Genome-wide association studies of salinity tolerance in local aman rice

The present study aimed to identify and characterize new sources of salt tolerance among 94 rice varieties from varied geographic origins. The genotypes were divided into five groups based on their morphological characteristics at both vegetative and reproductive stages using salinity scores from the Standard Evaluation System (SES). The experiment was designed as per CRD (Completely Randomized Design) with 2 sets of salinity treatments for 8 dS/meter and 12 dS/meter, respectively compared with one non-salinized control set. Using a Soil Plant Analysis Development (SPAD) meter, assessments of the apparent chlorophyll content (greenness) of the genotypes were done to comprehend the mechanism underlying their salt tolerance.  To evaluate molecular genetic diversity, a panel of 1 K RiCA SNP markers was employed. Utilizing TASSEL 5.0 software, 598 filtered SNPs were used for molecular analysis. Whole-genome association studies (GWAS) were also used to investigate panicle number per plant (pn, tiller number per plant (till), SPAD value (spad), sterility (percent) (str), plant height (ph) and panicle length (pl. It is noteworthy that these characteristics oversee conveying the visible signs of salt damage in rice. Based on genotype data, diversity analysis divided the germplasm groups into four distinct clusters (I, II, III and IV). For the traits studied, thirteen significant marker-trait associations were discovered. According to the phenotypic screening, seven germplasm genotypes namely Koijuri, Asha, Kajal, Kaliboro, Hanumanjata, Akundi and Dular, are highly tolerant to salinity stress. The greenness of these genotypes was found to be more stable over time, indicating that these genotypes are more resistant to stress. Regarding their tolerance levels, the GWAS analysis produced comparable results, supporting that salinity-tolerant genotypes having minor alleles in significant SNP positions showed more greenness during the stress period. The Manhattan plot demonstrated that at the designated significant SNP position, the highly tolerant genotypes shared common alleles. These genotypes could therefore be seen as important genomic resources for accelerating the development and release of rice varieties that are tolerant to salinity.

Exploring the Phenotypic and Genetic Variabilities in Yield and Yield-Related Traits of the Diallel-Crossed F5 Population of Aus Rice

Rice (Oryza sativa) is a major crop and a main food for a major part of the global population. Rice species have derived from divergent agro-climatic regions, and thus, the local germplasm has a large genetic diversity. This study investigated the relationship between phenotypic and genetic variabilities of yield and yield-associated traits in Aus rice to identify short-duration, high-yielding genotypes. Targeting this issue, a field experiment was carried out to evaluate the performance of 51 Aus rice genotypes, including 50 accessions in F5 generation and one short-duration check variety BINAdhan-19. The genotypes exhibited a large and significant variation in yield and its associated traits, as evidenced by a wide range of their coefficient of variance. The investigated traits, including days to maturity (DM), plant height (PH), panicle length (PL) and 1000-grain weight (TW) exhibited a greater genotypic coefficient of variation than the environmental coefficient of variation. In addition, the high broad-sense heritability of DM, PH, PL and TW traits suggests that the genetic factors significantly influence the observed variations in these traits among the F5 Aus rice accessions. This study also revealed that the grain yield per hill (GY) displayed a significant positive correlation with PL, number of filled grains per panicle (FG) and TW at both genotype and phenotype levels. According to the hierarchical and K-means cluster analyses, the accessions BU-R-ACC-02, BU-R-ACC-08 and R2-36-3-1-1 have shorter DM and relatively higher GY than other Aus rice accessions. These three accessions could be employed in the ongoing and future breeding programs for the improvement of short-duration and high-yielding rice cultivars.

