In the year 1971,the world’s biggest structural biology collaboration name—The Research Collaboratory for Structural Bioinformatics(RCSB),was formed to gather all the structural biologists at a single platform and t...In the year 1971,the world’s biggest structural biology collaboration name—The Research Collaboratory for Structural Bioinformatics(RCSB),was formed to gather all the structural biologists at a single platform and then extended out to be the world’s most extensive structural data repository named RCSB-Protein Data Bank(PDB)(https://www.rcsb.org/)that has provided the service for more than 50 years and continues its legacy for the discoveries and repositories for structural data.The RCSB has evolved from being a collaboratory network to a full-fledged database and tool with a huge list of protein structures,nucleic acid-containing structures,ModelArchive,and AlphaFold structures,and the best is that it is expanding day by day with computational advancement with tools and visual experiences.In this review article,we have discussed how RCSB has been a successful collaboratory network,its expansion in each decade,and how it has helped the ground-breaking research.The PDB tools that are helping the researchers,yearly data deposition,validation,processing,and suggestions that can help the developer improve for upcoming years are also discussed.This review will help future researchers understand the complete history of RCSB and its developments in each decade and how various future collaborative networks can be developed in various scientific areas and can be successful by keeping RCSB as a case study.展开更多
AIM: To understand which and how different miRNAs are implicated in the process of hepatic stellate cell (HSC) activation. METHODS: We used microarrays to examine the differential expression of miRNAs during in vitro ...AIM: To understand which and how different miRNAs are implicated in the process of hepatic stellate cell (HSC) activation. METHODS: We used microarrays to examine the differential expression of miRNAs during in vitro activation of primary HSCs (pHSCs). The transcriptome changes upon stable transfection of rno-miR-146a into an HSC cell line were studied using cDNA microarrays. Selected differentially regulated miRNAs were investigated by quantitative real-time polymerase chain reaction during in vivo HSC activation. The effect of miRNA mimics and inhibitor on the in vitro activation of pHSCs was also evaluated.RESULTS: We found that 16 miRNAs were upregulated and 26 were downregulated significantly in 10-d in vitro activated pHSCs in comparison to quiescent pHSCs. Overexpression of rno-miR-146a was characterized by marked upregulation of tissue inhibitor of metalloproteinase-3, which is implicated in the regulation of tumor necrosis factor-α activity. Differences in the regulation of selected miRNAs were observed comparing in vitro and in vivo HSC activation. Treatment with miR-26a and 29a mimics, and miR-214 inhibitor during in vitro activation of pHSCs induced significant downregulation of collagen type Ⅰ transcription. CONCLUSION: Our results emphasize the different regulation of miRNAs in in vitro and in vivo activated pHSCs. We also showed that miR-26a, 29a and 214 are involved in the regulation of collagen type I mRNA.展开更多
The treatment of shavings,trimmings and splits of leather waste from tanneries has a potential to generate value-added products. In this study enzymatic treatment of leather waste was performed. This method utilizes a...The treatment of shavings,trimmings and splits of leather waste from tanneries has a potential to generate value-added products. In this study enzymatic treatment of leather waste was performed. This method utilizes alkaline protease produced by Bacillus subtilis in our laboratory by submerged fermentation. Optimum conditions of pH,time duration,temperature and concentration of enzyme were determined for maximum degradation of leather waste. The amount of degradation was measured by the release of amino acid hydroxyproline. Amino acid composition in the hydrolysate obtained by the enzyme hydrolysis was determined. This relative simple biotreatment of leather waste may provide a practical and economical solution.展开更多
Objective:To assess the effect of L-carnitine supplementation during in vitro oocyte maturation and in vitro culture process of bovine oocytes.Methods:L-carnitine(3.8 mM)was added to maturation medium and the effect w...Objective:To assess the effect of L-carnitine supplementation during in vitro oocyte maturation and in vitro culture process of bovine oocytes.Methods:L-carnitine(3.8 mM)was added to maturation medium and the effect was assessed in the quality(Experiment 1)and in the cleavage and 4-cells stage(Experiment 2).Besides,the effect of L-carnitine addition on maturation medium(3.8 mM)and culture medium(1.5 mM)on embryo rate production was assessed.In Experiment 1,bovine oocytes from abattoir were randomly separated into two groups(the control group and L-carnitine group)forin vitro maturation.Matured oocytes were examined for cumulus cells expansion as an indicator of maturation,and the content of the mitochondrial activity,the presence of lipid droplets,the reduced glutathione,and the reactive oxygen species were measured by using specific fluorochromes.In Experiment 2,oocytes were matured as performed in Experiment 1,afterward fertilized and cultured until day 3,and cleavage rate and 4-cells stage rate were determinated.In Experiment 3,in vitro maturation and fertilization were done as performed in Experiment 2,but at day 3 of culture,each group of embryos was separated into two new groups,and L-carnitine(1.5 mM)was added in culture media until day 8.The cleavage and embryo development rate were determined on the basis with the oocytes put on maturation.Hatching rate was calculated from cleaved embryos.Results:The cumulus expansion rate at gradeⅢand mitochondrial activity were significantly higher in the L-carnitine group in comparison with the control group(P0.05).In addition,cleavage and the proportion of embryo development and hatching rate were similar for all groups(P>0.05).Conclusions:L-carnitine as a supplement in culture media improves the cumulus expansion and increases the mitochondrial activity during in vitro maturation process but has no apparent effect on the cleavage and development of bovine embryos.Further investigations of L-carnitine addition on in vitroculture are needed to test their effect on embryo quality.展开更多
