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The Bioinformatic Applications of Hi-c and Linked reads

中国植物病理学会2011年学术年会

作者： jack WESTWOOD SIMON c GrEON TrISNA TUNGADI ALEX M MUrPHY JOHN P cArr Department of Plant Sciences University of CambridgeCambridgeUK

＜正＞cucumber mosaic virus（cMV） is an economically important pathogen,which is transmitted by aphids in a non-persistent *** cMV coat protein is the only known factor required for aphid ***,we found that infection of Arabidopsis thaliana col-0 with severe strain Fny-cMV,but not cMV△2b（a cMV mutant in which the gene for the 2b protein is deleted）,enhanced resistance against aphids（Myzus persicea）（Westwood et al,unpublished data）,suggesting that 2b plays an important role in the

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GENOMIcS PrOTEOMIcS & BIOINFOrMATIcS 2024年第4期22卷 qzae048页

作者： Jiang, Libo Quail, Michael A. Fraser-Govil, jack Wang, Haipeng Shi, Xuequn Oliver, Karen Gomez, Esther Mellado Yang, Fengtang Ning, Zemin Shandong Univ Technol Sch Life Sci & Med Zibo 255049 Peoples R China Wellcome Sanger Inst Wellcome Genome Campus Cambridge CB10 1SA England Hainan Univ Coll Food Sci & Technol Haikou 570228 Peoples R China

Long-range sequencing grants insight into additional genetic information beyond what can be accessed by both short reads and modern long-read technology. Several new sequencing technologies, such as "Hi-c" and "Linked reads", produce long-range datasets for high-throughput and high-resolution genome analyses, which are rapidly advancing the field of genome assembly, genome scaffolding, and more comprehensive variant identification. In this review, we focused on five major long-range sequencing technologies: high-throughput chromosome conformation capture (Hi-c), 10X Genomics Linked reads, haplotagging, transposase enzyme linked long-read sequencing (TELL-seq), and single- tube long fragment read (stLFr). We detailed the mechanisms and data products of the five platforms and their important applications, evaluated the quality of sequencing data from different platforms, and discussed the currently available bioinformatics tools. This work will benefit the selection of appropriate long-range technology for specific biological studies.

关键词： Long-range NGS reads Hi-c Linked reads Genome assembly Quality assessment

Skin tissue engineering advances in severe burns:review and therapeutic applications

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Burns & Trauma 2016年第1期4卷 13-26页

作者： Alvin Wen choong chua Yik cheong Khoo Bien Keem Tan Kok chai Tan chee Liam Foo Si jack chong Singapore General Hospital Department of PlasticReconstructive andAesthetic Surgery20 College RoadAcademia Level 4Singapore 169845Singapore. Singapore General Hospital Skin Bank UnitBlock 4 Level 3Room 15Outram RoadSingapore 169608Singapore. Transplant Tissuecentre c/o Skin Bank UnitSingapore General HospitalBlock 4 Level 3 RoomA7Outram RoadSingapore 169608Singapore. Singapore General Hospital Skin Bank UnitBlock 4 Level 3Room 15Outram RoadSingapore 169608Singapore. Transplant Tissuecentre c/o Skin Bank UnitSingapore General HospitalBlock 4 Level 3 RoomA7Outram RoadSingapore 169608Singapore. Singapore General Hospital Department of PlasticReconstructive andAesthetic Surgery20 College RoadAcademia Level 4Singapore 169845Singapore. Singapore General Hospital Skin Bank UnitBlock 4 Level 3Room 15Outram RoadSingapore 169608Singapore.

current advances in basic stem cell research and tissue engineering augur well for the development of improved cultured skin tissue substitutes:a class of products that is still fraught with limitations for clinical *** the ability to grow autologous keratinocytes in-vitro from a small skin biopsy into sheets of stratified epithelium(within 3 to 4 weeks)helped alleviate the problem of insufficient donor site for extensive burn,many burn units still have to grapple with insufficient skin allografts which are used as intermediate wound coverage after burn *** offered by tissue-engineered skin dermal replacements to meet emergency demand have been used fairly *** the availability of these commercial products,they all suffer from the same problems of extremely high cost,sub-normal skin microstructure and inconsistent engraftment,especially in full thickness *** practice for severe burn treatment has since evolved to incorporate these tissue-engineered skin substitutes,usually as an adjunct to speed up epithelization for wound closure and/or to improve quality of life by improving the functional and cosmetic results *** review seeks to bring the reader through the beginnings of skin tissue engineering,the utilization of some of the key products developed for the treatment of severe burns and the hope of harnessing stem cells to improve on current practice.

