Sequence Analysis of Hypothetical Proteins from Helicobacter pylori 26695 to Identify Potential Virulence Factors

Ahmad Abu Turab Naqvi,Farah Anjum,Faez Iqbal Khan,Asimul Islam,Faizan Ahmad,Md. Imtaiyaz Hassan 한국유전체학회 2016 Genomics & informatics Vol.14 No.3

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

Sequence Analysis of Hypothetical Proteins from Helicobacter pylori 26695 to Identify Potential Virulence Factors

Naqvi, Ahmad Abu Turab,Anjum, Farah,Khan, Faez Iqbal,Islam, Asimul,Ahmad, Faizan,Hassan, Md. Imtaiyaz Korea Genome Organization 2016 Genomics & informatics Vol.14 No.3

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

Biochemical screening of Lactobacilli in midgut of wild Aedes aegypti mosquitoes. A step toward paratransgenesis candidate

Alhaji Hamisu Maimusa,Abu Hassan AHMAD,Nur Faeza Abu Kassim,Hamdan Ahmad,Hamady Dieng,Junaid RAHIM,Muhammad Ahmad DAHIRU 한국곤충학회 2019 Entomological Research Vol.49 No.2

This study was conducted to isolate and identify lactobacilli from larval and adult midgut of wild Aedes aegypti (Ae. aegypti) to find candidate bacteria for paratransgenic control. Characterization of the bacterial symbionts was done using Gram staining, motility test, catalase test, and biochemical tests, among others, and the morphological features were confirmed using a standard scheme that simplifies the identification of lactic acid bacteria. A total of 174 strains were isolated and identified, 135 strains from larval midgut and 39 strains from adult midgut (mean ± SE, 4.00 ± 0.72; P = 0.00). The isolated species were confirmed to be Lactobacillus fermentum, L. casei, L. acidophilus, L. viridescens, L. brevis and L. gasseri. It can be concluded that Ae. aegypti has the potential of harboring the cultivable bacterial symbionts. In conclusion, the isolated species were nominated for paratransgenic control, particularly L. fermentum, being found in large numbers from both larval and adulxt midgut.

Survival Analysis and Prognostic Factors for Colorectal Cancer Patients in Malaysia

Hassan, Muhammad Radzi Abu,Suan, Mohd Azri Mohd,Soelar, Shahrul Aiman,Mohammed, Noor Syahireen,Ismail, Ibtisam,Ahmad, Faizah Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.7

Background: Cancer survival analysis is an essential indicator for effective early detection and improvements in cancer treatment. This study was undertaken to document colorectal cancer survival and associated prognostic factors in Malaysians. Materials and Methods: All data were retrieved from the National Cancer Patient Registry-Colorectal Cancer. Only cases with confirmed diagnosis through histology between the year 2008 and 2009 were included. Retrieved data include socio-demographic information, pathological features and treatment received. Survival curves were plotted using the Kaplan-Meier method. Univariate analysis of all variables was then made using the Log-rank test. All significant factors that influenced survival of patients were further analysed in a multivariate analysis using Cox' regression. Results: Total of 1,214 patients were included in the study. The overall 3- and 5-year survival rates were 59.1% and 48.7%, respectively. Patients with localized tumours had better prognosis compared to those with advanced stage cancer. In univariate analysis, staging at diagnosis (p<0.001), primary tumour size (p<0.001), involvement of lymph nodes (p<0.001) and treatment modalities (p=0.001) were found to be predictors of survival. None of the socio-demographic characteristics were found to exert any influence. In Cox regression analysis, staging at diagnosis (p<0.001), primary tumour size (p<0.001), involvement of lymph nodes (p<0.001) and treatment modalities (p<0.001) were determined as independent prognostic factors of survival after adjusted for age, gender and ethnicity. Conclusions: The overall survival rate for colorectal cancer patients in Malaysia is similar to those in other Asian countries, with staging at diagnosis, primary tumor size, involvement of lymph node and treatment modalities having significant effects. More efforts are needed to improve national survival rates in future.

Repeated impact response of bio-inspired sandwich beam with arched and honeycomb bilayer core

Ahmad B.H. Kueh,Juin-Hwee Tan,Shukur Abu Hassan,Mat Uzir Wahit 국제구조공학회 2023 Structural Engineering and Mechanics, An Int'l Jou Vol.85 No.6

The article examines the impact response of the sandwich beam furnished by a novel bilayer core as inspired by the woodpecker’s head architecture under different repeatedly exerted low-velocity impact loadings by employing the finite element package, ABAQUS. The sandwich beam forms four essential parts comprising bottom and top carbon fiber reinforced polymer laminates encasing bilayer core made of laterally arched solid hot melt adhesive material and aluminum honeycomb. Impact loadings are implemented repeatedly with a steel hemisphere impactor for various impact energies, 7.28 J, 9.74 J, and 12.63 J. Essentially, the commonly concentrated stresses at the impact region are regulated away by the arched core in all considered cases thus reducing the threat of failure. The sandwich beam can resist up to 5 continual impacts at 7.28 J and 9.74 J but only up to 3 times repeated loads at 12.63 J before visible failure is noticed. In the examination of several key impact performance indicators under numerous loading cases, the proposed beam demonstrates favorably up to 1.3-11.2 higher impact resistance efficacies compared to existing designs, therefore displaying an improvement in repeated impact resistance of the new design.

