smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species

The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK. Communicated by Ramaswamy H. Sarma</p

Nanofabrication of Plasmonic Circuits Containing Single Photon Sources

Nanofabrication of photonic components based on dielectric loaded surface plasmon polariton waveguides (DLSPPWs) excited by single nitrogen vacancy (NV) centers in nanodiamonds is demonstrated. DLSPPW circuits are built around NV containing nanodiamonds, which are certified to be single-photon emitters, using electron-beam lithography of hydrogen silsesquioxane (HSQ) resist on silver-coated silicon substrates. A propagation length of 20 ± 5 μm for the NV single-photon emission is measured with DLSPPWs. A 5-fold enhancement in the total decay rate, and 58% coupling efficiency to the DLSPPW mode is achieved, indicating significant mode confinement. Finally, we demonstrate routing of single plasmons with DLSPPW-based directional couplers, revealing the potential of our approach for on-chip realization of quantum-optical networks

Efficient Coupling of a Single Diamond Color Center to Propagating Plasmonic Gap Modes

We report on coupling of a single nitrogen-vacancy (NV) center in a nanodiamond to the propagating gap mode of two parallel placed chemically grown silver nanowires. The coupled NV-center nanowire system is made by manipulating nanodiamonds and nanowires with the tip of an atomic force microscope cantilever. An efficient coupling of an NV-center to an easily accessible gap plasmon mode is demonstrated and we measure an enhancement of the spontaneous emission decay rate by a factor of 8.3

Chemotaxis gene clusters in <i>Burkholderia</i> strains SJ98, YI23, CCGE 1001, CCGE 1002 and CCGE 1003.

<p>Chemotaxis gene clusters in <i>Burkholderia</i> strains SJ98, YI23, CCGE 1001, CCGE 1002 and CCGE 1003.</p

Genome alignment of <i>Burkholderia</i> sp.

<p>SJ98 and <i>Burkholderia</i> sp. YI23.<b> </b></p

Genome Annotation of <i>Burkholderia</i> sp. SJ98 with Special Focus on Chemotaxis Genes

<div><p><i>Burkholderia</i> sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of <i>Burkholderia</i> sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that <i>Burkholderia</i> sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related <i>Burkholderia</i> strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium <i>E. coli</i> K12. It was found that strain SJ98 has 37 <i>che</i> genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (<a href="http://crdd.osdd.net/raghava/genomesrs/burkholderia/" target="_blank">http://crdd.osdd.net/raghava/genomesrs/burkholderia/</a>).</p></div

Characterization of <i>Burkholderia</i> sp. SJ98, <i>Burkholderia</i> sp. YI23, <i>Burkholderia</i> sp. CCGE 1001, <i>Burkholderia</i> sp. CCGE 1002 and <i>Burkholderia</i> sp. CCGE 1003.

<p>Characterization of <i>Burkholderia</i> sp. SJ98, <i>Burkholderia</i> sp. YI23, <i>Burkholderia</i> sp. CCGE 1001, <i>Burkholderia</i> sp. CCGE 1002 and <i>Burkholderia</i> sp. CCGE 1003.</p

Number of <i>che</i> gene homologs in <i>E.coli</i>, <i>B</i>. sp. SJ98, <i>B</i>. sp.YI23, <i>B</i>. sp. CCGE 1001, <i>B</i>. sp. CCGE 1002 and <i>B</i>. sp. CCGE 1003.

<p>Number of <i>che</i> gene homologs in <i>E.coli</i>, <i>B</i>. sp. SJ98, <i>B</i>. sp.YI23, <i>B</i>. sp. CCGE 1001, <i>B</i>. sp. CCGE 1002 and <i>B</i>. sp. CCGE 1003.</p

Additional file 1: Table S1. of CSmetaPred: a consensus method for prediction of catalytic residues

Datasets used in present work. List of pdb entries along with known catalytic residues from six datasets. (PDF 576 kb

Genome assembly results of <i>Burkholderia</i> sp. SJ98.

*<p>Scaffolds produced by assembly of Roche’s 454 FLX data.</p>**<p>Sequences (16 contigs and 1 scaffold) produced after gap filling of Assembly-1 by Illumina GA IIX data.</p>***<p>Contigs produced after the finishing of Assembly-3 (Sanger’s sequencing and manually by BLAST), final assembly.</p