Epigenetic Regulation of Nucleotide Excision Repair.

Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.

COVID-19 in Bangladesh: measuring differences in individual precautionary behaviors among young adults.

Aim: The novel coronavirus disease 2019 (COVID-19) is present in Bangladesh, and various control measures have been taken to flatten the epidemic curve. Due to the current demographic distribution in Bangladesh, young adults comprise almost one-third of the total population of the country. Therefore, their precautionary behavior is very important to ensure the success of preventive policies. This exploratory study examined the differences in the adoption of precautionary behaviors among young adults, and estimated and compared the predictors of precautionary behavior adoption among young adults living in the capital city Dhaka and a nearby district, Tangail. Subject and methods: A total of 350 respondents from each district participated in the study. ANOVA and two-sample t-tests were utilized to detect differences in precautionary behavior across demographic groups of young adults, and quantile regression modeling was used to find the predictors of adopting precautionary behaviors and to compare these predictors between the two districts. Results: Individuals who had a postgraduate education and had good mental health tended to show better precautionary behaviors in Dhaka. Female respondents from Tangail who had no psychological distress took precautionary behaviors more often than their male counterparts. However, no significant differences in the adoption of precautionary behaviors to prevent COVID-19 among young adults were found between the two districts. Better self-control ability, higher education and good mental health emerged as factors that significantly shaped the precautionary behaviors of young adults in this study. Conclusion: Having better knowledge did not ensure better adoption of precautionary behaviors among the participants. In effect, the government's strong intervention to keep people maintaining social distance and a strict lockdown in severely affected areas are probable immediate solutions.

Advanced Nanoengineering Approach for Target-Specific, Spatiotemporal, and Ratiometric Delivery of Gemcitabine-Cisplatin Combination for Improved Therapeutic Outcome in Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDAC) is an intractable malignancy with a dismal survival rate. Recent combination therapies have had a major impact on the improvement of PDAC prognosis. Nevertheless, clinically used combination regimens such as FOLFIRINOX and gemcitabine (Gem)/nab-paclitaxel still face major challenges due to lack of the safe and ratiometric delivery of multiple drugs. Here, a rationally designed mesoporous silica nanoparticle (MSN)-based platform is reported for the target-specific, spatiotemporal, ratiometric, and safe co-delivery of Gem and cisplatin (cisPt). It is shown that systemic administration of the nanoparticles results in synergistic therapeutic outcome in a syngeneic and clinically relevant genetically engineered PDAC mouse model that has rarely been used for the therapeutic evaluation of nanomedicine. This synergism is associated with a strategic engineering approach, in which nanoparticles provide redox-responsive controlled delivery and in situ differential release of Gem/cisPt drugs with the goal of overcoming resistance to Pt-based drugs. The platform is also rendered with additional tumor-specificity via a novel tumor-associated mucin1 (tMUC1)-specific antibody, TAB004. Overall, the platform suppresses tumor growth and eliminates the off-target toxicities of a highly toxic chemotherapy combination.

APE2 Is a General Regulator of the ATR-Chk1 DNA Damage Response Pathway to Maintain Genome Integrity in Pancreatic Cancer Cells.

The maintenance of genome integrity and fidelity is vital for the proper function and survival of all organisms. Recent studies have revealed that APE2 is required to activate an ATR-Chk1 DNA damage response (DDR) pathway in response to oxidative stress and a defined DNA single-strand break (SSB) in Xenopus laevis egg extracts. However, it remains unclear whether APE2 is a general regulator of the DDR pathway in mammalian cells. Here, we provide evidence using human pancreatic cancer cells that APE2 is essential for ATR DDR pathway activation in response to different stressful conditions including oxidative stress, DNA replication stress, and DNA double-strand breaks. Fluorescence microscopy analysis shows that APE2-knockdown (KD) leads to enhanced γH2AX foci and increased micronuclei formation. In addition, we identified a small molecule compound Celastrol as an APE2 inhibitor that specifically compromises the binding of APE2 but not RPA to ssDNA and 3'-5' exonuclease activity of APE2 but not APE1. The impairment of ATR-Chk1 DDR pathway by Celastrol in Xenopus egg extracts and human pancreatic cancer cells highlights the physiological significance of Celastrol in the regulation of APE2 functionalities in genome integrity. Notably, cell viability assays demonstrate that APE2-KD or Celastrol sensitizes pancreatic cancer cells to chemotherapy drugs. Overall, we propose APE2 as a general regulator for the DDR pathway in genome integrity maintenance.

Megacities as drivers of national outbreaks: The 2017 chikungunya outbreak in Dhaka, Bangladesh.

