Azra Yasmin

Relationship between heavy metals concentrations in egret species, their environment and food chain differences from two Headworks of Pakistan

Concentration of ten metals (Cd, Cr, Co, Cu, Fe, Li, Mn, Ni, Pb and Zn) were analyzed in the egg contents, prey and soil samples of little egret (Egretta garzetta) and cattle egret (Bubulcus ibis) from two Headworks to determine habitat and species-specific differences; to assess the importance of prey and habitat contamination as an exposure source for heavy metals. Concentration of Cu, Mn, Cr and Pb in egg contents, Fe, Co, Cu, Mn, Zn in prey and Fe, Co, Cu, Ni, Li in surface soils were significantly different (P<0.05). Mean metal concentrations of Cr, Pb and Cd were relatively higher in little egret whereas Cu and Mn were higher in the egg contents of cattle egret. The mean concentrations of Cu, Mn and Zn were higher in prey samples of cattle egrets and Cr, Cd and Pb in prey samples of little egrets. In soil samples collected from little egret heronries metal concentrations were higher except Cu and Ni. Correlation Analysis and Hierarchical Agglomerative Cluster Analysis (HACA) identified relatively similar associations of metals and their source identification. Metals such as Fe, Cu, Mn, and Li were related with geochemical origin from parent rock material as well as anthropogenic input whereas Cr, Cd, Pb, Ni, Co and Zn were associated mostly with anthropogenic activities. The study suggested that eggs are useful bio-monitor of local heavy metal contamination.

Genetic Deletions of GSTM1 and GSTT1 in Head and Neck Cancer: Review of the Literature from 2000 to 2012

Head and neck cancer is one of the leading causes of deaths worldwide. Two genes GSTM1 and GSTT1 involved in phase II of carcinogen detoxification have been frequently studied in the literature. Their null genotypes are thought to be associated with increased head and neck cancer risk. However, the published reviews are not up to date and many important papers have been skipped. The current literature review was restricted to the null genotypes of the GSTM1 and GSTT1 genes with special emphasis on the genotypic status. We found that the size of study sample varied greatly and the oral cavity cancer was more influenced by GSTM1 and GSTT1 gene deletions. With respect to ethnicity Asians are more prone to head and neck cancers with these null genotypes as compared to Europeans and Americans. The current review showed significant associations (OR=9.0, 95%CI; 1.4-9.5; OR=3.7, 95%CI; 1.4-9.5) of GSTM1 and GSTT1 null genotypes with head and neck cancers. Review confirms the data of previous reviews that GSTM1 and GSTT1 gene polymorphisms may be risk factors for cancer initiation.

In silico assessment of phosphorylation and O-β-GlcNAcylation sites in human NPC1 protein critical for Ebola virus entry.

Ebola is a highly pathogenic enveloped virus responsible for deadly outbreaks of severe hemorrhagic fever. It enters human cells by binding a multifunctional cholesterol transporter Niemann-Pick C1 (NPC1) protein. Post translational modification (PTM) information for NPC1 is crucial to understand Ebola virus (EBOV) entry and action due to changes in phosphorylation or glycosylation at the binding site. It is difficult and costly to experimentally assess this type of interaction, so in silico strategy was employed. Identification of phosphorylation sites, including conserved residues that could be possible targets for 21 predicted kinases was followed by interplay study between phosphorylation and O-β-GlcNAc modification of NPC1. Results revealed that only 4 out of 48 predicted phosphosites exhibited O-β-GlcNAc activity. Predicted outcomes were integrated with residue conservation and 3D structural information. Three Yin Yang sites were located in the α-helix regions and were conserved in studied vertebrate and mammalian species. Only one modification site S425 was found in β-turn region located near the N-terminus of NPC1 and was found to differ in pig, mouse, cobra and humans. The predictions suggest that Yin Yang sites may not be important for virus attachment to NPC1, whereas phosphosite 473 may be important for binding and hence entry of Ebola virus. This information could be useful in addressing further experimental studies and therapeutic strategies targeting PTM events in EBOV entry.

Plant growth-promoting potential of endophytic bacteria isolated from roots of wild Dodonaea viscosa L.

