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Gene regulatory networks

Chen Xu, Hao Zhang, Wei Gu, Huiqiao Wu, Yuanyuan Chen, Wenchao Zhou, Baifeng Sun, Xiaolong Shen, Zicheng Zhang, Yue Wang, Yang Liu, Wen Yuan
Ossification of the posterior longitudinal ligament (OPLL) presents as pathological heterotopic ossification of the spinal ligaments. However, its underlying molecular mechanism is still unclear. Our previous findings suggested that altered microRNA regulatory network are critical for the development of OPLL. Here, we set out to unveiling the detailed mechanism of those altered OPLL-specific microRNAs. We screened a set of differentially expressed OPLL-specific microRNAs from the previous sequencing data and showed that microRNA-10a actively modulates the ossification of posterior ligament cells in vitro...
June 15, 2018: Scientific Reports
Frank A Skraly, Madana M R Ambavaram, Oliver Peoples, Kristi D Snell
Although the return on investment over the last 20 years for mass screening of individual plant genes to improve crop performance has been low, the investment in these activities was essential to establish the infrastructure and tools of modern plant genomics. Complex traits such as crop yield are likely multigenic, and the exhaustive screening of random gene combinations to achieve yield gains is not realistic. Clearly, smart approaches must be developed. In silico analyses of plant metabolism and gene networks can move a trait discovery program beyond trial-and-error approaches and towards rational design strategies...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
Madana M R Ambavaram, Aminat Ali, Kieran P Ryan, Oliver Peoples, Kristi D Snell, Maria N Somleva
Increasing crop yield requires the coordination of multiple metabolic pathways spanning photosynthetic carbon fixation, central carbon metabolism, and finally targeted carbon deposition to end product. In this study, we used a transcriptome-based gene regulatory association network to search for transcription factor genes that could play a role in increasing carbon flow through pathways associated with these processes to increase biomass yield in switchgrass. Two novel switchgrass transcription factors, PvBMY1 (BioMass Yield 1, belonging to the APETALA2/Ethylene Response Factor family of transcription factors) and PvBMY3 (BioMass Yield 3, a member of the Nuclear-Factor Y family of transcription factors), with predicted roles in the regulation of photosynthesis and related metabolism were identified...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
Chris Kang, Boris Aguilar, Ilya Shmulevich
The origin of multicellularity in metazoa is one of the fundamental questions of evolutionary biology. We have modeled the generic behaviors of gene regulatory networks in isogenic cells as stochastic nonlinear dynamical systems-coupled Boolean networks with perturbation. Model simulations under a variety of dynamical regimes suggest that the central characteristic of multicellularity, permanent spatial differentiation (diversification), indeed can arise. Additionally, we observe that diversification is more likely to occur near the critical regime of Lyapunov stability...
May 2018: Physical Review. E
Henry Reyer, Michael Oster, Elizabeth Magowan, Eduard Murani, Helga Sauerwein, Dirk Dannenberger, Björn Kuhla, Siriluck Ponsuksili, Klaus Wimmers
Feed efficiency (FE) is a measure of the rate between feed intake and body weight gain and is subject to constant progress in pigs, based on extensive performance tests and analyses of physiological parameters. However, endocrine regulatory circuits which comprise the sensation and perception of intrinsic requirements and appropriate systemic responses have not yet been fully elucidated. It is hypothesized that the gut-brain-axis, which is a network of hierarchical anterior regulatory tissues, contributes largely to variations in FE...
June 15, 2018: Physiological Genomics
Yoonji Kim, Jaejik Kim
Dynamic system consisting of ordinary differential equations (ODEs) is a well-known tool for describing dynamic nature of gene regulatory networks (GRNs), and the dynamic features of GRNs are usually captured through time-course gene expression data. Owing to high-throughput technologies, time-course gene expression data have complex structures such as heteroscedasticity, correlations between genes, and time dependence. Since gene experiments typically yield highly noisy data with small sample size, for a more accurate prediction of the dynamics, the complex structures should be taken into account in ODE models...
June 15, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Liang Chen, Shilai Shi, Ninfei Jiang, Hira Khanzada, Ghulam Mustafa Wassan, Changlan Zhu, Xiaosong Peng, Jie Xu, Yujin Chen, Qiuying Yu, Xiaopeng He, Junru Fu, Xiaorong Chen, Lifang Hu, Linjuan Ouyang, Xiaotang Sun, Haohua He, Jianmin Bian
BACKGROUND: Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress. RESULTS: The lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition...
