S. M. Shahinul Islam

University of Rajshahi | RU · Institute of Biological Sciences

In this study, the effect of heat stress pretreatment factors on cell suspension culture of potato was investigated. The duration of stress pretreatment at 5–50 °C for 20 min was evaluated by measuring cell growth and viability using the trypan blue exclusion method. Data were collected by measuring the dry weight of suspended cells, duration of he...

Streptococcus mutans bacteria form a biofilm called plaque that causes oral diseases, including tooth decay. Therefore, inhibition of biofilm formation is essential to maintaining good oral health. The health and nutritional benefits of Cynodon dactylon are well documented, but very little is known about its use to treat against oral diseases. The...

Background: There are various varieties of habitats that have specific characteristics of water for the breeding of mosquito. A house-to-house cross-sectional entomological survey used to be carried out at per domestic area to become aware of larval breeding sites. Aedes aeygypti used to be primary vector and Aedes albopictus used to be predominant...

A shift in agricultural management from chemical to organic practices is expected to reduce environmental hazards and improve soil health and productivity in Bangladesh. To increase knowledge of the impact of probiotic cultures and organic farming practices on the physical and chemical properties of Bangladeshi soils, an investigation was carried o...

Congenital heart disease (CHD) is a congenital defect affecting the structure of the heart. Early detection can be done by auscultating the murmur and this could help to diagnosis the disease. This study was aimed to detect CHD by rapid evaluation of clinical features, findings and cardiac auscultation which will help to customize the future manage...

Proper management and selection of a single drug or multiple drugs for the treatment of diabetes is very important. The choice of treatment depends on a number of factors. With the proper treatment, the state of diabetes can be managed very smoothly. The main objective of this study was to compare the efficacy of insulin, biguanides and sulfonylure...

Cancer is a very alarming disease that affects many people in every year all over the world and also in Bangladesh. Under this study a descriptive cross-sectional study was conducted to assess the knowledge on oral health status and its care before, during and after therapy. Total 145 cancer patients were selected and interviewed through a semi-str...

The purpose of this study was to evaluate a randomized control trial protocol to assess the effectiveness of an oral care protocol on chemotherapy- and/ or radiation therapy-induced oral complications in cancer patients. It was a randomized, outcome assessor blinded study. Patients were randomly allotted to a control and intervention group. Out of...

The prevalence of prostatic carcinoma is the outcome of several factors including improved awareness the general population of the significance of carcinoma of the prostate and progresses in diagnostic approaches. The PSA is a probable prostate cancer tumor marker, although it cannot distinguish prostate cancer from BPH solely. To assess the useful...

Background: Diabetic autonomic neuropathy (DAN) is the most neglected major and widespread microvascular complication of type-2 diabetes mellitus, involving multiple body organs. DAN is a subtype of diabetic peripheral neuropathy.Objective: To investigate the relationship between the variability of HbA1c and diabetic autonomic neuropathy in type-2...

In search of alternative counter to harmful effects of chemical fertilizers on soils and environment, probiotic and organic manures-based fertilizer management options need to be evaluated. The experiments were designed as randomized complete block design (RCBD) consisting of three wheat varieties and nine soil amendment treatments. The result reve...

Pouzolzia sanguinea grows in tropical and sub-tropical regions of Bangladesh, used for a variety of purposes including pain, rheumatoid kidney diseases in traditional medicine. The crude ethanolic leaf extract of P. sanguinea with its different fractions (ethanol, n-hexane, and chloroform) was investigated for phytochemical constituents, in vitro a...

Under this study a total of nine treatments were considered for soil amendments where organic manures, chemical fertilizer and probiotics were used to evaluate the efficiency on growth and yield of wheat. On the basis of seedling disease incidence and chlorophyll presence parameters data were recorded on seedling infection at 14 days, seedling blig...

Diabetic peripheral neuropathy (DPN) patients frequently feel persistent pain, which is described as painful diabetic peripheral neuropathy (PDPN), which begins in both feet and frequently spreads to the calves, fingers, and hands. PDPN not only causes pain, but also affects patients' sleep, emotions, mental state, and everyday activities, resultin...

Mulberry is a very hard and quickly developing plant belongs to the family of Moraceae. The leaf of mulberry is exclusively utilized for feeding and rising of the silkworm (Bombyx mori) for the production of silk yarn. It is evaluated that mulberry silk contributes around 90% of the total worldwide raw silk production that contributed to socio-econ...

