PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene ...PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene was successfully cloned from the Vibrio alginolyticus HY9901 strain.A comprehensive analysis of the cloned gene was conducted using bioinformatics.Sequence analysis revealed that the total length of the phoR gene(GenBank accession No.:KJ958404.1)is 1299 bp,with the coding region containing a total of 432 amino acid residues.The phylogenetic tree of PhoR revealed that it belongs to the same subclade as V.diabolicus.The SMART program was employed for the purpose of functional domain prediction,which revealed that PhoR possesses three major functional domains:PAS(amino acids 98-166),HisKA(amino acids 205-272),and HATPase_c(amino acids 317-429).展开更多
Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indic...Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indicated that the total length of the sodB gene was 585 bp and that it could encode 194 amino acids.The predicted amino acid sequence derivation indicated that the molecular weight of the protein was approximately 21.56 kDa,with an isoelectric point of 4.95.Upon prediction of the N-terminal signal peptide structure of the protein,no significant signal peptide cleavage site was observed,indicating that the protein lacked both a signal peptide and a transmembrane region.The amino acid sequence contained an N-glycosylation site,a casein kinase II phosphorylation site,a microsomal C-terminal target signal site,and a manganese and iron superoxide dismutase signal site.The probability of intracytoplasmic localization of the SodB protein was 56.5%,which was analyzed according to the subcellular localization of the protein.The amino acid sequence of the sodB gene of V.alginolyticus exhibited 98%-100%homology to other Vibrio species,clustering into the same subfamily with V.parahaem,indicating a relatively close relationship between them.In the prediction of protein structure,the proportions ofα-helix,random coil,β-sheet,and extended strand were 48.45%,30.41%,5.67%,and 15.46%,respectively.The similarity to template 1dt0.1.A reached 71.58%.A PTM site analysis revealed the presence of phosphorylation,glycosylation,ubiquitination,sumoylation,acetylation,and methylation modification sites,as well as the absence of lactylation modification sites.展开更多
Over the last two decades, food allergens are being recognized as one of the food hazards. This serious food safety issue is being addressed in different countries not only in terms of their biological and clinical ch...Over the last two decades, food allergens are being recognized as one of the food hazards. This serious food safety issue is being addressed in different countries not only in terms of their biological and clinical characteristics, but also in terms of various standards of allergen management in food industries. This abnormal immune response caused by food allergens affects the quality of life especially in children and influences their overall health and retards normal growth, along with they suffer from ailments like eating disorders, depression, sometimes even death which is the most adverse impact of food allergy. Every country has their own set of guidelines to deal with the food allergens especially developed countries, food allergen guidelines is not well documented in developing countries. FAO/WHO is providing assistance to developing countries in strengthening their food safety guidelines. The Codex Alimentarius was formulated by the two organizations FAO/WHO in the year 1960; it is a collection of food standards in a integrated, codified style, together with associated material such as codes of hygiene and good manufacturing practices that should be followed by industries during various production stages of a food item. In both developed and developing nations, the Food Chemical Codex or the Codex Alimentarius aims to protect public health and implement fair trade practises for the trading of food items.展开更多
Molecular microbiological methods, such as competetive PCR, real-time PCR, denaturing gradient gel electrophoresis (DGGE) and large-scale parallel-pyrosequencing, require the extraction of sufficient quantity of high ...Molecular microbiological methods, such as competetive PCR, real-time PCR, denaturing gradient gel electrophoresis (DGGE) and large-scale parallel-pyrosequencing, require the extraction of sufficient quantity of high quality DNA from microbiologically and chemically complex matrices. Due to difficulties in the field to standardize/select the optimum DNA preservation-extraction methods in view of laboratories differences, this article attempts to present a straight-forward mathematical framework for comparing some of the most commonly used methods. To this end, as a case study, the problem of selecting an optimum sample preservation-DNA extraction strategy for obtaining total bacterial DNA from swine feces was considered. Two sample preservation methods (liquid nitrogen and RNAlater?) and seven extraction techniques were paired and compared under six quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A260/280 and A 260/230 ratios), duration of extraction, degradation degree of DNA, and cost. From a practical point of view, it is unlikely that a single sample preservation-DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic multi-criteria decision-making (MCDM) approach was used to compare the methods. As a result, the ZR Fecal DNA MiniPrepTM DNA extraction kit for samples preserved either with liquid nitrogen or RNAlater? were identified as potential optimum solutions for obtaining total bacterial DNA from swine feces. Considering the need for practicality for in situ applications, we would recommend liquid nitrogen as sample preservation method, along with the ZR Fecal DNA MiniPrepTM kit. Total bacterial DNA obtained by this strategy can be suitable for downstream PCR-based DNA analyses of swine feces.展开更多
