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Science Bulletin 2024年第6期69卷 784-791页

作者：李冠良陈程杰陈佩珂 blake c.meyers 夏瑞 State Key Laboratory for conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhou 510640China Key Laboratory of Biology and Germplasm Enhancement of Horticultural crops in South china Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510640China center Saint LouisMO 63132USA Division of Plant Science and Technology University of Missouri-ColumbiaColumbiaMO 65211USA

Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and *** various sRNA analysis tools have been developed for plants,the use of most of them depends on programming and command-line environments,which is a challenge for many wet-lab ***,current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive,normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final ***,we present sRNAminer,a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs:microRNAs(miRNAs),phased small interfering RNAs(phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).We constructed a curated or"golden"set of MIRNA and PHAS loci,which was used to assess the performance of sRNAminer in comparison to other existing *** results showed that sRNAminer outperformed these tools in multiple aspects,highlighting its *** addition,to enable an efficient evaluation of sRNA annotation results,we developed Integrative Genomics Viewer(IGV)-sRNA,a modified genome browser optimized from IGV and we incorporated it as a functional module in ***-sRNA can display a wealth of sRNA-specific features,enabling a more comprehensive understanding of sRNA *** and IGV-sRNA are both platform-independent software that can be run under all operating *** are now freely available at https://***/kli28/sRNAminer and https://***/cJchen/IG V-sRNA.

关键词： sRNAminer sRNA analysis miRNA PhasiRNA hc-siRNA IGV-sRNA

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An Integrated Workflow for DNA Methylation Analysis

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Journal of Genetics and Genomics 2013年第5期40卷 249-260页

作者： Pingchuan Li Feray Demirci Gayathri Mahalingam caghan Demirci Mayumi Nakano blake c.meyers Department of Plant & Soil Sciences Delaware Biotechnology InstituteUniversity of DelawareNewarkDE 19711USA

The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many *** methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and ***-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual *** we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data *** describe some applications for the analysis and interpretation of these *** laboratory provides public access to plant DNA methylation data via visualization tools available at our ＂Next-Gen Sequence＂ websites（http：//***）,along with small RNA,RNA-seq and other data types.

关键词： DNA methylation BS-seq Epigenetics

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Differential truncation and uridyiation patterns of microRNAs in plant hen1 mutants reveal distinct routes of microRNA turnover

Differential truncation and uridyiation patterns of microRNA...

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第十三届全国植物基因组学大会

作者： blake c.meyers Stacey A.Simon Katherine Petsch Marja Timmermans University of Delaware Dept.of Plant & Soil SciencesNewarkDE19711USA cold Spring Harbor Laboratory Cold Spring HarborNY 11724USA

miRNA levels depend on both biogenesis and *** methyltransferase HEN1 stabilizes plant miRNAs,animal piRNAs,and siRNAs in both kingdoms via 3’ terminal *** of HEN1 in plants results in non-templated oligouridylation and accelerated degradation of *** hen1 mutants from Arabidopsis,rice and maize,we found that the patterns of miRNA truncation and

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sRNAanno-a database repository of uniformly annotated small RNAs in plants

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Horticulture Research 2021年第1期8卷 746-753页

作者： chengjie chen Jiawei Li Junting Feng Bo Liu Lei Feng Xiaoling Yu Guanliang Li Jixian Zhai blake c.meyers Rui Xia State Key Laboratory for conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural UniversityGuangzhouChina Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhouChina Key Laboratory of Biology and Germplasm Enhancement of Horticultural crops in South china Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouGuangdong 510640China Guangdong Litchi Engineering Research center College of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510640China Department of Biology&Institute of Plant and Food Science Southern University of Science and TechnologyShenzhenGuangdong 518055China Donald Danforth Plant Science center Saint LouisMO 63132USA Division of Plant Sciences University of Missouri-ColumbiaColumbiaMO 65211USA