BACKGROUND: Several large outbreaks of chikungunya have been reported in the Indian Ocean region in the last decade. In 2017, an outbreak occurred in Dhaka, Bangladesh, one of the largest and densest megacities in the world. Population mobility and fluctuations in population density are important drivers of epidemics. Measuring population mobility during outbreaks is challenging but is a particularly important goal in the context of rapidly growing and highly connected cities in low- and middle-income countries, which can act to amplify and spread local epidemics nationally and internationally. METHODS: We first describe the epidemiology of the 2017 chikungunya outbreak in Dhaka and estimate incidence using a mechanistic model of chikungunya transmission parametrized with epidemiological data from a household survey. We combine the modeled dynamics of chikungunya in Dhaka, with mobility estimates derived from mobile phone data for over 4 million subscribers, to understand the role of population mobility on the spatial spread of chikungunya within and outside Dhaka during the 2017 outbreak. RESULTS: We estimate a much higher incidence of chikungunya in Dhaka than suggested by official case counts. Vector abundance, local demographics, and population mobility were associated with spatial heterogeneities in incidence in Dhaka. The peak of the outbreak in Dhaka coincided with the annual Eid holidays, during which large numbers of people traveled from Dhaka to other parts of the country. We show that travel during Eid likely resulted in the spread of the infection to the rest of the country. CONCLUSIONS: Our results highlight the impact of large-scale population movements, for example during holidays, on the spread of infectious diseases. These dynamics are difficult to capture using traditional approaches, and we compare our results to a standard diffusion model, to highlight the value of real-time data from mobile phones for outbreak analysis, forecasting, and surveillance.

Risk factors for non-communicable diseases in Bangladesh: findings of the population-based cross-sectional national survey 2018.

OBJECTIVES: To determine the national prevalence of risk factors of non-communicable diseases (NCD) in the adult population of Bangladesh. DESIGN: The study was a population-based national cross-sectional study. SETTING: This study used 496 primary sampling units (PSUs) developed by the Bangladesh Bureau of Statistics. The PSUs were equally allocated to each division and urban and rural stratum within each division. PARTICIPANTS: The participants were adults aged 18 to 69 years, who were usual residents of the households for at least 6 months and stayed the night before the survey. Out of 9900 participants, 8185 (82.7%) completed STEP-1 and STEP-2, and 7208 took part in STEP-3. PRIMARY AND SECONDARY OUTCOME: The prevalence of behavioural, physical and biochemical risk factors of NCD. Data were weighted to generate national estimates. RESULTS: Tobacco use was significantly (p<0.05) higher in the rural (45.2%) than the urban (38.8%) population. Inadequate fruit/vegetable intake was significantly (p<0.05) higher in the urban (92.1%) than in the rural (88.9%) population. The mean salt intake per day was higher in the rural (9.0 g) than urban (8.9 g) population. Among all, 3.0% had no, 70.9% had 1 to 2 and 26.2% had ≥3 NCD risk factors. The urban population was more likely to have insufficient physical activity (adjusted OR (AOR): 1.2, 95% CI: 1.2 to 1.2), obesity (AOR: 1.5, 95% CI: 1.5 to 1.5), hypertension (AOR: 1.3, 95% CI: 1.3 to 1.3), diabetes (AOR: 1.6, 95% CI: 1.6 to 1.6) and hyperglycaemia (AOR: 1.1, 95% CI: 1.1 to 1.1). CONCLUSIONS: Considering the high prevalence of the behavioural, physical and biochemical risk factors, diverse population and high-risk group targeted interventions are essential to combat the rising burden of NCDs.

APE1 senses DNA single-strand breaks for repair and signaling.

DNA single-strand breaks (SSBs) represent the most abundant type of DNA damage. Unrepaired SSBs impair DNA replication and transcription, leading to cancer and neurodegenerative disorders. Although PARP1 and XRCC1 are implicated in the SSB repair pathway, it remains unclear how SSB repair and SSB signaling pathways are coordinated and regulated. Using Xenopus egg extract and in vitro reconstitution systems, here we show that SSBs are first sensed by APE1 to initiate 3'-5' SSB end resection, followed by APE2 recruitment to continue SSB end resection. Notably, APE1's exonuclease activity is critical for SSB repair and SSB signaling pathways. An APE1 exonuclease-deficient mutant identified in somatic tissue from a cancer patient highlighted the significance of APE1 exonuclease activity in cancer etiology. In addition, APE1 interacts with APE2 and PCNA, although PCNA is dispensable for APE1's exonuclease activity. Taken together, we propose a two-step APE1/APE2-mediated mechanism for SSB end resection that couples DNA damage response with SSB repair in a eukaryotic system.

