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https://www.readbyqxmd.com/read/29471367/evolution-of-genes-associated-with-gynoecium-patterning-and-fruit-development-in-solanaceae
#1
Clara Inés Ortiz-Ramírez, Sayonara Plata-Arboleda, Natalia Pabón-Mora
Background and Aims: The genetic basis of fruit development has been extensively studied in Arabidopsis, where major transcription factors controlling valve identity (i.e. FRUITFULL), replum development (i.e. REPLUMLESS) and the differentiation of the dehiscence zones (i.e. SHATTERPROOF, INDEHISCENT and ALCATRAZ) have been identified. This gene regulatory network in other flowering plants is influenced by duplication events during angiosperm diversification. Here we aim to characterize candidate fruit development genes in the Solanaceae and compare them with those of Brassicaceae...
February 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29470863/the-evolution-of-mollusc-shells
#2
REVIEW
Carmel McDougall, Bernard M Degnan
Molluscan shells are externally fabricated by specialized epithelial cells on the dorsal mantle. Although a conserved set of regulatory genes appears to underlie specification of mantle progenitor cells, the genes that contribute to the formation of the mature shell are incredibly diverse. Recent comparative analyses of mantle transcriptomes and shell proteomes of gastropods and bivalves are consistent with shell diversity being underpinned by a rapidly evolving mantle secretome (suite of genes expressed in the mantle that encode secreted proteins) that is the product of (a) high rates of gene co-option into and loss from the mantle gene regulatory network, and (b) the rapid evolution of coding sequences, particular those encoding repetitive low complexity domains...
February 22, 2018: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/29470839/embryonic-neurogenesis-in-echinoderms
#3
REVIEW
Veronica F Hinman, Robert D Burke
The phylogenetic position of echinoderms is well suited to revealing shared features of deuterostomes that distinguish them from other bilaterians. Although echinoderm neurobiology remains understudied, genomic resources, molecular methods, and systems approaches have enabled progress in understanding mechanisms of embryonic neurogenesis. Even though the morphology of echinoderm larvae is diverse, larval nervous systems, which arise during gastrulation, have numerous similarities in their organization. Diverse neural subtypes and specialized sensory neurons have been identified and details of neuroanatomy using neuron-specific labels provide hypotheses for neural function...
February 22, 2018: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/29470492/memory-functions-reveal-structural-properties-of-gene-regulatory-networks
#4
Edgar Herrera-Delgado, Ruben Perez-Carrasco, James Briscoe, Peter Sollich
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and complexity of these models mean that their behaviour is not always intuitive and the underlying mechanisms can be difficult to decipher. For this reason, methods that simplify and aid exploration of complex networks are necessary. To this end we develop a broadly applicable form of the Zwanzig-Mori projection...
February 22, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29467540/identification-of-a-novel-microrna-mrna-regulatory-biomodule-in-human-prostate-cancer
#5
Yanqiong Zhang, Funeng Jiang, Huichan He, Jianheng Ye, Xia Mao, Qiuyan Guo, Shu-Lin Wu, Weide Zhong, Chin-Lee Wu, Na Lin
Our recent study identified a list of differentially expressed microRNAs (miRNAs) in human prostate cancer (PCa) tissues compared to adjacent benign prostate tissues. In the current study, to identify the crucial miRNA-mRNA regulatory biomodule involved into prostate carcinogenesis based on the previous miRNA expression profile in PCa, we proposed an integrated systematic approach which combined miRNA-mediated gene expression regulatory network analysis, experimental validations in vitro and in vivo, as well as clinical significance evaluation...
