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Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway

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Synthetic and Systems Biotechnology 2022年第2期7卷 738-749页

作者： Francesca V.Gambacorta Ellen R.Wagner Tyler B.jacobson Mary Tremaine Laura K.Muehlbauer Mick A.McGee justin j.Baerwald Russell L.Wrobel john F.Wolters Mike Place joshua j.Dietrich Dan Xie jose Serate Shabda Gajbhiye Lisa Liu Maikayeng Vang-smith joshua j.Coon Yaoping Zhang Audrey P.Gasch Daniel Amador-Noguez Chris Todd Hittinger Trey K.Sato brian F.Pfleger DOE Great Lakes Bioenergy Research Center University of Wisconsin-MadisonMadisonWIUSA Department of Chemical and Biological Engineering University of Wisconsin-MadisonMadisonWIUSA Laboratory of Genetics Center for Genomic Science InnovationUniversity of Wisconsin-MadisonMadisonWIUSA Department of Bacteriology University of Wisconsin-MadisonMadisonWIUSA Department of Chemistry University of Wisconsin-MadisonMadisonWIUSA Wisconsin Energy Institute J.F.Crow Institute for the Study of EvolutionUniversity of Wisconsin-MadisonMadisonWIUSA Department of Biomolecular Chemistry University of Wisconsin-MadisonMadisonWIUSA

Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces ***,we explore how two of these strategies,pathway re-localization and redox cofactor-balancing,affect the performance and physiology of isobutanol producing *** equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced(NADPH-dependent)or redox-balanced(NADH-dependent)ketol-acid reductoisomerase *** then conducted transcriptomic,proteomic and metabolomic analyses to elucidate molecular differences between the engineered *** localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic ***-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version,albeit at low overall pathway *** genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters,which are required cofactors for the dihydroxyacid dehydratase *** then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation,thereby increasing cellular iron *** resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold,demonstrating that both localizations can support flux to isobutanol.

关键词： Saccharomyces cerevisiae Isobutanol Functional genomics analysis Pathway localization Fe incorporation

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Acid-insoluble ash is a better indigestible marker than chromic oxide to measure apparent total tract digestibility in pigs

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Animal Nutrition 2021年第1期7卷 64-71页

作者： Susanto Prawirodigdo Neil j.Gannon brian j.Leury Frank R.Dunshea Faculty of Veterinary and Agricultural Sciences The University of MelbourneParkvilleVictoria3010Australia Balai Pengkajian Teknologi Pertanian Central java SemarangCentral Java50552Indonesia Biomin Singapore PO Box 2419ToowoombaQLD4350Australia Faculty of Biological Sciences The University of LeedsLeedsLS29JTUnited Kingdom

The aim of this study was to determine the apparent total tract digestibility(ATTD)of nutrients in cottonseed meal(CSM)and soybean meal(SBM)in simple carbohydrate and more complex wheat-based diets using 2 indigestible markers and total faecal ***-five Large White×Landrace boars(57.8 kg)were randomly allocated to either a pure wheat diet,40%CSM or SBM in either a sugar-starch-(1∶1)or wheat-based diet for 18 ***-insoluble ash(AIA)and chromic oxide(Cr2O3)were included in all diets as indigestible *** were offered(1,800 g/d per pig)in 3 meals/d from d 1 to 11 and 8 meals/d from d 12 to *** d 9,the pigs were moved to individual metabolism cages to allow total faecal *** d 18,the pigs were fed hourly for 8 *** the 8th meal,pigs were anaesthetized and digesta sampled from the terminal ileum and rectum before lethal *** were no differences between ATTD of nitrogen(N)determined using AIA as a marker and measured by total faecal *** the other hand,the ATrD of N of diets containing CSM in sugar-starch-or wheat-based diets and the pure wheat diet determined using Cr2O3 as a marker was less(-3.11%,-4.46%and-6.59%;P

关键词： Organic matter Pig Wheat Cottonseed meal Soybean meal Digestibility Nitrogen

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Potential for natural and enhanced attenuation of sulphanilamide in a contaminated chalk aquifer

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journal of Environmental Sciences 2017年第12期29卷 39-48页