The rice blast,caused by fungus Magnaporthe oryzae,is a major constraint to the world food security.Hyphal growth is the foundation of fungal development and proliferation of fungi.To investigate genes involved in hyp...The rice blast,caused by fungus Magnaporthe oryzae,is a major constraint to the world food security.Hyphal growth is the foundation of fungal development and proliferation of fungi.To investigate genes involved in hyphal growth of this fungus,digital gene expression tag profiling was used to compare a previously generated temperature-sensitive mutant which defect at hyphae growth and reduction on pathogenicity,with its related wildtype strain.416 genes were detected as differential expression,178 of which were specifically expressed in Guy-11 but down-regulated expression in the mutant.Functional classification analysis revealed the phenotype mutation may be mainly caused by a defection in translational and vacuole- related processes.The results and the protocol used will improve our knowledge on morphogenesis and promote the further study on M.oryzae pathogenesis.展开更多
An efficient calibration algorithm for an ambulatory audiometric test system is proposed. This system utilizes a personal digital assistant (PDA) device to generate the correct sound pressure level (SPL) from an audio...An efficient calibration algorithm for an ambulatory audiometric test system is proposed. This system utilizes a personal digital assistant (PDA) device to generate the correct sound pressure level (SPL) from an audiometric transducer such as an earphone. The calibrated sound intensities for an audio-logical examination can be obtained in terms of the sound pressure levels of pure-tonal sinusoidal signals in eight-banded frequency ranges (250, 500, 1 000, 2 000, 3 000, 4 000, 6 000 and 8 000 Hz), and with mapping of the input sound pressure levels by the weight coefficients that are tuned by the delta learning rule. With this scheme, the sound intensities, which evoke eight-banded sound pressure levels by 5 dB steps from a minimum of 25 dB to a maximum of 80 dB, can be generated without volume displacement. Consequently, these sound intensities can be utilized to accurately determine the hearing threshold of a subject in the ambulatory audiometric testing environment.展开更多
The coronavirus disease 2019(COVID-19)outbreak caused by the severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)developed into a global health emergency.Systemic microthrombus caused by SARS-CoV-2 infection is...The coronavirus disease 2019(COVID-19)outbreak caused by the severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)developed into a global health emergency.Systemic microthrombus caused by SARS-CoV-2 infection is a common complication in patients with COVID19.Cardiac microthrombosis as a complication of SARS-CoV-2 infection is the primary cause of cardiac injury and death in patietns with severe COVID-19.In this study,we performed single-cell sequencing analysis of the right ventricular free wall tissue from healthy donors,patients who died during the hypercoagulable period of characteristic coagulation abnormality(CAC),and patients who died during the fibrinolytic period of CAC.We collected 61,187 cells enriched in 24 immune cell subsets and 13 cardiac-resident cell subsets.We found that in the course of SARS-CoV-2 infected heart microthrombus,MYO1 Ehigh RASGEF1 Bhighmonocyte-derived macrophages promoted hyperactivation of the immune system and initiated the extrinsic coagulation pathway by activating chemokines CCL3,CCL5.This series of events is the main cause of cardiac microthrombi following SARS-CoV-2 infection.In a SARS-CoV-2 infected heart microthrombus,excessive immune activation is accompanied by an increase in cellular iron content,which in turn promotes oxidative stress and intensifies intercellular competition.This induces cells to alter their metabolic environment,resulting in increased sugar uptake via the glycosaminoglycan synthesis pathway.In addition,high levels of reactive oxygen species generated by elevated iron levels promote increased endogenous malondialdehyde synthesis in a subpopulation of cardiac endothelial cells.This exacerbates endothelial cell dysfunction and exacerbates the coagulopathy process.展开更多
The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biologic...The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing （NGS）-based studies, we propose a workflow that accounts for the unique characteris- tics of scRNA-seq data and primary objectives of single-cell studies.展开更多
文摘In the year 1971,the world’s biggest structural biology collaboration name—The Research Collaboratory for Structural Bioinformatics(RCSB),was formed to gather all the structural biologists at a single platform and then extended out to be the world’s most extensive structural data repository named RCSB-Protein Data Bank(PDB)(https://www.rcsb.org/)that has provided the service for more than 50 years and continues its legacy for the discoveries and repositories for structural data.The RCSB has evolved from being a collaboratory network to a full-fledged database and tool with a huge list of protein structures,nucleic acid-containing structures,ModelArchive,and AlphaFold structures,and the best is that it is expanding day by day with computational advancement with tools and visual experiences.In this review article,we have discussed how RCSB has been a successful collaboratory network,its expansion in each decade,and how it has helped the ground-breaking research.The PDB tools that are helping the researchers,yearly data deposition,validation,processing,and suggestions that can help the developer improve for upcoming years are also discussed.This review will help future researchers understand the complete history of RCSB and its developments in each decade and how various future collaborative networks can be developed in various scientific areas and can be successful by keeping RCSB as a case study.
