Rapid, accurate and serotype independent pipeline for in silico epitope mapping of SARS-CoV-2 antigens: a combined machine learning and Chou’s pseudo amino acid composition method

Here,a new integrated machine learning and Chou’s pseudo amino acid composition method has been proposed for in silico epitope mapping of severe acute respiratorysyndrome-like coronavirus antigens.For this,a training dataset including 266 linear B-cell epitopes,1,267 T-cell epitopes and 1,280 non-epitopes were prepared.The epitope sequences were then converted to numerical vectors using Chou’s pseudo amino acid composition method.The vectors were then introduced to the support vector machine,random forest,artificial neural network,and K-nearest neighbor algorithms for the classification process.The algorithm with the highest performance was selected for the epitope mapping procedure.Based on the obtained results,the random forest algorithm was the most accurate classifier with an accuracy of 0.934 followed by K-nearest neighbor,artificial neural network,and support vector machine respectively.Furthermore,the efficacies of predicted epitopes by the trained random forest algorithm were assessed through their antigenicity potential as well as affinity to human B cell receptor and MHC-I/II alleles using the VaxiJen score and molecular docking,respectively.It was also clear that the predicted epitopes especially the B-cell epitopes had high antigenicity potentials and good affinities to the protein targets.According to the results,the suggested method can be considered for developing specific epitope predictor software as well as an accelerator pipeline for designing serotype independent vaccine against the virus.

Physico-Chemical and Microbiological Quality Assessment of Supply Water around Dhaka City, Bangladesh

Dhaka is one of the most densely-populated megacities in the world. Water supply problem is acute in this city, but the quality of drinking water has tremendous importance as potability. This study was aimed at comparing various physicochemical and microbiological parameters which are very much relevant for the drinking water quality of Dhaka city of Bangladesh. A total of 80 samples from 11 collection point of different places were collected over ten months. After that, the samples were examined by a different measuring device for physicochemical parameter testing. Considering physicochemical parameters, all water samples were within the limit for pH. However, 53.75% water had unsatisfactory for chlorine level. Total Dissolve Solid (TDS), hardness, iron, and alkalinity based unsatisfactory were 28.75%, 15.0%, 8.75%, and 3.75% respectively. Five parameters had taken into consideration to measure the microbiological quality. The cultural and biochemical methods showed that 80 water samples have a different range of contamination. The total aerobic count was unsatisfactory for 53.75% samples. Sixty-one samples were found coliform contaminated that is 76.25% of the total samples and 58.75% sample was carried fecal substances. E. coli and Vibrio was unsatisfactory as 61.25% and13.75% respectively. This study revealed that how much safe is supplied water of a municipal water supplier.

Tissue Culture and Rapid Propagation of Platanus occidentalis L.

[ Objective ] The aim was to carry out study on the tissue culture of Platanus occldentalis L. so as to provide suitable method for propagation and preser- vation of fine strains. [ Method ] Four lines of P. occidentalis were used as test materials to explore the proliferation conditions of them on different mediums. [ Re- suit] The difference on the proliferation culture conditions among four clones, four media as well as the interaction of clones and media is extremely significant. The multiple comparisons result showed that the optimal proliferation medium for SX4, SX12, SJ28 and DY18 are ？,4, A2, A2 and A4. SX4 shows the best proliferation result. [ Conclusion] The result in this study has provided suitable method for propagation and preservation of fine strains and the material basis for further studies an P ,~rvirl.,,n^nli~

<i>In Vivo</i>Pharmacokinetic and Hemocompatible Evaluation of Lyophilization Induced Nifedipine Solid-Lipid Nanoparticle

Nifedipine-solid-lipid nanoparticles lyophilized with trehalose (NI-SLN-Tre) were prepared by the high pressure homogenization of a roll mixture consisting of NI and hydrogenated soybean phosphatidylcholine and dipalmitoylphosphatidylglycerol, and in vivo pharmacokinetic properties and their hemocompatibility were determined and compared with those of a NI-SLN suspension. The resulting pharmacokinetic data demonstrated that although no significant differences were observed between the time of peak concentration (Tmax), peak plasma concentration (Cmax), and the area under the curve (AUC0→∞) values of both administrated samples, NI tended to be absorbed to a much greater extent from the lyophilized NI-SLN-Tre suspensions because of the enhanced solvation of NI-SLN in gastrointestinal fluid, derived from formation of hydrogen bonds between the polar head groups of the lipids and the O-H groups of trehalose. Furthermore, the results of a hemolysis assay revealed that the NI-SLN and NI-SLN-Tre suspensions showed good hemocompatibility properties with hemolysis values of less than 5%. Taken together, the results of this study demonstrate that NI-SLN-Tre exhibits suitable pharmacokinetic properties and good biocompatibility.

