Cytoskeletal rearrangement occurs in variety of cellular processes and involves a wide spectrum of proteins. Gelsolin super family proteins control actin organization by severing and capping filament ends and nucleating actin assembly. Gelsolin is the founding member of this family and plays important role in pathogenesis of human neoplasia.This study aimed to investigate the germline mutations and expressional profile of Gelsolin in human breast cancer tissues. For germ line screening PCR-SSCP technique was used while expression was analyzed through quantitative real time PCR. Different types of mutations were observed in Gelsolin coding regions on exons 4, 10, 11, 14 and 15. These mutations include 3 missense nonsynonymous substitution mutations, 2 deletions, 1 insertion and 1 synonymous substitution mutation. Gelsolin transcript level was found significantly lower in breast tumor tissues compared to control samples (p=0.03). Low level of Gelsolin was found in metastatic patients (p=0.002) and patients who died from breast cancer (P=0.03) compared to disease free patients at final follow up. This study shows that level of Gelsolin is down regulated in breast cancer tissues and is linked with metastasis development and death in patients. It is concluded that genetic changes in coding regions of Gelsolin can potentially contribute to genetic instability. These genetic variations and expressional correlation with patient survival may prove to be of significant importance.

The aetiology of head and neck cancer (HNC) has been shown to be associated with genetic and certain environmental factors that produce DNA damage. Base excision repair (BER) genes are responsible for repair of DNA damage caused by reactive oxygen species and other electrophiles and therefore are good candidate susceptibility genes for HNC. Apurinic/apyrimidinic endonuclease-1 (APEX1) proteins have important functions in the BER pathway. In this case-control study, all exons of the APEX1 gene and its exon/intron boundaries were amplified in 300 HNC cases and 300 matched healthy controls and then analysed by single-stranded conformational polymorphism. Amplified products showing altered mobility patterns were sequenced and analysed. To confirm our observations, we examined APEX1 expression at mRNA level on 50 head and neck squamous cell carcinoma (HNSCC) and 50 normal control samples by quantitative real-time polymerase chain reaction. At germ line level, three novel mutations (13T > G, Ser129Arg and Val131Gly) of APEX1 were observed. The homozygous and heterozygous genotypes of APEX1 13T > G, Ser129Arg and Val131Gly appear to be significantly involved in the development of HNC. In the case of expressional level, APEX1 mRNA expression was positively correlated with tumour size, clinical stage and positive lymph node metastasis. Statistical analysis showed a significantly higher APEX1 mRNA level in HNC tumour tissue than in control samples. Our study demonstrated that APEX1 mutations and deregulation of APEX1 are associated with increased risk of HNC in the Pakistani population.

In first part of this study association between OGG1 polymorphisms and breast cancer susceptibility was explored by meta-analysis. Second part of the study involved 925 subjects, used for mutational analysis of OGG1 gene using PCR-SSCP and sequencing. Fifteen mutations were observed, which included five intronic mutations, four splice site mutations, two 3′UTR mutations, three missense mutations, and a nonsense mutation. Significantly (p < 0.001) increased (~29 fold) breast cancer risk was associated with a splice site variant g.9800972T>G and 3′UTR variant g.9798848G>A. Among intronic mutations, highest (~15 fold) increase in breast cancer risk was associated with g.9793680G>A (p < 0.009). Similarly ~14-fold increased risk was associated with Val159Gly (p < 0.01), ~17-fold with Gly221Arg (p < 0.005), and ~18-fold with Ser326Cys (p < 0.004) in breast cancer patients compared with controls, whereas analysis of nonsense mutation showed that ~13-fold (p < 0.01) increased breast cancer risk was associated with Trp375STOP in patients compared to controls. In conclusion, a significant association was observed between OGG1 germ line mutations and breast cancer risk. These findings provide evidence that OGG1 may prove to be a good candidate of better diagnosis, treatment, and prevention of breast cancer.

Our findings indicate that both genetic and epigenetic RB1 changes may contribute to the pathogenesis of HNC in the Pakistani population.

