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Article
Some Rapid Methods for Oral Treponema Detection
بعض الطرق السريعة في تشخيص جراثيم تريبونيما الفم

Author: Summaya A. Al- Hamdonii سمية عدنان صالح الحمدوني
Journal: Rafidain journal of science مجلة علوم الرافدين ISSN: 16089391 Year: 2012 Volume: 23 Issue: 3E Pages: 23-32
Publisher: Mosul University جامعة الموصل

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Abstract

The present study investigates the presence of four oral Treponemal species using rapid molecular methods. Subgingival fluid samples were obtained before and after one week of scaling and the nucleic acid was liberated from the bacterial cells to be used as a template for PCR. Specific primers for each Treponemal species targeted to16SrDNA sequence was depended.89% of samples were positive for Treponema sp., 88% of them were positive to the presence of more than one type. T. amylovorum, T. medium, T.socranskii, and T. vincentii were detected in 72%, 87%, 76 % , and 28% respectively with higher percentage at pocket depths >5 mm. Molecular method was able to detect Treponemal species even after scaling, however, in lower percentage than before it.

تبحث الدراسة الحالية عن وجود أربعة أنواع منTreponema الفم باستخدام الطرائق الجزيئية السريعة. تم الحصول على عينات من سائل تحت اللثة قبل وبعد اسبوع واحد من إجراءscaling وتم تحرير الحامض النووي من الخلايا البكتيرية لاستخدامه كقالباً في تفاعل PCR. تم اعتماد بوادئ متخصصة لتتابع16SrDNA لكل نوع Treponema. أظهرت النتائج أن 89% من العينات كانت موجبة لوجود Treponema sp.، 88% منها كانت موجبة لوجود أكثر من نوع واحد. شخصت الأنواع T. amylovorum ،T. medium، T. socranskii ، T. vincentii بنسبة 72%، 87%، 76%، 28% على التوالي وبنسبة أعلى عند عمق جيب 5< ملم. تمكنت الطرائق الجزيئية من الكشف عن هذه الأنواع بعد إجراء scaling لكن بنسبة اقل من نسبتها قبل إجراءscaling .

Keywords

Oral Treponema --- 16S rRNA --- PCR.


Article
Study of Phylogenetic Tree and Morphology of Aporrectodea Based on Mitochondrial Marker (16S rRNA gene) in Some Area South of Baghdad/ Iraq

Author: Najwa Sh. Ahmed1, Nebrass Faleh Chacain2, Falih Hamzah Edan3,Saad M. Nada1, Anas Noori Ibraheem1
Journal: Iraqi Journal of Biotechnology المجلة العراقية للتقانات الحياتية ISSN: 18154794 Year: 2015 Volume: 14 Issue: 2 Pages: 47-54
Publisher: Baghdad University جامعة بغداد

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Abstract

This study aimed to show the phylogenetic structure of Aporrectodea genus in order to verify its cladistics nature and its taxonomic validity. In this work, collection of Aporrectodea genus from three locations from South of Baghdad, (AL-Karrada, AL-Zafranya and New Baghdad) are studied. First, we used usual morphological characteristics to identify each species than molecular phylogenetic analyses are based on the sequences of mitochondrial 16S rRNA gene regions and used software MEGA6 and Raptorx software. Rresults of the two methods (MEGA 6 and Raptorx software) were cluster groups (organisms of 8 sample from Group1A and Group3) in one group and with distance equal to 0.006, clustering of group 2 as a single group, and reached the highest value between group 2 and group 1(B) with distance equal to 0.272 and to move away genetic traits, Raptorx software, conformation of protein for 16SrRNA appeared as a result of the similarity of Mega6. The marker mitochondrial 16S rRNA gene is a powerful tool for identifying species of earthworms and provides a useful complement to traditional morphological taxonomy.


