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Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts

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Journal of Integrative Plant Biology 2013年第7期55卷 576-585页

作者： Xiang Jin Qin Li Guanghui Xiao Yu-Xian Zhu State Key Laboratory of Protein and Plant gene research College of Life SciencesPeking University National Center for Plant gene research(Beijing)

We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 Unigenes. The average lengths of the U nigenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton Unigenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 Unigenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.

关键词： Cotton fiber deep sequencing expressed sequence tag assembly functional genomics Gossypium.

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Silencing hepatitis B virus covalently closed circular DNA: The potential of an epigenetic therapy approach

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World Journal of Gastroenterology 2021年第23期27卷 3182-3207页

作者： Prashika Singh Dylan Kairuz Patrick Arbuthnot Kristie Bloom Wits/SAMRC Antiviral gene Therapy research unit School of PathologyUniversity of the WitwatersrandJohannesburg 2050GautengSouth Africa

Global prophylactic vaccination programmes have helped to curb new hepatitis B virus(HBV)***,it is estimated that nearly 300 million people are chronically infected and have a high risk of developing hepatocellular *** such,HBV remains a serious health priority and the development of novel curative therapeutics is urgently *** HBV infection has been attributed to the persistence of the covalently closed circular DNA(cccDNA)which establishes itself as a minichromosome in the nucleus of *** the viral transcription intermediate,the cccDNA is responsible for producing new virions and perpetuating *** is dependent on various host factors for cccDNA formation and the minichromosome is amenable to epigenetic *** HBV proteins,X(HBx)and core(HBc)promote viral replication by modulating the cccDNA epigenome and regulating host cell *** includes viral and host gene expression,chromatin remodeling,DNA methylation,the antiviral immune response,apoptosis,and *** of the cccDNA minichromosome would result in a sterilizing cure;however,this may be difficult to *** therapies could permanently silence the cccDNA minichromosome and promote a functional *** review explores the cccDNA epigenome,how host and viral factors influence transcription,and the recent epigenetic therapies and epigenome engineering approaches that have been described.

关键词： Chronic hepatitis B virus Epigenetic gene silencing Functional cure Hepatocellular carcinoma Hepatitis B surface antigen

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Reproducing indolent B-cell lymphoma transformation with T-cell immunosuppression in LMP1/CD40-expressing mice

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Cellular & Molecular Immunology 2019年第4期16卷 412-414页

作者： Christelle Vincent-Fabert Alexis Saintamand Amandine David Mehdi Alizadeh François Boyer Nicolas Arnaud Ursula Zimber-Strobl Jean Feuillard Nathalie Faumont CNRS-UMR 7276 INSERM U1262 CRIBL University of Limogesand Hematology Laboratory of Dupuytren Hospital University Center(CHU)of LimogesLimogesFrance INSERM U917 University of Rennes 1RennesFrance LNPRM EFS BretagneRennesFrance research unit gene vectors Helmholtz Center MunichGerman Research Center for Environmental Health GmbHMunichGermany

Indolent B-cell lymphomas are a group of incurable cancers of the elderly that encompass various entities,such as chronic lymphocytic leukemia(CLL),follicular lymphoma(FL),and marginal zone lymphoma(MZL).All indolent lymphomas may evolve towards aggressive transformation with an increased proliferation index and decreased tumor doubling *** transformation,which is called Richter’s syndrome in CLL,is associated with an aggressive clinical course and poor *** least in CLL,transformation of an indolent B-cell clone is molecularly different from that of de novo diffuse large B-cell lymphomas.1 Aging is known to be associated with immune decline,with increased inflammation,decreased immune surveillance and increased onset of malignancies among the consequences.2 Progression of indolent B-cell lymphomas is likely to be associated with escape from immune surveillance.

