Pub Date : 2018-01-01Epub Date: 2018-01-10DOI: 10.1080/23312025.2018.1425196
Brandy A Smith, Christina R Mottishaw, Andria J Hendricks, Jason Mitchell, Stephanie Becker, Pamela S Ropski, Bomina Park, Marie Finkbeiner-Caufield, Barbara Garay-Nontol, R W Holman, Kenneth J Rodnick
Nonenzymatic glycation (NEG) begins with the non-covalent binding of a glucopyranose to a protein. The bound glucopyranose must then undergo structural modification to generate a bound electrophile that can reversibly form a Schiff base, which can then lead to Amadori intermediates, and ultimately to glycated proteins. Inorganic phosphate (Pi) is known to accelerate the glycation of human hemoglobin (HbA), although the specific mechanism(s) of Pi as an effector reagent have not been determined. The aim of this study was to determine whether Pi and a glucopyranose can concomitantly bind to HbA and react while bound within the early, noncovalent stages to generate electrophilic species capable of progress in NEG. 31P and 1HNMR of model reactions confirm that bimolecular reactions between Pi and glucopyranose occur generating modified glucose electrophiles. Computations of protein/substrate interactions predict that Pi can concomitantly bind with a glucopyranose in HbA pockets with geometries suitable for multiple acid/base mechanisms that can generate any of four transient electrophiles. Pi-facilitated mechanisms in the noncovalent stages predict that the glycation of β-Val1 of HbA to HbA1c is a "hot spot" because the β-Val1 pocket facilitates many more mechanisms than any other site. The mechanistic diversity of the Pi effect within the early noncovalent stages of NEG predicts well the overall site selectivity observed from the in vivo glycation of HbA in the presence of Pi. These insights extend our basic understanding of the NEG process and may have clinical implications for diabetes mellitus and even normal aging.
{"title":"Potential roles of inorganic phosphate on the progression of initially bound glucopyranose toward the nonenzymatic glycation of human hemoglobin: mechanistic diversity and impacts on site selectivity.","authors":"Brandy A Smith, Christina R Mottishaw, Andria J Hendricks, Jason Mitchell, Stephanie Becker, Pamela S Ropski, Bomina Park, Marie Finkbeiner-Caufield, Barbara Garay-Nontol, R W Holman, Kenneth J Rodnick","doi":"10.1080/23312025.2018.1425196","DOIUrl":"https://doi.org/10.1080/23312025.2018.1425196","url":null,"abstract":"<p><p>Nonenzymatic glycation (NEG) begins with the non-covalent binding of a glucopyranose to a protein. The bound glucopyranose must then undergo structural modification to generate a bound electrophile that can reversibly form a Schiff base, which can then lead to Amadori intermediates, and ultimately to glycated proteins. Inorganic phosphate (Pi) is known to accelerate the glycation of human hemoglobin (HbA), although the specific mechanism(s) of Pi as an effector reagent have not been determined. The aim of this study was to determine whether Pi and a glucopyranose can concomitantly bind to HbA and react while bound within the early, noncovalent stages to generate electrophilic species capable of progress in NEG. <sup>31</sup>P and <sup>1</sup>HNMR of model reactions confirm that bimolecular reactions between Pi and glucopyranose occur generating modified glucose electrophiles. Computations of protein/substrate interactions predict that Pi can concomitantly bind with a glucopyranose in HbA pockets with geometries suitable for multiple acid/base mechanisms that can generate any of four transient electrophiles. Pi-facilitated mechanisms in the noncovalent stages predict that the glycation of β-Val1 of HbA to HbA1c is a \"hot spot\" because the β-Val1 pocket facilitates many more mechanisms than any other site. The mechanistic diversity of the Pi effect within the early noncovalent stages of NEG predicts well the overall site selectivity observed from the <i>in vivo</i> glycation of HbA in the presence of Pi. These insights extend our basic understanding of the NEG process and may have clinical implications for diabetes mellitus and even normal aging.</p>","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":"4 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1425196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37096802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1525857
Michael Norén, S. Kullander
Abstract We present the complete mitochondrial genome and a phylogenetic analysis of the danionine cyprinid Betadevario ramachandrani, endemic to the Western Ghats in India. Bayesian phylogenetic analysis of all available mitochondrial genomes of Danionina show that B. ramachandrani is the most basal member of a clade also containing Devario, Microdevario and Microrasbora, and this clade is the sister group of Danio. Seven of 20 mitochondrial genomes downloaded from GenBank for phylogenetic analysis were found to be chimeric, including five curated reference genomes, and this did affect our phylogenetic analysis. At least three of these erroneous sequences have been used in other studies. There is reason to suspect that there are numerous chimeric mitogenomes in GenBank.
