Genome reduction is a common phenomenon in intracellular endosymbionts, parasites and pathogens. Because of substantial gene and functional loss, genome reduction precipitates reliance on the host for nutrition and energy supplies

Technologies that measure characteristics of large families of cellular molecules (e.g., genes, proteins, metabolites), have been collectively described by using the suffix ‘-omics’at the end of the name of the characteristic measured. Etymology of the suffix comes from the Latin suffix ‘-ome’, derived from mass or many.

Next Generation Sequencing (NGS) technology is becoming very popular in generating the short reads genomic or transcriptome data. Based on the type of sequencing technology, it offers diverse applications varying from genome assembly, gene expression analysis to epigenetic changes.

Incorporating digital and online tools to increase the options and flexibility in education is a rapidly growing area of pedagogy. Students can collaborate on projects without being in the same vicinity and download archived live lectures for further review, or access recorded lectures in case they missed it.

Botulinum Neurotoxins (BoNTs) bind the neuronal membrane of the host cell via dual interactions with both protein receptors and gangliosides. In order to decipher the molecular determinants for recognition of cell surface protein receptor synaptotagmins II (Syt-II) by the BoNT serotype B (BoNT/B), a high-level quantum chemical analysis was performed, on the basis of the 2.15 Å resolution x-ray crystal structure of the BoNT/B – Syt-II complex. The work resulted in the discovery of two interfaces of molecular recognition; the amphipathic α-helix of the protein receptor Syt-II interacts with BoNT/B by forming a hydrophobic interface on one side of the helix and a hydrophilic interface on the other side. The hydrophobic interface consists of residues Phe47, Leu50, Phe54, Phe55 and Ile58 of Syt-II interacting with residues Trp1178, Tyr1181, Tyr1183, Phe1194 and Phe1204 of BoNT/B. The hydrophilic interface is composed of residues Lys53 and Glu57 of Syt-II interacting with residues Lys1113, Asp1115, Ser1116 and Lys1192 of BoNT/B. Intermolecular interaction energies between BoNT/B and Syt-II were calculated by means of the supermolecular approach at the MP2 level with subsequent solvation energy correction. It was found that the energetic contribution of the hydrophobic interface toward binding of BoNT/B with Syt-II (-9.49 kcal/mol) is much stronger than that of the hydrophilic interface (-2.58 kcal/ mol). Furthermore, pair-wise intermolecular interaction analysis led to the findings that π-π stacking interactions among aromatic residues are the major molecular determinants for recognition of cell surface protein receptor Syt-II by the botulinum neurotoxin BoNT/B. These findings are significant since it was widely believed that the extreme toxicities of BoNTs have a lot to do with the high affinity and specificity of their binding to the neuronal membrane. It is expected that a detailed understanding of the intermolecular interactions responsible for the extreme specificity of molecular recognition between BoNT and its protein receptor as reported here will have far reaching implication for not only the rational design of potent protein toxin inhibitors targeting toxin-protein receptor binding interface but also the development of more suitable therapeutic neurotoxins.

Bioseqeunces such as protein, RNA and DNA, are made up of sequences of amino acids/nucleotides. The binding of biosequences among themselves is important for governing many biological processes of a living organism. The bindings are maintained by short segments of these biosequences, known as functional elements. Due to the importance of these functional elements, their presence is well conserved throughout evolution, allowing them to be discovered as patterns. As sequencing technologies continue to improve, the amount of biosequences is available in abundance. It is thus convenient and cost-effective if functional elements can be discovered from biosequences data computationally in an unsupervised manner without the need of prior knowledge or costly pre-preprocessing. In this paper, we aim to give a brief review of an unsupervised pattern discovery tool known as Aligned Pattern Clustering (or its software WeMineTM). It is developed to facilitate the discovery and analysis of patterns in biosequences, and has been applied in1) unsupervised identification of protein binding sites; 2) revealing functioning subgroup characteristics; and 3) identification of intra-protein, inter-protein and protein- DNA binding sites. In the era of ever-expanding biosequence data, we believe that this unsupervised pattern discovery approach would render a reliable, robust, and scalable method for scientific discovery and applications through leveraging the ever expanding volume of biosequences.

Biofilms keep the intimate relationship between human body and resident microbes. According to National Institutes of Health (NIH), the development of extracellular microbial communities, called biofilms contribute approximately 75% of pathogenic infections to human. The formation of biofilm confers several advantages during pathogen colonization and tolerates extreme conditions like exogenous stress caused by anti-infective agents. The interpretation and exploitation of anti-biofilm properties would help in future challenges, particularly in the control of human infections. The proven scientific evidence with regard to cellular association and exopolysaccharide production by probiotic bacteria could play an important role as anti-biofilm tools. These extracellular components may directly interact with the biofilms as they are actively transported to the bacterial environments via cytoplasmic membrane. The interactive ability of these extracellular metabolites to treat pathogenic biofilms is gaining significant research interest and their possibility to use as anti-biofilm agents. In this review, the extracellular probiotic bacterial markers and molecular approaches to control pathogenic biofilms have been reviewed and future perspectives and research interests are discussed as well.