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Journal of Integrative Plant Biology 2016年第4期58卷 282-283页

作者： Hailing Jin Special Issue EditorUC President's Chair Director of Genetics Genomics and Bioinformatics Graduate ProgramCenter for Plant Cell BiologyInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideUSA

Plants are constantly under attack by pathogens,pests,and parasites,resulting in severe consequences on global food production and human *** pathogens and pests find their ways to invade and communicate with their hos... 详细信息

关键词： communicate constantly sophisticated consequences microbial fight biotic evolved pathogen volatile

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The potential of plant proteins as antifungal agents for agricultural applications

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Synthetic and Systems Biotechnology 2022年第4期7卷 1075-1083页

作者： Tiffany Chiu Theo Poucet Yanran Li Graduate Program in Genetics GenomicsAnd Bioinformatics1140 Batchelor HallUniversity of California RiversideCalifornia92521USA Department of Chemical and Environmental Engineering University of CaliforniaRiversideCA92521USA

Fungal pathogens induce a variety of diseases in both plants and post-harvest food crops,resulting in significant crop losses for the agricultural *** the usage of chemical-based fungicides is the most common way to control these diseases,they damage the environment,have the potential to harm human and animal life,and may lead to resistant fungal ***,there is an urgent need for diverse and effective agricultural fungicides that are environmentally-and *** have evolved various mechanisms in their innate immune system to defend against fungal pathogens,including soluble proteins secreted from plants with antifungal *** proteins can inhibit fungal growth and infection through a variety of mechanisms while exhibiting diverse functionality in addition to antifungal *** this mini review,we summarize and discuss the potential of using plant antifungal proteins for future agricultural applications from the perspective of bioengineering and biotechnology.

关键词： antifungal potential crops

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Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA 156 Module by the Homeodomain Proteins PENNYWISE and POUND-FOOLISH in Arabidopsis

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Molecular Plant 2011年第6期4卷 1123-1132页

作者： Shruti Lal Leo Bryan Pacis Harley M.S. Smith Genetics Genomics and Bioinformatics Graduate Program University of California Riverside CA 92521 USA Center for Plant Cell Biology Institute of Integrative Genome Biology Department of Botany and Plant Sciences University of California Riverside CA 92521 USA

The morphology of inflorescences is regulated in part by the temporal and spatial events that regulate flower specification. In Arabidopsis, an endogenous flowering time pathway mediated by a subset of SQUAMOSA PROMOTER- BINDING PROTEIN-LIKE （SPL） transcription factors, including SPL3, SPL4, and SPL5, function to specify flowers by activating floral meristem identity genes. During shoot development, SPL3, SPL4, and SPL5 are post-transcriptionally regulated by microRNA156 （miR156）. The photoperiod regulated florigenic signal, FLOWERING LOCUS T （FT）, promotes floral induction, in part by activating SPL3, SPL4, and SPL5. In turn, these SPLs function in parallel with FT to specify flower meristems. Two related BELLl-like homeobox genes PENNYWISE （PNY） and POUND-FOOLISH （PNF） expressed in the shoot apical meristem are absolutely required for the specification of floral meristems. Genetic studies show that the floral specification function of FT depends upon PNYand PNF; however, the interplay between these homeodomain proteins and SPLs is not known. In this manuscript, we show that the photoperiodic floral induction of SPL3, SPL4, and SPL5 is dependent upon PNY and PNE Further, PNY and PNF also control SPL3, SPL4, and SPL5 expression by negatively regulating miR156. Lastly, ectopic expres- sion of SPL4 partially rescues the pny pnf non-flower-producing phenotype, while overexpression of SPL3 or SPL5 in pny pnf plants was unable to restore flower specification. These results suggest that：（1） SPL3, SPL4, and SPL5 function is dependent upon PNY and PNF, or （2） expression of multiple SPLs is required for floral specification in pny pnf plants.

关键词： Development meristem homeodomain flowering microRNA.

