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Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants

Journal of Integrative Agriculture 2024年第1期23卷 1-19页

作者： atiqur rahman Hasan Sofiur rahman Shakil Uddin Naima Sultana Shirin Akhter Ujjal Kumar Nath Shamsun Nahar Begum Mazadul Islam Afroz Naznin Nurul Amin Sharif Ahmed Akbar Hossain Department of Genetics and Plant Breeding Bangladesh Agricultural UniversityMymensingh 2202Bangladesh Plant Breeding Division Bangladesh Institute of Nuclear AgricultureMymensingh 2202Bangladesh Tuber Crop Research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Horticulture Research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Biotechnology Division Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh International Rice Research Institute Bangladesh OfficeDhaka 1213Bangladesh Division of Soil Science Bangladesh Wheat and Maize Research InstituteDinajpur 5200Bangladesh

The impact of epigenetic modifications like DNA methylation on plant phenotypes has expanded the possibilities for crop *** methylation plays a part in the regulation of both the chromatin structure and gene expression,and the enzyme involved,DNA methyltransferase,executes the methylation process within the plant *** regulating crucial biological pathways,epigenetic changes actively contribute to the creation of the ***,epigenome editing may assist in overcoming some of the drawbacks of genome editing,which can have minor off-target consequences and merely facilitate the loss of a gene’s *** drawbacks include gene knockout,which can have such off-target *** review provides examples of several molecular characteristics of DNA methylation,as well as some plant physiological processes that are impacted by these epigenetic changes in the *** also discuss how DNA alterations might be used to improve crops and meet the demands of sustainable and environmentally-friendly farming.

关键词： DNA methylation epigenetics CMS male sterility chromatin architecture gene expression higher plants

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GliomaCNN: An Effective Lightweight CNN Model in Assessment of Classifying Brain Tumor from Magnetic Resonance Images Using Explainable AI

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Computer Modeling in Engineering & Sciences 2024年第9期140卷 2425-2448页

作者： Md.atiqur rahman Mustavi Ibne Masum Khan Md Hasib M.F.Mridha Sultan Alfarhood Mejdl Safran Dunren Che Department of Computer Science and Engineering Ahsanullah University of Science and TechnologyDhaka1208Bangladesh Department of Computer Science and Software Engineering The University of Western AustraliaPerthWA 6009Australia Department of Computer Science American International University-BangladeshDhaka1229Bangladesh Department of Computer Science College of Computer and Information SciencesKing Saud UniversityP.O.Box 51178Riyadh11543Saudi Arabia School of Computing Southern Illinois UniversityCarbondale62901USA

Brain tumors pose a significant threat to human lives and have gained increasing attention as the tenth leading cause of global *** study addresses the pressing issue of brain tumor classification using Magnetic resonance imaging(MRI).It focuses on distinguishing between Low-Grade Gliomas(LGG)and High-Grade Gliomas(HGG).LGGs are benign and typically manageable with surgical resection,while HGGs are malignant and more *** research introduces an innovative custom convolutional neural network(CNN)model,*** stands out as a lightweight CNN model compared to its *** research utilized the BraTS 2020 dataset for its *** with the gradient-boosting algorithm,GliomaCNN has achieved an impressive accuracy of 99.1569%.The model’s interpretability is ensured through SHapley Additive exPlanations(SHAP)and Gradient-weighted Class Activation Mapping(Grad-CAM++).They provide insights into critical decision-making regions for classification *** challenges in identifying tumors in images without visible signs,the model demonstrates remarkable performance in this critical medical application,offering a promising tool for accurate brain tumor diagnosis which paves the way for enhanced early detection and treatment of brain tumors.

关键词： Deep learning magnetic resonance imaging convolutional neural networks explainable AI boosting algorithm ablation

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Nature’s Pharmacy under Siege: Investigating Antibiotic Resistance Pattern in Endophytic Bacteria of Medicinal Plants

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Advances in Microbiology 2024年第4期14卷 183-208页

作者： Bonoshree Sarkar Afroza Sultana Nabila Nawar Binti Farhana Tasnim Chowdhury Sadia Afrin Mohammad Fahim Taibur rahman atiqur rahman Infection Biology Laboratory Department of Biochemistry and Molecular Biology University of Dhaka Dhaka Bangladesh Department of Pathology University of Alabama at Birmingham Birmingham USA

