Pub Date : 2018-01-01Epub Date: 2018-05-14DOI: 10.4172/jpb.1000474
Li Liu, Stefanie Boyd, Mehraban Kavoussi, Lee A Bulla, Duane D Winkler
The Cry1Ab toxin produced by Bacillus thuringiensis binds to a conserved structural motif in the 12th ectodomain module (EC12) of BT-R1, a cadherin G protein-coupled receptor (GPCR) contained in the membrane of midgut epithelial cells of the tobacco hornworm Manduca sexta. Toxin binding transmits a signal into the cells and turns on a multi-step signal transduction pathway, culminating in cell death. Using chromatographically purified Cry1Ab and EC12 proteins, we demonstrated the direct formation of a stable complex between these two proteins in solution and visualized it on a native polyacrylamide gel. Moreover, we generated a fluorescent EC12 probe by converting the 36th residue to cysteine to enable maleimide-mediated conjugation of Alexa-488 fluorescent dye to EC12 by site-directed mutagenesis. In addition, we changed the 44th residue of EC12 to tryptophan, which greatly improved accuracy of protein quantification and traceability. Using the fluorescently labeled EC12 probe for direct and competitive binding assays, we were able to determine binding specificity in solution. These accomplishments will facilitate identification and characterization of the interface sequences for both the Cry1Ab toxin and BT-R1.
{"title":"Interaction of Fluorescently Labeled Cadherin G Protein-coupled Receptor with the Cry1Ab Toxin of Bacillus thuringiensis.","authors":"Li Liu, Stefanie Boyd, Mehraban Kavoussi, Lee A Bulla, Duane D Winkler","doi":"10.4172/jpb.1000474","DOIUrl":"https://doi.org/10.4172/jpb.1000474","url":null,"abstract":"<p><p>The Cry1Ab toxin produced by <i>Bacillus thuringiensis</i> binds to a conserved structural motif in the 12<sup>th</sup> ectodomain module (EC12) of BT-R<sub>1</sub>, a cadherin G protein-coupled receptor (GPCR) contained in the membrane of midgut epithelial cells of the tobacco hornworm <i>Manduca sexta</i>. Toxin binding transmits a signal into the cells and turns on a multi-step signal transduction pathway, culminating in cell death. Using chromatographically purified Cry1Ab and EC12 proteins, we demonstrated the direct formation of a stable complex between these two proteins in solution and visualized it on a native polyacrylamide gel. Moreover, we generated a fluorescent EC12 probe by converting the 36<sup>th</sup> residue to cysteine to enable maleimide-mediated conjugation of Alexa-488 fluorescent dye to EC12 by site-directed mutagenesis. In addition, we changed the 44<sup>th</sup> residue of EC12 to tryptophan, which greatly improved accuracy of protein quantification and traceability. Using the fluorescently labeled EC12 probe for direct and competitive binding assays, we were able to determine binding specificity in solution. These accomplishments will facilitate identification and characterization of the interface sequences for both the Cry1Ab toxin and BT-R<sub>1</sub>.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/jpb.1000474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36328634","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 : 2018-01-01Epub Date: 2018-12-11DOI: 10.4172/0974-276X.1000487
Li Liu, Stefanie D Boyd, Lee A Bulla, Duane D Winkler
The bacterium Bacillus thuringiensis (Bt) produces protoxin proteins in parasporal crystals. Proteolysis of the protoxin generates an active toxin which is a potent microbial insecticide. Additionally, Bt toxin genes have been introduced into genetically modified crops to produce insecticidal toxins which protect crops from insect invasion. The insecticidal activity of Cry toxins is mediated by specific interaction between toxins and their respective cellular receptors. One such toxin (Cry1Ab) exerts toxicity by first targeting the 12th ectodomain region (EC12) of the moth cadherin receptor BT-R1. Binding promotes a highly regulated signaling cascade event that concludes in oncotic-like cell death. We previously determined that conserved sequence motifs near the N- and C-termini of EC12 are critical for toxin binding in insect cells. Here, we have established that Cry1Ab specifically binds to EC12 as a soluble heterodimeric complex with extremely high affinity (Kd = 19.5 ± 1.6 nM). Binding assays using Cry1Ab toxin and a fluorescently labeled EC12 revealed that the heterodimeric complex is highly specific in that no such formation occurs between EC12 and other Cry toxins active against beetle and mosquito. Disruption of one or both terminal sequence motifs in EC12 eliminates complex formation. Until now, comprehensive biophysical characterization of Cry1Ab recognition and binding by the BT-R1 receptor was unresolved. The findings presented here provide insight on the molecular determinants in the Cry family of toxins and should facilitate the assessment and advancement of their use as pesticidal agents.