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Bile acid synthesis impedes tumor-specific T cell responses during liver cancer

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Science (New York, N.Y.) 2025年第6730期387卷 192-201页

作者： Varanasi, Siva Karthik Chen, Dan Liu, Yingluo Johnson, Melissa A. Miller, Cayla M. Ganguly, Souradipta Lande, Kathryn LaPorta, Michael A. Hoffmann, Filipe Araujo Mann, Thomas H. Teneche, Marcos G. Casillas, Eduardo Mangalhara, Kailash C. Mathew, Varsha Sun, Ming Jensen, Isaac J. Farsakoglu, Yagmur Chen, Timothy Parisi, Bianca Deota, Shaunak Havas, Aaron Lee, Jin Chung, H Kay Schietinger, Andrea Panda, Satchidananda Williams, April E. Farber, Donna L. Dhar, Debanjan Adams, Peter D. Feng, Gen-Sheng Shadel, Gerald S. Sundrud, Mark S. Kaech, Susan M. NOMIS Center for Immunobiology and Microbial Pathogenesis Salk Institute for Biological Studies La Jolla CA United States Department of Pathology School of Medicine University of California San Diego La Jolla CA United States Sanford Burnham Prebys Medical Discovery Institute La Jolla CA United States Department of Medicine School of Medicine University of California San Diego CA United States Razavi Newman Integrative Genomics and Bioinformatics Core Facility Salk Institute for Biological Studies La Jolla CA United States Department of Microbiology and Immunology Columbia University Irving Medical Center New York NY USA Department of Surgery Columbia University Irving Medical Center New York NY USA Regulatory Biology Laboratory Salk Institute for Biological Studies La Jolla CA United States Immunology Program Memorial Sloan Kettering Cancer Center New York NY USA Immunology and Microbial Pathogenesis Program Weill Cornell Graduate School of Medical Sciences New York NY USA Parker Institute for Cancer Immunotherapy New York NY USA Department of Microbiology and Immunology Geisel School of Medicine at Dartmouth Hanover NH USA Department of Medicine Geisel School of Medicine at Dartmouth Hanover NH USA Center for Digestive Health Dartmouth Health NH United States Dartmouth Cancer Center Dartmouth Health NH United States

The metabolic landscape of cancer greatly influences antitumor immunity, yet it remains unclear how organ-specific metabolites in the tumor microenvironment influence immunosurveillance. We found that accumulation of primary conjugated and secondary bile acids (BAs) are metabolic features of human hepatocellular carcinoma and experimental liver cancer models. Inhibiting conjugated BA synthesis in hepatocytes through deletion of the BA-conjugating enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) enhanced tumor-specific T cell responses, reduced tumor growth, and sensitized tumors to anti-programmed cell death protein 1 (anti-PD-1) immunotherapy. Furthermore, different BAs regulated CD8+ T cells differently;primary BAs induced oxidative stress, whereas the secondary BA lithocholic acid inhibited T cell function through endoplasmic reticulum stress, which was countered by ursodeoxycholic acid. We demonstrate that modifying BA synthesis or dietary intake of ursodeoxycholic acid could improve tumor immunotherapy in liver cancer model systems.

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Oryza CLIMtools:A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

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Plant Communications 2024年第4期5卷 145-165页

作者： Angel Ferrero-Serrano David Chakravorty Kobie J.Kirven Sarah M.Assmann Biology Department Pennsylvania State University208 Mueller LaboratoryUniversity ParkPA 16802USA Intercollege Graduate Degree Program in Bioinformatics and Genomics Pennsylvania State University208 Mueller LaboratoryUniversity ParkPA 16802USA

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their *** address this issue,we present Oryza CLIMtools(https://***/CLIMtools/oryza_v1.0/),thefirst resource for pan-genome prediction of climate-associated genetic variants in a crop *** CLIMtools consists of interactive web-based databases that enable the user to(1)explore the local environments of traditional rice varieties(landraces)in South-East Asia and(2)investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Ge-nomes *** demonstrate the value of these resources by identifying an interplay betweenflowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in *** quantitative trait locus analysis has suggested the impor-tance of heterotrimeric G proteins in the control of agronomic ***,we analyzed the climate associations of natural variants in the different heterotrimeric G protein *** identified a coordi-nated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits,including plant height and seed and panicle *** conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

关键词： Oryza sativa rice G by E adaptation flowering time GWAS OsHD2 OsSOC1 heterotrimeric G pro-tein OsRGA1 d1 OsGS3 OsDEP1 OsGGC2

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Nuclear Factor I/A Controls A-fiber Nociceptor Development

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Neuroscience Bulletin 2020年第7期36卷 685-695页

作者： Lu Qi Guangjuan Yin Yongchao Zhang Yeqi Tao Xiaohua Wu Richard M.Gronostajski Mengsheng Qiu Yang Liu College of Life Sciences Zhejiang UniversityHangzhou 310058China Zhejiang Key Laboratory of Organ Development and Regeneration Institute of Life SciencesHangzhou Normal UniversityHangzhou 310036China Department of Biochemistry Program in GeneticsGenomics and BioinformaticsCenter of Excellence in Bioinformatics and Life SciencesState University of New York at BuffaloBuffaloNY 14203USA