Exploration of the physical properties of the newly synthesized kagome superconductor LaIr3Ga2 using different exchange-correlation functionals

LaIr₃Ga₂ is a kagome superconductor with a superconducting temperature (T_c) of 5.16 K. Here, we present the physical properties of the LaIr₃Ga₂ kagome superconductor computed via the DFT method wherein six different exchange-correlation functionals were used. The lattice parameters obtained using different functionals are reasonable, with a slight variation compared to experimental values. The bonding nature was explored. The elastic constants (C_ij), moduli (B, G, Y), and Vickers hardness (H_v) were computed to disclose the mechanical behavior. The H_v values were estimated to be 2.56-3.16 GPa using various exchange-correlation functionals, indicating the softness of the kagome material. The Pugh ratio, Poisson's ratio, and Cauchy pressure revealed the ductile nature. In addition, mechanical stability was ensured based on the estimated elastic constants. The anisotropic mechanical behavior was confirmed via different anisotropic indices. The Debye temperature (Θ_D), melting temperature (T_m), and minimum thermal conductivity (k_min) were calculated to characterize the thermal properties and predict the potential of LaIr₃Ga₂ as a thermal barrier coating material. The electronic density of states was investigated in detail. The McMillan equation was used to estimate T_c, and the electron-phonon coupling constant (λ) was calculated to explore the superconducting nature. The important optical constants were also calculated to explore its possible optoelectronic applications. The values of reflectivity in the IR-visible region are about 62% to 80%, indicating that the compound under study is suitable as a coating to reduce solar heating. The obtained parameters were compared with previously reported parameters, where available.

Chemically stable new MAX phase V2SnC: a damage and radiation tolerant TBC material

Using density functional theory, the phase stability and physical properties, including structural, electronic, mechanical, thermal and vibrational with defect processes, of a newly synthesized 211 MAX phase V₂SnC are investigated for the first time. The obtained results are compared with those found in the literature for other existing M₂SnC (M = Ti, Zr, Hf, Nb, and Lu) phases. The formation of V₂SnC is exothermic and this compound is intrinsically stable in agreement with the experiment. V₂SnC has potential to be etched into 2D MXene. The new phase V₂SnC and existing phase Nb₂SnC are damage tolerant. V₂SnC is elastically more anisotropic than Ti₂SnC and less than the other M₂SnC phases. The electronic band structure and Fermi surface of V₂SnC indicate the possibility of occurrence of its superconductivity. V₂SnC is expected to be a promising TBC material like Lu₂SnC. The radiation tolerance in V₂SnC is better than that in Lu₂SnC.

Using density functional theory, the phase stability and physical properties, including structural, electronic, mechanical, thermal and vibrational with defect processes, of a newly synthesized 211 MAX phase V₂SnC are investigated for the first time.

Investigation of Pathogenic Escherichia Coli from Diarrheic Calves in Selective Area of Bangladesh

Molecular technique was used to investigate the prevalence of virulent diarrheic genes in pathogenic Escherichia coli and their antibiotic sensitivity patterns. A hundred samples from 100 different diarrheic calves from mid-north-western part of Bangladesh were screened for the presence of virulence factors associated with diarrhea. Following isolation and identification on the basis of cultural, morphological and biochemical properties, the presence of the virulence genes such as eaeA, bfpA, elt, est, stx1 and stx2 were examined using PCR. Antimicrobial susceptibility of 57 E. coli was determined by agar disk diffusion method for 8 antimicrobial agents. Out of 100 samples 57 (57%) were found to be positive for E. coli and their distribution rates according to their age, breed and sex were  66.7% ( 6 days old ), 85.7% (Sahiwal breed) and in  64.2 % (female calves) respectively. Among 57 E. coli isolates, only 16 isolates were analyzed for the detection of the said genes. Among them, only eaeA gene was detected in 2 E. coli isolates (12.5 %). Antibiotic resistance patterns revealed that Oxacillin, Rifampicin and Penicillin were  100% resistant followed by Erythromycin which was more than 80% resistant. In case of Amoxicillin and Tetracycline, about 59.65% and 61.40% were found to be resistant respectively whereas all 57 E. coli isolates showed moderately susceptible (30%) to Cefuroxime, a second generation Cephalosporin. Therefore, none of the eight antimicrobials studied can not be recommended as single best therapeutic agent for the treatment of neonatal calf diarrhea. In addition, this study indicated that diarrhea in calves in these locations can be ascribed to mainly Enteropathogenic E. coli (EPEC) which was atypical (only contained the eaeA genes but not bfpA). However, further studies are necessary to characterize the isolated eaeA gene positive E. coli by serotyping, tissue culture assay and other molecular techniques to find out the potentiality of those virulent genes contributing pathogenicity of E. coli causing diarrhea in calves.DOI: http://dx.doi.org/10.3329/bjvm.v13i1.23716Bangl. J. Vet. Med. (2015). 13 (1): 45-51