{"title":"\"The Defined Toxin-binding Region of the Cadherin G-protein Coupled Receptor, BT-R<sub>1</sub>, for the Active Cry1Ab Toxin of <i>Bacillus thuringiensis</i>\".","authors":"Li Liu, Stefanie D Boyd, Lee A Bulla, Duane D Winkler","doi":"10.4172/0974-276X.1000487","DOIUrl":"https://doi.org/10.4172/0974-276X.1000487","url":null,"abstract":"<p><p>The bacterium <i>Bacillus thuringiensis</i> (Bt) produces protoxin proteins in parasporal crystals. Proteolysis of the protoxin generates an active toxin which is a potent microbial insecticide. Additionally, Bt toxin genes have been introduced into genetically modified crops to produce insecticidal toxins which protect crops from insect invasion. The insecticidal activity of Cry toxins is mediated by specific interaction between toxins and their respective cellular receptors. One such toxin (Cry1Ab) exerts toxicity by first targeting the 12<sup>th</sup> ectodomain region (EC12) of the moth cadherin receptor BT-R<sub>1</sub>. Binding promotes a highly regulated signaling cascade event that concludes in oncotic-like cell death. We previously determined that conserved sequence motifs near the N- and C-termini of EC12 are critical for toxin binding in insect cells. Here, we have established that Cry1Ab specifically binds to EC12 as a soluble heterodimeric complex with extremely high affinity (K<sub>d</sub> = 19.5 ± 1.6 nM). Binding assays using Cry1Ab toxin and a fluorescently labeled EC12 revealed that the heterodimeric complex is highly specific in that no such formation occurs between EC12 and other Cry toxins active against beetle and mosquito. Disruption of one or both terminal sequence motifs in EC12 eliminates complex formation. Until now, comprehensive biophysical characterization of Cry1Ab recognition and binding by the BT-R<sub>1</sub> receptor was unresolved. The findings presented here provide insight on the molecular determinants in the Cry family of toxins and should facilitate the assessment and advancement of their use as pesticidal agents.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/0974-276X.1000487","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36948445","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}
A. Suvannasankha, C. Crean, Heather M Leyes, S. Wongsaengsak, Guihong Qi, Jong Won Kim, Mu Wang
Introduction: Quantitative proteomics approaches have provided insight into biomarkers of cancer and other diseases with high sensitivity, high specificity, and high analytical precision. Multiple Myeloma is an incurable, fatal blood cancers characterized by clonal expansion of plasma cells in the bone marrow. Current multiple myeloma proteomic research mainly focuses on serum biomarkers, not plasma cells, due to technical difficulties including a requirement for tumor cell isolation from bone marrow aspirates, tumor cell paucity and poor in vitro survival after isolation.Materials and methods: A global proteomic analysis was performed using sorted bone marrow plasma cells from normal donors and multiple myeloma patients and a large-scale quantitative mass spectrometry platform. A selected panel of up- and down-regulated proteins were validated by multiple-reaction-monitoring.Results: We identified a panel of 18 up- and down-regulated potential biomarkers of multiple myeloma, which can be further clinically validated for their potential use as disease-specific biomarkers or signature molecules for monitoring disease progression.Conclusion: The study demonstrates a good example of using proteomics as a tool for the development of clinical biomarkers for diagnosis, prognosis, and drug target discovery.