Noxious mechanical information is transmitted through molecularly distinct nociceptors,with pinprickevoked sharp sensitivity via A-fiber nociceptors marked by developmental expression of the neuropeptide Y receptor 2(Npy2 r)and von Frey filament-evoked punctate pressure information via unmyelinated C fiber nociceptors marked by ***,the molecular programs controlling their development are only beginning to be *** we demonstrate that Npy2 r-expressing sensory neurons are in fact divided into two groups,based on transient or persistent Npy2 r ***2 r-transient neurons are myelinated,likely including A-fiber nociceptors,whereas Npy2 r-persistent ones belong to unmyelinated pruriceptors that co-express *** then showed that the transcription factors NFIA and Runx1 are necessary for the development of Npy2 r-transient A-fiber nociceptors and MrgprD^+C-fiber nociceptors,***,mice with conditional knockout of Nfia,but not Runx1 showed a marked attenuation of pinprick-evoked nocifensive *** studies therefore identify a transcription factor controlling the development of myelinated nociceptors.

关键词： Dorsal root ganglion Acute pain Pinprick pain Npy2r Nppb Nociceptor A-fiber mechanonociceptor

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Repurposed Nrf2 activator dimethyl fumarate rescues muscle inflammation and fibrosis in an aggravated mdx mouse model of Duchenne muscular dystrophy

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Redox Biology 2025年 84卷 103676页

作者： Kourakis, Stephanie Timpani, Cara A. Bagaric, Ryan M. Qi, Bo Ali, Benazir A. Boyer, Rebecca Spiesberger, Guinevere Kandhari, Nitika Yan, Xu Kuang, Jujiao Tulangekar, Ankita de Haan, Judy B. Deveson-Lucas, Deanna Stupka, Nicole Fischer, Dirk Rybalka, Emma Institute for Health and Sport (IHeS) Victoria University Melbourne VIC Australia Inherited and Acquired Myopathies Program Australian Institute for Musculoskeletal Science (AIMSS) St Albans VIC Australia Department of Medicine – Western Health Melbourne Medical School The University of Melbourne St Albans VIC Australia Monash Genomics and Bioinformatics Platform Biomedical Discovery Institute Monash University Clayton VIC Australia Sarcopenia Research Program Australian Institute for Musculoskeletal Science (AIMSS) St Albans VIC Australia Basic Science Domain Oxidative Stress Laboratory Baker Heart and Diabetes Institute Melbourne VIC Australia Baker Department of Cardiometabolic Health University of Melbourne Parkville VIC Australia Division of Neuropediatric and Developmental Medicine University Children's Hospital of Basel (UKBB) Basel Switzerland

In inherited neuromuscular disease, Duchenne muscular dystrophy (DMD), glucocorticoids significantly slow disease progression yet impart side effects severe enough to preclude use in a significant proportion of patients. Extending our findings that acute treatment with FDA approved multiple sclerosis drug, dimethyl fumarate (DMF), rescues muscle pathology in juvenile mdx mice, we aimed to conduct tiered pre-clinical testing toward translation. To aggravate disease phenotype in adult mdx muscles that usually lack human equivalent muscle pathology, we used bi-weekly treadmill running for 4 weeks which increased plasma DMD biomarker, creatine kinase, by 2-fold and quadriceps fibrosis by ∼30 %. Using this model, we screened DMF for 5 weeks in a head-to-head comparison, and in combination, with standard-of-care prednisone (PRED), to model the most likely clinical trial scenario. We show comparable efficacy between DMF and PRED at reducing inflammation via NF-κB suppression and CD68⁺ macrophage infiltration. Moderate term DMF monotherapy had additional anti-fibrotic and anti-lipogenic effects on skeletal and cardiac muscle beyond those seen with PRED treatment, although combination therapy exacerbated fibrosis in quadriceps. Our study supports DMF as a repurposing candidate for DMD, especially for patients who cannot tolerate chronic glucocorticoid treatment. We also highlight the importance of evaluating combination therapy to identify potential off-target effects between emerging therapeutics and glucocorticoids towards better designed clinical trials. © 2025

关键词： Dimethyl fumarate Duchenne muscular dystrophy Muscle pathology Therapeutics

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The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription

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Nature Communications 2025年第1期16卷 1-19页

