Matematičeskaâ biologiâ i bioinformatika, May 1, 2024
Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long non... more Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long noncoding RNAs (lncRNAs), a type of noncoding RNA, are important for regulating inflammation and immunity. Despite this significance, there needs to be more published research on how lncRNAs are expressed in vitiligo cases and their potential roles in the biology of this skin condition. This study aims to elucidate the molecular landscape of vitiligo by analyzing gene expression profiles of vitiligo skin and normal skin. Two datasets, RNA-seq and microarray, were thoroughly investigated to identify differentially expressed (DE) genes and lncRNAs associated with vitiligo development. Functional enrichment analysis revealed biological processes and pathways influenced by dysregulated genes, highlighting intricate processes such as melanin biosynthesis and melanogenesis, shedding light on the complex regulatory networks involved in pigmentation and immune responses. Protein-protein interaction analysis highlighted significantly downregulated hub genes, including TYRP1, MLANA, MC1R, SLC45A2, PAX3, TYR, DCT, OCA2, PMEL, and SOX10, revealing significant functional relationships among identified hub genes within the network. RNA-seq data analysis uncovered DE-lncRNAs, emphasizing the regulatory role of lncRNAs in vitiligo. Moreover, the correlation analysis between the expression of lncRNAs and key genes associated with melanogenesis (OCA2, TYRP1, and PMEL) unveiled novel upregulated lncRNAs such as CRTC3-AS1, LCMT1-AS1, LINC02178 contributing to vitiligo development. Additionally, lncRNA-gene networks constructed based on key melanocyte-related genes provided insights into the molecular relationships relevant to vitiligo. Overall, this study offers a comprehensive understanding of vitiligo pathogenesis, identifying potential therapeutic targets and laying the foundation for future research in this critical area.
MicroRNAs are non-coding molecules 21–23 nucleotides long that are involved in post-transcription... more MicroRNAs are non-coding molecules 21–23 nucleotides long that are involved in post-transcriptional regulation of gene expression by mRNA silencing. There is evidence that miRNA activity is associated with various types of human cancer, such as breast cancer, colorectal cancer, ovarian cancer and hepatocellular carcinoma, as well as with clear cell renal cell carcinoma. In 2020, the incidence of kidney cancer worldwide was 319,016. Clear cell renal cell carcinoma is associated with loss or mutation of the VHL gene. The aim of this study was to identify miRNAs that are expressed differently in samples of normal kidney tissue and tissue affected by clear cell renal cell carcinoma. For this study, a public miRNA dataset from ArrayExpress was obtained and post-processed. Mapping, identification of known and new microRNAs, and quantification were performed using the miRDeep2 computer program from the DESeq R/Bioconductor package. We performed target identification and functional load ana...
Salinity is one of the major factors that limits geographical distribution of plants and adversel... more Salinity is one of the major factors that limits geographical distribution of plants and adversely affects crop productivity and quality. Here high-level expression of betaine aldehyde dehydrogenase (BADH) was reported in cultured explants of lettuce via plastid genetic engineering. Lettuce (Lactuca sativa) plant was primarily experimented for tolerance of betaine aldehyde (BA) and soudium chloride (NaCl) by tissue culture technique and it was found that the wild type lettuce tolerated 10 and 75 mM from each substance respectively. Genes required in this study were amplified by polymerase chain reaction (PCR) technique using specific forward and reverse primers, and these genes were BADH, prrn promoter and many other regulatory genes. Some of these genes were isolated from their hosts and some were obtained from previous work available at Daniell laboratory. All these genes beside many techniques for ligation, extension, sequencing, orientation confirmation were used to construct the cassette vector pLS-BADH-LS which carries the gene of interest. Homoplasmic transgenic plants exhibiting high levels of salt tolerance were regenerated from bombarded cell cultures via somatic embryogenesis. Transgenic lettuce plants expressing BADH grew in the presence of high concentrations of NaCl (up to 150 mM), the highest level of salt tolerance reported so far among genetically modified lettuce, and the tolerance to betaine aldehyde was 30 mM.
Journal of microbiology, biotechnology and food sciences, 2022
Coronavirus disease (COVID-19) appeared as outbreak in 2019 in Wuhan, China. It has been classifi... more Coronavirus disease (COVID-19) appeared as outbreak in 2019 in Wuhan, China. It has been classified as pandemic disease and more severe than predicted; with infections already recorded in a variety of countries. This study aims to confirm the COVID-19 infection through the following tests: hematological, C-reactive protein (CRP). Samples were collected from the infected patients and sent to the National Flu Center (Central Public Health Laboratory) for COVID-19 (positive or negative) diagnosis by the RT-PCR technique. In this study, sixty five of COVID-19 patients and twenty five of healthy control samples male and female were collected in Iraq. There are significant differences in the parameters of the hematological markers for patients in comparing with the control group and no significant differences were observed in Hb when RBC and GRAN percent rise in patients relative to the control group with P=0.0395 and P=0.0354 respectively comparing with the control group. White blood cel...
