123VCF: an intuitive and efficient tool for filtering VCF files.

BACKGROUND: The advent of Next-Generation Sequencing (NGS) has catalyzed a paradigm shift in medical genetics, enabling the identification of disease-associated variants. However, the vast quantum of data produced by NGS necessitates a robust and dependable mechanism for filtering irrelevant variants. Annotation-based variant filtering, a pivotal step in this process, demands a profound understanding of the case-specific conditions and the relevant annotation instruments. To tackle this complex task, we sought to design an accessible, efficient and more importantly easy to understand variant filtering tool. RESULTS: Our efforts culminated in the creation of 123VCF, a tool capable of processing both compressed and uncompressed Variant Calling Format (VCF) files. Built on a Java framework, the tool employs a disk-streaming real-time filtering algorithm, allowing it to manage sizable variant files on conventional desktop computers. 123VCF filters input variants in accordance with a predefined filter sequence applied to the input variants. Users are provided the flexibility to define various filtering parameters, such as quality, coverage depth, and variant frequency within the populations. Additionally, 123VCF accommodates user-defined filters tailored to specific case requirements, affording users enhanced control over the filtering process. We evaluated the performance of 123VCF by analyzing different types of variant files and comparing its runtimes to the most similar algorithms like BCFtools filter and GATK VariantFiltration. The results indicated that 123VCF performs relatively well. The tool's intuitive interface and potential for reproducibility make it a valuable asset for both researchers and clinicians. CONCLUSION: The 123VCF filtering tool provides an effective, dependable approach for filtering variants in both research and clinical settings. As an open-source tool available at https://project123vcf.sourceforge.io , it is accessible to the global scientific and clinical community, paving the way for the discovery of disease-causing variants and facilitating the advancement of personalized medicine.

Rational design of B-cell and T-cell multi epitope-based vaccine against Zika virus, an in silico study.

The Zika virus (ZKV) is a single-stranded positive-sense, enveloped RNA virus. Zika infection during pregnancy can cause congenital microcephaly, Guillain-Barré syndrome, miscarriage, and other CNS abnormalities. The world needs safe and effective vaccinations to fight against ZIKV infection since vaccination is generally regarded as one of the most effective ways to prevent infectious diseases. In the present work, we used immunoinformatics and docking studies to construct a vaccine containing multi-epitopes using the structural and non-structural proteins of ZKV. The structural models of ZKV proteins (PrE, PrM, NS1, and NS2A) were constructed using Pyre2 and RaptorX servers. The epitopes of B-cell, T-cell (HTL and CTL), and IFN-γ were predicted, and each epitope's immunogenic nature and physiochemical properties were confirmed. As an adjuvant, the CPG-Oligodeoxynucleotide, an agonist of Toll-like receptor 9 (TLR9), is associated to cytotoxic T-lymphocytes (CTL) epitopes via PAPAP linker. To assess the binding affinity and the tendency of the designed vaccine to induce an immune response through TLR9, molecular docking was done. In the next step, molecular dynamics (MD) simulation to 100 nanoseconds (ns) was used to evaluate the stability of the interaction of the designed vaccine with TLR9. The designed vaccine is predicted to be highly antigenic, non-toxic, soluble, and stable with low flexibility in MD simulation. MD studies indicated that the finalized vaccine-TLR9 docked complex was stable during simulation time. The vaccine construct is able to stimulate both humoral and cellular immune responses. We suppose that our constructed model of the vaccine may have the ability to induce the host immune response against ZKV. Further studies, including in vitro and in vivo experimental analyses, are needed to prove the constructed vaccine's efficacy with multi-epitopes.Communicated by Ramaswamy H. Sarma.

The effectiveness of existential psychotherapy on attitude to life and self-flourishing of educated women homemakers.