关键词： Burns Skin tissue engineering Stem cells cultured epithelial autografts Dermal substitutes Microskin grafting

Danish cohort of monozygotic inflammatory bowel disease twins: clinical characteristics and inflammatory activity

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World Journal of Gastroenterology 2016年第21期22卷 5050-5059页

作者： Frederik Trier Moller Lina Knudsen Marcus Harbord jack Satsangi Hannah Gordon Lene christiansen Kaare christensen Tine Jess Vibeke Andersen research Unit for Molecular Diagnostics Hospital of Southern Jutland Institute of regional Health research University of Southern Denmark Division of Epidemiology and Disease Surveillance Statens Serum Institut Department of Gastro-enterology Chelsea and Westminster Hospital centre for Molecular Medicine University of Edinburgh Western General Hospital Danish Ageing research centre Institute of Public Health University of Southern Denmark Department of clinical Medicine University of Aalborg

AIM: To describe the establishment of a Danish inflammatory bowel diseases (IBD) twin cohort with focus on concordance of treatment and inflammatory ***: We identified MZ twins, likely to be discordant or concordant for IBD, by merging information from the Danish Twin register and the National Patient register. The twins were asked to provide biological samples, questionnaires, and data access to patient files and public registries. Biological samples were collected via a mobile laboratory, which allowed for immediate centrifugation, fractionation, and storage of samples. The mean time from collection of samples to storage in the -80 °c mobile freezer was less than one hour. The diagnoses where validated using the copenhagen diagnostic ***: We identified 159 MZ IBD twin pairs, in a total of 62 (39%) pairs both twins agreed to participate. Of the supposed 62 IBD pairs, the IBD diagnosis could be confirmed in 54 pairs. The cohort included 10 concordant pairs, whereof some were discordant for either treatment or surgery. The 10 concordant pairs, where both pairs suffered from IBD, included eight cD/cD pairs, one Uc/Uc pair and one Uc/IBDU pair. The discordant pairs comprised 31 Uc, 5 IBDU (IBD unclassified), and 8 cD discordant pairs. In the co-twins not affected by IBD, calprotectin was above 100 μg/g in 2 participants, and above 50 μg/g in a further 5 ***: The presented IBD twin cohorts are an excellent resource for bioinformatics studies with proper adjustment for disease-associated exposures including medication and inflammatory activity in the co-twins.

关键词： Digestive system diseases Inflammatory bowel diseases crohn’ s disease Ulcerative colitis Epidemiologic studies Twins Biobank

Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis

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Zoological research 2023年第1期44卷 106-125页

作者： Yi-Tao Lin Ting Xu jack chi-Ho Ip Yanan Sun Ling Fang Tiangang Luan Yu Zhang Pei-Yuan Qian Jian-Wen Qiu Department of Biology Hong Kong Baptist UniversityHong Kong SARChina Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) GuangzhouGuangdong 511458China Department of Ocean Science Hong Kong University of Science and TechnologyHong Kong SARChina Instrumental Analysis&research center Sun Yat-Sen UniversityGuangzhouGuangdong 510875China State Key Laboratory of Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhouGuangdong 510875China Institute of Environmental and Ecological Engineering Guangdong University of TechnologyGuangzhouGuangdong 510006China college of Life Sciences and Oceanography Shenzhen UniversityShenzhenGuangdong 518060China

Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel(Gigantidas haimaensis) as a model, we explored this hostbacterial system by assembling the host transcriptome and genomes of its epibiotic campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing(SOX)multienzyme complex with the acquisition of sox B from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTcA) cycle to a calvin-Benson-Bassham(cBB)cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway(ru MP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine,isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and c-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.

关键词： Bathymodioline chemosynthesis cold seep Deep-sea adaptation Symbiosis

New interchange English for international communication

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chromosome Substitution Lines:Useful Genomic resources in cotton

2005年

作者： (美) jack c.richards Jonathan Hull Susan Proctor

本教材主要使用美国英语，但涉及许多国家、地区和文化，它强调在实际交流活动中培养语言，主要活动有主题讨论、语法结构、语言功能、词汇扩展和语言训练。

ISBN: (纸本)7560022049

关键词：英语

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棉花学报 2008年第S1期20卷 111-页

作者： SAHA Sukumar JENKINS Johnie N McArTY jack c STELLY David USDA-ArS crop Science research Laboratory P.O.Box 5367 Mississippi State Dept.Soil & crop Sciences TAMU college Station

The genus Gossypium is a very diverse one with about 50 ***,a very narrow germplasm base is presently being used for genetic improvement of Upland *** wild

关键词： cS

Taxonomy and phylogeny of hyaline‑spored coelomycetes

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Fungal Diversity 2020年第1期100卷 279-801页

