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https://read.qxmd.com/read/30779583/depletion-of-high-molecular-mass-proteins-for-the-identification-of-small-proteins-and-short-open-reading-frame-encoded-peptides-in-cellular-proteomes
#1
Liam Cassidy, Philipp T Kaulich, Andreas Tholey
The identification of small proteins and peptides (below ca. 100 to 150 amino acids) in complex biological samples is hampered by the dominance of higher molecular weight proteins. On the other hand, the increasing knowledge about alternative or short open reading frames creates a need for methods that allow the existence of the corresponding gene products to be proven in proteomics experiments. We present an acetonitrile-based precipitation methodology which depletes the majority of proteins above ca. 15 kDa...
February 19, 2019: Journal of Proteome Research
https://read.qxmd.com/read/30778890/biomethane-production-from-sugar-beet-pulp-under-cocultivation-with-clostridium-cellulovorans-and-methanogens
#2
Hisao Tomita, Fumiyoshi Okazaki, Yutaka Tamaru
This study was demonstrated with a coculture fermentation system using sugar beet pulp (SBP) as a carbon source combining the cellulose-degrading bacterium Clostridium cellulovorans with microbial flora of methane production (MFMP) for the direct conversion of cellulosic biomass to methane (CH4 ). The MFMP was taken from a commercial methane fermentation plant and extremely complicated. Therefore, the MFMP was analyzed by a next-generation sequencing system and the microbiome was identified and classified based on several computer programs...
February 18, 2019: AMB Express
https://read.qxmd.com/read/30767709/effects-of-amino-modified-biofilm-carriers-on-biogas-production-in-the-anaerobic-digestion-of-corn-straw
#3
Yongdi Liu, Chaoba Lin, Honghua Jia, Xiaoyu Yong, Xinxin Xie, Xiayuan Wu, Jun Zhou, Ping Wei
This paper studied the property of three different biofilm carriers added into the anaerobic digestion systems, a granular activated carbon, a polyacrylonitrile, and a polyacrylonitrile modified with diethylenetriamine (PAN-NH2 ). The PAN-NH2 system kept the maximum biogas and methane production, which were 42.69% and 37.29% higher than the control system, respectively. The value of pH and chemical oxygen demand, the content of total solid and volatile solid, volatile fatty acids concentration, coenzyme F420 concentration, and microbial community analysis were investigated during the anaerobic digestion process...
February 15, 2019: Environmental Technology
https://read.qxmd.com/read/30742498/response-of-methanogenic-archaea-from-siberian-permafrost-and-non-permafrost-environments-to-simulated-mars-like-desiccation-and-the-presence-of-perchlorate
#4
Paloma Serrano, Mashal Alawi, Jean-Pierre de Vera, Dirk Wagner
Numerous preflight investigations were necessary prior to the exposure experiment BIOMEX on the International Space Station to test the basic potential of selected microorganisms to resist or even to be active under Mars-like conditions. In this study, methanogenic archaea, which are anaerobic chemolithotrophic microorganisms whose lifestyle would allow metabolism under the conditions on early and recent Mars, were analyzed. Some strains from Siberian permafrost environments have shown a particular resistance...
February 2019: Astrobiology
https://read.qxmd.com/read/30737865/solubilization-of-organics-due-to-thermal-hydrolysis-pretreatment-and-the-shift-in-microbial-population-in-anaerobic-digestion
#5
Manisha S Berde, Domenec Jolis
A study was conducted to analyze the effect of solubilization due to thermal hydrolysis pretreatment on the microbial population responsible for anaerobic digestion at mesophilic temperature. Metagenomic and microbial population analysis was done on digesters receiving sludge with and without thermal hydrolysis pretreatment. The digester receiving thermal hydrolysis pretreatment was stable at lower detention times and showed a shift in microbial population with predominance of methane-producing population in comparison to conventional digesters receiving no thermal hydrolysis pretreatment...