Incidence and mortality rates of colorectal cancer in Malaysia

Muhammad Radzi Abu Hassan,Ibtisam Ismail,Mohd Azri Mohd Suan,Faizah Ahmad,Wan Khamizar Wan Khazim,Zabedah Othman,Rosaida Mat Said,Wei Leong Tan,Siti Rahmah @ Noor Syahireen Mohammed,Shahrul Aiman Soel 한국역학회 2016 Epidemiology and Health Vol.38 No.-

OBJECTIVES: This is the first study that estimates the incidence and mortality rate for colorectal cancer (CRC) patients in Malaysia by sex and ethnicity. METHODS: The 4,501 patients were selected from National Cancer Patient Registry-Colorectal Cancer data. Patient survival status was cross-checked with the National Registration Department. The age-standardised rate (ASR) was calculated as the proportion of CRC cases (incidence) and deaths (mortality) from 2008 to 2013, weighted by the age structure of the population, as determined by the Department of Statistics Malaysia and the World Health Organization world standard population distribution. RESULTS: The overall incidence rate for CRC was 21.32 cases per 100,000. Those of Chinese ethnicity had the highest CRC incidence (27.35), followed by the Malay (18.95), and Indian (17.55) ethnicities. The ASR incidence rate of CRC was 1.33 times higher among males than females (24.16 and 18.14 per 100,000, respectively). The 2011 (44.7%) CRC deaths were recorded. The overall ASR of mortality was 9.79 cases, with 11.85 among the Chinese, followed by 9.56 among the Malays and 7.08 among the Indians. The ASR of mortality was 1.42 times higher among males (11.46) than females (8.05). CONCLUSIONS: CRC incidence and mortality is higher in males than females. Individuals of Chinese ethnicity have the highest incidence of CRC, followed by the Malay and Indian ethnicities. The same trends were observed for the age-standardised mortality rate.

Contribution of the MLH1 -93G>A Promoter Polymorphism in Modulating Susceptibility Risk in Malaysian Colorectal Cancer Patients

Nizam, Zahary Mohd,Abdul Aziz, Ahmad Aizat,Kaur, Gurjeet,Abu Hassan, Muhammad Radzi,Mohd Sidek, Ahmad Shanwani,Lee, Yeong Yeh,Mazuwin, Maya,Ankathil, Ravindran Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.2

Background: Colorectal cancer (CRC) exists in a more common sporadic form and less common hereditary forms, associated with the Lynch syndrome, familial adenomatous polyposis (FAP) and other rare syndromes. Sporadic CRC is believed to arise as a result of close interaction between environmental factors, including dietary and lifestyle habits, and genetic predisposition factors. In contrast, hereditary forms such as those related to the Lynch syndrome result from inheritance of germline mutations of mismatch repair (MMR) genes. However, in certain cases, the influence of low penetrance alleles in familial colorectal cancer susceptibility is also undeniable. Aim: To investigate the genotype frequencies of MLH1 promoter polymorphism -93G>A and to determine whether it could play any role in modulating familial and sporadic CRC susceptibility risk. Methods: A case-control study comprising of 104 histopathologically confirmed CRC patients as cases (52 sporadic CRC and 52 Lynch syndrome patients) and 104 normal healthy individuals as controls was undertaken. DNA was extracted from peripheral blood and the polymorphism was genotyped employing PCR-RFLP methods. The genotypes were categorized into homozygous wild type, heterozygous and homozygous variants. The risk association between these polymorphisms and CRC susceptibility risk was calculated using binary logistic regression analysis and deriving odds ratios (ORs). Results: When risk association was investigated for all CRC patients as a single group, the heterozygous (G/A) genotype showed a significantly higher risk for CRC susceptibility with an OR of 2.273, (95%CI: 1.133-4.558 and p-value=0.021). When analyzed specifically for the 2 types of CRC, the heterozygous (G/A) genotype showed significantly higher risk for sporadic CRC susceptibility with and OR of 3.714, (95%CI: 1.416-9.740 and p-value=0.008). Despite high OR value was observed for Lynch syndrome (OR: 1.600, 95%CI: 0.715-3.581), the risk was not statistically significant (P=0.253). Conclusion: Our results suggest an influence of MLH1 promoter polymorphism -93G>A in modulating susceptibility risk in Malaysian CRC patients, especially those with sporadic disease.