作者： Umphred-Wilson, Katharine Ratnayake, Shashikala Tang, Qianzi Wang, Rui Chaudhary, Sneha Ghosh Ballachanda, Devaiah N. Trichka, Josephine Wisniewski, Jan Zhou, Lan Chen, Qingrong Meerzaman, Daoud Singer, Dinah S. Adoro, Stanley Experimental Immunology Branch National Cancer Institute National Institutes of Health Bethesda 20892 MD United States Immunology Training Program Department of Pathology Case Western Reserve University School of Medicine Cleveland 44106 OH United States Computational Genomics and Bioinformatics Branch Center for Biomedical Informatics & Information Technology National Cancer Institute National Institutes of Health Bethesda 20850 MD United States College of Animal Science and Technology Sichuan Agricultural University Chengdu 611130 China Department of Pathology and Genomic Medicine Houston Methodist Hospital Houston 77030 TX United States

Addiction to oncogene-rewired transcriptional networks is a therapeutic vulnerability in cancer cells, underscoring a need to better understand mechanisms that relay oncogene signals to the transcriptional machinery. Here, using human and mouse T cell acute lymphoblastic leukemia (T-ALL) models, we identify an essential requirement for the endosomal sorting complex required for transport protein CHMP5 in T-ALL epigenetic and transcriptional programming. CHMP5 is highly expressed in T-ALL cells where it mediates recruitment of the coactivator BRD4 and the histone acetyl transferase p300 to enhancers and super-enhancers that enable transcription of T-ALL genes. Consequently, CHMP5 depletion causes severe downregulation of critical T-ALL genes, mitigates chemoresistance and impairs T-ALL initiation by oncogenic NOTCH1 in vivo. Altogether, our findings uncover a non-oncogene dependency on CHMP5 that enables T-ALL initiation and maintenance. © This is a U.S. Government work and not under copyright protection in the US;foreign copyright protection may apply 2025.

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Evolution in Biological and Non-biological Systems: The Origins of Life

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Biological Theory 2013年第1期7卷 26-37页

作者： Salazar-Ciudad, Isaac Genomics Bioinformatics and Evolution Group Department of Genetics and Microbiology Universitat Autònoma de Barcelona Barcelona Spain Developmental Biology Program Institute of Biotechnology University of Helsinki Helsinki Finland

A replicator is simply something that makes copies of itself. There are hypothetical replicators (e.g., self-catalyzing chemical cycles) that are suspected to be unable to exhibit heritable variation. Variation in any of their constituent molecules would not lead them to produce offspring with those new variant molecules. Copying, such as in DNA replication or in xerox machines, allows any sequence to be remade and then sequence variations to be inherited. This distinction has been used against non-RNA-world hypotheses: without RNA replication systems have no capacity to exhibit heritable variation. However, is copying the only way to have heritable variation? This article suggests that evolution can happen without anything being copied and that, in fact, RNA copying is too complex to arise spontaneously as the first pre-biotic system. There would then be a historical gradation of systems from non-alive to alive in which the capacity to have heritable changes would progressively increase and in which copying, as in template-based RNA-replication, would be a crucial but relatively late event. In addition, this article proposes a way by which RNA replication could have arisen, after systems able to evolve arose, as a crucial innovation and how that innovation spread over existing evolutionary systems and became a major driver of subsequent evolution. © 2012, Konrad Lorenz Institute for Evolution and Cognition Research.

关键词： Compartment-first Development Evolution Generative systems Origins of life

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Commentary on whole-grain intake and pancreatic cancer risk-the danish,diet,cancer and health cohort by Schacht et al.

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Hepatobiliary Surgery and Nutrition 2021年第5期10卷 702-704页

作者： Rick J.Jansen Department of Public Health GenomicsPhenomicsand Bioinformatics ProgramCenter for Immunization Research and Education(CIRE)Center for Diagnostic and Therapeutic Strategies in Pancreatic CancerNorth Dakota State UniversityFargoNDUSA

In their manuscript,“Whole-Grain Intake and Pancreatic Cancer Risk-The Danish,Diet,Cancer and Health Cohort”,Schacht et al.(1)report that total whole-grain product(per 50 g/d serving)intake was significantly associated with lower incidence of pancreatic cancer(HR:0.93;95%CI:0.86,1.00).A sex-specific analysis revealed that this association only held among ***,neither total whole-grain(per 16-g serving)or specific individual whole-grain products and cereals were significantly associated with lower pancreatic cancer *** this commentary,I will describe some of the assumptions and biases associated with assessing dietary intake and attempting to find associations with disease.

关键词： intake cancer

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