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.

Seroprevalence of specific Brucella infection of cattle in Bangladesh Agricultural University Veterinary Clinics and its surrounding areas

Rahman, Md. Siddiqur,Alam, Nur,Rahman, A.K.M. Anisur,Huque, A.K.M. Fazlul,Ahasan, Md. Shamim,Song, Hee-Jong The Korean Society of Veterinary Service 2009 韓國家畜衛生學會誌 Vol.32 No.3

A cross sectional survey was conducted to determine the seroprevalence of brucellosis in cattle in Bangladesh Agricultural University (BAU) Veterinary Clinics, in BAU Dairy Farm and Vabokhali from June 2008 to November 2008. A total of 200 serum samples were collected from BAU Veterinary Clinic, from BAU Dairy Farm and Vabokhali. Among the serum samples 143 sera samples were collected from BAU Veterinary Clinic, 42 serum samples from BAU Dairy Farm and 15 serum samples from Vabokhali. Sera were separated from blood samples and tested with specific Brucella abortus antigen (BAA) test and B. melitensis antigen (BMA) test. The overall seroprevalence of brucellosis in cattle was 5% in BAA and 0.5% in BMA. It was observed that, a significant higher prevalence of B. abortus was found in female than male. An insignificant higher prevalence of brucellosis was found in adult cattle (aged above 5 years), in cross breed cattle, in cattle with grazing, cattle breed by natural breeding, and in pregnant cows. Although insignificant but a higher prevalence of brucellosis was found in aged cattle than young cattle, cross bred cattle, pregnant cattle than non pregnant cattle, cattle with grazing. A higher prevalence of brucellosis was found in female cattle than male.

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

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.

Comparing Satisfaction/Dissatisfaction and Public Confidence in the ITS Environment in Public and Private Transportation

( Anisur Rahman ),( Yoon C. Cho ) 서암순창장학회 2017 Journal of Marketing Thought Vol.4 No.2

Although Intelligent Transport Systems (ITS) is widely used both in public and private transportation, the factors that influence satisfaction and public confidence seem to differ between the two modes of transportation. The purpose of this study is to compare the justice dimensions that influence satisfaction and public confidence in the context of ITS in public and private transportation and to explore implications for Citizen/Customer Relationship Management (CRM) and public policy. This study finds that in public transportation, policy planners should focus on freedom to communicate views and opinions, ease of engaging commuting, adaptability of commuting to reflect individual circumstances, manner and behavior of service personnel, and provision of caring, individual attention towards passengers. In private transportation, policy planners should focus on manner and behavior of the service personnel, and provision of caring, individual attention towards passengers.

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.

Characteristics of bovine pulmonary parasites in Bangladesh

Rahman, A. K. M. Anisur,Begum, Nurjahan,Rahman, Md Siddiqur,Song, Hee-Jong The Korean Society of Veterinary Service 2009 韓國家畜衛生學會誌 Vol.32 No.1

In a cross-sectional abattoir survey of bovine pulmonary diseases in Mymensingh, during September 2001 to April 2002, subclinical Dictyocaulus viviparous infection was found in mesoendemic level in Bangladeshi adult zebu cattle. The number of mature lung worms varied from $1{\sim}18$ in individual lungs. One to five mature lung worms were most frequent (74.2%) followed by 6 to 10(19.3%) and $11{\sim}18$ (6.5%). Of the total 123 mature worms collected from 31 lungs, there were 50 (40.7%) male and 73 (59.3%) female worms. The female lungworms (mean length 14.41mm) were significantly (P<0.01) larger than the male lungworms (mean length 11.28mm). The number of hydatid cysts varied from $1{\sim}80$ in individual lungs. One to five ($1{\sim}5$) cysts were recorded most commonly (76.0%) followed by $11{\sim}80$ (20.0%) and $6{\sim}10$ (4%). The size (diameter) of the hydatid cysts ranged from $2{\sim}12cm$. Of the total 203 hydatid cysts collected from 31 lungs 45 (22.2%) cysts were fertile and 158 (77.8%) cyst were sterile.

Incorporation of anisotropic scattering into the method of characteristics

RAHMAN ANISUR,이덕중 한국원자력학회 2022 Nuclear Engineering and Technology Vol.54 No.9

In this study, we incorporate an anisotropic scattering scheme involving spherical harmonics into the method of characteristics (MOC). The neutron transport solution in a light water reactor can be significantly improved because of the impact of an anisotropic scattering source with the MOC flat source approximation. Several problems are selected to verify the proposed scheme and investigate its effects and accuracy. The MOC anisotropic scattering source is based on the expansion of spherical harmonics with Legendre polynomial functions. The angular flux, scattering source, and cross section are expanded in terms of the surface spherical harmonics. Later, the polynomial is expanded to achieve the odd and even parity of the source components. Ultimately, the MOC angular and scalar fluxes are calculated from a combination of two sources. This paper presents various numerical examples that represent the hot and cold conditions of a reactor core with boron concentration, burnable absorbers, and control rod materials, with and without a reflector or baffle. Moreover, a small critical core problem is considered which involves significant neutron leakage at room temperature. We demonstrate that an anisotropic scattering source significantly improves solution accuracy for the small core high-leakage problem, as well as for practical large core analyses