Article
Isolation and identification of Citrobacter freundii from chicken meat samples using cultural and molecular techniques

Authors: Marwa Hameed AlKhafaji --- Mohammed Hayder Hashim
Journal: Iraqi Journal of Science المجلة العراقية للعلوم ISSN: 00672904/23121637 Year: 2018 Volume: 59 Issue: 3A Pages: 1216-1224
Publisher: Baghdad University جامعة بغداد

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Abstract

Because of Citrobacter freundii medical and economical importance and that there are only little local studies about it, this study aimed to isolate and identify this important bacterial species from others that have a similar biochemical and morphological characteristics. Twenty five chicken meat samples were collected randomly from local markets in Baghdad city during 2017; Citrobacter was isolated from the collected samples using selective and differential media and identified using biochemical tests, the identification was confirmed using Vitek 2 compact and polymerase chain reaction for 16S rRNA and the isolated bacteria identified as C. freundii.


Article
Identification Pseudomonas aeruginosa by 16s rRNA gene for Differentiation from Other Pseudomonas Species that isolated from Patients and environment
تشخيص بكتريا Pseudomonas aeruginosa بـجين 16s rRNAلتفريقها عن بقية انواع جنسها المعزولة من المرضى والبيئة

Authors: Abeer A. Marhoon محمد ابراهيم الطائي --- Ismail H.Aziz اسماعيل حسين عزيز --- Mohammed E. Altaai عبير علي مرهون
Journal: Baghdad Science Journal مجلة بغداد للعلوم ISSN: 20788665 24117986 Year: 2014 Volume: 11 Issue: 2 عدد خاص بالمؤتمر النسوي الثاني Pages: 1028-1034
Publisher: Baghdad University جامعة بغداد

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Abstract

Pseudomonas aeruginosa is a common and major opportunistic human pathogen, its causes many and dangersinfectious diseases due to death in some timesex: cystic fibrosis , wounds inflammation , burns inflammation , urinary tract infection , other many infections otitis external , Endocarditis , nosocomial infection and also causes other blood infections (Bacteremia). thereforebecomes founding fast and exact identification of P. aeruginosafrom samples culture very important.However, identification of this species may be problematic due to the marked phenotypic variabilitydemonstrated by samples isolates and the presence of other closely related species. To facilitate species identification, we used 16S ribosomal DNA(rRNA) sequence data toidentify genus- and species-specific 16S rRNA signature sequences,its account a stable part of the geneticcode. Based on these sequences we designed simple, rapid, and accurate PCR assays that allow the differentiation of P. aeruginosa from Pseudomonas species and other pathogen genus ,also this test considered as the most specific than the other diagnostic tests like API (20) which give 70% while the 16SrRNA test give more than 90 %.

تعد بكتريا الـPseudomonas aeruginosa الاكثر شيوعا وخطورة من بين الممرضات الانتهازية التي تصيب الانسان ،اذ تسبب العديد من الامراض المعدية الخطرة التي تؤدي الى الموت في بعض الاحيان مثال ذلك التكيس الليفي ، التهاب الجروح، التهاب الحروق ، التهاب المجاري البولية ، والعديد من الاصابات الاخرى . لذلك اصبح من المهم جدا ايجاد طريقة سريعة ودقيقة لتشخيص بكتريا الـ Pseudomonas aeruginosa من العينات المرضية المزروعة على الاوساط الزرعية وذلك لان تشخيص هذا النوع يواجه مشكلة التغاير في النمط المظهري الملحوظ في العينات المعزولة التي تحتوي على العديد من الانواع المتقاربة جدا فيما بينها وابسط طريقة للتفريق بين هذه الانواع هي استخدام الـ 16SrRNA الذي يعطي تشخيصا للجنس والنوع اذ يعد الشفرة الوراثية الثابتة للنوع وبذلك . هدفت هذه الدراسه الى ايجاد تشخيص سريع وبسيط ودقيق بتقنيةPCR يهيأ لنا تشخيص بكتريا الـPseudomonas aeruginosaوتفريقها عن باقي انواع جنسها واجناس مرضيه اخرى وكذلك يعتبر هذا الاختبار الأدق من بين الاختبارات التشخيصية الاخرى مثل الـAPI (20) حيث يعطي نسبة 70% في حين يعطي التشخيص بالـ16SrDNA اكثر من %90.