作者： Karen A.Bennett Simon D.Kelly Xiangyu Tang brian j.Reid School of Environmental Sciences University of East AngliaNorwich Research ParkNorwich NR4 7TJUK Food and Environmental Protection Laboratory International Atomic Energy Agency1400 ViennaAustria Key Laboratory of Mountain Surface Processes and Ecological Regulation Institute of Mountain Hazards and EnvironmentChinese Academyof SciencesChengdu 610041China

Understanding antibiotic biodegradation is important to the appreciation of their fate and removal from the environment. In this research an Isotope Ratio Mass Spectrometry（IRMS）method was developed to evaluate the extent of biodegradation of the antibiotic,sulphanilamide, in contaminated groundwater. Results indicted an enrichment in δ^（13）C of8.44‰ from-26.56（at the contaminant source） to-18.12‰（300 m downfield of the source）.These results confirm reductions in sulphanilamide concentrations（from 650 to 10 mg/L）across the contaminant plume to be attributable to biodegradation（56%） vs. other natural attenuation processes, such as dilution or dispersion（42%）. To understand the controls on sulphanilamide degradation ex-situ microcosms assessed the influence of sulphanilamide concentration, redox conditions and an alternative carbon source. Results indicated, high levels of anaerobic capacity（~50% mineralisation） to degrade sulphanilamide under high（263 mg/L）, moderate（10 mg/L） and low（0.02 mg/L） substrate concentrations. The addition of electron acceptors; nitrate and sulphate, did not significantly enhance the capacity of the groundwater to anaerobically biodegrade sulphanilamide. Interestingly, where alternative carbon sources were present, the addition of nitrate and sulphate inhibited sulphanilamide biodegradation. These results suggest, under in-situ conditions, when a preferential carbon source was available for biodegradation, sulphanilamide could be acting as a nitrogen and/or sulphur source. These findings are important as they highlight sulphanilamide being used as a carbon and a putative nitrogen and sulphur source, under prevailing iron reducing conditions.

关键词： Antibiotics Sulphonamide Groundwater contamination Biodegradation Stable isotope fractionation IRMS

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Reply to Letter by Dr. Christoph Kupferschmid： Commentary on ＂Countries with high circumcision prevalence have lower prostate cancer mortality＂

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Asian journal of Andrology 2016年第6期18卷 950-951页

作者： Mitchell S Wachtel Shengping Yang brian j Morris Texas Tech University Health Sciences Center Lubbock Texas USA School of Medical Sciences University of Sydney Sydney New South Wales Australia

Dear Editor, We thank Dr. Kupferschmid for his interest in our study, which examined male circumcision （MC） and prostate cancer mortality〉2 Considerable strong evidence has been accumulated since 1951.3 Most of his references4-10 do not address MC and the risk of death from prostate cancer. That is a different question than MC and the risk of developing prostate cancer, which none of his references validly assess. One reference addressed bacterial colonization,6 not prostate cancer. Another7 concerned sexually transmitted infections and prostate cancer.

关键词： EPIDEMIOLOGY RISK

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Characteristics of lipids and their feeding value in swine diets

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journal of Animal Science and Biotechnology 2016年第3期7卷 249-271页

作者： brian j.Kerr Trey A.Kellner Gerald C.Shurson USDA-ARS-National Laboratory for Agriculture and the Environment AmesIA 50011USA Department of Animal Science Iowa State UniversityAmesIA 50011USA Department of Animal Science University of MinnesotaSt.PaulMN 55108USA

In livestock diets, energy is one of the most expensive nutritional components of feed formulation. Because lipids are a concentrated energy source, inclusion of lipids are known to affect growth rate and feed efficiency, but are also known to affect diet palatability, feed dustiness, and pellet quality. In reviewing the literature, the majority of research studies conducted on the subject of lipids have focused mainly on the effects of feeding presumably high quality lipids on growth performance, digestion, and metabolism in young animals. There is, however, the wide array of composition and quality differences among lipid sources available to the animal industry making it essential to understand differences in lipid composition and quality factors affecting their digestion and metabolism more fully. In addition there is often confusion in lipid nomenclature, measuring lipid content and composition, and evaluating quality factors necessary to understand the true feeding value to animals. Lastly, advances in understanding lipid digestion, post-absorption metabolism, and physiological processes（e.g., cell division and differentiation, immune function and inflammation）; and in metabolic oxidative stress in the animal and lipid peroxidation, necessitates a more compressive assessment of factors affecting the value of lipid supplementation to livestock diets. The following review provides insight into lipid classification, digestion and absorption, lipid peroxidation indices, lipid quality and nutritional value, and antioxidants in growing pigs.