{"title":"Proteomic Characterization of Plasma Cells from Patients with Multiple Myeloma","authors":"A. Suvannasankha, C. Crean, Heather M Leyes, S. Wongsaengsak, Guihong Qi, Jong Won Kim, Mu Wang","doi":"10.4172/JPB.1000461","DOIUrl":"https://doi.org/10.4172/JPB.1000461","url":null,"abstract":"Introduction: Quantitative proteomics approaches have provided insight into biomarkers of cancer and other diseases with high sensitivity, high specificity, and high analytical precision. Multiple Myeloma is an incurable, fatal blood cancers characterized by clonal expansion of plasma cells in the bone marrow. Current multiple myeloma proteomic research mainly focuses on serum biomarkers, not plasma cells, due to technical difficulties including a requirement for tumor cell isolation from bone marrow aspirates, tumor cell paucity and poor in vitro survival after isolation.Materials and methods: A global proteomic analysis was performed using sorted bone marrow plasma cells from normal donors and multiple myeloma patients and a large-scale quantitative mass spectrometry platform. A selected panel of up- and down-regulated proteins were validated by multiple-reaction-monitoring.Results: We identified a panel of 18 up- and down-regulated potential biomarkers of multiple myeloma, which can be further clinically validated for their potential use as disease-specific biomarkers or signature molecules for monitoring disease progression.Conclusion: The study demonstrates a good example of using proteomics as a tool for the development of clinical biomarkers for diagnosis, prognosis, and drug target discovery.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000461","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324899","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}
Despite the fact that “omic” technologies (including genomic, epigenomic, transcriptomic, proteomic and metabolomic technologies) are becoming widely used in various medical fields, their use in psychiatry is still very limited. Assessing suicidal behavior in psychiatric practice consists mostly of semi-structured questionnaires or various self-assessing scales. Information obtained this way is rather subjective. Therefore, our proteomic approach may provide more valid and objective way how to assess suicidality in daily clinical practice by finding possible candidates for biomarkers of suicidal behavior. In the present short communication, we present and discuss the results of our pilot proteomic study of cerebrospinal fluid (CSF) in two adult suicidal patients post-mortem (males, average age: 55, cause of death: hanging, no concomitant medication, no medical history), two adult controls post-mortem (males, average age: 55, cause of death: heart attack, no concomitant medication, no medical history) and two adult controls in-vivo (females, average age: 55, diagnosis: hydrocephalus, no concomitant medication – samples were drawn before the medication was taken). Samples of CSF in-vivo were included in this study to confirm the presence of identified proteins in living subjects and also to define their levels in CSF. Per subject, 5 ml of CSF was collected and post-mortem interval (PMI) did not exceed 32 hours. The protocol and informed consents for this study were approved by local ethical committee.
{"title":"Proteomic Analysis of Cerebrospinal Fluid in Suicidal Patients - A Pilot Study","authors":"Semancikova Erika, Tkáčiková Soňa, Talian Ivan, B. Peter, Hertelyová Zdenka, Tomečková Vladimíra","doi":"10.4172/JPB.1000476","DOIUrl":"https://doi.org/10.4172/JPB.1000476","url":null,"abstract":"Despite the fact that “omic” technologies (including genomic, epigenomic, transcriptomic, proteomic and metabolomic technologies) are becoming widely used in various medical fields, their use in psychiatry is still very limited. Assessing suicidal behavior in psychiatric practice consists mostly of semi-structured questionnaires or various self-assessing scales. Information obtained this way is rather subjective. Therefore, our proteomic approach may provide more valid and objective way how to assess suicidality in daily clinical practice by finding possible candidates for biomarkers of suicidal behavior. In the present short communication, we present and discuss the results of our pilot proteomic study of cerebrospinal fluid (CSF) in two adult suicidal patients post-mortem (males, average age: 55, cause of death: hanging, no concomitant medication, no medical history), two adult controls post-mortem (males, average age: 55, cause of death: heart attack, no concomitant medication, no medical history) and two adult controls in-vivo (females, average age: 55, diagnosis: hydrocephalus, no concomitant medication – samples were drawn before the medication was taken). Samples of CSF in-vivo were included in this study to confirm the presence of identified proteins in living subjects and also to define their levels in CSF. Per subject, 5 ml of CSF was collected and post-mortem interval (PMI) did not exceed 32 hours. The protocol and informed consents for this study were approved by local ethical committee.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000476","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324715","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}
A short presentation is given of a recent book on the origin of life with the intent of explain the basic mechanisms and questions to the interested layman. In spite of the elementary nature of the book, a reflexion on the main principles driving the life emergence are discussed from an informational perspective that can be useful in many mathematical and computational trends of biological modeling.
{"title":"A Marvelous Accident: The Birth of Life","authors":"V. Manca","doi":"10.4172/JPB.1000479","DOIUrl":"https://doi.org/10.4172/JPB.1000479","url":null,"abstract":"A short presentation is given of a recent book on the origin of life with the intent of explain the basic mechanisms and questions to the interested layman. In spite of the elementary nature of the book, a reflexion on the main principles driving the life emergence are discussed from an informational perspective that can be useful in many mathematical and computational trends of biological modeling.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000479","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324764","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}
It is a recurring limiting factor to obtain sufficient concentrations of soluble proteins using in vitro methodologies. Solubility is an independent characteristic of a protein which can be determined using amino acid compositions under specific experimental conditions. The present study aims at the prediction of protein solubility by adapting machine learning based approaches using the primary structure information. The features involve amino acid compositional features as well as the physiochemical properties of the amino acids i.e. canonical value, hydrophobicity, solubility index and solubility score. For a dataset of 6372 protein sequences (4850 soluble protein sequences and 1522 insoluble protein sequences), all the four features were calculated. Using the calculated values, four different prediction models were developed based on Multilayer Perceptron (MLP), Random Forest (RF), Decision Tree (DT), and Naive Bayes Classifier (NBC). For performance evaluation, MCC, F-measure, accuracy, precision and recall rate are determined. Among all the four prediction models, MLP has been observed to be the most accurate model for the prediction of protein solubility with an accuracy rate of 95.92%, followed by RF and NBC. The proposed model, based on MLP, can be used for predicting protein solubility as a preprocess of experimental predictions. The method is resource and time efficient, and can help in predicting solubility of proteins instead of laborious and hectic experimental work.
