Cogent Biology最新文献_第10页

Investigation of intrinsic dynamics of enzymes involved in metabolic pathways using coarse-grained normal mode analysis 利用粗粒度正态分析研究参与代谢途径的酶的内在动力学

Cogent Biology Pub Date : 2017-01-01 DOI: 10.1080/23312025.2017.1291877

Sarah M. Meeuwsen, An Nam Hodac, Lauren M. Adams, Ryan D. McMunn, Maxwell S. Anschutz, Kari J. Carothers, Rachel E. Egdorf, Peter M. Hanneman, Jonathan P. Kitzrow, Cynthia K. Keonigsberg, Óscar López-Martínez, P. A. Matthew, Ethan H. Richter, Jonathan E. Schenk, Heidi L. Schmit, M. Scott, Eva M. Volenec, S. Hati

{"title":"Investigation of intrinsic dynamics of enzymes involved in metabolic pathways using coarse-grained normal mode analysis","authors":"Sarah M. Meeuwsen, An Nam Hodac, Lauren M. Adams, Ryan D. McMunn, Maxwell S. Anschutz, Kari J. Carothers, Rachel E. Egdorf, Peter M. Hanneman, Jonathan P. Kitzrow, Cynthia K. Keonigsberg, Óscar López-Martínez, P. A. Matthew, Ethan H. Richter, Jonathan E. Schenk, Heidi L. Schmit, M. Scott, Eva M. Volenec, S. Hati","doi":"10.1080/23312025.2017.1291877","DOIUrl":"https://doi.org/10.1080/23312025.2017.1291877","url":null,"abstract":"Abstract Intrinsic dynamics of proteins are known to play important roles in their function. In particular, collective dynamics of a protein, which are defined by the protein’s overall architecture, are important in promoting the active site conformation that favors substrate binding and effective catalysis. The primary sequence of a protein, which determines its three-dimensional structure, encodes unique dynamics. The intrinsic dynamics of a protein actually link protein structure to its function. In the present study, coarse-grained normal mode analysis was performed to examine the intrinsic dynamic patterns of 24 different enzymes involved in primary metabolic pathways. We observed that each metabolic enzyme exhibits unique patterns of motions, which are conserved across multiple species and functionally relevant. Dynamic cross-correlation matrices (DCCMs) are visibly identical for a given enzyme family but significantly different from DCCMs of other protein families, reinforcing that proteins with similar function exhibit a similar pattern of motions. The present work also reasserted that correct identification of unknown proteins is possible based on their intrinsic mobility patterns.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2017.1291877","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48277448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Hepatoprotective activity of Ganoderma lucidium (Curtis) P. Karst against cyclophosphamide-induced liver injury in mice 灵芝对环磷酰胺所致小鼠肝损伤的保护作用

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1267421

H. Pham, L. Hoang, V. Phung

引用次数: 4

Comparing cork quality from Hafir-Zarieffet mountain forest (Tlemcen, Algeria) vs. Tagus basin Montado (Benavente, Portugal) 阿尔及利亚特莱姆森Hafir-Zarieffet山林与葡萄牙贝纳文特塔古斯盆地Montado的软木质量比较

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1236431

Amina Ghalem, I. Barbosa, R. Bouhraoua, Augusta Costa

{"title":"Comparing cork quality from Hafir-Zarieffet mountain forest (Tlemcen, Algeria) vs. Tagus basin Montado (Benavente, Portugal)","authors":"Amina Ghalem, I. Barbosa, R. Bouhraoua, Augusta Costa","doi":"10.1080/23312025.2016.1236431","DOIUrl":"https://doi.org/10.1080/23312025.2016.1236431","url":null,"abstract":"Abstract In the southwestern Mediterranean Basin, cork oaks (Quercus suber L.) are periodically harvested for their cork. This natural product is valued by its homogeneity which heightens the importance of characterizing cork tissue discontinuities, or cork pores. Cork porosity profile in natural cork planks has been reported to be affected by forest management practices but, so far, has been scarcely addressed. We characterize the cork porosity profile in two contrasting cork oak woodland; at a mountain forest, in Western Algeria (absence of forest management) and at a peneplain “montado,” in southern Portugal (intensively managed toward the optimization of cork production). Image analysis techniques were applied on transverse sections of more than 40 cork samples from both woodland, and a stepwise discriminant analysis was used to discriminate between the cork pore features data-sets. Cork porosity profiles were similar between regions but; in the cork samples from Algeria, cork pores were having higher values for linear dimensions of pores (length and perimeter) and contrasting shape values (roundness) which depreciate cork quality, when compared to the cork samples from Portugal. However, improved woodland management strategies at Algeria should ensure adequate cork homogeneity and suitability for more valuable cork products.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2016.1236431","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Differential biochemical response of rice (Oryza sativa L.) genotypes against rice blast (Magnaporthe oryzae) 水稻(Oryza sativa L.)基因型对稻瘟病的不同生化反应

