Prediction of Antimicrobial Peptides Based on Sequence Alignment and Feature Selection Methods

Antimicrobial peptides (AMPs) represent a class of natural peptides that form a part of the innate immune system, and this kind of ‘nature's antibiotics’ is quite promising for solving the problem of increasing antibiotic resistance. In view of this, it is highly desired to develop an effective computational method for accurately predicting novel AMPs because it can provide us with more candidates and useful insights for drug design. In this study, a new method for predicting AMPs was implemented by integrating the sequence alignment method and the feature selection method. It was observed that, the overall jackknife success rate by the new predictor on a newly constructed benchmark dataset was over 80.23%, and the Mathews correlation coefficient is 0.73, indicating a good prediction. Moreover, it is indicated by an in-depth feature analysis that the results are quite consistent with the previously known knowledge that some amino acids are preferential in AMPs and that these amino acids do play an important role for the antimicrobial activity. For the convenience of most experimental scientists who want to use the prediction method without the interest to follow the mathematical details, a user-friendly web-server is provided at http://amp.biosino.org/

The Critical Role of 12-Methyl Group of Anthracycline Dutomycin to Its Antiproliferative Activity

Anthracycline dutomycin is a tetracyclic quinone glycoside produced by Streptomyces minoensis NRRL B-5482. SW91 is a C-12 demethylated dutomycin derivative, which was identified in our previous research. In vitro cytotoxicity and apoptosis assays of these two compounds were conducted to demonstrate their antiproliferation activities. The results showed that both dutomycin and SW91 block cells at the S phase, whereas dutomycin shows more significant inhibition of cell growth. Their interactions with calf thymus DNA (CT-DNA) were investigated, with dutomycin exhibiting higher binding affinity. The molecular docking demonstrated that the 12-methyl group makes dutomycin attach to the groove of DNA. These findings suggest that dutomycin has binding higher affinity to DNA and impairs DNA replication resulting in more significant antitumor activity

DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Abstract Background The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynamics in some specialized cellular environments. However, the large-scale generation of single-cell RNA-seq (scRNA-seq) data collected at multiple time points remains a challenge to effective measurement gene expression patterns in transcriptome analysis. Results We present an algorithm based on the Dynamic Time Warping score (DTWscore) combined with time-series data, that enables the detection of gene expression changes across scRNA-seq samples and recovery of potential cell types from complex mixtures of multiple cell types. Conclusions The DTWscore successfully classify cells of different types with the most highly variable genes from time-series scRNA-seq data. The study was confined to methods that are implemented and available within the R framework. Sample datasets and R packages are available at https://github.com/xiaoxiaoxier/DTWscore

Mechanisms Controlling MicroRNA Expression in Tumor

MicroRNAs (miRNAs) are widely present in many organisms and regulate the expression of genes in various biological processes such as cell differentiation, metabolism, and development. Numerous studies have shown that miRNAs are abnormally expressed in tumor tissues and are closely associated with tumorigenesis. MiRNA-based cancer gene therapy has consistently shown promising anti-tumor effects and is recognized as a new field in cancer treatment. So far, some clinical trials involving the treatment of malignancies have been carried out; however, studies of miRNA-based cancer gene therapy are still proceeding slowly. Therefore, furthering our understanding of the regulatory mechanisms of miRNA can bring substantial benefits to the development of miRNA-based gene therapy or other combination therapies and the clinical outcome of patients with cancer. Recent studies have revealed that the aberrant expression of miRNA in tumors is associated with promoter sequence mutation, epigenetic alteration, aberrant RNA modification, etc., showing the complexity of aberrant expression mechanisms of miRNA in tumors. In this paper, we systematically summarized the regulation mechanisms of miRNA expression in tumors, with the aim of providing assistance in the subsequent elucidation of the role of miRNA in tumorigenesis and the development of new strategies for tumor prevention and treatment

Financial indicators of security of the banking system as indicators of competitiveness

