The Experts below are selected from a list of 294 Experts worldwide ranked by ideXlab platform
You-liang Zheng - One of the best experts on this subject based on the ideXlab platform.
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The impact of single nucleotide polymorphism in monomeric Alpha-Amylase Inhibitor genes from wild emmer wheat, primarily from Israel and Golan
BMC evolutionary biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Background Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection.
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the impact of single nucleotide polymorphism in monomeric Alpha Amylase Inhibitor genes from wild emmer wheat primarily from israel and golan
BMC Evolutionary Biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection. Three hundred and forty-eight sequences encoding monomeric Alpha-Amylase Inhibitors (WMAI) were obtained from 14 populations of wild emmer wheat. The frequency of SNPs in WMAI genes was 1 out of 16.3 bases, where 28 SNPs were detected in the coding sequence. The results of purifying and the positive selection hypothesis (p < 0.05) showed that the sequences of WMAI were contributed by both natural selection and co-evolution, which ensured conservation of protein function and inhibition against diverse insect Amylases. The majority of amino acid substitutions occurred at the C-terminal (positive selection domain), which ensured the stability of WMAI. SNPs in this gene could be classified into several categories associated with water, temperature, and geographic factors, respectively. Great diversity at the WMAI locus, both between and within populations, was detected in the populations of wild emmer wheat. It was revealed that WMAI were naturally selected for across populations by a ratio of dN/dS as expected. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. A sharp genetic divergence over very short geographic distances compared to a small genetic divergence between large geographic distances also suggested that the SNPs were subjected to natural selection, and ecological factors had an important evolutionary role in polymorphisms at this locus. According to population and codon analysis, these results suggested that monomeric Alpha-Amylase Inhibitors are adaptively selected under different environmental conditions.
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Sequence variations and haplotype identification of wheat dimeric Alpha-Amylase Inhibitor genes in einkorn wheats.
Biochemical genetics, 2007Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:This study characterizes 80 dimeric Alpha-Amylase Inhibitor genes from 68 accessions of the einkorn wheats Triticum urartu, T. boeoticum, and T. monococcum. The mature protein coding sequences of WDAI genes were analyzed. Nucleotide sequence variations in these regions resulted from base substitution and/or indel mutations. Most of the WDAI gene sequences from T. boeoticum and all sequences from T. monococcum had one nucleotide insertion in the coding region, such that these Alpha-Amylase Inhibitor sequences could not encode the correct mature proteins. We identified 21 distinct haplotypes from the diploid wheat WDAI gene sequences. A main haplotype was found in 15 gene samples from the A(u) genome and 35 gene samples from the A(m) genome. The T. monococcum and T. boeoticum accessions shared the same main haplotype, with 25 samples from T. monococcum and 10 from T. boeoticum. The WDAI gene sequences from the A(u) and A(m) genomes could be obviously clustered into two clades, but the sequences from the A(m) genome of T. boeoticum and T. monococcum could not be clearly distinguished. The phylogenetic analysis revealed that the WDAI gene sequences from the A(m) genome had accumulated fewer variations and evolved at a slower rate than the sequences from the A(u) genome. Although some accessions from only one or two areas had unique mutations at the same position, the diversity of WDAI gene sequences in diploid wheat showed little relationship to the origin of the accessions.
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Molecular characterization of dimeric Alpha-Amylase Inhibitor genes in wheat and development of genome allele-specific primers for the genes located on chromosome 3BS and 3DS
Journal of Cereal Science, 2006Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Eviatar Nevo, Bernard R. Baum, You-liang ZhengAbstract:Alpha-Amylase Inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as an energy source. For weevil control, Alpha-Amylase Inhibitors and their genes could be used to genetically engineer weevil resistant seeds. Thirty genes encoding dimeric Alpha-Amylase Inhibitors were isolated from Triticum aestivum L. 'Chinese Spring' and characterized by nucleotide and amino acid sequence analysis. Eleven representative Alpha-Amylase Inhibitor genes were identified, and the deduced amino acid sequences of these genes were of high coherence (95.1%). These Inhibitors and others obtained from the wheat EST database were clustered into three groups, the genes from 'Chinese Spring' were present in each group. Specific primer sets were designed for each group, based on the SNPs of these genes, and the chromosome locations of each group of Inhibitor genes investigated by amplification of the 'Chinese Spring' ditelosomic lines. There were two and one groups of Inhibitor genes on chromosomes 3BS and 3DS, respectively, whereas no group of Inhibitor genes was found on chromosome 3AS. Thus, the primer set for each group of Inhibitor genes was genome allele-specific. The two known Inhibitors, 0.53 and 0.19, were located on chromosomes 3BS and 3DS, respectively. The validity of the three genome allele-specific primer sets was confirmed by amplifications in 15 accessions of Triticum urartu, Triticum monococcum, Aegilops tauschii and Triticum dicoccoides. These results gave further support at the molecular level, that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat are encoded by a multigene family.