{"title":"Prediction of Protein Solubility using Primary Structure Compositional Features: A Machine Learning Perspective","authors":"N. Rasool, Waqar Hussain, S. Mahmood","doi":"10.4172/JPB.1000458","DOIUrl":"https://doi.org/10.4172/JPB.1000458","url":null,"abstract":"It is a recurring limiting factor to obtain sufficient concentrations of soluble proteins using in vitro methodologies. Solubility is an independent characteristic of a protein which can be determined using amino acid compositions under specific experimental conditions. The present study aims at the prediction of protein solubility by adapting machine learning based approaches using the primary structure information. The features involve amino acid compositional features as well as the physiochemical properties of the amino acids i.e. canonical value, hydrophobicity, solubility index and solubility score. For a dataset of 6372 protein sequences (4850 soluble protein sequences and 1522 insoluble protein sequences), all the four features were calculated. Using the calculated values, four different prediction models were developed based on Multilayer Perceptron (MLP), Random Forest (RF), Decision Tree (DT), and Naive Bayes Classifier (NBC). For performance evaluation, MCC, F-measure, accuracy, precision and recall rate are determined. Among all the four prediction models, MLP has been observed to be the most accurate model for the prediction of protein solubility with an accuracy rate of 95.92%, followed by RF and NBC. The proposed model, based on MLP, can be used for predicting protein solubility as a preprocess of experimental predictions. The method is resource and time efficient, and can help in predicting solubility of proteins instead of laborious and hectic experimental work.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46164699","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}
S. Oy, Kukharenko Ap, O. Kozlov, Dubey Iy, Tkachuk Zy
2'-5'-linked triadenylates present the class of low molecular compounds, capable of regulating various cell functions. Their main function is the activation of ribonuclease L – the main enzyme of the innate immunity. Their dephosphorylation results in loss of this function, which, on the other hand grants them a handful of new, yet undiscovered abilities. Aim: Study the concentration-dependend influence of dephosphorylated 2'-5'-linked tradenylates on the protein kinases activity. Methods: Protein kinases were titrated with radioactively labeled ATP. After that the radioactivity value was determined with the use of scintillation counter. Results: We have found out that 2'-5'-linked are capable of changing the biological activity of various protein kinases by altering the amount of ATP they can potentially cleave. Conclusions: We suggest that this effect could occur to the specific changes in protein kinases structure.
{"title":"2'-5'-Linked Triadenylates Act as Protein Kinase Activity Modulators","authors":"S. Oy, Kukharenko Ap, O. Kozlov, Dubey Iy, Tkachuk Zy","doi":"10.4172/JPB.1000457","DOIUrl":"https://doi.org/10.4172/JPB.1000457","url":null,"abstract":"2'-5'-linked triadenylates present the class of low molecular compounds, capable of regulating various cell functions. Their main function is the activation of ribonuclease L – the main enzyme of the innate immunity. Their dephosphorylation results in loss of this function, which, on the other hand grants them a handful of new, yet undiscovered abilities. \u0000Aim: Study the concentration-dependend influence of dephosphorylated 2'-5'-linked tradenylates on the protein kinases activity. \u0000Methods: Protein kinases were titrated with radioactively labeled ATP. After that the radioactivity value was determined with the use of scintillation counter. \u0000Results: We have found out that 2'-5'-linked are capable of changing the biological activity of various protein kinases by altering the amount of ATP they can potentially cleave. \u0000Conclusions: We suggest that this effect could occur to the specific changes in protein kinases structure.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000457","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45774096","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}
S. Mukhtar, Ahmad Zaheer, Dalaq Aiysha, K. Malik, Samina Mehnaz
Microbial enzymes play a key role as metabolic catalysts, leading to their diverse applications and use in various industries. The constant search for novel microbial enzymes has led to improvisations in the industrial processes which is the key for profit growth. Actinomycetes form a significant group of microbial populations in soil, plant tissues and marine environments. Actinomycetes produce many valuable extracellular enzymes which can decompose a variety of organic materials. Enzymes produced by Actinomycetes and applied in different industries are cellulases, proteases, amylases, lipases xylanases, chitinases, cutinases and pectinases. Actinomycetes identified from the extreme environments are known to be producers of novel enzymes with great industrial potential. This review attempts to summarize the applications of enzymes from Actinomycetes in different industries such as food, medicine, pulp and paper, detergent, textile, agriculture and biorefineries.
