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https://www.readbyqxmd.com/read/28738195/proteomic-and-genetics-insights-on-the-response-of-the-bacteriocinogenic-lactobacillus-sakei-crl1862-during-biofilm-formation-on-stainless-steel-surface-at-10%C3%A2-c
#1
Mariana Pérez-Ibarreche, Lucía M Mendoza, Graciela Vignolo, Silvina Fadda
Some lactic acid bacteria have the ability to form biofilms on food-industry surfaces and this property could be used to control food pathogens colonization. Lactobacillus sakei CR1862 was selected considering its bacteriocinogenic nature and ability to adhere to abiotic surfaces at low temperatures. In this study, the proteome of L. sakei CRL1862 grown either under biofilm on stainless steel surface and planktonic modes of growth at 10°C, was investigated. Using two-dimensional gel electrophoresis, 29 out of 43 statistically significant spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry...
July 4, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28736244/the-use-of-stable-isotopes-in-the-study-of-human-pathophysiology
#2
Evelina Charidemou, Tom Ashmore, Julian L Griffin
The growing prevalence of metabolic diseases including fatty liver disease and Type 2 diabetes has increased the emphasis on understanding metabolism at the mechanistic level and how it is perturbed in disease. Metabolomics is a continually expanding field that seeks to measure metabolites in biological systems during a physiological stimulus or a genetic alteration. Typically, metabolomics studies provide total pool sizes of metabolites rather than dynamic flux measurements. More recently there has been a resurgence in approaches that use stable isotopes (e...
July 20, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28733443/direct-metabolic-interrogation-of-dihydrotestosterone-biosynthesis-from-adrenal-precursors-in-primary-prostatectomy-tissues
#3
Charles Dai, Yoon-Mi Chung, Evan Kovac, Ziqi Zhu, Jianneng Li, Cristina Magi-Galluzzi, Andrew J Stephenson, Eric A Klein, Nima Sharifi
Purpose: A major mechanism of castration-resistant prostate cancer (CRPC) involves intratumoral biosynthesis of dihydrotestosterone (DHT) from adrenal precursors. We have previously shown that adrenal-derived androstenedione (AD) is the preferred substrate over testosterone (T) for 5α-reductase expressed in metastatic CRPC, bypassing T as an obligate precursor to DHT. However, the metabolic pathway of adrenal-derived DHT biosynthesis has not been rigorously investigated in the setting of primary disease in the prostate...
July 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28733212/the-peroxyl-radical-induced-oxidation-of-escherichia-coli-ftsz-and-its-single-tryptophan-mutant-y222w-modifies-specific-side-chains-generates-protein-cross-links-and-affects-biological-function
#4
Elizabeth Escobar-Álvarez, Fabian Leinisch, Gissela Araya, Octavio Monasterio, Lasse G Lorentzen, Eduardo Silva, Michael J Davies, Camilo López-Alarcón
FtsZ (filamenting temperature-sensitive mutant Z) is a key protein in bacteria cell division. The wild-type Escherichia coli FtsZ sequence (FtsZwt) contains three tyrosine (Tyr, Y) and sixteen methionine (Met, M) residues. The Tyr at position 222 is a key residue for FtsZ polymerization. Mutation of this residue to tryptophan (Trp, W; mutant Y222W) inhibits GTPase activity resulting in an extended time in the polymerized state compared to FtsZwt. Protein oxidation has been highlighted as a determinant process for bacteria resistance and consequently oxidation of FtsZwt and the Y222W mutant, by peroxyl radicals (ROO•) generated from AAPH (2,2'-azobis(2-methylpropionamidine) dihydrochloride) was studied...
July 18, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28732885/fouling-resistant-pvdf-carboxymethyl-chitosan-composite-nanofiltration-membranes-for-humic-acid-removal
#5
Kavitha Ekambaram, Mohan Doraisamy
In this work, carboxymethyl chitosan without a crosslinking agent was blended with polyvinylidene fluoride using non solvent induced phase inversion process. Carboxymethyl chitosan was synthesized using monochloroacetic acid and isopropanol and its structural elucidation was done. Synthesized carboxymethyl chitosan was incorporated with PVDF and investigated for its casting dope viscosity, x-ray photoelectron spectroscopy, thermal gravimetric analysis, mechanical properties, contact angle, scanning electron microscopy, atomic force microscopy and filtration studies...