June 15, 2018: BMC Genomics
Yun Lu, Wei Gao, Lu-Qi Huang
miRNA (microRNA) is a kind of important endogenous non-coding small RNA, which mainly regulates the expression of target gene at the post-transcriptional level by splicing and translation inhibition and it plays an important role in the synthesis of plant secondary metabolites, especially for medicinal plants, the secondary metabolites are mostly active ingredients, which are the basis of medicinal effects. It is of great significance to study the biosynthetic pathways and complex regulatory networks of secondary metabolites of medicinal plants...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Luming Yang, Hanqiang Liu, Jianyu Zhao, Yupeng Pan, Siyuan Cheng, Calvin D Lietzow, Changlong Wen, Xiaolan Zhang, Yiqun Weng
Plants employ tight genetic control to integrate intrinsic growth signals and environmental cues to enable organ growth to a defined size. Many genes contributing to cell proliferation and/or cell expansion and consequently organ size control have been identified, but the regulatory pathways are poorly understood. Here we have characterized a cucumber littleleaf (ll) mutant which exhibits smaller organ sizes but more lateral branches than the wildtype. The small organ size in ll was due to a reduction of both cell number and cell size...
June 14, 2018: Plant Journal: for Cell and Molecular Biology
Chao-Qiang Lai, Caren E Smith, Laurence D Parnell, Yu-Chi Lee, Dolores Corella, Paul Hopkins, Bertha A Hidalgo, Stella Aslibekyan, Michael A Province, Devin Absher, Donna K Arnett, Katherine L Tucker, Jose M Ordovas
Background: The putative functional variant -265T>C (rs5082) within the APOA2 promoter has shown consistent interactions with saturated fatty acid (SFA) intake to influence the risk of obesity. Objective: The aim of this study was to implement an integrative approach to characterize the molecular basis of this interaction. Design: We conducted an epigenome-wide scan on 80 participants carrying either the rs5082 CC or TT genotypes and consuming either a low-SFA (<22 g/d) or high-SFA diet (≥22 g/d), matched for age, sex, BMI, and diabetes status in the Boston Puerto Rican Health Study (BPRHS)...
June 12, 2018: American Journal of Clinical Nutrition
Jie-Ling Lai, Dong-Jie Tang, Yu-Wei Liang, Ren Zhang, Qi Chen, Zhen-Ping Qin, Zhen-Hua Ming, Ji-Liang Tang
The RNA chaperone, Hfq, is known to play extensive roles in bacterial growth and development. More recently, it has been shown to be required for virulence in many human and animal bacterial pathogens. Despite these studies little is known about the role Hfq plays in phytopathogenic bacteria. In this study, we show Hfq is required for full virulence of the crucifer black rot pathogen Xanthomonas campestris pv. campestris (Xcc). We demonstrate that an Xcc hfq deletion strain is highly attenuated for virulence in Chinese radish and shows a severe defect in the production of virulence factors including extracellular enzymes and extracellular polysaccharide...
June 14, 2018: Environmental Microbiology Reports
Zhigang Qu, Zhe Quan, Qi Zhang, Zhenyu Wang, Qingxu Song, Xinming Zhuang, Changfeng Fu, Feng Xu, Yadong Liu, Yuanyi Wang, Zheng Wang, Yi Liu
The present study aimed to identify novel intervertebral disc degeneration (IDD)‑associated long noncoding (lnc)RNAs and genes. The lncRNA and mRNA microarray dataset GSE56081 was downloaded from the Gene Expression Omnibus database and included 5 samples from patients with degenerative lumbar nucleus pulposus and 5 normal controls. Differentially expressed lncRNAs or differentially expressed genes (DEGs) were identified and co‑expression network analysis was performed followed by functional analysis for genes in the network...
June 5, 2018: Molecular Medicine Reports
Hongwei Gao, Xuanrong Chen, Zhiqun Shang, Yuanjie Niu
Long non-coding RNAs (lncRNAs) make up a significant portion of transcripts that are not translated into proteins and lncRNAs were previously thought to be transcriptional noise. Recently, there has been increased interest in lncRNAs due to their diverse functions in human cancers. At present, lncRNAs are considered to be the main component of the competing endogenous RNA (ceRNA) network due to their regulatory role in protein-coding gene expression by acting as microRNA (miRNA) sponges. However, the function of the lncRNA-mediated ceRNA network in renal cell carcinoma remains unknown...