The present study was focused to detect leading elements that control gene expression in genetica... more The present study was focused to detect leading elements that control gene expression in genetically modified tomato by using conventional PCR technique.These common elements in all GM. plants are CaMV-35S promoter isolated from cauliflower mosaic virus and T-Nos terminator from the Agrobacterium tumefaciens. Seventy eight tomato genotypes were collected from Iraqiinstitutions and markets. The experiment was conducted in the Institute of Genetic Engineering/University of Baghdad/ Iraq and Directorate of Seeds Testing and Certification/Ministry of Agriculture/ Iraq. The tomato DNA samples were extracted manually by ChexadecylTrimethyl-Ammonium-Bromide (CTAB) method. When measuring the optical density (OD) of the tomato samples, most purity values were found to be between (1.7-1.9).Two specific primers of CaMV-35S promoter, Nos terminator supplied by Canadian Alpha DNA Company, AccuPower®PCR Pre mix PCR supplied by Korean Bioneer Company and positive control (plasmid) supplied by Dr. ...
Background and Objectives: Staphylococcus aureus is an opportunistic human pathogen that causes a... more Background and Objectives: Staphylococcus aureus is an opportunistic human pathogen that causes a variety of diseases. Staphylococcal biofilms are a source of chronic and continual infections. This study was conducted to estimate the distribution of agr among different isolates of S. aureus and their relationship with biofilm. Also, it was aimed to check the association of operon agr with virulence factors (seb, eta, spa and tst v8) and study the effect of biosynthesis silver nanoparticles on the function of the agr system. Materials and Methods: Out of 580 clinical specimens, 100 S. aureus isolates were isolated and identified based on cultural, morphological, and different biochemical tests, in addition to molecular identification using PCR with specific primer 16SrRNA. For biofilm detection, the fungi synthesized silver nanoparticles were used to check its effect on agr system. Results: The biofilm producer among S. aureus was 61% and non-biofilm producer isolates were 39%. It wa...
Background: The main problem in treatment of leukemia patients is the chemotherapy resistance whi... more Background: The main problem in treatment of leukemia patients is the chemotherapy resistance which is a main concern in recent years. The cause of chemotherapy drug resistance is related to MDR gene which is located on chromosome 7 (7q21-31) and it is mainly connected with energy-dependent efflux (P-glycoprotein). This study was conducted to assess the correlation between MDR polymorphism and chemotherapy efficiency with Vincristine in a sample of Iraqi Acute Myeloid Leukemia (AML) patients. Methods: The blood sample of 200 AML patients and 200 controls were collected and the frequency of rs2032582 was calculated through sequencing and then the role of different genetic patterns was evaluated on cancer cells by MTT assay. Results: The results indicate that GG and TT genotypes (20 and 20.5% from total patients count) are more frequent in Iraqi AML patients than other genetic patterns in MDR gene and also the genotype TA is more sensitive to Vincristine chemotherapy than other genoty...
The uric acid is a waste product of the living cell, produced by xanthine oxidase, which contribu... more The uric acid is a waste product of the living cell, produced by xanthine oxidase, which contributes up to 60% of the total plasma antioxidant activity in healthy subjects. The study provides data relating serum uric acid, glucose levels and blood hypertension. Seventy nine patients with pregnancy diabetes mellitus, 25 normal healthy with pregnancy, 25 DM patients, and fifty normal healthy persons, where seen from February till July 2017, in Al-Semawa General Hospital, were participated in the study. The results revealed a highly significant difference (P<0.001) in uric acid, glucose level and hypertension in almost pregnancy diabetic patients and DM patients when compared to control group. In conclusion, this study found that pregnancy women at the early development stage of glucose disorders had a significantly of hyperuricemia and in clinical practices, measurement of serum uric acid level may help to identify the risk of hypertension.
Human cytomegalovirus (HCMV) is a well known hallmark of increasing morbidity and mortality in hu... more Human cytomegalovirus (HCMV) is a well known hallmark of increasing morbidity and mortality in humans with acquired impairment in innate and adaptive immunity indicating high seroprevalence rate of 83%. This study aims to identify novel drug targets as disease biomarkers in HCMV-infected hosts. Thereby datasets were collected from NCBI SRA Database and were further analyzed through RNA-seq pipeline to identify differentially expressed genes between HCMV-infected hosts and healthy individuals. Subsequently functional enrichment analysis of highly signi cant genes was performed through enrichR. RNA-seq analysis identi ed 1974 differentially expressed genes in HCMV-infected hosts including 678 over-modulated and 1028 down-modulated genes. Nevertheless, present DGE analysis study has reported novel drug targets including 5 protein-coding genes (RRAGD, SPINK1, NAP1L2, PKIG and LXN) and 2 pseudogenes (EEF1A1P38, WFDC21P). Additionally dysregulated genes have been found to be highly enriched in immune system related biological processes mainly Toll-like receptor signaling pathway, NODlike receptor signaling pathway, PI3K-Akt signaling pathway, TNF signaling pathway and IL-17 signaling pathway indicating positive correlation between dysregulated immune-system mechanisms and HCMV replication. Hence this study has proposed novel therapeutic targets for early detection and treatment of HCMV infection that would positively in uence public health. However wet laboratory explorations are required to ensure safety and e cacy of proposed drug targets.
The role of microRNAs (miRNAs) in the pathogenesis of cardiovascular disease has been extensively... more The role of microRNAs (miRNAs) in the pathogenesis of cardiovascular disease has been extensively studied. miRNAs have been highlighted as an important physiological regulator for activities like cardiac protection. miRNAs are present in the circulation, and they have been investigated as physiological markers, especially in the condition of heart failure. However, there is less compelling verification that miRNAs can outperform traditional biomarkers. However, clinical evidence is still required. In this review article, we explored the feasibility of miRNAs as diagnostic biomarkers for heart failure in a systematic study. Searching in the PubMed database to identify miRNA molecules that are differentially expressed between groups of patients with heart failure or heart disease and controls, throughout the investigation, we discovered no significant overlap in differentially expressed miRNAs. Only four miRNAs (“miR-126,” “miR-150-5p,” “hsa-miR-233,” and “miR-423-5p”) were differenti...