{"title":"The enigmatic Betadevario ramachandrani (Teleostei: Cyprinidae: Danioninae): phylogenetic position resolved by mitogenome analysis, with remarks on the prevalence of chimeric mitogenomes in GenBank","authors":"Michael Norén, S. Kullander","doi":"10.1080/23312025.2018.1525857","DOIUrl":"https://doi.org/10.1080/23312025.2018.1525857","url":null,"abstract":"Abstract We present the complete mitochondrial genome and a phylogenetic analysis of the danionine cyprinid Betadevario ramachandrani, endemic to the Western Ghats in India. Bayesian phylogenetic analysis of all available mitochondrial genomes of Danionina show that B. ramachandrani is the most basal member of a clade also containing Devario, Microdevario and Microrasbora, and this clade is the sister group of Danio. Seven of 20 mitochondrial genomes downloaded from GenBank for phylogenetic analysis were found to be chimeric, including five curated reference genomes, and this did affect our phylogenetic analysis. At least three of these erroneous sequences have been used in other studies. There is reason to suspect that there are numerous chimeric mitogenomes in GenBank.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1525857","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46394658","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1469387
R. Sadhukhan, N. Brown, D. Ouellette, D. Banach, D. Filoti, David Winarta, Reema Raghavendra, Silvino Sousa, Anhdao T. Darcy, L. Alessandri, A. Ivanov, Sahana Bose, Lucia Eaton, G. Preston, J. Freeman, I. Correia
Abstract Injecting anti-tumor necrosis factor (TNF)α antibodies into patient joints at the site of inflammation, inter-articular (IA) delivery, has demonstrated modest success for treatment of Spondyloarthritis (SpA), Rheumatoid Arthritis (RA), and osteoarthritis. However, IA delivery is not the treatment route of choice due to rapid clearance from the site of administration. Elastin-like polypeptides (ELPs) are reported to undergo phase transition; forming reversible aggregates above their transition temperature, which when injected into IA space have a 25-fold longer half-life compared to the soluble form. Here, we fused an ELP repeat to the C-terminus of each heavy chain of an anti-TNFα monoclonal antibody (mAb) and provide detailed characterization of the fusion IgG molecule. Expression and purification yielded homogenous protein confirmed by gels, hydrophobic-interaction chromatography, Capilary Electrophoresis (CE), Mass Spectrometry (MS), and analytical ultracentrifugation. The ELPs altered hydrophobicity and pI of the parent mAb and new elastic properties were imparted to the molecule; forming large stable complexes with a hydrodynamic radius of 40 nm above 39°C that dissociated into soluble, active monomer below 37°C. The fusion mAb retained its affinity and ability to neutralize TNFα as determined by surface plasmon resonance and cell-based assay, respectively, with equal potency to unmodified anti-TNFα mAb. Differential-scanning calorimetry studies show stabilization of adjacent CH2 and CH3 domains in the fusion molecule and the aggregated molecule was found to be fully functional after 7 days at 37°C. For the first time, we reveal architecture of an ELP-fusion mAb and binding to antigen using single-particle-transmission-electron microscopy. Unstructured ELP was visualized at the C-terminus and binding to antigen was shown at the N-terminus. Collectively, these studies indicate that it is possible to impart elastic properties to a monoclonal antibody while retaining purity, stability, and ability to effectively bind and neutralize antigen.
