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In silico Comparison of Simple Sequence Repeats in High Nucleotides-Rich Genomes of Microorganism
Fakher Rahim
Pakistan Journal of Biological Sciences , 2008,
Abstract: This study determined the distribution of a specific group of Simple Sequence Repeats (SSRs), in genome sequences of 7 chromosomes (Shigella flexneri 2a str 301 and 2457 T, Shigella sonnei, E. coli K12, M. tuberculosis, M. leprae and S. saprophytycus) have downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs. The data obtained in the present study show that: (i) Tandem repeats are widely distributed throughout the genomes. (ii) SSRs are differentially distributed among coding and non-coding regions in investigated Shigella genomes. (iii) Total frequency of SSRs in non-coding regions is higher than coding regions. (iv) In all investigated chromosomes ratio of Tri-nucleotide SSRs are much higher than randomized genomes and Di nucleotide SSRs are lower. (v) Ratio of total and mono-nucleotide SSRs in real genome is higher than randomized genomes in E. coli K12, Sh. flexneri str 301 and S. saprophyticus, while it is lower in Sh. flexneri str 2457T, Sh. sonnei and M. tuberculosis and it is approximately same in M. leprae. (vi) Frequency of codon repetitions are vary considerably depending on the type of encoded amino acid.
Microcytic hypochromic anemia patients with thalassemia : Genotyping approach
Rahim Fakher
Indian Journal of Medical Sciences , 2009,
Abstract: Background: Microcytic hypochromic anemia is a common condition in clinical practice, and alpha-thalassemia has to be considered as a differential diagnosis. Aims: This study was conducted to evaluate the frequency of α-gene, β-gene and hemoglobin variant numbers in subjects with microcytic hypochromic anemia. Setting And Designs: Population-based case-control study in the Iranian population. Materials And Methods: A total of 340 subjects from southwest part of Iran were studied in the Research Center of Thalassemia and Hemoglobinopathies (RCTH), Iran. Genotyping for known a- and b-gene mutations was done with gap-PCR and ARMS. In cases of some rare mutations, the genotyping was done with the help of other techniques such as RFLP and ARMS-PCR. Statistical Analysis: Statistical analysis was carried out by SPSS 11.5 and an independent-sample t test. Results: Out of the total 340 individuals, 325 individuals were evaluated to have microcytic hypochromic anemia based on initial hematological parameters such as MCV< 80 fl; MCH < 27 pg; the remaining 15 patients were diagnosed with no definite etiology. The overall frequency of -α3.7 deletion in 325 individuals was 20.3%. The most frequent mutations were IVS II-I, CD 36/37 and IVS I-110 with frequencies of 6.31%, 5.27% and 1.64%, respectively. Only, there was a significant difference between beta-thalassemia trait and beta-thalassemia major with regard to MCV (P < 0.05) and MCH (P < 0.05) indices, and also MCH index between beta-thalassemia trait and Hb variants (P < 0.05). Conclusion: Molecular genotyping provides a rapid and reliable method for identification of common, rare and unknown a- and b-gene mutations, which help to diagnose unexplained microcytosis and thus prevent unnecessary iron supplementation.
An in Silico Development of Selective Inhibitor for Histamine Receptors
Fakher Rahim
Biotechnology , 2010,
Abstract: This study aimed to design a reliable homology model of human histamine H1 and H4 receptors (hH1R, hH4R), that would guide future biochemical and genetic efforts in its evaluation as a potential therapeutic target. Furthermore, these accurate models could aid in the structure-based inhibitor design for antagonists against the histamine H1 and H4 receptors. The homologous protein sequences of histamine receptors were retrieved from the NCBI REFSEQ which by using the sequence alignment program ClustalW alignment of the human histamine receptors sequence with Bovine Rhodopsin was conducted to locate the homology aligned regions. The present study found that Asp107 and Asn198 are in favorable positions for anchoring histamine. Identification of novel interaction sites for antagonist binding mutational data suggest a crucial role for Asp107, Trp158, Phe 432 and Phe 435 in antagonist binding. This study identified several novel amino acids at the binding site. Binding mode analysis of known H1 antagonists four known H1 antagonists (mepyramine, acrivastine, desloratadine, loratadine) were docked successfully to the binding site of the hH1R model by FlexiDock. The ligand used for optimizing the receptor model, the pharmacophore constraints and the different scoring functions applied in high throughput docking had all significant effect on the results. This research identified 16 compounds with 7 significant H4 activities representing an overall hit rate of 5.2%. To the best of our knowledge, this is one of the largest structure-based virtual screenings, where the virtual hits were confirmed by an in vitro assay. Moreover, this is the first structure-based drug design study reported on the hH4R. After the virtual screening, we identified several novel ligands with significant H4 affinity. These scaffolds can serve as starting points in the development of potent and selective H4 ligands in future.
