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An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

genomics, Proteomics & Bioinformatics 2016年第6期14卷 371-378页

作者： Jitendra Kumar Manoj Kumar Shashank Gupta Vasim Ahmed Manu Bhambi Rajesh Pandey Nat Singh Chauhan Department of Biochemistry Maharshi Dayanand UniversityRohtak 124001India Ayurgenomics Unit Translational Research and Innovative Science Through AyurgeomicsCouncil of Scientific and Industrial ResearchInstitute of Genomics and Integrative BiologyNew Delhi 110020India

Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight （〉 23 kb） metagenomic DNA （260/280 ratio 〉 1.8） with a good yield （55.8 ± 3.8 ng/mg of feces）. We also confirm that there is very low human genomic DNA contamination （eubacterial： human genomic DNA marker genes = 227.9：1） in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX＋. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for cultureindependent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.

关键词： Metagenomic DNAextraction Gut microbiome Human feces 16S rRNA

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A functional tacrolimus-releasing nerve wrap for enhancing nerve regeneration following surgical nerve repair

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Neural Regeneration Research 2025年第1期20卷 291-304页

作者： Simeon C.Daeschler Katelyn J.W.So Konstantin Feinberg Marina Manoraj Jenny Cheung Jennifer Zhang Kaveh Mirmoeini JPaul Santerre Tessa Gordon Gregory HBorschel SickKids Research Institute Neuroscience and Mental Health ProgramTorontoONCanada Institute of Biomaterials and Biomedical Engineering University of TorontoTorontoONCanada Indiana University School of Medicine IndianapolisINUSA Division of Plastic and Reconstructive Surgery the Hospital for Sick ChildrenTorontoONCanada translational biology and Engineering Program Ted Rogers Centre for Heart ResearchInstitute of Biomedical EngineeringFaculty of DentistryUniversity of TorontoTorontoONCanada

Axonal regeneration following surgical nerve repair is slow and often incomplete,resulting in poor functional recovery which sometimes contributes to lifelong ***,there are no FDA-approved therapies available to promote nerve *** accelerates axonal regeneration,but systemic side effects presently outweigh its potential benefits for peripheral nerve *** authors describe herein a biodegradable polyurethane-based drug delivery system for the sustained local release of tacrolimus at the nerve repair site,with suitable properties for scalable production and clinical application,aiming to promote nerve regeneration and functional recovery with minimal systemic drug *** is encapsulated into co-axially electrospun polycarbonate-urethane nanofibers to generate an implantable nerve wrap that releases therapeutic doses of bioactive tacrolimus over 31 *** and drug loading are adjustable for applications in small and large caliber nerves,and the wrap degrades within 120 days into biocompatible *** released from the nerve wrap promotes axon elongation in vitro and accelerates nerve regeneration and functional recovery in preclinical nerve repair models while off-target systemic drug exposure is reduced by 80%compared with systemic *** its surgical suitability and preclinical efficacy and safety,this system may provide a readily translatable approach to support axonal regeneration and recovery in patients undergoing nerve surgery.

关键词： biodegradable local drug delivery nerve injury nerve regeneration nerve wrap tacrolimus

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Intranasal nerve growth factor bypasses the blood-brain barrier and affects spinal cord neurons in spinal cord injury

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Neural Regeneration Research 2014年第10期9卷 1025-1030页

作者： Luigi Aloe Patrizia Bianchi Alberto De Bellis Marzia Soligo Maria Luisa Rocco Cellular biology and Neurobiology Institute National Research Council(CNR) Maria Rosaria Maglione Foundation Onlus NapoliItaly Intitute of translational Pharmacology National Research Council(CNR)

The purpose of this work was to investigate whether, by intranasal administration, the nerve growth factor bypasses the blood-brain barrier and turns over the spinal cord neurons and if such therapeutic approach could be of value in the treatment of spinal cord injury. Adult Sprague-Dawley rats with intact and injured spinal cord received daily intranasal nerve growth factor administration in both nostrils for 1 day or for 3 consecutive weeks. We found an in-creased content of nerve growth factor and enhanced expression of nerve growth factor receptor in the spinal cord 24 hours after a single intranasal administration of nerve growth factor in healthy rats, while daily treatment for 3 weeks in a model of spinal cord injury improved the deifcits in locomotor behaviour and increased spinal content of both nerve growth factor and nerve growth factor receptors. These outcomes suggest that the intranasal nerve growth factor bypasses blood-brain barrier and affects spinal cord neurons in spinal cord injury. They also suggest exploiting the possible therapeutic role of intranasally delivered nerve growth factor for the neuroprotection of damaged spinal nerve cells.

