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In silico identification and characterization of common epitope-based peptide vaccine for Nipah and Hendra viruses

Asian Pacific Journal of Tropical Medicine 2017年第6期10卷 601-608页

作者： Chayan Kumar Saha Mahbub Hasan Saddam Hossain Asraful Jahan Abul Kalam Azad Department of genetic Engineering & Biotechnology Shahjalal University of Science and Technology Department of genetic Engineering & Biotechnology University of Chittagong

Objective: To explore a common B-and T-cell epitope-based vaccine that can elicit an immune response against encephalitis causing genus Henipaviruses, Hendra virus(He V) and Nipah virus(Ni V). Methods: Membrane proteins F, G and M of He V and Ni V were retrieved from the protein database and subjected to different bioinformatics tools to predict antigenic B-cell epitopes. Best B-cell epitopes were then analyzed to predict their T-cell antigenic potentiality. Antigenic B-and T-cell epitopes that shared maximum identity with He V and Ni V were selected. Stability of the selected epitopes was predicted. Finally, the selected epitopes were subjected to molecular docking simulation with HLA-DR to confirm their antigenic potentiality in silico. Results: One epitope from G proteins, one from M proteins and none from F proteins were selected based on their antigenic potentiality. The epitope from the G proteins was stable whereas that from M was unstable. The M-epitope was made stable by adding flanking dipeptides. The 15-mer G-epitope(VDPLRVQWRNNSVIS) showed at least 66% identity with all Ni V and He V G protein sequences, while the 15-mer M-epitope(GKLEFRRNNAIAFKG) with the dipeptide flanking residues showed 73% identity with all Ni V and He V M protein sequences available in the database. Molecular docking simulation with most frequent MHC class-II(MHC II) and class-I(MHC I) molecules showed that these epitopes could bind within HLA binding grooves to elicit an immune response. Conclusions: Data in our present study revealed the notion that the epitopes from G and M proteins might be the target for peptide-based subunit vaccine design against He V and Ni V. However, the biochemical analysis is necessary to experimentally validate the interaction of epitopes individually with the MHC molecules through elucidation of immunity induction.

关键词： Hendra virus Nipah virus Epitope Encephalitis Docking Flanking dipeptides

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Association between low molecular polypeptide 7 single nucleotide polymorphism and response to therapy in hepatitis C virus infection

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World Journal of Hepatology 2013年第3期5卷 97-103页

作者： Moataza H Omran Basma E Fotouh Samar S Youssef Noha E Ibrahim Wael Nabil EL-Sayed M Mahdy Wafaa G Shosha Mostafa K El-Awady Microbial Biotechnology Department Genetic Engineering Division National Research Center Chemistry Department Faculty of Science Helwan University

AIM: To investigate the relationship between low molecular polypeptide-7 (LMP-7) gene polymorphism and response to interferon (IFN) therapy in chronic hepatitis C virus (HCV) patients. METHODS: LMP-7 polymorphism at codon 49 with nucleotide substitution from A to C was amplified in 104 chronic HCV patients of genotype 4. The amplicons were digested with restriction endonuclease Bsm I and the produced restriction fragment length polymorphism was analyzed. Patients received IFN + regional blood volume therapy for 48 wk and the frequency of thissingle nucleotide polymorphism (SNP) was statistically correlated with treatment response. The exclusion criteria for these patients were stated by the national health program for treating viral hepatitis. Main exclusion criteria included co-infection with hepatitis B virus or schistosomiasis, thyroid dysfunction, uncontrolled diabetes mellitus, history of long term drug or alcohol intake and autoimmune hepatitis. Multivariate analyses were done to correlate LMP-7 SNP plus several factors such as age, gender, weight, serum alpha-fetoprotein (AFP) and alanine aminotransferase levels, liver activity, fibrosis score and viral load with response to therapy. RESULTS: The data presented in this study clearly demonstrated statistically significant differences between sustained virological response (SVR) (defined as the absence of HCV RNA levels in the patient's sera at least 6 mo after discontinuation of treatment) and non-response (NR) (where HCV RNA levels in the patient's sera never become undetectable for 6 mo during or after treatment). Variables were described as odds ratio with 95%CI. The data were considered significant if P values were ≤ 0.05; highly significant if P < 0.01 and very highly significant if P < 0.001. Current data showed that 91.7% of patients carrying LMP-7 C/C allele were associated with SVR, while the other two genotypes C/A and A/A were associated with NR patients, 83.3% and 64.3% respectively, showing that g