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Detection of single nucleotide polymorphisms in 24 kDa dimeric Alpha-Amylase Inhibitors from cultivated wheat and its diploid putative progenitors.
Biochimica et biophysica acta, 2005Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:Seventeen new genes encoding 24 kDa family dimeric Alpha-Amylase Inhibitors had been characterized from cultivated wheat and its diploid putative progenitors. And the different Alpha-Amylase Inhibitors in this family, which were determined by coding regions single nucleotide polymorphisms (cSNPs) of their genes, were investigated. The amino acid sequences of 24 kDa Alpha-Amylase Inhibitors shared very high coherence (91.2%). It indicated that the dimeric Alpha-Amylase Inhibitors in the 24 kDa family were derived from common ancestral genes by phylogenetic analysis. Eight Alpha-Amylase Inhibitor genes were characterized from one hexaploid wheat variety, and clustered into four subgroups, indicating that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat were encoded by multi-gene. Forty-five cSNPs, including 35 transitions and 10 transversions, were found, and resulted in a total of ten amino acid changes. The cSNPs at the first site of a codon cause much more nonsynonymous (92.9%) than synonymous mutations, while nonsynonymous and synonymous mutations were almost equal when the cSNPs were at the third site. It was observed that there was Ile105 instead of Val105 at the active region Val104-Val105-Asp106-Ala107 of the Alpha-Amylase Inhibitor by cSNPs in some Inhibitors from Aegilops speltoides, diploid and hexaploid wheats.
Ji-rui Wang - One of the best experts on this subject based on the ideXlab platform.
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The impact of single nucleotide polymorphism in monomeric Alpha-Amylase Inhibitor genes from wild emmer wheat, primarily from Israel and Golan
BMC evolutionary biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Background Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection.
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the impact of single nucleotide polymorphism in monomeric Alpha Amylase Inhibitor genes from wild emmer wheat primarily from israel and golan
BMC Evolutionary Biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection. Three hundred and forty-eight sequences encoding monomeric Alpha-Amylase Inhibitors (WMAI) were obtained from 14 populations of wild emmer wheat. The frequency of SNPs in WMAI genes was 1 out of 16.3 bases, where 28 SNPs were detected in the coding sequence. The results of purifying and the positive selection hypothesis (p < 0.05) showed that the sequences of WMAI were contributed by both natural selection and co-evolution, which ensured conservation of protein function and inhibition against diverse insect Amylases. The majority of amino acid substitutions occurred at the C-terminal (positive selection domain), which ensured the stability of WMAI. SNPs in this gene could be classified into several categories associated with water, temperature, and geographic factors, respectively. Great diversity at the WMAI locus, both between and within populations, was detected in the populations of wild emmer wheat. It was revealed that WMAI were naturally selected for across populations by a ratio of dN/dS as expected. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. A sharp genetic divergence over very short geographic distances compared to a small genetic divergence between large geographic distances also suggested that the SNPs were subjected to natural selection, and ecological factors had an important evolutionary role in polymorphisms at this locus. According to population and codon analysis, these results suggested that monomeric Alpha-Amylase Inhibitors are adaptively selected under different environmental conditions.
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Sequence variations and haplotype identification of wheat dimeric Alpha-Amylase Inhibitor genes in einkorn wheats.
