An in-silico approach to design potential siRNAs against the ORF57 of Kaposi's sarcoma-associated herpesvirus

Rahman, Anisur,Gupta, Shipan Das,Rahman, Md. Anisur,Tamanna, Saheda Korea Genome Organization 2021 Genomics & informatics Vol.19 No.4

Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.

Evaluation of Bio-Control Efficacy of Trichoderma Strains against Alternaria alternata Causing Leaf Blight of Ashwagandha [Withania somnifera (L.) Dunal]

Md. Ahsanur Rahman,Md. Arifur Rahman,Zakiah Rahman Moni,Mohammad Anisur Rahman 강원대학교 산림과학연구소 2020 Journal of Forest Science Vol.36 No.3

Ashwagandha is an important ancient medicinal crops, being affected with many diseases, among which leaf blight caused by Alternaria alternata has become the constraint resulting in huge yield losses. Continuous usage of chemical methods leads to environment, soil and water pollution. Whereas biological control of diseases is long lasting, inexpensive, eco-friendly and harmless to target organisms. In this context, it is aimed to evaluate five Trichoderma strains viz. Trichoderma virens IMI-392430, T. pseudokoningii IMI-392431, T. harzianum IMI-392432, T. harzianum IMI-392433 and T. harzianum IMI-392434 as bio-control efficacy against A. alternata and growth promoting effect in Ashwagandha. All the Trichoderma strains had varied antagonistic effects against the pathogen. In dual culture technique, the strain T. harzianum IMI-392433 showed maximum percentage inhibition of mycelial growth (54.89%) followed by T. harzianum IMI-392432 (53.83%), T. harzianum IMI-392434 (48.94%) and T. virens IMI-392430, (43.62%) against the pathogen, while the least inhibition percentage was observed with the T. pseudokoningii IMI-392431 (36.60%). The culture filtrate of the Trichoderma strain, T. harzianum IMI-392433 recorded highest inhibition on the mycelial growth (39.05%) and spore germination (80.77%) of pathogen and the lowest was recorded in T. pseudokoningii IMI-392431 (20.45 and 50%). Moreover, seeds treated with spore suspension of the strain T. harzianum IMI-392433 reduced the percentages of disease severity index significantly. The strain T. harzianum IMI-392433 also significantly increased seed germination %, seedling vigor and growth of Ashwagandha. The correlation matrix showed that root yield per plant of Ashwagandha had significant and positive correlation with plant height (r=0.726**), number of leaf (r=0.514**), number of primary branch (r=0.820**), number of secondary branch (r=0.829**), fresh plant weight (r=0.887**), plant dry weight (r=0.613**), root length (r=0.824**), root diameter (r=0.786**), root dry weight (r=0.739**) and fresh root weight (r=0.731**). The significant and negative correlation (r=-0.336**) was observed with the root yield and percentages of disease severity index. The study recognized that the T. harzianum IMI-392433 strain performed well in inhibiting the mycelial growth and reduced the percentages of disease severity index of pathogen as well as increased the plant growth in Ashwagandha.

Women’s coping strategies and help-seeking practices : Some observations on domestic violence in rural Bangladesh

Anisur Rahman KHAN 이화여자대학교 아시아여성학센터 2015 Asian Journal of Women's Studies(AJWS) Vol.21 No.3

This article examines the coping strategies and help-seeking practices of women victims of domestic violence perpetrated by their husbands in rural Bangladesh. By drawing on 39 semi-structured in-depth interviews, conducted in eight rural settings in Netrokona and Mymensingh districts, it was found that the abused women tried to cope with domestic violence in many ways. Making their marriages work at any cost was their prime motivation in coping with violence. Moreover, they tolerated domestic violence because they were concerned about their own future and that of their children. At times, some women spoke back to their husbands. In extreme cases, some left the abusive relationships. With regard to helpseeking, they largely sought assistance from informal networks, such as parents, relatives, neighbors, community leaders and community-based NGOs and only a few sought formal support from legal and institutional agencies. It was noted that the dynamics of both the coping strategies and help-seeking practices were very complex. Women’s vulnerabilities were well-exposed in both cases. Neither informal nor formal support could ensure sufficient protection for women. Sometimes, seeking help aggravated women’s condition in many ways. It is, therefore, suggested that the existing drawbacks in both informal and formal support mechanisms must be eliminated in order to render appropriate services to the victims.