关键词： nerve regeneration spinal cord injury nerve growth factor intranasal delivery blood-brain barrier motor function leptin neuroprotection rats neural regeneration

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Unraveling brain aging through the lens of oral microbiota

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Neural Regeneration Research 2025年第7期20卷 1930-1943页

作者： Qinchao Hu Si Wang Weiqi Zhang Jing Qu Guang-Hui Liu State Key Laboratory of Membrane biology Institute of ZoologyChinese Academy of SciencesBeijingChina Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhouGuangdong ProvinceChina Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders Xuanwu HospitalCapital Medical UniversityBeijingChina Aging translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijingChina CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina University of Chinese Academy of Sciences BeijingChina Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijingChina Aging Biomarker Consortium BeijingChina State Key Laboratory of Stem Cell and Reproductive biology Institute of ZoologyChinese Academy of SciencesBeijingChina Beijing Institute for Stem Cell and Regenerative Medicine BeijingChina

The oral cavity is a complex physiological community encompassing a wide range of *** of oral microbiota can lead to various oral infectious diseases,such as periodontitis and tooth decay,and even affect systemic health,including brain aging and neurodegenerative *** studies have highlighted how oral microbes might be involved in brain aging and neurodegeneration,indicating potential avenues for intervention *** this review,we summarize clinical evidence demonstrating a link between oral microbes/oral infectious diseases and brain aging/neurodegenerative diseases,and dissect potential mechanisms by which oral microbes contribute to brain aging and *** also highlight advances in therapeutic development grounded in the realm of oral microbes,with the goal of advancing brain health and promoting healthy aging.

关键词： Alzheimer's disease brain aging multiple sclerosis neurodegeneration neurodegenerative diseases oral microbiota Parkinson's disease periodontitis bacteria Porphyromonas gingivalis

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MAWBP and MAWD inhibit proliferation and invasion in gastric cancer

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World Journal of Gastroenterology 2013年第18期19卷 2781-2792页

作者： Dong-Mei Li Jun Zhang Wen-Mei Li Jian-Tao Cui Yuan-Ming Pan Si-Qi Liu Rui Xing You-Yong Lu Laboratory of Molecular Oncology Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Peking University Cancer Hospital/Institute Department of Biochemistry and Molecular biology School of Medicine Shihezi University Beijing Institute of genomics Chinese Academy of Sciences

AIM: To investigate role of putative mitogen-activated protein kinase activator with WD40 repeats (MAWD)/ MAWD binding protein (MAWBP) in gastric cancer (GC). METHODS: MAWBP and MAWD mRNA expression level was examined by real-time reverse transcriptasepolymerase chain reaction and semi-quantitative polymerase chain reaction in six GC cell lines. Western blotting was used to examine the protein expression levels. We developed GC cells that stably overexpressed MAWBP and MAWD, and downregulated expression by RNA interference assay. Proliferation and migration of these GC cells were analyzed by 3-(4,5-dimethyl2-thiazolyl)-2,5-diphenyl tetrazolium bromide (MTT), soft agar, tumorigenicity, migration and transwell assays. The effect of expression of MAWBP and MAWD on transforming growth factor (TGF)-β1-induced epithelialmesenchymal transition (EMT) was examined by transfection of MAWBP and MAWD into GC cells. We detected the levels of EMT markers E-cadherin, N-cadherin and Snail in GC cells overexpressing MAWBP and MAWD by Western blotting. The effect of MAWBP and MAWD on TGF-β signal was detected by analysis of phosphorylation level and nuclear translocation of Smad3 using Western blotting and immunofluorescence. RESULTS: Among the GC cell lines, expression of endogenous MAWBP and MAWD was lowest in SGC7901 cells and highest in BGC823 cells. MAWBP and MAWD were stably overexpressed in SGC7901 cells and knocked down in BGC823 cells. MAWBP and MAWD inhibited GC cell proliferation in vitro and in vivo . MTT assay showed that overexpression of MAWBP and MAWD suppressed growth of SGC7901 cells (P < 0.001), while knockdown of these genes promoted growth of BGC823 cells (P < 0.001). Soft agar colony formation experiments showed that overexpression of MAWBP and MAWD alone or together reduced colony formation compared with vector group in SGC7901 (86.25±8.43, 12.75±4.49, 30±6.41 vs 336.75±22.55, P < 0.001), and knocked-down MAWBP and MAWD demonstrated opposite effects (131.25±16.