Changes in the biting activity of a dengue vector relative to larval and adult nutritional histories: Implications for preventive measures

Hamady Dieng,Ooi Seow Hui,Ahmad Abu Hassan,Fatimah Abang,Idris Abd Ghani,Tomomitsu Satho,Fumio Miake,Hamdan Ahmad,Yuki Fukumitsu,Wan Fatma Zuharah,Abdul Hafiz Ab Majid,Nur Faeza Abu Kassim,Nur Aida Ha 한국응용곤충학회 2015 Journal of Asia-Pacific Entomology Vol.18 No.3

Themagnitude of dengue transmission depends largely on the level of human–vector contact. Therefore, knowledge regarding the biting periodicity ofmosquitoes is crucial to determine transmission periods' risk, and in planning personal protection measures. Dengue vectors are day-active and endure transitory periods of starvation overnight. However, it is unclear howtheir blood feeding activity pattern is related to body sizewhen temporarily deprived of their main source of energy — sugar. We examined the changes in Aedes albopictus diurnal biting activity, taking into account larval nutritional history and adult starvation. Overall, large body size and nonstarvation conditions were associated with better blood feeding success, but these parameters did not significantly modify the timing of first blood feeding attempt. Females of both sizes showed significant temporal variations in their blood feeding activities. Under conditions of starvation, blood meal uptake was much greater in large females from morning to evening. Similar variations of feeding activity were observed in small females, except in the morning. Under non-starvation conditions, the blood feeding activity of small mosquitoes tended to decrease over time, whereas blood meal uptake activity was high and remained almost constant from morning to evening for larger mosquitoes. Thiswork emphasizes the importance of body size and hunger on the dynamics of vector–host interaction and has important implications for the development of novel strategies for the prevention of disease transmission. Knowingwhen dengue vectors actively bite during the day can help in timing effective personal protective measures.

Analysis of Hereditary Nonpolyposis Colorectal Cancer in Malay Cohorts using Immunohistochemical Screening

Juhari, Wan Khairunnisa Wan,Rahman, Wan Faiziah Wan Abdul,Sidek, Ahmad Shanwani Mohd,Hassan, Muhammad Radzi Abu,Noordin, Khairul Bariah Ahmad Amin,Zakaria, Andee Dzulkarnaen,Macrae, Finlay,Zilfalil, B Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.9

Background: Lynch syndrome (LS) is an inherited predisposition to colorectal, endometrial (uterine) and other cancers. Although most cancers are not inherited, about 5 percent (%) of people who have colorectal or endometrial cancer have the Lynch syndrome. It involves the alteration of mismatch repair (MMR) genes; MLH1, MSH2, MSH6 or PMS2. In this study, we analyzed the expression of MMR proteins in colorectal cancer in a Malay cohort by immunohistochemistry. Materials and Methods: A total of 17 patients were selected fulfilling one of the Bethesda criteria: colorectal cancer diagnosed in a patient aged less than 50 years old, having synchronous and metachronous colorectal cancer or with a strong family history. Immunohistochemical staining was performed on paraffin embedded tumour tissue samples using four antibodies: MLH1, MSH2, MSH6 and PMS2. Results: Twelve out of 17 patients (70.6%) were noted to have a family history. A total of 41% (n=7) of the patients had abnormal immunohistochemical staining with one or more of the four antibodies. Loss of expression were noted in 13 tumour tissues with a negative staining score <4. Of 13 tumour tissues, four showed loss expression of MLH1. For PMS2, loss of expression were noted in five cases. Both MSH2 and MSH6 showed loss of expression in two tumour tissues respectively. Conclusions: Revised Bethesda criteria and immunohistochemical analysis constituted a convenient approach and is recommended to be a first-line screening for Lynch syndrome in Malay cohorts.

Temporal distribution of larval Chironomidae (Diptera) in experimental rice fields in Penang, Malaysia

S.A. Al-Shami,Md Rawi Che Salmah,Ahmad Abu Hassan,Mohd Nor Siti Azizah 한국응용곤충학회 2010 Journal of Asia-Pacific Entomology Vol.13 No.1

The distribution and abundance of chironomid larvae were investigated in experimental rice fields at the Bukit Merah Agricultural Experimental Research Station, Penang, Northern Malaysia. The mean density of chironomid larvae during the period of the study (including two cultivation seasons) was 121 larvae m−2. Chironomus kiiensis (48.6%) was the most abundant species, while four other species, Polypedilum trigonus (4.8%), Tanytarsus formosanus (22.6%), Tanypus punctipennis (13.9%), and Clinotanypus sp. (10.1%) occurred less frequently, although they were present during all wet phases of rice cultivation. Generally, water depth, rice plant height, conductivity, and nitrate–nitrogen content of the water only weakly influenced the abundance of the larvae. Other environmental parameters such as pH, dissolved oxygen, daytime water temperature, total suspended solids, phosphate, and sediment total organic matter did not significantly affect larval populations. The community structure of chironomids in this rice agroecosystem followed the dynamic changes of the field including agronomic practices, patterns of water availability, and phases of rice plant growth.