Better differential diagnosis of iron deficiency anemia from beta-thalassemia trait
Fakher Rahim,Bijan Keikhaei
Turkish Journal of Hematology , 2009,
Abstract: Objective: Iron deficiency anemia (IDA) and beta-thalassemia trait ( -TT) are the most common forms of microcytic anemia. This study was conducted to compare the validity of various discrimination indices in differentiating β-TT from IDA by calculating their sensitivity, specificity and Youden's index.Methods: Totally 323 subjects (173 children and 150 adults) with microcytic anemia were involved in this study. We calculated 10 discrimination indices in all patients with IDA and β-TT. We divided the patients into two different groups as younger or older than 10 years. Results: None of the indices showed sensitivity and specificity of 100% in the patients older than 10 years, and in the patients younger than 10 years, only Shine & Lal index showed sensitivity close to 90% and specificity of 100%. The most accurate discriminative index for patients younger than 10 years was Shine & Lal and for those older than 10 years it was RDW index. According to Youden's index, Shine & Lal and RBC count showed the greatest diagnostic value in patients younger than 10 years and RDW and RBC count indices in those older than 10 years. Conclusion: None of the indices was completely sensitive and specific in differentiation between β-TT and IDA. Mean and median mean cell Hb density (MCHD) were very close to normal values in both IDA and β-TT patients, but in the case of mean density of Hb/liter (MDHL), we found that the mean and median were significantly higher than normal values in β-TT and lower than normal values in IDA patients. In our study, Youden's index of RBC and Shine & Lal were the highest and most reliable indices in differentiating β-TT from IDA in the patients younger than 10 years. For patients older than 10 years, the most reliable discrimination indices were RBC and RDW.
Assessment of Motility and Survival Rate of Asthenospermic Men's Sperm Cultured in Media Plus Leukemia Inhibitor Factor
Fakher Rahim,Ghasem Saki
International Journal of Pharmacology , 2010,
Abstract: As our knowledge no report was given about effect of leukemia inhibitor factor on sperm motility and survival rate of asthenospermic infertile men. That's why this study was decided to review the effects of Leukemia Inhibitor Factor (LIF) with different concentrations of 0, 3, 5, 10, 50 ng mL-1 on motility and survival rate of asthenospermic infertile men. Semen samples of 15 asthenospermic men who referred to IVF unit of Imam Khomeini Hospital, Ahvaz, Iran were collected and put in incubator under condition 5% CO2 in air at 37°C for 45-30 min then total sperm count was done first, then calculate the motile sperm with a degree a and b. In this study, we evaluated only samples that had sperm motility percent of more than 30%. After that time from every sample about 10 μL removed and culture in different media. Every drop was evaluated 6, 24, 48 h after cultured of sperm in it for motility and survival rate of sperm. Statistical analysis shows that the forward motility of sperm cultured for 6 h in media with and without of LIF is not significant (p>0.05) but after 24 h the forward motility and survival rate of sperm cultured in media with 10 and 50 ng mL-1 of LIF significantly increased (p<0.05) and after 48 h the forward motility and as well as survival rate of sperm cultured in media with 50 ng mL-1 of LIF significantly increased (p<0.05). The conclusion from this study is that certain concentrations of leukemia inhibitor factor can increase the motility and survival rate of sperm.
