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https://www.readbyqxmd.com/read/27879393/natural-variation-of-molecular-and-morphological-gibberellin-responses
#1
Youn-Jeong Nam, Dorota Herman, Jonas Blomme, Eunyoung Chae, Mikiko Kojima, Frederik Coppens, Véronique Storme, Twiggy Van Daele, Stijn Dhondt, Hitoshi Sakakibara, Detlef Weigel, Dirk Inzé, Nathalie Gonzalez
Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis thaliana (Arabidopsis). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories...
November 22, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27877118/contexts-paired-with-junk-food-impair-goal-directed-behavior-in-rats-implications-for-decision-making-in-obesogenic-environments
#2
Michael D Kendig, Ambrose M K Cheung, Joel S Raymond, Laura H Corbit
The high prevalence of obesity and related metabolic diseases calls for greater understanding of the factors that drive excess energy intake. Calorie-dense palatable foods are readily available and often are paired with highly salient environmental cues. These cues can trigger food-seeking and consumption in the absence of hunger. Here we examined the effects of palatable food-paired environmental cues on control of instrumental food-seeking behavior. In Experiment 1, adult male rats received exposures to one context containing three "junk" foods (JFs context) and another containing chow (Chow context)...
2016: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/27874013/crystal-structure-of-fabz-acp-complex-reveals-a-dynamic-seesaw-like-catalytic-mechanism-of-dehydratase-in-fatty-acid-biosynthesis
#3
Lin Zhang, Jianfeng Xiao, Jianrong Xu, Tianran Fu, Zhiwei Cao, Liang Zhu, Hong-Zhuan Chen, Xu Shen, Hualiang Jiang, Liang Zhang
Fatty acid biosynthesis (FAS) is a vital process in cells. Fatty acids are essential for cell assembly and cellular metabolism. Abnormal FAS directly correlates with cell growth delay and human diseases, such as metabolic syndromes and various cancers. The FAS system utilizes an acyl carrier protein (ACP) as a transporter to stabilize and shuttle the growing fatty acid chain throughout enzymatic modules for stepwise catalysis. Studying the interactions between enzymatic modules and ACP is, therefore, critical for understanding the biological function of the FAS system...
December 2016: Cell Research
https://www.readbyqxmd.com/read/27872959/corynebacterium-glutamicum-for-sustainable-bioproduction-from-metabolic-physiology-to-systems-metabolic-engineering
#4
Judith Becker, Gideon Gießelmann, Sarah Lisa Hoffmann, Christoph Wittmann
Since its discovery 60 years ago, Corynebacterium glutamicum has evolved into a workhorse for industrial biotechnology. Traditionally well known for its remarkable capacity to produce amino acids, this Gram-positive soil bacterium, has become a flexible, efficient production platform for various bulk and fine chemicals, materials, and biofuels. The central turnstile of all these achievements is our excellent understanding of its metabolism and physiology. This knowledge base, together with innovative systems metabolic engineering concepts, which integrate systems and synthetic biology into strain engineering, has upgraded C...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27869296/segmented-linear-modeling-of-cho-fed-batch-culture-and-its-application-to-large-scale-production
#5
Bassem Ben Yahia, Boris Gourevitch, Laetitia Malphettes, Elmar Heinzle
We describe a systematic approach to model CHO metabolism during biopharmaceutical production across a wide range of cell culture conditions. To this end, we applied the metabolic steady state concept. We analyzed and modeled the production rates of metabolites as a function of the specific growth rate. First, the total number of metabolic steady state phases and the location of the breakpoints were determined by recursive partitioning. For this, the smoothed derivative of the metabolic rates with respect to the growth rate were used followed by hierarchical clustering of the obtained partition...
November 7, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27869177/repressor-logic-modules-assembled-by-rolling-circle-amplification-platform-to-construct-a-set-of-logic-gates
#6
Hua Wei, Bo Hu, Suming Tang, Guojie Zhao, Yifu Guan
Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27869104/comparative-analysis-of-the-volatile-metabolomes-of-pseudomonas-aeruginosa-clinical-isolates
#7
Heather D Bean, Christiaan A Rees, Jane E Hill
Pseudomonas aeruginosa is a nearly ubiquitous Gram-negative organism, well known to occupy a multitude of environmental niches and cause human infections at a variety of bodily sites, due to its metabolic flexibility, secondary to extensive genetic heterogeneity at the species level. Because of its dynamic metabolism and clinical importance, we sought to perform a comparative analysis on the volatile metabolome (the 'volatilome') produced by P. aeruginosa clinical isolates. In this study, we analyzed the headspace volatile molecules of 24 P...