INTRODUCTION: Women make up half of the world's population and play a critical role in the health and well-being of the family and society. The purpose of this study is to determine the effectiveness of existential psychotherapy on attitude to life and self-flourishing of educated women homemakers. METHODS: A quasiexperimental study with the pretest-posttest design is used in this work. The research population included 68 homemakers with university education who live in Neyshabur, Iran. Sampling method was available. The women were randomly assigned into two groups: intervention and control groups. The women in the intervention group participated in 10 sessions of existential therapy group. The data collection tool was a questionnaire of Life Regard Index (LRI) and Human Flourishing Questionnaire (HFQ). The data were analyzed by the SPSS software version 21 using Chi-square, independent t-test, and paired t-test while P < 0.05 considered as a significant level. RESULTS: Scores of attitude to life and self-flourishing in educated homemakers before intervention were not significantly different in the two groups. Independent t-test showed that self-flourishing was significantly increased in the intervention group (90.88 ± 15.27) compared to the control group (79.64 ± 15.87) (P = 0.004). The attitude to life was significantly increased in the intervention group (35.79 ± 14.21) compared to the control group (27.50 ± 8.77) (P = 0.005). CONCLUSIONS: The results of this study emphasize that existential group therapy is effective in attitude to life, and self-flourishing of educated homemakers. This therapy can also be used to enhance individual and social abilities the importance and impact of existential psychotherapy on enhancing capabilities such as a positive attitude to life and self-flourishing.

Improvement of Selenomonas ruminantium ß-xylosidase thermal stability by replacing buried free cysteines via site directed mutagenesis.

ß-xylosidase is an essential enzyme for breakdown of xylan to d-xylose. It has a significant potential application value for medicine, food, paper and pulp, and biofuel industries. Due to the negative consequences caused by buried free cysteine residues, mutational substitution of such residues is often accompanied by a notable increase in thermal stability. To characterize the role of cysteine residues in the structure, function and stability of Selenomonas ruminantium ß-d-Xylosidase (SXA), we prepared and evaluated wild-type and four cysteines- deficient SXA proteins. Buried cysteine residues were replaced with. In comparison with the wild-type, the Km values of the mutants remained relatively constant while their kcat values decreased. The C101V and C286V displayed higher thermal stability than the wild-type at 55 and 60 °C. Conformational changes of the secondary and tertiary structure as derived from circular dichroism and fluorescence spectroscopy revealed that changing a buried cysteine to a hydrophobic residue could lead to an increase in thermal stability with minimal perturbation of the wild-type protein structure. In addition to experimental methods, the stability of WT SXA and C101V and C286V mutants at 333 K was also studied by MD simulation. Our theoretical data had a good agreement with the experimental results.

Synergistic effect of programmed cell death protein 1 blockade and secondary lymphoid tissue chemokine in the induction of anti-tumor immunity by a therapeutic cancer vaccine.

The use of DNA vaccines has become an attractive approach for generating antigen-specific cytotoxic CD8+ T lymphocytes (CTLs), which can mediate protective antitumor immunity. The potency of DNA vaccines encoding weakly immunogenic tumor-associated antigens (TAAs) can be improved by using an adjuvant injected together with checkpoint antibodies. In the current study, we evaluated whether the therapeutic effects of a DNA vaccine encoding human papilloma virus type 16 (HPV-16) E7 can be enhanced by combined application of an immune checkpoint blockade directed against the programmed death-1 (PD-1) pathway and secondary lymphoid tissue chemokine (SLC) also known as CCL21 adjuvant, in a mouse cervical cancer model. The therapeutic effects of the DNA vaccine in combination with CCL21 adjuvant plus PD-1 blockade was evaluated using a tumor growth curve. To further investigate the mechanism underlying the antitumor response, cytolytic and lymphocyte proliferation responses in splenocytes were measured using non-radioactive cytotoxicity and MTT assays, respectively. Vascular endothelial growth factor (VEGF) and IL-10 expression in the tumor and the levels of IFN-γ and IL-4 in supernatants of spleno-lymphocyte cultures were measured using ELISA. The immune efficacy was evaluated by in vivo tumor regression assay. The results showed that vaccination with a DNA vaccine in combination with the CCL21 adjuvant plus PD-1 blockade greatly enhanced cytotoxic T lymphocyte production and lymphocyte proliferation rates and greatly inhibited tumor progression. Moreover, the vaccine in combination with adjuvant and blockade significantly reduced intratumoral VEGF, IL-10 and splenic IL-4 but induced the expression of splenic IFN-γ. This formulation could be an effective candidate for a vaccine against cervical cancers and merits further investigation.