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Using high-throughput data and dynamic flux balance modeling techniques to identify points of constraint in xylose utilization in Saccharomyces cerevisiae

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Systems Microbiology and Biomanufacturing 2021年第1期1卷 58-75页

作者： William Hohenschuh Ronald E.Hector Frank Chaplen Ganti S.Murthy Oregon State University CorvallisUSA USDA ARSNCAURPeoriaUSA present address:EMD Serono inc. RocklandUSA present address:Indian Institute of Technology-Indore IndoreIndia

Background Several enzymes and cofactors have been identified as contributing to the slow utilization of xylose by xylose-fermenting strains of Saccharomyces ***,there has been no consensus on which of these possible bottle-necks are the most important to address.A previous strain characterization study from our lab suggested that insufficient NAD+limits fermentation and may be the most important bottleneck affecting utilization of xylose for the production of *** development and validation of a genome scale dynamic flux balance model would help to verify the existence and extent of this and other metabolic bottlenecks and suggest solutions to guide future strain development thereby minimiz-ing bottleneck impact on process *** A dynamic flux balance model was developed to identify bottlenecks in several strains of ***,both with wild-type pentose phosphate pathway expression and with the pathway over ***1 was found to be limiting in the oxidative portion of the pentose phosphate pathway under oxygen replete *** pathway is used to regenerate *** oxygen limiting conditions,respiration of xylose was limited by the lack of oxygen as a terminal electron *** production was also limited under these conditions due to the inability to balance NAD+/*** model suggests the use of the anaplerotic glyoxylate pathway to improve NAD+/NADH balance,increasing ethanol produc-tion by 50%while producing succinate as a coproduct at upwards of 20 g/*** In the production of high value chemicals from biomass,the use of the respiratory metabolism is a waste of feedstock *** previously identified in the oxidative pentose phosphate pathway are currently only relevant under oxygen-replete conditions and cannot impact the partitioning of carbon between the respiratory and fermentative *** future efforts on the non-respiratory balancing of NAD+/NADH,perhaps through th

关键词： Xylose Ethanol Biofuel Lignocellulose Metabolic bottlenecks Flux balance analysis Modeling Cofactor imbalance Glyoxylate pathway NAD+ NADH

Autonomy in materials research: a case study in carbon nanotube growth

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npj Computational Materials 2016年第1期2卷 25-30页

作者： Pavel Nikolaev Daylond Hooper Frederick Webber Rahul Rao Kevin Decker Michael Krein Jason Poleski Rick Barto Benji Maruyama Air Force Research Laboratory Materials and Manufacturing DirectorateRXASWPAFBDaytonOHUSA UES inc DaytonOHUSA Lockheed Martin Advanced Technology Laboratories Cherry HillNJUSA present address:Air Force Research Laboratory RHCIWPAFBOH 45433 and Infoscitex IncDaytonOH 45431USA present address:Air Force Research Laboratory 711 Human Performance WingHuman Effectiveness DirectorateRHASWPAFBDaytonOH 45433USA

Advances in materials are an important contributor to our technological progress,and yet the process of materials discovery and development itself is *** current research process is human-centred,where human researchers design,conduct,analyse and interpret experiments,and then decide what to do *** have built an Autonomous Research System(ARES)—an autonomous research robot capable of first-of-its-kind closed-loop iterative materials *** exploits advances in autonomous robotics,artificial intelligence,data sciences,and high-throughput and in situ techniques,and is able to design,execute and analyse its own experiments orders of magnitude faster than current research *** applied ARES to study the synthesis of singlewalled carbon nanotubes,and show that it successfully learned to grow them at targeted growth *** has broad implications for the future roles of humans and autonomous research robots,and for human-machine *** believe autonomous research robots like ARES constitute a disruptive advance in our ability to understand and develop complex materials at an unprecedented rate.