Small RNAs(sRNAs)are essential regulatory molecules,and there are three major sRNA classes in plants:microRNAs(miRNAs),phased small interfering RNAs(phased siRNAs or phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).Excluding miRNAs,the other two classes are not well annotated or available in public databases for most sequenced plant *** performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly *** results are available via an online repository called sRNAanno(***).compared with other public plant sRNA databases,we obtained was much more miRNA annotations,which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA *** also provides free access to genomic information for>22,721 PHAS loci and>22 million hc-siRNA loci annotated from these 143 plant *** miRNA and PHAS loci can be easily browsed to view their main features,and a collection of archetypal trans-acting siRNA 3(TAS3)genes were annotated separately for quick *** facilitate the ease of sRNA annotation,sRNAanno provides free service for sRNA annotations to the *** summary,the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs.

关键词： sRNA database repository

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A modular microfluidic platform to study how fluid shear stress alters estrogen receptor phenotype in ER+breast cancer cells

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Microsystems & Nanoengineering 2024年第1期10卷 287-299页

作者： Braulio Andrés Ortega Quesada Jonathan cuccia Rachael coates blake Nassar Ethan Littlefield Elizabeth c.Martin Adam T.Melvin cain Department of chemical Engineering Louisiana State UniversityBaton RougeLA 70803USA Department of chemical and Biological Engineering Clemson UniversityClemsonSC 29634USA Biological and Agricultural Engineering Louisiana State UniversityBaton RougeLA 70803USA Department Medicine Section Hematology and Medical OncologyTulane UniversityNew OrleansLA 70118USA

Metastatic breast cancer leads to poor prognoses and worse outcomes in patients due to its invasive behavior and poor response to *** is still unclear what biophysical and biochemical factors drive this more aggressive phenotype in metastatic cancer;however recent studies have suggested that exposure to fluid shear stress in the vasculature could cause *** this study a modular microfluidic platform capable of mimicking the magnitude of fluid shear stress(FSS)found in human vasculature was designed and *** device provides a platform to evaluate the effects of FSS on McF-7 cell line,an estrogen receptor positive(ER+)breast cancer cell line,during circulation in the *** of the effects of FSS on McF-7 cells was carried out utilizing two approaches:single cell analysis and bulk *** single cell analysis,cells were trapped in a microarray after exiting the serpentine channel and followed by immunostaining on the device(on-chip).Bulk analysis was performed after cells were collected in a microtube at the outlet of the microfluidic serpentine channel for western blotting(off-chip).It was found that cells exposed to an FSS magnitude of 10 dyn/cm^(2) with a residence time of 60 s enhanced expression of the proliferation marker Ki67 in the McF-7 cell line at a single cell *** understand possible mechanisms for enhanced Ki67 expression,on-chip and off-chip analyses were performed for pro-growth and survival pathways ERK,AKT,and JAK/*** demonstrated that after shearing the cells phosphorylation of p-AKT,p-mTOR,and p-STAT3 were ***,there was no change in p-ERK1/*** is a mediator of ER rapid signaling,analysis of phosphorylated ERαwas carried out and no significant differences between sheared and non-sheared populations were *** together these results demonstrate that FSS can increase phosphorylation of proteins associated with a more aggressive phenotype in circulating cancer *** findin

关键词： fluid breast estrogen

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存在问题的不均匀性焊缝及其预防方法

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国外机车车辆工艺 1996年第1期 12-15页

作者： John c.meyers 冒一平

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Using physiological conditions to assess current and future habitat use of a Subarctic frog

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Integrative Zoology 2023年第1期18卷 2-14页

作者： Thomas P.HASTINGS blake R.HOSSAcK LeeAnn FISHBAcK Jon M.DAVENPORT Department of Biology Appalachian State UniversityBooneNorth CarolinaUSA U.S.Geological Survey Northern Rocky Mountain Science Centerand Wildlife Biology ProgramW.A.Franke College of Forestry&ConservationUniversity of MontanaMissoulaMontanaUSA churchill Northern Studies centre ChurchillManitobaCanada