Diabetic peripheral neuropathy (DPN) is one of the most common long-term microvascular complications of diabetes. This study was undertaken to investigate the association of HbA1c variability with diabetic peripheral neuropathy (sensory and motor) in patients with type-2 diabetes. In this cross-sectional study, a total of 150 type-2 diabetic patien...

In genome-wide quantitative trait locus (QTL) mapping studies, multiple quantitative traits are often measured along with the marker genotypes. Multi-trait QTL (MtQTL) analysis, which includes multiple quantitative traits together in a single model, is an efficient technique to increase the power of QTL identification. The two most widely used clas...

Qualitative and quantitative studies were done on leaf epidermal characteristics with special reference to stomatal features to find out the impact of environmental condition on twenty four accessions of Cynodon dactylon (L.) Pers. collected from different ecological habitats of Bangladesh. The foliar epidermal peels from both surfaces of mature le...

Application of chemical substances as stress pre-treatment factors may positively influence androgenetic responses in cereal and other crops. AgNO3 is an anti-ethylene compounds that played a significant role in combination with other chemicals for anther culture responses in cereal and other crop plants. For this study two local wheat cultivars vi...

Sixteen potato genotypes were assessed for drought tolerance through morphophysiological characteristics using stress tolerance trait index (STTI), principal component analysis (PCA), and cluster analysis (CA). Two to three wk old nodal segments explants (1.0 to 2.0 cm long) derived from in vitro grown sprouts were cultured on MS medium that contai...

Multivariate simple interval mapping (SIM) is one of the most popular approaches for multiple quantitative trait locus (QTL) analysis. Both maximum likelihood (ML) and least squares (LS) multivariate regression (MVR) are widely used methods for multi-trait SIM. ML-based MVR (MVR-ML) is an expectation maximization (EM) algorithm based iterative and...

Leaf morphology of crop plants has significant value in agronomy. Leaf rolling in rice plays a vital role to increase grain yield. However, collective information on the rolling leaf (RL) genes reported to date, and different comparative bioinformatics studies of their sequences are still incomplete. This bioinformatics study was designed to invest...

Morphological, phenotypical and yield attributing characteristics of 20 mulberry genotypes were evaluated. Genotypic and phenotypic variations, heritability, genetic advance and correlation co-efficient were also estimated. It was found that the phenotypic co-efficient of variation (PCV) was higher (97.68%) than genotypic co-efficient of variation...

Simple interval mapping (SIM) is one of the most popular approaches for genome wide single quantitative trait locus (QTL) analysis. Maximum likelihood (ML) and ordinary least squares (OLS) regression are widely used methods for SIM. However, these approaches are very sensitive to outliers and provide misleading results in presence of phenotypic con...

Morphological, phenotypical and yield attributing characteristics of 20 mulberry genotypes were evaluated. Genotypic and phenotypic variations, heritability, genetic advance and correlation coefficient were also estimated. It was found that the phenotypic coefficient of variation (PCV) was higher (97.68%) than genotypic coefficient of variation (GC...

Callus induction and its subsequent regeneration is an important issue to study the genetic variability in breeding and biotechnological program. Under this study, various physiological characteristics of calli were evaluated based on ten (10) indigenous and six (6) exotic potato genotypes. Correlation matrix, mean rank, and standard deviation of r...

Simple interval mapping (SIM) is one of the most popular approaches for genome-wide single quantitative trait locus (QTL) analysis. Maximum likelihood (ML) and least squares (LS) regressions are widely used methods for SIM. However, these approaches are very complex and time-consuming in terms of statistical computation. In this study, we have intr...

Lung cancer is the most important health risk for human in worldwide. Non-small cell lung cancer (NSCLC) is the most common cause of premature death from malignant disease. The aim of the study was to determine the pathways and expression profile of the genes to discover molecular signature at RNA and protein levels which could serve as potential d...

This study was performed on in vitro bioassay screening for salt tolerance of ten native and six exotic potato genotypes in Bangladesh. Single node was used to evaluate salinity tolerance especially on biomass production. Five different concentrations of NaCl (0 = control, 100, 150, 200 and 250 mM) were used in addition to MS medium and evaluated s...

Classification of samples into one or more populations is one of the main objectives of gene expression data (GED) analysis. Many machine learning algorithms were employed in several studies to perform this task. However, these studies did not consider the outliers problem. GEDs are often contaminated by outliers due to several steps involve in the...

Mulberry genetic resource is increasingly being recognized as one of the basic key component for sustainable silk production under changing climatic condition. In this investigation, analysis of multivariate was done to assess the diversity in 20 mulberry genotypes (includes indigenous and exotic) for leaf yield and its growth attributes. The analy...