关键词： Hepatitis C virus Interferon therapy Low molecular mass polypeptide Host gene Single nucleotide polymorphism

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Optimization and modeling of glyphosate biodegradation by a novel Comamonas odontotermitis P2 through response surface methodology

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Pedosphere 2020年第5期30卷 618-627页

作者： Sadiqa FIRDOUS Samina IQBAL Samina ANWAR Soil and Environmental Biotechnology division National Institute for Biotechnology and Genetic Engineering(NIBGE)Faisalabad 38000(Pakistan) Pakistan Institute of Engineering and Applied Sciences(PIEAS) NiloreIslamabad 45650(Pakistan)

Glyphosate is an important organophosphonate herbicide used to eliminate grasses and herbaceous plants in many vegetation management *** extensive use is causing environmental pollution,and consequently,there is a need to remove it from the environment using an eco-friendly and cost-effective *** a step to address this problem,a novel bacterial strain Comamonas odontotermitis F2,capable to utilize glyphosate as a carbon(C)and/or phosphorus(P)source,was isolated from a glyphostate-contaminated field soil in Australia and *** surface methodology(RSM)employing a 2^3 full factorial central composite design was used to optimize glyphosate degradation by *** P2 under various culture *** strain *** P2 was proficient in degrading 1.5 g L^-1 glyphosate completely within 104 *** optimal conditions for the degradation of glyphosate were found to be pH 7.4,29.9℃,and an inoculum density of 0.54 g L^-1,resulting in a maximum degradation of 90%.Sequencing of glyphosate oxidoreductase(GOX)and C-P lyase(phnJ)genes from *** P2 revealed 999c and 93%identities to already reported bacterial GOX and phnJ genes,*** presence of these two genes in *** indicates its potential to degrade glyphosate through GOX and C-P lyase metabolic *** study demonstrates the potential of *** P2 for efficient degradation of glyphosate,which can be exploited for remediation of glyphosate.

关键词： bacterial strain central composite rotatable design glyphosate oxidoreductase high-performance liquid chromatography inoculum density organophosphonate herbicide remediation

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Molecular Markers and Candidate Genes for Thermo-Sensitive Genic Male Sterile in Rice

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Rice science 2019年第3期26卷 147-156,I0008-I0012页

作者： Sudthana KHLAIMONGKHON Sriprapai CHAKHONKAEN Keasinee PITNGAM Khanittha DITTHAB Numphet SANGARWUT Natjaree PANYAWUT Thiwawan WASINANON Chareerat MONGKOLSIRIWATANA Julapark CHUNWONGSE Amorntip MUANGPROM Center for Agricultural Biotechnology Kasetsart University National Center for genetic Engineering and Biotechnology National Science and Technology Development Agency division of genetics Faculty of Liberal Arts and Science Kasetsart University

The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations derived from crosses between IR68301 S, an indica TGMS rice line, and IR14632(tropical japonica), Supanburi 91062(indica) and IR67966-188-2-2-1(tropical japonica), *** 1:3 ratio between sterile and normal pollen of F_2 plants from the three populations revealed that TGMS is controlled by a single recessive gene. Bulked segregant analysis using simple sequence repeat(SSR) and insertion-deletion(InDel) markers were used to identify markers linked to the tms gene. The linkage analysis based on the three populations indicated that the tms locus was located on chromosome 2 covering the same area. Using IR68301S × IR14632 F_2 population, the results showed that the tms locus was located between SSR marker RM12676 and InDel marker 2gAP0050058. The genetic distance from the tms gene to these two flanking markers were 1.10 and 0.82 cM, *** marker 2gAP004045 located between these two markers showed complete co-segregation with the TGMS phenotype. In addition, InDel marker vf0206114052 showed 2.94 cM linked to the tms gene using F_2 populations of IR68301S × Supanburi 91062. These markers are useful tool for developing new TGMS lines by marker-assisted selection. There were ten genes located between the two flanking markers RM12676 and 2gAP0050058. Using quantitative real-time PCR for expression analysis, 7 of the 10 genes showed expression in panicles, and response to temperatures. These genes could be the candidate gene controlling TGMS in IR68301S.