October 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28731563/improving-fructose-utilization-and-butanol-production-by-clostridium-acetobutylicum-via-extracellular-redox-potential-regulation-and-intracellular-metabolite-analysis
#6
Li-Jie Chen, You-Duo Wu, Chuang Xue, Feng-Wu Bai
Jerusalem artichoke (JA) can grow well in marginal lands with high biomass yield, and thus is a potential energy crop for biorefinery. The major biomass of JA is from tubers, which contain inulin that can be easily hydrolyzed into a mixture of fructose and glucose, but fructose utilization for producing butanol as an advanced biofuel is poor compared to glucose-based ABE fermentation by Clostridium acetobutylicum. In this article, the impact of extracellular redox potential (ORP) on the process was studied using a mixture of fructose and glucose to simulate the hydrolysate of JA tubers...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28729868/the-c4-model-grass-setaria-is-a-short-day-plant-with-secondary-long-day-genetic-regulation
#7
Andrew N Doust, Margarita Mauro-Herrera, John G Hodge, Jessica Stromski
The effect of photoperiod (day:night ratio) on flowering time was investigated in the wild species, Setaria viridis, and in a set of recombinant inbred lines (RILs) derived from a cross between foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis). Photoperiods totaled 24 h, with three trials of 8:16, 12:12 and 16:8 light:dark hour regimes for the RIL population, and these plus 10:14 and 14:10 for the experiments with S. viridis alone. The response of S. viridis to light intensity as well as photoperiod was assessed by duplicating photoperiods at two light intensities (300 and 600 μmol...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28727725/redgem-systematic-reduction-and-analysis-of-genome-scale-metabolic-reconstructions-for-development-of-consistent-core-metabolic-models
#8
Meric Ataman, Daniel F Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727429/elliptic-cylinder-airborne-sampling-and-geostatistical-mass-balance-approach-for-quantifying-local-greenhouse-gas-emissions
#9
Jovan M Tadić, Anna M Michalak, Laura T Iraci, Velibor Ilic, Sébastien C Biraud, Daniel R Feldman, Thaopaul V Bui, Matthew S Johnson, Max Loewenstein, Seongeun Jeong, Marc L Fischer, Emma L Yates, Ju-Mee Ryoo
In this study, we explore observational, experimental, methodological and practical aspects of the flux quantification of greenhouse gases from local point sources by using in-situ airborne observations, and suggest a series of conceptual changes to improve flux estimates. We address the major sources of uncertainty reported in previous studies by modifying (1) the shape of the typical flight path, (2) the modeling of covariance and anisotropy, and (3) the type of interpolation tools used. We show that a cylindrical flight profile offers considerable advantages compared to traditional profiles collected as curtains, although this new approach brings with it the need for a more comprehensive subsequent analysis...
July 20, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28727166/hepatocytes-contribute-to-residual-glucose-production-in-a-mouse-model-for-glycogen-storage-disease-type-ia
#10
Brenda S Hijmans, Andreas Boss, Theo H van Dijk, Maud Soty, Henk Wolters, Elodie Mutel, Albert K Groen, Terry G J Derks, Gilles Mithieux, Arend Heerschap, Dirk-Jan Reijngoud, Fabienne Rajas, Maaike H Oosterveer
It is a longstanding enigma how glycogen storage disease (GSD) type I patients retain a limited capacity for endogenous glucose production (EGP) despite the loss of glucose-6-phosphatase (G6Pase) activity. Insight into the source of residual EGP is of clinical importance given the risk of sudden death in these patients, but so far contradictory mechanisms have been proposed. We investigated G6Pase-independent EGP in hepatocytes isolated from a liver-specific GSD Ia mouse model (L-G6pc(-/-) mice), and performed real-time analysis of hepatic glucose fluxes and glycogen metabolism in L-G6pc(-/-) mice using state-of-the-art stable isotope methodologies...
July 20, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28726776/autophagosome-maturation-mediated-by-rab7-contributes-to-neuroprotection-of-hypoxic-preconditioning-against-global-cerebral-ischemia-in-rats
#11
Lixuan Zhan, Siyuan Chen, Kongping Li, Donghai Liang, Xinyong Zhu, Liu Liu, Zhiwei Lu, Weiwen Sun, En Xu
Autophagy disruption leads to neuronal damage in hypoxic-ischemic brain injury. Rab7, a member of the Rab GTPase superfamily, has a unique role in the regulation of autophagy. Hypoxic preconditioning (HPC) provides neuroprotection against transient global cerebral ischemia (tGCI). However, the underlying mechanisms remain poorly understood. Thus, the current study explored the potential molecular mechanism of the neuroprotective effect of HPC by investigating how Rab7 mediates autophagosome (AP) maturation after tGCI in adult rats...
July 20, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28725675/comparisons-of-elisa-and-western-blot-assays-for-detection-of-autophagy-flux
#12
Sung-Hee Oh, Yong-Bok Choi, June-Hyun Kim, Conrad C Weihl, Jeong-Sun Ju
We analyzed autophagy/mitophagy flux in vitro (C2C12 myotubes) and in vivo (mouse skeletal muscle) following the treatments of autophagy inducers (starvation, rapamycin) and a mitophagy inducer (carbonyl cyanide m-chlorophenylhydrazone, CCCP) using two immunodetection methods, ELISA and Western blotting, and compared their working range, accuracy, and reliability. The ELISAs showed a broader working range than that of the LC3 Western blots (Table 1). Table 2 showed that data value distribution was tighter and the average standard error from the ELISA was much smaller than those of the Western blot, directly relating to the accuracy of the assay...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28725442/identification-of-dust-storm-origin-in-south-west-of-iran
#13
Parya Broomandi, Bahram Dabir, Babak Bonakdarpour, Yousef Rashidi
BACKGROUND: Deserts are the main sources of emitted dust, and are highly responsive to wind erosion. Low content of soil moisture and lack of vegetation cover lead to fine particle's release. One of the semi-arid bare lands in Iran, located in the South-West of Iran in Khoozestan province, was selected to investigate Sand and Dust storm potential. METHODS: This paper focused on the metrological parameters of the sampling site, their changes and the relationship between these changes and dust storm occurrence, estimation of Reconaissance Drought Index, the Atterberg limits of soil samples and their relation with soil erosion ability, the chemical composition, size distribution of soil and airborne dust samples, and estimation of vertical mass flux by COMSALT through considering the effect of saffman force and interparticle cohesion forces during warm period (April-September) in 2010...