Species with especially close dependence on the environment to meet physiological requirements,such as ectotherms,are highly susceptible to the impacts of climate *** change is occurring rapidly in the Subarctic and Arctic,but there is limited knowledge on ectotherm physiology in these *** investigated how environmental conditions and habitat characteristics inﬂuence the physiological conditions and habitat use of wood frogs(Rana sylvatica)in a Subarctic landscape near churchill,Manitoba(canada).We used plaster models to estimate water loss rates and surface body temperatures among different habitat types and at speciﬁc locations used by radio-tracked *** loss(R2=0.67)and surface temperature(R2=0.80)of plaster models was similar to that of live ***-based water loss rates were greater in tundra habitat than in boreal forest and ecotone *** use of wood frogs was strongly tied with available surface moisture and decreased water loss rates that were observed with plaster *** conditions,such as wind speed and ground tem-perature,explained 58%and 91%of the variation in water balance and temperature of plaster *** physiological conditions may be challenging for semi-aquatic ectotherms in environments vulnerable to future cli-mate *** ability to predict physiological conditions based on environmental conditions,as demonstrated in our study,can help understand how wildlife will respond to climatic changes.

关键词： Arctic climate change landscape physiology water balance wood frog

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Integrative multi-omics and systems bioinformatics in translational neuroscience:A data mining perspective

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药物分析学报:英文版 2023年第8期13卷 836-850页

作者： Lance M.O'connor blake A.O'connor Su Bin Lim Jialiu Zeng chih Hung Lo college of Biological Sciences University of MinnesotaMinneapolisMN55455USA School of Pharmacy University of WisconsinMadisonWI53705USA Department of Biochemistry and Molecular Biology Ajou University School of MedicineSuwon16499South Korea Lee Kong chian School of Medicine Nanyang Technological UniversitySingapore308232Singapore

Bioinformatic analysis of large and complex omics datasets has become increasingly useful in modern day biology by providing a great depth of information,with its application to neuroscience termed *** mining of omics datasets has enabled the generation of new hypotheses based on differentially regulated biological molecules associated with disease mechanisms,which can be tested experimentally for improved diagnostic and therapeutic targeting of neurodegenerative ***,integrating multi-omics data using a systems bioinformatics approach will advance the understanding of the layered and interactive network of biological regulation that exchanges systemic knowledge to facilitate the development of a comprehensive human brain *** this review,we first summarize data mining studies utilizing datasets from the individual type of omics analysis,including epigenetics/epigenomics,transcriptomics,proteomics,metabolomics,lipidomics,and spatial omics,pertaining to Alzheimer's disease,Parkinson's disease,and multiple *** then discuss multi-omics integration approaches,including independent biological integration and unsupervised integration methods,for more intuitive and informative interpretation of the biological data obtained across different omics *** further assess studies that integrate multi-omics in data mining which provide convoluted biological insights and offer proof-of-concept proposition towards systems bioinformatics in the reconstruction of brain ***,we recommend a combination of high dimensional bioinformatics analysis with experimental validation to achieve translational neuroscience applications including biomarker discovery,therapeutic development,and elucidation of disease *** conclude by providing future perspectives and opportunities in applying integrative multi-omics and systems bioinformatics to achieve precision phenotyping of neurodegenerative diseases and towards personaliz

关键词： Multi-omics integration Systems bioinformatics Data mining Human brain profile reconstruction Translational neuroscience

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Biological insights in non-small cell lung cancer

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cancer Biology & Medicine 2023年第7期20卷 500-518页

作者： Rafael Rosell Anisha Jain Jordi codony-Servat Eloisa Jantus-Lewintre blake Morrison Jordi Barretina Ginesta María González-cao Germans Trias i Pujol Research Institute Badalona 08028Spain IOR Hospital Quiron-DexeusBarcelona 08028Spain Department of Microbiology JSS Academy of Higher Education&ResearchMysuru 570015India Pangaea Oncology Hospital Quiron-DexeusBarcelona 08028Spain Department of Biotechnology Universitat Politècnica de ValenciaMixed Unit TRIAL(General University Hospital of Valencia Research Foundation and Príncipe Felipe Research Center)CIBERONCValencia 46014Spain Sumitomo Pharma Oncology Inc.CambridgeMA and LehiUT 84043USA