关键词： Digestion Energy Lipids Peroxidation Pigs

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Atomic and Close-to-Atomic Scale Manufacturing:A Review on Atomic Layer Removal Methods Using Atomic Force Microscopy

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Nanomanufacturing and Metrology 2020年第3期3卷 167-186页

作者： Paven Thomas Mathew brian j.Rodriguez Fengzhou Fang Centre of Micro/Nano Manufacturing Technology(MNMT-Dublin) University College DublinDublin D04V1W8Ireland School of Physics University College DublinBelfieldDublin D04 V1W8Ireland Conway Institute of Biomolecular and Biomedical Research University College DublinBelfield.Dublin D04V1W8Ireland State Key Laboratory of Precision Measuring Technology and Instruments Centre of Micro/Nano Manufacturing TechnologyMNMT.Tianjin UniversityTianjin 300072China

Manufacturing at the atomic scale is the next generation of the industrial *** and close-to-atomic scalemanufacturing(ACSM)helps to achieve *** force microscopy(AFM)is a promising method for this purposesince an instrument to machine at this small scale has not yet been *** the need for increasing the number ofelectronic components inside an integrated circuit chip is emerging in the present-day scenario,methods should be adoptedto reduce the size of connections inside the *** can be achieved using ***,connecting moleculeswith the electrodes and then to the external world is *** must be laid to make this possible for *** layer removal,down to one atom,can be employed for this ***,theoretical works are beingperformed extensively to study the interactions happening at the molecule-electrode junction,and how electronic transportis affected by the functionality and robustness of the *** theoretical studies can be verified experimentally only if nano electrodes are *** is widely used in the semiconductor industry to fabricate electronic ***,carbon-based materials such as highly oriented pyrolytic graphite,gold,and silicon carbide find applications inthe electronic device manufacturing ***,ACSM of these materials should be developed *** paperpresents a review on the state-of-the-art research performed on material removal at the atomic scale by electrochemical andmechanical methods of the mentioned materials using AFM and provides a roadmap to achieve effective mass productionof these devices.

关键词： Atomic force microscopy Atomic-scale manufacturing Molecular scale devices Electrochemistry ACSM ManufacturingⅢ

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Optimising mesh size with escape gaps in a dual-species portunid-trap fishery

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Aquaculture and Fisheries 2020年第6期5卷 308-316页

作者： Matt K.Broadhurst Daniel j.Tolhurst brian Hughes Vincent Raoult Timothy M.smith Troy F.Gaston NSW Department of Primary Industries Fisheries Conservation Technology UnitNational Marine Science CentrePO Box 4321Coffs HarbourNSW2450Australia Marine and Estuarine Ecology Unit School of Biological SciencesUniversity of QueenslandBrisbaneQLD4072Australia The Roslin Institute and Royal(Dick)School of Veterinary Studies University of EdinburghEaster BushMidlothianEH259RGUnited Kingdom Hunter Local Land Services PO Box 440TareeNSW2430Australia School of Environmental and Life Sciences University of NewcastleOurimbahNSW2258Australia

In south-eastern Australia,the same baited,round traps(comprising 50–57-mm mesh netting)are used to target giant mud,Scylla serrata and blue swimmer crabs,Portunus armatus in spatially separated *** fisheries are characterised by the common,problematic discarding of undersized portunids(<85 and 65 mm carapace length;CL for *** and ***)and fish(yellowfin bream,Acanthopagrus australis).This poor selectivity was addressed here in two experiments assessing the utility of(1)traps partially or completely covered in larger mesh(91 mm to match the minimum legal size of the smaller ***),and then(2)any cumulative benefits of fitting species-specific escape *** experiment 1,there were no differences among catches of legal-sized portunids associated with either partial,or complete trap coverage with larger *** of mesh coverage,both designs of 91-mm traps also retained significantly fewer(by up to 42%)undersized *** and *** experiment 2,replicate traps completely covered in 91-mm mesh were tested against conventional traps comprising 56-mm mesh,and traps with the same mesh sizes,but also three escape gaps configured for either ***(46×120 mm)or ***(36×120 mm)(*** treatments in total).All modified traps maintained catches of legal-sized ***,and only the 91-mm traps with escape gaps caught fewer legal-sized *** undersized ***,*** and ***(mean catches reduced by up to 49%)were retained in all larger-meshed than small-meshed traps,and in all of those traps with escape gaps(by up to 95%)than *** there were no significant cumulative benefits of escape gaps in largermeshed traps(measured by a statistical interaction),there was a trend of fewer unwanted catches *** data support configuring portunid traps with mesh sizes matching the morphology of the smallest legal-sized target ***,simply retroactively fitting escape gaps in existing,smaller-m

