scholarly journals Identification of Helicobacter pylori Membrane Proteins Using Sequence-Based Features

2022 ◽  
Vol 2022 ◽  
pp. 1-7
Author(s):  
Mujiexin Liu ◽  
Hui Chen ◽  
Dong Gao ◽  
Cai-Yi Ma ◽  
Zhao-Yue Zhang
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Cross Validation ◽  
Cost Effective ◽  
Vital Role ◽  
Support Vector ◽  
Sequence Information ◽  
Common Risk Factor ◽  
Proposed Model ◽  
H Pylori

Helicobacter pylori (H. pylori) is the most common risk factor for gastric cancer worldwide. The membrane proteins of the H. pylori are involved in bacterial adherence and play a vital role in the field of drug discovery. Thus, an accurate and cost-effective computational model is needed to predict the uncharacterized membrane proteins of H. pylori. In this study, a reliable benchmark dataset consisted of 114 membrane and 219 nonmembrane proteins was constructed based on UniProt. A support vector machine- (SVM-) based model was developed for discriminating H. pylori membrane proteins from nonmembrane proteins by using sequence information. Cross-validation showed that our method achieved good performance with an accuracy of 91.29%. It is anticipated that the proposed model will be useful for the annotation of H. pylori membrane proteins and the development of new anti-H. pylori agents.

DEEPSMP: A deep learning model for predicting the ectodomain shedding events of membrane proteins

2020 ◽  
Vol 18 (03) ◽  
pp. 2050017
Author(s):  
Zhongbo Cao ◽  
Wei Du ◽  
Gaoyang Li ◽  
Huansheng Cao
Keyword(s):  
Membrane Proteins ◽  
Cross Validation ◽  
Short Term Memory ◽  
Characteristic Curve ◽  
Attention Mechanism ◽  
Training Dataset ◽  
Sequence Information ◽  
Dense Layer ◽  
Ectodomain Shedding ◽  
Proposed Model

Membrane proteins play essential roles in modern medicine. In recent studies, some membrane proteins involved in ectodomain shedding events have been reported as the potential drug targets and biomarkers of some serious diseases. However, there are few effective tools for identifying the shedding event of membrane proteins. So, it is necessary to design an effective tool for predicting shedding event of membrane proteins. In this study, we design an end-to-end prediction model using deep neural networks with long short-term memory (LSTM) units and attention mechanism, to predict the ectodomain shedding events of membrane proteins only by sequence information. Firstly, the evolutional profiles are encoded from original sequences of these proteins by Position-Specific Iterated BLAST (PSI-BLAST) on Uniref50 database. Then, the LSTM units which contain memory cells are used to hold information from past inputs to the network and the attention mechanism is applied to detect sorting signals in proteins regardless of their position in the sequence. Finally, a fully connected dense layer and a softmax layer are used to obtain the final prediction results. Additionally, we also try to reduce overfitting of the model by using dropout, L2 regularization, and bagging ensemble learning in the model training process. In order to ensure the fairness of performance comparison, firstly we use cross validation process on training dataset obtained from an existing paper. The average accuracy and area under a receiver operating characteristic curve (AUC) of five-fold cross-validation are 81.19% and 0.835 using our proposed model, compared to 75% and 0.78 by a previously published tool, respectively. To better validate the performance of the proposed model, we also evaluate the performance of the proposed model on independent test dataset. The accuracy, sensitivity, and specificity are 83.14%, 84.08%, and 81.63% using our proposed model, compared to 70.20%, 71.97%, and 67.35% by the existing model. The experimental results validate that the proposed model can be regarded as a general tool for predicting ectodomain shedding events of membrane proteins. The pipeline of the model and prediction results can be accessed at the following URL: http://www.csbg-jlu.info/DeepSMP/ .

Endoscopic Biopsy Pathology of Helicobacter pylori Gastritis

1999 ◽  
Vol 123 (9) ◽  
pp. 778-781 ◽  
Author(s):  
Maher Toulaymat ◽  
Sharon Marconi ◽  
Jane Garb ◽  
Christopher Otis ◽  
Shirin Nash
Keyword(s):  
Helicobacter Pylori ◽  
Specific Antibody ◽  
Cost Effective ◽  
Endoscopic Biopsy ◽  
Immunohistochemical Method ◽  
Labor Costs ◽  
Chronic Active Gastritis ◽  
Cost Effective Method ◽  
H Pylori ◽  
Helicobacter Pylori Gastritis