Diabetes mellitus is a form of metabolic disorder where patients are incapable to organize g... more Diabetes mellitus is a form of metabolic disorder where patients are incapable to organize glucose metabolism. The most common types are Type I and Type II, constituting about 10% and 90% of cases, respectively. The cause of type I diabetes, which usually spreads in children and adolescents, is the disability of the endocrine system to produce insulin. On the other hand, The most common type of diabetes, type II diabetes, is often presented in adults. It is usually presented as a collection of insulin deficiency and insulin resistance. This work was done to estimate the count of microbiota in diabetics to find an appraoch for detection and follow-up treatment. The count of two types of bacteria Lactobacillus and Bifidobacterium was determined using qPCR based on the standard curve that was created from the serial decimal dilution of samples containing an unknown number of bacteria taken from probiotic capsules. The main results of this study show that the Lactobacillus count w...
1ST SAMARRA INTERNATIONAL CONFERENCE FOR PURE AND APPLIED SCIENCES (SICPS2021): SICPS2021
Determine the glucose regulatory role of decaffeinated Green Tea extract in reduces the metastasi... more Determine the glucose regulatory role of decaffeinated Green Tea extract in reduces the metastasis and cell viability of MCF7 cell line
Network Modeling Analysis in Health Informatics and Bioinformatics
Haemophilus influenzae is a pathogen that causes invasive bacterial infections in humans. The hig... more Haemophilus influenzae is a pathogen that causes invasive bacterial infections in humans. The highest prevalence lies in both young children and adults. Generally, there are no vaccines available that target all the strains of Haemophilus influenzae. Hence, the purpose of this research is to employ bioinformatics and immunoinformatics approaches to design a Multi-Epitope Vaccine candidate employing the pathogenic cell division protein FtsN that specifically combat all the Haemophilus influenzae strains. The current research focuses on developing subunit vaccine in contrast to vaccines generated from the entire pathogen. This will be accomplished by combining multiple bioinformatics and immunoinformatics approaches. As a result, prospective T cells (helper T lymphocyte and cytotoxic T lymphocytes) and B cells epitopes were investigated. The human leukocyte antigen allele having strong associations with the antigenic and overlapping epitopes were chosen, with 70% of the total coverage of the world population. To construct a linked vaccine design, multiple linkers were used. To increase the immunogenic profile, an adjuvant was linked using EAAAK linker. The final vaccine construct with 149 amino acids was obtained after adjuvants and linkers were added. The developed Multi-Epitope Vaccine has a high antigenicity as well as viable physiochemical features. The 3D conformation was modeled and undergoes refinement and validation using bioinformatics methods. Furthermore, protein-protein molecular docking analysis was performed to predict the effective binding poses of Multi-Epitope Vaccine with the Toll-like receptor 4 protein. Besides, vaccine underwent the codon translational optimization and computational cloning to verify the reliability and proper Multi-Epitope Vaccine expression. In addition, it is necessary to conduct experiments and research in the laboratory to demonstrate that the vaccine that has been developed is immunogenic and protective.
Lettuce is one of the most important edible plant worldwide. At the time that lettuce is the cand... more Lettuce is one of the most important edible plant worldwide. At the time that lettuce is the candidate plant to carry the foreign vaccine gene for human. The B subunits of toxin of Vibrio cholerae (CTB) are candidate vaccine antigens. This research was conduct to express CTB gene in lettuce chloroplast. Genes required in this study were obtained by polymerase chain reaction (PCR) technique using specific forward and reverse primers, and these genes were CTB, BADH, prrn promoter and many other regulatory genes. Some of these genes were isolated from their hosts and some were obtained from previous work available at Daniell laboratory. All these genes beside many techniques for ligation, extension, sequencing, orientation confirmation were used to construct the cassette vector pLS-BADH-LS-CTB which carries the gene of interest. In this work the CTB gene with BADH gene were transferred to the chloroplast of lettuce plant and selection of transgenic plant was performed on the MS medium containing BA and NaCl without any antibiotic selectable marker. Integration of an unmodified CTB-coding sequence into chloroplast genomes (up to 1000 copies per cell) resulted in the accumulation of up to 6.2% of total soluble lettuce leaves protein as functional oligomers (620-fold higher expression levels than that of the unmodified CTB gene expressed via the nuclear genome). PCR and Southern blot analyses confirmed stable integration of the CTB gene and BADH gene into the chloroplast genome in addition to the integration in the right orientation and in specific region between trnaI\trnA.Western blot analysis showed that the chloroplast synthesized CTB assembled into oligomers and were antigenically identical with purified native CTB.