{"title":"Engineering elastic properties into an anti-TNFα monoclonal antibody","authors":"R. Sadhukhan, N. Brown, D. Ouellette, D. Banach, D. Filoti, David Winarta, Reema Raghavendra, Silvino Sousa, Anhdao T. Darcy, L. Alessandri, A. Ivanov, Sahana Bose, Lucia Eaton, G. Preston, J. Freeman, I. Correia","doi":"10.1080/23312025.2018.1469387","DOIUrl":"https://doi.org/10.1080/23312025.2018.1469387","url":null,"abstract":"Abstract Injecting anti-tumor necrosis factor (TNF)α antibodies into patient joints at the site of inflammation, inter-articular (IA) delivery, has demonstrated modest success for treatment of Spondyloarthritis (SpA), Rheumatoid Arthritis (RA), and osteoarthritis. However, IA delivery is not the treatment route of choice due to rapid clearance from the site of administration. Elastin-like polypeptides (ELPs) are reported to undergo phase transition; forming reversible aggregates above their transition temperature, which when injected into IA space have a 25-fold longer half-life compared to the soluble form. Here, we fused an ELP repeat to the C-terminus of each heavy chain of an anti-TNFα monoclonal antibody (mAb) and provide detailed characterization of the fusion IgG molecule. Expression and purification yielded homogenous protein confirmed by gels, hydrophobic-interaction chromatography, Capilary Electrophoresis (CE), Mass Spectrometry (MS), and analytical ultracentrifugation. The ELPs altered hydrophobicity and pI of the parent mAb and new elastic properties were imparted to the molecule; forming large stable complexes with a hydrodynamic radius of 40 nm above 39°C that dissociated into soluble, active monomer below 37°C. The fusion mAb retained its affinity and ability to neutralize TNFα as determined by surface plasmon resonance and cell-based assay, respectively, with equal potency to unmodified anti-TNFα mAb. Differential-scanning calorimetry studies show stabilization of adjacent CH2 and CH3 domains in the fusion molecule and the aggregated molecule was found to be fully functional after 7 days at 37°C. For the first time, we reveal architecture of an ELP-fusion mAb and binding to antigen using single-particle-transmission-electron microscopy. Unstructured ELP was visualized at the C-terminus and binding to antigen was shown at the N-terminus. Collectively, these studies indicate that it is possible to impart elastic properties to a monoclonal antibody while retaining purity, stability, and ability to effectively bind and neutralize antigen.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1469387","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44897331","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1576016
{"title":"Retraction: Using pgRNA-Cas9 system to knockout MKL1 inhibited cell migration and proliferation","authors":"","doi":"10.1080/23312025.2018.1576016","DOIUrl":"https://doi.org/10.1080/23312025.2018.1576016","url":null,"abstract":"","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1576016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43785840","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1431474
M. Billah, S. M. Rana, N. Akter, M. S. Hossain
Abstract Objective: Type 2 Diabetes Mellitus is one of the most serious and common public health problems and metabolic disorder in both developed and developing countries. Diabetic patient may suffer from imbalanced electrolyte and lipid profile due to complications of diabetes mellitus and the medication they receive. Electrolytes and lipids have noteworthy roles, and changes in their concentrations provide significant signs of disease progression in a number of non-communicable diseases like diabetes. As there is a very few study of electrolyte and lipid profile in young Bangladeshi female diabetic patients, we investigated to identify the status of serum electrolytes and lipid profile with fasting blood glucose levels in type 2 diabetic female subjects with age ranging from 20 to 30. Subjects: Thirty-five female type 2 diabetes mellitus patients and 15 non-diabetic healthy control female volunteers of 20–30 age were recruited to determine serum glucose, electrolytes (Na+, K+, Cl−, and HCO3−), and lipid profiles (total cholesterol, triglyceride, HDL, and LDL). Result: The mean levels of electrolytes except K+ and lipid profile except HDL were found significantly higher (p < 0.001) in comparison with control group. While, there was significant (p < 0.05) decrease in the serum levels of K + and HDL in all diabetics. Conclusion: These results presented some variations from other research having different age and sex. Therefore, it can be concluded that there might have an effect of age and sex differences on lipid and electrolyte profile. This abnormal biochemical profile could be a noteworthy sign of diabetes associated disease and may have great potential as a diagnostic tool in clinical practice.