关键词： hybrid rice thermo-sensitive genic male sterility insertion/deletion simple sequence repeat marker-assisted selection

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Effects of inter-culture, arabinogalactan proteins, and hydrogen peroxide on the plant regeneration of wheat immature embryos

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Journal of Integrative Agriculture 2015年第1期14卷 11-19页

作者： ZHANG Wei WANG Xin-min FAN Rong YIN Gui-xiang WANG Ke DU Li-pu XIAO Le-le YE Xing-guo National Key Facility of Crop Gene Resources and genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences division of Agricultural and Environmental Science School of BiosciencesUniversity of Nottingham

The regeneration rate of wheat immature embryo varies among genotypes, howbeit many elite agriculture wheat varieties have low regeneration rates. Optimization of tissue culture conditions and attempts of adding signal molecules are effective ways to increase plant regeneration rate. Inter-culture is one of ways that have not been investigated in plant tissue culture. Moreover, the use of arabinogalactan proteins （AGPs） and hydrogen peroxide （H202） have been reported to increase regeneration rate in a few plant species other than wheat. The current research pioneeringly uses inter-culture of immature embryos of different wheat genotypes, and also investigates impacts of AGP and H2O2 on the induction of embryogenic calli and plant regeneration. As a result, high-frequency regeneration wheat cultivars Kenong 199 （KN 199） and Xinchun 9 （XC9）, together with low-frequency regeneration wheat line Chinese Spring （CS）, presented striking increase in the induction of embryogenic calli and plant regeneration rate of CS through inter-culture strategy, up to 52.19 and 67.98%, respectively. Adding 50 to 200 mg L-1 AGP or 0.005 to 0.01‰ H2O2 to the callus induction medium, enhanced growth of embryogenic calli and plant regeneration rate in quite a few wheat genotypes. At 50 mg L-1 AGP application level in callus induction medium plant regeneration rates of 8.49,409.06 and 283.16% were achieved for Jimai 22 （JM22）, Jingdong 18 （JD18） and Yangmai 18 （YM18）, respectively; whereas at 100 mg L-1 AGP level, CS （105.44%）, Chuannong 16 （CN16）（80.60%） and Ningchun 4 （NC4）（62.87%） acted the best. Moreover CS （79.05%）, JM22 （7.55%）, CN16 （101.87%）, YM18 （365.56%）, Yangmai 20 （YM20）（10.48%）, and CB301 （187.40%） were more responsive to 0.005 %o of H2O2, and NC4 （35.37%） obtained the highest shoot regeneration rates at 0.01%o of H2O2. Overall, these two methods, inter-culture and AGP （or H2O2） application, can be further applied to wheat transgenic research.

关键词： wheat immature embryos plant regeneration inter-culture arabinogalactan proteins hydrogen peroxide

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Bioaugmentation of a novel bacterial consortium in cotton-planted soil for lambda-cyhalothrin degradation

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Pedosphere 2024年第6期34卷 1100-1110页

作者： Samina ANWAR Anusha LIAQAT Asma MUNIR Muhammad F.ASHRAF Samina IQBAL Soil & Environmental Biotechnology division National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering &Applied Sciences (NIBGE-CPIEAS) Department of Chemistry Government College Women University