Atherosclerosis is one of the most important coronary artery disease (CAD) caused by lipid accumu... more Atherosclerosis is one of the most important coronary artery disease (CAD) caused by lipid accumulation, hypertension, smoking, and many other factors such as environmental and genetic factors. It has been recorded that genetic variations in rs10757278 and rs1333049 are correlated with CAD. In the present study, 100 blood samples were collected (50 CAD patients and 50 appeared to be healthy controls), who referred to Ibn-Albytar general hospital/in Bagdad city for heart disease from February to March 2019. Genotyping for two SNPs rs10757278 and rs1333049, were done by Tetra ARMS method. For the rs10757278 polymorphism, the GG genotype verses to AA genotype was significantly associated with the risk of CAD (OR=5.16, 95% CI:1.02-26.0, P=0.047). For the rs10757278 polymorphism, there was no significant associatin between genotypes and the susceptibiulity to CAD. In the present study, the rs10757278 polymorphism showed an association with CAD.
Risankizumab, a humanized monoclonal antibody that targets interleukin-23 p19 subunit, was develo... more Risankizumab, a humanized monoclonal antibody that targets interleukin-23 p19 subunit, was developed for the treatment of psoriasis. This work characterizes risankizumab pharmacokinetics in Japanese and Chinese healthy subjects compared with white healthy subjects and in Japanese patients with moderate to severe plaque psoriasis,generalized pustular psoriasis,or erythrodermic psoriasis.A phase 1,single-dose study evaluated risankizumab pharmacokinetics and safety/tolerability in healthy white (18 and 300 mg subcutaneous [SC]), Japanese (18, 90, and 300 mg SC and 200, 600, and 1200 mg intravenous [IV]), and Chinese (18, 90, and 300 mg SC) subjects; pharmacokinetic data were analyzed using noncompartmental methods. Risankizumab pharmacokinetic data from phase 2/3 studies in Japanese patients with plaque psoriasis, generalized pustular psoriasis, or erythrodermic psoriasis following multiple SC doses of 75 mg or 150 mg were analyzed using a population pharmacokinetic approach along with data from the phase 1 and global phase 1 to 3 studies. Risankizumab plasma exposures (peak plasma concentration and area under the concentration-time curve) were approximately dose-proportional across 18-to 300-mg SC or 200-to 1200-mg IV doses. Risankizumab terminal elimination half-life (harmonic mean 27-34 days) was comparable across doses and ethnicities. Risankizumab exposures were approximately 20% to 30% higher in Japanese and Chinese healthy subjects compared with white healthy subjects or in Japanese patients compared with non-Japanese patients. After accounting for bodyweight differences, risankizumab exposures were comparable across ethnicities. Overall, there was no ethnic impact on risankizumab pharmacokinetics, and the small difference in exposure due to body weight has no clinical relevance.
Prostatic hyperplasia is benign tumor occur in prostate. Benign prostatic hyperplasia is common d... more Prostatic hyperplasia is benign tumor occur in prostate. Benign prostatic hyperplasia is common disease in old men. The incidence of disease arises with increase in age. The patient with benign prostatic hyperplasia are estimated 20% of men in 40s old, and 90% in of men in 80s old, and main causes of prostatic hyperplasia are unknown but there is evidence referring to genetic and hormonal disorders that may cause the disease. This study includes 60 patients with prostatic hyperplasia with an average age of 64 years old and 30 samples as a control with same age group. The study obtained that there was significant association (P 0.05) between PSA (KLK3) and prostatic hyperplasia. Result also mentions that there was significant decrease in testosterone level and significant increase in dihydrotestosterone level. The present study for KLK2 and KLK3 genes showed molecular variation in both genes, varied between polymorphism and allele polymorphism. PCR amplification of specific primers of KLK2 gene showed polymorphisms ranged between 14%, 8%, 10%, and 6% in each KLK2a, KLK2b, KLK2c, and KLK2d primers respectively, while the allele polymorphism in KLK2c amplification with primer reaches 18% of patient. PCR amplification of specific primers of KLK3 gene showed polymorphisms ranged between 10%, 6%, 2%, and 4% in each KLK3a, KLK3b, KLK3c, and KLK3d primer respectively, and allele variation was not detected in amplification product of KLK3.
Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagno... more Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagnostic molecular marker for different types of cancer, identifying the importance of liquid biopsy. The aim of this review was to evaluate the prognostic and diagnostic performance of Arthrobacter luteus (ALU) repeat in tumor. Following a thorough review of the literature published from January, 2000 to September 2021, 36 studies were included. All of the study descriptions were analyzed. According to several studies, there were increased concentrations of ALU repetitive elements in cancer patients, while these concentrations were decreased in control, benign, different cancer stage, and other diseases. The total ALU (115 and 247) sequence levels are potential biomarkers for the purpose of investigations and cancer prognosis.
Risankizumab is a humanized anti-interleukin-23 monoclonal antibody in development for the treatm... more Risankizumab is a humanized anti-interleukin-23 monoclonal antibody in development for the treatment of several inflammatory diseases. This work characterized the pharmacokinetics of risankizumab and evaluated covariates that may affect its exposures using phase I and II trial data in subjects with psoriasis and Crohn's disease. Plasma concentration measurements from a phase I study and a phase II study in subjects with psoriasis (n = 157; single doses of 0.01-5 mg/kg intravenously, 0.25-1 mg/kg subcutaneously, and 18 mg subcutaneously, and multiple doses of 90 and 180 mg subcutaneously), and a phase II study in subjects with Crohn's disease (n = 115; doses of 200 or 600 mg intravenously every 4 weeks followed by 180 mg subcutaneously every 8 weeks) were analyzed using non-linear mixed-effects modeling. The model was qualified using bootstrap and simulation-based diagnostics. A two-compartment model with first-order absorption and elimination described the pharmacokinetics o...