With the rapid development of high-throughput DNA microarray technologies, researchers can measure expression profiles of thousands of genes simultaneously with low costs. These massive amounts of gene expression (GE) data often contain missing values or outliers due to various reasons of data generating process. Most of the statistical methods wer...

This study was carried out to improve an efficient protocol for in vitro callus induction and plant regeneration using Bangladeshi barley genotypes collected from BARI, Gazipur, Bangladesh. After sterilization embryos were separated carefully from mature seeds of six barley genotypes (BB-1, BB-2, BB-3, BB-4, BB-5 and BB-6) and cultured them in MS m...

Interphase nuclear phenotype in different accessions (Acc.) of Cynodon dactylon studied in the present experiment showed chromocentric nuclear organization and the chromocenters were found to be visible clearly. The chromocenter numbers were not same and sometimes it was found to be significantly less and never more than total number of chromosomes...

Simple interval mapping (SIM) is one of the most popular approaches for genome-wide single quantitative trait locus (QTL) analysis. Maximum likelihood (ML) and ordinary least squares (OLS) regression are widely used methods for SIM. However, these approaches are very sensitive to outliers and provide misleading results in presence of phenotypic con...

Background: Identification of differentially expressed genes (DEGs) under two or more experimental conditions is an important task for elucidating the molecular basis of phenotypic variation. In the recent years, next generation sequencing (RNA-seq) has become very attractive and competitive alternative to the microarrays because of reducing the c...

Distribution as well as adaptation of Cynodon dactylon to different ecological zones of Bangladesh is mainly dependant on weather and adaphic factors of their respective habitats. Generally, it is a warm season perennial grass species that initiates growth in the vernal season and its growth continues rapidly when moisture is adequate and they find...

Lung cancer is one of the most important health risks worldwide for human. Non-small cell lung cancer (NSCLC) is the most common cause of premature death from malignant disease. This study provides in-depth insights from systems biology analyses to identify molecular to inform systemic drug targeting in NSCLC. Gene expression profiles from non smal...

Background and objectives: Identification of cancer biomarkers that are differentially expressed (DE) between two biological conditions is an important task in many microarray studies. There exist several methods in the literature in this regards and most of these methods designed especially for unpaired samples, those are not suitable for paired s...

In many line crossing experiments of genome-wise quantitative trait loci (QTL) mapping studies, multiple phenotypic traits are measured simultaneously. The most common approach to detect the important QTLs controlling these quantitative traits is to analyze the collected data on multiple traits separately for each trait. However, such approach may...

Background: Identification of cancer biomarkers that are differentially expressed (DE) 15 under two biological conditions is an important task in many microarray studies. There exist 16 several methods in the literature in this regards and most of these methods designed especially for 17 unpaired samples, which does not satisfy the requirements of...

Background Productivity of important crop rice is greatly affected by salinity. The plant hormone jasmonate plays a vital role in salt stress adaptation, but also evokes detrimental side effects if not timely shut down again. As novel strategy to avoid such side effects, OsJAZ8, a negative regulator of jasmonate signalling, is expressed under contr...

p>To determine the effect of light and dark on callus induction and plant regeneration from five different explants of three tobacco varieties were studied. Normal white light (3000 lux) and dark conditions were considered for callus induction. Among the explants earliest callusing initiated at 5th day from nodal segment and the highest amount of c...

p>The main purpose of gene expression data analysis is to identify the biomarker genes by comparing the gene expression levels between two different groups or conditions. There are several methods to select biomarker genes and many comparative studies have been performed to select the appropriate method. However, they did not consider the problems...

p>Simple interval mapping (SIM) is one of the most important techniques for the identification of quantitative trait locus (QTL). Most of the approaches of SIM are very sensitive to phenotypic outliers and produce misleading results. There is a robust approach of SIM only for F₂population. However, there is no robust SIM meth...

Background: Metabolomics is a relatively new and dominant branch of bioinformatics. Metabolite expression level controls the phenotypic characteristics of any organism. Recently, breast cancer is the leading type of cancer in women across the world, accounting for 25% of all cases. In 2012, it was seen that due to breast cancer, there were 1.68 mil...

Abstract: One of the main objectives of genomics is the identification of important genes in the genome which are responsible for a particular phenotypic trait like blood pressure, complex disease like cancer, drought tolerance, etc. Quantitative trait locus (QTL) analysis is the most popular and widely used statistical methods for the identificati...