February 8, 2019: Water Environment Research: a Research Publication of the Water Environment Federation
https://read.qxmd.com/read/30713681/chemically-defined-lactose-based-autoinduction-medium-for-site-specific-incorporation-of-non-canonical-amino-acids-into-proteins
#6
Michael Muzika, Natali H Muskat, Shani Sarid, Oshrit Ben-David, Ryan A Mehl, Eyal Arbely
Genetic code expansion technology enables the site-specific incorporation of dozens of non-canonical amino acids (NCAAs) into proteins expressed in live cells. The NCAAs can introduce various chemical functionalities into proteins, ranging from natural post-translational modifications, to spectroscopic probes and chemical handles for bioorthogonal reactions. These chemical groups provide powerful tools for structural, biochemical, and biophysical studies, which may require significant quantities of recombinantly expressed proteins...
July 17, 2018: RSC Advances
https://read.qxmd.com/read/30709765/efficient-biogas-production-from-cattle-manure-in-a-plug-flow-reactor-a-large-scale-long-term-study
#7
Lili Dong, Guangli Cao, Xianzhang Guo, Tianshu Liu, Jiwen Wu, Nanqi Ren
In this study, a large-scale plug flow reactor has been operated at a hydraulic retention time of 25 d with substrate concentration of total solids (7-10%) under a temperature of 37-40 °C with a working volume of 3.85 × 104 m3 and dispose 1504 m3 /d of waste for three years. The average monthly biogas production was 7.45 × 104 m3 . At stable stage, the volume biogas, methane production rate and methane content reached 1.07 m3 /m3· d, 0.58 m3 /m3· d and 56.4%, respectively. Moreover, the specific biogas and methane yields of substrate removal efficiency were up to 0...
January 23, 2019: Bioresource Technology
https://read.qxmd.com/read/30680878/thiol-based-redox-sensing-in-the-methyltransferase-associated-sensor-kinase-rdms-in-methanosarcina-acetivorans
#8
Kerstin Fiege, Nicole Frankenberg-Dinkel
Organisms have evolved signal transduction systems to quickly adapt their lifestyle to internal and environmental changes. While protein kinases and two-component systems are widely distributed in Bacteria, they are also found in Archaea, but are less diversified and abundant. In this work, we analyzed the function of the kinase RdmS and its role in a putative two-component system in the methanogenic archaeon Methanosarcina acetivorans. RdmS is encoded upstream of the regulator MsrF, which activates the expression of the corrinoid/methyltransferase fusion protein MtsD...
January 24, 2019: Environmental Microbiology
https://read.qxmd.com/read/30677634/effects-of-pig-slurry-acidification-on-methane-emissions-during-storage-and-subsequent-biogas-production
#9
Sang-Ryong Shin, Seongwon Im, Alsayed Mostafa, Mo-Kwon Lee, Yeo-Myeong Yun, Sae-Eun Oh, Dong-Hoon Kim
In addition to undesirable odorous gases, substantial amounts of greenhouse gases (GHG), particularly methane (CH4 ), are generated during the storage of livestock manure. To reduce the CH4 emissions, first, pig slurry (PS) was stored for 40 d at 30 °C after adjusting the pH at 5.0-7.0 using H2 SO4 solution. In the control (non-acidified PS), 3.7 kg CO2 eq./ton PS of CH4 emissions was detected, which was reduced to 1.8, 0.9, 0.4, 0.2, and 0.1 kg CO2 eq./ton PS at pH 7.0, 6.5, 6.0, 5.5, and 5.0, respectively...
January 16, 2019: Water Research
https://read.qxmd.com/read/30671309/effects-of-nickel-and-cobalt-on-methane-production-and-methanogen-abundance-and-diversity-in-paddy-soil
#10
Tianwei Wang, Zhaoxia Li, Xueping Chen, Xi-En Long
Background: Paddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition. Methods: An incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil...