На сучасному етапі розвитку економіки особливо гостро постає проблема досягнення конкурентоспроможного стану банківської сис- теми України, що неможливо без забезпечення її фінансової безпеки

Ubiquitylation Functions in the Calcium Carbonate Biomineralization in the Extracellular Matrix

<div><p>Mollusks shell formation is mediated by matrix proteins and many of these proteins have been identified and characterized. However, the mechanisms of protein control remain unknown. Here, we report the ubiquitylation of matrix proteins in the prismatic layer of the pearl oyster, <em>Pinctada fucata</em>. The presence of ubiquitylated proteins in the prismatic layer of the shell was detected with a combination of western blot and immunogold assays. The coupled ubiquitins were separated and identified by Edman degradation and liquid chromatography/mass spectrometry (LC/MS). Antibody injection <em>in vivo</em> resulted in large amounts of calcium carbonate randomly accumulating on the surface of the nacreous layer. These ubiquitylated proteins could bind to specific faces of calcite and aragonite, which are the two main mineral components of the shell. In the <em>in vitro</em> calcium carbonate crystallization assay, they could reduce the rate of calcium carbonate precipitation and induce the calcite formation. Furthermore, when the attached ubiquitins were removed, the functions of the EDTA-soluble matrix of the prismatic layer were changed. Their potency to inhibit precipitation of calcium carbonate was decreased and their influence on the morphology of calcium carbonate crystals was changed. Taken together, ubiquitylation is involved in shell formation. Although the ubiquitylation is supposed to be involved in every aspect of biophysical processes, our work connected the biomineralization-related proteins and the ubiquitylation mechanism in the extracellular matrix for the first time. This would promote our understanding of the shell biomineralization and the ubiquitylation processes.</p> </div

Ubiquitylation of <i>P. fucata</i> matrix proteins.

<p>(A) The ubiquitylated proteins were characterized by western blotting of EDTA extracts of nacre and prisms separated from the shell. The ubiquitylated proteins were mainly present in the EDTA-soluble matrix of calcitic prisms. P-ESM, EDTA-soluble matrix of the prismatic layer; P-EISM, the EDTA-insoluble matrix of the prismatic layer; N-ESM, EDTA-soluble matrix of the nacreous layer; N-EISM, the denatured fraction of the EDTA-insoluble matrix of the nacreous layer. (B) Time-course reaction of isopeptidase with the EDTA-soluble matrix fraction of the prismatic layer. Reaction products were analyzed by western blotting. The reaction was performed at 37°C with a volume of 15 µL containing 0.1 µM of isopeptidase, 2 µg of substrate, for the indicated times. Mono Ubi, mono-ubiquitin. (C) Amino acid sequence of ubiquitin showing the residues identified by Edman degradation (underlined) and the peptide sequences identified by LC-MS analysis (red highlights).</p

Chitin-binding assay.

<p>Lane 1, water-washings; lane 2, 0.2 M NaCl-washings; lane 3, 1 M acetic acid-washings; lane 4, extract with detergent-SDS/β-mercaptoethanol for 10 min at 100°C. GST was used as a negative control.</p

The physiological functions of the ubiquitylated proteins were inhibited by antibody injection.

<p>(A) SEM image of the inner surface of the low dosage antibody-injected group. The stair-like growth pattern was disturbed. (B) Enlargement of the box shown in (A), illustrating the crystals deposited on the inner nacreous layer surface. (C) SEM image of the inner surface of the high dosage antibody-injected group. More crystals were randomly accumulated. (D) Enlargement of the box shown in (C), illustrating that the crystals were linked together to form a new layer. (E) SEM image of the inner surface of preimmune rabbit serum injected <i>P. fucata</i> shell showing the stair-like growth pattern. (F) Enlargement of the box shown in (E), illustrating the flat tablets. (G) Energy-dispersive x-ray spectroscopy analysis of the deposition (black asterisk) shown in (D). Scale bars, 200 µm in (A) and (C); 50 µm in (E); 25 µm in (B) and (D); 10 µm in (F).</p