One of the main objectives of genomics is the identification of important genes in the genome which are responsible for a particular phenotypic trait like blood pressure, complex disease like cancer, drought tolerance, etc. Quantitative trait locus (QTL) analysis is the most popular and widely used statistical methods for the identification of impo...

p>An efficient callus induction and plant regeneration system has been developed using three local soybean ( Glycine max L.) varieties. All the varieties showed good callusing (78.30 ‐ 88.80%) from shoot tip (ST) in MS + 3.0 mg/l 2,4‐D + 1.0 mg/l BAP. Best callus induction and embryo formation were recorded in T₅ for BS‐6 as 88.80 and 81...

Abstract: Background: Metabolomics data generation and quantification are different from other types of molecular “omics” data in bioinformatics. Mass spectrometry (MS) based (gas chromatography mass spectrometry (GC-MS), liquid chromatography mass spectrometry (LC-MS), etc.) metabolomics data frequently contain missing values that make some quant...

Patient classification through feature selection (FS) based on gene expression data (GED) has already become popular to the research communities. T-test is the well-known statistical FS method in GED analysis. However, it produces higher false positives and lower accuracies for small sample sizes or in presence of outliers. To get rid from the shor...

Identification of differentially expressed (DE) genes with two or more conditions is an important task for discovery of few biomarker genes. Significance Analysis of Microarrays (SAM) is a popular statistical approach for identification of DE genes for both small- and large-sample cases. However, it is sensitive to outlying gene expressions and pro...

In drug invention and early disease prediction of lung cancer, metabolomic biomarker detection is very important. Mortality rate can be decreased, if cancer is predicted at the earlier stage. Recent diagnostic techniques for lung cancer are not prognosis diagnostic techniques. However, if we know the name of the metabolites, whose intensity levels...

An efficient callus induction and plant regeneration system has been developed using salt and heat as pre-treatment factors for three barley genotypes viz. BB-3, BB-6 and BHL-18. Different concentrations of NaCl (1.5, 2.5, 3.5, 4.5, 5.5 and 6.5 g/L) were used and its effects were determined on the basis of the viability of callus (CV), plant regene...

Dendrobium hybrid orchid is popular in orchid commercial industry due to its short life cycle and ability to produce various types of flower colours. This study was conducted to identify the morphological, biochemical and scanning electron microscopy (SEM) analysis in the Dendrobium sonia-28 orchid plants. In this study, 0.05 and 0.075 % of colchic...

Somatic embryos were induced from leaf and shoot explants of Vanda tessellata (Roxb.) Hook. ex G. Don cultured on MS medium supplemented with BAP, NAA and Kn. BAP (0.5 mg/l) and Kn (1.0 mg/l) showed better performance on somatic embryogenesis with embryos forming mostly near the cut ends of stem and leaf surfaces. Maturation of somatic embryos were...

Figure S1: Plot of smallest β-weight for simulation study 1. (a) In absence of outliers. (b) One outlier with each of 10% genes. Where the smallest β-weight represents the minimum value of 20 β-weights for 20 samples for each gene. The outlier genes are indicated in red color. The gray line indicates the maximum value of cutoff, λ = 0.13 for outlyi...

An experiment was done on encapsulation using in vitro-derived nodal segments in MS medium containing sodium alginate and SA for cold preservation and conversion into plantlet in potato cv. Asterix. Encapsulated (having certain amount of SA) and non-encapsulated nodal segments were stored at low temperature (4 o C) for different storage periods. At...

An organism’s complete set of DNA is called its genome. Genomics is the sub discipline of genetics devoted to the genetic mapping, DNA sequencing and functional analysis of genomes. Genomics is widely used in human health, animal health, agriculture, environmental development and industries. The main objective of genome analysis is the identificati...

An efficient callus induction and regeneration system has been developed for BARI barley-6 during this study. Seed-derived embryos were used as explant sources for callus induction. The highest frequency of callus induction (71.38%) was obtained when 3.5 mg/l 2,4-D was provided to seeds for 4 days prior to culture. The lowest callusing (15.55%) was...

Under this study an efficient protocol on mass propagation of Cymbidium finlaysonianum an epiphytic Malaysian wild orchid has been established using axenic culture. To obtain an axenic seed culture, it is important to perform an adequate a disinfection procedure in tissue culture. Four nutrient media viz. MS, ½MS, KC and VW were evaluated on In vit...

Over the last decade Genome-wide association studies (GWAS) have evolved into a powerful and widely used tool for investigating the genetic architecture of complex traits or diseases. The recent technical advances in high-throughput genotyping technologies make the possibility of performing GWAS very feasible. A number of popular open source R pack...