Article
Molecular diagnosis and DNA fingerprinting based on IS6110 of Mycobacterium tuberculosis isolated from patients in Iraq

Author: Mothanna A. S. Almahdawi1 , Ahmmed A. Mankhi2 , Mohammed M. Kdban1
Journal: Iraqi Journal of Biotechnology المجلة العراقية للتقانات الحياتية ISSN: 18154794 Year: 2018 Volume: 17 Issue: 1 Pages: 51-59
Publisher: Baghdad University جامعة بغداد

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Abstract

Polymerase chain reaction assay (PCR) used for the detection of Mycobacterium tuberculosis strain and fingerprint study. Ten positive cultures on Lowenstein Jensen (LJ) media were collected from specialized center of chest and respiratory diseaseBaghdad .genomic DNA was extracted from all isolates and subjected to genetic characterization by (PCR) methods. two specific primers were used in pcr analysis for detection 16S rRNA and insertion sequence IS6110 where commonly used as a target of Mycobacterium. The result of gel electrophoresis showed that all isolates belong to Mycobacterium, and a sequence showed that 99% identity in sequence of 16S rRNA of M. tuberculosis and there is one nucleotide changes, the isolate submission in gen bank NCBI with accession number (MG03060) and 100 identity in sequence of IS6110 of M. tuberculosis. The isolate showed there is Ten polymorphism diversity according to copy number of IS6110 that have, where 80% of M.tuberculosis has large copy number (6_10) and 20% have low copy number (1-5) of isolate. This study showed that M.tuberculosis isolated in Iraq belong to two groups. Polymorphism groups depended on copy number of IS6110.


Article
Isolation and identification of Streptococcus mutans from dental caries patients at Thi-Qar province/Iraq

Authors: Hamza Sh. Abd Al-Zahra --- Manal B. Saleh
Journal: JOURNAL OF THI-QAR SCIENCE مجلة علوم ذي قار ISSN: 19918690 Year: 2018 Volume: 6 Issue: 4 Pages: 22-27
Publisher: Thi-Qar University جامعة ذي قار

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Abstract

Dental caries is one of an important common human infectious disease that can lead to loss of tooth structure, it is occur due to the metabolic activation of the plague microorganisms especially Streptococcus mutans bacterium. Eighteen samples from saliva and dental plaque were collected from patients with dental caries active at ages from (7-25) years from Specialized dental hospital and dental clinics at Thi-Qar province during the period from November to December 2016.Thirty-three isolates belong Streptococcus mutans were identified by cultural methods, biochemical tests and Api 20 Strep. system, while twenty-eight isolates identified by using Polymerase Chain Reaction (PCR) technique and sequencing of 16S rRNA gene with 507 bp, whereas by using 16S rRNA gene the result confirmed that these isolates were belong to Streptococcus mutans. The aim of study is Isolation and identification of Streptococcus mutans bacterium from the dental caries and dental biofilm patients at Thi-Qar province by of 16S rRNA gene


Article
Molecular feature of lasB gene of Pseudomonas aeruginosa isolated from different clinical sources

Author: Molecular feature of lasB gene of Pseudomonas aeruginosa isolated from different clinical sources
Journal: JOURNAL OF THI-QAR SCIENCE مجلة علوم ذي قار ISSN: 19918690 Year: 2018 Volume: 6 Issue: 4 Pages: 163-166
Publisher: Thi-Qar University جامعة ذي قار