2019: PeerJ
https://read.qxmd.com/read/30669050/electro-driven-methanogenic-microbial-community-diversity-and-variability-in-the-electron-abundant-niche
#11
Weiwei Cai, Wenzong Liu, Zhaojing Zhang, Kai Feng, Ge Ren, Chuanliang Pu, Jiaqi Li, Ye Deng, Aijie Wang
The underlying dynamics of microbial (bacteria and archaea) communities ecologically responding to an applied potential are critical to achieving the goal of enhancing bioenergy recovery but are not sufficiently understood. We built a MEC-AD mode that increased methane production rate by several times (max. 3.8 times) during the startup period compared to control AD, changed the absence or presence of external voltage to provide the pre-, dur-, and post- samples for microbial analysis. From a time and spatially dependent community analysis of electrode-respiring bacteria and methanogens, the corresponding Geobacter developed under the influence of external voltage, pairing with methanogens in the anodic and cathodic biofilm to generate methane...
January 14, 2019: Science of the Total Environment
https://read.qxmd.com/read/30654102/fungal-bioaugmentation-of-anaerobic-digesters-fed-with-lignocellulosic-biomass-what-to-expect-from-anaerobic-fungus-orpinomyces-sp
#12
Çağrı Akyol, Orhan Ince, Mahir Bozan, E Gozde Ozbayram, Bahar Ince
Energy-efficient biogas reactors are often designed and operated mimicking natural microbial ecosystems such as the digestive tracts of ruminants. Anaerobic fungi play a crucial role in the degradation of lignocellulose-rich fiber thanks to their high cellulolytic activity. Fungal bioaugmentation is therefore at the heart of our understanding of enhancing anaerobic digestion (AD). The efficiency of bioaugmentation with anaerobic fungus Orpinomyces sp. was evaluated in lignocellulose-based AD configurations...
January 8, 2019: Bioresource Technology
https://read.qxmd.com/read/30634152/effects-of-tylosin-ciprofloxacin-and-sulfadimidine-on-mcra-gene-abundance-and-the-methanogen-community-during-anaerobic-digestion-of-cattle-manure
#13
Xin Zhang, Jie Gu, Xiaojuan Wang, Kaiyu Zhang, Yanan Yin, Ranran Zhang, Sheqi Zhang
This study evaluated how tylosin (TYL), ciprofloxacin (CIP), and sulfadimidine (SM2 ) affected biogas and CH4 production during anaerobic digestion (AD) via their effects on the key genes related to methane production and the methanogenic community. The results showed that TYL, CIP, and SM2 reduced the production of methane during AD by 7.5%, 21.9%, and 16.0%, respectively. After AD for five days, CIP strongly inhibited the mcrA gene, where its abundance was 49% less than that in the control. TYL and SM2 decreased the abundances of Spirochaeta and Fibrobacteres during AD...
December 18, 2018: Chemosphere
https://read.qxmd.com/read/30628235/-impacts-of-sludge-characteristics-on-anaerobic-digestion-with-microwave-pretreatment-and-archaeal-community-structure-analysis
#14
Ping Fang, An-Ping Tang, Xing-Min Fu, Wei Li, Yang Wen, Juan Tong, Yuan-Song Wei
Sludge characteristics is an important factor in sludge pretreatment and anaerobic digestion (AD) efficiency. Therefore, waste sludge of anaerobic-anoxic-aerobic (A2 O) and A2 O-membrane bioreactor (MBR) wastewater treatment processes from a full-scale wastewater treatment plant were taken, and the variations of sludge characteristics and performance during microwave pretreatment and AD were compared. The succession of archaeal community structure during the sludge treatment was also investigated. A2 O waste sludge showed better biodegradability than A2 O-MBR waste sludge did, with 16...