Matematičeskaâ biologiâ i bioinformatika, May 1, 2024
Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long non... more Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long noncoding RNAs (lncRNAs), a type of noncoding RNA, are important for regulating inflammation and immunity. Despite this significance, there needs to be more published research on how lncRNAs are expressed in vitiligo cases and their potential roles in the biology of this skin condition. This study aims to elucidate the molecular landscape of vitiligo by analyzing gene expression profiles of vitiligo skin and normal skin. Two datasets, RNA-seq and microarray, were thoroughly investigated to identify differentially expressed (DE) genes and lncRNAs associated with vitiligo development. Functional enrichment analysis revealed biological processes and pathways influenced by dysregulated genes, highlighting intricate processes such as melanin biosynthesis and melanogenesis, shedding light on the complex regulatory networks involved in pigmentation and immune responses. Protein-protein interaction analysis highlighted significantly downregulated hub genes, including TYRP1, MLANA, MC1R, SLC45A2, PAX3, TYR, DCT, OCA2, PMEL, and SOX10, revealing significant functional relationships among identified hub genes within the network. RNA-seq data analysis uncovered DE-lncRNAs, emphasizing the regulatory role of lncRNAs in vitiligo. Moreover, the correlation analysis between the expression of lncRNAs and key genes associated with melanogenesis (OCA2, TYRP1, and PMEL) unveiled novel upregulated lncRNAs such as CRTC3-AS1, LCMT1-AS1, LINC02178 contributing to vitiligo development. Additionally, lncRNA-gene networks constructed based on key melanocyte-related genes provided insights into the molecular relationships relevant to vitiligo. Overall, this study offers a comprehensive understanding of vitiligo pathogenesis, identifying potential therapeutic targets and laying the foundation for future research in this critical area.
MicroRNAs are non-coding molecules 21–23 nucleotides long that are involved in post-transcription... more MicroRNAs are non-coding molecules 21–23 nucleotides long that are involved in post-transcriptional regulation of gene expression by mRNA silencing. There is evidence that miRNA activity is associated with various types of human cancer, such as breast cancer, colorectal cancer, ovarian cancer and hepatocellular carcinoma, as well as with clear cell renal cell carcinoma. In 2020, the incidence of kidney cancer worldwide was 319,016. Clear cell renal cell carcinoma is associated with loss or mutation of the VHL gene. The aim of this study was to identify miRNAs that are expressed differently in samples of normal kidney tissue and tissue affected by clear cell renal cell carcinoma. For this study, a public miRNA dataset from ArrayExpress was obtained and post-processed. Mapping, identification of known and new microRNAs, and quantification were performed using the miRDeep2 computer program from the DESeq R/Bioconductor package. We performed target identification and functional load ana...
Salinity is one of the major factors that limits geographical distribution of plants and adversel... more Salinity is one of the major factors that limits geographical distribution of plants and adversely affects crop productivity and quality. Here high-level expression of betaine aldehyde dehydrogenase (BADH) was reported in cultured explants of lettuce via plastid genetic engineering. Lettuce (Lactuca sativa) plant was primarily experimented for tolerance of betaine aldehyde (BA) and soudium chloride (NaCl) by tissue culture technique and it was found that the wild type lettuce tolerated 10 and 75 mM from each substance respectively. Genes required in this study were amplified by polymerase chain reaction (PCR) technique using specific forward and reverse primers, and these genes were BADH, prrn promoter and many other regulatory genes. Some of these genes were isolated from their hosts and some were obtained from previous work available at Daniell laboratory. All these genes beside many techniques for ligation, extension, sequencing, orientation confirmation were used to construct the cassette vector pLS-BADH-LS which carries the gene of interest. Homoplasmic transgenic plants exhibiting high levels of salt tolerance were regenerated from bombarded cell cultures via somatic embryogenesis. Transgenic lettuce plants expressing BADH grew in the presence of high concentrations of NaCl (up to 150 mM), the highest level of salt tolerance reported so far among genetically modified lettuce, and the tolerance to betaine aldehyde was 30 mM.
Journal of microbiology, biotechnology and food sciences, 2022
Coronavirus disease (COVID-19) appeared as outbreak in 2019 in Wuhan, China. It has been classifi... more Coronavirus disease (COVID-19) appeared as outbreak in 2019 in Wuhan, China. It has been classified as pandemic disease and more severe than predicted; with infections already recorded in a variety of countries. This study aims to confirm the COVID-19 infection through the following tests: hematological, C-reactive protein (CRP). Samples were collected from the infected patients and sent to the National Flu Center (Central Public Health Laboratory) for COVID-19 (positive or negative) diagnosis by the RT-PCR technique. In this study, sixty five of COVID-19 patients and twenty five of healthy control samples male and female were collected in Iraq. There are significant differences in the parameters of the hematological markers for patients in comparing with the control group and no significant differences were observed in Hb when RBC and GRAN percent rise in patients relative to the control group with P=0.0395 and P=0.0354 respectively comparing with the control group. White blood cel...
