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Colorectal cancer (CRC) is one of the leading causes of death in Saudi Arabia. CRC mostly affects older age groups, but now a days it also appears frequently at a young age. However, the complete genetic etiology of CRC remains unknown. To identify the genetic factors responsible for this cancer type and to search for biomarkers for early diagnosis and prevention, we collected sixteen CRC tumor tissue samples and six normal colon tissues and extracted mRNA and synthesized cDNA. We then performed microarray transcriptomic profiling of Saudi patients with colon cancer. Gene expression was analyzed using Partek Genomics Suite, and principal component analysis (PCA) was performed to separate the different clusters of colon cancer and healthy tissues. Distinct differences in gene expression profiles were observed between colon cancer and normal tissue samples. Subsequently, we validated gene expression using real-time PCR. We found that the C-X-C motif chemokine ligand 8 (CXCL8) gene was expressed most in CRC samples. CXCL8 expressed 25.6 folds more in CRC tissues than in healthy tissues. In conclusion, we found that CXCL8 is the chief biomarker gene that is expressed most in CRC and plays an important role in tumor progression and metastasis.

Lynch syndrome is inherited in an autosomal dominant mode. Lynch syndrome is caused by impairment of one or more of the various genes (most frequently MLH1 and MSH2) involved in mismatch repair. In this study, whole genome comparative genomic hybridization array (array CGH) based genomic analysis was performed on twelve Saudi Lynch syndrome patients. A total of 124 chromosomal alterations (structural loss) were identified at mean log2 ratio cut off value of ±0.25. We also found structural loss in 2p21-p16.3, 3p23-p14.2, 7p22.1 and 1p34.1-p33 regions. These findings were subsequently validated by real time quantitative PCR showing downregulation of MSH2, MSH6, EPCAM, MLH1, PMS2 and MUTYH genes. These findings shall help in establishing database for alterations in mismatch repair genes underlying Lynch syndrome in Saudi population as well as to determine the incidence ratio of these disorders. Guided counselling will subsequently lead to the prevention and eradication of Lynch Syndrome in the local population. Keywords: Familial colorectal cancer, Lynch syndrome, arrayCGH, Mismatch repair genes

Colorectal cancer (CRC) is one of the leading causes of death in Saudi Arabia. CRC mostly affects older age groups, but now a days it also appears frequently at a young age. However, the complete genetic etiology of CRC remains unknown. To identify the genetic factors responsible for this cancer type and to search for biomarkers for early diagnosis and prevention, we collected sixteen CRC tumor tissue samples and six normal colon tissues and extracted mRNA and synthesized cDNA. We then performed microarray transcriptomic profiling of Saudi patients with colon cancer. Gene expression was analyzed using Partek Genomics Suite, and principal component analysis (PCA) was performed to separate the different clusters of colon cancer and healthy tissues. Distinct differences in gene expression profiles were observed between colon cancer and normal tissue samples. Subsequently, we validated gene expression using real-time PCR. We found that the C-X-C motif chemokine ligand 8 (CXCL8) gene was expressed most in CRC samples. CXCL8 expressed 25.6 folds more in CRC tissues than in healthy tissues. In conclusion, we found that CXCL8 is the chief biomarker gene that is expressed most in CRC and plays an important role in tumor progression and metastasis.

