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Highly Aligned Ternary Nanofiber Matrices Loaded with MXene Expedite Regeneration of Volumetric Muscle Loss

Nano-Micro Letters 2024年第4期16卷 269-292页

作者： Moon Sung Kang Yeuni Yu Rowoon Park Hye Jin Heo Seok Hyun Lee Suck Won Hong Yun Hak Kim Dong‑Wook Han Department of Cogno‑Mechatronics Engineering College of Nanoscience and NanotechnologyPusan National UniversityBusan 46241Republic of Korea Medical Research Institute School of MedicinePusan National UniversityYangsan 50612Republic of Korea Department of Anatomy School of MedicinePusan National UniversityYangsan 50612Republic of Korea Engineering Research Center for Color‑Modulated Extra‑Sensory Perception Technology Pusan National UniversityBusan 46241Republic of Korea Department of Biomedical Informatics School of MedicinePusan National UniversityYangsan 50612Republic of Korea Periodontal Disease Signaling Network Research Center and Dental and Life Science Institute School of DentistryPusan National UniversityYangsan 50612Republic of Korea BIO‑IT Fusion Technology Research Institute Pusan National UniversityBusan 46241Republic of Korea present address:Osstem Implant inc. Seoul 07789Republic of Korea

Current therapeutic approaches for volumetric muscle loss(VML)face challenges due to limited graft availability and insufficient bioactivities.To overcome these limitations,tissue-engineered scaffolds have emerged as a promising alternative.In this study,we developed aligned ternary nanofibrous matrices comprised of poly(lactide-co-ε-caprolactone)integrated with collagen and Ti_(3)C_(2)T_(x)MXene nanoparticles(NPs)(PCM matrices),and explored their myogenic potential for skeletal muscle tissue regeneration.The PCM matrices demonstrated favorable physicochemical properties,inc.uding structural uniformity,alignment,microporosity,and hydrophilicity.In vitro assays revealed that the PCM matrices promoted cellular behaviors and myogenic differentiation of C2C12 myoblasts.Moreover,in vivo experiments demonstrated enhanced muscle remodeling and recovery in mice treated with PCM matrices following VML injury.Mechanistic insights from next-generation sequencing revealed that MXene NPs facilitated protein and ion availability within PCM matrices,leading to elevated intracellular Ca^(2+)levels in myoblasts through the activation of inducible nitric oxide synthase(i NOS)and serum/glucocorticoid regulated kinase 1(SGK1),ultimately promoting myogenic differentiation via the m TOR-AKT pathway.Additionally,upregulated i NOS and inc.eased NO–contributed to myoblast proliferation and fiber fusion,thereby facilitating overall myoblast maturation.These findings underscore the potential of MXene NPs loaded within highly aligned matrices as therapeutic agents to promote skeletal muscle tissue recovery.

关键词： Ti_(3)C_(2)T_(x)MXene nanoparticle Ternary nanofibrous matrices Myogenesis Regeneration of volumetric muscle loss Next generation sequencing

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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, inc.uding 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 inc.ease expression of a biosynthetic gene, thereby modulating essential oil composition.

关键词： aromatic plant essential oil genome mint Verticillium wilt

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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 cerevisiae.However,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 ethanol.The 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 economics.Results A dynamic flux balance model was developed to identify bottlenecks in several strains of S.cerevisiae,both with wild-type pentose phosphate pathway expression and with the pathway over expressed.ZWF1 was found to be limiting in the oxidative portion of the pentose phosphate pathway under oxygen replete conditions.This pathway is used to regenerate NADPH.Under oxygen limiting conditions,respiration of xylose was limited by the lack of oxygen as a terminal electron acceptor.Ethanol production was also limited under these conditions due to the inability to balance NAD+/NADH.The model suggests the use of the anaplerotic glyoxylate pathway to improve NAD+/NADH balance,inc.easing ethanol produc-tion by 50%while producing succinate as a coproduct at upwards of 20 g/l.Conclusion In the production of high value chemicals from biomass,the use of the respiratory metabolism is a waste of feedstock carbon.Bottlenecks 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 pathways.Focusing future efforts on the non-respiratory balancing of NAD+/NADH,perhaps through the glyoxylate pathway,would improve the economics

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

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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 worldwide.This disease is characterized by photoreceptor degeneration,eventually leading to complete blindness.Autosomal dominant(adRP)has been associated with mutations in at least four ubiquitously expressed genes encoding pre-mRNA splicing factors—Prp3,Prp8,Prp31 and PAP1.Biological 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 elucidated.To investigate the in vivo function of these adRP-associated splicing factor genes,we examined Drosophila in which expression of fly Prp31 homolog was down-regulated.Sequence 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 patients.Such transgenic DmPrp31RNAi flies provide a useful tool for identifying genetic modifiers or interacting genes for Prp31.Expression of the human Prp31 in these animals leads to a partial rescue of the eye phenotype.Our results indicate that the Drosophila CG6876 is the fly ortholog of mammalian Prp31 gene.