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Abstract

The study was carried out through a period from June to November 2017 from out-patients and in-patients of Al-Hussein Teaching Hospital in Thi-Qar province South of Iraq. A sum of 132 specimens from the hospital facility condition and different clinical samples of various patients were randomly collected and analyzed for diagnosis of Pseudomonas aeruginosa. These clinical specimens were included wound, burn, ear swabs, urine and sputum specimens. Every single specimen was screened to detect of P. aeruginosa by culturing on suitable media, and 36 isolates of P. aeruginosa were distinguished through biochemical tests and using API 20NE system for confirmation the isolates. All P. aeruginosa isolates were tested against nine antimicrobial discs in vitro. They revealed that having different classes and the results demonstrated that variable resistance to the anti-microbial agents. In attempting to the recognizable proof of P. aeruginosa having the DNA, Polymerase chain reaction (PCR) was utilized in light of particular groundwork for 16S rRNA genetic marker. The results demonstrated that PCR has observed to be quick and sensitive and particular for recognizable proof of P. aeruginosa. Furthermore, 16S rRNA was utilized as confirmation feature, while lasB detected as virulence gene also to utilize as pathogenesis quality of the bacteria


Article
Molecular Study of 16SrRNA Gene in Enterobacteriaceae isolated from Iraqi Patients

Authors: Ilham Abdul Hadi Khalaf --- Ahmed Mohamed Turkey --- Shahad Hisham Mahmood
Journal: Al-Nahrain Journal of Science مجلة النهرين للعلوم ISSN: (print)26635453,(online)26635461 Year: 2018 Volume: 00 Issue: 1 Pages: 78-87
Publisher: Al-Nahrain University جامعة النهرين

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Abstract

This study included the collection of 204 clinical and non-clinical samples from Ibn-Al-Baladi childbirth Hospital, Al-Yarmouk Teaching Hospital and Imam Ali Hospital in Baghdad, from both genders of different ages. The collected samples were distributed according to the collection source (urine, wounds, burns, feces, Tigris River water in Baghdad and soil samples). A total of 31 isolates of Escherichia coli (48.43 %), 15 isolates Klebsiella pneumoniae (23.43 %), 10 isolates of Enterobacter cloacae (15.62 %) and 8 isolates of proteus mirabilis (12.50 %) were isolated and identified based on microscopic culture, conventional methods, VITEK 2 and molecular identification of 16 SrRNA gene. Our investigations indicated that Escherichia coli and Klebsiella pneumoniae species represent the most frequent isolates, whereas both Enterobacter cloacae and Proteus mirabilis were the less frequent species. The results of the analysis of the sequencing of selected 21 isolates were deposited in the National Center for Biotechnology Information (NCBI) belong to the four species (From LC314477.1 to LC314497.1).


Article
ISOLATION AND IDENTIFICATION OF BACTERIA THAT PRODUCE AMYLASE
عزل وتشخيص البكتريا المنتجة لانزيم الاميليز

Authors: Jasim . M . Awda جاسم محمد عودة1 --- Ali . H. Fayyadh علي حسين فياض
Journal: iraq journal of market research and consumer protection المجلة العراقية لبحوث السوق وحماية المستهلك ISSN: ISSN/ 20713894/ EISSN/25236180 Year: 2018 Volume: 10 Issue: 1 Pages: 17-26
Publisher: Baghdad University جامعة بغداد

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Abstract

Thirty six bacteria were isolated from various sourcesc (soil, starch, cooked rice and other foods) and subjected to a series of primary screening tests to obtain the optimal isolation to production of amylase. The volume of producing zone by logal indicator for (Seven) isolates of the secondary screening by measuring the enzymatic activity and specific enzymatic activity. The isolate A4 was found to be the most efficient for production of amylase. Then this isolate was diagnosed through microscopic, vitek 2 system technique. in addition by gentic diagnesis through gene 16s of the genes nitrogen bases by use the polymerase chain reaction (PCR) which reached 1256 bases. In comparison to the available information at the National Center for Biotechnology Information (NCBI), the isolation was found to be Bacillus subtilis