Single-Strand Break End Resection in Genome Integrity: Mechanism and Regulation by APE2.

DNA single-strand breaks (SSBs) occur more than 10,000 times per mammalian cell each day, representing the most common type of DNA damage. Unrepaired SSBs compromise DNA replication and transcription programs, leading to genome instability. Unrepaired SSBs are associated with diseases such as cancer and neurodegenerative disorders. Although canonical SSB repair pathway is activated to repair most SSBs, it remains unclear whether and how unrepaired SSBs are sensed and signaled. In this review, we propose a new concept of SSB end resection for genome integrity. We propose a four-step mechanism of SSB end resection: SSB end sensing and processing, as well as initiation, continuation, and termination of SSB end resection. We also compare different mechanisms of SSB end resection and DSB end resection in DNA repair and DNA damage response (DDR) pathways. We further discuss how SSB end resection contributes to SSB signaling and repair. We focus on the mechanism and regulation by APE2 in SSB end resection in genome integrity. Finally, we identify areas of future study that may help us gain further mechanistic insight into the process of SSB end resection. Overall, this review provides the first comprehensive perspective on SSB end resection in genome integrity.

Chikungunya outbreak (2017) in Bangladesh: Clinical profile, economic impact and quality of life during the acute phase of the disease.

BACKGROUND: Chikungunya virus causes mosquito-transmitted infection that leads to extensive morbidity affecting substantial quality of life. Disease associated morbidity, quality of life, and financial loss are seldom reported in resources limited countries, such as Bangladesh. We reported the acute clinical profile, quality of life and consequent economic burden of the affected individuals in the recent chikungunya outbreak (May to September 2017) in Dhaka city, Bangladesh. METHODS: We conducted a cross-sectional study during the peak of chikungunya outbreak (July 24 to August 5, 2017) to document the clinical profiles of confirmed cases (laboratory test positive) and probable cases diagnosed by medical practitioners. Data related to clinical symptoms, treatment cost, loss of productivity due to missing work days, and quality of life during their first two-weeks of symptom onset were collected via face to face interview using a structured questionnaire. World Health Organization endorsed questionnaire was used to assess the quality of life. RESULTS: A total of 1,326 chikungunya cases were investigated. Multivariate analysis of major clinical variables showed no statistically significant differences between confirmed and probable cases. All the patients reported joint pain and fever. Other more frequently reported symptoms include headache, loss of appetite, rash, myalgia, and itching. Arthralgia was polyarticular in 56.3% of the patients. Notably, more than 70% patients reported joint pain as the first presenting symptom. About 83% of the patients reported low to very low overall quality of life. Nearly 30% of the patients lost more than 10 days of productivity due to severe arthropathy. CONCLUSIONS: This study represents one of the largest samples studied so far around the world describing the clinical profile of chikungunya infection. Our findings would contribute to establish an effective syndromic surveillance system for early detection and timely public health intervention of future chikungunya outbreaks in resource-limited settings like Bangladesh.

APE2 promotes DNA damage response pathway from a single-strand break.

As the most common type of DNA damage, DNA single-strand breaks (SSBs) are primarily repaired by the SSB repair mechanism. If not repaired properly or promptly, unrepaired SSBs lead to genome stability and have been implicated in cancer and neurodegenerative diseases. However, it remains unknown how unrepaired SSBs are recognized by DNA damage response (DDR) pathway, largely because of the lack of a feasible experimental system. Here, we demonstrate evidence showing that an ATR-dependent checkpoint signaling is activated by a defined plasmid-based site-specific SSB structure in Xenopus HSS (high-speed supernatant) system. Notably, the distinct SSB signaling requires APE2 and canonical checkpoint proteins, including ATR, ATRIP, TopBP1, Rad9 and Claspin. Importantly, the SSB-induced ATR DDR is essential for SSB repair. We and others show that APE2 interacts with PCNA via its PIP box and preferentially interacts with ssDNA via its C-terminus Zf-GRF domain, a conserved motif found in >100 proteins involved in DNA/RNA metabolism. Here, we identify a novel mode of APE2-PCNA interaction via APE2 Zf-GRF and PCNA C-terminus. Mechanistically, the APE2 Zf-GRF-PCNA interaction facilitates 3'-5' SSB end resection, checkpoint protein complex assembly, and SSB-induced DDR pathway. Together, we propose that APE2 promotes ATR-Chk1 DDR pathway from a single-strand break.