Complications of CT-Guidance Fine Needle Biopsy in Intra-Thoracic Masses
Mohammad Davoudi,Fakher Rahim
Iranian Journal of Radiology , 2010,
Abstract: Background/Objective: CT scan guided fine needle biopsy of the chest lesions is an increasingly popular technique, but may have complications of which pneumothorax is the most common. The purpose of this study was to observe the complications of needle biopsy of chest lesions guided by CT scan among the studied patients. "nPatients and Methods: This is a descriptive epidemiologic study. All patients who were referred to Imam Khomeini Hospital, Ahwaz from 2005 to 2007 as an indication for chest lesion biopsy were studied. Snapshot files on lung CT scan regarding the lesion size and depth measurements and the biopsy samples obtained were sent to pathology. After the biopsy, the patients' CT scan was to act as the presence or absence of symptoms, proper action was made of "nResults: Among 102 patients studied, 85 patients (83.4%) were uncomplicated, but eight patients (7.9%) suffered from pneumothorax. In this study, there was no correlation found between the size of the lesion and the severity of complications, but between the location of the lesion and the complications caused there was statistically significant difference. "nConclusion: The needle biopsy guided by CT scan is a suitable diagnostic method due to low complications in many cases.
The Study of Developmental Capacity of Vitrified Mouse Blastocysts in Different Straws after Transfer to Mouse Pseudo Pregnant
Ghasem Saki,Fakher Rahim,lida Moradi
Pakistan Journal of Biological Sciences , 2008,
Abstract: Vitrification is the commonly used method for long-term storage of pre-implantation mammalian embryos. It is an essential part of assisted reproductive technologies. The re-expansion rate, pregnancy and birth rate of vitrified blastocysts using CPS were compared with OPS and Conventional Straw. Female NMRI mice were injected with Gonadotrophins in order induce them for super ovulation. At that time the mice were sacrified by cervical dislocation and dissected of mouse abdomen. The uterine horns were existed blastocysts were collected in PBS and randomly allocated to four groups: vitrification in CPS, conventional straw, OPS and untreated controls. The vitrification solution was EFS40%. After storage for 1 month in liquid nitrogen, the blastocysts were thawed in 0.5 M sucrose for in vitro culture in M16 medium. After 6 h of culture, the numbers of expanded blastocysts was recorded and ready for transfer to uterus of pseudo pregnant mouse. The re-expansion rate of the CPS group (72.1%) was significantly higher (p<0.05) than OPS (52.55) and C.S. (38.6%) groups. The pregnancy (70%) and birth rate (45%) of blastocysts in CPS were similar to those of fresh blastocysts (80% and 45.5%) and the pregnancy (10%) and birth rate (5.1%) in Conventional Straws lower than OPS (20 and 7.5%), but were not significantly different. Mouse blastocysts vitrified using CPS had a better result compared with OPS and Conventional Straw. The value of CPS for vitrification of blastocysts may also merit investigation.
Application of diagnostic methods and molecular diagnosis of hemoglobin disorders in Khuzestan province of Iran
Fakher Rahim,Bijan Kaeikhaei,Taghi Akbari
Indian Journal of Human Genetics , 2007,
Abstract: Background : The hemoglobinopathies refer to a diverse group of inherited disorders characterized by a reduced synthesis of one or more globin chains (thalassemias) or the synthesis of structurally abnormal hemoglobin (Hb). The thalassemias often coexist with a variety of structural Hb variants giving rise to complex genotypes and an extremely wide spectrum of clinical and hematological phenotypes. Hematological and biochemical investigations and family studies provide essential clues to the different interactions and are fundamental to DNA diagnostics of the Hb disorders. Although DNA diagnostics have made a major impact on our understanding and detection of the hemoglobinopathies, DNA mutation testing should never be considered a shortcut or the test of first choice in the workup of a hemoglobinopathy. Materials and Methods: A careful three-tier approach involving: (1) Full blood count (2) Special hematological tests, followed by (3) DNA mutation analysis, provides the most effective way in which to detect primary gene mutations as well as gene-gene interactions that can influence the overall phenotype. With the exception of a few rare deletions and rearrangements, the molecular lesions causing hemoglobinopathies are all identifiable by PCR-based techniques. Furthermore, each at-risk ethnic group has its own combination of common Hb