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Article
In silico Modeling of Beta-lactamase Protein Acinetobacter baumannii

Author: Taif M. Abdul-Hussein1 , Hasan M. Abo Almaali2 , Shurook M.K. Saadedin1 , Wifaq M. Al-Wattar3
Journal: Iraqi Journal of Biotechnology المجلة العراقية للتقانات الحياتية ISSN: 18154794 Year: 2019 Volume: 18 Issue: 1 Pages: 37-42
Publisher: Baghdad University جامعة بغداد

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Abstract

The most common mechanism of resistance to β-lactam antibiotics in gram-negative bacteria is the production of β-lactamases that hydrolyze the drug. Results that have been obtained from some servers that have been used in this study were gave a poor quality and prediction. SWISS MODEL server results gave more promising result as it had 92% query coverage. Validated was done for the model study by using QMEAN score, Ramachandran plot and ProSA server. 3D Refine and Mod Refiner were used for model refinement. Finally, ProSA server have been used in order to revalidate the model.


Article
In Silico Investigations of some Adverse Effects of Anticancer Drugs used in Iraq
دراسات حاسوب لبعض الجوانب السلبية للأدوية المضادة للسرطان المستعملة في العراق

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Abstract

Abstract: Adverse effects of anticancer drugs used in Iraq (30 drugs) were studied using in Silico approaches represented by using T.E.S.T v. 4.1 software. Results showed that 50% of drugs were mutagenic and 91% of them caused developmental toxicity .There was positive relationship between mutagenicity and developmental toxicity and the correlation coefficient was (r=0.779) . Most mutagenic activity caused by alkylating drugs (30.77%) and less than that by intercalating drugs (23.08%). Developmental toxicity mainly resulted from drugs affected the enzymes and receptors (29.41%) while drugs interact with tubulin resulted in (17.65%) of toxicity cases. The rest of percentages were due to other factors which some of them were unknown. There was no relationship between the number of rings (in general) in drug molecule and the mutagenicity and developmental toxicity. Other parameters such as number of rotatable bonds، HB donors and HB acceptors had no effect on mutagenicity and developmental toxicity.

درست بعض الجوانب السلبية الناجمة عن استعمال بعض الأدوية المضادة للسرطان المستعملة في العراق ( 30 دواء) باستعمال الحاسوب . أسفرت النتائج عند استعمال برنامج T.E.S.T v. 4.1 ان%50 من الأدوية لها فعالية تطفيرية وان %91 منها لها تأثيرات على التطور وعلى المدى البعيد ، وكانت العلاقة موجبة بين القابلية التطفيرية وسمية التطور اذ بلغ معامل الارتباط (r=0.779) وكانت اغلب حالات التطفير ناتجة عن عمليات الألكلة ( حوالي 30.77%) وبدرجة اقل عن عمليات الحشر (23.08%) ، اما سمية التطور فكانت ناتجة بشكل أساسي عن التأثير في الإنزيمات والمستلمات (29.41%) في حين كان التداخل مع Tubulin بدرجة اقل (17.65%) وشغلت العوامل المتعددة الأخرى التي بعضها غير معروف باقي النسب في كلا الحالتين . لم تكن هناك علاقة بين عدد الحلقات (العامة) الموجودة في الدواء مع حالة التطفير او سمية التطور . ولا توجد علاقة بين مؤشرات أخرى مثل عدد الأواصر الحرة Rotatable bonds او HB donors و HB acceptorsمع الجوانب السلبية المدروسة .


Article
In Silico and in Vitro Evaluation of Real Time PCR Assay for Detection of Staphylococcus aureus

Authors: Al-Shaimaa Muhammed Saeed Al-Rawi --- Abdul Kareem A. Al-Kazaz --- Majeed Arsheed Sabbah --- Mohammed Mahdi Al-Zubaidi
Journal: Al-Nahrain Journal of Science مجلة النهرين للعلوم ISSN: (print)26635453,(online)26635461 Year: 2017 Volume: 20 Issue: 1 Pages: 126-131
Publisher: Al-Nahrain University جامعة النهرين

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Abstract

Many research groups developed real time PCR assays for identification of Methicillin-resistant Staphylococcus aureus (MRSA). They designed different primers and probes in their assays. Gene mecA is the target identification of MRSA by PCR assay. The aim of this study is using in silico approach to identify the best primers and probe for real time PCR identification mecA gene. Published primers and probes were analyzed in silico to select the best for real time PCR identification of mecA gene. The selected primers and probe successfully used for real time amplification of twenty MRSA tested. This study reveals the importance of in silico approach for designing diagnostic assays shorten the cost and the time. [DOI: 10.22401/JNUS.20.1.18]


Article
Association of PPARG gene polymorphism (Pro 12 Ala) with the risk of type 2 diabetes mellitus (T2DM) incidence in sample of Iraqi patients