Microbiome and metabolome dysbiosis analysis in impaired glucose tolerance for the prediction of progression to diabetes mellitus

Gut microbiota and circulating metabolite dysbiosis predate important pathological changes in glucose metabolic disorders;however,comprehensive studies on impaired glucose tolerance(IGT),a diabetes mellitus(DM)precursor,are lacking.Here,we perform metagenomic sequencing and metabolomics on 47 pairs of individuals with IGT and newly diagnosed DM and 46 controls with normal glucose tolerance(NGT);patients with IGT are followed up after 4 years for progression to DM.Analysis of baseline data reveals significant differences in gut microbiota and serum metabolites among the IGT,DM,and NGT groups.In addition,13 types of gut microbiota and 17 types of circulating metabolites showed significant differences at baseline before IGT progressed to DM,including higher levels of Eggerthella unclassified,Coprobacillus unclassified,Clostridium ramosum,L-valine,L-norleucine,and L-isoleucine,and lower levels of Eubacterium eligens,Bacteroides faecis,Lachnospiraceae bacterium 3_1_46FAA,Alistipes senegalensis,Megaspaera elsdenii,Clostridium perfringens,α-linolenic acid,10E,12Z-octadecadienoic acid,and dodecanoic acid.A random forest model based on differential intestinal microbiota and circulating metabolites can predict the progression from IGT to DM(AUC=0.87).These results suggest that microbiome and metabolome dysbiosis occur in individuals with IGT and have important predictive values and potential for intervention in preventing IGT from progressing to DM.

Hand-holding and releasing between the anion and cation to change their macroscopic behavior in water

Despite the similarity of ionic liquid and zwitterion, their some properties such as conductivity and hydrophobicity are different. Here we developed a novel phosphonium salt having a dynamic covalent bond between anion and cation, enabling reversible structural shift between free ion pair and zwitterion. With the phosphonium salt, control of the macroscopic phase behavior in aqueous solution, i.e. forming mono-or biphasic systems, upon exposure to an acid or base was reversibly achieved, based on the structural shift of the phosphonium salt. CO_2/N_2 bubbling reversibly changed the phase behavior as well as acid/base, leading to green separation systems.

Current scenario and challenges of plastic pollution in Bangladesh:a focus on farmlands and terrestrial ecosystems

Plastic is considered one of the most indispensable commodities in our daily life.At the end of life,the huge ever-growing pile of plastic waste(PW)causes serious concerns for our environment,including agricultural farmlands,groundwater quality,marine and land ecosystems,food toxicity and human health hazards.Lack of proper infrastructure,financial backup,and technological advancement turn this hazardous waste plastic management into a serious threat to developing countries,especially for Bangladesh.A comprehensive review of PW generation and its consequences on environment in both global and Bangladesh contexts is presented.The dispersion routes of PW from different sources in different forms(microplastic,macroplastic,nanoplastic)and its adverse effect on agriculture,marine life and terrestrial ecosystems are illustrated in this work.The key challenges to mitigate PW pollution and tackle down the climate change issue is discussed in this work.Moreover,way forward toward the design and implementation of proper PW management strategies are highlighted in this study.

Role of T cells in cancer immunotherapy:Opportunities and challenges

Immunotherapies boosting the immune system's ability to target cancer cells are promising for the treatment of various tumor types,yet clinical responses differ among patients and cancers.Recently,there has been increasing interest in novel cancer immunotherapy practices aimed at triggering T cell-mediated anti-tumor responses.Antigen-directed cytotoxicity mediated by T lymphocytes has become a central focal point in the battle against cancer utilizing the immune system.The molecular and cellular mechanisms involved in the actions of T lymphocytes have directed new therapeutic approaches in cancer immunotherapy,including checkpoint blockade,adoptive and chimeric antigen receptor(CAR)T cell therapy,and cancer vaccinology.This review addresses all the strategies targeting tumor pathogenesis,including metabolic pathways,to evaluate the clinical significance of current and future immunotherapies for patients with cancer,which are further engaged in T cell activation,differentiation,and response against tumors.

Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients

The Omicron variant of the severe acute respiratory syndrome coronavirus 2(SARS‑CoV‑2)infected a substantial proportion of Chinese population,and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment.We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles,plus viral,bacterial,and fungal content,as well as virulence factors and examined their relationships to 28-day mortality were examined.In addition,the bronchoalveolar lavage fluid(BALF)samples from invasive ventilated hospital/community-acquired pneumonia patients(HAP/CAP)sampled in 2019 were included for comparison.Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages,with no difference in 28-day mortality between them.Compared to HAP/CAP cohort,invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract;and in the COVID-19 non-survivors,we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane,higher abundance of opportunistic pathogens including bacterial Alloprevotella,Caulobacter,Escherichia-Shigella,Ralstonia and fungal Aspergillus sydowii and Penicillium rubens.Correlational analysis further revealed significant associations between host immune responses and microbial compositions,besides synergy within viral,bacterial,and fungal pathogens.Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients,providing the basis for future clinical treatment and reduction of fatality.

