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https://www.readbyqxmd.com/read/28920469/the-canonical-way-to-make-a-heart-%C3%AE-catenin-and-plakoglobin-in-heart-development-and-remodeling
#1
Oksana O Piven, Cecilia L Winata
The main mediator of the canonical Wnt pathway, β-catenin, is a major effector of embryonic development, postnatal tissue homeostasis, and adult tissue regeneration. The requirement for β-catenin in cardiogenesis and embryogenesis has been well established. However, many questions regarding the molecular mechanisms by which β-catenin and canonical Wnt signaling regulate these developmental processes remain unanswered. An interesting question that emerged from our studies concerns how β-catenin signaling is modulated through interaction with other factors...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28918935/dense-intra-adipose-sympathetic-arborizations-are-essential-for-cold-induced-beiging-of-mouse-white-adipose-tissue
#2
Haochen Jiang, Xiaofan Ding, Ying Cao, Huanhuan Wang, Wenwen Zeng
Efferent signals from the central nervous system represent a key layer of regulation of white adipose tissue (WAT). However, the mechanism by which efferent neural signals control WAT metabolism remains to be better understood. Here, we exploit the volume fluorescence-imaging technique to visualize the neural arborizations in mouse inguinal WAT at single-fiber resolution. The imaging reveals a dense network of sympathetic arborizations that had been previously undetected by conventional methods, with sympathetic fibers being in close apposition to > 90% of adipocytes...
September 5, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28918332/control-of-absence-epilepsy-seizures-in-specific-relay-nuclei-of-thalamus
#3
Bing Hu, Xiaoqiang Zou, Yu Guo, Zhejia Yang, Feng Shi, Wangyuan Dong
In this paper, we used a classic basal ganglia-corticothalamic model(BGCT) to study the onset and control mechanism of absence epilepsy in specific relay nuclei (SRN) of thalamus. It was found that the seizure state may appear in SRN by turning the coupling strength -vsr and signal transmission delay τ on the route "Thalamic reticular nuclei (TRN) of thalamus ⟶ SRN ". With increasing of -vsr, the seizure state appeared two times, and its onset mechanism has not been discussed in previous studies. The seizure activity can be well controlled by adjusting the activation level of the substantia nigra pars reticulata (SNr) in basal ganglia, which is a main output tissue to the corticothalamic system through two direct inhibitory pathways "SNr ⟶ SRN" and "SNr ⟶ TRN " in our model...
September 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28918159/identification-of-circular-rna-in-the-bombyx-mori-silk-gland
#4
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Bombyx mori is an economically important holometabolous lepidopteran insect. In B. mori endogenous noncoding RNAs such as microRNAs (miRNAs) and Piwi-interacting RNAs play crucial biological functions in metamorphosis and sex determination. In addition, circular RNAs (circRNAs) have been recently identified as noncoding RNAs in most common model organisms and show potential as gene regulators. However, to date, there have been few studies on the circRNAs present in the B. mori genome conducted to date. Here, we identified 3916 circRNAs by deep circular transcriptome sequencing using the silk gland of B...
September 13, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28916541/a-proteomic-atlas-of-insulin-signalling-reveals-tissue-specific-mechanisms-of-longevity-assurance
#5
Luke S Tain, Robert Sehlke, Chirag Jain, Manopriya Chokkalingam, Nagarjuna Nagaraj, Paul Essers, Mark Rassner, Sebastian Grönke, Jenny Froelich, Christoph Dieterich, Matthias Mann, Nazif Alic, Andreas Beyer, Linda Partridge
Lowered activity of the insulin/IGF signalling (IIS) network can ameliorate the effects of ageing in laboratory animals and, possibly, humans. Although transcriptome remodelling in long-lived IIS mutants has been extensively documented, the causal mechanisms contributing to extended lifespan, particularly in specific tissues, remain unclear. We have characterized the proteomes of four key insulin-sensitive tissues in a long-lived Drosophila IIS mutant and control, and detected 44% of the predicted proteome (6,085 proteins)...
September 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28915785/seed-maturation-associated-transcriptional-programs-and-regulatory-networks-underlying-genotypic-difference-in-seed-dormancy-and-size-weight-in-wheat-triticum-aestivum-l
#6
Yuji Yamasaki, Feng Gao, Mark C Jordan, Belay T Ayele
BACKGROUND: Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype...