关键词： Drosophila photoreceptor degeneration retinitis pigmentosa Prp31

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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 evolution.The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages.In 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 kingdom.We characterize over 2250000 PPR motifs in over 400000 proteins.In 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 liverworts.We show that rather than a single expansion,most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity.We 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 co-factors.Finally,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

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Excitotoxicity, calcium and mitochondria: a triad in synaptic neurodegeneration

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Translational Neurodegeneration 2022年第1期11卷 917-930页

作者： Manish Verma Britney N.Lizama Charleen T.Chu Department of Pathology University of Pittsburgh School of MedicinePittsburghPA 15261USA Department of Ophthalmology University of Pittsburgh School of MedicinePittsburghPA 15261USA Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of MedicinePittsburghPA 15261USA McGowan Institute for Regenerative Medicine University of Pittsburgh School of MedicinePittsburghPA 15261USA Center for Protein Conformational Diseases University of PittsburghPittsburghPA 15261USA Center for Neuroscience University of PittsburghPittsburghPA 15261USA present address:Astellas Pharma inc. 9 Technology DriveWestboroughMA 01581USA.

Glutamate is the most commonly engaged neurotransmitter in the mammalian central nervous system,acting to mediate excitatory neurotransmission.However,high levels of glutamatergic input elicit excitotoxicity,contribut-ing to neuronal cell death following acute brain injuries such as stroke and trauma.While excitotoxic cell death has also been implicated in some neurodegenerative disease models,the role of acute apoptotic cell death remains controversial in the setting of chronic neurodegeneration.Nevertheless,it is clear that excitatory synaptic dysregula-tion contributes to neurodegeneration,as evidenced by protective effects of partial N-methyl-D-aspartate receptor antagonists.Here,we review evidence for sublethal excitatory injuries in relation to neurodegeneration associated with Parkinson’s disease,Alzheimer’s disease,amyotrophic lateral sclerosis and Huntington’s disease.In contrast to classic excitotoxicity,emerging evidence implicates dysregulation of mitochondrial calcium handling in excitatory post-synaptic neurodegeneration.We discuss mechanisms that regulate mitochondrial calcium uptake and release,the impact of LRRK2,PINK1,Parkin,beta-amyloid and glucocerebrosidase on mitochondrial calcium transporters,and the role of autophagic mitochondrial loss in axodendritic shrinkage.Finally,we discuss strategies for normalizing the flux of calcium into and out of the mitochondrial matrix,thereby preventing mitochondrial calcium toxicity and excitotoxic dendritic loss.While the mechanisms that underlie inc.eased uptake or decreased release of mitochondrial calcium vary in different model systems,a common set of strategies to normalize mitochondrial calcium flux can prevent excitatory mitochondrial toxicity and may be neuroprotective in multiple disease contexts.

关键词： Mitochondrial calcium Mitochondrial calcium uniporter NCLX antiporter Parkinson’s disease Alzheimer’s disease LRRK2 PINK1 Beta-amyloid Mitophagy Excitotoxicity Amyotrophic lateral sclerosis Huntington’s disease Glucocerebrosidase

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Histone Lysine Methyltransferase SDG8 Is Involved in Brassinosteroid-Regulated Gene Expression in Arabidopsis thaliana

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Molecular Plant 2014年第8期7卷 1303-1315页

作者： Xiaolei Wang Jiani Chen Zhouli Xie Sanzhen Liu Trevor Nolan Huaxun Ye Mingcai Zhang Hongqing Guo Patrick S. Schnable Zhaohu Li Yanhai Yin State Key Laboratory of Plant Physiology and Biochemistry Department of Agronomy College of Agronomy and Biotechnology ChinaAgricultural University Beijing 100193 PR China Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 USA Department of Agronomy Iowa State University Ames IA 50011 USA present address: Department of Plant Pathology Kansas State University Manhattan KS 66506-5502 USA present address: Du Pont Pioneer inc. Johnston IA USA Data2Bio LLC Ames IA 50011-3650 USA