February 21, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29467500/a-tomato-mads-box-protein-slcmb1-regulates-ethylene-biosynthesis-and-carotenoid-accumulation-during-fruit-ripening
#6
Jianling Zhang, Zongli Hu, Qiyuan Yao, Xuhu Guo, Vanluc Nguyen, Fenfen Li, Guoping Chen
The MADS-box transcription factors play essential roles in many physiological and biochemical processes of plants, especially in fruit ripening. Here, a tomato MADS-box gene, SlCMB1, was isolated. SlCMB1 expression declined with the fruit ripening from immature green to B + 7 (7 days after Breaker) fruits in the wild type (WT) and was lower in Nr and rin mutants fruits. Tomato plants with reduced SlCMB1 mRNA displayed delayed fruit ripening, reduced ethylene production and carotenoid accumulation. The ethylene production in SlCMB1-RNAi fruits decreased by approximately 50% as compared to WT...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29467471/network-analysis-of-coronary-artery-disease-risk-genes-elucidates-disease-mechanisms-and-druggable-targets
#7
Harri Lempiäinen, Ingrid Brænne, Tom Michoel, Vinicius Tragante, Baiba Vilne, Tom R Webb, Theodosios Kyriakou, Johannes Eichner, Lingyao Zeng, Christina Willenborg, Oscar Franzen, Arno Ruusalepp, Anuj Goel, Sander W van der Laan, Claudia Biegert, Stephen Hamby, Husain A Talukdar, Hassan Foroughi Asl, Gerard Pasterkamp, Hugh Watkins, Nilesh J Samani, Timo Wittenberger, Jeanette Erdmann, Heribert Schunkert, Folkert W Asselbergs, Johan L M Björkegren
Genome-wide association studies (GWAS) have identified over two hundred chromosomal loci that modulate risk of coronary artery disease (CAD). The genes affected by variants at these loci are largely unknown and an untapped resource to improve our understanding of CAD pathophysiology and identify potential therapeutic targets. Here, we prioritized 68 genes as the most likely causal genes at genome-wide significant loci identified by GWAS of CAD and examined their regulatory roles in 286 metabolic and vascular tissue gene-protein sub-networks ("modules")...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29467401/dyngenie3-dynamical-genie3-for-the-inference-of-gene-networks-from-time-series-expression-data
#8
Vân Anh Huynh-Thu, Pierre Geurts
The elucidation of gene regulatory networks is one of the major challenges of systems biology. Measurements about genes that are exploited by network inference methods are typically available either in the form of steady-state expression vectors or time series expression data. In our previous work, we proposed the GENIE3 method that exploits variable importance scores derived from Random forests to identify the regulators of each target gene. This method provided state-of-the-art performance on several benchmark datasets, but it could however not specifically be applied to time series expression data...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29467369/transcriptomic-signature-of-drought-response-in-pearl-millet-pennisetum-glaucum-l-and-development-of-web-genomic-resources
#9
Sarika Jaiswal, Tushar J Antala, M K Mandavia, Meenu Chopra, Rahul Singh Jasrotia, Rukam S Tomar, Jashminkumar Kheni, U B Angadi, M A Iquebal, B A Golakia, Anil Rai, Dinesh Kumar
Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29467363/enhancing-hi-c-data-resolution-with-deep-convolutional-neural-network-hicplus
#10
Yan Zhang, Lin An, Jie Xu, Bo Zhang, W Jim Zheng, Ming Hu, Jijun Tang, Feng Yue
Although Hi-C technology is one of the most popular tools for studying 3D genome organization, due to sequencing cost, the resolution of most Hi-C datasets are coarse and cannot be used to link distal regulatory elements to their target genes. Here we develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. We demonstrate that HiCPlus can impute interaction matrices highly similar to the original ones, while only using 1/16 of the original sequencing reads...
February 21, 2018: Nature Communications
https://www.readbyqxmd.com/read/29467265/-apterous-a-specifies-dorsal-wing-patterns-and-sexual-traits-in-butterflies
#11
Anupama Prakash, Antónia Monteiro
Butterflies have evolved different colour patterns on their dorsal and ventral wing surfaces to serve different signalling functions, yet the developmental mechanisms controlling surface-specific patterning are still unknown. Here, we mutate both copies of the transcription factor apterous in Bicyclus anynana butterflies using CRISPR/Cas9 and show that apterous A, expressed dorsally, functions both as a repressor and modifier of ventral wing colour patterns, as well as a promoter of dorsal sexual ornaments in males...
February 28, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29467254/bdnf-activates-an-nfi-dependent-neurodevelopmental-timing-program-by-sequestering-nfatc4
#12
Baojin Ding, Paul R Dobner, Debra Mullikin-Kilpatrick, Wei Wang, Hong Zhu, Chi-Wing Chow, John W Cave, Richard M Gronostajski, Daniel L Kilpatrick
How intrinsic and extrinsic signals are coordinated to regulate synaptic maturation and its timing is an important question for neurodevelopment and its disorders. Here, we investigated the influence of the neurotrophin BDNF on the developmental timing of a dendrite/synapse-related gene program controlled by Nuclear Factor One (NFI) in maturing cerebellar granule neurons (CGNs). BDNF accelerated the onset of NFI-regulated late-gene expression and NFI temporal occupancy in CGN cultures in a MEK5/ERK5-dependent manner...
February 21, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29467216/molecular-basis-for-sterol-transport-by-start-like-lipid-transfer-domains
#13
Florian A Horenkamp, Diana P Valverde, Jodi Nunnari, Karin M Reinisch
Lipid transport proteins at membrane contact sites, where two organelles are closely apposed, play key roles in trafficking lipids between cellular compartments while distinct membrane compositions for each organelle are maintained. Understanding the mechanisms underlying non-vesicular lipid trafficking requires characterization of the lipid transporters residing at contact sites. Here, we show that the mammalian proteins in the lipid transfer proteins anchored at a membrane contact site (LAM) family, called GRAMD1a-c, transfer sterols with similar efficiency as the yeast orthologues, which have known roles in sterol transport...