基金Supported by Institute of Bioengineering and Nanotechnology (Biomedical Research Council, Agency for Science, Technology and Research, Singapore)
文摘AIM: To understand which and how different miRNAs are implicated in the process of hepatic stellate cell (HSC) activation. METHODS: We used microarrays to examine the differential expression of miRNAs during in vitro activation of primary HSCs (pHSCs). The transcriptome changes upon stable transfection of rno-miR-146a into an HSC cell line were studied using cDNA microarrays. Selected differentially regulated miRNAs were investigated by quantitative real-time polymerase chain reaction during in vivo HSC activation. The effect of miRNA mimics and inhibitor on the in vitro activation of pHSCs was also evaluated.RESULTS: We found that 16 miRNAs were upregulated and 26 were downregulated significantly in 10-d in vitro activated pHSCs in comparison to quiescent pHSCs. Overexpression of rno-miR-146a was characterized by marked upregulation of tissue inhibitor of metalloproteinase-3, which is implicated in the regulation of tumor necrosis factor-α activity. Differences in the regulation of selected miRNAs were observed comparing in vitro and in vivo HSC activation. Treatment with miR-26a and 29a mimics, and miR-214 inhibitor during in vitro activation of pHSCs induced significant downregulation of collagen type Ⅰ transcription. CONCLUSION: Our results emphasize the different regulation of miRNAs in in vitro and in vivo activated pHSCs. We also showed that miR-26a, 29a and 214 are involved in the regulation of collagen type I mRNA.
文摘The treatment of shavings,trimmings and splits of leather waste from tanneries has a potential to generate value-added products. In this study enzymatic treatment of leather waste was performed. This method utilizes alkaline protease produced by Bacillus subtilis in our laboratory by submerged fermentation. Optimum conditions of pH,time duration,temperature and concentration of enzyme were determined for maximum degradation of leather waste. The amount of degradation was measured by the release of amino acid hydroxyproline. Amino acid composition in the hydrolysate obtained by the enzyme hydrolysis was determined. This relative simple biotreatment of leather waste may provide a practical and economical solution.
基金This study was funded by the Administrative Department of Science Technology and Innovation(COLCIENCIAS)(Grant No.727,2015).
文摘Objective:To assess the effect of L-carnitine supplementation during in vitro oocyte maturation and in vitro culture process of bovine oocytes.Methods:L-carnitine(3.8 mM)was added to maturation medium and the effect was assessed in the quality(Experiment 1)and in the cleavage and 4-cells stage(Experiment 2).Besides,the effect of L-carnitine addition on maturation medium(3.8 mM)and culture medium(1.5 mM)on embryo rate production was assessed.In Experiment 1,bovine oocytes from abattoir were randomly separated into two groups(the control group and L-carnitine group)forin vitro maturation.Matured oocytes were examined for cumulus cells expansion as an indicator of maturation,and the content of the mitochondrial activity,the presence of lipid droplets,the reduced glutathione,and the reactive oxygen species were measured by using specific fluorochromes.In Experiment 2,oocytes were matured as performed in Experiment 1,afterward fertilized and cultured until day 3,and cleavage rate and 4-cells stage rate were determinated.In Experiment 3,in vitro maturation and fertilization were done as performed in Experiment 2,but at day 3 of culture,each group of embryos was separated into two new groups,and L-carnitine(1.5 mM)was added in culture media until day 8.The cleavage and embryo development rate were determined on the basis with the oocytes put on maturation.Hatching rate was calculated from cleaved embryos.Results:The cumulus expansion rate at gradeⅢand mitochondrial activity were significantly higher in the L-carnitine group in comparison with the control group(P0.05).In addition,cleavage and the proportion of embryo development and hatching rate were similar for all groups(P>0.05).Conclusions:L-carnitine as a supplement in culture media improves the cumulus expansion and increases the mitochondrial activity during in vitro maturation process but has no apparent effect on the cleavage and development of bovine embryos.Further investigations of L-carnitine addition on in vitroculture are needed to test their effect on embryo quality.
