Adjusting for heterogeneity of experimental data in genetic evaluation of dry matter intake in dairy cattle

The objectives of the present study were (i) to find the best fitted model for repeatedly measured daily dry matter intake (DMI) data obtained from different herds and experiments across lactations and (ii) to get better estimates of the genetic parameters and better genetic evaluations. After editing, there were 572,512 daily DMI records of 3,495 animals (Holstein cows) from 11 different herds across 13 lactations and the animals were under 110 different nutritional experiments. The fitted model for this data set was a univariate repeated‐measure animal model (called model 1) in which additive genetic and permanent environmental (within and across lactations) effects were fitted as random. Model 1 was fitted as two distinct models (called models 2 and 3) based on alternative fixed effect corrections. For unscaled data, each model (models 2 and 3) was fitted as a homoscedastic (HOM) model first and then as a heteroscedastic (HET) model. Then, data were scaled by multiplying with particular herd‐scaling factors, which were calculated by accounting for heterogeneity of phenotypic within‐herd variances. Models were selected based on cross‐validation and prediction accuracy results. Scaling factors were re‐estimated to determine the effectiveness of accounting for herd heterogeneity. Variance components and respective heritability and repeatability were estimated based on a pedigree‐based relationship matrix. Results indicated that the model fitted for scaled data showed better fit than the models (HOM or HET) fitted for unscaled data. The heritability estimates of the models 2 and 3 fitted for scaled data were 0.30 and 0.08, respectively. The repeatability estimates of the model fitted for scaled data ranged from 0.51 to 0.63. The re‐estimated scaling factor after accounting for heterogeneity of residual variances was close to 1.0, indicating the stabilization of residual variances and herd accounted for most of the heterogeneity. The rank correlation of EBVs between scaled and unscaled data ranged from 0.96 to 0.97.     

Effects of phosphorus and potassium addition on growth and nodula- tion of Dalbergia sissoo in the nursery

A study was conducted to test the influence of different inorganic fertilizers （phosphorous and potassium） on the nodulation and growth of Dalbergia sissoo grown in the nursery. Before seeds sowing, different combinations of P, K fertilizers were incorporated with the nutrient-deficient natural forest soils, and then amended with cowdung （soil： cowdung = 3：1）. Nodulation status （nodule number, shape, fresh weight, dry weight and color） in the roots and the plant growth parameters （length of shoot and root, collar diameter, fresh and dry weight of shoot and root） were recorded 60 days after seeds sowing. Nodulation status and growth of the plants varied significantly （P〈0.05） in the soils amended with fertilizers in comparison to the control. The highest nodule number （62）, fresh （0.50 g） and dry （0.07 g） weights were recorded with the dose of PK at the rate of 160 kg/hm2. Nodule shape and color also varied widely in different treatments. In case of plant growth parameters, shoot and root length, collar diameter, fresh and dry weight of the plants took on a significant difference （P〈0.05） among various combination of fertilizers. From the study, it is revealed that PK at the rate of 160 kg/hm^2 fertilizer with soil and cowdung mixture （soil： eowdung = 3：1） is recommended for optimum growth and nodule formation of D. sissoo in degraded soils at a nursery level.     

ANTIVIRAL EFFECTS OF BACTERIOCIN AGAINST ANIMAL-TO-HUMAN TRANSMITTABLE MUTATED SARS-COV-2: A SYSTEMATIC REVIEW

• Identification of bacteriocin sources• Classification of bacteriocins• Antiviral pathways of bacteriocinsThe COVID-19 infections caused by SARS-CoV-2 have resulted in millions of people being infected and thousands of deaths globally since November 2019. To date, no unique therapeutic agent has been developed to slow the progression of this pandemic. Despite possessing antiviral traits the potential of bacteriocins to combat SARS-CoV-2 infection has not been fully investigated. This review summarizes the mechanisms by which bacteriocins can be manipulated and implemented as effective virus entry blockers with infection suppression potential properties to highly transmissible viruses through comprehensive immune modulations that are potentially effective against COVID-19. These antimicrobial peptides have been suggested as effective antiviral therapeutics and therapeutic supplements to prevent rapid virus transmission. This review also provides a new insight into the cellular and molecular alterations which have made SARS-CoV-2 self-modified with diversified infection patterns. In addition, the possible applications of antimicrobial peptides through both natural and induced mechanisms in infection prevention perspectives on changeable virulence cases are comprehensively analyzed. Specific attention is given to the antiviral mechanisms of the molecules along with their integrative use with synthetic biology and nanosensor technology for rapid detection. Novel bacteriocin based therapeutics with cutting-edge technologies might be potential substitutes for existing time-consuming and expensive approaches to fight this newly emerged global threat.     