Dodonaea viscosa, a wild and perennial shrub that can tolerate harsh environmental conditions, was used for the isolation of its endophytic bacteria and their potential was explored for the promotion of Canola growth. The bacteria identified through 16S rRNA gene sequencing, belonged to ten different genera namely Inquilinus, Xanthomonas, Pseudomonas, Rhizobium, Brevundimonas, Microbacterium, Bacillus, Streptomyces, Agrococcus and Stenotrophomonas. All the strains produced small amount of IAA (indole acetic acid) in the absence of tryptophan and comparatively more in the presence of tryptophan. All the bacterial strains were positive for ammonia production, cellulase and pectinase activity, but few of them showed phosphate solubilization, siderophore and hydrogen cyanide production. Only three strains showed ACC (1-aminocyclopropane-1-carboxylate) deaminase activity when tested using in-vitro enzyme assay. Members of genera Bacillus, Pseudomonas and Streptomyces showed positive chitinase, protease and antifungal activity against two phytopathogenic fungi Aspergillus niger and Fusarium oxysoprum, while members of Xanthomonas, Pseudomonas and Bacillus showed significant root elongation of Canola which could be related with their positive plant-growth-promoting (PGP) traits. Among the three plant growth promoting Bacillus strains, B. idriensis is never reported before for its PGP activities. These results showed the potential of Dodonaea viscosa endophytic bacteria as PGPBs, which in future can be further explored for their host range/molecular mechanisms.

Arsenic and fluoride removal by potato peel and rice husk (PPRH) ash in aqueous environments

ABSTRACT Finding appropriate adsorbent may improve the quality of drinking water in those regions where arsenic (As) and fluoride (F−) are present in geological formations. In this study, we evaluated the efficiency of potato peel and rice husk ash (PPRH-ash)-derived adsorbent for the removal of As and F from contaminated water. Evaluation was done in batch adsorption experiments, and the effect of pH, initial adsorbate concentration, contact time, and adsorbent dose were studied. Characteristics of adsorbents were analyzed using scanning electron micropcope (SEM) and Fourier transform infrared (FTIR) spectroscopy. Both the Langmuir and Freundlich isotherm models fitted well for F− and As sorption process. The maximum adsorption capacity of adsorbent for As and F− was 2.17 μg g−1 and 2.91 mg g−1, respectively. The As and Fi removal was observed between pH 7 and 9. The sorption process was well explained with pseudo-second order kinetic model. Arsenic adsorption was not decreased in the presence of carbonate and sulfate. Results from this study demonstrated potential utility of this agricultural biowaste, which could be developed into a viable filtration technology for As and F− removal in As- and F-contaminated water streams.

Understanding properties of the master effector of phage shock operon in Mycobacterium tuberculosis via bioinformatics approach

The phage shock protein (Psp) is a part of the Psp operon, which assists in safeguarding the survival of bacterium in stress and shields the cell against proton motif force challenge. It is strongly induced by bacterium allied phages, improperly localized mutant porins and various other stresses. Master effector of the operon, PspA has been modeled and simulated, illustrating how it undergoes significant conformational transition at the far end in Mycobacterium tuberculosis. Association of this key protein of the operon influences action of Psp system on the whole. We are further working on the impact of phosphorylation perturbation and changes in the structure of PspA during complex formation with other moieties of interest.

Prostate cancer and glutathione S-transferase deletions.

GSTM1 and GSTT1 gene polymorphisms have been studied in many populations to evaluate their association with prostate cancer risk with contrasting results. The current study was aimed to find out the association of GSTM1 and GSTT1 gene polymorphisms with prostate cancer in Pakistani men. This case control study included pathologically confirmed prostate cancer patients and age matched male controls. Epidemiological data was collected by a standard questionnaire and presence or absence of GSTM1 and GSTT1 gene was observed by multiplex PCR using CYP1A1 as housekeeping gene. Prostate cancer was more prevalent in age of >60 years and most of the patients were at stage IV (70 %) and have undergone surgery. Family history of cancer, smoking, metastasis and surgery were found to be significant (P<0.05) risk factors in prostate cancer development. Gleason score 7 was most prevalent (40.5 %) in prostate cancer patients. Source of drinking water, residential area, occupation, eating habits and number of family members had no association (P>0.05) with prostate cancer risk. No significant association was found when comparing GSTM1 (OR=0.78) and GSTT1 (OR=0.89) gene deletions with prostate cancer risk. Smoking and TNM staging were also not associated with deletion of GSTM1 and GSTT1 genes. Comparison of dual null deletion of both genes with prostate cancer also showed non-significant associations. Deletion of GSTM1 gene at stage IV prostate cancer patients was significantly higher compared with other stages of cancer while no significance was shown by GSTT1 gene deletion. GSTM1, GSTT1 and deletion of both GSTM1 and GSTT1 genes do not contribute towards increased risk of prostate cancer in Pakistani population.