关键词： lymphoma Richter transformation

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Mitigation on self-discharge behaviors via morphological control of hierarchical Ni-sulfides/Ni-oxides electrodes for long-life-supercapacitors

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Journal of Materials Science & Technology 2022年第18期113卷 217-228页

作者： Dhananjay Mishra Niraj Kumar Ajit Kumar SeungGi Seo SungHun Jin Department of Electronic Engineering Incheon National UniversityIncheon 406-772 and also with Convergence Research Center for Insect VectorsIncheon National UniversityRepublic of Korea

To cope up with the sustainable energy storage goals for supercapacitors(SCs),the self-discharge in SC electrodes is a significant hurdle,and thereby,nickel sulfide(NS)with high conductivity is adopted as a test vehicle for understanding the morphological evolution effects for long-life ***,honeycomb-like NS is hierarchically formed over hydrothermally grown nickel oxide(NO)via successive ionic layer adsorption reaction(SILAR)*** heterostructure shows a fivefold improvement in specific capacitance from 348 F g^(−1) to 2077 F g^(−1)at 1 mV s^(−1) over bare ***,the remarkable upliftment of capacitance retention is achieved from 60.7%to 92.3%even after 3000 cycles via morphological control of NS/NO hetero-structure with the help of highly conductive *** importantly,the self-discharge behaviors and synergistic role of leakage current associated with morphological evolution via NS overcoating are studied in *** particular,the self-discharge mitigation from 45%(NO)to 35%(NS20/NO)due to the NS/NO heterostructure and the behind mechanism are ascribed to the activated-controlled Faradaic reaction coupled with a charge *** study emphasizes the potential importance of composite heterostructure by tuning the electrical conductivity and morphological adjustment NO via consecutive overcoating of NS through SILAR as a novel *** enhances charge storage,redox kinetics,and the mitigation of self-discharge properties of the active electrode *** practical validation on sustainable energy storage,NS20/NO supercapacitors illuminate the LED for 35%longer than NO after one-time charging,potentially beneficial for the next generation SCs.

关键词： Morphological evolution Self-discharge SILAR overcoating Supercapacitors Heterostructure

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The Arabidopsis Anaphase-Promoting Complex/Cyclosome Subunit 1 is Critical for Both Female Gametogenesis and Embryogenesis

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Journal of Integrative Plant Biology 2013年第1期55卷 64-74页

作者： Yanbing Wang Yingnan Hou Hongya Gu Dingming Kang Zhang-Liang Chen Jingjing Liu Li-Jia Qu State Key Laboratory of Protein and Plant gene research College of Life Sciences Peking University College of Agronomy and Biotechnology China Agricultural University The National Plant gene research Center

Anaphase-promoting complex/cyclosome （APC/C）, a multisubunit E3 ligase, plays a critical role in cell cycle control, but the functional characterization of each subunit has not yet been completed. To investigate the function of APC1 in Arabidopsis, we analyzed four mutant alleles of APC1, and found that mutation in APC1 resulted in significantly reduced plant fertility, accumulation of cyclin B, and disrupted auxin distribution in embryos. The three mutant alleles apcl-1, apcl-2 and apcl-3 shared variable defects in female gametogenesis including degradation, abnormal nuclear number, and disrupted polarity of nuclei in the embryo sac as well as in embryogenesis, in which embryos were arrested at multiple stages. All of these defects are similar to those previously identified in apc4. The mutant apcl-4, in which the T-DNA was inserted after the transmembrane domain at the C-terminus, showed much more severe phenotypes; that is, most of the ovules were arrested at the one-nucleate female gametophyte stage （stage FG1）. In the apcl apc4 double mutants, the fertility was further reduced by one-third in apcl-ll＋ apc4-1/＋, and in some cases no ovules even survived in siliques of apcl-4/＋ apc4-1/＋. Our data thus suggest that APC1, an essential component of APC/C, plays a synergistic role with APC4 both in female gametogenesis and in embryogenesis.