There is an increased interest in the extraction of nucleic acids from various environmental samples since culture-independent molecular techniques contribute to deepen and broaden the understanding of a greater porti...There is an increased interest in the extraction of nucleic acids from various environmental samples since culture-independent molecular techniques contribute to deepen and broaden the understanding of a greater portion of uncultivable microorganisms. Due to difficulties to select the optimum DNA extraction method in view of downstream molecular analyses, this article presents a straightforward mathematical framework for comparing some of the most commonly used methods. Four commercial DNA extraction kits and two physical-chemical methods (bead-beating and freeze-thaw) were compared for the extraction of DNA under several quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A260/280 and A260/230 ratios), degradation degree of DNA, easiness of PCR amplification, duration of extraction, and cost per extraction. From a practical point of view, it is unlikely that a single DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) was employed to compare the methods. The PowerSoil? DNA Isolation Kit was systematically defined as the best performing method for extracting DNA from soil samples. More specifically, for soil:manure and soil:manure:biochar mixtures, the PowerSoil?DNA Isolation Kit method performed best, while for neat soil samples its alternative version gained the first rank.展开更多
Due to the increased demand for ready-to-eat(RTE)minimally processed foods,alternatives to chemical and thermal preservation methods to maintain food safety are highly demanded.A significant safety hazard in RTE food ...Due to the increased demand for ready-to-eat(RTE)minimally processed foods,alternatives to chemical and thermal preservation methods to maintain food safety are highly demanded.A significant safety hazard in RTE food products is the growth of the foodborne pathogen Listeria monocytogenes(L.monocytogenes).After processing,recontamination or cross-contamination of L.monocytogenes in RTE food products may occur and the lack of cooking can lead to an increased risk of listeriosis.Further,some RTE food products(e.g.cheese and cured meat)can have a long processing period and shelf life,thus allowing for the growth and proliferation of L.monocytogenes in the food matrix.Lactic acid bacteria(LAB)are generally recognized as safe probiotics and have been proposed as a biological control approach to eliminate foodborne pathogens including L.monocytogenes.LAB have been reported to extend the shelf life of food products and inhibit pathogen proliferation via growth competition and metabolite production.LAB are native microflora of many RTE foods,but only certain LAB may inhibit pathogen growth.Therefore,the specificity of LAB species should be employed in their use in RTE foods.This review will discuss the antimicrobial mechanisms of LAB against L.monocytogenes,selective use of LAB in food matrices,and their uses in food processing and packaging.展开更多
Riparian buffers,located in the transition zone between terrestrial and aquatic ecosystems,are a hotspot for nitrogen(N)removal through denitrification.Earthworms are abundant in riparian buffers and may enhance denit...Riparian buffers,located in the transition zone between terrestrial and aquatic ecosystems,are a hotspot for nitrogen(N)removal through denitrification.Earthworms are abundant in riparian buffers and may enhance denitrification.This study investigated earthworm demographics of three earthworm functional groups(anecic,epigeic,and endogeic)and denitrifier activity in temporarily flooded and non-flooded riparian soils from April to October 2012 in southern Quebec,Canada.Nine earthworm species,mostly endogeic,were found in the temporarily flooded soil,while only six earthworm species were found in the non-flooded soil.On average,there were 11.7 times more earthworms with 12.4 times greater biomass(P<0.05)found in the temporarily flooded soil than in the non-flooded soil.The denitrification enzyme activity(DEA)was of similar magnitude in temporarily flooded and non-flooded soils,with temporal variation associated with rainfall patterns.Endogeic earthworm biomass was positively correlated(P<0.05)with DEA,while epigeic earthworm biomass was positively correlated(P<0.05)with 16S rRNA gene copies and nosZ gene copies from bacteria,indicating an association between earthworm functional groups and denitrifier activity in riparian soils.Stepwise multiple regressions showed that DEA in riparian soils could be predicted using soil moisture,inorganic N concentration,and earthworm functional groups,suggesting that endogeic and epigeic earthworms contributed to denitrifier activity in riparian soils.展开更多
基金Supported by Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean UniversityNational Natural Science Foundation of China(32073015)+1 种基金Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802)Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007).