关键词： robot artificial autonomous

The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

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Molecular Plant 2020年第2期13卷 215-230页

作者： Bernard Gutmann Santana Royan Mareike Schallenberg-Rudinger Henning Lenz Ian R.Castleden Rose McDowell Michael AVacher Julian Tonti-Filippini Charles SBond Volker Knoop Ian D.Small Australian Research Council Centre of Excellence in Plant Energy Biology The University of Western AustraliaCrawleyPerth 6009WAAustralia School of Molecular Sciences The University of Western AustraliaCrawleyPerth 6009WAAustralia IZMB-Institut fur Zellulare und Molekulare Botanik Abteilung Molekulare EvolutionUniversitat BonnKirschallee 153115 BonnGermany present address:EditForce inc. West zone#429Kyushu University744 MotookaNishi-KuFukuokaJapan present address:IBG-2:Plant Sciences Forschungszentrum Jiilich GmbH52425 JulichGermany present address:Australian eHealth Research Centre Commonwealth Scientific and Industrial Research OrganisationFloreatPerth 6014WAAustralia

The RNA-binding pentatricopeptide repeat(PPR)family comprises hundreds to thousands of genes in most plants,but only a few dozen in algae,indicating massive gene expansions during land plant *** nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant *** this study,we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family,focusing on the proteins typically associated with RNA editing,which show the most spectacular variation in numbers and domain composition across the plant *** characterize over 2250000 PPR motifs in over 400000 *** lycophytes,polypod ferns,and hornworts,nearly 10%of expressed protein-coding genes encode putative PPR editing factors,whereas they are absent from algae and complex-thalloid *** show that rather than a single expansion,most land plant lineages with high numbers of editing factors have continued to generate novel sequence *** identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing ***,using the sequence variations across the datasets,we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors,given their phylogenetic distribution and sequence characteristics.

关键词： RNA editing RNA-binding protein organelles

Draft Genome Sequence of Mentha Iongifolia and Development of Resources for Mint Cultivar Improvement

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Molecular Plant 2017年第2期10卷 323-339页

作者： Kelly J. Vining Sean R. Johnson Amirhossein Ahkami Iris Lange Amber N. Parrish Susan C. Trapp Rodney B. Croteau Shannon C.K. Straub Iovanna Pandelova B. Markus Lange Department of Horticulture Oregon State University Corvallis OR 97331 USA M. J. Murdock Metabolomics Laboratory Institute of Biological Chemistry Washington State University Pullman WA 99164-6340 USA Department of Biology Hobart and William Smith Colleges Geneva NY 14456 USA present address: Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory (EMSL) Richiand WA 99354 USA present address: Medifluidics inc. Fort Collins. CO 80525 USA

The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verti- cillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid ge- homes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha Iongifolia （L.） Huds., a diploid species ancestral to cultivated peppermint and spearmint. The 353 Mb genome contains 35 597 predicted protein-coding genes, including 292 disease resistance gene homologs, and nine genes determining essential oil characteristics. A genetic linkage map ordered 1397 genome scaffolds on 12 pseudochromosomes. More than two million simple sequence repeats were identified, which will facilitate molecular marker development. The M. Iongifolia genome is a valuable resource for both metabolic engineering and molecular breeding. This is exemplified by employing the genome sequence to clone and functionally characterize the promoters in a peppermint cultivar, and demonstrating the utility of a glandular trichome-specific promoter to increase expression of a biosynthetic gene, thereby modulating essential oil composition.

关键词： aromatic plant essential oil genome mint Verticillium wilt

The splicing factor Prp31 is essential for photoreceptor development in Drosophila

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Protein & Cell 2010年第3期1卷 267-274页

作者： Payal Ray Xiaoyan Luo Elizabeth J.Rao Amina Basha Elvin A.Woodruff III Jane Y.Wu Department of Neurology Northwestern University Feinberg Medical SchoolChicagoIL 60611USA Magnify inc. 2316 Riverside DrNashvilleTN 37216USA present address:Trumbull College Yale UniversityNew HavenCT 06511USA

Retinitis pigmentosa is a leading cause of blindness and a progressive retinal disorder,affecting millions of people *** disease is characterized by photoreceptor degeneration,eventually leading to complete *** dominant(adRP)has been associated with mutations in at least four ubiquitously expressed genes encoding pre-mRNA splicing factors—Prp3,Prp8,Prp31 and *** function of adRPassociated splicing factor genes and molecular mechanisms by which mutations in these genes cause cell-type specific photoreceptor degeneration in humans remain to be *** investigate the in vivo function of these adRP-associated splicing factor genes,we examined Drosophila in which expression of fly Prp31 homolog was *** analyses show that CG6876 is the likely candidate of Drosophila melanogaster Prp31 homolog(DmPrp31).Predicted peptide sequence for CG6876 shows 57%similarity to the Homo sapiens Prp31 protein(HsPrp31).Reduction of the endogenous Prp31 by RNAi-mediated knockdown speci-fically in the eye leads to reduction of eye size or complete absence of eyes with remarkable features of photoreceptor degeneration and recapitulates the bimodal expressivity of human Prp31 mutations in adRP *** transgenic DmPrp31RNAi flies provide a useful tool for identifying genetic modifiers or interacting genes for *** of the human Prp31 in these animals leads to a partial rescue of the eye *** results indicate that the Drosophila CG6876 is the fly ortholog of mammalian Prp31 gene.

