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biological regulatory network

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https://www.readbyqxmd.com/read/28228108/expression-profiling-and-bioinformatic-analyses-suggest-new-target-genes-and-pathways-for-human-hair-follicle-related-micrornas
#1
Lara M Hochfeld, Thomas Anhalt, Céline S Reinbold, Marisol Herrera-Rivero, Nadine Fricker, Markus M Nöthen, Stefanie Heilmann-Heimbach
BACKGROUND: Human hair follicle (HF) cycling is characterised by the tight orchestration and regulation of signalling cascades. Research shows that micro(mi)RNAs are potent regulators of these pathways. However, knowledge of the expression of miRNAs and their target genes and pathways in the human HF is limited. The objective of this study was to improve understanding of the role of miRNAs and their regulatory interactions in the human HF. METHODS: Expression levels of ten candidate miRNAs with reported functions in hair biology were assessed in HFs from 25 healthy male donors...
February 22, 2017: BMC Dermatology
https://www.readbyqxmd.com/read/28227870/identifying-disease-network-perturbations-through-regression-on-gene-expression-and-pathway-topology-analysis
#2
Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Kyriakos Sgarbas, Panos Balomenos, Georgios N Dimitrakopoulos, Anastasios Bezerianos, Aristidis G Vrahatis
In Systems Biology, network-based approaches have been extensively used to effectively study complex diseases. An important challenge is the detection of network perturbations which disrupt regular biological functions as a result of a disease. In this regard, we introduce a network based pathway analysis method which isolates casual interactions with significant regulatory roles within diseased-perturbed pathways. Specifically, we use gene expression data with Random Forest regression models to assess the interactivity strengths of genes within disease-perturbed networks, using KEGG pathway maps as a source of prior-knowledge pertaining to pathway topology...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226784/parameter-estimation-for-gene-regulatory-networks-a-two-stage-mcmc-bayesian-approach
#3
Niannan Xue, Wei Pan, Yike Guo, Niannan Xue, Wei Pan, Yike Guo, Wei Pan, Yike Guo, Niannan Xue
Genetic regulatory networks have emerged as a useful way to elucidate the biochemical pathways for biological functions. Yet, determination of the exact parametric forms for these models remain a major challenge. In this paper, we present a novel computational approach implemented in C++ to solve this inverse problem. This takes the form of an optimization stage first after which Bayesian filtering takes place. The key advantage of such a flexible, general and robust approach is that it provides us with a joint probability distribution of the model parameters instead of single estimates, which we can propagate to final predictions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226783/learning-a-probabilistic-boolean-network-model-from-biological-pathways-and-time-series-expression-data
#4
Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra, Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra, Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra
The problem of inferring a stochastic model for gene regulatory networks is addressed here. The prior biological data includes biological pathways and time-series expression data. We propose a novel algorithm to use both of these data to construct a Probabilistic Boolean Network (PBN) which models the observed dynamics of genes with a high degree of precision. Our algorithm constructs a pathway tree and uses the time-series expression data to select an optimal level of tree, whose nodes are used to infer the PBN...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225764/cynomolgus-macaques-naturally-infected-with-trypanosoma-cruzi-i-exhibit-an-overall-mixed-pro-inflammatory-modulated-cytokine-signature-characteristic-of-human-chagas-disease
#5
Danielle Marquete Vitelli-Avelar, Renato Sathler-Avelar, Armanda Moreira Mattoso-Barbosa, Nicolas Gouin, Marcelo Perdigão-de-Oliveira, Leydiane Valério-Dos-Reis, Ronaldo Peres Costa, Silvana Maria Elói-Santos, Matheus de Souza Gomes, Laurence Rodrigues do Amaral, Andréa Teixeira-Carvalho, Olindo Assis Martins-Filho, Edward J Dick, Gene B Hubbard, Jane F VandeBerg, John L VandeBerg
BACKGROUND: Non-human primates have been shown to be useful models for Chagas disease. We previously reported that natural T. cruzi infection of cynomolgus macaques triggers clinical features and immunophenotypic changes of peripheral blood leukocytes resembling those observed in human Chagas disease. In the present study, we further characterize the cytokine-mediated microenvironment to provide supportive evidence of the utility of cynomolgus macaques as a model for drug development for human Chagas disease...