Antibiotic resistance poses a significant global health threat, necessitating a thorough understanding of its prevalence in various ecological contexts. Medicinal plants, renowned for their therapeutic properties, host endophytic bacteria that produce bioactive compounds. Understanding antibiotic resistance dynamics in these bacteria is vital for human health and antibiotic efficacy preservation. In this study, we investigated antibiotic resistance profiles in endophytic bacteria from five medicinal plants: Thankuni, Neem, Aparajita, Joba, and Snake plant. We isolated and characterized 113 endophytic bacteria, with varying resistance patterns observed against multiple antibiotics. Notably, 53 strains were multidrug-resistant (MDR), with 14 exhibiting extensive drug resistance (XDR). Thankuni-associated bacteria displayed 44% MDR and 11% XDR, while Neem-associated bacteria showed higher resistance (60% MDR, 13% XDR). Aparajita-associated bacteria had lower resistance (22% MDR, 6% XDR), whereas Joba-associated bacteria exhibited substantial resistance (54% MDR, 14% XDR). Snake plant-associated bacteria showed 7% MDR and 4% XDR. Genus-specific distribution revealed Bacillus (47%), Staphylococcus (21%), and Klebsiella (11%) as major contributors to MDR. Our findings highlight diverse drug resistance patterns among plant-associated bacteria and underscore the complexity of antibiotic resistance dynamics in diverse plant environments. Identification of XDR strains emphasizes the severity of the antibiotic resistance problem, warranting further investigation into contributing factors.

关键词： Antibiotic Resistance Endophytic Bacteria Medicinal Plants Drug Resistance

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Entropy Quantization of Schwarzschild Black Hole

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Communications in Theoretical Physics 2019年第3期71卷 307-311页

作者： M.atiqur rahman Department of Applied Mathematics Rajshahi University

The surface gravity of Schwarzschild black hole can be quantized from the test particle moving around different energy states analog to the Bohr's atomic model. We have quantized the Hawking temperature and entropy of Schwarzschild black hole from quantization of surface gravity. We also have shown that the change of entropy reduces to zero when the boundary shrinks to very small size.

关键词： Hawking temperature entropy Schwarzschild black hole

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COVID-19: Challenges and viewpoints from low-and-middle-income Asian countries perspectives

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Journal of Safety Science and Resilience 2020年第2期1卷 70-72页

作者： Yasmin Jahan atiqur rahman Graduate School of Biomedical and Health Sciences Hiroshima University1-2-3 Minami-kuHiroshima-shi 734-0046Japan Department of Society and Culture(IKOS) Division Ageing and Social ChangeLinköping UniversitySweden

The crisis of coronavirus disease(COVID-19)is growing and has a potential impact on low-and-middle-income countries(LMICs),particularly in Asian regions,which,have reported less so *** main purpose of this article is to discuss the challenges of COVID-19 management in Asian LMICs and propose some future guidelines to control the transmission and *** to a highly dense population,low-resourced health system,lack of testing kit,and tracing,the ultimate impact could be *** is highly likely that Asian LMICs were not in the center of receiving high priority by the international community in order to take effective prevention *** might upsurge *** the symptoms,mode of transmission varies largely due to a number of unknown clinical features of the virus,defining a risk group only based on some limited criteria such as age and disease with comorbidity could be *** some of the Asian LMICs launched contact tracing ***,the study has identified several healthcare challenges in Asian LMICs such as shortage of supply of PPE,inadequate long-term care services,the socio-cultural differences which require utmost *** addition,to control infection and enhance prevention,some pertinent problems need to be *** on that,some multifactorial approaches can be taken in line with international ***,this paper recommends developing a strong and resilient healthcare monitoring system.

关键词： COVID-19 Asian Low-middle income countries Challenges control Prevention

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Association of Host Interferon-γ Gene Polymorphism with Toxoplasma gondii Infection in Pregnant Women of Bangladesh

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American Journal of Molecular Biology 2023年第3期13卷 156-169页

作者： Nasrin Akter Sonia Tamanna Molie rahman atiqur rahman Akm Mahbub Hasan Taibur rahman Laboratory of Infection Biology Department of Biochemistry and Molecular Biology University of Dhaka Dhaka Bangladesh Laboratory of Reproductive Health Department of Biochemistry and Molecular Biology University of Dhaka Dhaka Bangladesh Bangladesh Institute of Research and Rehabilitation in Diabetes Endocrine and Metabolic Disorders Dhaka Bangladesh