关键词： Drosophila photoreceptor degeneration retinitis pigmentosa Prp31

Development and characterization of Saccharomyces cerevisiae strains genetically modified to over-express the pentose phosphate pathway regulating transcription factor STB5 in the presence of xylose

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Systems Microbiology and Biomanufacturing 2021年第1期1卷 42-57页

作者： William Hohenschuh Ronald E.Hector Jeffrey A.Mertens Ganti S.Murthy Biological and Ecological Engineering Oregon State University116 Gilmore HallCorvallisOR 97331USA USDA ARSNCAURPeoriaIL 61604USA present address:EMD Serono inc. RocklandMA 02370USA present address:Biosciences and Biomedical Engineering Indian Institute of Technology-IndorePOD 1A704 Khandwa RoadSimrolMadhya Pradesh 453552India

Background Several enzymes in the pentose phosphate pathway of Saccharomyces cerevisiae have been identified as relating to the constraint of xylose consumption and conversion to ***,no strategy has been proposed for simultaneous regulation of all contributing *** multiple enzymes contribute to constraint,over expression of a native transcription factor controlling the entire constraining pathway may provide optimal pathway wide *** characterization of this strain on both pure sugars and lignocellulosic hydrolysates would provide an opportunity to identify additional bot-tlenecks not addressed by the modification of the pentose phosphate pathway expression *** A series of strains were developed expressing STB5 and PGI1 under the control of a novel xylose inducible *** transcription of STB5 and its regulatory targets was verified via *** statistically significant difference was found in terms of xylose consumption or ethanol yield in these strains versus control *** consumption through both the fermentative and respiratory pathways appeared to be related to oxygen availability and culture density with high-density(low oxygen)cultures consuming xylose more slowly than low-density *** maximum specific consumption rate for high-density cultures was 0.21 g xylose/gDCW/h versus 0.41 g xylose/gDCW/h in lower density *** similar ethanol yields at high and low density(approximately 0.25 g ethanol/g xylose)suggest that the maximum rate of fermentation is linked to the rate of respiration in a stoichiometric *** This study did not find evidence supporting the pentose phosphate pathway constraint identified in other ***,NAD+availability mediated by oxygen availability and citric acid cycle flux was suggested to limit *** increased aeration could provide increased conversion of NAD+to NADH(and a stoichiometric increase in fermen-tatio

关键词： Xylose Ethanol Biofuel Lignocellulose Metabolic bottlenecks STB5 Xylose inducible NAD+/NADH Cofactor imbalance Saccharomyces cerevisiae

Interannual and Decadal Variability of Landfalling Tropical Cyclones in the Southeast Coastal States of the United States

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Advances in Atmospheric Sciences 2002年第4期19卷 677-686页

作者： Li'an Xie Leonard J. Pietrafesa Kejian Wu Department of Marine Earth and Atmospheric Sciences North Carolina Slate University Box 8208 27695-8208 Raleigh North Carolina USA present address: Institute of Physical Oceanography The Ocean University of Qingdao 266003 Qingdao

The interannual variability of the Atlantic tropical cyclone (TC) frequency is well known. Separately, recent studies have also suggested that a much longer, multidecadal (40-60 year) trend might be emerging from the recent increase in Atlantic TC activity. However, the overall structure of the intrinsic frequencies (or temporal modes) of Atlantic TC activity is not yet known. The focus of this study is to systematically an-alyze the intrinsic frequencies of Atlantic TC activity using hurricane and tropical storm landfall data collec-ted along the southeast coast(SEC) of the United States, Based on an Empirical Mode Decomposition (EMD) analysis of the frequency of landfall TCs along the SEC from 1887-1999, we have found that Atlantic TC activity has four primary, temporal modes. The interannual and multidecadal modes reported in the published literature are two such modes. After identifying all primary modes, the relative importance of each mode and its physical cause can be analyzed. For example, the most energetic mode is the interannual mode (2-7 year period). This mode is known to be associated with the 2-7 year El Nino/ La Ni na cycle. The average number of annual landfalling TCs along (he SEC decreased by 24% during El Nino years, but did not show significant increase during weak and moderate La Nina years. However, intense La Nina years were generally associated with more than average landfalling TCs along the SEC. The effects of El Nino and La Nina also became more significant when only hurricanes were considered. The significance of the effects of El Nino and La Nina on landfalling TCs and hurricanes in different US southeast coastal states showed significant differences.

