Detection of human cytomegalovirus genome in malignant gliomas by in situ hybridization technique

Background: Human Cytomegalovirus ( HCMV ), lies dormant in the glial cells , and can be reactivated under conditions of inflammation and immunosuppression. In vitro, the virus can transform cells and dysregulate many cellular pathways involved in oncogenesis. This study was conducted to detect HCMV matrix-protein mRNA using In Situ Hybridization technique in glial brain tumor tissues compared to normal brain tissues and the presence of cytomegalic inclusion bodies in brain tumor tissues. Patients and Method: Thirty eight of glial tumor specimens were obtained in paraffin blocks compared to eight normal brain autopsy specimens which were age and sex matched with the study group as a control group. ISH was conducted tissue sections using a biotinylated Long DNA Probe for CMV Matrix Protein together with in-situ hybridization (ISH) detection kit. Results: The biotinylated probe specific for mRNA encoded HCMV – Matrix Protein showed hybridization with viral nucleic acids in 34 cases(out of 38)of malignant glial tumor specimens representing (73.9% ) of the total study groups . All cases with high grades astrocytoma revealed a positive hybridization in a percentage of 32.6% from 15 cases with grade III, and 10 ( 21.7% ) cases with grade IV astrocytoma. Nine out of 38 cases with grade III astrocytoma representing (23.7%), 7 (18.4 %) cases with glioblastoma multiforme and 2 oligodendroglioma cases(5.3 %), revealed inclusion bodies on histological examination. Conclusions: HCMV may play a role in the glioma pathogenesis. In Situ Hybridization test proved to be a very sensitive and specific technique for the detection of HCMV mRNA in tissues. Epidemiological, histopathological identification of cytomegalic inclusion bodies , and molecular studies are necessary to confirm the association of HCMV related human cancers in general Iraqi population

The effect of laser radiation on DNA damage and repair

Background: The effect of Helium Neon laser (He-Ne 632.8 nm) was reported to protect cells from damage. We studied lymphocyte cells pre irradiated with (UVC 260 nm) to induce DNA damage. Investigations were carried using gel electrophoresis and test for cell viability. It has also been reported that effect depends on incubation period after damage. The extent of damage to the cells depends on the period of irradiation with UVC also on its intensity. Objective: In this work we studied the effect of UVC on DNA damage and cell survival Also study of the effect of He-Ne laser on cell survival after all being pre irradiated with UVC light and its protective effect on DNA post UV damage. Method: This study was conducted in pathology department post graduate laboratory - College of medicine-Baghdad University. The total number of samples was (147). Blood samples were collected from healthy donors came to the blood bank, the amount of blood drown varies from 5ml to 7ml in heparin tubes .The work was carried out during the period between November 2010 to August 2011. In this experiments examination of samples was carried out to test the radiation effect on cell viability by using trypan blue dye, the experiments were preformed after 1, 24 and 72 hours post UVC irradiation to test the repair development. In other experiments Gel electrophoresis were carried out on samples to study the effect of radiation on the DNA fragmentation. Result: Results reveal a reduced DNA fragmentation appeared on gel electrophoresis experiments as the smear length is reduced significantly for both UV10 and UV20 , other results for cell viability tests revelled that He-Ne can increase survival of cells pre irradiated with UVC irradiation giving (66%, 57%, 70%( improvement in UV exposure for10 min and (59%,56%,59%) improvement for UV exposure for 20 min respectively . Conclusion: The effect of the laser in the improvement of cell survival may be attributed to the induction of endogenous radioprotectore and probably enzymes induced by laser irradiation which may be either reduce the free radical by scavenging effect or by improved cell repair, we may conclude that He-Ne laser can protect cells from radiation damag

Detection of Human papillomavirus in surface epithelial ovarian carcinoma using in situ hybridization technique

Background: The role of Human papillomaviruses (HPV) in the etiology of ovarian cancer remains unclear and the results are controversial. Several studies have verified the presence of HPV DNA in both malignant and benign ovarian tumors. Objectives: Determine the percentage of detection of HPV high (16&18) and low risk types (6&11) in surface epithelial ovarian carcinoma compared to benign and control groups. Materials And Methods: Molecular detection and genotyping of HPV DNA were performed in 76 ovarian tissue blocks by using in situ hybridization (ISH) technique for detecting and localization of high risk HPV (16 and 18) and low risk HPV (6&11) types. Results: The presence of ISH signals for HPV DNA in benign group (71%) was higher than that found in malignant group (64%). HPV 16 was the most predominant type followed by HPV18, 6, and 11 respectively in both malignant and benign groups. High risk HPV were presented with low score and high intensity in both malignant and benign tumors. Low risk HPV types were detected in high score and intensity in benign tumors which significantly differed from that with malignant tumors, which revealed low score and low intensity. The percentage of co-infection of low risk HPV6&11 in benign group was higher (16.9%) than malignant group (7.1%). Only significant difference was found in combination of both high and low risk HPV types. Conclusions: This finding reflects a possible role of HPV virus in the carcinogenesis of ovarian tumors. HPV infection may play a relative role in the pathogenesis of ovarian carcinomas or it could facilitate its progression

Forkhead box P3 gene expression and chromosomal analysis in a sample of Iraqi patients with multiple sclerosis