Evaluation of Firmness and Sweetness Index of Tomatoes using Hyperspectral Imaging

( Anisur Rahman ),( Mohammad Akbar Faqeerzada ),( Rahul Joshi ),( Byoung-kwan Cho ) 한국농업기계학회 2017 한국농업기계학회 학술발표논문집 Vol.22 No.1

The objective of this study was to evaluate firmness, and sweetness index (SI) of tomatoes (Lycopersicum esculentum) by using hyperspectral imaging (HSI) in the range of 1000-1400 nm. The mean spectra of the 95 matured tomato samples were extracted from the hyperspectral images, and the reference firmness and sweetness index of the same sample were measured and calibrated with their corresponding spectral data by partial least squares (PLS) regression with different preprocessing method. The results showed that the regression model developed by PLS regression based on Savitzky-Golay (S-G) second-derivative preprocessed spectra resulted in better performance for firmness, and SI of tomatoes compared to models developed by other preprocessing methods, with correlation coefficients (rpred) of 0.82, and 0.74 with standard error of prediction (SEP) of 0.86 N, and 0.63 respectively. Then, the feature wavelengths were identified using model-based variable selection method, i.e., variable important in projection (VIP), resulting from the PLS regression analyses and finally chemical images were derived by applying the respective regression coefficient on the spectral image in a pixel-wise manner. The resulting chemical images provided detailed information on firmness, and sweetness index (SI) of tomatoes. Therefore, these research demonstrated that HIS technique has a potential for rapid and non-destructive evaluation of the firmness and sweetness index of tomatoes.

Hollow silica nanosphere having functionalized interior surface with thin manganese oxide layer: nanoreactor framework for size-selective Lewis acid catalysis

Anisur, Rahman Md,Shin, Jongmin,Choi, Hyung Ho,Yeo, Kyung Min,Kang, Eun Joo,Lee, In Su Royal Society of Chemistry 2010 Journal of materials chemistry Vol.20 No.47

<P>A novel selective nanoscale etching process that generated a well defined hollow nanostructure was developed by treating manganese oxide nanoparticles with a hydroxylamine solution. This selective etching process was used for exploiting a novel method of differentially functionalizing the internal surface of a hollow silica shell with a catalytically active Mn<SUB>3</SUB>O<SUB>4</SUB> layer and creating a novel nanoreactor framework. The nanoreactor fabricated by the newly developed method catalyzed the cyanosilylation reactions of various aromatic aldehydes with size and shape selectivity. Moreover, the substrate selectivity in the cyanosilylation reactions was efficiently tuned by modifying the outer silica shell with silane coupling reagents.</P> <P>Graphic Abstract</P><P>Nanoscale etching process generated a nanoreactor framework, consisting of a hollow and porous silica shell and a functionalized interior surface with Mn<SUB>3</SUB>O<SUB>4</SUB> layer, which catalyzes cyanosilylation reactions with size selectivity. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c0jm02647f'> </P>

Attenuation of p-dimethylaminoazobenzene initiated genotoxicity and cytotoxicity in mice by the combined treatment of a traditional homeopathic remedy Chelidonium Majus 200C and vitamin-C

Anisur Rahman Khuda-Bukhsh,Surjyo Jyoti Biswas,Susanta Roy Karmakar 셀메드 세포교정의약학회 2012 셀메드 (CellMed) Vol.2 No.4

The homeopathic remedy Chelidonium majus 200C (Chel-200) is traditionally used by homeopathic practitioners in liver ailments arising out of hepatotoxicity. The present investigation was aimed at examining whether vitamin C (L-ascorbic acid or AA), used in both traditional and orthodox medicines, can show better effects when used in combination with Chel-200, in favorably modifying the toxicological effects induced by the chronic feeding of p-dimethylaminoazobenzene (p-DAB, initiator) and phenobarbital (PB, promoter) in mice for 7 days through 120 days to induce hepatotoxicity and liver tumors. Mice were euthanized at 7, 15, 30, 60, 90, and 120 days of carcinogen feeding to assess various cytogenetical, biochemical and histological changes occurring in them. In a placebo controlled study, Chel-200 or the respective placebo (Alcohol-200C or Alc, “vehicle” of homeopathic drug), was orally administered to toxicant-fed mice. Sub-groups of the mice receiving Chel-200 were also fed either AA or an Alc placebo and their individual and conjoint effects were studied against the respective controls, to evaluate if the combination therapy of Chel-200 with AA can be of additional help in the amelioration of the toxicities generated by the toxicants. The combined feeding of Chel- 200 and AA appeared to reduce the cytotoxic and genotoxic effects significantly, when compared to either only the Chel-200 or AA fed group. A similar trend was also obtained in the results of scanning and transmission electron microscopic studies of the livers. Experiments in other mammalian models are warranted to confirm if these drugs in combination could be used in palliative care of human patients with liver diseases including cancer.