作者： Wen‑Jing Li Eric H.c.McKenzie Jian‑Kui(jack)Liu D.Jayarama Bhat Dong‑Qin Dai Erio camporesi Qing Tian Sajeewa S.N.Maharachchikumbura Zong‑Long Luo Qiu‑Ju Shang Jin‑Feng Zhang Narumon Tangthirasunun Samantha c.Karunarathna Jian‑chu Xu Kevin D.Hyde Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China World Agroforestry centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China center of Excellence in Fungal research Mae Fah Luang UniversityChiang Rai 57100Thailand Mushroom research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand Landcare research Manaaki Whenua Private Bag 92170AucklandNew Zealand School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China No.128/1‑J Azad Cooperative Housing SocietyCurcaP.O.Goa VelhaGoa 403108India center for Yunnan Plateau Biological resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnan 655011People’s Republic of China A.M.B.Gruppo Micologico Forlivese“Antonio Cicognani”Via Roma 18ForlìItaly A.M.B circolo Micologico“Giovanni carini” C.P.314BresciaItaly Societàper gli Studi Naturalistici della romagna C.P.143BagnacavalloRAItaly college of Agriculture and Biological Sciences Dali UniversityDali 671003YunnanPeople’s Republic of China Department of Biology Faculty of ScienceKing Mongkut’s Institute of TechnologyLadkrabangChalongkrung Rd.Ladkrabang DistrictBangkok 10520Thailand

coelomycete is a general term used for asexual fungi which produce conidia in fruiting bodies:pycnidial,acervular,cupulate,pycnothyria or stromatic *** group contains numerous plant pathogenic,saprobic and endophytic species associated with a wide range of ***,morphological characters and host associations have been used as criteria to identify and classify coelomycetes,and this has resulted in a poor understanding of their generic and species *** based taxonomic studies have provided a better outlook of the phylogenetic and evolutionary trends in ***,the present outcomes represent only a preliminary step towards the understanding of *** genera have not been revisited since they were first *** present study revises the classification of the hyaline-spored coelomycetes and provides a modern taxonomic framework based on both morphology and *** total,248 genera were investigated,of which less than 100 are known to have sequence ***-locus sequence data analyses of 28S nrDNA,18S nrDNA,ITS,rNA polymerase II second largest subunit(rpb2),and part of the translation elongation factor 1-alpha gene(tef1)andβ-tubulin(tub2)gene regions were *** a result,three new genera and 23 new species are *** addition,three new links between sexual and asexual genera are *** are 138 genera that lack sequence data,and these are treated as Ascomycota,genera incertae *** drawings and descriptions are provided based on the examination of types and fresh collections and on the literature.

关键词： 26 new taxa Ascomycota Asexual morphs Basidiomycota

Effects of Plant Density on Boll retention and Yield of cotton in the Mid-South

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American Journal of Plant Sciences 2017年第4期8卷 891-906页

作者： jack c. Mccarty Johnie N. Jenkins russell W. Hayes Martin J. Wubben Genetics and Sustainable Agriculture research Unit Crop Science Research Laboratory USDA-ARS Starkville MS USA

The number of cotton (Gossypium hirsutum L.) plants being grown per unit of land area has gained attention due to the technology fees associated with seed containing value added traits. We investigated boll retention, yield, and yield components of cotton grown with reduced stands of 20% to 40% from the uniform planting pattern of four seeds per 30.5 cm of row. Five field experiments were conducted from 2012-2014 using eight treatments arranged in a randomized complete design with six replications. Yield and yield component data were collected. The plant one-row skip one-row treatment resulted in significant yield losses across all five experiments compared to the uniform planting pattern. Treatments with 20% stand reductions did not result in lower total yields;however, each plant in these treatments had to produce two additional bolls to maintain yield. Treatments which had at least 61 cm skips, 40% stand reduction, resulted in lower yields. Treatments had minor affects on boll weight, and lint percentage. The uniform planting pattern produced 67% of its yield from position one bolls compared to about 50% for treatments with reduced stands. reduced stand treatments produced about 20% of their yield on monopodial branches compared to 10% for the uniform treatment. With modern precision planting equipments, opportunities exist to reduce seed rate and maintain yield;however, many production risk factors must also be considered before a reduced seeding rate is adopted.

关键词： cotton Plant Population Fruit retention Plant Skips

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陆地卫星多光谱扫描器热波段的校准

激光与红外 1980年第3期 65-71页

作者： jack c.Lansing 苏广

陆地卫星3号携带的多光谱扫描器,第一次在前四个可见光波段的基础上增加一对地球景物红外发射敏感的第五波段。而前四个波段敏感反射的太阳辐照。本文描述了第五波段的设计特点:探测器观察反射镜反射的冷环境所构成的热基准,调增益增量... 详细信息

陆地卫星3号携带的多光谱扫描器,第一次在前四个可见光波段的基础上增加一对地球景物红外发射敏感的第五波段。而前四个波段敏感反射的太阳辐照。本文描述了第五波段的设计特点:探测器观察反射镜反射的冷环境所构成的热基准,调增益增量以保持动态范围而不影响信噪比。用一大面积黑体源完成热波段的地面校准。在测试中,探测器和仪器温渡是变化的。取得的数据通过加权最小二乘方法推导的校准算几法分析。分析后所得数值可和热真空测试数据的余数对照,以验证校准是否适当。从空间获得的数据可用以验证一适当的函数,此函数可从扫描器信号中求出信号辐射强度,文中对这一工作方式作了介绍。

关键词：红外源辐射源扫描器探测器黑体辐射强度景物陆地卫星波段