关键词： tropical cyclone empirical mode decomposition El Nino decadal variability

Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

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Plant Communications 2024年第8期5卷 1-17页

作者： Xiaotong Liu Daisuke Igarashi Rachel A.Hillmer Thomas Stoddard You Lu Kenichi Tsuda Chad L.Myers Fumiaki Katagiri Department of Plant and Microbial Biology University of Minnesota-Twin CitiesSt PaulMN 55108USA Department of Computer Science and Engineering University of Minnesota-Twin CitiesMinneapolisMN 55455USA Bioinformatics and Computational Biology Graduate Program University of Minnesota-Twin CitiesMinneapolisMN 55455USA Institute for Innovation Ajinomoto Co.Inc.KawasakiJapan State Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China present address:225 S 6th St MinneapolisMN 55402USA present address:Biotalys Inc.2520 Meridian Parkway Suite 480DurhamNC 27713USA present address:Life Sciences Institute and Department of Cell and Developmental Biology University of Michigan Medical SchoolAnn ArborMI 48109USA

Rapid plant immune responses in the appropriate cells are needed for effective defense against *** transcriptome analysis is often used to describe overall immune responses,collection of transcriptome data with sufficient resolution in both space and time is *** reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a Pseudomonas syringae strain expressing the effector AvrRpt2,which induces effector-triggered immunity in ***-peak time-course patterns are prevalent among thousands of upregulated *** implemented a multicompartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each *** decomposed peaks reveal an“echoing”pattern:the peak times of the first and second peaks correlate well across most upregulated *** demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to ***,the peak decomposition has extracted spatial information from the time-course *** echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types.A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered *** of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor *** discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

关键词： Arabidopsis Pseudomonas syringae plant immune response multi-compartment model WRKY transcription factors resilient immune signaling network

Modelling in vitro gametogenesis using induced pluripotent stem cells:a review

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Cell Regeneration 2023年第1期12卷 53-66页

作者： Maria Victoria Romualdez‑Tan present address:Repro Optima Center for Reproductive Health Inc.Ground Floor JRDC Bldg.Osmena Blvd.Capitol SiteCebu City 6000Philippines Cebu Doctors University Hospital Cebu CityPhilippines

In vitro gametogenesis(IVG)has been a topic of great interest in recent years not only because it allows for further exploration of mechanisms of germ cell development,but also because of its prospect for innovative medical applications especially for the treatment of *** of the mechanisms underlying gamete development in vivo has inspired scientists to attempt to recapitulate the entire process of gametogenesis in *** earlier studies have established IVG methods largely using pluripotent stem cells of embryonic origin,the scarcity of sources for these cells and the ethical issues involved in their use are serious limitations to the progress of IVG research especially in ***,with the emergence of induced pluripotent stem cells(iPSCs)due to the revolutionary discovery of dedifferentiation and reprogramming factors,IVG research has progressed remarkably in the last *** paper extensively reviews developments in IVG using ***,the paper presents key concepts from groundwork studies on IVG including earlier researches demonstrating that IVG methods using embryonic stem cells(ESCs)also apply when using *** for the derivation of iPSCs are briefly discussed,highlighting the importance of generating transgene-free iPSCs with a high capacity for germline transmission to improve efficacy when used for *** main part of the paper discusses recent advances in IVG research using iPSCs in various stages of *** addition,current clinical applications of IVG are presented,and potential future applications are *** IVG is still faced with many challenges in terms of technical issues,as well as efficacy and safety,novel IVG methodologies are emerging,and IVG using iPSCs may usher in the next era of reproductive medicine sooner than *** raises both ethical and social concerns and calls for the scientific community to cautiously develop IVG technology to ensure it is not only effica

关键词： In-vitro gametogenesis Artificial gametes Germ cell derivation Primordial germ cell-like cells Induced pluripotent stem cells