{"title":"Actinomycetes: A Source of Industrially Important Enzymes","authors":"S. Mukhtar, Ahmad Zaheer, Dalaq Aiysha, K. Malik, Samina Mehnaz","doi":"10.4172/JPB.1000456","DOIUrl":"https://doi.org/10.4172/JPB.1000456","url":null,"abstract":"Microbial enzymes play a key role as metabolic catalysts, leading to their diverse applications and use in various industries. The constant search for novel microbial enzymes has led to improvisations in the industrial processes which is the key for profit growth. Actinomycetes form a significant group of microbial populations in soil, plant tissues and marine environments. Actinomycetes produce many valuable extracellular enzymes which can decompose a variety of organic materials. Enzymes produced by Actinomycetes and applied in different industries are cellulases, proteases, amylases, lipases xylanases, chitinases, cutinases and pectinases. Actinomycetes identified from the extreme environments are known to be producers of novel enzymes with great industrial potential. This review attempts to summarize the applications of enzymes from Actinomycetes in different industries such as food, medicine, pulp and paper, detergent, textile, agriculture and biorefineries.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000456","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43725681","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}
Zongfu Cao, Lei Wang, Yilu Chen, Ruikun Cai, Jianbo Lu, Yufei Yu, Cuixia Chen, Feng Gu, Juhua Yang, Xu Ma
Background: The relationships among phenotypes, genes, and variants play a key role for monogenic disorders in the era of precision medicine. Information about this is erupting with the current rapid development of genomic technology. However, it is time-consuming and error-prone to manually capture the information from the literature. Thus, how to capture this information rapidly and accurately is a bottleneck to be solved. Results: Here, we present VarfromPDB, an automated and integrated method to mine the genes and variants related to a Mendelian disorder from multiple public curated databases and literature. To demonstrate the procedure, feasibility and application, we used a monogenic disorder, Joubert syndrome, as an example to capture the related genes from multiple sources including HPO, OrphaNet, ClinVar, UniProt and PubMed abstracts. The captured gene list is more comprehensive than that from DisGeNET and DISEASES databases. Conclusion: VarfromPDB is a an automated and integrated tool to compile the up-to-date disease-genevariant database with comprehensive. It is valuable for genetic researchers and has great potential in facilitating the application of genetic testing for precision medicine. The source code for VarfromPDB is freely available at https://CRAN.R-project.org/package=VarfromPDB.
{"title":"VarfromPDB: An Automated and Integrated Tool to Mine Disease-Gene-Variant Relations from the Public Databases and Literature","authors":"Zongfu Cao, Lei Wang, Yilu Chen, Ruikun Cai, Jianbo Lu, Yufei Yu, Cuixia Chen, Feng Gu, Juhua Yang, Xu Ma","doi":"10.4172/JPB.1000455","DOIUrl":"https://doi.org/10.4172/JPB.1000455","url":null,"abstract":"Background: The relationships among phenotypes, genes, and variants play a key role for monogenic disorders in the era of precision medicine. Information about this is erupting with the current rapid development of genomic technology. However, it is time-consuming and error-prone to manually capture the information from the literature. Thus, how to capture this information rapidly and accurately is a bottleneck to be solved. \u0000Results: Here, we present VarfromPDB, an automated and integrated method to mine the genes and variants related to a Mendelian disorder from multiple public curated databases and literature. To demonstrate the procedure, feasibility and application, we used a monogenic disorder, Joubert syndrome, as an example to capture the related genes from multiple sources including HPO, OrphaNet, ClinVar, UniProt and PubMed abstracts. The captured gene list is more comprehensive than that from DisGeNET and DISEASES databases. \u0000Conclusion: VarfromPDB is a an automated and integrated tool to compile the up-to-date disease-genevariant database with comprehensive. It is valuable for genetic researchers and has great potential in facilitating the application of genetic testing for precision medicine. The source code for VarfromPDB is freely available at https://CRAN.R-project.org/package=VarfromPDB.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000455","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44314383","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 : 2017-11-22DOI: 10.4172/0974-276X-C1-102
A. Dunker
{"title":"Intrinsically disordered protein, alternative splicing, and post-translational modification: A toolkit for developmental biology","authors":"A. Dunker","doi":"10.4172/0974-276X-C1-102","DOIUrl":"https://doi.org/10.4172/0974-276X-C1-102","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915769","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}
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