September 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28915634/dna-methylation-signature-of-long-noncoding-rna-genes-during-human-pre-implantation-embryonic-development
#7
Jingyu Li, Wei Han, Xiaoli Shen, Shubiao Han, Hong Ye, Guoning Huang
DNA methylation have crucial roles in regulating the expression of developmental genes during mammalian pre-implantation embryonic development (PED). However, the DNA methylation dynamic pattern of long noncoding RNA (lncRNA) genes, one type of epigenetic regulators, in human PED have not yet been demonstrated. Here, we performed a comprehensive analysis of lncRNA genes in human PED based on public reduced representation bisulphite sequencing (RRBS) data. We observed that both lncRNA and protein-coding genes complete the major demethylation wave at the 2-cell stage, whereas the promoters of lncRNA genes show higher methylation level than protein-coding genes during PED...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915238/a-high-resolution-atlas-of-gene-expression-in-the-domestic-sheep-ovis-aries
#8
Emily L Clark, Stephen J Bush, Mary E B McCulloch, Iseabail L Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C Bruce Whitelaw, Tom C Freeman, Kim M Summers, Alan L Archibald, David A Hume
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28914394/bioinformatics-based-identification-of-methylated-differentially-expressed-genes-and-related-pathways-in-gastric-cancer
#9
Hao Li, Jing-Wei Liu, Shuang Liu, Yuan Yuan, Li-Ping Sun
BACKGROUND AND AIMS: The aim of the study was to identify methylated-differentially expressed genes (MDEGs) in gastric cancer and investigate their potential pathways. METHODS: Expression profiling (GSE13911 and GSE29272) and methylation profiling (GSE25869 and GSE30601) data were obtained from GEO DataSets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology and pathway enrichment analyses were performed for the MDEGs...
September 15, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28913594/developmental-trajectory-of-the-prefrontal-cortex-a-systematic-review-of-diffusion-tensor-imaging-studies
#10
Sónia S Sousa, Edson Amaro, Alberto Crego, Óscar F Gonçalves, Adriana Sampaio
Fluctuations in gray and white matter volumes in addition to the fibers' reorganization and refinement of synaptic connectivity apparently happen in a particular temporo-spatial sequence during the dynamic and prolonged process of cerebral maturation. These developmental events are associated with regional modifications of brain tissues and neural circuits, contributing to networks' specialization and enhanced cognitive processing. According to several studies, improvements in cognitive processes are possibly myelin-dependent and associated to white matter maturation...
September 15, 2017: Brain Imaging and Behavior
https://www.readbyqxmd.com/read/28913343/exacerbating-and-reversing-lysosomal-storage-diseases-from-yeast-to-humans
#11
REVIEW
Tamayanthi Rajakumar, Andrew B Munkacsi, Stephen L Sturley
Lysosomal storage diseases (LSDs) arise from monogenic deficiencies in lysosomal proteins and pathways and are characterized by a tissue-wide accumulation of a vast variety of macromolecules, normally specific to each genetic lesion. Strategies for treatment of LSDs commonly depend on reduction of the offending metabolite(s) by substrate depletion or enzyme replacement. However, at least 44 of the ~50 LSDs are currently recalcitrant to intervention. Murine models have provided significant insights into our understanding of many LSD mechanisms; however, these systems do not readily permit phenotypic screening of compound libraries, or the establishment of genetic or gene-environment interaction networks...
August 25, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28911967/applications-of-nuclear-magnetic-resonance-in-lipid-analyses-an-emerging-powerful-tool-for-lipidomics-studies
#12
REVIEW
Jingbo Li, Thomas Vosegaard, Zheng Guo
The role of lipids in cell, tissue, and organ physiology is crucial; as many diseases, including cancer, diabetes, neurodegenerative, and infectious diseases, are closely related to absorption and metabolism of lipids. Mass spectrometry (MS) based methods are the most developed powerful tools to study the synthetic pathways and metabolic networks of cellular lipids in biological systems; leading to the birth of an emerging subject lipidomics, which has been extensively reviewed. Nuclear magnetic resonance (NMR), another powerful analytical tool, which allows the visualization of single atoms and molecules, is receiving increasing attention in lipidomics analyses...