Agro-Morphological,Physico-Chemical and Molecular Characterization of Rice Germplasm with Similar Names of Bangladesh

Thirty-one duplicate and similar named rice germplasms of Bangladesh were studied to assess the genetic variation for the agro-morphological and physico-chemical traits and simple sequence repeat banding patterns during 2009–2012 at Bangladesh Rice Research Institute. The range of variations within the cultivar groups showed higher degree. The principal component analysis showed that the first five components with vector values 1 contributed 82.90% of the total variations. The cluster analysis grouped the genotypes into four clusters, where no duplicate germplasm was found. The highest number(11) of genotypes was constellated in cluster I and the lowest(3) in cluster II. The intra- and inter-cluster distances were the maximum in cluster I(0.93) and between clusters I and IV(24.61), respectively, and the minimum in cluster IV(0.62) and between clusters I and III(5.07), respectively. The cluster mean revealed that the crosses between the genotypes of cluster I with those of clusters II and IV would exhibit high heterosis for maximum good characters. A total of 350 alleles varied from 3(RM277) to 14(RM21) with an average of 7.8 per locus were detected at 45 microsatellite loci across the 31 rice accessions. The gene diversity ranged from 0.48 to 0.90 with an average of 0.77, and the polymorphism information content values from 0.44(RM133) to 0.89(RM206) with an average of 0.74. RM206, RM21, RM55, RM258 and RM433 were considered as the best markers on the basis of their higher polymorphism information content values. The dendrogram from unweighted pair-group method with arithmetic average clustering also classified the genotypes into four groups, where group IV comprised of 20 genotypes and group III of one genotype, but no duplicate was found. Finally, similar and duplicate named rice germplasms need to be conserved in gene bank as are distinct from each other.     

Expression of Toll-like receptors and downstream genes in lipopolysaccharide-induced porcine alveolar macrophages

The aim of the present study was to determine the age-related kinetic changes of Toll-like receptors (TLRs) and downstream genes expression, and secretion of cytokine in lipopolysaccharide (LPS) stimulated porcine alveolar macrophages (AM). For this purpose, AMs were isolated from 5-day-old newborn piglets and 120-day-old young pigs. mRNA expression and cytokine measurement was determined by quantitative real-time PCR and ELISA, respectively. First, AMs were incubated for 24 h in the absence or presence of increasing concentrations of LPS. Results showed the up-regulation of TLRs 2, 4, 5 and 9 mRNA from all concentrations of LPS used, as compared to non-stimulated cells, and TLR4 was the highest expression in both ages (P<0.05). Furthermore, quantitative analysis demonstrated increased expression of mRNAs encoding TLRs 2, 4, 5 and 9, LBP, CD14, MD2, MyD88, IRAK4 and TRAF6 in both ages in a time-dependant manner (P<0.05). Overall, LPS inducible mRNA for TLR4, LBP, CD14 and MyD88 had higher expression in newborn piglets compared with those of young pigs (P<0.05). The level of cytokine protein IL6 and TNFα in supernatant fluid significantly varied with time of incubation and age of animals. Their concentration increased immediately at 1 h after LPS stimulation and remained significantly higher up to 48 h in both ages. Production of pro-inflammatory cytokine protein IL6 and TNFα in supernatant was significantly higher in young pigs than those of piglets. This study suggests that differential age-related changes in the expression of TLRs and downstream genes, and pro-inflammatory cytokine could contribute to a different age-related innate immune response during pulmonary infection. Further investigation is warranted to determine the precise effects of LPS on porcine AMs by means of a functional study across a wider age range.     

Anti-Alzheimer’s Molecules Derived from Marine Life: Understanding Molecular Mechanisms and Therapeutic Potential

Alzheimer’s disease (AD) is a devastating neurodegenerative disease and the most common cause of dementia. It has been confirmed that the pathological processes that intervene in AD development are linked with oxidative damage to neurons, neuroinflammation, tau phosphorylation, amyloid beta (Aβ) aggregation, glutamate excitotoxicity, and cholinergic deficit. Still, there is no available therapy that can cure AD. Available therapies only manage some of the AD symptoms at the early stages of AD. Various studies have revealed that bioactive compounds derived from marine organisms and plants can exert neuroprotective activities with fewer adverse events, as compared with synthetic drugs. Furthermore, marine organisms have been identified as a source of novel compounds with therapeutic potential. Thus, there is a growing interest regarding bioactive compounds derived from marine sources that have anti-AD potentials. Various marine drugs including bryostatin-1, homotaurine, anabaseine and its derivative, rifampicins, anhydroexfoliamycin, undecylprodigioisin, gracilins, 13-desmethyl spirolide-C, and dictyostatin displayed excellent bioavailability and efficacy against AD. Most of these marine drugs were found to be well-tolerated in AD patients, along with no significant drug-associated adverse events. In this review, we focus on the drugs derived from marine life that can be useful in AD treatment and also summarize the therapeutic agents that are currently used to treat AD.     

