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metabolic network

Duntao Shu, Baogang Zhang, Yanling He, Gehong Wei
Nitrogen-transforming microorganisms play pivotal roles for the microbial nitrogen-cycling network in the anammox granular system. However, little is known about the effects of inorganic carbon (IC) stresses on the assemblage patterns and functional profiles of abundant and rare taxa. Herein, the community assemblage and functional traits of abundant and rare sub-communities were investigated. Results revealed that insufficient IC had adverse influences on the process performance, while anammox activity could be recovered by IC addition...
June 9, 2018: Bioresource Technology
María Banqueri, Marta Méndez, Jorge L Arias
Subjects' early life events will affect them later in life. When these events are stressful, such as child abuse in humans or repeated maternal separation in rodents, subjects can show some behavioral and brain alterations. This study used young adult female Wistar rats that were maternally raised (AFR), maternally separated from post-natal day (PND) 1 to PND10 (MS10), or maternally separated from PND1 to PND21 (MS21), in order to assess the effects of maternal separation (MS) on spatial learning and memory, as well as cognitive flexibility, using the Morris Water Maze (MWM)...
June 14, 2018: Neurobiology of Learning and Memory
Eleni A Greenwood, Lauri A Pasch, Marcelle I Cedars, Richard S Legro, Esther Eisenberg, Heather G Huddleston
OBJECTIVE: To test the hypothesis that insulin resistance is associated with depression risk in polycystic ovary syndrome (PCOS). DESIGN: Secondary analysis of data from a multicenter randomized trial. SETTING: Multicenter university-based clinical practices. PATIENT(S): Seven hundred thirty-eight women with PCOS by modified Rotterdam criteria seeking pregnancy enrolled in a randomized clinical trial comparing clomiphene citrate versus letrozole...
June 13, 2018: Fertility and Sterility
Rachel S Kelly, Bo L Chawes, Kevin Blighe, Yamini V Virkud, Damien C Croteau-Chonka, Michael J McGeachie, Clary B Clish, Kevin Bullock, Juan C Celedón, Scott T Weiss, Jessica A Lasky-Su
BACKGROUND: Single-omic analyses have provided some insight into the basis of lung function in asthmatic children, but the underlying biological pathways are still poorly understood. METHODS: Weighted gene co-expression network analysis (WGCNA) was used to identify modules of co-regulated gene transcripts and metabolites in blood, among 325 children with asthma from the 'Genetic Epidemiology of Asthma in Costa Rica' study. The biology of modules associated with lung function; as measured by FEV1 , FEV1 /FVC-ratio, bronchodilator response, and airway responsiveness to methacholine, was explored...
June 13, 2018: Chest
Pingping Zhu, Jian Zhang, Yujie Chen, Shanshan Yin, Mingming Su, Guoxiang Xie, Kim L R Brouwer, Changxiao Liu, Ke Lan, Wei Jia
Host-gut microbiota metabolic interactions are closely associated with health and disease. A manifestation of such co-metabolism is the vast structural diversity of bile acids (BAs) involving both oxidative stereochemistry and conjugation. Herein, we describe the development and validation of a LC-MS-based method for the analysis of human C24 BA metabolome in serum and urine. The method has high throughput covering the discrimination of oxidative stereochemistry of unconjugated species in a 15-min analytical cycle...
June 16, 2018: Analytical and Bioanalytical Chemistry
Bei Wang, Qijiang Jin, Xiao Zhang, Neil S Mattson, Huihui Ren, Jing Cao, Yanjie Wang, Dongrui Yao, Yingchun Xu
Flooding severely limits plant growth even for some aquatic plants. Although much work has been done on submergence response of some important crop plants, little is known about the response mechanism of aquatic plants, i.e. lotus (Nelumbo nucifera). In this study, we investigated the genome-wide regulation lotus genes in response to submergence stress by high-throughput mRNA sequencing. A total of 4002 differentially expressed genes (DEGs) in lotus upon submergence stress. Among them, 1976 genes were up-regulated and 2026 down-regulated...
June 15, 2018: Scientific Reports
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Ratnam Wickneswari
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes...
June 15, 2018: Scientific Reports
Cristiana Gomes de Oliveira Dal'Molin, Lake-Ee Quek, Pedro A Saa, Robin Palfreyman, Lars Keld Nielsen
The compartmentalization of C4 plants increases photosynthetic efficiency, while constraining how material and energy must flow in leaf tissues. To capture this metabolic phenomenon, a generic plant metabolic reconstruction was replicated into four connected spatiotemporal compartments, namely bundle sheath (B) and mesophyll (M) across the day and night cycle. The C4 leaf model was used to explore how amenable polyhydroxybutyrate (PHB) production is with these four compartments working cooperatively. A strategic pattern of metabolite conversion and exchange emerged from a systems-level network that has very few constraints imposed; mainly the sequential two-step carbon capture in mesophyll, then bundle sheath and photosynthesis during the day only...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
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
Colin P McNally, Elhanan Borenstein
BACKGROUND: Metabolic dependencies between microbial species have a significant impact on the assembly and activity of microbial communities. However, the evolutionary origins of such dependencies and the impact of metabolic and genomic architecture on their emergence are not clear. RESULTS: To address these questions, we developed a novel framework, coupling a reductive evolution model with a multi-species genome-scale metabolic model to simulate the evolution of two-species microbial communities...