variants and thalassemia mutations. In Iran, there are many different forms of a and β thalassemia. Increasingly, different Hb variants are being detected and their effects per se or in combination with the thalassemias, provide additional diagnostic challenges. Results:We did step-by-step diagnosis workup in 800 patients with hemoglobinopathies who referred to Research center of Thalassemia and Hemoglobinopathies in Shafa Hospital of Ahwaz Joundishapour University of medical sciences, respectively. We detected 173 patients as iron deficiency anemia (IDA) and 627 individuals as thalassemic patients by use of different indices. We have successfully detected 75% (472/627) of the β -thalassemia mutations by using amplification refractory mutation system (ARMS) technique and 19% (130/627) of the β -thalassemia mutations by using Gap-PCR technique and 6% (25/627) as Hb variants by Hb electrophoresis technique. We did prenatal diagnosis (PND) for 176 couples which had background of thalassemia in first pregnancy. Result of PND diagnosis in the first trimester was 35% (62/176) affected fetus with β -thalassemia major and sickle cell disease that led to termination of the pregnancy. Conclusion:Almost all hemoglobinopathies can be
Effect of forced swimming stress on count, motility and fertilization capacity of the sperm in adult rats
Saki Ghasem,Rahim Fakher,Alizadeh Karim
Journal of Human Reproductive Sciences , 2009,
Abstract: Aims: The purpose of this study was to determine whether 50 days of forced swimming stress applied to adult male rats affects count, motility and fertilization capacity of sperm. Settings and Design: It is a prospective study designed in vitro. Materials and Methods: A total 30 adult male wistar rats were used in this study. All rats were divided into two equal groups (n = 15): (1) control group and (2) experimental group. Animals of the experimental group were submitted to force swimming stress for 3 min in water at 32°C daily for 50 days. Then, all male rats were sacrificed, the right epididymides were removed and sperm concentration and motility were determined. The sperm suspension was added to the ova. Fertilization capacity was assessed by counting two-cell embryos 24-26 h after completion of fertilization in vitro. Statistical Analysis Used: Data are reported as mean ± SD and percentage. The difference between the control and experimental groups was determined by the unpaired t-test. Results: The mean and standard deviation of sperm concentration in the control and experimental groups were 60.8 ± 9.3 10 6 /ml and 20.4 ± 5.3 10 6 /ml, respectively. There was a statistical difference of P < 0.05 between the two groups in terms of sperm concentration. The percentage of motility in the experimental group was significantly different ( P < 0.05). The same results were obtained in case of fertility ( P < 0.05). Stress caused by forced swimming was observed by a significant increase in the latency of the pain response in the hot-plate test ( P < 0.05). Conclusions: These results suggest that forced swimming stress in time course equal or more than spermatogenesis period, i.e. 48-50 days in the rat will be significantly effective to reduce the number and motility of sperms as well as the fertilization capacity.
Effect of forced swimming stress on in-vivo fertilization capacity of rat and subsequent offspring quality
Saki Ghasem,Rahim Fakher,Vaysi Ozra
Journal of Human Reproductive Sciences , 2010,
Abstract: Aims: This study aimed to determine the effect of 50 days of forced swimming stress on fertilization capacity of rat and subsequent offspring quality. Setting and Design: The prospective study designed in vivo. Materials and Methods: Total 90 Wistar rats including 30 adult male (3 months of age, weighing 210 ± 10.6 g) and 60 female rats (3 months of age, weighing 230 ± 12.2 g) were engaged in this study. Male rats were randomly divided in two equal groups (n=15): Control and experimental groups. Animals of the experimental group were submitted to forced swimming stress for 3 min in water at 32oC daily for 50 days. Then all adult male rats were mated with normal females (2 per each male) for 7 days. Female rats were sacrificed and autopsy was performed on day 20 of pregnancy when uterus and ovaries were examined for the number of corpora lutea, dead and live fetuses, embryo resorption, implantation sites, and fetus weight. Conclusion: Results of this study have important implications for families attempting pregnancy. Stress pursuant to life events may have a negative impact on in vivo fertilization capacity of male rats and subsequent offspring quality.
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