关键词： Arabidopsis anaphase-promoting complex/cyclosome (APC/C) APC1 APC4 female gametogenesis embryogenesis synergistic role

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gene therapy for spinal muscular atrophy:perspectives on the possibility of optimizing SMN1 delivery to correct all neurological and systemic perturbations

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Neural Regeneration research 2025年第7期20卷 2011-2012页

作者： Sharon J.Brown Rafael J.Yáñez-Muñoz Heidi R.Fuller School of Pharmacy and Bioengineering Keele UniversityKeeleUK Wolfson Center for Inherited Neuromuscular Disease TORCH BuildingRJAH Orthopaedic HospitalOswestryUK *** Center of Gene and Cell TherapyDepartment of Biological SciencesSchool of Life Sciences and the EnvironmentRoyal Holloway University of LondonEghamUK

Spinal muscular atrophy(SMA)is a genetic condition that results in selective lower motor neuron loss with concomitant muscle weakness and *** genetic cause of SMA was understood in 1995 when loss or impairment of the survival motor neuron 1(SMN1)gene was identified as the main contributing factor(Lefebvre et al.,1995).This,in combination with the discovery that humans have a“back-up”gene,SMN2,which can produce low levels(approximately 10%)of the full-length functional SMN protein,has led to the generation of SMA-specific gene *** was traditionally classified according to age of symptom onset and developmental milestones achieved,with life expectancy and severity varying between ***,SMN2 copy number is used as a proxy for the prediction of disease severity,with higher SMN2 copy number typically being associated with reduced severity of SMA,although this relationship is not absolute:some individuals with low SMN2 copy number have less severe SMA phenotypes and vice ***,the etiology of SMA is further complicated by other factors,such as non-typical nucleotide variants and SMN2-independent modifiers of disease severity.

关键词： atrophy traditionally absolute

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Progress and prospects of engineered sequence-specific DNA modulating technologies for the management of liver diseases

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World Journal of Hepatology 2015年第6期7卷 859-873页

作者： Samantha A Nicholson Buhle Moyo Patrick B Arbuthnot Wits/SA MRC Antiviral gene Therapy research unit School of Pathology Health Sciences Faculty University of the Witwatersrand

Liver diseases are one of the leading causes of mortality in the world. The hepatic illnesses, which include inherited metabolic disorders, hemophilias and viralhepatitides, are complex and currently difficult to treat. The maturation of gene therapy has heralded new avenues for developing effective intervention for these diseases. DNA modification using gene therapy is now possible and available technology may be exploited to achieve long term therapeutic benefit. The ability to edit DNA sequences specifically is of paramount importance to advance gene therapy for application to liver diseases. Recent development of technologies that allow for this has resulted in rapid advancement of gene therapy to treat several chronic illnesses. Improvements in application of derivatives of zinc finger proteins(ZFPs), transcription activator-like effectors(TALEs), homing endonucleases(HEs) and clustered regularly interspaced palindromic repeats(CRISPR) and CRISPR associated(Cas) systems have been particularly important. These sequence-specific technologies may be used to modify genes permanently and also to alter gene transcription for therapeutic purposes. This review describes progress in development of ZFPs, TALEs, HEs and CRISPR/Cas for application to treating liver diseases.

关键词： gene therapy Zinc fingers Transcriptionactivator-like effectors Clustered regularly interspacedshort palindromic repeats Homing endonucleases Liver diseases

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Taxonomic studies of Phlebotomus sergenti (parrot) (diptera:psychodidae) and its evolutionary relationship with its closest allies

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Asian Pacific Journal of Tropical Medicine 2008年第3期1卷 13-19页

作者： Juma Khan Kakarsulemankhel In-charge of Arthropod vectors & Helminths research Center for Advanced Studies in Vaccinology & Biotechnology(CASVAB)Brewery RoadQuettaPakistan

In the survey,the work was done to develop taxonomic record of sand fly Phlebotomus(paaphlebotomus) sergenti (Parrot) collected for the first time from new epidemic localities of cutaneous leishmaniasis in Dera Ghazi Khan(Pakistan).In view of the published reports about the detection of Leishmania major,the causative agent of cutaneous leishmaniasis from this species in many countries,the correct identification of this species becomes of significant value in the study of epidemiology of ***,in order to facilitate zoologists and medical researchers in its correct identification,taxonomic characters of ***(parrot) is studied in details with special reference to its mouth parts,male and female genitalia.A key is also given to P. sergentii(parrot) and its closest *** this light its relationships with its closest allies is also briefly discussed.