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1264162

P. Anushree, R. Naik, R. Satbhai, A. Gaikwad, C. Nimbalkar, J. Bahler

{"title":"Differential biochemical response of rice (Oryza sativa L.) genotypes against rice blast (Magnaporthe oryzae)","authors":"P. Anushree, R. Naik, R. Satbhai, A. Gaikwad, C. Nimbalkar, J. Bahler","doi":"10.1080/23312025.2016.1264162","DOIUrl":"https://doi.org/10.1080/23312025.2016.1264162","url":null,"abstract":"Abstract The disease-free (control) and blast infected leaf samples of 11 rice genotypes were evaluated for activity profile of defense-related and antioxidative enzymes. The amplification genomic DNA with two SSR markers RM124 and RM224 were also performed for identification of blast resistance and susceptible genotypes. The activity of chitinase, PAL and β-glucosidase of post pathogen-infected leaf samples increased significantly in all rice genotypes, thought the increase was comparable less in to blast susceptible genotypes Chimansal and EK-70. The activity of antioxidative enzymes was comparatively higher in the infected leaf of blast resistant genotypes recording highest increase in NLR-20104 and KJT-5. The activity of defense-related and antioxidative enzymes in the disease-free leaf samples differed among the genotypes and was even higher in the two blast susceptible genotypes. RM144 and RM224 SSR primers clearly amplified in blast resistant KJT-5, NLR-20104, KJT-2, Tetep genotypes whereas RM144 missing in susceptible Chimansal but prominently present in susceptible genotype EK-70. This study revealed that higher level of induction of defense-related and antioxidative enzymes and presence of specific amplified fragments with RM144 and RM224 could be useful for screening the resistant and susceptible rice genotypes against Magnaporthe oryzae.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2016.1264162","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Antioxidant and antidiabetic potential of Myrothamnus flabellifolius found in Botswana 产自博茨瓦纳的松果木的抗氧化和抗糖尿病潜能

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1275403

T. Kwape, R. Majinda, P. Chaturvedi

引用次数: 9

Comparison of visual observation and emission intensity of resazurin for antimicrobial properties of hexane, dichloromethane, methanol and water extracts from a brown alga, Turbinaria ornata 褐藻Turbinaria ornata中己烷、二氯甲烷、甲醇和水提取物的抑菌效果及释放强度比较

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1225877

Kar-Yee Tye, S. Gan, S. Lim, S. Tan, Chen-Ai Chen, S. Phang

{"title":"Comparison of visual observation and emission intensity of resazurin for antimicrobial properties of hexane, dichloromethane, methanol and water extracts from a brown alga, Turbinaria ornata","authors":"Kar-Yee Tye, S. Gan, S. Lim, S. Tan, Chen-Ai Chen, S. Phang","doi":"10.1080/23312025.2016.1225877","DOIUrl":"https://doi.org/10.1080/23312025.2016.1225877","url":null,"abstract":"Abstract Marine natural products have been increasingly found to be a promising source of drug candidates for fighting human diseases. The present study was carried out to assess the antimicrobial properties of a brown alga, Turbinaria ornata. Hexane, dichloromethane, methanol, and water extracts were tested against 23 micro-organisms including Gram-positive and negative bacteria, yeasts, and fungi. The disk diffusion method was employed followed by modified resazurin microtitre assay (REMA). The results obtained from modified REMA using both methods of colorimetric and fluorometric were compared. The best antimicrobial activity was recorded in dichloromethane extract for disk diffusion. Further, modified REMA showed inhibition in Bacillus cereus, Bacillus subtilis, Staphylococcus aureus ATCC 25923, S. aureus, Staphylococcus epidermidis, Staphylococcus saprophyticus, Enterococcus faecalis, Pseudomonas aeruginosa ATCC 27853, Candida parapsilosis ATCC 22019, Candida guilliermondii ATCC 6260, and Saccharomyces cerevisiae. Both methods of modified REMA were substantially in agreement with each other based on Cohen’s kappa statistical analysis (κ value = 0.712; p < 0.0005). Our findings suggested that T. ornata dichloromethane extract has the potential to be used as a source of antimicrobial compounds.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2016.1225877","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Acute and sub-acute toxicity studies on the effect of Senna alata in Swiss Albino mice 番泻草对瑞士白化病小鼠急性和亚急性毒性研究