November 8, 2018: Huan Jing Ke Xue= Huanjing Kexue
https://read.qxmd.com/read/30599328/increased-biodegradability-of-low-grade-coal-wastewater-in-anaerobic-membrane-bioreactor-by-adding-yeast-wastes
#15
Yeo-Myeong Yun, Myungchan Kim, Hyojeon Kim, Dong-Hoon Kim, Eilhann E Kwon, Seoktae Kang
Demineralization is required in upgrading low-grade coal to serve as an alternative energy resource for the production of fuel and valuable chemicals but generates a large amount of low-grade coal wastewater (LCWW). The objective of this study was to investigate the effects of a co-substrate on an anaerobic membrane bioreactor (AnMBR) treating LCWW. CH4 was not produced during the operation fed by LCWW alone. When yeast wastes (YW) were supplemented, there was a gradual increase in the biodegradability of LCWW, achieving 182 CH4 mL/g COD with 58% COD removal efficiency...
December 29, 2018: Journal of Environmental Management
https://read.qxmd.com/read/30584962/mechanism-of-process-imbalance-of-long-term-anaerobic-digestion-of-food-waste-and-role-of-trace-elements-in-maintaining-anaerobic-process-stability
#16
Wanli Zhang, Bin Chen, Aimin Li, Lei Zhang, Rundong Li, Tianhua Yang, Wanli Xing
This study investigated mechanism of process imbalance of long-term anaerobic digestion (AD) of food waste (FW) and role of trace elements (TEs) in maintaining process stability. AD of FW was strongly inhibited by volatile fatty acids (VFA, mainly propionate). The deficiency of essential TEs in FW was the fundamental reason. TEs contents in digester gradually decreased with regular substrate feeding and digestate discharge, which greatly limited growth and metabolism of hydrogenotrophic methanogens and Methanosarcina...
December 17, 2018: Bioresource Technology
https://read.qxmd.com/read/30572955/comparative-analysis-of-deep-sequenced-methanogenic-communities-identification-of-microorganisms-responsible-for-methane-production
#17
Adam Pyzik, Martyna Ciezkowska, Pawel S Krawczyk, Adam Sobczak, Lukasz Drewniak, Andrzej Dziembowski, Leszek Lipinski
BACKGROUND: Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways...
December 20, 2018: Microbial Cell Factories
https://read.qxmd.com/read/30555446/ammonia-inhibition-of-anaerobic-volatile-fatty-acid-degrading-microbial-communities
#18
Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Sabine Kleinsteuber, Hauke Harms, Florian Centler
Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM...
2018: Frontiers in Microbiology
https://read.qxmd.com/read/30539258/a-short-term-stimulation-of-ethanol-enhances-the-effect-of-magnetite-on-anaerobic-digestion
#19
Caiqin Wang, Weilong Qiao, Hui Chen, Xiangyang Xu, Liang Zhu
Conductive iron oxides (CIO) have been proved recently to facilitate the anaerobic microbial syntrophy based on the direct interspecies electron transfer (DIET) in batch experiments. However, the effect of CIO was always insignificant in anaerobic digestion (AD) reactor especially when the DIET-based syntrophic partners were absent. In this study, the effect of magnetite on performance of AD system with sucrose as a sole carbon source was investigated, but limited enhancement was achieved during the first 36-day operation...
December 12, 2018: Applied Microbiology and Biotechnology
https://read.qxmd.com/read/30528903/graphene-facilitates-biomethane-production-from-protein-derived-glycine-in-anaerobic-digestion
#20
Richen Lin, Chen Deng, Jun Cheng, Ao Xia, Piet N L Lens, Stephen A Jackson, Alan D W Dobson, Jerry D Murphy
Interspecies electron transfer is a fundamental factor determining the efficiency of anaerobic digestion (AD), which involves syntrophy between fermentative bacteria and methanogens. Direct interspecies electron transfer (DIET) induced by conductive materials can optimize this process offering a significant improvement over indirect electron transfer. Herein, conductive graphene was applied in the AD of protein-derived glycine to establish DIET. The electron-producing reaction via DIET is thermodynamically more favorable and exhibits a more negative Gibbs free energy value (-60...
November 22, 2018: iScience
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