Biochemical genetics, 2007Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:This study characterizes 80 dimeric Alpha-Amylase Inhibitor genes from 68 accessions of the einkorn wheats Triticum urartu, T. boeoticum, and T. monococcum. The mature protein coding sequences of WDAI genes were analyzed. Nucleotide sequence variations in these regions resulted from base substitution and/or indel mutations. Most of the WDAI gene sequences from T. boeoticum and all sequences from T. monococcum had one nucleotide insertion in the coding region, such that these Alpha-Amylase Inhibitor sequences could not encode the correct mature proteins. We identified 21 distinct haplotypes from the diploid wheat WDAI gene sequences. A main haplotype was found in 15 gene samples from the A(u) genome and 35 gene samples from the A(m) genome. The T. monococcum and T. boeoticum accessions shared the same main haplotype, with 25 samples from T. monococcum and 10 from T. boeoticum. The WDAI gene sequences from the A(u) and A(m) genomes could be obviously clustered into two clades, but the sequences from the A(m) genome of T. boeoticum and T. monococcum could not be clearly distinguished. The phylogenetic analysis revealed that the WDAI gene sequences from the A(m) genome had accumulated fewer variations and evolved at a slower rate than the sequences from the A(u) genome. Although some accessions from only one or two areas had unique mutations at the same position, the diversity of WDAI gene sequences in diploid wheat showed little relationship to the origin of the accessions.
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Molecular characterization of dimeric Alpha-Amylase Inhibitor genes in wheat and development of genome allele-specific primers for the genes located on chromosome 3BS and 3DS
Journal of Cereal Science, 2006Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Eviatar Nevo, Bernard R. Baum, You-liang ZhengAbstract:Alpha-Amylase Inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as an energy source. For weevil control, Alpha-Amylase Inhibitors and their genes could be used to genetically engineer weevil resistant seeds. Thirty genes encoding dimeric Alpha-Amylase Inhibitors were isolated from Triticum aestivum L. 'Chinese Spring' and characterized by nucleotide and amino acid sequence analysis. Eleven representative Alpha-Amylase Inhibitor genes were identified, and the deduced amino acid sequences of these genes were of high coherence (95.1%). These Inhibitors and others obtained from the wheat EST database were clustered into three groups, the genes from 'Chinese Spring' were present in each group. Specific primer sets were designed for each group, based on the SNPs of these genes, and the chromosome locations of each group of Inhibitor genes investigated by amplification of the 'Chinese Spring' ditelosomic lines. There were two and one groups of Inhibitor genes on chromosomes 3BS and 3DS, respectively, whereas no group of Inhibitor genes was found on chromosome 3AS. Thus, the primer set for each group of Inhibitor genes was genome allele-specific. The two known Inhibitors, 0.53 and 0.19, were located on chromosomes 3BS and 3DS, respectively. The validity of the three genome allele-specific primer sets was confirmed by amplifications in 15 accessions of Triticum urartu, Triticum monococcum, Aegilops tauschii and Triticum dicoccoides. These results gave further support at the molecular level, that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat are encoded by a multigene family.
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Detection of single nucleotide polymorphisms in 24 kDa dimeric Alpha-Amylase Inhibitors from cultivated wheat and its diploid putative progenitors.
Biochimica et biophysica acta, 2005Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:Seventeen new genes encoding 24 kDa family dimeric Alpha-Amylase Inhibitors had been characterized from cultivated wheat and its diploid putative progenitors. And the different Alpha-Amylase Inhibitors in this family, which were determined by coding regions single nucleotide polymorphisms (cSNPs) of their genes, were investigated. The amino acid sequences of 24 kDa Alpha-Amylase Inhibitors shared very high coherence (91.2%). It indicated that the dimeric Alpha-Amylase Inhibitors in the 24 kDa family were derived from common ancestral genes by phylogenetic analysis. Eight Alpha-Amylase Inhibitor genes were characterized from one hexaploid wheat variety, and clustered into four subgroups, indicating that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat were encoded by multi-gene. Forty-five cSNPs, including 35 transitions and 10 transversions, were found, and resulted in a total of ten amino acid changes. The cSNPs at the first site of a codon cause much more nonsynonymous (92.9%) than synonymous mutations, while nonsynonymous and synonymous mutations were almost equal when the cSNPs were at the third site. It was observed that there was Ile105 instead of Val105 at the active region Val104-Val105-Asp106-Ala107 of the Alpha-Amylase Inhibitor by cSNPs in some Inhibitors from Aegilops speltoides, diploid and hexaploid wheats.
Jay K Udani - One of the best experts on this subject based on the ideXlab platform.
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Systematic Review and Meta-Analysis of a Proprietary Alpha-Amylase Inhibitor from White Bean (Phaseolus vulgaris L.) on Weight and Fat Loss in Humans.