Groundwater is a major source of water supply for domestic and irrigation uses in semiarid, remote but rapidly developing Kilasaifullah district part of Zhob River Basin, located at Pakistan–Afghanistan Border. Zhob River is among few major rivers of perennial nature in Balochistan, which flows from WSW to ENE and falls in Gomal River, a tributary of Indus River. Keeping in view the important geopolitical position and rapid development of the region, this study is primarily focused on groundwater chemistry for contamination sources as well as agriculture development. Water samples from open and tube wells are analyzed and calculated for electrical conductivity (EC), total dissolved solids (TDS), turbidity, pH, K+, Na+, Ca2+, Mg2+, HCO, Cl−, NO, SO, PO, sodium percent (Na%), sodium adsorption ratio (SAR), Kelly's index (KI), and heavy metals (Fe, Cu, Cr, Zn, Pb, and Mn). On the basis of the chemical constituents two zones within the study area are identified and possible causes of the contaminants are pointed out. Two recharge areas were responsible for the different chemical results in groundwater, e.g., zone A was recharged from NNW saline geological formations (Nisai, Khojak, Multana, Bostan formations, and Muslim Bagh ophiolites), which are concentrated with high sodium and chloride. On the other hand Zone B was sourced from SSW from carbonate rich rocks (Alozai, Loralai, Parh formations, and Muslim Bagh ophiolites). The groundwater is classified as C2–S1, C3–S1, C3–S2, C4–S2 on the basis of EC and SAR values which indicate that most of the water of both zones can be used for irrigation safely except the samples plotted in C3–S2 and C4–S2 categories which could be dangerous for soil and crops. Groundwater samples are plotted in good to permissible limits with some samples excellent to good and few samples belong to doubtful category based on sodium percent. Groundwater of zone A is unsuitable for irrigation use due to higher values of KI (more than one) but water of zone B are good for irrigation based on KI. In general, water of both zones is suitable for irrigation but care should be taken during the selection of crops which are sensitive to alkalinity or sodium hazards particularly in zone A.

Stratigraphical and sedimentological analyses of Late Neoproterozoic successions in Lesser Himalaya are combined herein with palaeogeographical considerations and comparisons with equivalent successions in India and South China. The succession starts with the Hazara Formation, which contains complete and incomplete Bouma sequences suggesting its deposition in deep marine turbidite settings. The overlying Tanawal Formation, rich in massive sandstone, shale and siltstone, was deposited in shallow marine conditions, as indicated by the presence of parallel lamination, large scale tabular, trough cross-and hummocky cross-stratifications. The Tanawal Formation facies shift laterally from proximal (south-southeast) to distal (north-northwest). The glaciogenic Tanaki Boulder Bed, overlying the Tanawal Formation, was deposited during the Maronian glaciation. It is equivalent to the Blaini Formation of India, and to the Sinian diamictites of South China. The Abbottabad Formation of Cambrian age overlies the Tanaki Boulder Bed, and is composed of dolomite, chert nodules and phosphate-rich packages; similar successions are documented in India and South China at the same stratigraphical interval. The similarities of the Neoproterozoic successions of Lesser Himalaya (both in Pakistan and India) and South China suggests their possible proximity during the break-up of Rodinia and the assembly of the Gondwana Supercontinent.

Cyclin D1 plays a key role in cell cycle control, particularly in the transition from G1 to S phase, regulated by cyclin-dependent kinases. The objective of the present study was to screen the cyclin D1 gene (CCND1) for polymorphisms in patients with head and neck cancer (HNC). Genomic DNA was isolated from blood samples of 380 HNC patients and 350 controls. In a hospital-based case-control study using the PCR-SSCP technique we found 3 novel germline mutations: g3578C>A, g3475G>C and g3383delA. The commonly reported guanine to adenine polymorphisms in exon 4 g7656G>A (rs9344) and g10861C>A (rs7177) in 3'UTR of CCND1 were also observed. The calculated frequencies of the g7656G>A (rs9344) polymorphism in GG, GA and AA genotypes were 27.3%, 38.6%, and 33.9% in HNC cases, and 44.2%, 29.4%, and 26.2% in normal healthy controls, respectively. Adjusted by age (in years), sex and smoking status, multivariate logistic regression analysis showed that the AA and GA genotypes were associated with a significantly increased risk (OR 1.34, 95% CI 1.03-1.64, p=0.028) for HNC. The CCND1 AA genotype variant was associated with an increased risk in individuals who were <40 years old (OR 1.45, 95% CI 1.02-2.08, p=0.04). In conclusion, it is suggested that the CCND1 G/A polymorphism is associated with the early onset of HNC and may contribute to HNC susceptibility in a Pakistani population.

DNA repair gene polymorphisms have been implicated as susceptibility factors in cancer development. It is possible that DNA repair polymorphisms may also influence the risk of gene mutation. Polymorphisms in the DNA repair gene XRCC1 have been indicated to have a contributive role in DNA adduct formation and an increased risk of cancer development. 300 head and neck cancer patients and 150 controls were included in this study. PCR-single-strand conformation polymorphism and DNA sequencing were used to analyze the whole exonic region of XRCC1 in head and neck cancer patients. Sequence analysis revealed two missense and two silent mutations in our study. Frequency of silent mutations; Pro206Pro (rs915927) and Gln632Gln (rs3547) was calculated as 0.16 (16 %) and 0.30 (30 %) respectively. Whereas, the frequency of missense mutations; Arg399Gln (rs25487) and Tyr576Asn (rs2307177) was calculated as 0.27 (27 %) and 0.28 (28 %) respectively. In our study, incidence of these mutations was found higher in larynx cancer (p < 0.005) as compared to oral cavity and pharynx cancer. Our finding suggests that the polymorphic XRCC1 gene may contribute to risk of developing head and neck cancer. To our knowledge, this is the first report that XRCC1 is associated with increased risk of head and neck cancer in a Pakistani population.