The present study was focused to detect leading elements that control gene expression in genetica... more The present study was focused to detect leading elements that control gene expression in genetically modified tomato by using conventional PCR technique.These common elements in all GM. plants are CaMV-35S promoter isolated from cauliflower mosaic virus and T-Nos terminator from the Agrobacterium tumefaciens. Seventy eight tomato genotypes were collected from Iraqiinstitutions and markets. The experiment was conducted in the Institute of Genetic Engineering/University of Baghdad/ Iraq and Directorate of Seeds Testing and Certification/Ministry of Agriculture/ Iraq. The tomato DNA samples were extracted manually by ChexadecylTrimethyl-Ammonium-Bromide (CTAB) method. When measuring the optical density (OD) of the tomato samples, most purity values were found to be between (1.7-1.9).Two specific primers of CaMV-35S promoter, Nos terminator supplied by Canadian Alpha DNA Company, AccuPower®PCR Pre mix PCR supplied by Korean Bioneer Company and positive control (plasmid) supplied by Dr. ...
Background and Objectives: Staphylococcus aureus is an opportunistic human pathogen that causes a... more Background and Objectives: Staphylococcus aureus is an opportunistic human pathogen that causes a variety of diseases. Staphylococcal biofilms are a source of chronic and continual infections. This study was conducted to estimate the distribution of agr among different isolates of S. aureus and their relationship with biofilm. Also, it was aimed to check the association of operon agr with virulence factors (seb, eta, spa and tst v8) and study the effect of biosynthesis silver nanoparticles on the function of the agr system. Materials and Methods: Out of 580 clinical specimens, 100 S. aureus isolates were isolated and identified based on cultural, morphological, and different biochemical tests, in addition to molecular identification using PCR with specific primer 16SrRNA. For biofilm detection, the fungi synthesized silver nanoparticles were used to check its effect on agr system. Results: The biofilm producer among S. aureus was 61% and non-biofilm producer isolates were 39%. It wa...
Background: The main problem in treatment of leukemia patients is the chemotherapy resistance whi... more Background: The main problem in treatment of leukemia patients is the chemotherapy resistance which is a main concern in recent years. The cause of chemotherapy drug resistance is related to MDR gene which is located on chromosome 7 (7q21-31) and it is mainly connected with energy-dependent efflux (P-glycoprotein). This study was conducted to assess the correlation between MDR polymorphism and chemotherapy efficiency with Vincristine in a sample of Iraqi Acute Myeloid Leukemia (AML) patients. Methods: The blood sample of 200 AML patients and 200 controls were collected and the frequency of rs2032582 was calculated through sequencing and then the role of different genetic patterns was evaluated on cancer cells by MTT assay. Results: The results indicate that GG and TT genotypes (20 and 20.5% from total patients count) are more frequent in Iraqi AML patients than other genetic patterns in MDR gene and also the genotype TA is more sensitive to Vincristine chemotherapy than other genoty...
The uric acid is a waste product of the living cell, produced by xanthine oxidase, which contribu... more The uric acid is a waste product of the living cell, produced by xanthine oxidase, which contributes up to 60% of the total plasma antioxidant activity in healthy subjects. The study provides data relating serum uric acid, glucose levels and blood hypertension. Seventy nine patients with pregnancy diabetes mellitus, 25 normal healthy with pregnancy, 25 DM patients, and fifty normal healthy persons, where seen from February till July 2017, in Al-Semawa General Hospital, were participated in the study. The results revealed a highly significant difference (P<0.001) in uric acid, glucose level and hypertension in almost pregnancy diabetic patients and DM patients when compared to control group. In conclusion, this study found that pregnancy women at the early development stage of glucose disorders had a significantly of hyperuricemia and in clinical practices, measurement of serum uric acid level may help to identify the risk of hypertension.
Human cytomegalovirus (HCMV) is a well known hallmark of increasing morbidity and mortality in hu... more Human cytomegalovirus (HCMV) is a well known hallmark of increasing morbidity and mortality in humans with acquired impairment in innate and adaptive immunity indicating high seroprevalence rate of 83%. This study aims to identify novel drug targets as disease biomarkers in HCMV-infected hosts. Thereby datasets were collected from NCBI SRA Database and were further analyzed through RNA-seq pipeline to identify differentially expressed genes between HCMV-infected hosts and healthy individuals. Subsequently functional enrichment analysis of highly signi cant genes was performed through enrichR. RNA-seq analysis identi ed 1974 differentially expressed genes in HCMV-infected hosts including 678 over-modulated and 1028 down-modulated genes. Nevertheless, present DGE analysis study has reported novel drug targets including 5 protein-coding genes (RRAGD, SPINK1, NAP1L2, PKIG and LXN) and 2 pseudogenes (EEF1A1P38, WFDC21P). Additionally dysregulated genes have been found to be highly enriched in immune system related biological processes mainly Toll-like receptor signaling pathway, NODlike receptor signaling pathway, PI3K-Akt signaling pathway, TNF signaling pathway and IL-17 signaling pathway indicating positive correlation between dysregulated immune-system mechanisms and HCMV replication. Hence this study has proposed novel therapeutic targets for early detection and treatment of HCMV infection that would positively in uence public health. However wet laboratory explorations are required to ensure safety and e cacy of proposed drug targets.
The role of microRNAs (miRNAs) in the pathogenesis of cardiovascular disease has been extensively... more The role of microRNAs (miRNAs) in the pathogenesis of cardiovascular disease has been extensively studied. miRNAs have been highlighted as an important physiological regulator for activities like cardiac protection. miRNAs are present in the circulation, and they have been investigated as physiological markers, especially in the condition of heart failure. However, there is less compelling verification that miRNAs can outperform traditional biomarkers. However, clinical evidence is still required. In this review article, we explored the feasibility of miRNAs as diagnostic biomarkers for heart failure in a systematic study. Searching in the PubMed database to identify miRNA molecules that are differentially expressed between groups of patients with heart failure or heart disease and controls, throughout the investigation, we discovered no significant overlap in differentially expressed miRNAs. Only four miRNAs (“miR-126,” “miR-150-5p,” “hsa-miR-233,” and “miR-423-5p”) were differenti...