Foods (Basel Switzerland), 2018Co-Authors: Jay K Udani, Ollie Tan, Jhanna Pamela L MolinaAbstract:The aim of this meta-analysis was to examine the evidence for the effectiveness of a proprietary Alpha-Amylase Inhibitor from white bean (Phaseolus vulgaris L.) supplementation interventions in humans on modification of body weight and fat mass. A systematic literature search was performed using three databases: PubMed, the Cochrane collaboration, and Google Scholar. In addition, the manufacturer was contacted for internal unpublished data, and finally, the reference section of relevant original research and review papers were mined for additional studies. Eleven studies were selected for the meta-analysis of weight loss (a total of 573 subjects), and three studies for the meta-analysis of body fat reduction (a total of 110 subjects), as they fulfilled the inclusion criteria. Phaseolus vulgaris supplementation showed an average effect on weight loss difference of −1.08 kg (95% CI (confidence interval), −0.42 kg to −1.16 kg, p < 0.00001), and the average effect on body fat reduction was 3.26 kg (95% CI, −2.35 kg to −4.163 kg, p = 0.02). This meta-analysis found statistically significant effects of Phaseolus vulgaris supplementation on body weight and body fat.
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a proprietary Alpha Amylase Inhibitor from white bean phaseolus vulgaris a review of clinical studies on weight loss and glycemic control
Nutrition Journal, 2011Co-Authors: Marilyn L Barrett, Jay K UdaniAbstract:Obesity, and resultant health hazards which include diabetes, cardiovascular disease and metabolic syndrome, are worldwide medical problems. Control of diet and exercise are cornerstones of the management of excess weight. Foods with a low glycemic index may reduce the risk of diabetes and heart disease as well as their complications. As an alternative to a low glycemic index diet, there is a growing body of research into products that slow the absorption of carbohydrates through the inhibition of enzymes responsible for their digestion. These products include Alpha-Amylase and glucosidase Inhibitors. The common white bean (Phaseolus vulgaris) produces an Alpha-Amylase Inhibitor, which has been characterized and tested in numerous clinical studies. A specific and proprietary product named Phase 2® Carb Controller (Pharmachem Laboratories, Kearny, NJ) has demonstrated the ability to cause weight loss with doses of 500 to 3000 mg per day, in either a single dose or in divided doses. Clinical studies also show that Phase 2 has the ability to reduce the post-prandial spike in blood glucose levels. Experiments conducted incorporating Phase 2 into food and beverage products have found that it can be integrated into various products without losing activity or altering the appearance, texture or taste of the food. There have been no serious side effects reported following consumption of Phase 2. Gastro-intestinal side effects are rare and diminish upon extended use of the product. In summary, Phase 2 has the potential to induce weight loss and reduce spikes in blood sugar caused by carbohydrates through its Alpha-Amylase inhibiting activity.
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a proprietary Alpha Amylase Inhibitor from white bean phaseolus vulgaris a review of clinical studies on weight loss and glycemic control
Nutrition Journal, 2011Co-Authors: Marilyn L Barrett, Jay K UdaniAbstract:Obesity, and resultant health hazards which include diabetes, cardiovascular disease and metabolic syndrome, are worldwide medical problems. Control of diet and exercise are cornerstones of the management of excess weight. Foods with a low glycemic index may reduce the risk of diabetes and heart disease as well as their complications. As an alternative to a low glycemic index diet, there is a growing body of research into products that slow the absorption of carbohydrates through the inhibition of enzymes responsible for their digestion. These products include Alpha-Amylase and glucosidase Inhibitors. The common white bean (Phaseolus vulgaris) produces an Alpha-Amylase Inhibitor, which has been characterized and tested in numerous clinical studies. A specific and proprietary product named Phase 2® Carb Controller (Pharmachem Laboratories, Kearny, NJ) has demonstrated the ability to cause weight loss with doses of 500 to 3000 mg per day, in either a single dose or in divided doses. Clinical studies also show that Phase 2 has the ability to reduce the post-prandial spike in blood glucose levels. Experiments conducted incorporating Phase 2 into food and beverage products have found that it can be integrated into various products without losing activity or altering the appearance, texture or taste of the food. There have been no serious side effects reported following consumption of Phase 2. Gastro-intestinal side effects are rare and diminish upon extended use of the product. In summary, Phase 2 has the potential to induce weight loss and reduce spikes in blood sugar caused by carbohydrates through its Alpha-Amylase inhibiting activity.