Expression dynamics of Toll-like receptors mRNA and cytokines in porcine peripheral blood mononuclear cells stimulated by bacterial lipopolysaccharide

The Toll-like receptor (TLR)4 is critical for the recognition of Gram-negative bacterial lipopolysaccharide (LPS) but in porcine peripheral blood mononuclear cells (PBMCs) it may cooperate with other TLRs and lead to the production of inflammatory cytokines. Therefore, we analyzed TLR1-10 mRNA expression in porcine PBMCs stimulated with LPS over time (1-48 h) by using quantitative real-time PCR and cytokine proteins level by ELISA in culture supernatant. TLR1-10 mRNA was detectable in porcine PBMCs. When compared with the control (non-stimulated), TLR1 mRNA were increased (p<0.05) at 3 h after challenge with 1 μg/ml LPS, whereas TLR1 and TLR2 mRNA were increased (p<0.01) at 6 h after challenge with 10 μg/ml LPS. TLR4 increased (p<0.001) at 3h after challenge with LPS and remained constant. TLR5 and TLR6 mRNA increased (p<0.05) at 9 h and 1 h after of LPS stimulation, respectively. The mRNA of CD14 and MD2 were increased (p<0.001) at 1h after LPS stimulation. Additionally, at most of the time analyzed, the mRNA expression increased with the dose of LPS. The LPS concentration had influence (p<0.05) on all the TLRs expression except TLR10; whereas time had effect (p<0.05) on all TLRs expression except TLR2, 3, 6 and 10. When compared to the control, the cytokines IL1b, IL8 and TNFα proteins were increased (p<0.001) immediately at 1 h after LPS stimulation and remained constant till 48 h. IL12b was increased (p<0.001) 12 h after challenge with 10 μg/ml of LPS. Although IL8 level was the highest, the higher (p<0.05) expression of all these inflammatory cytokines indicate that upon interacting with TLRs, LPS exerted inflammatory response in PBMCs through the production of Th1 type cytokines. The production of cytokines was influenced (p<0.001) by both the dose of LPS and the stimulation time. Hence, the porcine PBMCs are likely able to express all members of TLRs.     

SSR-based population structure,molecular diversity and identity cards of Ziziphus species from Pakistan and China

Genetic Resources and Crop Evolution - Research work on the genetic diversity within Pakistani and Chinese Ziziphus species is limited, and to date, no single report on the application of DNA...     

Genotypic variability in plant water status of French bean under drought stress

Seven genotypes of French bean (Phaseolus vulgaris L.) were evaluated under semi-controlled conditions at the Bangabandhu Sheikh Mujibur Rahman Agricultural University, Bangladesh to analyze genotypic variability in leaf water status under water stress. The plants were grown under two moisture regimes, viz. 80% field capacity (FC) and 50% FC throughout the growing season. The genotypes showed significant variation in water relation traits. Genotypes BB24 and BB43 maintained higher relative water content (RWC), but lower turgid weight/dry weight ratio (TW/DW) and water uptake capacity (WUC). When drought susceptibility index (DSI) among the genotypes was considered, BB24 was found the most tolerant to drought and BB04 was the most susceptible one. A close positive relationship between leaf TW/DW and DSI under drought was recorded (R ² = 0.627). Leaf TW/DW was decreased considerably due to water stress by 10% in genotype BB24 followed by BB43 (13%), and both BARI bushbean-2 and BB04 (19%). Stomatal aperture and whole plant transpiration rate were found minimal in the BB24 and BB43 compared to that of BB04 and BARI bushbean-2. Considering these water relation traits, genotypes BB24 and BB43 may be considered as relatively tolerant to tissue dehydration. The study also revealed that the TW/DW, WUC, stomatal aperture, and whole plant transpiration rate was negatively and significantly associated with yield; however, the RWC was positively correlated with yield under water stress conditions.     

The use of fermented soybean meal and squid by-product blend as a substitute for fish meal in practical diets for climbing perch,Anabas testudienus (Bloch, 1792), pond culture: Growth performance and economics analysis

A feeding trial was conducted to evaluate the effects of different ratios of fish meal (FM) to a fermented blend (FB: fermented soybean meal and squid by-product blend) on growth and economic performance of climbing perch, Anabas testudineus (Bloch, 1792), in earthen ponds. Five diets were prepared where FB was substituted for 0 (D1), 25 (D2), 50 (D3), 75 (D4), or 100% FM protein (D5), while a commercial diet (D6) was used for comparison. Triplicate groups of fish (1.03 ± 0.07 g) were fed twice daily up to satiation for 70 days in earthen ponds. No significant (P > 0.05) differences were found in growth performance of fish fed D1, D2, D3, and D6 diets, while fish growth decreased significantly (P < 0.05) in D4 and D5 groups. Feed intake decreased (P < 0.05) with the increasing levels of FB with no significant difference in the feed conversion ratio, which ranged from 1.98 to 2.08. The fish survival decreased significantly in D5 alone. While considering the overall production, the total yield and economic return were found to be highest in D2 (64176.7 TK ha^?1) and lowest in D5 (14418.3 Tk. ha^?1). Based on the present experimental condition, it is concluded that FB can economically be included in aquafeed as a substitute for up to 50% of FM protein from the diets of climbing perch.