Extensive use of lambda-cyhalothrin（LC） for agricultural and domestic pest control leads to the accumulation of its residues in soil and water,which poses a serious threat to the *** of LC at the point source is the most effective way to avoid its spread and harmful ***,this study was planned to investigate the potential of indigenously isolated bacteria for the remediation of LC in cotton-vegetated *** potent LC-degrading bacteria,Brucella intermedia Halol,Alcaligenes faecalis CH1S,and Aquamicrobium terrae CH1T,were isolated from a pyrethroid-contaminated soil.A consortium CHST comprising these three strains was found to exhibit a higher potential for LC degradation as compared to the individual *** degradation of LC by CHST was optimized for four varying factors,i.e.,pH,inoculum density（ID）,carbon source（CS）,and initial pesticide（i.e.,LC）concentration（PC）,by applying Taguchi design of *** contributions of these factors to the biodegradation of LC were found to be in the order of pH> CS> PC> *** enhanced degradation of LC（84%） was attained at pH 7.0 in minimum salt medium containing 10 mg L-1LC and 3% *** consortium CHST was also augmented in sterilized and unsterilized soil microcosms at three PCs,i.e.,2,5,and 10 mg *** 21 d of incubation,complete LC degradation was achieved at 2 mg kg-1PC in sterilized as well as unsterilized soil,whereas at higher PCs,the extent of degradation was comparatively *** PC of 5 mg kg-1,88% and 96% LC degradation were observed in sterilized and unsterilized soils,respectively,compared to 79% and90% degradation at 10 mg kg-1,*** biodegradation,the major metabolite of LC,i.e.,3-phenoxybenzoic acid,was produced and further *** a cotton-planted soil spiked with 10 mg kg-1LC,the consortium degraded 91.8% LC,as well as improving the agronomic parameters of the cotton *** a nutshell,the consortium CHST was found to be a promising

关键词： 3-phenoxybenzoic acid bioremediation HPLC analysis pesticide point source of contamination pyrethroids Taguchi design of experiment

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characterization OF β-THALASSEMIA MUTATIONS IN CHINESE USING OLIGONUCLEOTIDE HYBRIDIZATION WITH AMPLIFIED DNA

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Chinese Science Bulletin 1990年第3期35卷 261-262页

作者：黄淑帧周霞娣朱皓任兆瑞曾溢滔 Laboratory of Medical genetics Shanghai Children's Hospital division of Gene Diagnosis National Center of Genetic Medicine Shanghai 200040 PRC

β-Thalassemia is a relatively common monogenic disorder in China. Up to the present, over 60 different mutations have been found to cause β-thalassemia in the world; and each ethnic group or population carries its own mutant alleles. It is of great significance to study β-thal mutations among the Chinese people for understanding the pathogenesis of the disease, the relationships between different races and the migration of populations as well as prevention and therapy of β-thalassemia.

关键词： alleles mutant populations migration ethnic pathogenesis DNA prevention carries globin

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A Simple,Efficient and Rapid Method for Good Quality DNA Extraction from Rice Grains

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Rice science 2017年第2期24卷 119-122页

作者： Abu Ashfaqur SAJIB Mohammad Ashraful Islam BHUIYA Roksana HUQUE Department of genetic Engineering and Biotechnology University of DhakaDhaka 1000Bangladesh Food Technology division Institute of Food and Radiation BiologyAtomic Energy Research EstablishmentSavar 1349Bangladesh

An efficient and good DNA extraction protocol should be simple, affordable and yield enough DNA with high quality. Rice(Oryza sativa L.) DNA extraction methods often use seedlings or leaves rather than the grains and tend to be time-consuming, involve multiple steps, and use hazardous chemicals and expensive enzymes. Rice grains offer several benefits over seedlings and leaves as a source of DNA for genetic analysis. However, these benefits are underutilized because the bulk of a rice grain is made up of starch. It is particularly important, but difficult to get rid of the starch while extracting DNA from rice grains. This co-precipitated polysaccharide is a known inhibitor of DNA polymerase activity in polymerase chain reaction(PCR). We describe here a very simple and highly affordable Chelex~?-100 based DNA extraction method from rice grains. It does not require any hazardous chemicals or enzymes. This method reproducibly extracts DNA with good purity indices(A_(260)/A_(230) and A_(260)/A_(280) values), but requires only a few steps.