Detection of Chlamydia trachomatis by immunological and genetic methods in female sex workers and the local female population of reproductive age in Mymensingh, Bangladesh.

To investigate the accurate prevalence of genital Chlamydia trachomatis infection in Mymensingh, a local area in central-northern Bangladesh, 40 female sex workers (FSW) and 110 sexually active women (SAW, non-FSW) of reproductive age from a local community with clinical symptoms were examined by an immunochromatography test (ICT) and plasmid-based polymerase chain reaction (PCR) during a 1-year period from July 2011 to June 2012 using the endocervical swab as a specimen. By ICT and/or PCR, the C. trachomatis detection rate was 58% and 27% in FSW and SAW, respectively, showing a significant difference (P < 0.01). Two C. trachomatis strains from FSW were determined to be serovar D by ompA-based PCR and sequencing analysis. The highest prevalence was found among women aged 15 to 35 years. A lower socioeconomic status was considered to be an important risk factor for C. trachomatis infection in FSW but not in SAW. This is the first study to determine the prevalence of C. trachomatis infections in FSW and SAW in the same local area in Bangladesh.

PCR-based detection of Leishmania DNA in skin samples of post kala-azar dermal leishmaniasis patients from an endemic area of Bangladesh.

Post kala-azar dermal leishmaniasis (PKDL) is a sequel of visceral leishmaniasis (VL) and PKDL patients are an important reservoir for anthroponotic transmission of VL. Therefore, diagnosis and treatment of PKDL is important for the kala-azar elimination program in South Asia, including Bangladesh. While definitive diagnosis of PKDL is still based on microscopy, despite the low sensitivity of this method of diagnosis, PCR for identification of kinetoplast DNA (kDNA) from Leishmania parasites is expected to be a rapid and sensitive diagnostic method. We attempted PCR-based diagnosis from skin biopsy specimens and compared PCR to other available detection methods in order to determine the acceptability and feasibility of the PCR diagnostic method in an endemic area of VL in Bangladesh. Both skin biopsy specimens and blood samples were collected from 110 patients suspected to have PKDL from 6 subdistrict health complexes in Mymensingh, Bangladesh. Using microscopy, we identified 32 samples (29.1%) that were positive for Leishmania. Immunochromatography tests indicated that 85 samples (77.3%) were positive for Leishmania. In contrast, a total of 104 (94.5%) samples tested positive using nested PCR, while unaffected portions of skin from PKDL patients tested negative. Sequencing analysis of the PCR products indicated that the amplified portion had more than 98% nucleotide sequence identity to the Leishmania donovani reference strain, D10. These findings indicate that the PCR method using a skin biopsy is highly sensitive and useful for confirmatory diagnosis of PKDL.

Graphical estimation of the dual-enzyme kinetic parameters for Cr(VI) reduction.

Chromium(VI) (Cr(VI)) contamination of soil and groundwater is a major environmental concern. Bioreduction of Cr(VI) by Shewanella oneidensis MR-1 (MR-1) can be considered a feasible option to reduce the toxic and mobile Cr(VI) to the less toxic and less mobile chromium(III) (Cr(III)). The reaction rate expression for Cr(VI) reduction is nonlinear and the rate constants are evaluated by employing nonlinear optimization techniques. The outcome of the optimization techniques, in general, depends on the initial estimate of the kinetic parameters which is not always available. A graphical approach based on sound mathematical reasoning has been developed which is accurate, simpler to use, and can provide the best initial estimate for nonlinear optimization.

Estimating the dual-enzyme kinetic parameters for Cr (VI) reduction by Shewanella oneidensis MR-1 from soil column experiments.

Hexavalent chromium (Cr (VI)) contamination of soil and groundwater is considered a major environmental concern. Bioreduction of Cr (VI) to trivalent chromium (Cr (III)) can be considered an effective technology in remediating Cr (VI) contaminated sites. Among the Cr (VI) reducing bacteria, Shewanella oneidensis MR-1 (MR-1) is relatively effective. Reduction of Cr (VI) by MR-1 is defined by the dual-enzyme kinetic model. The feasibility of bioreduction of Cr (VI) is usually evaluated by performing batch experiments which may not accurately represent the subsurface environment. The objective of this paper is to present a rational approach to determine the dual-enzyme reaction kinetics of Cr (VI) reduction by MR-1 from continuous flow soil column experiments which more accurately simulate the subsurface environment. Kinetic parameters obtained from soil column data were found to be much smaller than that obtained from batch data. The stable enzyme induced reaction rate was found to be 127th and the average deactivating enzyme induced reaction rate was 117th of the corresponding values obtained from batch reactor data as reported in literature.