Diabetes mellitus is a form of metabolic disorder where patients are incapable to organize g... more Diabetes mellitus is a form of metabolic disorder where patients are incapable to organize glucose metabolism. The most common types are Type I and Type II, constituting about 10% and 90% of cases, respectively. The cause of type I diabetes, which usually spreads in children and adolescents, is the disability of the endocrine system to produce insulin. On the other hand, The most common type of diabetes, type II diabetes, is often presented in adults. It is usually presented as a collection of insulin deficiency and insulin resistance. This work was done to estimate the count of microbiota in diabetics to find an appraoch for detection and follow-up treatment. The count of two types of bacteria Lactobacillus and Bifidobacterium was determined using qPCR based on the standard curve that was created from the serial decimal dilution of samples containing an unknown number of bacteria taken from probiotic capsules. The main results of this study show that the Lactobacillus count w...
1ST SAMARRA INTERNATIONAL CONFERENCE FOR PURE AND APPLIED SCIENCES (SICPS2021): SICPS2021
Determine the glucose regulatory role of decaffeinated Green Tea extract in reduces the metastasi... more Determine the glucose regulatory role of decaffeinated Green Tea extract in reduces the metastasis and cell viability of MCF7 cell line
Network Modeling Analysis in Health Informatics and Bioinformatics
Haemophilus influenzae is a pathogen that causes invasive bacterial infections in humans. The hig... more Haemophilus influenzae is a pathogen that causes invasive bacterial infections in humans. The highest prevalence lies in both young children and adults. Generally, there are no vaccines available that target all the strains of Haemophilus influenzae. Hence, the purpose of this research is to employ bioinformatics and immunoinformatics approaches to design a Multi-Epitope Vaccine candidate employing the pathogenic cell division protein FtsN that specifically combat all the Haemophilus influenzae strains. The current research focuses on developing subunit vaccine in contrast to vaccines generated from the entire pathogen. This will be accomplished by combining multiple bioinformatics and immunoinformatics approaches. As a result, prospective T cells (helper T lymphocyte and cytotoxic T lymphocytes) and B cells epitopes were investigated. The human leukocyte antigen allele having strong associations with the antigenic and overlapping epitopes were chosen, with 70% of the total coverage of the world population. To construct a linked vaccine design, multiple linkers were used. To increase the immunogenic profile, an adjuvant was linked using EAAAK linker. The final vaccine construct with 149 amino acids was obtained after adjuvants and linkers were added. The developed Multi-Epitope Vaccine has a high antigenicity as well as viable physiochemical features. The 3D conformation was modeled and undergoes refinement and validation using bioinformatics methods. Furthermore, protein-protein molecular docking analysis was performed to predict the effective binding poses of Multi-Epitope Vaccine with the Toll-like receptor 4 protein. Besides, vaccine underwent the codon translational optimization and computational cloning to verify the reliability and proper Multi-Epitope Vaccine expression. In addition, it is necessary to conduct experiments and research in the laboratory to demonstrate that the vaccine that has been developed is immunogenic and protective.
Lettuce is one of the most important edible plant worldwide. At the time that lettuce is the cand... more Lettuce is one of the most important edible plant worldwide. At the time that lettuce is the candidate plant to carry the foreign vaccine gene for human. The B subunits of toxin of Vibrio cholerae (CTB) are candidate vaccine antigens. This research was conduct to express CTB gene in lettuce chloroplast. Genes required in this study were obtained by polymerase chain reaction (PCR) technique using specific forward and reverse primers, and these genes were CTB, BADH, prrn promoter and many other regulatory genes. Some of these genes were isolated from their hosts and some were obtained from previous work available at Daniell laboratory. All these genes beside many techniques for ligation, extension, sequencing, orientation confirmation were used to construct the cassette vector pLS-BADH-LS-CTB which carries the gene of interest. In this work the CTB gene with BADH gene were transferred to the chloroplast of lettuce plant and selection of transgenic plant was performed on the MS medium containing BA and NaCl without any antibiotic selectable marker. Integration of an unmodified CTB-coding sequence into chloroplast genomes (up to 1000 copies per cell) resulted in the accumulation of up to 6.2% of total soluble lettuce leaves protein as functional oligomers (620-fold higher expression levels than that of the unmodified CTB gene expressed via the nuclear genome). PCR and Southern blot analyses confirmed stable integration of the CTB gene and BADH gene into the chloroplast genome in addition to the integration in the right orientation and in specific region between trnaI\trnA.Western blot analysis showed that the chloroplast synthesized CTB assembled into oligomers and were antigenically identical with purified native CTB.