Background: Multiple Sclerosis disease is a demyelination process which interferes with the neuronal signal transmission, thus leading to different cognitive and physical dysfunctions like optic neuritis, motor, sensory and coordination problems. Recently many researches have been directed toward studying the relation between some genes and multiple sclerosis. Among the important genes to be studied in multiple sclerosis is the forkhead box P3 gene expression. Objectives: The aims of the present work were to study the expression of forkhead box P3 gene by real time polymerase chain reaction, and to perform chromosomal analysis on the multiple sclerosis patients peripheral blood lymphocytes. Patients and methods: A case-control study was performed using real time polymerase chain reaction technique to measure the relative expression of forkhead box P3 gene in peripheral blood leukocytes of 25 newly diagnosed untreated multiple sclerosis patients and comparing them with that of 25 apparently healthy controls, in addition to performing chromosomal analysis on multiple sclerosis patients peripheral blood lymphocytes. Results: Significant down-regulation in forkhead box P3 gene was detected in multiple sclerosis patients in comparison to controls. Chromosomal analysis that was performed for multiple sclerosis patients revealed normal results. Conclusion: Multiple sclerosis is associated with significant change in forkhead box P3 gene expression that can be measured by real time polymerase chain reaction technique. Furthermore, multiple sclerosis is not associated with gross chromosomal abnormalities

MicroRNAs (20a, 146a, 155, and 145) expressions in a sample of Iraqi patients with multiple sclerosis

Background: Multiple sclerosis is a devastating central nervous system autoimmune disorder that is characterized by a series of inflammations, demyelinations, and neurodegenerations that affect the brain and spinal cord. The epigenetic studies specially micro Ribonucleic acid expression represent an important field of researches that probably uncover the obscurities behind the multiple sclerosis pathogenesis. Objectives: to study the expression of micro Ribonucleic acids (20a, 146a, 155, and 145) in multiple sclerosis patients by the use of real time polymerase chain reaction. Patients and Methods: A case-control study was performed using real time polymerase chain reaction technique to measure the relative expression of micro Ribonucleic acids (20a, 146a, 155, and 145) in peripheral blood leukocytes of 25 newly diagnosed untreated multiple sclerosis patients and comparing them with that of 25 clinically apparent healthy controls . Results: Studying of micro Ribonucleic acids expression in multiple sclerosis patients revealed a significant down-regulation in micro Ribonucleic acid-20a while up- regulation of micro Ribonucleic acid-155 expression in multiple sclerosis patients in comparison to controls. Micro Ribonucleic acids -146a and 145 were not associated with significant changes in its expression in multiple sclerosis patients in comparison to controls. Conclusion: multiple sclerosis is associated with significant changes in micro Ribonucleic acids expression including micro Ribonucleic acid-20a, and micro Ribonucleic acid-155 but not micro Ribonucleic acid 146a and-145 that can be measured by real time polymerase chain reaction technique

Molecular characterization of glucose-6-phosphate dehydrogenase deficient variants in Baghdad city - Iraq

Background: Although G6PD deficiency is the most common genetically determined blood disorder among Iraqis, its molecular basis has only recently been studied among the Kurds in North Iraq, while studies focusing on Arabs in other parts of Iraq are still absent. Methods: A total of 1810 apparently healthy adult male blood donors were randomly recruited from the national blood transfusion center in Baghdad. They were classified into G6PD deficient and non-deficient individuals based on the results of methemoglobin reduction test (MHRT), with confirmation of deficiency by subsequent enzyme assays. DNA from deficient individuals was studied using a polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) for four deficient molecular variants, namely G6PD Mediterranean (563 C®T), Chatham (1003 G®A), A- (202 G®A) and Aures (143 T®C). A subset of those with the Mediterranean variant, were further investigated for the 1311 (C®T) silent mutation. Results: G6PD deficiency was detected in 109 of the 1810 screened male individuals (6.0%). Among 101 G6PD deficient males molecularly studied, the Mediterranean mutation was detected in 75 cases (74.3%), G6PD Chatham in 5 cases (5.0%), G6PD A- in two cases (2.0%), and G6PD Aures in none. The 1311 silent mutation was detected in 48 out of the 51 G6PD deficient males with the Mediterranean variant studied (94.1%). Conclusions: Three polymorphic variants namely: the Mediterranean, Chatham and A-, constituted more than 80% of G6PD deficient variants among males in Baghdad. Iraq. This observation is to some extent comparable to othe

Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders

The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The knowledge translation status in selected Eastern-Mediterranean universities and research institutes.

A serious worldwide effort to strengthen research based knowledge translation (KT) has begun in recent years and some countries, particularly developed ones, are trying to incorporate KT in their health and health research systems. Keeping in mind the recent economic depression and the need to perform more efficient research, we aimed to assess and compare the KT status of selected health research institutes in the Eastern Mediterranean Regions' countries, and to identify their strengths and weaknesses in the field.After finding the focal points that would steer the focus group discussions (FGDs) and help complete the 'Self Assessment Tool for Research Institutes' (SATORI) tool, each focal point held two FGDs in which researchers, research authorities and other individuals specified in detail further in the study were held. The scores obtained by each institute were evaluated quantitatively, and the transcriptions were analyzed qualitatively with OpenCode software.For ease of analysis the 50 items of the SATORI were classified into 7 main domains: 'priority setting', 'research quality and timeliness', 'researchers' KT capacities', 'facilities and pre-requisites of KT', 'processes and regulations supporting KT', 'interaction with research users', and 'promoting and evaluating the use of knowledge'. Based on the scoring system, the strongest domain was 'research quality and timeliness'. 'Priority setting' was the weakest domain of all. The remaining domains were more or less equal in strength and were not in a favorable state. The qualitative findings confirmed the quantitative findings.The main problem, it seems, is that a KT climate does not exist in the region. And despite the difference in the contexts, there are many similarities in the region's institutes included in this study. Collaborative efforts can play a role in creating this climate by steering countries towards KT and suggesting regional strategic directions according to their needs