Author: Shaymaa S. Abd Alrazzaq , Ismail A. Abdul-hassan
Journal: Iraqi Journal of Biotechnology المجلة العراقية للتقانات الحياتية ISSN: 18154794 Year: 2018 Volume: 17 Issue: 3 Pages: 112-123
Publisher: Baghdad University جامعة بغداد

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Abstract

Diabetes mellitus is a combination of heterogeneous disorders commonly presenting with episodes of hyperglycaemia and glucose intolerance, as a result of lack of insulin, defective insulin action, or both . PPARG gene variant ( pro 12 ala) has been linked to risk of development of diabetes mellitus . this study was carried out to examine whether the polymorphism of PPARG gene are correlated with the incidence of type 2 diabetes mellitus (T2DM) in Iraqi population. Diabetic patients (n=50) and apparently healthy control subject (n=50), were enrolled genotyping of PPARG gene SNP (rs1801282) were determined by using Taqman genotyping assay. The results showed that the distribution of genotypes and alleles frequencies at (rs1801282) SNP of PPARG gene, as related with CC , CG and combined CG+CC genotypes, G allele seem to be a protective allele, therefore, the presence of both heterozygous and homozygous mutants may reduce the risk of T2DM (the frequency of CG+GC mutants were 68% in apparently healthy control individuals and 50% in T2DM patients). In contrast, there is wild CC genotype (50 versus 32% in T2DM and control group, respectively, X2=6.93; P<0.01; OR=1.272).


Article
In Silico Model for Lung Cancer Prediction Based on TP53 mutations Using Neural Network

Authors: Ban Nadeem Dhannoon --- Zahraa Naser Shahweli
Journal: Al-Nahrain Journal of Science مجلة النهرين للعلوم ISSN: (print)26635453,(online)26635461 Year: 2018 Volume: 00 Issue: 1 Pages: 196-201
Publisher: Al-Nahrain University جامعة النهرين

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Abstract

In silico models have become well known in the current decade because they assist researchers and specialists in organizing and analyzing big data. To complete their work, these models require powerful techniques and algorithms, the most important of which are machine learning algorithms. This work utilizes the Relief F algorithm for feature selection and trains the back propagation neural network (BPNN) algorithm on the UMD TP53 all-2012-R1-US database for lung cancer. Lung cancer is the most commonly diagnosed cancer among women and men, and can be predicted from mutations that occur in the TP53 tumor suppressor gene. Five measures are used to estimate performance: sensitivity and specificity are important dimensions utilized to obtain the receiver operating characteristic (ROC) curve; accuracy and F measure are necessary to determine algorithm precision; and Matthews correlation coefficient (MCC), which is the most important measure, provides the right criterion for classification algorithms. The Relief F and BPNN algorithms achieve satisfactory results that reach 99.41 for sensitivity, 95.39 for specificity, 99.04 for accuracy, 99.47 for F measure, and 0.93 for MCC.


Article
In silico Identification to Potential Drug siRNA Using Statistical Methods in Helicobacter pylori
.دراسه حاسوبيه لتشخيص التواليات الدوائية siRNA الاكفأ باستخدام طرق احصائية لبكتريا Helicobacter pylori

Author: Al Rikabi, Z. H. زينب هاتف عباس
Journal: karbala journal of pharmaceutical sciences مجلة كربلاء للعلوم الصيدلانية ISSN: 70272221 Year: 2014 Issue: 8 Pages: 26-37
Publisher: Kerbala University جامعة كربلاء

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Abstract

Helicobacter pylori a causative influence risk of carcinogenesis which has developed resistance to drugs. The present study was carried out to identify potential drug targets in H. pylori by design of potent siRNA. To reach the goal, the collection essential gene for H. pylori and host from DEG, then a variety of bioinformatics databases studying Blastp Database of essential genes, Blastp from NCBI and KEGG, for selection non-homologous genes, then the software OligoWalk to design siRNA. The study concluded to get seven (7) essential membrane protein of H. pylori to become drug target, then subjected to find siRNA which are shorter than 21 nt about 2423 siRNA, 110 siRNA (Effective siRNA rules), 56 siRNA (ratio GC (35%-60%)), 50 siRNA (Desired position), 30 siRNA (Probability range between (0.70-0.91)), 20 siRNA (Secondary structures), 8 siRNA (Drug target), this steps respectively. Conclusion: Eight (8) siRNA which could use as potential drug target for resistant of Helicobacter pylori 26695.