Human toxoplasmosis is caused by the intracellular protozoan parasite Toxoplasma gondii. Although T. gondii infection is generally asymptomatic for most of the immunocompetent adults, severe complications may occur particularly in pregnant women and immunocompromised individual. Host cell immunity plays a critical role in parasite differentiation and persistence in the host. Therefore, genetic polymorphism in the host immune genes, for instance interferon-γ gene could be linked with possibility of T. gondii infection. The objective of the study was to verify the link between the single nucleotide polymorphisms (SNPs) in the IFN-γ gene of pregnant women and T. gondii infection through correlating with anthropometric and sociodemographic parameters. In this study, ninety-two (N = 92) pregnant women (16 - 40 years) and healthy controls (N = 95) with similar age ranges were included. Among them, 25% (n = 23) pregnant women were seropositive for T. gondii IgG antibodies by Rapid Test Assay. Allelic and genotypic frequencies of IFN-γ +874T/A (rs2430561) SNPs were evaluated by using ARMS-PCR. The distribution of the A and T alleles in the specific position of the IFN-γ gene in the T. gondii-infected pregnant women and the control groups did not differ significantly, according to the data. However, we found a higher frequency (13.04%) of A/A genotype in T. gondii infected pregnant women as compared to non-infected individuals (8.70%), demonstrating that T. gondii infection susceptibility may be increased by homozygosity for the A allele. Further studies are to be needed to find out the link between host gene polymorphism and T. gondii infection in Bangladesh.

关键词： T. gondii Pregnant Women Seroprevalence IFN-γ Gene Polymorphism

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Analysis of Proteotranscriptomics Landscape Reveals Differentially Regulated Pathways in Toxoplasma gondii Infected Mouse Liver

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Computational Molecular Bioscience 2022年第1期12卷 20-57页

作者： Tanzina Tarannum Md. Saruar Alam atiqur rahman Sajib Chakraborty Hossain Uddin Shekhar Taibur rahman Laboratory of Infection Biology Department of Biochemistry and Molecular Biology University of Dhaka Dhaka Bangladesh Laboratory Clinical Biochemistry and Translational Medicine Department of Biochemistry and Molecular Biology University of Dhaka Dhaka Bangladesh

Toxoplasma gondii (T. gondii) an intracellular protozoan parasite, infects mammals including human population world-wide. Upon primary infection, the parasite contributes to mild flu like symptoms in immune competent host, but life threatening complication is seen in immune compromised patients and in pregnant women. Understanding the host-parasite interaction is critical for understanding the pathogenesis and biology parasite reactivation in the host. In this study, we used proteotrasncriptomics analyses by integrating the transcriptomics and proteomics data of T. gondii infected mouse liver to uncover the effector molecules responsible for disease pathogenesis that can be used as candidate markers for diagnosis and drug target. With this aim, we systematically integrated transcriptomicand proteomic data, representing the parasite infected mouse liver. Out of 2758 differentially expressed genes (DEGs) and 301 differentially expressed proteins (DEPs), 159 overlapping genes were identified. Among them, 86 genes were upregulated and 72 were downregulated in their respective mRNA and protein levels in the infected condition. Gene Ontology (GO) analysis revealed that the upregulated genes were mostly associated with immune system processes whereas the downregulated genes were involved in oxidation-reduction process and metabolism of lipid, and fatty acids. Protein-protein interaction (PPI) network analysis uncovered an interaction-hub including, Psmb8, Psmb9 and Tap1 for upregulated proteins and Cyp1A2, Cyp4A10 and Cyp3A11 for down-regulated proteins. Further studies are needed to validating these effector molecules. These molecules are likely to play a vital role in disease pathogenesis, as well as can be used as potential diagnostic marker and drug target candidates.

关键词： Toxoplasma gondii Transcriptome Proteome Mouse Liver Differentially Expressed Genes and Proteins Gene Ontology Analysis Protein-Protein Interaction Hub-Proteins Homology Modeling Effector Molecules

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Mitochondrial DNA mutations-candidate biomarkers for breast cancer diagnosis in Bangladesh

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Chinese Journal of Cancer 2012年第9期31卷 449-454页

作者： Gazi Nurun Nahar Sultana atiqur rahman Abu Din Ahmed Shahinuzzaman Rowshan Ara Begum Chowdhury Faiz Hossain Centre for Advanced Research in Sciences University of DhakaDhaka 1000Bangladesh Department of Microbiology University of DhakaDhaka 1000Bangladesh Department of Genetic Engineering and Biotechnology University of DhakaDhaka 1000Bangladesh National Cancer Research Institute and Hospital MohakhaliDhaka 1212Bangladesh East West University MohakhaliDhaka 1212Banglades