Atherosclerosis is one of the most important coronary artery disease (CAD) caused by lipid accumu... more Atherosclerosis is one of the most important coronary artery disease (CAD) caused by lipid accumulation, hypertension, smoking, and many other factors such as environmental and genetic factors. It has been recorded that genetic variations in rs10757278 and rs1333049 are correlated with CAD. In the present study, 100 blood samples were collected (50 CAD patients and 50 appeared to be healthy controls), who referred to Ibn-Albytar general hospital/in Bagdad city for heart disease from February to March 2019. Genotyping for two SNPs rs10757278 and rs1333049, were done by Tetra ARMS method. For the rs10757278 polymorphism, the GG genotype verses to AA genotype was significantly associated with the risk of CAD (OR=5.16, 95% CI:1.02-26.0, P=0.047). For the rs10757278 polymorphism, there was no significant associatin between genotypes and the susceptibiulity to CAD. In the present study, the rs10757278 polymorphism showed an association with CAD.
Risankizumab, a humanized monoclonal antibody that targets interleukin-23 p19 subunit, was develo... more Risankizumab, a humanized monoclonal antibody that targets interleukin-23 p19 subunit, was developed for the treatment of psoriasis. This work characterizes risankizumab pharmacokinetics in Japanese and Chinese healthy subjects compared with white healthy subjects and in Japanese patients with moderate to severe plaque psoriasis,generalized pustular psoriasis,or erythrodermic psoriasis.A phase 1,single-dose study evaluated risankizumab pharmacokinetics and safety/tolerability in healthy white (18 and 300 mg subcutaneous [SC]), Japanese (18, 90, and 300 mg SC and 200, 600, and 1200 mg intravenous [IV]), and Chinese (18, 90, and 300 mg SC) subjects; pharmacokinetic data were analyzed using noncompartmental methods. Risankizumab pharmacokinetic data from phase 2/3 studies in Japanese patients with plaque psoriasis, generalized pustular psoriasis, or erythrodermic psoriasis following multiple SC doses of 75 mg or 150 mg were analyzed using a population pharmacokinetic approach along with data from the phase 1 and global phase 1 to 3 studies. Risankizumab plasma exposures (peak plasma concentration and area under the concentration-time curve) were approximately dose-proportional across 18-to 300-mg SC or 200-to 1200-mg IV doses. Risankizumab terminal elimination half-life (harmonic mean 27-34 days) was comparable across doses and ethnicities. Risankizumab exposures were approximately 20% to 30% higher in Japanese and Chinese healthy subjects compared with white healthy subjects or in Japanese patients compared with non-Japanese patients. After accounting for bodyweight differences, risankizumab exposures were comparable across ethnicities. Overall, there was no ethnic impact on risankizumab pharmacokinetics, and the small difference in exposure due to body weight has no clinical relevance.
Prostatic hyperplasia is benign tumor occur in prostate. Benign prostatic hyperplasia is common d... more Prostatic hyperplasia is benign tumor occur in prostate. Benign prostatic hyperplasia is common disease in old men. The incidence of disease arises with increase in age. The patient with benign prostatic hyperplasia are estimated 20% of men in 40s old, and 90% in of men in 80s old, and main causes of prostatic hyperplasia are unknown but there is evidence referring to genetic and hormonal disorders that may cause the disease. This study includes 60 patients with prostatic hyperplasia with an average age of 64 years old and 30 samples as a control with same age group. The study obtained that there was significant association (P 0.05) between PSA (KLK3) and prostatic hyperplasia. Result also mentions that there was significant decrease in testosterone level and significant increase in dihydrotestosterone level. The present study for KLK2 and KLK3 genes showed molecular variation in both genes, varied between polymorphism and allele polymorphism. PCR amplification of specific primers of KLK2 gene showed polymorphisms ranged between 14%, 8%, 10%, and 6% in each KLK2a, KLK2b, KLK2c, and KLK2d primers respectively, while the allele polymorphism in KLK2c amplification with primer reaches 18% of patient. PCR amplification of specific primers of KLK3 gene showed polymorphisms ranged between 10%, 6%, 2%, and 4% in each KLK3a, KLK3b, KLK3c, and KLK3d primer respectively, and allele variation was not detected in amplification product of KLK3.
Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagno... more Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagnostic molecular marker for different types of cancer, identifying the importance of liquid biopsy. The aim of this review was to evaluate the prognostic and diagnostic performance of Arthrobacter luteus (ALU) repeat in tumor. Following a thorough review of the literature published from January, 2000 to September 2021, 36 studies were included. All of the study descriptions were analyzed. According to several studies, there were increased concentrations of ALU repetitive elements in cancer patients, while these concentrations were decreased in control, benign, different cancer stage, and other diseases. The total ALU (115 and 247) sequence levels are potential biomarkers for the purpose of investigations and cancer prognosis.
Risankizumab is a humanized anti-interleukin-23 monoclonal antibody in development for the treatm... more Risankizumab is a humanized anti-interleukin-23 monoclonal antibody in development for the treatment of several inflammatory diseases. This work characterized the pharmacokinetics of risankizumab and evaluated covariates that may affect its exposures using phase I and II trial data in subjects with psoriasis and Crohn's disease. Plasma concentration measurements from a phase I study and a phase II study in subjects with psoriasis (n = 157; single doses of 0.01-5 mg/kg intravenously, 0.25-1 mg/kg subcutaneously, and 18 mg subcutaneously, and multiple doses of 90 and 180 mg subcutaneously), and a phase II study in subjects with Crohn's disease (n = 115; doses of 200 or 600 mg intravenously every 4 weeks followed by 180 mg subcutaneously every 8 weeks) were analyzed using non-linear mixed-effects modeling. The model was qualified using bootstrap and simulation-based diagnostics. A two-compartment model with first-order absorption and elimination described the pharmacokinetics o...
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Papers by Ahmed Suleiman