文摘PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene was successfully cloned from the Vibrio alginolyticus HY9901 strain.A comprehensive analysis of the cloned gene was conducted using bioinformatics.Sequence analysis revealed that the total length of the phoR gene(GenBank accession No.:KJ958404.1)is 1299 bp,with the coding region containing a total of 432 amino acid residues.The phylogenetic tree of PhoR revealed that it belongs to the same subclade as V.diabolicus.The SMART program was employed for the purpose of functional domain prediction,which revealed that PhoR possesses three major functional domains:PAS(amino acids 98-166),HisKA(amino acids 205-272),and HATPase_c(amino acids 317-429).
基金Supported by Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean UniversityNational Natural Science Foundation of China(32073015)+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indicated that the total length of the sodB gene was 585 bp and that it could encode 194 amino acids.The predicted amino acid sequence derivation indicated that the molecular weight of the protein was approximately 21.56 kDa,with an isoelectric point of 4.95.Upon prediction of the N-terminal signal peptide structure of the protein,no significant signal peptide cleavage site was observed,indicating that the protein lacked both a signal peptide and a transmembrane region.The amino acid sequence contained an N-glycosylation site,a casein kinase II phosphorylation site,a microsomal C-terminal target signal site,and a manganese and iron superoxide dismutase signal site.The probability of intracytoplasmic localization of the SodB protein was 56.5%,which was analyzed according to the subcellular localization of the protein.The amino acid sequence of the sodB gene of V.alginolyticus exhibited 98%-100%homology to other Vibrio species,clustering into the same subfamily with V.parahaem,indicating a relatively close relationship between them.In the prediction of protein structure,the proportions ofα-helix,random coil,β-sheet,and extended strand were 48.45%,30.41%,5.67%,and 15.46%,respectively.The similarity to template 1dt0.1.A reached 71.58%.A PTM site analysis revealed the presence of phosphorylation,glycosylation,ubiquitination,sumoylation,acetylation,and methylation modification sites,as well as the absence of lactylation modification sites.
文摘Over the last two decades, food allergens are being recognized as one of the food hazards. This serious food safety issue is being addressed in different countries not only in terms of their biological and clinical characteristics, but also in terms of various standards of allergen management in food industries. This abnormal immune response caused by food allergens affects the quality of life especially in children and influences their overall health and retards normal growth, along with they suffer from ailments like eating disorders, depression, sometimes even death which is the most adverse impact of food allergy. Every country has their own set of guidelines to deal with the food allergens especially developed countries, food allergen guidelines is not well documented in developing countries. FAO/WHO is providing assistance to developing countries in strengthening their food safety guidelines. The Codex Alimentarius was formulated by the two organizations FAO/WHO in the year 1960; it is a collection of food standards in a integrated, codified style, together with associated material such as codes of hygiene and good manufacturing practices that should be followed by industries during various production stages of a food item. In both developed and developing nations, the Food Chemical Codex or the Codex Alimentarius aims to protect public health and implement fair trade practises for the trading of food items.
文摘Molecular microbiological methods, such as competetive PCR, real-time PCR, denaturing gradient gel electrophoresis (DGGE) and large-scale parallel-pyrosequencing, require the extraction of sufficient quantity of high quality DNA from microbiologically and chemically complex matrices. Due to difficulties in the field to standardize/select the optimum DNA preservation-extraction methods in view of laboratories differences, this article attempts to present a straight-forward mathematical framework for comparing some of the most commonly used methods. To this end, as a case study, the problem of selecting an optimum sample preservation-DNA extraction strategy for obtaining total bacterial DNA from swine feces was considered. Two sample preservation methods (liquid nitrogen and RNAlater?) and seven extraction techniques were paired and compared under six quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A260/280 and A 260/230 ratios), duration of extraction, degradation degree of DNA, and cost. From a practical point of view, it is unlikely that a single sample preservation-DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic multi-criteria decision-making (MCDM) approach was used to compare the methods. As a result, the ZR Fecal DNA MiniPrepTM DNA extraction kit for samples preserved either with liquid nitrogen or RNAlater? were identified as potential optimum solutions for obtaining total bacterial DNA from swine feces. Considering the need for practicality for in situ applications, we would recommend liquid nitrogen as sample preservation method, along with the ZR Fecal DNA MiniPrepTM kit. Total bacterial DNA obtained by this strategy can be suitable for downstream PCR-based DNA analyses of swine feces.