June 6, 2018: Oncology Reports
Wanassa Beroual, Matteo Brilli, Emanuele G Biondi
Caulobacter crescentus represents a remarkable model system to investigate global regulatory programs in bacteria. In particular, several decades of intensive study have revealed that its cell cycle is controlled by a cascade of master regulators, such as DnaA, GcrA, CcrM, and CtrA, that are responsible for the activation of functions required to progress through DNA replication, cell division and morphogenesis of polar structures (flagellum and stalk). In order to accomplish this task, several post-translational (phosphorylation and proteolysis) and transcriptional mechanisms are involved...
2018: Frontiers in Genetics
Brett T Chiquet, Qiuping Yuan, Eric C Swindell, Lorena Maili, Robert Plant, Jeffrey Dyke, Ryan Boyer, John F Teichgraeber, Matthew R Greives, John B Mulliken, Ariadne Letra, Susan H Blanton, Jacqueline T Hecht
Orofacial development is a multifaceted process involving tightly regulated genetic signaling networks, that when perturbed, lead to orofacial abnormalities including cleft lip and/or cleft palate. We and others have shown an association between the cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) gene and nonsyndromic cleft lip with or without cleft palate (NSCLP). Further, we demonstrated that knockdown of Crispld2 in zebrafish alters neural crest cell migration patterns resulting in abnormal jaw and palate development...
June 13, 2018: European Journal of Human Genetics: EJHG
Laura P M H de Rooij, Derek C H Chan, Ava Keyvani Chahi, Kristin J Hope
Normal hematopoiesis is sustained through a carefully orchestrated balance between hematopoietic stem cell (HSC) self-renewal and differentiation. The functional importance of this axis is underscored by the severity of disease phenotypes initiated by abnormal HSC function, including myelodysplastic syndromes and hematopoietic malignancies. Major advances in the understanding of transcriptional regulation of primitive hematopoietic cells have been achieved, however, the post-transcriptional regulatory layer that may impinge on their behavior remains underexplored by comparison...
June 13, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
James C Hart, Nicholas A Ellis, Michael B Eisen, Craig T Milller
Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus)...
June 13, 2018: PLoS Genetics
Gustavo H Esteves, Luiz F L Reis
MOTIVATION: Gene expression data analysis is of great importance for modern molecular biology, given our ability to measure the expression profiles of thousands of genes and enabling studies rooted in systems biology. In this work, we propose a simple statistical model for the activation measuring of gene regulatory networks, instead of the traditional gene co-expression networks. RESULTS: We present the mathematical construction of a statistical procedure for testing hypothesis regarding gene regulatory network activation...
June 13, 2018: Statistical Applications in Genetics and Molecular Biology
Erin Wall, Nadim Majdalani, Susan Gottesman
RcsB, a response regulator of the FixJ/NarL family, is at the center of a complex network of regulatory inputs and outputs. Cell surface stress is sensed by an outer membrane lipoprotein, RcsF, which regulates interactions of the inner membrane protein IgaA, lifting negative regulation of a phosphorelay. In vivo evidence supports a pathway in which histidine kinase RcsC transfers phosphate to phosphotransfer protein RcsD, resulting in phosphorylation of RcsB. RcsB acts either alone or in combination with RcsA to positively regulate capsule synthesis and synthesis of small RNA (sRNA) RprA as well as other genes, and to negatively regulate motility...
June 13, 2018: Annual Review of Microbiology
Ying-Ping Gai, Shuo-Shuo Yuan, Ya-Nan Zhao, Huai-Ning Zhao, Hua-Liang Zhang, Xian-Ling Ji
Environmental stresses are major constraints that limit the leaf productivity and quality of mulberry. LncRNAs have emerged as important regulators in response to biotic and abiotic stresses in plants. However, the functions and mechanisms of most lncRNAs remain largely unknown. A novel lncRNA designated as MuLnc1 was found to be cleaved by mul-miR3954 and produce secondary siRNAs in a 21 nt phase in mulberry. It was demonstrated that one of the siRNAs produced, si161579, can silence the expression of the calmodulin-like protein gene CML27 of mulberry ( MuCML27 )...
2018: Frontiers in Plant Science
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