Genetic variations and head and neck cancer risks

Variations in CYP1A1, GSTM1, GSTT1 and GSTP1 in head and neck cancer have been frequently found in literature. But these studies give an overview of these genetic variations in different populations. The current mini review focus on the analysis of these genetic variations at DNA, mRNA and protein levels in the same study group. Eight publications were reviewed on the same study samples yielding results at DNA, mRNA and protein levels. At DNA level, CYP1A1 showed significantly higher mutations in head and neck cancer patients compared to controls at g.2842A>C and g.2842_2843insT. GSTM1 and GSTT1 showed deletion polymorphisms and heterozygous deletion confers protection against cancer. Mutations were also found in GSTP1 at g.2848A>T, g.2849G>A, g.1074delC and g.1466delC. mRNA and protein expressional analysis revealed underexpression of CYP1A1, loss or underexpression of GSTM1 and GSTT1 and overexpression of GSTP1. In addition an unusual intronic variant of GSTP1 mRNA was also found, retaining the intronic portion between exons. The current review gives a complete study overview regarding CYP1A1, GSTM1, GSTT1 and GSTP1 variations at DNA, mRNA and protein levels in head and neck cancer. The review is helpful in designing a new experiment or gene therapy for head and neck cancer patients.

NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach

Gene-environment interaction studies have led to the identification of genetic mutations in individuals with increased susceptibility to pollution related diseases. rs1800566 polymorphism of NQO1, leading to P187S missense mutation in the transcribed antioxidant protein, causes individuals carrying this mutation more prone to NO2 induced lung inflammatory injury. Here, we report significant structural and functional changes incurred by NQO1 antioxidant protein as a result of alteration in its nucleotide (C609T) and hence, protein sequence. Detailed insights were obtained regarding the prospective impact of this mutation on the structural stability of normal and mutated NQO1 protein, using a myriad of bioinformatic tools and webservers. Structure analysis showed no significant change at secondary level. A change in the native backbone conformation was observed due to formation of a hydrogen bond. Hydrophobicity and phosphorylation properties, decisive factors for functioning and stability of NQO1 were considerably influenced by P187S mutation. Computational study of the properties of a polymorph linked with NOx induced lung injury sheds light on the molecular basis of this polymorphism and endorses previous findings, reported by the scientists working in this domain.

Entangling Relation of Micro RNA-let7, miRNA-200 and miRNA-125 with Various Cancers

Involvement of micro RNAs (miRNA) is currently the focus for cancer studies as they effect the post transcriptional expression of different genes. Let-7 family is among the firstly discovered miRNAs that play important role in cell proliferation and dysregulation leading to cell based diseases including cancer. Another family, miRNA-200 prevents transformation of cell to malignant form and tumor formation by interacting with epidermal mesenchymal transition (EMT). Similarly miRNA-125 controls apoptosis and proliferation by affecting multiple genes involved in transcription, immunological defense, resistance against viral and bacterial infections that ultimately leads to cell proliferation, metastasis and finally cancer. All of these micro RNAs are known to be either upregulated or downregulated in various cancers. Current review is focused to elaborate the role of these three families of micro RNAs on different genes that ultimately cause cancer. In conclusion we can say that the miRNAs discussed here are mostly downregulated in various cancers with some exceptions when upregulation of miRNA-125 may be attributed to cancer formation.Involvement of micro RNAs (miRNA) is currently the focus for cancer studies as they effect the post transcriptional expression of different genes. Let-7 family is among the firstly discovered miRNAs that play important role in cell proliferation and dysregulation leading to cell based diseases including cancer. Another family, miRNA-200 prevents transformation of cell to malignant form and tumor formation by interacting with epidermal mesenchymal transition (EMT). Similarly miRNA-125 controls apoptosis and proliferation by affecting multiple genes involved in transcription, immunological defense, resistance against viral and bacterial infections that ultimately leads to cell proliferation, metastasis and finally cancer. All of these micro RNAs are known to be either upregulated or downregulated in various cancers. Current review is focused to elaborate the role of these three families of micro RNAs on different genes that ultimately cause cancer. In conclusion we can say that the miRNAs discussed here are mostly downregulated in various cancers with some exceptions when upregulation of miRNA-125 may be attributed to cancer formation.