The plant steroid hormones, brassinosteroids （BRs）, play important roles in plant growth, development, and responses to environmental stresses. BRs signal through receptors localized to the plasma membrane and other signaling components to regulate the BES1/BZR1 family of transcription factors, which modulates the expression of thousands of genes. How BESl/BZR1 and their interacting proteins function to regulate the large number of genes are not com- pletely understood. Here we report that histone lysine methyltransferase SDG8, implicated in histone 3 lysine 36 diand trimethylation （H3K36me2 and me3）, is involved in BR-regulated gene expression. BES1 interacts with SDG8, directly or indirectly through IWSl, a transcription elongation factor involved in BR-regulated gene expression. The knockout mutant sdg8 displays a reduced growth phenotype with compromised BR responses. Global gene expression studies demonstrated that, while BR regulates about 5000 genes in wild-type plants, the hormone regulates fewer than 700 genes in sdg8 mutant. In addition, more than half of BR-regulated genes are differentially affected in sdg8 mutant. A Chromatin Immunoprecipitation （CHIP） experiment showed that H3K36me3 is reduced in BR-regulated genes in the sdg8 mutant. Based on these results, we propose that SDG8 plays an essential role in mediating BR-regulated gene expression. Our results thus reveal a major mechanism by which histone modifications dictate hormonal regulation of gene expression.

关键词： brassinosteroid histone modifications gene regulation.

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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 ethanol.However,no strategy has been proposed for simultaneous regulation of all contributing enzymes.If multiple enzymes contribute to constraint,over expression of a native transcription factor controlling the entire constraining pathway may provide optimal pathway wide regulation.Further 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 pattern.Results A series of strains were developed expressing STB5 and PGI1 under the control of a novel xylose inducible promoter.inc.eased transcription of STB5 and its regulatory targets was verified via qRT-PCR.No statistically significant difference was found in terms of xylose consumption or ethanol yield in these strains versus control strains.Xylose 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 cultures.The 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 cultures.Statistically 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 fashion.Conclusion This study did not find evidence supporting the pentose phosphate pathway constraint identified in other works.Instead,NAD+availability mediated by oxygen availability and citric acid cycle flux was suggested to limit fermentation.While inc.eased aeration could provide inc.eased conversion of NAD+to NADH(and a stoichiometric inc.ease in fermen-tation flux),this inc.ease would not be expected impr

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

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Improved Growth and Stress Tolerance in the Arabidopsis oxtl Mutant Triggered by Altered Adenine Metabolism

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Molecular Plant 2012年第6期5卷 1310-1332页

作者： Suchada Sukrong Kil-Young Yun Patrizia Stadler Charan Kumar Tony Facciuolo Barbara A.Moffatt Deane L.Falconec Department of Plant and Soil Science University of KentuckyLexingtonKY 40546USA present address:Department of Pharmacognosy Faculty of Pharmaceutical SciencesChulalongkorn UniversityBangkokThailand Department of Biological Sciences University of MassachusettsOne University AvenueLowellMA 01854USA present address:Fungi and Plant Co.Ltd Chungcheongbuk-doRepublic of Korea Department of Biology University of WaterlooWaterlooOntarioCanada

Plants perceive and respond to environmental stresses with complex mechanisms that are often associ- ated with the activation of antioxidant defenses. A genetic screen aimed at isolating oxidative stress-tolerant lines of Arabidopsis thaliana has identified oxtl, a line that exhibits improved tolerance to oxidative stress and elevated temperature but displays no apparent deleterious growth effects under non-stress conditions. Oxtl harbors a muta- tion that arises from the altered expression of a gene encoding adenine phosphoribosyltransferase （APT1）, an enzyme that converts adenine to adenosine monophosphate （AMP）, indicating a link between purine metabolism, whole-plant growth responses, and stress acclimation. The oxtl mutation results in decreased APT1 expression that leads to reduced enzymatic activity. Correspondingly, oxtl plants possess elevated levels of adenine. Decreased APT enzyme activity dir- ectly correlates with stress resistance in transgenic lines that ectopically express APT1. The metabolic alteration in oxtl plants also alters the expression of several antioxidant defense genes and the response of these genes to oxidative chal- lenge. Finally, it is shown that manipulation of adenine levels can induce stress tolerance to wild-type plants. Collectively, these results show that alterations in cellular adenine levels can trigger stress tolerance and improve growth, leading to inc.eases in plant biomass. The results also suggest that adenine might play a part in the signals that modulate responses to abiotic stress and plant growth.

关键词： abiotic/oxidative environmental stress acclimation priming purine signaling salvage pathway thermotolerance.

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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 slow.Our current research process is human-centred,where human researchers design,conduct,analyse and interpret experiments,and then decide what to do next.We have built an Autonomous Research System(ARES)—an autonomous research robot capable of first-of-its-kind closed-loop iterative materials experimentation.ARES 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 methods.We applied ARES to study the synthesis of singlewalled carbon nanotubes,and show that it successfully learned to grow them at targeted growth rates.ARES has broad implications for the future roles of humans and autonomous research robots,and for human-machine partnering.We 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

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