BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization

Chloroplasts are organelles found in cells of green plants and eukaryotic algae that conduct photosynthesis. Knowing a protein’s subchloroplast location provides in-depth insights about the protein’s function and the microenvironment where it interacts with other molecules. In this paper, we present BS-KNN, a bit-score weighted K-nearest neighbor method for predicting proteins’ subchloroplast locations. The method makes predictions based on the bit-score weighted Euclidean distance calculated from the composition of selected pseudo-amino acids. Our method achieved 76.4% overall accuracy in assigning proteins to 4 subchloroplast locations in cross-validation. When tested on an independent set that was not seen by the method during the training and feature selection, the method achieved a consistent overall accuracy of 76.0%. The method was also applied to predict subchloroplast locations of proteins in the chloroplast proteome and validated against proteins in Arabidopsis thaliana. The software and datasets of the proposed method are available at https://edisk.fandm.edu/jing.hu/bsknn/bsknn.html

Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food

BACKGROUND: Toxin-antitoxin (TA) systems are commonly found in bacteria and Archaea, and it is the most common mechanism involved in bacterial programmed cell death or apoptosis. Recently, MazF, the toxin component of the toxin-antitoxin module, has been categorized as an endoribonuclease, or it may have a function similar to that of a RNA interference enzyme. RESULTS: In this paper, with comparative data and phylogenetic analyses, we are able to identify several potential MazF-conserved motifs in limited subsets of foodborne pathogens and probiotic strains and further provide a molecular basis for the development of engineered/synthetic probiotic strains for the mitigation of foodborne illnesses. Our findings also show that some probiotic strains, as fit as many bacterial foodborne pathogens, can be genetically categorized into three major groups based on phylogenetic analysis of MazF. In each group, potential functional motifs are conserved in phylogenetically distant species, including foodborne pathogens and probiotic strains. CONCLUSION: These data provide important knowledge for the identification and computational prediction of functional motifs related to programmed cell death. Potential implications of these findings include the use of engineered probiotic interventions in food or use of a natural probiotic cocktail with specificity for controlling targeted foodborne pathogens

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens

The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health

MOESM1 of Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis

Additional file 1: Table S1. Numbers and proportions of general COG-associated functional genes for Clostridium perfringens strains Del1 and JP55. Table S2. The comparisons of virulence genes among Clostridium perfringens CP Del1, and 2 reference strains CP4 and ATCC13124

MOESM1 of Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis

Additional file 1: Table S1. Numbers and proportions of general COG-associated functional genes for Clostridium perfringens strains Del1 and JP55. Table S2. The comparisons of virulence genes among Clostridium perfringens CP Del1, and 2 reference strains CP4 and ATCC13124

Liquid Crystal Enabled Dynamic Nanodevices

Inspired by the anisotropic molecular shape and tunable alignment of liquid crystals (LCs), investigations on hybrid nanodevices which combine LCs with plasmonic metasurfaces have received great attention recently. Since LCs possess unique electro-optical properties, developing novel dynamic optical components by incorporating nematic LCs with nanostructures offers a variety of practical applications. Owing to the large birefringence of LCs, the optical properties of metamaterials can be electrically or optically modulated over a wide range. In this review article, we show different elegant designs of metasurface based nanodevices integrated into LCs and explore the tuning factors of transmittance/extinction/scattering spectra. Moreover, we review and classify substantial tunable devices enabled by LC-plasmonic interactions. These dynamically tunable optoelectronic nanodevices and components are of extreme importance, since they can enable a significant range of applications, including ultra-fast switching, modulating, sensing, imaging, and waveguiding. By integrating LCs with two dimensional metasurfaces, one can manipulate electromagnetic waves at the nanoscale with dramatically reduced sizes. Owing to their special electro-optical properties, recent efforts have demonstrated that more accurate manipulation of LC-displays can be engineered by precisely controlling the alignment of LCs inside small channels. In particular, device performance can be significantly improved by optimizing geometries and the surrounding environmental parameters

Strengthening mechanisms of graphene coated copper under nanoindentation

We conduct molecular dynamics simulations to investigate the strengthening mechanisms of monolayer graphene coated copper during nanoindentation. It was found that the fracture of the graphene coating includes three stages: (i) initiation of decagon defects, (ii) growth of decagon defects, and (iii) formation of pearl necklace like structure. After the graphene breaks, the intact graphene coating around the indentation still plays a role in strengthening the copper substrate. The shear modulus mismatch and the lattice mismatch at the interface result in the image and misfit stresses, which act as a barrier to impede dislocations to slip out of the copper surface, thereinto, the image stress is the dominant. In addition, it is interesting to observe pristmatic partial dislocation loop and twinning planes during the indentation