Background: Breast cancer is a multifactorial disease with the highest frequency in females. Genetic and environmental factors can cause mutation in several genes like tyrosine kinase, JAK2 gene which may initiate cancer. Molecular analysis of mutations in the JAK2 gene along with determination of environmental, clinical and haematological risk factors associated with breast cancer patients is need of hour to improve patient's healthcare. Somatic JAK2 valine-to-phenylalanine (617 codon) mutation is one of the widely prevalent mutations. Methods: Blood was collected from seventy breast cancer patients after their consent. The questionnaire included risk factors, age group, locality, number of children, tumor type, family history, time of initial diagnosis, no of cycles/month, water conditions and exposure to radiations. Molecular analysis were carried out from genomic DNA using Sanger sequencing and allele-specific PCR to check the V617F point mutation. Results: The breast cancer risk factors includes unfiltered water (68.57%), urban (58.57%), menopause (55.71%), family history of cancer (18.57%), tumor grades (II, 37.14% and III, 35.71%), consanguineous marriages (44.28%) and having more than 3–4 children (45.71%). Prevalence of breast cancer was higher after the age of 35 and maximum at 35–50. In allele-specific PCR of 70 patients, 25 patients were wild type (229 bp), 25 patients were with partially deleted gene (200 bp), and 20 patient had shown no or less than 40 bp size fragments. In Sanger's sequencing of 70 BC cases, 18% were found to be positive for V617F point mutation, including 6 homozygous (T/T) and 7 heterozygous (G/T) mutations at nucleotide position 1849 in exon 14 of the JAK2 gene. Conclusions: Environmental and clinical risk factors were associated with breast cancer which can be overcome by improving awareness of associated risks, health facilities and reducing stress. Keywords: Breast cancer, JAK2, V617F mutation, Allele-specific PCR, Sanger’s sequencing

Objective: Phosphorous is an essential micronutrient of plants and involved in critical biological functions. In nature, phosphorous is mostly present in immobilized inorganic mineral and in the fixed organic form including phytic acid and phosphoesteric compounds. However, the bioavailability of bound phosphorous could be enhanced by the use of phosphate solubilizing microorganisms such as bacteria and fungi. The phytases are widespread in an environment and have been isolated from different sources comprising bacteria and fungi. Methodology: In current studies, we show the successful use of gamma rays and EMS (Ethyl Methane Sulphonate) mutagenesis for enhanced activity of phytases in a fungal strain Sporotrichum thermophile. Results: We report an improved strain ST2 that could produce a clear halo zone around the colony, up to 24 mm. The maximum enzymatic activity was found of 382 U/mL on pH 5.5. However, the phytase activity was improved to 387 U/ml at 45 °C. We also report that the mutants produced through EMS showed the greater potential for phytase production. Conclusion: The current study highlights the potential of EMS mutagenesis for strain improvement over physical mutagens. Keywords: Gamma rays, EMS mutagenesis, Fungus, Phosphate solubilizer

Objective: Maize is an important crop for fodder, food and feed industry. The present study explores the plant-microbe interactions as alternative eco-friendly sustainable strategies to enhance the crop yield. Methodology: Bacterial diversity was studied in the rhizosphere of maize by culture-dependent and culture-independent techniques by soil sampling, extraction of DNA, amplification of gene of interest, cloning of desired fragment and library construction. Results: Culturable bacteria were identified as Achromobacter, Agrobacterium, Azospirillum, Bacillus, Brevibacillus, Bosea, Enterobacter, Microbacterium, Pseudomonas, Rhodococcus, Stenotrophomonas and Xanthomonas genera. For culture-independent approach, clone library of 16S ribosomal RNA gene was assembled and 100 randomly selected clones were sequenced. Majority of the sequences were related to Firmicutes (17%), Acidobacteria (16%), Actinobacteria (17%), Alpha-Proteobacteria (7%), Delta-proteobacteria (4.2%) and Gemmatimonadetes (4.2%) However, some of the sequences (30%) were novel that showed no homologies to phyla of cultured bacteria in the database. Diversity of diazotrophic bacteria in the rhizosphere investigated by analysis of PCR-amplified nifH gene sequence that revealed abundance of sequences belonging to genera Azoarcus (25%), Aeromonas (10%), Pseudomonas (10%). The diazotrophic genera Azotobacter, Agrobacterium and Zoogloea related nifH sequences were also detected but no sequence related to Azospirillum was found showing biasness of the growth medium rather than relative abundance of diazotrophs in the rhizosphere. Conclusion: The study provides a foundation for future research on focussed isolation of the Azoarcus and other diazotrophs found in higher abundance in the rhizosphere. Keywords: Azospirillum, Diazotrophs, 16S rRNA, nifH, Metagenomics