Abstract Objectives.—To describe the endoscopic biopsy pathology of Helicobacter pylori gastritis, compare bacterial detection by immunohistochemistry using a specific antibody with the Genta stain, and to compare the relative costs of the 2 techniques. Design.—One hundred cases of gastritis identified as positive for H pylori by Genta stain and 100 cases considered negative by the same technique were stained using an anti-H pylori–specific polyclonal antibody. Laboratory reagent and labor costs for the 2 methods were compared. Results.—Chronic active gastritis with lymphoid follicles was significantly associated with H pylori infection (P < .0001). The immunohistochemical method had a sensitivity of 97% and a specificity of 98% compared with the Genta stain, with strong agreement for grading density of organisms (κ = 0.85; P < .001). Reagent costs were similar for both methods, but immunohistochemistry using an autoimmunostainer required less dedicated technical time and hence was less expensive than the Genta stain. Conclusions.—Immunohistochemistry using a specific antibody is an accurate and cost-effective method for H pylori detection in gastric biopsies.

iRNAD: a computational tool for identifying D modification sites in RNA sequence

2019 ◽  
Vol 35 (23) ◽  
pp. 4922-4929 ◽  
Author(s):  
Zhao-Chun Xu ◽  
Peng-Mian Feng ◽  
Hui Yang ◽  
Wang-Ren Qiu ◽  
Wei Chen ◽  
...  
Keyword(s):  
Computational Models ◽  
Operating Characteristic ◽  
Cross Validation ◽  
Characteristic Curve ◽  
Support Vector ◽  
Final Model ◽  
Rna Sequence ◽  
Functional Roles ◽  
Proposed Model ◽  
User Friendly

Abstract Motivation Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA. Results We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model. Availability and implementation A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.

Prevalence of Helicobacter pylori cagA and vacA Genes and Their Correlation with Gastrointestinal Diseases

2020 ◽  
Vol EJMM29 (4) ◽  
pp. 151-156
Author(s):  
Amr M. El-Sabbagh ◽  
Ahmed H. Yassen ◽  
Maha M abdelsalam
Keyword(s):  
Helicobacter Pylori ◽  
Gastrointestinal Diseases ◽  
Vital Role ◽  
Gastroduodenal Disease ◽  
Urease Test ◽  
Cytotoxin Associated Gene A ◽  
Gastrointestinal Illnesses ◽  
Clinical Illness ◽  
H Pylori ◽  
Variant Genes

Background: Helicobacter pylori (H. pylori) is a gram-negative bacterium, producing gastric ulcer, mild to severe gastritis, gastric carcinoma and lymphoma to the gastric mucosa-associated lymphoid tissue through many virulence influences. Among the virulence factors identified; vacuolating cytotoxin A (vacA) and cytotoxin-associated gene A (cagA) play an important role. Objective: In this study, we try to discover the relation between vacA variant and cagA genes with the clinical illness occurring in H. pylori patients Methodology: One hundred and forty patients were included in our study. Dual biopsy samples were taken from the stomach; one was examined by the urease test, and the other one was stored at −80°C for DNA extraction followed by PCR. The existence of H. pylori in the tissue was recognized by the existence of glmM gene and its detection by PCR. All the positive samples were additionally tested by PCR for the occurrence of cagA and vacA variant genes. Results: Our study demonstrated that cagA and vacA genes were found among 50% and 57% respectively of H. pylori patients complaining from gastrointestinal illnesses and that vacA s1/s2 was the main genotype found in H. pylori persons with gastroduodenal disease. Significant relation between vacA s1 gene and cagA gene was found. Conclusion: vacA s1 genotype has a vital role in upper gastrointestinal illnesses progress.

scholarly journals Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions

2014 ◽  
Vol 2014 ◽  
pp. 1-4 ◽  
Author(s):  
Pengmian Feng ◽  
Ning Jiang ◽  
Nan Liu
Keyword(s):  
Cost Effective ◽  
Dnase I ◽  
Support Vector ◽  
Jackknife Test ◽  
Dnase I Hypersensitive Sites ◽  
Proposed Model ◽  
Hypersensitive Sites ◽  
Dna Elements ◽  
Genomic Regions ◽  
Regulatory Dna

DNase I hypersensitive sites (DHS) associated with a wide variety of regulatory DNA elements. Knowledge about the locations of DHS is helpful for deciphering the function of noncoding genomic regions. With the acceleration of genome sequences in the postgenomic age, it is highly desired to develop cost-effective computational methods to identify DHS. In the present work, a support vector machine based model was proposed to identify DHS by using the pseudo dinucleotide composition. In the jackknife test, the proposed model obtained an accuracy of 83%, which is competitive with that of the existing method. This result suggests that the proposed model may become a useful tool for DHS identifications.

scholarly journals Cholesterol Enhances Helicobacter pylori Resistance to Antibiotics and LL-37

2011 ◽  
Vol 55 (6) ◽  
pp. 2897-2904 ◽  
Author(s):  
David J. McGee ◽  
Alika E. George ◽  
Elizabeth A. Trainor ◽  
Katherine E. Horton ◽  
Ellen Hildebrandt ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Lipid A ◽  
Polymyxin B ◽  
Defined Medium ◽  
Vital Role ◽  
Content Type ◽  
The Two Cultures ◽  
H Pylori ◽  
The Impact