Ze-hong Yan - One of the best experts on this subject based on the ideXlab platform.
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The impact of single nucleotide polymorphism in monomeric Alpha-Amylase Inhibitor genes from wild emmer wheat, primarily from Israel and Golan
BMC evolutionary biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Background Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection.
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the impact of single nucleotide polymorphism in monomeric Alpha Amylase Inhibitor genes from wild emmer wheat primarily from israel and golan
BMC Evolutionary Biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection. Three hundred and forty-eight sequences encoding monomeric Alpha-Amylase Inhibitors (WMAI) were obtained from 14 populations of wild emmer wheat. The frequency of SNPs in WMAI genes was 1 out of 16.3 bases, where 28 SNPs were detected in the coding sequence. The results of purifying and the positive selection hypothesis (p < 0.05) showed that the sequences of WMAI were contributed by both natural selection and co-evolution, which ensured conservation of protein function and inhibition against diverse insect Amylases. The majority of amino acid substitutions occurred at the C-terminal (positive selection domain), which ensured the stability of WMAI. SNPs in this gene could be classified into several categories associated with water, temperature, and geographic factors, respectively. Great diversity at the WMAI locus, both between and within populations, was detected in the populations of wild emmer wheat. It was revealed that WMAI were naturally selected for across populations by a ratio of dN/dS as expected. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. A sharp genetic divergence over very short geographic distances compared to a small genetic divergence between large geographic distances also suggested that the SNPs were subjected to natural selection, and ecological factors had an important evolutionary role in polymorphisms at this locus. According to population and codon analysis, these results suggested that monomeric Alpha-Amylase Inhibitors are adaptively selected under different environmental conditions.
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Sequence variations and haplotype identification of wheat dimeric Alpha-Amylase Inhibitor genes in einkorn wheats.
Biochemical genetics, 2007Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:This study characterizes 80 dimeric Alpha-Amylase Inhibitor genes from 68 accessions of the einkorn wheats Triticum urartu, T. boeoticum, and T. monococcum. The mature protein coding sequences of WDAI genes were analyzed. Nucleotide sequence variations in these regions resulted from base substitution and/or indel mutations. Most of the WDAI gene sequences from T. boeoticum and all sequences from T. monococcum had one nucleotide insertion in the coding region, such that these Alpha-Amylase Inhibitor sequences could not encode the correct mature proteins. We identified 21 distinct haplotypes from the diploid wheat WDAI gene sequences. A main haplotype was found in 15 gene samples from the A(u) genome and 35 gene samples from the A(m) genome. The T. monococcum and T. boeoticum accessions shared the same main haplotype, with 25 samples from T. monococcum and 10 from T. boeoticum. The WDAI gene sequences from the A(u) and A(m) genomes could be obviously clustered into two clades, but the sequences from the A(m) genome of T. boeoticum and T. monococcum could not be clearly distinguished. The phylogenetic analysis revealed that the WDAI gene sequences from the A(m) genome had accumulated fewer variations and evolved at a slower rate than the sequences from the A(u) genome. Although some accessions from only one or two areas had unique mutations at the same position, the diversity of WDAI gene sequences in diploid wheat showed little relationship to the origin of the accessions.
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Molecular characterization of dimeric Alpha-Amylase Inhibitor genes in wheat and development of genome allele-specific primers for the genes located on chromosome 3BS and 3DS
Journal of Cereal Science, 2006Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Eviatar Nevo, Bernard R. Baum, You-liang ZhengAbstract:Alpha-Amylase Inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as an energy source. For weevil control, Alpha-Amylase Inhibitors and their genes could be used to genetically engineer weevil resistant seeds. Thirty genes encoding dimeric Alpha-Amylase Inhibitors were isolated from Triticum aestivum L. 'Chinese Spring' and characterized by nucleotide and amino acid sequence analysis. Eleven representative Alpha-Amylase Inhibitor genes were identified, and the deduced amino acid sequences of these genes were of high coherence (95.1%). These Inhibitors and others obtained from the wheat EST database were clustered into three groups, the genes from 'Chinese Spring' were present in each group. Specific primer sets were designed for each group, based on the SNPs of these genes, and the chromosome locations of each group of Inhibitor genes investigated by amplification of the 'Chinese Spring' ditelosomic lines. There were two and one groups of Inhibitor genes on chromosomes 3BS and 3DS, respectively, whereas no group of Inhibitor genes was found on chromosome 3AS. Thus, the primer set for each group of Inhibitor genes was genome allele-specific. The two known Inhibitors, 0.53 and 0.19, were located on chromosomes 3BS and 3DS, respectively. The validity of the three genome allele-specific primer sets was confirmed by amplifications in 15 accessions of Triticum urartu, Triticum monococcum, Aegilops tauschii and Triticum dicoccoides. These results gave further support at the molecular level, that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat are encoded by a multigene family.
