratory arrest (S-IRA) that results in sudden death unless resuscitation is rapidly instituted...
May 25, 2017: Epilepsy Research
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