关键词： Bycatch Escape gap Mesh size Portunid

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Recent advances in the utilization of insects as an ingredient in aquafeeds:A review

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Animal Nutrition 2022年第4期11卷 334-349页

作者： Sahya Maulu Sandra Langi Oliver j.Hasimuna Dagoudo Missinhoun brian P.Munganga Buumba M.Hampuwo Ndakalimwe Naftal Gabriel Mabrouk Elsabagh Hien Van Doan Zulhisyam Abdul Kari Mahmoud A.O.Dawood Centre for Innovative Approach Zambia(CIAZ) Plot No.119825ChalalaLusakaZambia Faculty of Agriculture and Environmental Sciences Muni UniversityP.O.Box 725AruaUganda National Aquaculture Research and Development Centre Department of FisheriesMinistry of Fisheries and LivestockKitweP.O Box 22797Zambia Department of Zoology and Aquatic Sciences School of Natural ResourcesCopperbelt UniversityKitweP.O Box 21692Zambia Department of Aquaculture and Fisheries Science Faculty of Natural ResourcesLilongweUniversity ofNatural Resources(LUANAR)P.O.Box 219LilongweMalawi Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization Ministry of AgricultureFreshwater Fisheries Research CenterChinese Academy of Fishery SciencesWuxi 214081JiangsuChina World Fish Zambia Office Lunbansenshi Close Plot 18944Olympia ParkLusakaZambia h Department of Fisheries and Ocean Sciences University of NamibiaPrivate Bag 462HentiesbayNamibia Department of Animal Production and Technology Faculty of Agricultural Sciences and TechnologiesNigde€Omer Halisdemir UniversityNigde 51240Turkey Department of Nutrition and Clinical Nutrition Faculty of Veterinary MedicineKafrelsheikh UniversityKafrelsheikh 33516Egypt Department of Animal and Aquatic Sciences Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Innovative Agriculture Research Center Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Faculty of Agro Based Industry Universiti Malaysia KelantanJeli Campus17600 JeliMalaysia Department of Animal Production Faculty of AgricultureKafrelsheikh UniversityEgypt The Center for Applied Research on the Environment and Sustainability The American University in Cairo11835 CairoEgypt

The aquafeed industry continues to expand in response to the rapidly growing aquaculture ***,the identification of alternative protein sources in aquatic animal diets to replace conventional sources due to cost and sustainability issues remains a major ***,insects have shown tremendous results as potential replacers of fishmeal in *** present study aimed to review the utilization of insects in aquafeeds and their effects on aquatic animals’growth and feed utilization,immune response and disease resistance,and fish flesh quality and *** many insect species have been investigated in aquaculture,the black soldier fly(Hermetia illucens),and the mealworm(Tenebrio molitor)are the most studied and most promising insects to replace fishmeal in ***,insect rearing conditions and biomass processing methods may affect the product’s nutritional composition,digestibility,shelf life and required insect inclusion level by aquatic ***,insect-recommended inclusion levels for aquatic animals vary depending on the insect species used,biomass processing method,and test ***,while an appropriate inclusion level of insects in aquafeed provides several nutritional and health benefits to aquatic animals,more studies are needed to establish optimum requirements levels for different aquaculture species at different stages of development and under different culture systems.

关键词： Aquaculture Aquafeed Alternative protein source Immune response Insect

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Identification of C9-C11 unsaturated aldehydes as prediction markers of growth and feed intake for non-ruminant animals fed oxidized soybean oil

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journal of Animal Science and Biotechnology 2020年第4期11卷 1033-1046页

作者： jieyao Yuan brian j.Kerr Shelby M.Curry Chi Chen Department of Food Science and Nutrition University of Minnesota1334 Eckles AvenueSt.PaulMN 55108USA USDA-ARS National Laboratory for Agriculture and the Environment 1015 N.University Boulevard2165 NSRICAmesIA 50011USA Oak Ridge Institute for Science and Education Oak RidgeTNUSA.