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Detection of single nucleotide polymorphisms in 24 kDa dimeric Alpha-Amylase Inhibitors from cultivated wheat and its diploid putative progenitors.
Biochimica et biophysica acta, 2005Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:Seventeen new genes encoding 24 kDa family dimeric Alpha-Amylase Inhibitors had been characterized from cultivated wheat and its diploid putative progenitors. And the different Alpha-Amylase Inhibitors in this family, which were determined by coding regions single nucleotide polymorphisms (cSNPs) of their genes, were investigated. The amino acid sequences of 24 kDa Alpha-Amylase Inhibitors shared very high coherence (91.2%). It indicated that the dimeric Alpha-Amylase Inhibitors in the 24 kDa family were derived from common ancestral genes by phylogenetic analysis. Eight Alpha-Amylase Inhibitor genes were characterized from one hexaploid wheat variety, and clustered into four subgroups, indicating that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat were encoded by multi-gene. Forty-five cSNPs, including 35 transitions and 10 transversions, were found, and resulted in a total of ten amino acid changes. The cSNPs at the first site of a codon cause much more nonsynonymous (92.9%) than synonymous mutations, while nonsynonymous and synonymous mutations were almost equal when the cSNPs were at the third site. It was observed that there was Ile105 instead of Val105 at the active region Val104-Val105-Asp106-Ala107 of the Alpha-Amylase Inhibitor by cSNPs in some Inhibitors from Aegilops speltoides, diploid and hexaploid wheats.
Yu-ming Wei - One of the best experts on this subject based on the ideXlab platform.
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The impact of single nucleotide polymorphism in monomeric Alpha-Amylase Inhibitor genes from wild emmer wheat, primarily from Israel and Golan
BMC evolutionary biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Background Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection.
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the impact of single nucleotide polymorphism in monomeric Alpha Amylase Inhibitor genes from wild emmer wheat primarily from israel and golan
BMC Evolutionary Biology, 2010Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Mei Deng, Eviatar Nevo, You-liang ZhengAbstract:Various enzyme Inhibitors act on key insect gut digestive hydrolases, including Alpha-Amylases and proteinases. Alpha-Amylase Inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric Alpha-Amylase Inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection. Three hundred and forty-eight sequences encoding monomeric Alpha-Amylase Inhibitors (WMAI) were obtained from 14 populations of wild emmer wheat. The frequency of SNPs in WMAI genes was 1 out of 16.3 bases, where 28 SNPs were detected in the coding sequence. The results of purifying and the positive selection hypothesis (p < 0.05) showed that the sequences of WMAI were contributed by both natural selection and co-evolution, which ensured conservation of protein function and inhibition against diverse insect Amylases. The majority of amino acid substitutions occurred at the C-terminal (positive selection domain), which ensured the stability of WMAI. SNPs in this gene could be classified into several categories associated with water, temperature, and geographic factors, respectively. Great diversity at the WMAI locus, both between and within populations, was detected in the populations of wild emmer wheat. It was revealed that WMAI were naturally selected for across populations by a ratio of dN/dS as expected. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. A sharp genetic divergence over very short geographic distances compared to a small genetic divergence between large geographic distances also suggested that the SNPs were subjected to natural selection, and ecological factors had an important evolutionary role in polymorphisms at this locus. According to population and codon analysis, these results suggested that monomeric Alpha-Amylase Inhibitors are adaptively selected under different environmental conditions.
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Sequence variations and haplotype identification of wheat dimeric Alpha-Amylase Inhibitor genes in einkorn wheats.