2017: Journal of Environmental Health Science & Engineering
https://www.readbyqxmd.com/read/28725384/emissions-of-methane-from-northern-peatlands-a-review-of-management-impacts-and-implications-for-future-management-options
#14
REVIEW
Mohamed Abdalla, Astley Hastings, Jaak Truu, Mikk Espenberg, Ülo Mander, Pete Smith
Northern peatlands constitute a significant source of atmospheric methane (CH 4). However, management of undisturbed peatlands, as well as the restoration of disturbed peatlands, will alter the exchange of CH 4 with the atmosphere. The aim of this systematic review and meta-analysis was to collate and analyze published studies to improve our understanding of the factors that control CH 4 emissions and the impacts of management on the gas flux from northern (latitude 40° to 70°N) peatlands. The analysis includes a total of 87 studies reporting measurements of CH 4 emissions taken at 186 sites covering different countries, peatland types, and management systems...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28724354/novel-plasmodium-falciparum-metabolic-network-reconstruction-identifies-shifts-associated-with-clinical-antimalarial-resistance
#15
Maureen A Carey, Jason A Papin, Jennifer L Guler
BACKGROUND: Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. RESULTS: Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724103/nematode-community-response-to-green-infrastructure-design-in-a-semiarid-city
#16
Mitchell A Pavao-Zuckerman, Christine Sookhdeo
Urbanization affects ecosystem function and environmental quality through shifts in ecosystem fluxes that are brought on by features of the built environment. Green infrastructure (GI) has been suggested as a best management practice (BMP) to address urban hydrologic and ecological impacts of the built environment, but GI practice has only been studied from a limited set of climatic conditions and disciplinary approaches. Here, we evaluate GI features in a semiarid city from the perspective of soil ecology through the application of soil nematode community analysis...
May 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28721404/accurate-determination-of-the-charge-transfer-efficiency-of-photoanodes-for-solar-water-splitting
#17
Dino Klotz, Daniel A Grave, Avner Rothschild
The oxygen evolution reaction (OER) at the surface of semiconductor photoanodes is critical for photoelectrochemical water splitting. This reaction involves photo-generated holes that oxidize water via charge transfer at the photoanode/electrolyte interface. However, a certain fraction of the holes that reach the surface recombine with electrons from the conduction band, giving rise to the surface recombination loss. The charge transfer efficiency, ηt, defined as the ratio between the flux of holes that contribute to the water oxidation reaction and the total flux of holes that reach the surface, is an important parameter that helps to distinguish between bulk and surface recombination losses...
July 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28720902/comparative-genomic-analysis-of-paenibacillus-sp-ssg-1-and-its-closely-related-strains-reveals-the-effect-of-glycometabolism-on-environmental-adaptation
#18
Hui Xu, Shishang Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dairong Qiao, Yu Cao, Yi Cao
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28719204/norditerpenoids-and-dinorditerpenoids-from-the-seeds-of-podocarpus-nagi-as-cytotoxic-agents-and-autophagy-inducers
#19
Zhe-Ling Feng, Le-Le Zhang, Yuan-Dong Zheng, Qian-Yu Liu, Jing-Xin Liu, Lu Feng, Li Huang, Qing-Wen Zhang, Jin-Jian Lu, Li-Gen Lin
Nine new norditerpenoids and dinorditerpenoids, 2-oxonagilactone A (1), 7β-hydroxynagilactone D (2), nagilactones K and L (3 and 4), 3β-hydroxynagilactone L (5), 2β-hydroxynagilactone L (6), 3-epi-15-hydroxynagilactone D (7), 1α-chloro-2β,3β,15-trihydroxynagilactone L (8), and 15-hydroxynagilactone L (9), were isolated from the seeds of Podocarpus nagi, along with eight known analogues. The structures of the new compounds were established based on detailed NMR and HRESIMS analysis, as well as from their ECD spectra...
July 18, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28718926/ets-nocv-decomposition-of-the-reaction-force-the-hcn-cnh-isomerization-reaction-assisted-by-water
#20
Silvia Díaz, Mateusz Z Brela, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Artur Michalak
The partitioning of the reaction force based on the extended-transition-state natural orbital for chemical valence (ETS-NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered ("reactant perspective" and "product perspective")...
July 18, 2017: Journal of Computational Chemistry
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