February 21, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29467003/extracellular-%C3%AE-synuclein-levels-are-regulated-by-neuronal-activity
#14
Kaoru Yamada, Takeshi Iwatsubo
BACKGROUND: α-Synuclein is a presynaptic protein abundant in the cytoplasmic compartment of neurons, whereas its presence in the extracellular space has also been observed under physiological conditions. Extracellular α-synuclein has pathological significance, exhibiting cellular toxicity and impairment of synaptic transmission. Notably, misfolded α-synuclein drives the cell-to-cell propagation of pathology via the extracellular space. However, the primary mechanism that regulates the extracellular levels of α-synuclein remains to be determined...
February 22, 2018: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/29466876/srebp2-contributes-to-cisplatin-resistance-in-ovarian-cancer-cells
#15
Lei Zheng, Li Li, Yun Lu, Fangfang Jiang, Xiu-An Yang
This study is to investigate transcription factors involved in cisplatin resistance in ovarian cancer cells. The transcriptome of cisplatin resistant and sensitive A2780 epithelial ovarian cancer cells was obtained from GSE15372. Ovarian transcriptome data GSE62944 was downloaded from TCGA and applied for transcription regulatory network analysis. The analysis results were confirmed using quantitative polymerase chain reaction. The roles of SREBP2 in cisplatin-resistant cells were investigated by RNA inference and cell viability analysis...
January 1, 2018: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29466699/unveiling-network-based-functional-features-through-integration-of-gene-expression-into-protein-networks
#16
REVIEW
Mahdi Jalili, Tom Gebhardt, Olaf Wolkenhauer, Ali Salehzadeh-Yazdi
Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype-phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies...
February 18, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29466696/uhrf1-regulates-cdh1-via-promoter-associated-non-coding-rnas-in-prostate-cancer-cells
#17
Elena Magnani, Filippo Macchi, Monica Mancini, Vanessa Lomazzi, Sara Cogliati, Christian Pistore, Martina Mandruzzato, Anne-Catherine Dock-Bregeon, Ian Marc Bonapace
Non-coding RNAs (ncRNAs) transcribed from the promoter and the downstream region can affect the expression of the corresponding coding genes. It has been shown that sense-directed ncRNAs arising from the promoter region of the E-cadherin gene (CDH1) mediate its repression. Here, we show that an antisense-directed ncRNA (paRCDH1-AS) transcribed from the CDH1 promoter is necessary for its expression. paRCDH1-AS acts as a hooking scaffold by recruiting the epigenetic regulators, UHRF1, DNMT3A, SUV39H1 and SUZ12, involved in CDH1 repression...
February 18, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29465812/the-role-of-salt-for-immune-cell-function-and-disease
#18
REVIEW
Ralf Willebrand, Markus Kleinewietfeld
The immune system evolved to protect organisms from invading pathogens. A network of pro- and anti-inflammatory cell types equipped with special effector molecules guarantees efficient elimination of intruders like viruses and bacteria. However, imbalances can lead to an exceeding response of effector cells incurring autoimmune or allergic diseases. An interplay of genetic and environmental factors contributes to autoimmune diseases and recent studies provided evidence for an impact of dietary habits on the immune status and related disorders...
February 21, 2018: Immunology
https://www.readbyqxmd.com/read/29465290/global-integrated-analysis-of-methylomes-and-transcriptomes-from-laser-capture-microdissected-bronchial-and-alveolar-cells-in-human-lung
#19
Xiao Dong, Miao Shi, Moonsook Lee, Rafael Toro, Silvia Gravina, Weiguo Han, Shoya Yasuda, Tao Wang, Zhengdong Zhang, Jan Vijg, Yousin Suh, Simon D Spivack
Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells...
February 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29464057/construction-of-key-signal-regulatory-network-in-metastatic-colorectal-cancer
#20
Lu Qi, Yanqing Ding
There are many stages in the development and metastasis of colorectal cancer (CRC). In this study, we compared the differential expression genes in different stages of metastatic CRC. Then, we screened the continuously up-regulated genes and the continuously down-regulated genes that were associated with the development and metastasis of CRC. After analyzing the intersection of differential expression genes in each stage, we screened the continuously up-regulated genes and deviated genes in the extracellular matrix and the continuously down-regulated genes and deviated genes in the mitochrondia of CRC...
January 19, 2018: Oncotarget
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