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28224498/differential-gene-expression-dex-and-alternative-splicing-events-ase-for-temporal-dynamic-processes-using-hmms-and-hierarchical-bayesian-modeling-approaches
#6
Sunghee Oh, Seongho Song
In gene expression profile, data analysis pipeline is categorized into four levels, major downstream tasks, i.e., (1) identification of differential expression; (2) clustering co-expression patterns; (3) classification of subtypes of samples; and (4) detection of genetic regulatory networks, are performed posterior to preprocessing procedure such as normalization techniques. To be more specific, temporal dynamic gene expression data has its inherent feature, namely, two neighboring time points (previous and current state) are highly correlated with each other, compared to static expression data which samples are assumed as independent individuals...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28219524/the-function-and-transcriptome-analysis-of-a-bzip-transcription-factor-cgap1-in-colletotrichum-gloeosporioides
#7
Xiaoyu Li, Yateng Wu, Zhiqiang Liu, Chenghui Zhang
Colletotrichum gloeosporioides is an important pathogen of anthracnose, which is able to infect numerous crops in tropical and subtropical regions, causing great economic losses. To investigate the fungal response to host-generated reactive oxygen species (ROS), we cloned and characterized the CgAP1 gene of C. gloeosporioides. CgAP1 encoded a bZIP transcription factor which had a bZIP DNA-binding domain and two cysteine-rich domains structurally and functionally related to Saccharomyces cerevisiae YAP1. Deletion of CgAP1 in C...
April 2017: Microbiological Research
https://www.readbyqxmd.com/read/28219342/effects-of-exposure-to-streptococcus-iniae-on-microrna-expression-in-the-head-kidney-of-genetically-improved-farmed-tilapia-oreochromis-niloticus
#8
Jun Qiang, Fanyi Tao, Jie He, Lanyi Sun, Pao Xu, Wenjin Bao
BACKGROUND: Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28218277/mir-203-enhances-let-7-biogenesis-by-targeting-lin28b-to-suppress-tumor-growth-in-lung-cancer
#9
Yong Zhou, Hongwei Liang, Zhicong Liao, Yanbo Wang, Xiuting Hu, Xi Chen, Lin Xu, Zhibin Hu
Human cancers often exhibit increased microRNA (miRNA) biogenesis and global aberrant expression of miRNAs; thus, targeting the miRNA biogenesis pathway represents a novel strategy for cancer therapy. Here, we report that miR-203 enhances the biogenesis of tumor suppressor let-7 in lung cancer by directly targeting LIN28B. Specially, we found that the LIN28B protein levels were dramatically increased in lung cancer tissues, but its mRNA levels did not differ significantly, suggesting that a post-transcriptional mechanism is involved in LIN28B regulation...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217746/integrated-regulatory-and-metabolic-networks-of-the-marine-diatom-phaeodactylum-tricornutum-predict-the-response-to-rising-co2-levels
#10
Jennifer Levering, Christopher L Dupont, Andrew E Allen, Bernhard O Palsson, Karsten Zengler
Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean's primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom's metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels...
January 2017: MSystems
https://www.readbyqxmd.com/read/28216162/genome-wide-identification-of-glabra3-downstream-genes-for-anthocyanin-biosynthesis-and-trichome-formation-in-arabidopsis
#11
Chenhao Gao, Dong Li, Changyu Jin, Shaowei Duan, Shuanghui Qi, Kaige Liu, Hanchen Wang, Haoli Ma, Jiangbo Hai, Mingxun Chen
GLABRA3 (GL3), a bHLH transcription factor, has previously proved to be involved in anthocyanin biosynthesis and trichome formation in Arabidopsis, however, its downstream targeted genes are still largely unknown. Here, we found that GL3 was widely present in Arabidopsis vegetative and reproductive organs. New downstream targeted genes of GL3 for anthocyanin biosynthesis and trichome formation were identified in young shoots and expanding true leaves by RNA sequencing. GL3-mediated gene expression was tissue specific in the two biological processes...
February 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28214944/the-vascular-plants-open-system-of-growth
#12
REVIEW
Alice Basile, Marco Fambrini, Claudio Pugliesi
What is fascinating in plants (true also in sessile animals such as corals and hydroids) is definitely their open and indeterminate growth, as a result of meristematic activity. Plants as well as animals are characterized by a multicellular organization, with which they share a common set of genes inherited from a common eukaryotic ancestor; nevertheless, circa 1.5 billion years of evolutionary history made the two kingdoms very different in their own developmental biology. Flowering plants, also known as angiosperms, arose during the Cretaceous Period (145-65 million years ago), and up to date, they count around 235,000 species, representing the largest and most diverse group within the plant kingdom...