November 21, 2016: Journal of Breath Research
https://www.readbyqxmd.com/read/27867851/percutaneous-endoscopic-treatment-for-urinary-stones-in-pediatric-patients-where-we-are-now
#8
Paolo Caione, Giuseppe Collura, Michele Innocenzi, Mauro De Dominicis, Simona Gerocarni Nappo, Nicola Capozza
BACKGROUND: Percutaneous nephrolithotomy (PCNL) has been adopted for pyelo-calyceal stones treatment in pediatric patients, starting from the 90's. Very recently, miniaturization of endoscopic instruments allowed less invasive procedures with low complication rate. We reviewed our experience on upper tract stone treatment utilizing two different percutaneous accesses, focusing on the recent new miniaturized devices offered for pediatric renal stones. METHODS: Patients presenting upper tract urinary stones observed from January 2011 to December 2015 and treated by percutaneous renal access were prospectively evaluated: age, sex, metabolic issues, associated abnormalities, treatment modalities, hospital stay and complication rate were recorded in a specific database...
October 2016: Translational pediatrics
https://www.readbyqxmd.com/read/27867422/classyfire-automated-chemical-classification-with-a-comprehensive-computable-taxonomy
#9
Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S Wishart
BACKGROUND: Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27860522/the-ambrosia-symbiosis-from-evolutionary-ecology-to-practical-management
#10
Jiri Hulcr, Lukasz L Stelinski
The ambrosia beetle-fungus farming symbiosis is more heterogeneous than previously thought. There is not one but many ambrosia symbioses. Beetlefungus specificity is clade-dependent and ranges from strict to promiscuous. Each new origin has evolved a new mycangium. The most common relationship with host trees is colonization of freshly dead tissues, but there are also parasites of living trees, vectors of pathogenic fungi, and beetles living in rotten trees with a wood-decay symbiont. Most of these strategies are driven by fungal metabolism whereas beetle ecology is evolutionarily more flexible...
November 16, 2016: Annual Review of Entomology
https://www.readbyqxmd.com/read/27857205/principles-of-proteome-allocation-are-revealed-using-proteomic-data-and-genome-scale-models
#11
Laurence Yang, James T Yurkovich, Colton J Lloyd, Ali Ebrahim, Michael A Saunders, Bernhard O Palsson
Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments...
November 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27856908/characterization-of-a-dynamic-metabolon-producing-the-defense-compound-dhurrin-in-sorghum
#12
Tomas Laursen, Jonas Borch, Camilla Knudsen, Krutika Bavishi, Federico Torta, Helle Juel Martens, Daniele Silvestro, Nikos S Hatzakis, Markus R Wenk, Timothy R Dafforn, Carl Erik Olsen, Mohammed Saddik Motawia, Björn Hamberger, Birger Lindberg Møller, Jean-Etienne Bassard
Metabolic highways may be orchestrated by the assembly of sequential enzymes into protein complexes, or metabolons, to facilitate efficient channeling of intermediates and to prevent undesired metabolic cross-talk while maintaining metabolic flexibility. Here we report the isolation of the dynamic metabolon that catalyzes the formation of the cyanogenic glucoside dhurrin, a defense compound produced in sorghum plants. The metabolon was reconstituted in liposomes, which demonstrated the importance of membrane surface charge and the presence of the glucosyltransferase for metabolic channeling...
November 18, 2016: Science
https://www.readbyqxmd.com/read/27856638/regulation-of-pyruvate-dehydrogenase-kinase-4-in-the-heart-through-degradation-by-the-lon-protease-in-response-to-mitochondrial-substrate-availability
#13
Clair Crewe, Christopher Schafer, Irene Lee, Michael Kinter, Luke I Szweda
Cardiac metabolic inflexibility is driven by robust up-regulation of pyruvate dehydrogenase kinase 4 (PDK4) and phosphorylation-dependent inhibition of pyruvate dehydrogenase (PDH) within a single day of feeding mice a high fat diet. In the current study, we have discovered that PDK4 is a short-lived protein (t1/2 ~1 h) and is specifically degraded by the mitochondrial protease, Lon. Lon does not rapidly degrade PDK1 and 2 indicating specificity toward the PDK isoform that is a potent modulator of metabolic flexibility...
November 17, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27856353/urolithiasis-in-renal-transplant-donors-and-recipients-an-update
#14
REVIEW
Ahmed M Harraz, Ahmed I Kamal, Ahmed A Shokeir
Urolithiasis in the context of renal transplant is a quite rare event that requires keeping a higher index of suspicion and vigilance. Donors with incidentally discovered asymptomatic renal stones "donor gifted lithiasis" are potentially considered for donation should they are not recurrent stone formers and in the absence of active biochemical disorders. Stone clearance from the donors can be done before donation using shock wave lithotripsy and/or flexible ureteroscopy. Ex vivo ureteroscopy at time of transplant is equally feasible and safe...