{"title":"Analysis of serum electrolyte and lipid profile in young Bangladeshi female with Type II Diabetes","authors":"M. Billah, S. M. Rana, N. Akter, M. S. Hossain","doi":"10.1080/23312025.2018.1431474","DOIUrl":"https://doi.org/10.1080/23312025.2018.1431474","url":null,"abstract":"Abstract Objective: Type 2 Diabetes Mellitus is one of the most serious and common public health problems and metabolic disorder in both developed and developing countries. Diabetic patient may suffer from imbalanced electrolyte and lipid profile due to complications of diabetes mellitus and the medication they receive. Electrolytes and lipids have noteworthy roles, and changes in their concentrations provide significant signs of disease progression in a number of non-communicable diseases like diabetes. As there is a very few study of electrolyte and lipid profile in young Bangladeshi female diabetic patients, we investigated to identify the status of serum electrolytes and lipid profile with fasting blood glucose levels in type 2 diabetic female subjects with age ranging from 20 to 30. Subjects: Thirty-five female type 2 diabetes mellitus patients and 15 non-diabetic healthy control female volunteers of 20–30 age were recruited to determine serum glucose, electrolytes (Na+, K+, Cl−, and HCO3−), and lipid profiles (total cholesterol, triglyceride, HDL, and LDL). Result: The mean levels of electrolytes except K+ and lipid profile except HDL were found significantly higher (p < 0.001) in comparison with control group. While, there was significant (p < 0.05) decrease in the serum levels of K + and HDL in all diabetics. Conclusion: These results presented some variations from other research having different age and sex. Therefore, it can be concluded that there might have an effect of age and sex differences on lipid and electrolyte profile. This abnormal biochemical profile could be a noteworthy sign of diabetes associated disease and may have great potential as a diagnostic tool in clinical practice.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1431474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47911796","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1471779
Habtamu Abera Goshu, Wu Xiao Yun, M. Chu, P. Bao, P. Yan
Abstract Single nucleotide polymorphisms (SNPs) are common markers used for population genetics studies. Recently, copy number variations (CNVs) have been used to study genetic and phenotypic diversity within and among populations. Therefore, studies of the genetics of CNVs are important in the context of understanding evolutionary changes and genomic selection based upon genetic and phenotypic variation. The aim of this study was to analyse the distribution of the choline kinase beta (CHKB), Krüpple-like factor 6 (KLF6), glypican 1(GPC1) and cholinergic receptor muscarinic 3 (CHRM3) genes in five representative Chinese domestic yak breeds. The data generated by qPCR was transformed into log2 ratio and analysed using GraphPad (PRISM). The results show that the CNVs of CHKB, KLF6, and GPC1 genes presented more copy number losses in Tianzhu, Gannan and Plateau yak populations compared with the Datong and polled yak having relatively more copy number gains. However, the CHRM3 CNV showed more copy number gains in five yak populations. Therefore, these results indicate that there are relatively more copy number losses (deletion) in the yak populations; supporting the hypothesis that log2 ratio is more powerful at detecting loss than gain in copy number types. Taken together, these data provide information on the application genome CNVs in population genetics and suggest that the CNVs of the genes could exert a significant effect on phenotypic differences in yak populations.
{"title":"Population genetic copy number variation of CHKB, KLF6, GPC1 and CHRM3 genes in Chinese domestic yak (Bos grunniens) breeds","authors":"Habtamu Abera Goshu, Wu Xiao Yun, M. Chu, P. Bao, P. Yan","doi":"10.1080/23312025.2018.1471779","DOIUrl":"https://doi.org/10.1080/23312025.2018.1471779","url":null,"abstract":"Abstract Single nucleotide polymorphisms (SNPs) are common markers used for population genetics studies. Recently, copy number variations (CNVs) have been used to study genetic and phenotypic diversity within and among populations. Therefore, studies of the genetics of CNVs are important in the context of understanding evolutionary changes and genomic selection based upon genetic and phenotypic variation. The aim of this study was to analyse the distribution of the choline kinase beta (CHKB), Krüpple-like factor 6 (KLF6), glypican 1(GPC1) and cholinergic receptor muscarinic 3 (CHRM3) genes in five representative Chinese domestic yak breeds. The data generated by qPCR was transformed into log2 ratio and analysed using GraphPad (PRISM). The results show that the CNVs of CHKB, KLF6, and GPC1 genes presented more copy number losses in Tianzhu, Gannan and Plateau yak populations compared with the Datong and polled yak having relatively more copy number gains. However, the CHRM3 CNV showed more copy number gains in five yak populations. Therefore, these results indicate that there are relatively more copy number losses (deletion) in the yak populations; supporting the hypothesis that log2 ratio is more powerful at detecting loss than gain in copy number types. Taken together, these data provide information on the application genome CNVs in population genetics and suggest that the CNVs of the genes could exert a significant effect on phenotypic differences in yak populations.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1471779","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46318656","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1530493
Oscar M. Rollano-Peñaloza, S. Widell, P. Mollinedo, A. Rasmusson
Abstract To investigate the symbiotic interaction of Trichoderma harzianum Rifai on Chenopodium quinoa Willd. in isolation, we studied axenic co-culture of the T. harzianum isolates T-22 and BOL-12QD and the C. quinoa cultivars Kurmi and Maniqueña real. Neither T-22 nor BOL-12QD affected seedling growth during two days of co-culture in the early growth phase of rapid primary root extension. However, after longer axenic co-culture, T-22 and BOL-12 were found to significantly inhibit the overall growth of C. quinoa cv. Kurmi and Real, affecting also vitality parameters as seen for chlorophyll and betalains. Lateral root development was strongly inhibited in all plant−fungal combinations, leaving stunted lateral roots. These results suggest that T. harzianum has a general capacity to inhibit the growth of C. quinoa plants with a main effect on the lateral root development.