Constitutive expression of codon optimized Trichoderma reesei TrCel5A in Pichia pastoris using GAP promoter

To address the deficient activity of TrCel5A in naturally secreted cellulase preparation,this study used the GAP promoter to induce constitutive expression of Trichoderma reesei TrCel5A in Pichia pastoris.A recombinant TrCel5A was screened out after gene optimization,synthesis,and expression.The biochemical and enzymatic properties of the new recombinant were characterized.As a result,optimization of shake-flask fermentation of the recombinant was obtained at 28℃,2%inoculum volume,an initial pH of 6.0,as well as glycerol and Tween-80 additions of 30 g/L and 6 g/L,respectively.Under the above-optimized conditions,the recombinant produced 14.8 U/mL of the enzyme activity at 96 h of fermentation.To further enhance enzyme production,pilot-scale cultivation was evaluated using 5-L bioreactors.Using high-cell-density fermentation,the recombinant strain increased enzyme activity to 130.4 U/ml and protein content to 2.49 g/L.In addition,the kinetic factors,including K_(m) and V_(max) values for TrCel5A,were detected to be 5.1 mg/mL and 265.9μmol/(min.mg),respectively.Thus,TrCel5A was effectively expressed in P.pastoris under the GAP promoter,and it demonstrated its potential in commercially relevant enzyme hydrolysis of lignocellulosic biomass.

miR-16-5p enhances sensitivity to RG7388 through targeting PPM1D expression(WIP1)in Childhood Acute Lymphoblastic Leukemia

Aim:Given the encouraging results of the p53-Mdm2 inhibitor RG7388 in clinical trials and the vital function of miR-16-5p in suppressing cell proliferation,the aim of the present study was to investigate the combined impact of RG7388 and miR-16-5p overexpression on the childhood acute lymphoblastic leukemia(chALL).Methods:miRTarBase and miRDB,along with KEGG and STRING databases,were used to predict miR-16-5p target genes and explore protein-protein interaction networks,respectively.B-and T-lymphoblastic cell lines,in addition to patient primary cells,were treated with RG7388.Ectopic overexpression of miR-16-5p in Nalm6 cell line was induced through cell electroporation and transfection of microRNA mimics was confirmed by qRT-PCR.Cell viability was evaluated using the MTT assay.Western blot analyses were performed to evaluate the effects of RG7388 and miR-16-5p upregulation on the protein levels of p53 and its downstream target genes in chALL cells.Paired sample t-test was employed for statistical analyses.Results:MTT assay showed RG7388-induced cytotoxicity in wild-type p53 Nalm6 cell line and p53 functional patient primary cells.However,CCRF-CEM and p53 non-functional leukemic cells indicated drug resistance.Western blot analyses validated the bioinformatics results,confirming the downregulation of WIP1,p53 stabilization,as well as overexpression of p21WAF1 and Mdm2 proteins in Nalm6 cells transfected with miR-16-5p.Moreover,enhanced sensitivity to RG7388 was observed in the transfected cells.Conclusion:This is the first study indicating the mechanistic importance of miR-16-5p overexpression in chALL and its inhibitory role in leukemia treatment when combined with the p53-Mdm2 antagonist,RG7388.These findings might be useful for researchers and clinicians to pave the way for better management of chALL.

A dsRNA-degrading nuclease(dsRNase2)limits RNAi efficiency in the Asian corn borer(Ostrinia furnacalis)

The efficiency of RNA interference(RNAi)varies substantially among different insect species.Rapid degradation of double-stranded RNA(dsRNA)by dsRNA-degrading nucleases(dsRNases)has been implicated to cause low RNAi efficiency in several insect species.In this study,we identified four dsRNase genes(OfdsRNaseL Ofd-sRNase2,OfdsRNase3 and OfdsRNase4)from the Asian corn borer(Ostrinia furnacalis)transcriptome database.Bioinformatic analyses showed that each deduced protein sequence contained endonuclease NS domains and signal peptides.Gene expression analysis revealed that OfdsRNase2 was exclusively expressed in the midgut of larvae.RNAi efficiency was investigated in 2-d-old fifth-instar larvae(high expression of dsRNase2)and 2-d-old pupae(low expression of dsRNase2)by feeding or injecting dsRNA targeting a marker gene that encodes the lethal giant larvae protein(OfLgl).Our results showed that OfLgl only partially silenced the expression of OfLgl in pupae,but not in larvae,suggesting that OfdsRNase2 could contribute to lower RNAi efficiency in larval stages.This hypothesis was supported by our RNAi-of-RNAi experiment using a tissue culture technique where the silencing efficiency against the reporter gene,OfHexl,was significantly improved after knockdown of OfdsRNase2.When double luciferase assays were performed to evaluate the role of the four dsRNases in vitro,only OfdsRNase2 expressed in S2 cells significantly affected RNAi efficiency by degrading dsRNA.Taken together,our results suggested that the degradation of dsRNA by OfdsRNase2 in the midgut contributed to low RNAi efficiency in O.furnacalis larvae.