To determine the effect of light and dark on callus induction and plant regeneration from five different explants of three tobacco varieties were studied. Normal white light (3000 lux) and dark conditions were considered for callus induction. Among the explants earliest callusing initiated at 5 th day from nodal segment and the highest amount of ca...

Vanda tessellata is an endangered and medicinal orchid that is effective to cure various diseases e.g. dyspepsia, bronchitis, inflammations, piles, hiccup etc. The purpose of this study was to determine phytochemical constitutes and antimicrobial activity using extracts from whole plant of Vanda tessellata. The various solvent extracts such as chlo...

A rapid and an efficient protocol for germination of immature seeds of Vanda tessellata, PLBs development and plant regeneration system have been developed. The results indicate that immature capsules performed better in terms of germination (100.0%) and development of PLBs (90.0%). Around 45-60 days old PLBs were transferred to half strength of MS...

Three Bangladeshi barley genotypes viz. BARI barley‐1, 3 and 6 were selected for this study to evaluate the efficiency of callus induction and plant regeneration. The effect of five doses of AgNO3 singly, and combined with amino acids (L‐ proline, L‐glutamine) on callus induction and plant regeneration efficiency was evaluated using BARI barley‐3 a...

An efficient protocol for protocorm like bodies (PLBs) was development and its regeneration through direct somatic embryogenesis was standardized for Rhynchostylis retusa (L.). Somatic embryos were developed from leaf and roots and cultured in MS medium supplemented with different combinations of phytohormones either individually or in combination....

Corn silk (stigma of female flower) is used medicinally against some diseases caused by various pathogenic bacteria. The present study was aimed to identify some medicinal properties of corn silk and investigate its antimicrobial activities in different solvents viz., ethanol, chloroform and methanol extracts (10 mg/ml each) in comparison to strept...

An efficient protocol on callus induction (CI) and its subsequent regeneration (PR) systems has been standardized for four wheat varieties viz. 'Balaka', 'Bijoy', 'Kheri' and 'Prodip' in Bangladesh. Nine plant growth regulators (PGRs) either single or in combination were assessed for callus formation and plant regeneration. The cultivar 'Bijoy' pro...

Rhynchostylis retusa is a monopodial, epiphytic orchid. Owing to its high commercial value in the floricultural industry, mass propagation provides an alternative means of satisfying the demand. Unfortunately, conventional propagation is slow and difficult, suggesting in vitro methods for mass multiplication may be more appropriate. In this case ge...

A laboratory scale bioreactor system has been developed using nutrient spray technology for in vitro mass production of potato microtubers. Its effectiveness on the production of microtubers was investigated and compared with conventional liquid and semi-solid culture systems through bioreactor. Optimal culture conditions such as spray intervals, v...

Under this study an efficient protocol on callus induction (CI) and plant regeneration (PR) was developed using immature (IE) and mature embryos (ME) of four maize varieties viz. Barnali, Mohar, Khoi bhutta and Shuvra. For callus induction three basal media viz. MS, N6 and 6N1 were used where different concentration of 2,4-D (0.5, 1.0, 1.5, 2.0 mg/...

Through anther and microspore culture methods, complete homozygous plants can be produced within a year as compared to the long inbreeding method. Isolated microspore culture is one of the most important techniques for rapid development of haploid plants. The efficiency of this method is influenced by several factors such as cultural conditions, gr...

An efficient protocol has been developed for in vitro seed germination and for growth and development of protocorm likes bodies (PLBs) from three indigenous orchid species namely Acampe premorsa (Roxb.), Agrostophylum khasianum L. and Phalaenopsis cornorerris. We tested three media and among them PM was found to be the best because of the greatest...

Rhynchostylis retusa is a monopodial, epiphytic and medicinal orchid. The phytochemical screening and antimicrobial activities of different extract (methanol, ethanol, chloroform and hexane) of Rhynchostylis retusa was applied on five different bacteria (gram positive: Staphylococcus aureus & Bacillus subtilis; gram negative: Vibrio cholerae, Esche...

Rapid development of embryoids and the efficiency of regeneration by anther culture was observed in two barley genotypes. Five semi-solid media viz. MS, B5, N6, FHG and AMS 3 were used for embryo induction as well as plant regeneration. Harvested spikes were pretreated with cold for 2, 4, 6, 8, 10, 12, 14 or 16 days at 4°C in the dark. Cold pretrea...

An efficient protocol for micropropagation using the axenic pseudobulb derived from in vitro germinated seedlings of Cymbidium finlaysonianum Lindl was developed. The immature seeds were germinated on MS0 basal medium for seedling development. In vitro grown seedlings responded well and stimulated pseudobulb formation with benzylamino purine (BAP)...