关键词： Gastric cancer Mitogen-activated protein kinase activator with WD40 repeats binding protein Mitogen-activated protein kinase activator with WD40 repeats Invasion Transforming growth factor-β Epithelial-mesenchymal transition

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Biofunctionalized semiconductor quantum dots for virus detection

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Journal of Semiconductors 2023年第2期44卷 25-39页

作者： Yingqi Liang Guobin Mao Junbiao Dai Yingxin Ma CAS Key Laboratory of Quantitative Engineering biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Virus is a kind of microorganism and possesses simple structure and contains one nucleic acid,which must be replicated using the host cell *** causes large-scale infectious diseases and poses serious threats to the health,social well-being,and economic conditions of millions of people ***,there is an urgent need to develop novel strategies for accurate diagnosis of virus infection to prevent disease *** dots(QDs)are typical fluorescence nanomaterials with high quantum yield,broad absorbance range,narrow and size-dependent emission,and good ***-based nanotechnology has been found to be effective method with rapid response,easy operation,high sensitivity,and good specificity,and has been widely applied for the detection of different ***,until now,no systematic and critical review has been published on this important research ***,in this review,we aim to provide a comprehensive coverage of various QDs-based virus detection *** fundamental investigations have been reviewed,including information related to the synthesis and biofunctionalization of QDs,QDs-based viral nucleic acid detection strategies,and QDs-based *** challenges and perspectives regarding the potential application of QDs for virus detection is also discussed.

关键词： quantum dot synthesis and biofunctionalization virus detection molecule biology detection immunoassays

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Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

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Journal of Animal Science and Biotechnology 2019年第2期10卷 283-292页

作者： Xiao Wang Mogens SandΦ Lund Peipei Ma Luc Janss Haja N.Kadarmideen Guosheng Su Center for Quantitative Genetics and genomics Department of Molecular Biology and GeneticsAarhus UniversityTjeleDenmark School of Agriculture and biology Shanghai Jiaotong UniversityShanghaiChina.

Background: Genotyping by sequencing(GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock ***: Chip array(Chip) and four depths of GBS data was simulated. After quality control(call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS(GBSc), true genotypes for the GBS loci(GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, ***: The current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths.

关键词： Genomic prediction Genotype correction Genotyping by sequencing Simulation

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Epigenetic regulation of genes during development: A conserved themefrom flies to mammals

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Journal of Genetics and genomics 2008年第7期35卷 413-429页

作者： Dasari Vasanthi Rakesh K Mishra Centre for Cellular and Molecular biology Council for Scientific and Industrial Research Uppal Road Hyderabad 500007 India

Eukaryotic genome is organized in form of chromatin within the nucleus. This organization is important for compaction of DNA as well as for the proper expression of the genes. During early embryonic development, genomic packaging receives variety of signals to eventually set up cell type specific expression patterns of genes. This process of regulated chromatinization leads to ＂cell type specific epigenomes＂. The expression states attained during differentiation process need to be maintained subsequently throughout the life of the organism. Epigenetic modifications are responsible for chromatin dependent regulatory mechanism and play a key role in maintenance of the expression state-a process referred to as cellular memory. Another key feature in the packaging of the genome is formation of chromatin domains that are thought to be structural as well as functional units of the higher order chromatin organization. Boundary elements that function to define such domains set the limits of regulatory elements and that of epigenetic modifications. This connection of epigenetic modification, chromatin structure and genome organization has emerged from several studies. Hox genes are among the best studied in this context and have led to the significant understanding of the epigenetic regulation during development. Here we discuss the evolutionarily conserved features of epigenetic mechanisms emerged from studies on homeotic gene clusters.