{"title":"Trichoderma harzianum T-22 and BOL-12QD inhibit lateral root development of Chenopodium quinoa in axenic co-culture","authors":"Oscar M. Rollano-Peñaloza, S. Widell, P. Mollinedo, A. Rasmusson","doi":"10.1080/23312025.2018.1530493","DOIUrl":"https://doi.org/10.1080/23312025.2018.1530493","url":null,"abstract":"Abstract To investigate the symbiotic interaction of Trichoderma harzianum Rifai on Chenopodium quinoa Willd. in isolation, we studied axenic co-culture of the T. harzianum isolates T-22 and BOL-12QD and the C. quinoa cultivars Kurmi and Maniqueña real. Neither T-22 nor BOL-12QD affected seedling growth during two days of co-culture in the early growth phase of rapid primary root extension. However, after longer axenic co-culture, T-22 and BOL-12 were found to significantly inhibit the overall growth of C. quinoa cv. Kurmi and Real, affecting also vitality parameters as seen for chlorophyll and betalains. Lateral root development was strongly inhibited in all plant−fungal combinations, leaving stunted lateral roots. These results suggest that T. harzianum has a general capacity to inhibit the growth of C. quinoa plants with a main effect on the lateral root development.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1530493","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45253367","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1453319
S. A. Fuller, B. Beck, Matthew E. McEntire, E. Peatman, J. Abernathy
Abstract Hybrid striped bass is a major aquaculture species in the United States. Artificial breeding of this species can introduce large variation in growth during production to market size. To assess the genetic and nutrigenomic basis behind growth variability in these hybrids, fingerlings (n = 5072) from 47 families were size-matched and communally grown in earthen ponds for 115 days. Families were then ranked by weight gain and individuals from the three fastest growing (mean 240.8 ± 9.75 g; 242.0 ± 11.52 mm) and three slowest growing families (mean 153.5 ± 52.38 g; 223.3 ± 21.31 mm) were collected for liver RNA sequencing. As expected, growth characteristics in hybrid striped bass are highly heritable (p < 0.0001). Through differential gene expression analysis we identified 86 genes that were responsive between groups including 40 up-regulated (1.89˂fold-change < 7.66) and 46 down-regulated (−1.71 > fold-change ˃−4.59) genes in the largest fish. This included two somatic growth-related genes, growth factor receptor gene and a gene encoding an insulin-like growth factor binding protein, that may directly explain some of the genetic variation between families. Several additional genes involved in metabolic pathways such as glycolysis/gluconeogenesis and lipid biosynthesis were also revealed. The candidate gene list may also provide some evidence that both physiological and behavioral factors may be influencing growth differences in communally reared fish.