Breast cancer is a major health problem that affects more than 24% of women in Bangladesh. Furthermore, among low-income countries including Bangladesh, individuals have a high risk for developing breast cancer. This study aimed to identify candidate mitochondrial DNA (mtDNA) biomarkers for breast cancer diagnosis in Bangladeshi women to be used as a preventive approach. We screened the blood samples from 24 breast cancer patients and 20 healthy controls to detect polymorphisms in the D-loop and the ND3-and ND4-coding regions of mtDNA by direct sequencing. Among 14 distinct mutations, 10 polymorphisms were found in the D-loop, 3 were found in the ND3-coding region, and 1 was found in the ND4-coding region. The frequency of two novel polymorphisms in the D-loop, one at position 16290 (Tins) and the other at position 16293 (A-del), was higher in breast cancer patients than in control subjects (position 16290: odds ratio = 6.011, 95% confidence interval = 1.2482 to 28.8411, P = 0.002; position 16293: odds ratio = 5.6028, 95% confidence interval = 1.4357 to 21.8925, P = 0.010). We also observed one novel mutation in the ND3-coding region at position 10316 (A > G) in 69% of breast cancer patients but not in control subjects. The study suggests that two novel polymorphisms in the D-loop may be candidate biomarkers for breast

关键词：线粒体DNA突变生物标志物孟加拉国乳腺癌诊断基因编码区基因多态性 D-loop区

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Multi-functional pharmacological credence of triterpenoid 16-hydroxy betulinic acid isolated from Mikania cordata

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中国药理学与毒理学杂志 2018年第4期32卷 253-254页

作者： M. Oliur rahman Shah Alam SIDDIQUI atiqur rahman Mohammad Ahsanul AKBAR Mohammad Ajmal ALI Department of Botany University of Dhaka Dhaka 1000 Bangladesh Department ofApplied Chemistry and Chemical Engineering Islamic University Kushtia 7003 Bangladesh Department of Clinical Pharmacy and Pharmacology University of Dhaka Dhaka 1

OBJECTIVE To isolate and characterize bioactive compound from traditionally important medicinal plant Mikania cordata,and to investigate muti-faced pharmacological activities of the isolated *** A triterpeenoid,16-hydroxy betulinic acid(16 HBA) was isolated from Mikania cordata leaf and the structure of the compound was determined by NMR spectroscopic *** activity of 16 HBA was tested by disc diffusion method and minimum inhibitory concentration(MIC) against the tested microorganisms was *** analgesic property of 16 HBA was tested using acetic acid-induced writhes in mice and hot plate thermal stimulation in *** anti-inflammatory activity was studied using carrageenin-induced paw edema *** antipyretic potential of 16 HBA was evaluated by using yeast-induced hyperthermia in *** The triterpenoid 16 HBA showed potent antibacterial activity with inhibition zone of diameter ranging from 12.0~17.5 mm and antifungal activity with mycelial growth inhibition ranges from 37.6%~54.5%.The MIC values for antibacterial and antifungal activities ranged from 31.5~125 and 250~1000 μg·mL-1 *** compound(50 and100 mg·kg^(-1) body weight) showed potent peripheral and central analgesic activity having 55.19% and41% of writhing inhibition at 90 min after administration of the compound and the highest 55.98%,79.18% elongation of reaction time,*** anti-inflammatory activity screening,the compound(100 mg·kg^(-1)) revealed the highest 77.08% edema inhibition at 4 h after administration of *** antipyretic assay,16 HBA exhibited a strong antipyretic effect in yeast-induced *** The present study confirmed that 16-hydroxy betulinic acid isolated from Mikania cordata has potent antimicrobial,analgesic,anti-inflammatory and antipyretic *** results can be seen as scientific support for the traditional and folklore usage of Mikania cordata in Bangladesh for the treatment of differen

关键词：药用植物薇甘菊活性化学物药物分析

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Infection of <i>Toxoplasma gondii</i>in Humans and Livestock Animals: An Emerging Silent Threat for Bangladesh

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Open Journal of Medical Microbiology 2018年第4期8卷 109-117页

作者： Taibur rahman atiqur rahman Sajib Chakraborty Department of Biochemistry and Molecular Biology University of Dhaka Dhaka Bangladesh

Toxoplasma gondii is an intracellular, zoonotic protozoan parasite that causes toxoplasmosis. It can potentially infect almost all mammalian and avian hosts including one-third of the human population world-wide. The major target group of the parasite includes immunocompromised patients (e.g. AIDS, cancer, organ transplantation) and fetus bearing pregnant women where it develops toxoplasmic encephalitis, myocarditis, chorioretinitis and abnormal fetal brain development or stillbirths respectively. In this review, we have presented the current status of T. gondii infection in livestock animals and human population in Bangladesh to assess the country-wide relative risk. Although exact prevalence is difficult to predict due to the scarcity of data, nevertheless existing literature suggests that 16% - 39% humans and 8% - 70% domestic animals are infected with T. gondii, which implies Bangladeshi population is at high risk of toxoplasmosis. Furthermore, we have proposed a potential area of research to decipher the genetic diversity and transmission routes of T. gondii infection into Bangladeshi population.

关键词： Toxoplasma gondii Seroprevalence Livestock Animals Humans Bangladesh

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