November 14, 2016: International Journal of Surgery
https://www.readbyqxmd.com/read/27847299/an-mrspec-database-query-and-visualization-engine-with-applications-as-a-clinical-diagnostic-and-research-tool
#15
Filip Miscevic, Justin Foong, Benjamin Schmitt, Susan Blaser, Michael Brudno, Andreas Schulze
PURPOSE: Proton magnetic resonance spectroscopy (MRspec), one of the very few techniques for in vivo assessment of neuro-metabolic profiles, is often complicated by lack of standard population norms and paucity of computational tools. METHODS: 7035 scans and clinical information from 4430 pediatric patients were collected from 2008 to 2014. Scans were conducted using a 1.5T (n=3664) or 3T scanner (n=3371), and with either a long (144ms, n=5559) or short echo time (35ms, n=1476)...
November 9, 2016: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/27836842/microdiversification-of-a-pelagic-polynucleobacter-species-is-mainly-driven-by-acquisition-of-genomic-islands-from-a-partially-interspecific-gene-pool
#16
Matthias Hoetzinger, Johanna Schmidt, Jitka Jezberová, Ulrike Koll, Martin W Hahn
: Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome are clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located...
November 11, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27834209/metabolite-pools-and-carbon-flow-during-c4-photosynthesis-in-maize-13co2-labeling-kinetics-and-cell-type-fractionation
#17
Stéphanie Arrivault, Toshihiro Obata, Marek Szecówka, Virginie Mengin, Manuela Guenther, Melanie Hoehne, Alisdair R Fernie, Mark Stitt
Worldwide efforts to engineer C4 photosynthesis into C3 crops require a deep understanding of how this complex pathway operates. CO2 is incorporated into four-carbon metabolites in the mesophyll, which move to the bundle sheath where they are decarboxylated to concentrate CO2 around RuBisCO. We performed dynamic (13)CO2 labeling in maize to analyze C flow in C4 photosynthesis. The overall labeling kinetics reflected the topology of C4 photosynthesis. Analyses of cell-specific labeling patterns after fractionation to enrich bundle sheath and mesophyll cells revealed concentration gradients to drive intercellular diffusion of malate, but not pyruvate, in the major CO2-concentrating shuttle...
November 7, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27834193/impact-of-polypharmacy-on-antiretroviral-prescription-in-people-living-with-hiv
#18
Giovanni Guaraldi, Marianna Menozzi, Stefano Zona, Andrea Calcagno, Ana R Silva, Antonella Santoro, Andrea Malagoli, Giovanni Dolci, Chiara Mussi, Cristina Mussini, Matteo Cesari, Saye H Khoo
OBJECTIVES: To evaluate the relationship between polypharmacy and ART, delivered as conventional multi-tablet three-drug regimens, single-tablet regimens or less-drug regimens (simplified mono or dual regimens). METHODS: We conducted a cross-sectional analysis of electronic data from the prospective Modena HIV Metabolic Clinic Cohort Study. We included the last clinical observation for each patient from January 2006 to December 2015. Polypharmacy was defined as the use of five or more medications (excluding ART)...
November 9, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/27829583/bacillus-subtilis-gntr-regulation-modified-to-devise-artificial-transient-induction-systems
#19
Parastoo Majidian, Junko Kuse, Kosei Tanaka, Hamid Najafi, Mehrshad Zeinalabedini, Shinji Takenaka, Ken-Ichi Yoshida
We modified GntR regulation in Bacillus subtilis to devise transient induction systems. GntR is the repressor antagonized by gluconate to induce transcription of the gntRKPZ operon for gluconate catabolism. On the other hand, the gnt operon is repressed by glucose via carbon catabolite repression involving CcpA/P-ser-HPr, which binds to two cre sites: one located in the gnt promoter region and the other within the gntR coding region. We initiated gntKPZ encoding of enzymes for gluconate catabolism expressed independently from the operon; this allowed constitutive degradation of gluconate...
November 8, 2016: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/27829138/targeting-stromal-glutamine-synthetase-in-tumors-disrupts-tumor-microenvironment-regulated-cancer-cell-growth
#20
Lifeng Yang, Abhinav Achreja, Tsz-Lun Yeung, Lingegowda S Mangala, Dahai Jiang, Cecil Han, Joelle Baddour, Juan C Marini, Joseph Ni, Ryuichi Nakahara, Stephen Wahlig, Lisa Chiba, Sun Hye Kim, Joshua Morse, Sunila Pradeep, Archana Sidalaghatta Nagaraja, Monika Haemmerle, Noh Kyunghee, Mathew Derichsweiler, Thomas Plackemeier, Imelda Mercado-Uribe, Gabriel Lopez-Berestein, Tyler Moss, Prahlad T Ram, Jinsong Liu, Xiongbin Lu, Samuel C Mok, Anil K Sood, Deepak Nagrath
Reactive stromal cells are an integral part of tumor microenvironment (TME) and interact with cancer cells to regulate their growth. Although targeting stromal cells could be a viable therapy to regulate the communication between TME and cancer cells, identification of stromal targets that make cancer cells vulnerable has remained challenging and elusive. Here, we identify a previously unrecognized mechanism whereby metabolism of reactive stromal cells is reprogrammed through an upregulated glutamine anabolic pathway...
November 8, 2016: Cell Metabolism
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