关键词： epigenetic Hox cluster chromatin boundary Polycomb group tirthorax group cellular memory

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Influence of quasispecies on virological responses and disease severity in patients with chronic hepatitis C

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World Journal of Gastroenterology 2008年第5期14卷 701-708页

作者： Deepak Kumar Abdul Malik Mohammad Asim Anita Chakravarti Rakha H Das Premashis Kar Department of Medicine Department of Microbiology Maulana Azad Medical College New Delhi 110002 IndiaDeepak Comparative Genomics Unit Institute of Genomics and Integrative Biology Delhi University Campus Mall Road Delhi 110007 India Department of Microbiology Maulana Azad Medical College New Delhi 110002 IndiaDeepak Comparative genomics Unit Institute of Genomics and Integrative Biology Delhi University Campus Mall Road Delhi 110007 India Department of Microbiology Maulana Azad Medical College New Delhi 110002 India

AIM:To elucidate the influence of quasispecies on virological response and disease severity in patients with chronic hepatitis C. METHODS:Forty seven patients with hepatitis C [32 with chronic active hepatitis (CAH), 9 with cirrhosis, and 6 with hepatocellular carcinoma (HCC)] were screened for the presence of quasispecies by single stranded conformational polymorphism (SSCP) analysis in the hypervariable region (HVR) and non-structural 5B (NS5B) viral genes of hepatitis C virus. The 41 patients excluding those with HCC were on therapy and followed up for a year with the determination of virological response and disease severity. Virus isolated from twenty three randomly selected patients (11 non-responders and 12 showing a sustained virological response) was sequenced for the assessment of mutations. RESULTS:The occurrence of quasispecies was proportionately higher in patients with HCC and cirrhosis than in those with CAH, revealing a significant correlation between the molecular evolution of quasispecies and the severity of disease in patients with hepatitis C. The occurrence of complex quasispecies has a significant association (P < 0.05) with the non-responders, and leads to persistence of infection. Significant differences (P < 0.05) in viral load (log10 IU/mL) were observed among patients infected with complex quasispecies (CQS), those infected with simple quasispecies (SQS) and those with no quasispecies (NQS), after 12 wk (CQS-5.2 ± 2.3, SQS-3.2 ± 1.9, NQS-2.8 ± 2.4) and 24 wk (CQS-3.9 ± 2.2, SQS-3.0 ± 2.2, NQS-2.1 ± 2.3) in the HVR region. However, a statistically significant difference (P < 0.05) was observed between the viral loads of patients infected with CQS and those infected with NQS in NS5B viral gene after 24 wk (CQS-3.9 ± 2.2, SQS-3.0 ± 2.2, and NQS-2.1 ± 2.3) and 48 wk (CQS-3.1 ± 2.7, SQS-2.3 ± 2.4, NQS-2.0 ± 2.3) of therapy. Disease severity was significantly associated with viral load during therapy. The strains isolated from non-responders sho

关键词： Hepatitis C virus Single-strand conformational polymorphism Quasispecies Virological response Interferon therapy

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添加糖与儿童心血管病风险的关系

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中华高血压杂志 2016年第10期24卷 937-937页

作者：刘莉叶鹏 Vos MB Kaar JL Welsh JA Van Horn LV Feig DI Anderson CA Patel MJ Cruz Munos J Krebs NF Xanthakos SA Johnson RK American Heart Association Nutrition Committee of the council on Lifestyle and Cardiometabolic Health council on Clinical Cardiology Council on Cardiovascular Disease in the Young council on Cardiovascular and Stroke Nurs-ing Council on Epidemiology and Prevention council on func-tional genomics and translational biology council on Hypertension

不良的生活方式行为是导致全球可预防疾病的原因。膳食中添加糖可使其富含能量但营养差,且可增加发展为肥胖、心血管病、高血压、肥胖相关的癌症和龋齿的风险。方法和结果：美国心脏协会对目前的科学证据进行审查和分级,探讨添加糖对儿... 详细信息

不良的生活方式行为是导致全球可预防疾病的原因。膳食中添加糖可使其富含能量但营养差,且可增加发展为肥胖、心血管病、高血压、肥胖相关的癌症和龋齿的风险。方法和结果：美国心脏协会对目前的科学证据进行审查和分级,探讨添加糖对儿童心血管健康的影响。

关键词：心血管病风险儿童糖美国心脏协会心血管健康预防疾病生活方式

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