June 15, 2018: BMC Systems Biology
Anton Strunov, Lidiya V Boldyreva, Evgeniya N Andreyeva, Gera A Pavlova, Julia V Popova, Alena V Razuvaeva, Alina F Anders, Fioranna Renda, Alexey V Pindyurin, Maurizio Gatti, Elena Kiseleva
BACKGROUND: S2 cells are one of the most widely used Drosophila melanogaster cell lines. A series of studies has shown that they are particularly suitable for RNAi-based screens aimed at the dissection of cellular pathways, including those controlling cell shape and motility, cell metabolism, and host-pathogen interactions. In addition, RNAi in S2 cells has been successfully used to identify many new mitotic genes that are conserved in the higher eukaryotes, and for the analysis of several aspects of the mitotic process...
June 15, 2018: BMC Biology
Marie-Laure Erffelinck, Alain Goossens
Plants are sessile organisms. Therefore, they developed the capacity to quickly respond to biotic and abiotic environmental stresses, for instance by producing a broad spectrum of bioactive specialized metabolites. In this defense response, the jasmonate phytohormones can instigate a signaling cascade that leads to the specific elicitation and reprograming of numerous metabolic pathways. Recent research progress has provided several insights into the regulatory networks of many specialized metabolic pathways, mainly at the transcriptional level...
June 15, 2018: Planta Medica
Sheng-Min Guo, Jian-Xiong Wang, Jin Li, Fang-Yuan Xu, Quan Wei, Hai-Ming Wang, Hou-Qiang Huang, Si-Lin Zheng, Yu-Jie Xie, Chi Zhang
Osteoarthritis (OA) significantly influences the quality life of people around the world. It is urgent to find an effective way to understand the genetic etiology of OA. We used weighted gene coexpression network analysis (WGCNA) to explore the key genes involved in the subchondral bone pathological process of OA. Fifty gene expression profiles of GSE51588 were downloaded from the Gene Expression Omnibus database. The OA-associated genes and gene ontologies were acquired from JuniorDoc. Weighted gene coexpression network analysis was used to find disease-related networks based on 21756 gene expression correlation coefficients, hub-genes with the highest connectivity in each module were selected, and the correlation between module eigengene and clinical traits was calculated...
June 15, 2018: Journal of Cellular Biochemistry
Helen A Fletcher, Mitali Chatterjee, Andrea Cooper, Tracy Hussell, Paul M Kaye, Joann Prior, Rajko Reljic, Samantha Vermaak, Martin Vordermeier, Ann Williams, Helen McShane
For several complex intracellular pathogens, we have an urgent need for effective vaccines and yet there are common barriers to vaccine development. These diseases, including tuberculosis, leishmaniasis, leprosy and melioidosis, cause a huge burden of disease and disproportionately affect low and middle income countries. They are therefore often neglected due to the marginalisation of affected populations and the poor predicted commercial return on investment. Barriers to vaccine development include an incomplete understanding of protective immunity and translation from the bench into clinical vaccine trials...
2018: F1000Research
Peipei Huang, Shuting Xiong, Jingliang Kang, Jie Mei, Jian-Fang Gui
Sexual size dimorphism is an interesting phenomenon occurred in many fish species. Wildtype zebrafish exhibits a significant sexual dimorphism in body size at the adult stage. Previous studies indicated that sexual size dimorphism was eliminated in stat5b -mutated zebrafish. Herein, the comparative transcriptome analysis was conducted to observe the genes and pathways involved in sexual size dimorphism. The number of male-biased and female-biased genes was much less in the liver of stat5b mutant zebrafish than in wildtype...
2018: Frontiers in Physiology
María I Herrera, Lucas D Udovin, Nicolás Toro-Urrego, Carlos F Kusnier, Juan P Luaces, Matilde Otero-Losada, Francisco Capani
Metabolic syndrome (MetS) is a cluster of risk factors that lead to microvascular dysfunction and chronic cerebral hypoperfusion (CCH). Long-standing reduction in oxygen and energy supply leads to brain hypoxia and protein misfolding, thereby linking CCH to Alzheimer's disease. Protein misfolding results in neurodegeneration as revealed by studying different experimental models of CCH. Regulating proteostasis network through pathways like the unfolded protein response (UPR), the ubiquitin-proteasome system (UPS), chaperone-mediated autophagy (CMA), and macroautophagy emerges as a novel target for neuroprotection...
2018: Frontiers in Neuroscience
Alessandra Vella, Mario Mascalchi
Single-photon emission computed tomography (SPECT) and positron emission tomography (PET) with different radiotracers enable regional evaluation of blood flow and glucose metabolism, of receptors and transporters of several molecules, and of abnormal deposition of peptides and proteins in the brain. The cerebellum has been used as a reference region for different radiotracers in several disease conditions. Whole-brain voxel-wise analysis is not affected by a priori knowledge bias and should be preferred. SPECT and PET have contributed to establishing the cerebellum role in motion, cognition, and emotion control in physiologic and pathophysiologic conditions...
2018: Handbook of Clinical Neurology
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
Fang-Fang Fan, Fei-Fei Guo, Wen Zhang, Yi Zhang, Hong-Jun Yang, Yi Zhang, De-Feng Li, Jing Zhang, Jing-Jing Zhang
In this study, a computer-based network pharmacology approach was applied to investigate the potential mechanism and important components of Rhodiola crenulata in the protection of H9c2 cells against hydrogen peroxide (H₂O₂)-induced oxidative stress. The intestinal absorption liquid of R. crenulata enhanced the cell viability, maintained cell morphology and inhibited cell apoptosis in the H₂O₂-induced oxidative stress in H9c2. Then, computer-based network pharmacology was used to analyze the relevant mechanism...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
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