{"title":"Heritability of growth traits and correlation with hepatic gene expression among hybrid striped bass exhibiting extremes in performance","authors":"S. A. Fuller, B. Beck, Matthew E. McEntire, E. Peatman, J. Abernathy","doi":"10.1080/23312025.2018.1453319","DOIUrl":"https://doi.org/10.1080/23312025.2018.1453319","url":null,"abstract":"Abstract Hybrid striped bass is a major aquaculture species in the United States. Artificial breeding of this species can introduce large variation in growth during production to market size. To assess the genetic and nutrigenomic basis behind growth variability in these hybrids, fingerlings (n = 5072) from 47 families were size-matched and communally grown in earthen ponds for 115 days. Families were then ranked by weight gain and individuals from the three fastest growing (mean 240.8 ± 9.75 g; 242.0 ± 11.52 mm) and three slowest growing families (mean 153.5 ± 52.38 g; 223.3 ± 21.31 mm) were collected for liver RNA sequencing. As expected, growth characteristics in hybrid striped bass are highly heritable (p < 0.0001). Through differential gene expression analysis we identified 86 genes that were responsive between groups including 40 up-regulated (1.89˂fold-change < 7.66) and 46 down-regulated (−1.71 > fold-change ˃−4.59) genes in the largest fish. This included two somatic growth-related genes, growth factor receptor gene and a gene encoding an insulin-like growth factor binding protein, that may directly explain some of the genetic variation between families. Several additional genes involved in metabolic pathways such as glycolysis/gluconeogenesis and lipid biosynthesis were also revealed. The candidate gene list may also provide some evidence that both physiological and behavioral factors may be influencing growth differences in communally reared fish.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1453319","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41909128","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1488511
M. Tahir, Syed Inayat Ali Shah, G. Zaman, S. Muhammad
Abstract This article discusses the Ebola virus, which is also known as Ebola haemorrhagic. Ebola virus is a transmitter virus, and the transmitting agents are wild animals, whereas in the human population it transmits from human to human. We consider the Susceptible-Exposed-Infected-Recovered (SEIR) model for our study, where the population is affected by Ebola virus by wild and domestic animals. First, we formulate the proposed model. Then, the key value, , is obtained, which is the reproductive number of the concerned model. After that, stability analyses, both local and endemic stabilities, are carried out for disease-free equilibria and endemic equilibria and we show that both are stable. Global stability at the disease-free as well as at endemic equilibrium was found to be successfully stable. For global stability at both levels, we define the Lapnuov function, finally, numerical simulation of the Runge–Kutta method is presented for the proposed model.
{"title":"Ebola virus epidemic disease its modeling and stability analysis required abstain strategies","authors":"M. Tahir, Syed Inayat Ali Shah, G. Zaman, S. Muhammad","doi":"10.1080/23312025.2018.1488511","DOIUrl":"https://doi.org/10.1080/23312025.2018.1488511","url":null,"abstract":"Abstract This article discusses the Ebola virus, which is also known as Ebola haemorrhagic. Ebola virus is a transmitter virus, and the transmitting agents are wild animals, whereas in the human population it transmits from human to human. We consider the Susceptible-Exposed-Infected-Recovered (SEIR) model for our study, where the population is affected by Ebola virus by wild and domestic animals. First, we formulate the proposed model. Then, the key value, , is obtained, which is the reproductive number of the concerned model. After that, stability analyses, both local and endemic stabilities, are carried out for disease-free equilibria and endemic equilibria and we show that both are stable. Global stability at the disease-free as well as at endemic equilibrium was found to be successfully stable. For global stability at both levels, we define the Lapnuov function, finally, numerical simulation of the Runge–Kutta method is presented for the proposed model.","PeriodicalId":10412,"journal":{"name":"Cogent Biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/23312025.2018.1488511","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45648372","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}
Pub Date : 2018-01-01DOI: 10.1080/23312025.2018.1536315
Martha P. Olivas-Sánchez, C. Vital-García, J. P. Flores-Márgez, A. Mora-Covarrubias, F. Clemente-Sánchez
Abstract Mule deer historic range in Mexico has declined dramatically in the last decade. Forage availability and quality at the Chihuahuan Desert may play an important role sustaining populations at the southern end of their current distribution. We evaluated forage availability and quality at the end of a 3-year drought at two different localities in the Chihuahuan Desert: Old Net and Pulpit, we measured plant availability and quality, diet content and calculated diet preference indices. Vegetation at Old Net consisted primarily of both succulents (47%) and trees-shrubs (42%) while Pulpit had more grasses (60%) and herbs (24%) (P < 0.005). Feces collected at the Pulpit presented a high proportion of herbs (44%), while those collected at Old Net contained more trees and shrubs (53%). Preference index suggests that mule deer prefer herbs and overlook grasses, but there is no strong selection for any particular plant. Our results suggest that forage is appropriate to sustain mule deer populations, however, we found considerable variation in both localities suggesting a patchy landscape. More information regarding forage nutritional status and diet preferences can enhance our understanding on mule deer population dynamics in the Chihuahuan Desert.
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