Background: The benefits of using the oxidized oils from rendering and recycling as an economic source of lipids and energy in animal feed always coexist with the concerns that diverse degradation products in these oxidized oils can negatively affect animal health and performance. Therefore, the quality markers that predict growth performance could be useful when feeding oxidized oils to non-ruminants. However, the correlations between growth performance and chemical profiles of oxidized oils have not been well examined. In this study, six thermally oxidized soybean oils(OSOs) with a wide range of quality measures were prepared under different processing temperatures and processing durations, including 45 °C-336 h;67.5 °C-168 h;90 °C-84 h;135 °C-42 h;180 °C-21 h;and225 °C-10.5 h. Broilers and nursery pigs were randomly assigned to diets containing either unheated control soybean oil or one of six OSOs. Animal performance was determined by measuring body weight gain, feed intake,and gain to feed ratio. The chemical profiles of OSOs were first evaluated by common indicative tests, including peroxide value, thiobarbituric acid reactive substances, p-anisidine value, free fatty acids, oxidized fatty acids,unsaponifiable matter, insoluble impurities, and moisture, and then analyzed by the liquid chromatography-mass spectrometry-based chemometric ***: Among common quality indicators, p-anisidine value(An V), which reflects the level of carbonyl compounds,had the greatest inverse correlation with the growth performance of both broilers and pigs, followed by free fatty acids and oxidized fatty acids. Among the 17 aldehydes identified in OSOs, C9-C11 alkenals, especially 2-decenal and 2-undecenal, had stronger inverse correlations(r jor lipid oxidation products contributing to the An V, ind

关键词： Aldehydes Broiler Growth performance Pig Thermally oxidized soybean oil

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Isolation and Identification of Pseudo Seven-Coordinate Ru(Ⅲ)Intermediate Completing the Catalytic Cycle of Ru-bda Type of Water Oxidation Catalysts

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CCS Chemistry 2022年第7期4卷 2481-2490页

作者： Tianqi Liu Ge Li Nannan Shen Linqin Wang brian j.j.Timmer Shengyang Zhou Biaobiao Zhang Alexander Kravchenko Bo Xu Marten S.G.Ahlquist Licheng Sun Department of Chemistry School of Engineering Sciences in ChemistryBiotechnologyand HealthKTH Royal Institute of TechnologyStockholm 10044 Department of Theoretical Chemistry and Biology School of Engineering Sciences in ChemistryBiotechnologyand HealthKTH Royal Institute of TechnologyStockholm 10691 State Key Laboratory of Radiation Medicine and Protection School for Radiological and Interdisciplinary Sciences(RAD-X)Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhou 215123 Center of Artificial Photosynthesis for Solar Fuels School of ScienceWestlake UniversityHangzhou 310024 Nanotechnology and Functional Materials Department of Materials Sciences and EngineeringThe Angstrom LaboratoryUppsala UniversityUppsala 75103 Institute of Artificial Photosynthesis(IAP) State Key Laboratory of Fine ChemicalsDalian University of Technology(DUT)Dalian 116024

Isolation of RuⅢ-bda(17-electron specie)complex with an aqua ligand(2-electron donor)is challenging due to violation of the 18-electron *** considerable efforts have been dedicated to mechanistic studies of water oxidation by the Ru-bda family,the structure and initial formation of the Ru^(Ⅲ)-bda aqua complex are still ***,we challenge this often overlooked step by designing a pocketshape Ru-based complex *** computational studies showed that 1 possesses the crucial hydrophobicity at the Ru^(V)(O)state as well as similar probability of access of terminal O to solvent water molecules when compared with classic Ru-bda *** characterization of single-crystal structures at the Ru^(Ⅱ) and Ru^(Ⅲ) states,a pseudo seven-coordinate“ready-togo”aqua ligand with Ru^(Ⅲ)…O distance of 3.62A was *** aqua ligand was also found to be part of a formed hydrogen-bonding network,providing a good indication of how the Ru^(Ⅲ)-OH_(2)complex is formed.

关键词： Ru-bda water oxidation pseudo seven-coordinate Ru^(Ⅲ)-OH_(2)intermediate water preorganization

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