基金supported by the Natural Science Foundation of Zhejiang Province,China(Y3110028 and LQ12C14003)
文摘The rice blast,caused by fungus Magnaporthe oryzae,is a major constraint to the world food security.Hyphal growth is the foundation of fungal development and proliferation of fungi.To investigate genes involved in hyphal growth of this fungus,digital gene expression tag profiling was used to compare a previously generated temperature-sensitive mutant which defect at hyphae growth and reduction on pathogenicity,with its related wildtype strain.416 genes were detected as differential expression,178 of which were specifically expressed in Guy-11 but down-regulated expression in the mutant.Functional classification analysis revealed the phenotype mutation may be mainly caused by a defection in translational and vacuole- related processes.The results and the protocol used will improve our knowledge on morphogenesis and promote the further study on M.oryzae pathogenesis.
基金supported by the grant of the Korean Ministry of Education, Science and Technology (The Regional Core Research Program/Chungbuk BIT Research-Oriented University Consortium)
文摘An efficient calibration algorithm for an ambulatory audiometric test system is proposed. This system utilizes a personal digital assistant (PDA) device to generate the correct sound pressure level (SPL) from an audiometric transducer such as an earphone. The calibrated sound intensities for an audio-logical examination can be obtained in terms of the sound pressure levels of pure-tonal sinusoidal signals in eight-banded frequency ranges (250, 500, 1 000, 2 000, 3 000, 4 000, 6 000 and 8 000 Hz), and with mapping of the input sound pressure levels by the weight coefficients that are tuned by the delta learning rule. With this scheme, the sound intensities, which evoke eight-banded sound pressure levels by 5 dB steps from a minimum of 25 dB to a maximum of 80 dB, can be generated without volume displacement. Consequently, these sound intensities can be utilized to accurately determine the hearing threshold of a subject in the ambulatory audiometric testing environment.
基金supported by the National Key Research and Development Program of China(2022YFF1203204)the National Natural Science Foundation of China Joint Fund for Regional Innovation and Development(U23A20269).
文摘The coronavirus disease 2019(COVID-19)outbreak caused by the severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)developed into a global health emergency.Systemic microthrombus caused by SARS-CoV-2 infection is a common complication in patients with COVID19.Cardiac microthrombosis as a complication of SARS-CoV-2 infection is the primary cause of cardiac injury and death in patietns with severe COVID-19.In this study,we performed single-cell sequencing analysis of the right ventricular free wall tissue from healthy donors,patients who died during the hypercoagulable period of characteristic coagulation abnormality(CAC),and patients who died during the fibrinolytic period of CAC.We collected 61,187 cells enriched in 24 immune cell subsets and 13 cardiac-resident cell subsets.We found that in the course of SARS-CoV-2 infected heart microthrombus,MYO1 Ehigh RASGEF1 Bhighmonocyte-derived macrophages promoted hyperactivation of the immune system and initiated the extrinsic coagulation pathway by activating chemokines CCL3,CCL5.This series of events is the main cause of cardiac microthrombi following SARS-CoV-2 infection.In a SARS-CoV-2 infected heart microthrombus,excessive immune activation is accompanied by an increase in cellular iron content,which in turn promotes oxidative stress and intensifies intercellular competition.This induces cells to alter their metabolic environment,resulting in increased sugar uptake via the glycosaminoglycan synthesis pathway.In addition,high levels of reactive oxygen species generated by elevated iron levels promote increased endogenous malondialdehyde synthesis in a subpopulation of cardiac endothelial cells.This exacerbates endothelial cell dysfunction and exacerbates the coagulopathy process.
基金supported by Baylor Research Institute start-up funding,USA to WL
文摘The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing （NGS）-based studies, we propose a workflow that accounts for the unique characteris- tics of scRNA-seq data and primary objectives of single-cell studies.