Objective: To study the putative effects of Advanced Oxidation Protein Products (AOPPs) and Advanced Glycation End Products (AGEs) in the development and progression of cardiovascular disease (CVD). Methodology: AGEs, AOPPs, e-NOS, lipid profile, circulating stress and inflammatory biomarkers were evaluated among fifty cardiovascular patients and fifty controls. Independent student’s t-test was done for statistical analysis. Results: The malondialdehyde mean level in CVD patients (5.45 nmol/ml) was significantly higher than control (1.36 nmol/ml) (p value = 0.018). Nitric oxide in CVD patients (55.72 ng/ml) was remarkably increased as compared to normal subjects (19.19 ng/ml). A significant change in the mean serum level of AGEs in CVD patients (2.74 ng/ml) and normal individuals (0.85 ng/ml) was recorded (p value = 0.000). The AOPPs also showed significant increased levels in CVD group (132.07 ng/ml) in comparison with normal subjects (83.05 ng/ml) (p value = 0.011). The mean eNOS serum level in CVD group (15.50 U/L) was higher than control group (11.28 U/L) (p value = 0.004). Cardiovascular disease patients, in comparison with healthy controls, showed increased level of total cholesterol (5.48 mmol/L vs 4.45 mmol/L), triglycerides (2.59 mmol/L vs 1.24 mmol/L), and low density lipoprotein (2.47 mmol/L vs 2.31 mmol/L) along with decrease in high density lipoprotein (1.39 mmol/L vs 1.74 mmol/L). The mean MMP-11 serum levels in CVD group (98.69 ng/ml) was almost double of control group (45.60 ng/ml) (p value = 0.017). The mean serum level of TNF-α and IL1-α were 32.16 pg/ml and 6.64 pg/ml in CVD patient. The significant decreasing trend of SOD (p value = 0.041), CAT (p value = 0.018), GSH (p value = 0.036) and GRx (p value = 0.029) but increasing drift of GPx (0.023) level was observed in CVD patients. Conclusion: This study provides strong evidence that CVD patients presented with elevated oxidative stress, enhanced inflammation and lipid profile in their serum. Therefore, the study strongly approves that AGEs, AOPPs, inflammatory and lipoxidative biomarkers hold predictive potential in causing and aggravating the disease, thus by controlling these factors CVD progression can be inhibited. Keywords: Cardiovascular diseases, Advanced glycation end products, Advanced oxidation protein products, Endothelial nitric oxide synthase, Matrix metalloproteinase-11

Background: Cancer patients when treated with different chemotherapeutic drugs often develop mild to severe sight threatening diseases during or after chemotherapy. The mechanism involved in the pathogenesis of ocular toxicities is poorly understood. Oxidative stress, inflammation and MMPs (angiogenic factor) are involved in the progression of chemotherapy related ocular disorders. Materials and methods: The concentration of oxidative stress markers such as MDA, NO and levels of different antioxidant molecules such as SOD, CAT, GSH, GPx, GPr, VIT A, VIT E and VIT C present in the serum of chemotherapy treated patients (n = 50) and in normal persons (n = 20) were estimated by the direct spectrophotometric method while the concentration of TNF-α and MMP-9 activity were determined using human TNF-α and MMP-9 ELISA kits. Results: The concentration of SOD and CAT (0.356 ± 0.05 μg/dl and 1.26 ± 0.01 μmol/mol of protein) was significantly lower as compared to that (1.09 ± 0.03 μg/dl and 3.99 ± 0.04 μmol/mol of protein) in controls. The levels of GPx (0.06 ± 0.01 mmol/dl) in the cancer patients were much lower than those in the controls (0.78 ± 0.06 mmol/dl). Lower level of GSH (0.96 ± 0.003 μg/dl) in serum of the diseased group was observed as compared to healthy group (7.26 ± 1.40 μg/dl). The level of Vit A, Vit C and Vit E was lower in systemic circulation of cancer patients (109.99 ± 6.35 μg/ml, 1.26 ± 0.36 μg/ml and 1.29 ± 0.191 μg/ml) as compared to control subjects (166.35 ± 14.26 μg/ml, 3.25 ± 0.099 μg/ml and 6.354 ± 2.26 μg/ml) respectively. The concentration of nitric oxide was significantly higher in the cancer patients (45.26 ± 6.35 ng/ml) than that in the normal subjects (16.35 ± 3.26 ng/ml). The higher concentration of MDA (8.65 ± 3.26 nmol/ml) was observed in the patients than normal ones (1.254 ± 0.065 nmol/ml). The quantity of TNF-α was significantly higher in chemotherapy treated patients (32.68 ± 4.33 pg/ml) as compared to the control group (20.979 ± 1.98 pg/ml). Significantly higher concentration of MMP-9 (40.26 ± 3.26 ng/ml) was observed in the cancer patients than the controls (7.256 ± 1.95 ng/ml). Conclusion: Lower levels of antioxidant enzymes and non-enzymatic small molecules and higher levels of oxidative stress and inflammatory clinical parameters such as NO, MDA, TNF-α and MMP-9 may be involved in the pathogenesis of systemic chemotherapy related ocular complications such as cataract, glaucoma, blepharitis, retinitis pigmentosa, macular degeneration, pterygium and retinal degeneration. Keywords: Oxidative stress, Cancer, Chemotherapeutic drugs, TNF-α, MMPs, Ocular complications