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1272166

S. Roy, B. Ukil, L. M. Lyndem

引用次数: 20

Catechins from green tea modulate neurotransmitter transporter activity in Xenopus oocytes 绿茶中的儿茶素调节爪蟾卵母细胞的神经递质转运活性

Cogent Biology Pub Date : 2016-12-31 DOI: 10.1080/23312025.2016.1261577

Y. Wang, T. Engelmann, Y.F. Xu, W. Schwarz, T. Hsu

引用次数: 6

Isolation and purification of phytocystatin from almond: Biochemical, biophysical, and immunological characterization 从杏仁中分离纯化植物胱抑素:生化、生物物理和免疫学特性

Cogent Biology Pub Date : 2016-12-17 DOI: 10.1080/23312025.2016.1262489

A. A. Siddiqui, Peerzada Shariq Shaheen Khaki, A. Sohail, Tarique Sarwar, B. Bano

{"title":"Isolation and purification of phytocystatin from almond: Biochemical, biophysical, and immunological characterization","authors":"A. A. Siddiqui, Peerzada Shariq Shaheen Khaki, A. Sohail, Tarique Sarwar, B. Bano","doi":"10.1080/23312025.2016.1262489","DOIUrl":"https://doi.org/10.1080/23312025.2016.1262489","url":null,"abstract":"Abstract It is well known that fruit nuts contain wide variety of flavonoids and various proteins, consumption of which has been associated with the reduced risk of chronic diseases. Cystatins, a family of cysteine proteinase inhibitors, ubiquitously present in all cells serve various important and critical physiological functions. In this study a phytocystatin with molecular mass of 63.4 kDa was purified to homogeneity by a three-step process including ammonium sulfate fractionation (50–70%), acetone precipitation, and gel filtration chromatography on Sephacryl S100-HR column. The purified inhibitor migrated as single band under native and SDS-PAGE. The Ki values for purified inhibitor with papain, ficin, and bromelain were found to be 45.45, 83.33, and 90.9 nM, respectively, suggesting higher affinity of the inhibitor for papain as compared to ficin and bromelain. Phytocystatin was stable in broad pH and temperature range. Purified cystatin appeared to be antigenic as observed in western blot analysis. ITC assay data show a binding stoichiometry of 0.870 ± 0.03 sites for cystatin and papain interaction which indicated that cystatin is surrounded by nearly one papain molecule. FTIR, UV, and fluorescence studies showed significant conformational changes on cystatin–papain complex formation. Purified cystatin was found to possess 36.8% α-helical content as observed by CD spectroscopy.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2016.1262489","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

The spontaneous juvenile alopecia (jal) mutation in mice is associated with the insertion of an IAP element in the Gata3 gene 小鼠自发性幼年脱发(jal)突变与Gata3基因中IAP元素的插入有关

Cogent Biology Pub Date : 2016-12-14 DOI: 10.1080/23312025.2016.1264691

M. E. Connor, T. R. King

{"title":"The spontaneous juvenile alopecia (jal) mutation in mice is associated with the insertion of an IAP element in the Gata3 gene","authors":"M. E. Connor, T. R. King","doi":"10.1080/23312025.2016.1264691","DOIUrl":"https://doi.org/10.1080/23312025.2016.1264691","url":null,"abstract":"Abstract Background: A combination of genetic fine-mapping and complementation testing was used previously to assign the juvenile alopecia mutation (abbreviated jal) to the GATA binding protein 3 (Gata3) gene on Chromosome 2 in mice. However, sequence analysis of Gata3 exons (including coding and noncoding regions) revealed no differences between wild type C3H/HeJ and co-isogenic C3H/HeJ-jal/J mutant mice. Results: Using a PCR-based scanning method, here we have tested the hypothesis that jal might result from insertion of a transposable element in or near the Gata3 gene. We show that the jal mutation is specifically associated with an intracisternal A particle (IAP) element of the I∆1 subtype that has transposed to Intron 3–4 in the Gata3 gene, and use the same panel of recombinants used previously to fine-map jal to show that this IAP element and jal are located within the same small genetic interval. Conclusion: Transposition of an IAP element of the I∆1 subtype into Intron 3–4 of the mutant Gata3jal allele is the likely cause of the juvenile alopecia phenotype in mutant mice.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2016.1264691","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2