عزلت 36 بكتريا من مصادر مختلفة (التربة والنشا والارز المطبوخ وبعض الاغذية الاخرى) وأخضعت لمجموعة من اختبارات الغربلة الأولية للحصول على العزلة الأكفأ في انتاج أنزيم الأميليز من خلال حجم الهالة المتكونة بكاشف (لوكال) إذ اختيرت7 عزلات للغربلة الثانوية من خلال قياس الفعالية الأنزيمية والفعالية النوعية للانزيم وتبين ان العزلة التي رمز لها A4 كانت الاكفأ في انتاج انزيم الاميليز, ثم جرى تشخيص هذه العزلة من خلال الفحوصات المجهرية والمزرعية وبتقنية جهازVitek 2 System فضلاً عن التشخيص الجيني من خلال جين 16S بالكشف عن تسلسل القواعد النتروجينية للجين باستعمال تفاعل البلمرة المتسلسل (PCR) والذي بلغ حجمة 1256 قاعدة وبالمقارنة مع ما متوفر من معلومات في المركز الوطني لمعلومات التقنية الحيوية NCBI, تبين ان العزلة تعود الىBacillus subtilis.


Article
XYLANASE PRODUCTION FROM LOCAL BACTERIAL ISOLATE
انتاج الزايلينيز من عزلة بكتريا محلية

Author: Al-Badran & Al-Shamary البدران والشمري
Journal: Iraqi Journal of Agricultural Science مجلة العلوم الزراعية العراقية ISSN: 00750530/24100862 Year: 2019 Volume: 50 Issue: 3 Pages: 759-767
Publisher: Baghdad University جامعة بغداد

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Abstract

Seventeen local isolates of Bacillus were isolated from soil to produce extracellular xylanase under submerged fermentation process by using xylan as carbon sole source. All isolates were subjected to quantitative scanning to select the most efficient one. The highest activity of xylanase (2680u/ml) was obtained from isolate Bacillus sp RS1. The isolate identified by 16SrRNA gene sequence of Bacillus subtilis ( accuracy of 99%)which was matched with sequence of Bacillus subtilis VBN25 that recorded in Genebank under the Accession Number of MG027675.1.Extracted xylan from agricultural waste by acidic method(papyrus, sun flower stalks, Ibaa Wheat type, Furat wheat type and Abo Ghraib wheat type)were used as the substrate for xylanase production from Bacillus. The results showed that the papyrus gave the highest amount of xylan (187.6 µg/ml) as compared with that of the sun flower stalks, Ibaa Wheat type, Furat wheat type and Abo Ghraib wheat type(161.3, 161.6, 157.6, 157.2) µ g/ml respectively. The results indicated that the highest xylanase activity was 2800 u/ml produced by Bacillus subtilus when Papyrus xylan was used.

تم الحصول على سبعة عشر عزلة محلية لبكتريا Bacillus منتجة لانزيم الزايلنيز Xylanase باستعمال نظام تخمرات المزارع المغمورة بأستعمال الزايلان Xylan مصدرا وحيدا للكاربون، تم الحصول عليها من التربة. خضعت جميع العزلات للغربلة الكمية لاختيار الاكثر كفاءة في انتاج الانزيم، اعلى فعالية لانزيم الزايلنيز بلغت 2680 وحدة /مل ، تم الحصول عليها من العزلة Bacillus sp RS1. شخصت العزلة جزيئيا بالاعتماد على تتابعات القواعد النتروجينية للجين 16S rRNAعلى انها Bacillus subtilus وبنسبة تطابق 99%بالمقارنة مع تتابعات القواعد النتروجينية للعزلة العالمية Bacillus subtilis VBN25 في بنك الجينات NCBI بالرقم MG027675.1. استعمل الزايلان المستخلص من الفضلات الزراعية(البردي وسيقان زهرة الشمس والحنطة اصناف اباء وفرات وابو غريب) .اكدت النتائج ان اعلى نسبة من الزايلان تم الحصول عليها من البردي g/ml) µ (187.6 بالمقارنة مع سيقان زهرة الشمس والحنطة اصناف (اباء وفرات وابو غريب) حيث بلغت كمية الزايلان (161.3, 161.6, 157.6, 157.2)مايكروغرام/مل على التوالي. اكدت النتائج ان اعلى فعالية لانزيم الزايلنيز تم الحصول عليها من زايلان القصب حيث بلغت 2800 وحدة/مل باستعمال بكتريا . Bacillus subtilis

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