Objective: Phosphate (P) and zinc (Zn) are essential plant nutrients required for nodulation, nitrogen-fixation, plant growth and yield. Mostly applied P and Zn nutrients in the soil are converted into unavailable form. A small number of soil microbes have the ability to transform unsolvable forms of P and Zn to an available form. P-Zn-solubilizing rhizobacteria are potential alternates for P and Zn supplement. In the present study, the effect of two P-Zn-solubilizing bacterial strains (Bacillus sp. strain AZ17 and Pseudomonas sp. strain AZ5) was evaluated on the growth of chickpea plant. Methodology: Both strains were purified from the rhizospheric soil of chickpea plant grown-up in sandy soil and rain-fed area (Thal desert). In vitro, both strains solubilize P and Zn as well both strain produce IAA and organic acids. In the field experiments, conducted in the rain-fed area, the positive influence of inoculation with both bacterial isolates AZ5 and AZ17 on chickpea growth was observed. Results: The application of inoculum (strains AZ5 and AZ17) resulted in up to 17.47% and 17.34% increase in grain yield of both types of chickpea grown in fertilized and non-fertilized soil, respectively over non-inoculated control. Strain AZ5 was the most effective inoculum, increasing up to 17.47%, 16.04%, 26.32%, 22.53%, 26.12% and 22.59% in grain yield, straw weight, nodules number, dry weight of nodules, Zn uptake and P uptake respectively, over control. Conclusion: These results indicated that Pseudomonas sp. strain AZ5 and Bacillus sp. strain AZ17 can serve as effective microbial inocula for chickpea, particularly in the rain-fed area. Keywords: 16S rRNA, Bacillus, Pseudomonas, Organic acids, IAA, Rain-fed

Nigella sativa (NS) or black cumin is a dark, thin, and crescent-shaped, seeded shrub belonging to the Ranunculaceae family commonly growing on Mediterranean coasts in Saudi Arabia, northern Africa and Asia. They have amazing curative and therapeutic features that make them one of the most popular, safe, non-detrimental, and cytoprotective medicinal plant that can be used for prevention and treatment of many complicated diseases. Originally, N. sativa was used to treat migraines and allergy, and researches have shown its effectiveness in destroying cancer cells as well. The gastro protective effect of NS oil and its constituents has also been reported earlier; however, the complete perception on etiology and pathogenesis of gastric ulcer is not yet clear. Herein, we attempt to unveil some of the potential mechanisms exhibited by NS in preventing problems related to gastric ulcers. Gastric ailments like ulcers and tumors are the most common disorders of the gastro-intestinal tract in the present day life of the industrialized world. Gastric ulcer being a multifaceted problem exhibits complex etiology and is the fourth most common cause of cancer mortality. Drug interactions and toxicity are the main hindrances in chemotherapy. The existing merits and demerits of modern-day drugs make us turn toward the plant kingdom which may provide a valuable resource of novel potent natural compounds for pharmaceuticals or alternately, as dietary supplements. In this context, the revered phytotherapeutic N. sativa comes as a promising savior in today’s times. This review aims to summarize, both the functional and disease-related effects in the area of gastroenterology.