Comparison between prostate volume and intravesical prostatic protrusion in detecting bladder outlet obstruction due to benign prostatic hyperplasia

The objectives of this study were to determine and compare the correlation of intravesical prostatic protrusion (IPP) and prostate volume (PV) with bladder outlet obstruction (BOO). This study was conducted in the department of urology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh, between July 2009 to September 2010. Fifty benign prostatic hyperplasia (BPH) patients were included in the study. Their evaluation consisted of history along with International Prostate Symptoms Score (IPSS), digital rectal examination (DRE), transabdominal ultrasonography to measure prostate volume, intravesical prostatic protrusion & post voidal residual (PVR) urine and pressure-flow studies to detect bladder outflow obstruction (BOO). Statistical analysis included Unpaired ‘t’ test, Chisquare test and Spearman’s Rank correlation test. Receiver Operator Characteristic (ROC) curves were used to compare the correlation of PV and IPP with BOO. Mean prostate volume was significantly larger in bladder outlet obstructed patients (P<0.05). Mean IPP was significantly greater in obstructed patients (P<0.001). Area under ROC curve was 0.700 for PV and 0.821 for IPP. Prostate volume & intravesical prostatic protrusion measured through transabdominal ultrasonography are noninvasive and accessible method that significantly correlates with bladder outlet obstruction in patients with benign prostatic hyperplasia and the correlation of IPP is much more stronger than that of prostate volume. Introduction Benign prostatic hyperplasia (BPH) is one of the most common diseases in elderly men. The prevalence of histological BPH increases with age and appears in approximately 40% of men aged 50- 60 years and in approximately 90% of men aged more than 80 years1. Benign prostatic hyperplasia may lead to prostatic enlargement, bladder outlet obstruction (BOO) and lower urinary tract symptoms (LUTS). But the symptoms and obstruction do not entirely depend on prostate’s size. In contrast, intravesical prostatic protrusion (IPP) has been found to correlate with BOO2. IPP is a morphological change due to overgrowth of prostatic median and lateral lobes into the bladder and may lead to diskinetic movement of bladder during voiding. This IPP would cause more obstruction than if there were no protrusion and just enlargement of lateral lobes, as the strong bladder contraction could force open a channel between the lobes3. Several studies have previously demonstrated that the ultrasonographic measurement of IPP is able to detect BOO in BPH patients quickly and non-invasively4. This study was designed to diagnose BOO through non-invasive methods and aimed to define the correlationDOI: http://dx.doi.org/10.3329/bmrcb.v38i1.10446  Bangladesh Med Res Counc Bull 2012; 38: 14-17

A high pressure Ca-VI phase between 158 and 180 GPa: stability, electronic structure and superconductivity

We have performed ab initio calculations for a new high pressure phase of Ca-VI between 158 and 180 GPa. The study includes elastic parameters of monocrystalline and polycrystalline aggregates, electronic band structure, lattice dynamics and superconductivity. The calculations show that the orthorhombic Pnma structure is mechanically and dynamically stable in the pressure range studied. The structure is superconducting over the entire pressure range and the calculated T(c) (24.7 K with μ* = 0.1) is maximum at 172 GPa, which is close to the experimentally observed value of 25 K at 161 GPa.