关键词： DNA extraction rice grain Chelex■-100

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Phosphorus Starvation Tolerance in Rice Through Combined Physiological,Biochemical,and Proteome Analyses

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Rice science 2023年第6期30卷 613-631页

作者： Prathap V Suresh KUMAR Nand Lal MEENA Chirag MAHESHWARI Monika DALAL Aruna TYAGI division of Biochemistry Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi 110012India division of Germplasm Evaluation National Bureau of Plant Genetic ResourcesNew Delhi 110012India National Institute for Plant Biotechnology New Delhi 110012India

Phosphorus(P) deficiency limits the growth,development,and productivity of *** better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for the development of P-efficient rice cultivars,a pair of contrasting rice genotypes(Pusa-44 and NIL-23) was applied to investigate the morpho-physio-biochemical and proteomic variation under P-starvation *** rice genotypes were grown hydroponically in a PusaRich medium with adequate P(16 mg/kg,+P) or without P(0 mg/kg,-P) for 30 d.P-starvation manifested a significant reductions in root and shoot biomass,shoot length,leaf area,total chlorophyll,and P,nitrogen and starch contents,as well as protein kinase *** stress increased root-to-shoot biomass ratio,root length,sucrose content,and acid phosphatase activity,particularly in the P-tolerant genotype(NIL-23).Comparative proteome analysis revealed several P metabolism-associated proteins(including OsCDPKs,OsMAPKs,OsCPKs,OsLecRK2,and OsSAPks) to be expressed in the shoot of NIL-23,indicating that multiple protein kinases were involved in P-starvation/deficiency ***,the up-regulated expression of OsrbcL,OsABCG32,OsSUS5,OsPoll-like B,and ClpC2 proteins in the shoot,and OsACA9,OsACA8,OsSPS2F,OsPP2C15,and OsBiP3 in the root of NIL-23,indicated their role in P-starvation stress control through the Pup1 QTL. Thus,our findings indicated that-P stress-responsive proteins,in conjunction with morpho-physio-biochemical modulations,improved PUE and made NIL-23 a P-deficiency tolerant genotype due to the introgression of the Pup1 QTL in the Pusa-44 background.

关键词： phosphorus deficiency Pup1 QTL protein kinase acid phosphatase proteome analysis rice

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Variants of genes encoding collagens and matrix metalloproteinase system increased the risk of aortic dissection

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Science China(Life Sciences) 2017年第1期60卷 57-65页

作者： Zongzhe Li Chengming Zhou Lun Tan Peng Chen Yanyan Cao Chenze Li Xianqing Li Jiangtao Yan Hesong Zeng Dao-Wu Wang Dao-Wen Wang division of Cardiology Departments of Internal Medicine and Genetic Diagnosis CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and Technology Department of Cardiology the First Affiliated HospitalNanjing Medical University

Aortic dissection （AD） is a devastating, heterogeneous condition of aorta. The homeostasis between collagens and matrix metalloproteases （MMPs）/tissue inhibitors of MMPs （TIMPs） system in the extracellular matrix plays an important role for structure and functions of aorta. However, our knowledge on association between variants of genes in this system and pathogenesis of AD is very limited. We analyzed all yet known coding human genes of collagens （45 genes）, MMPs/TIMPs （27 genes） in 702 sporadic AD patients and in 163 matched healthy controls, by using massively targeted next-generation and Sanger sequencing. To define the pathogenesis of potential disease-causing candidate genes, we performed transcriptome sequencing and pedigree co-segregation analysis in some genes and generated Col5a2 knockout rats. We identified 257 pathogenic or likely pathogenic variants which involved 88.89% （64/72） genes in collagens-MMPs/TIMPs system and accounted for 31.05% （218/702） sporadic AD patients. In them, 84.86% patients （185/218） carried one variant, 12.84% two variants and 2.30% more than two variants. Importantly, we identified 52 novel probablY pathogenic loss-of-function （LOF） variants （20 nonsense, 16 frameshift, 14 splice sites, one stop-loss, one initiation codon） in 11.06% （50/452） AD patients, which were absent in 163 controls （P=2.5-10-5）. Transcriptome sequencing revealed that identified variants induced dyshomeostasis in expression of collagens-TIMPs/MMPs systems. The Col5a2-/- rats manifested growth retardation and aortic dysplasia. Our study provides a first comprehensive map of genetic alterations in collagens-MMPs/TIMPs system in sporadic AD patients and suggests that variants of these genes contribute largely to AD pathogenesis.

关键词： aortic dissection collagen matrix metalloproteinase next-generation sequencing genetic diagnosis

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