بكتريا Helicobacter pylori من المسببات المرضيه الخطرة لاحداث التسرطن والتي تطورت لمقاومة العقاقير. وقدأجريت هذه الدراسة لتحديد أهداف دوائية ل H. pylori بتصميم تواليات صغيره قويه التاثير من .siRNA للوصولللهدف، تم جمع الجينات الاساسية ل H. pylori والمضيف )الإنسان( من قاعده بيانات ،وتم استخدام العديد من برامجياتالمعلوماتية الحيوية blastp من قاعده البيانات DEG و NCBI وباستخدام Blastp كما استخدمت KEGG لاختتيارالجينات غير المتجانسة. وتم استخدام برنامج OlioWalk لايجاد siRNA واستخلصت الدراسه للوصول الى سبعه منالبروتينات الغشائية الاساسية ل H.pylori لتصبح اهدافا دوائية، ثم اختضعت لايجاد siRNA والتي تكون أقصر من21 نيوكلتيد والبالغ عددها 4242 siRNA 111 ، siRNA )ختاضعة قواعد تصميم siRNA الفعال(، 65 siRNA)ضمن حدود GC ٪ المطلوبه (35%-60%) (، و 61 siRNA )ضمن الموقع المطلوب(، 21 siRNA )ذات احتماليهعاليه تراوحت بين 0.70-0.91) 41 ،) siRNA )الهياكل الثانوية(، 8 siRNA )اهدافا دوائية( على التوالي. الاستنتاج:ثمانية تواليات صغيره من نيوكلتيدات ) (siRNA تمثل اهدافا دوائية لمقاومه بكتريا Helicobacter pylori 26695 .


Article
Single Nucleotide Polymorphism SNP Analysis of Exon6FollistatinGene Relatedtopolycystic Ovarian Syndrome inThiQar Governorate.

Author: EnasAbd-AlkareemJabaar
Journal: Journal of University of Babylon مجلة جامعة بابل ISSN: 19920652 23128135 Year: 2018 Volume: 26 Issue: 4 Pages: 293-307
Publisher: Babylon University جامعة بابل

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Abstract

Follistatin has been identifiedas a nominee gene for polycystic ovary syndrome (PCOS) from relationship studies.Acting to control the developmentof ovarian follicles and as an antagonist to aromatase action, changes in Follistatinrole or expression may affect main features of PCOS alteration.The aim of the recent study was to study the association of FST gene to define if genomicdifferencesarerelated with phenotypic structures of PCOS patients in a case–control suggestion study.Methods:This study involved 30 women with PCOS and 20 healthy women, whowerematched by their ageand anthropometric and biochemical profiles.The study was designed to examine theseparation of deoxyribonucleic acid (DNA), and genotype analysis was done for all the study participants using PCR-SNP.Results:Polymorphisms (SNPs) in the exon 6 FST gene region were determined for PCOS patients and controls, it was found that PCOS patientshad17 SNP in different samples, and after performing amino acid sequences alignment for these SNPs, it was observed that the last two SNPs of sample C12 constituted a non-synonym mutation, and the functional conformation of the produced FST gene weremodified with regard to exon 6 in the genotype C12. When this exonic SNP appears in the three-dimensional structure of the resulting proteins of C12 genotypes, the positively charged amino acid, Asp, is converted into another positively charged amino acid, His, in position 331 of the whole amino acid sequence of FST protein.The conclusionis that this, in turn doesn’t change the final phenotypic manifestation of the protein, and there was no alteration in the phenotypes of the PCOS patients.

يعرف الفولستاتينعلى انه من اكثر الجينات ارتباطا بمرض تكيس المبايض اذ انه يعمل على السيطرة على نمو الحويصلات المبيض وكذلك السيطرة على فعالية انزيم الاروماتيز وان أي تغيير في هذا الجين يؤدي الى زيادة امراضية النساء المصابات بتكيس المبايض وان الهدف من الدراسة الحالية هو دراسة العلاقة بين الجين المذكور ومرض تكيس المبايض مقارنة مع النساء الطبيعيات.تضمنت هذ الدراسة 30 امراة مصابة بتكيس المبايض و20 امراة غير مصابة و تمت المقارنة بينهن من الناحية المظهرية وقياس المعايير الهرمونية وكذلك دراسة التغيرات الجينية.لقد وجد من نتائج الدراسة ان النساء المصابات بتكيس المبايض يعانين من الزيادة في الوزن وكذلك ظهور شعر في مناطق غير مرغوب بها وزيادة في هرمون اللوتيني ونقصان في الهرمون المولد للحويصلات اما من الناحية الجينية فقد لوحظ وجود 17 تغير جيني عند النساء المصابات بتكيس المبايض وبعد مطابقة هذه التغيرات الجينية مع التغيرات المحتملة في البروتين وجد ان فقط 2 من التغيرات الجينية التي تسمى الطفرة الوراثية الصامتة التي تؤدي الى التغير من بروتين موجب الشحنة الى بروتين موجب الشحنة ايضا الا انه هذا التغير لا يؤثر على التغيرات المظهرية او امراضية تكيس المبايض .

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