Biochemical genetics, 2007Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:This study characterizes 80 dimeric Alpha-Amylase Inhibitor genes from 68 accessions of the einkorn wheats Triticum urartu, T. boeoticum, and T. monococcum. The mature protein coding sequences of WDAI genes were analyzed. Nucleotide sequence variations in these regions resulted from base substitution and/or indel mutations. Most of the WDAI gene sequences from T. boeoticum and all sequences from T. monococcum had one nucleotide insertion in the coding region, such that these Alpha-Amylase Inhibitor sequences could not encode the correct mature proteins. We identified 21 distinct haplotypes from the diploid wheat WDAI gene sequences. A main haplotype was found in 15 gene samples from the A(u) genome and 35 gene samples from the A(m) genome. The T. monococcum and T. boeoticum accessions shared the same main haplotype, with 25 samples from T. monococcum and 10 from T. boeoticum. The WDAI gene sequences from the A(u) and A(m) genomes could be obviously clustered into two clades, but the sequences from the A(m) genome of T. boeoticum and T. monococcum could not be clearly distinguished. The phylogenetic analysis revealed that the WDAI gene sequences from the A(m) genome had accumulated fewer variations and evolved at a slower rate than the sequences from the A(u) genome. Although some accessions from only one or two areas had unique mutations at the same position, the diversity of WDAI gene sequences in diploid wheat showed little relationship to the origin of the accessions.
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Molecular characterization of dimeric Alpha-Amylase Inhibitor genes in wheat and development of genome allele-specific primers for the genes located on chromosome 3BS and 3DS
Journal of Cereal Science, 2006Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, Eviatar Nevo, Bernard R. Baum, You-liang ZhengAbstract:Alpha-Amylase Inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as an energy source. For weevil control, Alpha-Amylase Inhibitors and their genes could be used to genetically engineer weevil resistant seeds. Thirty genes encoding dimeric Alpha-Amylase Inhibitors were isolated from Triticum aestivum L. 'Chinese Spring' and characterized by nucleotide and amino acid sequence analysis. Eleven representative Alpha-Amylase Inhibitor genes were identified, and the deduced amino acid sequences of these genes were of high coherence (95.1%). These Inhibitors and others obtained from the wheat EST database were clustered into three groups, the genes from 'Chinese Spring' were present in each group. Specific primer sets were designed for each group, based on the SNPs of these genes, and the chromosome locations of each group of Inhibitor genes investigated by amplification of the 'Chinese Spring' ditelosomic lines. There were two and one groups of Inhibitor genes on chromosomes 3BS and 3DS, respectively, whereas no group of Inhibitor genes was found on chromosome 3AS. Thus, the primer set for each group of Inhibitor genes was genome allele-specific. The two known Inhibitors, 0.53 and 0.19, were located on chromosomes 3BS and 3DS, respectively. The validity of the three genome allele-specific primer sets was confirmed by amplifications in 15 accessions of Triticum urartu, Triticum monococcum, Aegilops tauschii and Triticum dicoccoides. These results gave further support at the molecular level, that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat are encoded by a multigene family.
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Detection of single nucleotide polymorphisms in 24 kDa dimeric Alpha-Amylase Inhibitors from cultivated wheat and its diploid putative progenitors.
Biochimica et biophysica acta, 2005Co-Authors: Ji-rui Wang, Yu-ming Wei, Ze-hong Yan, You-liang ZhengAbstract:Seventeen new genes encoding 24 kDa family dimeric Alpha-Amylase Inhibitors had been characterized from cultivated wheat and its diploid putative progenitors. And the different Alpha-Amylase Inhibitors in this family, which were determined by coding regions single nucleotide polymorphisms (cSNPs) of their genes, were investigated. The amino acid sequences of 24 kDa Alpha-Amylase Inhibitors shared very high coherence (91.2%). It indicated that the dimeric Alpha-Amylase Inhibitors in the 24 kDa family were derived from common ancestral genes by phylogenetic analysis. Eight Alpha-Amylase Inhibitor genes were characterized from one hexaploid wheat variety, and clustered into four subgroups, indicating that the 24 kDa dimeric Alpha-Amylase Inhibitors in cultivated wheat were encoded by multi-gene. Forty-five cSNPs, including 35 transitions and 10 transversions, were found, and resulted in a total of ten amino acid changes. The cSNPs at the first site of a codon cause much more nonsynonymous (92.9%) than synonymous mutations, while nonsynonymous and synonymous mutations were almost equal when the cSNPs were at the third site. It was observed that there was Ile105 instead of Val105 at the active region Val104-Val105-Asp106-Ala107 of the Alpha-Amylase Inhibitor by cSNPs in some Inhibitors from Aegilops speltoides, diploid and hexaploid wheats.