关键词： Sandflies Pakistan

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Advances in the treatment of autism spectrum disorder:Wharton jelly mesenchymal stem cell transplantation

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World Journal of Methodology 2025年第1期15卷 72-79页

作者： Serdar Kabatas ErdinçCivelek Eyüp Can Savrunlu Umut Karaaslan Özlem Yıldız Erdal Karaöz Department of Neurosurgery University of Health Sciences TurkeyGaziosmanpaşa Training and Research HospitalIstanbul 34255Türkiye Department of Pediatric Allergy-Immunology Institute of Health Sciences Marmara UniversityIstanbul 34865Türkiye Center for Stem Cell&gene Therapy research and Practice University of Health Sciences TurkeyIstanbul 34255Türkiye Department of Child and Adolescent Psychiatry University of Health SciencesGaziosmanpaşa Training and Research HospitalIstanbul 34255Türkiye Department of Child and Adolescent Psychiatry Kocaeli University Faculty of MedicineKocaeli 41001Türkiye Center for Regenerative Medicine and Stem Cell research&Manufacturing Liv HospitalIstanbul 34340Türkiye Department of Histology and Embryology Istinye UniversityFaculty of MedicineIstanbul 34010Türkiye Center for Stem Cell and Tissue Engineering research and Practice Istinye UniversityIstanbul 34340Türkiye

BACKGROUND Autism spectrum disorder(ASD)is a complex neurodevelopmental disorder with multifaceted *** recent studies,neuroinflammation and immune dysregulation have come to the forefront in its *** are studies suggesting that stem cell therapy may be effective in the treatment of *** To evolve the landscape of ASD treatment,focusing on the potential benefits and safety of stem cell *** A detailed case report is presented,displaying the positive outcomes observed in a child who underwent intrathecal and intravenous Wharton’s jelly-derived mesenchymal stem cells(WJ-MSCs)transplantation combined with *** The study demonstrates a significant improvement in the child’s functional outcomes(Childhood Autism Rating Scale,Denver 2 Developmental Screening Test),especially in language and gross motor *** serious side effects were encountered during the 2-year *** The findings support the safety and effectiveness of WJ-MSC transplantation in managing ASD.

关键词： Autism spectrum disorder Neurorehabilitation Stem cell transplantation Wharton jelly mesenchymal stem cells Inflammation

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Journal of Integrative Plant Biology 2012年第10期54卷 814-827页

作者： Guo Luo Hongya Gu Jingjing Liu Li-Jia Qu State Key Laboratory for Protein and Plant gene research College of Life SciencesPeking-Tsinghua Center of Life SciencesPeking UniversityBeijing 100871China The National Plant gene research Center Beijing 100101China

Ubiquitination of proteins is one of the critical regulatory mechanisms in eukaryotes. In higher plants, protein ubiquitination plays an essential role in many biological processes, including hormone signaling, photomorphogenesis, and pathogen defense. However, the roles of protein ubiquitination in the repro- ductive process are not clear. In this study, we identified four plant-specific RING-finger genes designated Aberrant_Pollen Development 1_ （APD1） to APD4, as regulators of pollen mitosis II （PMII） in Arabidopsis thaliana （L.）. The apdl apd2 double mutant showed a significantly increased percentage of bicellular-like pollen at the mature pollen stage. Further downregulation of the APD3 and APD4 transcripts in apdl apd2 by RNA interference （RNAi） resulted in more severe abnormal bicellular-like pollen phenotypes than in apdl apd2, suggesting that cell division was defective in male gametogenesis. All of the four genes were expressed in multiple stages at different levels during male gametophyte development. Confocal analysis using green florescence fusion proteins （GFP） GFP-APD1 and GFP-APD2 showed that APDs are associated with intracellular membranes. Furthermore, APD2 had E2-dependent E3 ligase activity in vitro, and five APD2-interacting proteins were identified. Our results suggest that these four genes may be involved, redundantly, in regulating the PMII process during male gametogenesis.

关键词： Male gametogenesis pollen mitosis II RING-finger E3 ligase Arabidopsis.

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