ABSTRACTThe human gastric pathogenHelicobacter pyloristeals host cholesterol, modifies it by glycosylation, and incorporates the glycosylated cholesterol onto its surface via a cholesterol glucosyltransferase, encoded bycgt. The impact of cholesterol onH. pyloriantimicrobial resistance is unknown.H. pyloristrain 26695 was cultured in Ham's F12 chemically defined medium in the presence or absence of cholesterol. The two cultures were subjected to overnight incubations with serial 2-fold dilutions of 12 antibiotics, six antifungals, and seven antimicrobial peptides (including LL-37 cathelicidin and human alpha and beta defensins). Of 25 agents tested, cholesterol-grownH. pyloricells were substantially more resistant (over 100-fold) to nine agents than wereH. pyloricells grown without cholesterol. These nine agents included eight antibiotics and LL-37.H. pyloriwas susceptible to the antifungal drug pimaricin regardless of cholesterol presence in the culture medium. Acgtmutant retained cholesterol-dependent resistance to most antimicrobials but displayed increased susceptibility to colistin, suggesting an involvement of lipid A. Mutation oflpxE, encoding lipid A1-phosphatase, led to loss of cholesterol-dependent resistance to polymyxin B and colistin but not other antimicrobials tested. Thecgtmutant was severely attenuated in gerbils, indicating that glycosylation is essentialin vivo. These findings suggest that cholesterol plays a vital role in virulence and contributes to the intrinsic antibiotic resistance ofH. pylori.

scholarly journals Specific Antibodies in Sera and Gastric Aspirates of Symptomatic and Asymptomatic Helicobacter pylori-Infected Subjects

1998 ◽  
Vol 5 (3) ◽  
pp. 288-293 ◽  
Author(s):  
A. Mattsson ◽  
A. Tinnert ◽  
A. Hamlet ◽  
H. Lönroth ◽  
I. Bölin ◽  
...  
Keyword(s):  
Duodenal Ulcer ◽  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Immunosorbent Assay ◽  
Antibody Responses ◽  
Enzyme Linked Immunosorbent Assay ◽  
Duodenal Ulcers ◽  
Specific Antibodies ◽  
Antibody Titers ◽  
H Pylori

ABSTRACT In this study we have determined systemic and local antibody responses against different Helicobacter pylori antigens inH. pylori-infected and noninfected subjects. In addition, we studied whether differences in antibody responses between patients with duodenal ulcers and asymptomatic H. pylori carriers might explain the different outcomes of infection. Sera and in most instances gastric aspirates were collected from 19 duodenal ulcer patients, 15 asymptomatic H. pylori carriers, and 20 noninfected subjects and assayed for specific antibodies against different H. pylori antigens, i.e., whole membrane proteins (MP), lipopolysaccharides, flagellin, urease, the neuraminyllactose binding hemagglutinin HpaA, and a 26-kDa protein, by enzyme-linked immunosorbent assay. The H. pylori-infected subjects had significantly higher antibody titers against MP, flagellin, and urease in both sera and gastric aspirates compared with the noninfected subjects. Furthermore, the antibody titers against HpaA were significantly elevated in sera but not in gastric aspirates from the infected subjects. However, no differences in antibody titers against any of the tested antigens could be detected between the duodenal ulcer patients and the asymptomatic H. pyloricarriers, either in sera or in gastric aspirates.

Open-Source Essential Protein Prediction Model by Integrating Chi-Square and Support Vector Machine

2020 ◽  
Vol 11 (3) ◽  
pp. 38-56
Author(s):  
S. R. Mani Sekhar ◽  
Siddesh G. M. ◽  
Sunilkumar S. Manvi
Keyword(s):  
Support Vector Machine ◽  
Open Source ◽  
Vital Role ◽  
Support Vector ◽  
Chi Square ◽  
Essential Proteins ◽  
Topological Features ◽  
Proposed Model ◽  
Protein Prediction ◽  
Svm Model

Identification and analysis of protein play a vital role in drug design and disease prediction. There are several open-source applications that have been developed for identifying essential proteins which are based on biological or topological features. These techniques infer the possibility of proteins to be essential by using the network topology and feature selection, which can ignore some of the features to reduce the complexity and, subsequently, results in less accuracy. In the paper, the authors have used selenium driver to scrap the dataset. Later, the authors integrated the chi-square method with support vector machine for the prediction of essential proteins in baker yeast. Here, chi-square is a test of dissimilarity used for altering the record, and afterward, the support vector machine is used to classify the test dataset. The results show that the proposed model Chi-SVM model achieves an accuracy of 99.56%, whereas BC and CC achieved an accuracy of 84.0% and 86.0%. Finally, the proposed model is validated using Statistical performance measures such as PPA, NPA, SA, and STA.

