PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method

Although, existing methods have been successful in predicting phage (or bacteriophage) virion proteins (PVPs) using various types of protein features and complex classifiers, such as support vector machine and naïve Bayes, these two methods do not allow interpretability. However, the characterization and analysis of PVPs might be of great significance to understanding the molecular mechanisms of bacteriophage genetics and the development of antibacterial drugs. Hence, we herein proposed a novel method (PVPred-SCM) based on the scoring card method (SCM) in conjunction with dipeptide composition to identify and characterize PVPs. In PVPred-SCM, the propensity scores of 400 dipeptides were calculated using the statistical discrimination approach. Rigorous independent validation test showed that PVPred-SCM utilizing only dipeptide composition yielded an accuracy of 77.56%, indicating that PVPred-SCM performed well relative to the state-of-the-art method utilizing a number of protein features. Furthermore, the propensity scores of dipeptides were used to provide insights into the biochemical and biophysical properties of PVPs. Upon comparison, it was found that PVPred-SCM was superior to the existing methods considering its simplicity, interpretability, and implementation. Finally, in an effort to facilitate high-throughput prediction of PVPs, we provided a user-friendly web-server for identifying the likelihood of whether or not these sequences are PVPs. It is anticipated that PVPred-SCM will become a useful tool or at least a complementary existing method for predicting and analyzing PVPs

SCMRSA: a New Approach for Identifying and Analyzing Anti-MRSA Peptides Using Estimated Propensity Scores of Dipeptides.

Staphylococcus aureus is deemed to be one of the major causes of hospital and community-acquired infections, especially in methicillin-resistant S. aureus (MRSA) strains. Because antimicrobial peptides have captured attention as novel drug candidates due to their rapid and broad-spectrum antimicrobial activity, anti-MRSA peptides have emerged as potential therapeutics for the treatment of bacterial infections. Although experimental approaches can precisely identify anti-MRSA peptides, they are usually cost-ineffective and labor-intensive. Therefore, computational approaches that are able to identify and characterize anti-MRSA peptides by using sequence information are highly desirable. In this study, we present the first computational approach (termed SCMRSA) for identifying and characterizing anti-MRSA peptides by using sequence information without the use of 3D structural information. In SCMRSA, we employed an interpretable scoring card method (SCM) coupled with the estimated propensity scores of 400 dipeptides. Comparative experiments indicated that SCMRSA was more effective and could outperform several machine learning-based classifiers with an accuracy of 0.960 and Matthews correlation coefficient of 0.848 on the independent test data set. In addition, we employed the SCMRSA-derived propensity scores to provide a more in-depth explanation regarding the functional mechanisms of anti-MRSA peptides. Finally, in order to serve community-wide use of the proposed SCMRSA, we established a user-friendly webserver which can be accessed online at http://pmlabstack.pythonanywhere.com/SCMRSA. SCMRSA is anticipated to be an open-source and useful tool for screening and identifying novel anti-MRSA peptides for follow-up experimental studies

Time-lapse of biofilms under flow conditions.

<p><i>B</i>. <i>thailandensis</i> E264 biofilm after treated with 16×MIC of CAZ in MVBM and 0.1×MVBM under flow condition using Bioflux microfluidics platform with flow rate 0.5 dyn/cm² at 37 °C for 16 h. Black arrows indicated the starting time when changing of bacterial morphology was observed after treated with CAZ. The scale bar indicates 50 μm. Experiments were performed three times and representative examples are shown. The movies were shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194946#pone.0194946.s001" target="_blank">S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194946#pone.0194946.s004" target="_blank">S4</a> Figs.</p

Dead and live cells in 2-day old biofilm of <i>B</i>. <i>pseudomallei</i> K96243 and <i>B</i>. <i>thailandensis</i> E264 after treated with 16×MIC of each antibiotic in MVBM and 0.1×MVBM for 16 h.

<p>(A) Live/Dead ratios of <i>B</i>. <i>pseudomallei</i> K96243 and <i>B</i>. <i>thailandensis</i> E264. Data are the mean value of live/dead ratios from 6 random areas. *<i>p</i> < 0.01 compared to control in the same medium, ^#<i>p</i> < 0.01 compared to the same antibiotic in MVBM. The 3D reconstruction of <i>B</i>. <i>pseudomallei</i> K96243 (B) and <i>B</i>. <i>thailandensis</i> E264 (C) biofilm stained with LIVE/DEAD BacLight Bacterial Viability kit; SYTO 9 showing live cells in green and propidium iodide showing dead cells in red (10× objective).</p

Susceptibility of <i>B</i>. <i>pseudomallei</i> K96243 and <i>B</i>. <i>thailandensis</i> E264 in planktonic and biofilm forms to the tested antibiotics determined by Calgary biofilm device.

<p>Susceptibility of <i>B</i>. <i>pseudomallei</i> K96243 and <i>B</i>. <i>thailandensis</i> E264 in planktonic and biofilm forms to the tested antibiotics determined by Calgary biofilm device.</p

Anserine/Carnosine-Rich Extract from Thai Native Chicken Suppresses Melanogenesis via Activation of ERK Signaling Pathway

Skin hyperpigmentation is an aesthetic problem that leads to psychosocial issues. Thus, skin whitening agents from agro- and poultry-industrial co-products are considered high economic value ingredients of interest for sustainable application. Therefore, this study aimed to determine the cosmeceutical potential of anserine/carnosine-rich chicken extract (ACCE) from the Thai native chicken Pradu Hang Dam Mor Kor 55 (PD) meat. The chemical composition was identified and quantified using the HPLC-UV method. Then, the antioxidation potential of the extract was compared to that of L-anserine and L-carnosine, using 1,1-diphenyl-2-picrylhydrazyl assay and shikonin-induced production of reactive oxygen species in CCD-986Sk cell models, and the anti-melanogenesis effect in the MNT-1 melanoma cell line model was investigated. Furthermore, related mechanisms were identified using colorimetric tyrosinase assay and the Western blot technique. The ACCE was composed of L-anserine and L-carnosine as two major constituents. In a dose-dependent manner, ACCE, L-anserine, and L-carnosine manifested significant antioxidation potential and significant reduction of melanin production. Activation of the extracellular signal-regulated kinase (ERK) signaling pathway and inhibition of tyrosinase activity of ACCE were demonstrated as the mechanisms of the anti-melanogenesis effect. In conclusion, ACCE has been revealed as a potential cosmeceutical agent due to its antioxidation and anti-melanogenic activity in association with L-anserine and L-carnosine composition and biomolecular regulating ability. Therefore, further studies and development should be considered to support the utilization of anserine/carnosine-rich chicken extract in the cosmetic industry for economic value creation and sustainability

Planktonic bacterial growth curve.

<p>Growth curve of <i>B</i>. <i>pseudomallei</i> K96243 (A) and <i>B</i>. <i>thailandensis</i> E264 (B) cultured in MVBM, 0.1×MVBM and PBS at 37°C for 72 h. Data are the mean value of two independent experiments carried out in sextuplicate.</p