Quality Analysis of Stored Bell Peppers Using Near-Infrared Hyperspectral Imaging

Rahman, Anisur,Faqeerzada, Mohammad Akbar,Joshi, Rahul,Lohumi, Santosh,Kandpal, Lalit Mohan,Lee, Hoonsoo,Mo, Changyeun,Kim, Moon Sung,Cho, Byoung-Kwan American Society of Agricultural and Biological En 2018 Transactions of the ASABE Vol.61 No.4

<P>Abstract. The objective of this study was to predict the moisture content (MC), soluble solids content (SSC), and titratable acidity (TA) content in bell peppers during storage (18°C, 85% relative humidity) over 12 days, based on near-infrared hyperspectral imaging (NIR-HSI) in the 1000-1500 nm wavelength range. The mean spectra of 148 mature bell peppers were extracted from the hyperspectral images, and multivariate calibration models were built using partial least squares (PLS) regression with different preprocessing spectra techniques. The most effective wavelengths were selected using the variable importance in projection (VIP) technique, which selected optimal variables for the target quality parameters of bell peppers from a full set of variables. Subsequently the selected variables were used to develop a PLS-VIP model for simplifying the prediction model. The MC, SSC, and TA content in bell peppers during storage changed from 90.7% to 93.0%, from 6.1%Brix to 7.3%Brix, and from 0.222% to 0.334%, respectively. The PLS regression model with MC, SSC, and TA content resulted in coefficients of determination (R<SUP>2</SUP>pred) of 0.83, 0.85, and 0.7, with standard errors of prediction (SEP) of 0.08%, 0.075%Brix, and 0.013%, respectively, using SNV preprocessed spectra for MC and TA content and Savitzky-Golay (S-G) second-order derivatives preprocessed spectra for SSC of bell peppers. By contrast, the prediction results yielded R<SUP>2</SUP>pred of 0.69, 0.75, and 0.68, respectively, with SEP values of 0.103%, 0.107%Brix, and 0.011% when the PLS-VIP model was employed. The PLS-VIP model simplified the calibration model by selecting the most important variables in terms of their responsiveness to bell pepper quality properties. The results revealed that HSI coupled with multivariate analysis can be used successfully to predict the MC, SSC, and TA content in bell peppers. Keywords: Fruit quality, Hyperspectral imagery, Image analysis, Spectral analysis, Stored bell pepper.</P>

Disesae-Modigying Drugs in Rheumatoid Arthritis

Rahman, Anisur,Ahmed, salma,Underwood, Martin Medical Publications Korea 2002 Medical Progress Vol.24 No.8

Pulmonary diseases in slaughtered cattle 4. Pathology of pulmonary lesions

Rahman Akm Anisur,Nooruddin Md,Hossain M Mokbul,Rahman M Siddiqur,Hossain Mohammad Arif,Song Hee-Jong The Korean Society of Veterinary Service 2006 韓國家畜衛生學會誌 Vol.29 No.4

A study of pulmonary diseases in the slaughtered cattle (n = 125) of Mymensingh town was conducted to study pathological findings using the standard methods from September 2001 through April 2002. The pulmonary lesions observed in this study included congestion, emphysema, anthracosis, pleuritis abscess and hemorrhage. The histopathological findings of congestion were characterized by hemorrhage, a large number of leukocytes infiltration in the lumen of the alveoli, bronchitis, bronchiolitis, proliferation of fibrous connective tissue and hyperplasia of bronchiolar epithelia. Histopathologically, emphysema was identified by the distended alveoli with thin and atrophied alveolar walls. In anthracosis, carbon particles were found in stroma and alveolar lumen. In pleuritic lesions, there was a proliferation of fibrous connective tissue along with the infiltration of mononuclear reactive cells. Abscesses were characteristic of the accumulation of neutrophils surrounded by immature fibroblasts forming a capsule like structure.

3-D Image Reconstruction Techniques for Plant and Animal Morphological Analysis - A Review

( Anisur Rahman ),( Changyeun Mo ),( Byoung-kwan Cho ) 한국농업기계학회 2017 바이오시스템공학 Vol.42 No.4

Purpose: This review focuses on the major 3-D image reconstruction techniques and their applications in plant and animal morphological analysis. Methods &Results: This paper begins with an overview of major 3-D image reconstruction techniques and their basic principles. Subsequently, their applications in plant and animal morphological analysis are reviewed. A discussion on the limitations and future research direction of 3-D imaging techniques for accurate, fast measurements and modeling of plant and animal morphological analysis follows. Conclusions: Owing to the increasing demand for plant and animal morphological analysis, the application of 3-D imaging techniques will increase in popularity among researchers and the agricultural industry.