scholarly journals In Haitian women and preschool children, iron absorption from wheat flour-based meals fortified with sodium iron EDTA is higher than that from meals fortified with ferrous fumarate, and is not affected by Helicobacter pylori infection in children

2017 ◽  
Vol 118 (4) ◽  
pp. 273-279 ◽  
Author(s):  
Isabelle Herter-Aeberli ◽  
Kerline Eliancy ◽  
Yanick Rathon ◽  
Cornelia U. Loechl ◽  
Joseline Marhône Pierre ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Preschool Children ◽  
Wheat Flour ◽  
Geometric Mean ◽  
Cost Effective ◽  
Haitian Women ◽  
Ferrous Fumarate ◽  
Fe Isotopes ◽  
Women And Children ◽  
H Pylori

AbstractFe fortification of wheat flour was proposed in Haiti to combat Fe deficiency, but Fe bioavailability from fortificants has never been investigated in Haitian women or preschool children, two key target groups. We aimed to investigate the bioavailability of ferrous fumarate (FeFum), NaFeEDTA and their combination from fortified wheat flour. We recruited twenty-two healthy mother–child pairs in Port au Prince, Haiti, for an Fe-absorption study. We administered stable Fe isotopes as FeFum or NaFeEDTA individually in low-extraction wheat flour bread rolls consumed by all participants in a randomised, cross-over design. In a final, identical meal, consumed only by the women, FeFum+NaFeEDTA was administered. We measured Fe absorption by using erythrocyte incorporation of stable isotopes 14 d after consumption of each meal, and determined Fe status, inflammatory markers and Helicobacter pylori infection. Fe absorption (geometric mean was 9·24 (95 % CI 6·35, 13·44) and 9·26 (95 % CI 7·00, 12·31) from FeFum and 13·06 (95 % CI 9·23, 19·10) and 12·99 (95 % CI 9·18, 18·39) from NaFeEDTA in mothers and children, respectively (P<0·05 between compounds). Fe absorption from FeFum+NaFeEDTA was 11·09 (95 % CI 7·45, 17·34) and did not differ from the other two meals. H. pylori infection did not influence Fe absorption in children. In conclusion, in Haitian women and children, Fe absorption from NaFeEDTA was 40 % higher than from FeFum, and the combination FeFum+NaFeEDTA did not significantly increase Fe absorption compared with FeFum alone. In the context of Haiti, where the high costs of NaFeEDTA may not be affordable, the use of FeFum at 60 mg Fe/kg flour may be a preferable, cost-effective fortification strategy.

scholarly journals Bismuth Containing Quadruple Therapy versus Tailored Therapy as first-line treatments for Helicobacter pylori infection in a high clarithromycin resistance area

2019 ◽  
Author(s):  
Byoung Wook Bang ◽  
Jong Beom Shin ◽  
Eun Jung Ko ◽  
Kye Sook Kwon ◽  
Yong Woon Shin ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Cost Effective ◽  
Medical Costs ◽  
Rapid Urease Test ◽  
First Line ◽  
Tailored Therapy ◽  
Quadruple Therapy ◽  
Clarithromycin Resistance ◽  
Urease Test ◽  
H Pylori

Abstract Background Increasing clarithromycin resistance has led to the need for an alternative first-line therapy for the eradication of Helicobacter pylori (H. pylori) in Korea, and bismuth containing quadruple therapy (BQT) and tailored therapy (TT) have been proposed as alternative regimens. The aim of this study was to compare the eradication rates of BQT and TT as first-line H. pylori eradication therapies. Methods H. pylori infection was diagnosed using the rapid urease test or dual-priming oligonucleotide-based multiplex polymerase chain reaction (DPO-PCR) during endoscopy. Patients positive for H. pylori were divided into two groups; those tested using the rapid urease test received empirical BQT (the BQT group) whereas those tested by DPO-PCR received TT (the TT group). Eradication rates, adverse events, and overall medical costs, which included diagnostic test and eradication regimen costs, were compared. Results Three hundred and sixty patients were included in the study (TT group 178, BQT group 182). The modified intention-to-treat eradication rates of BQT and TT were 88.2% (142/161) and 80.3% (118/147), respectively (p=0.055), and corresponding eradication rates in the per-protocol population were 88.8% (142/160) and 81.4% (118/145) (p=0.07). Compliance and adverse event rates were similar in the two groups. Average medical costs were $ 90.3 per patient in the TT group and $ 75.5 in the BQT group (p=0.000). Conclusions Empirical BQT and tailored therapy were similar in terms of H. pylori eradication rate, safety, and tolerability, but BQT was more cost-effective.

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