文摘There is an increased interest in the extraction of nucleic acids from various environmental samples since culture-independent molecular techniques contribute to deepen and broaden the understanding of a greater portion of uncultivable microorganisms. Due to difficulties to select the optimum DNA extraction method in view of downstream molecular analyses, this article presents a straightforward mathematical framework for comparing some of the most commonly used methods. Four commercial DNA extraction kits and two physical-chemical methods (bead-beating and freeze-thaw) were compared for the extraction of DNA under several quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A260/280 and A260/230 ratios), degradation degree of DNA, easiness of PCR amplification, duration of extraction, and cost per extraction. From a practical point of view, it is unlikely that a single DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) was employed to compare the methods. The PowerSoil? DNA Isolation Kit was systematically defined as the best performing method for extracting DNA from soil samples. More specifically, for soil:manure and soil:manure:biochar mixtures, the PowerSoil?DNA Isolation Kit method performed best, while for neat soil samples its alternative version gained the first rank.
文摘Due to the increased demand for ready-to-eat(RTE)minimally processed foods,alternatives to chemical and thermal preservation methods to maintain food safety are highly demanded.A significant safety hazard in RTE food products is the growth of the foodborne pathogen Listeria monocytogenes(L.monocytogenes).After processing,recontamination or cross-contamination of L.monocytogenes in RTE food products may occur and the lack of cooking can lead to an increased risk of listeriosis.Further,some RTE food products(e.g.cheese and cured meat)can have a long processing period and shelf life,thus allowing for the growth and proliferation of L.monocytogenes in the food matrix.Lactic acid bacteria(LAB)are generally recognized as safe probiotics and have been proposed as a biological control approach to eliminate foodborne pathogens including L.monocytogenes.LAB have been reported to extend the shelf life of food products and inhibit pathogen proliferation via growth competition and metabolite production.LAB are native microflora of many RTE foods,but only certain LAB may inhibit pathogen growth.Therefore,the specificity of LAB species should be employed in their use in RTE foods.This review will discuss the antimicrobial mechanisms of LAB against L.monocytogenes,selective use of LAB in food matrices,and their uses in food processing and packaging.
基金Funding for this work was provided by the Natural Sciences and Engineering Research Council of Canada(NSERC)(Grant#2383823-10).
文摘Riparian buffers,located in the transition zone between terrestrial and aquatic ecosystems,are a hotspot for nitrogen(N)removal through denitrification.Earthworms are abundant in riparian buffers and may enhance denitrification.This study investigated earthworm demographics of three earthworm functional groups(anecic,epigeic,and endogeic)and denitrifier activity in temporarily flooded and non-flooded riparian soils from April to October 2012 in southern Quebec,Canada.Nine earthworm species,mostly endogeic,were found in the temporarily flooded soil,while only six earthworm species were found in the non-flooded soil.On average,there were 11.7 times more earthworms with 12.4 times greater biomass(P<0.05)found in the temporarily flooded soil than in the non-flooded soil.The denitrification enzyme activity(DEA)was of similar magnitude in temporarily flooded and non-flooded soils,with temporal variation associated with rainfall patterns.Endogeic earthworm biomass was positively correlated(P<0.05)with DEA,while epigeic earthworm biomass was positively correlated(P<0.05)with 16S rRNA gene copies and nosZ gene copies from bacteria,indicating an association between earthworm functional groups and denitrifier activity in riparian soils.Stepwise multiple regressions showed that DEA in riparian soils could be predicted using soil moisture,inorganic N concentration,and earthworm functional groups,suggesting that endogeic and epigeic earthworms contributed to denitrifier activity in riparian soils.