September 11, 2017: Progress in Lipid Research
https://www.readbyqxmd.com/read/28903493/editor-s-highlight-formulation-and-toxicology-evaluation-of-the-intrathecal-ayx1-dna-decoy-in-sprague-dawley-rats
#13
Julien Mamet, David C Yeomans, Tony L Yaksh, Donald C Manning, Scott Harris
The longevity of pain after surgery is debilitating and limits the recovery of patients. AYX1 is a double-stranded, unprotected, 23 base-pair oligonucleotide designed to reduce acute post-surgical pain and prevent its chronification with a single intrathecal perioperative dose. AYX1 mimics the DNA sequence normally bound by EGR1 on chromosomes, a transcription factor transiently induced in the dorsal root ganglia-spinal cord network following a noxious input. AYX1 binds to EGR1 and prevents it from launching waves of gene regulation that are necessary to maintain pain over time...
September 1, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28901494/molecular-mechanisms-of-pathogenesis-in-hepatocellular-carcinoma-revealed-by-rna%C3%A2-sequencing
#14
Yao Liu, Zhe Yang, Feng Du, Qiao Yang, Jie Hou, Xiaohong Yan, Yi Geng, Yaning Zhao, Hua Wang
The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants...
September 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28901463/microrna-expression-profiles-and-networks-in-placentas-complicated-with-selective-intrauterine-growth-restriction
#15
Hong Wen, Lu Chen, Jing He, Jun Lin
The microRNA (miRNA) profiles of placentas complicated with selective intrauterine growth restriction (sIUGR) are unknown. In the present study, the sIUGR‑associated placental miRNA expression was investigated using microarray and confirmatory reverse transcriptase‑quantitative polymerase chain reaction studies. Placenta samples around the individual insertion region for each umbilical cord were collected from monochorionic twins complicated with (n=17) or without sIUGR (control, n=16). miRNA profile analysis was performed on two sIUGR cases and one control using an Affymetrix microRNA 4...
September 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28899360/biological-networks-in-parkinson-s-disease-an-insight-into-the-epigenetic-mechanisms-associated-with-this-disease
#16
Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
BACKGROUND: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT: We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28899340/regulatory-network-changes-between-cell-lines-and-their-tissues-of-origin
#17
Camila M Lopes-Ramos, Joseph N Paulson, Cho-Yi Chen, Marieke L Kuijjer, Maud Fagny, John Platig, Abhijeet R Sonawane, Dawn L DeMeo, John Quackenbush, Kimberly Glass
BACKGROUND: Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28893605/oscillator-networks-with-tissue-specific-circadian-clocks-in-plants
#18
REVIEW
Keisuke Inoue, Takashi Araki, Motomu Endo
Many organisms rely on circadian clocks to synchronize their biological processes with the 24-hour rotation of the earth. In mammals, the circadian clock consists of a central clock in the suprachiasmatic nucleus and peripheral clocks in other tissues. The central clock is tightly coupled to synchronize rhythmicity and can organize peripheral clocks through neural and hormonal signals. In contrast to mammals, it has long been assumed that the circadian clocks in each plant cell is able to be entrained by external light, and they are only weakly coupled to each other...
September 8, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28892639/genetic-networks-in-plant-vascular-development
#19
Raili Ruonala, Donghwi Ko, Ykä Helariutta
Understanding the development of vascular tissues in plants is crucial because the evolution of vasculature enabled plants to thrive on land. Various systems and approaches have been used to advance our knowledge about the genetic regulation of vasculature development, from the scale of single genes to networks. In this review, we provide a perspective on the major approaches used in studying plant vascular development, and we cover the mechanisms and genetic networks underlying vascular tissue specification, patterning, and differentiation...
September 11, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28892370/mass-spectrometry-based-chemical-cartography-of-a-cardiac-parasitic-infection
#20
Laura-Isobel McCall, James T Morton, Jean A Bernatchez, Jair L Siqueira-Neto, Rob Knight, Pieter C Dorrestein, James H McKerrow
Trypanosoma cruzi parasites are the causative agents of Chagas disease, a leading infectious form of heart failure whose pathogenesis is still not fully characterized. In this work, we applied untargeted liquid chromatography-tandem mass spectrometry to heart sections from T. cruzi-infected and uninfected mice. We combined molecular networking and 3-dimensional modeling to generate chemical cartographical heart models. This approach revealed for the first time preferential parasite localization to the base of the heart and regiospecific distributions of nucleoside derivatives and eicosanoids, which we correlated to tissue-damaging immune responses...
September 11, 2017: Analytical Chemistry
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