February 18, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28212624/understanding-the-response-to-endurance-exercise-using-a-systems-biology-approach-combining-blood-metabolomics-transcriptomics-and-mirnomics-in-horses
#13
Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Eric Barrey, Jesús Maria López, Laurence Le Moyec
BACKGROUND: Endurance exercise in horses requires adaptive processes involving physiological, biochemical, and cognitive-behavioral responses in an attempt to regain homeostasis. We hypothesized that the identification of the relationships between blood metabolome, transcriptome, and miRNome during endurance exercise in horses could provide significant insights into the molecular response to endurance exercise. For this reason, the serum metabolome and whole-blood transcriptome and miRNome data were obtained from ten horses before and after a 160 km endurance competition...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212091/multistability-and-bifurcation-analysis-of-inhibitory-coupled-cyclic-genetic-regulatory-networks-with-delays
#14
Guang Ling, Zhi-Hong Guan, Bin Hu, Qiang Lai, Yonghong Wu
Many biological systems have the conspicuous property to present more than one stable state and diverse rhythmic behaviors. A closed relationship between these complex dynamic behaviors and cyclic genetic structures has been witnessed by pioneering works. In this paper, a typical structure of inhibitory coupled cyclic genetic networks is introduced to further enlighten this mechanism of stability and biological rhythms of living cells. The coupled networks consist two identical cyclic genetic subnetworks, which inhibit each other directly...
February 14, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28210797/mathematical-modelling-of-clostridial-acetone-butanol-ethanol-fermentation
#15
REVIEW
Thomas Millat, Klaus Winzer
Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the production of industrial-relevant solvents, solventogensis. In recent decades, mathematical models have been employed to elucidate the complex interlinked regulation and conditions that determine these two distinct metabolic states and govern the transition between them. In this review, we discuss these models with a focus on the mechanisms controlling intra- and extracellular changes between acidogenesis and solventogenesis...
February 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28208755/micrornas-new-insight-in-modulating-follicular-atresia-a-review
#16
REVIEW
Tesfaye Worku, Zia Ur Rehman, Hira Sajjad Talpur, Dinesh Bhattarai, Farman Ullah, Ngabu Malobi, Tesfaye Kebede, Liguo Yang
Our understanding of the post-transcriptional mechanisms involved in follicular atresia is limited; however, an important development has been made in understanding the biological regulatory networks responsible for mediating follicular atresia. MicroRNAs have come to be seen as a key regulatory actor in determining cell fate in a wide range of tissues in normal and pathological processes. Profiling studies of miRNAs during follicular atresia and development have identified several putative miRNAs enriched in apoptosis signaling pathways...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28207000/spatial-transcriptomic-analysis-of-cryosectioned-tissue-samples-with-geo-seq
#17
Jun Chen, Shengbao Suo, Patrick Pl Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28205554/the-oncoppi-network-of-cancer-focused-protein-protein-interactions-to-inform-biological-insights-and-therapeutic-strategies
#18
Zenggang Li, Andrei A Ivanov, Rina Su, Valentina Gonzalez-Pecchi, Qi Qi, Songlin Liu, Philip Webber, Elizabeth McMillan, Lauren Rusnak, Cau Pham, Xiaoqian Chen, Xiulei Mo, Brian Revennaugh, Wei Zhou, Adam Marcus, Sahar Harati, Xiang Chen, Margaret A Johns, Michael A White, Carlos Moreno, Lee A D Cooper, Yuhong Du, Fadlo R Khuri, Haian Fu
As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein-protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4...
February 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28202516/modeling-the-genetic-regulation-of-cancer-metabolism-interplay-between-glycolysis-and-oxidative-phosphorylation
#19
Linglin Yu, Mingyang Lu, Dongya Jia, Jianpeng Ma, Eshel Ben-Jacob, Herbert Levine, Benny A Kaipparettu, Jose' N Onuchic
Abnormal metabolism is a hallmark of cancer, yet its regulation remains poorly understood. Cancer cells were considered to utilize primarily glycolysis for ATP production, referred to as the Warburg effect. However, recent evidence suggests that oxidative phosphorylation (OXPHOS) plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and OXPHOS. Integrating information from literature, we constructed a regulatory network of genes and metabolites from which we extracted a core circuit containing HIF-1, AMPK, and ROS...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28198367/usp9x-regulates-ets-1-ubiquitination-and-stability-to-control-nras-expression-and-tumorigenicity-in-melanoma
#20
Harish Potu, Luke F Peterson, Malathi Kandarpa, Anupama Pal, Hanshi Sun, Alison Durham, Paul W Harms, Peter C Hollenhorst, Ugur Eskiocak, Moshe Talpaz, Nicholas J Donato
ETS transcription factors are commonly deregulated in cancer by chromosomal translocation, overexpression or post-translational modification to induce gene expression programs essential in tumorigenicity. Targeted destruction of these proteins may have therapeutic impact. Here we report that Ets-1 destruction is regulated by the deubiquitinating enzyme, Usp9x, and has major impact on the tumorigenic program of metastatic melanoma. Ets-1 deubiquitination blocks its proteasomal destruction and enhances tumorigenicity, which could be reversed by Usp9x knockdown or inhibition...
February 15, 2017: Nature Communications
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