Lung oncogenesis relies on intracellular cysteine to overcome oxidative *** tumor types,including non-small cell lung cancer(NScLc),upregulate the system x-c cystine/glutamate antiporter(xcT)through overexpression of the cystine transporter SLc7A11,thus sustaining intracellular cysteine levels to support glutathione *** factor erythroid 2-related factor 2(NRF2)serves as a master regulator of oxidative stress resistance by regulating SLc7A11,whereas Kelch-like EcH-associated protein(KEAP1)acts as a cytoplasmic repressor of the oxidative responsive transcription factor *** in KEAP1/NRF2 and p53 induce SLc7A11 activation in *** cystine is crucial in supplying the intracellular cysteine levels necessary to combat oxidative *** in cystine availability lead to iron-dependent lipid peroxidation,thus resulting in a type of cell death called *** inhibitors of xcT(either SLc7A11 or GPX4)induce ferroptosis of NScLc cells and other tumor *** cystine uptake is impaired,the intracellular cysteine pool can be sustained by the transsulfuration pathway,which is catalyzed by cystathionine-B-synthase(cBS)and cystathionine g-lyase(cSE).The involvement of exogenous cysteine/cystine and the transsulfuration pathway in the cysteine pool and downstream metabolites results in compromised cD8^(+)T cell function and evasion of immunotherapy,diminishing immune response and potentially reducing the effectiveness of immunotherapeutic *** is a previously unrecognized form of regulated cell *** NScLcs driven by EGFR,ALK,or KRAS,selective inhibitors induce pyroptotic cell death as well as *** targeted therapy,the mitochondrial intrinsic apoptotic pathway is activated,thus leading to the cleavage and activation of ***,gasdermin E is activated,thus leading to permeabilization of the cytoplasmic membrane and cell-lytic pyroptosis(indicated by characte

关键词： Solute carrier family 7 member 11(SLc7A11) nuclear factor erythroid 2-related factor 2(NRF2) ferroptosis pyroptosis KRAS G12c allele-specific inhibitors non-small cell lung cancer(NScLc)

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Nanostructure and thermal power of highly-textured and single-crystal-like Bi_(2)Te_(3) thin films

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Nano Research 2022年第3期15卷 2382-2390页

作者： Heng Zhang Jamo Momand Joshua Levinsky Qikai Guo Xiaotian Zhu Gert H ten Brink Graeme R.blake George Palasantzas Bart J.Kooi Zernike Institute for Advanced Materials University of GroningenNijenborgh 49747 AG GroningenThe Netherlands

Bi_(2)Te_(3)-based alloys are known to have outstanding thermoelectric *** structure–property relations have been studied,still,detailed analysis of the atomic and nano-scale structure of Bi_(2)Te_(3)thin film in relation to their thermoelectric properties remains poorly ***,highly-textured(HT)and single-crystal-like(ScL)Bi_(2)Te_(3)films have been grown using pulsed laser deposition(PLD)on Si wafer covered with(native or thermal)SiOx and mica *** films are highly textured with c-axis out-of-plane,but the in-plane orientation is random for the films grown on oxide and single-crystal-like for the ones grown on *** power factor of the film on thermal oxide is about four times higher(56.8μW·cm^(−1)·K^(−2))than that of the film on mica(12.8μW·cm^(−1)·K^(−2)),which is comparable to the one of the polycrystalline ingot at room temperature(RT).Reduced electron scattering in the textured thin films results in high electrical conductivity,where the ScL film shows the highest ***,its Seebeck coefficient shows a low *** measured properties are correlated with the atomic structure details unveiled by scanning transmission electron *** instance,the high concentration of stacking defects observed in the HT film is considered responsible for the increase of Seebeck coefficient compared to the ScL *** study demonstrates the influence of nanoscale structural effects on thermoelectric properties,which sheds light on tailoring thermoelectric thin films towards high performance.

关键词： Bi_(2)Te_(3)films highly-textured structure single-crystal-like structure thermoelectric properties pulsed laser deposition

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