Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus

Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.</jats:p

Transcriptomic Response of White Lupin Roots to Short-Term Sucrose Treatment

White lupin (Lupinus albus) has become a model plant for understanding plant adaptations to phosphorus (P) and iron (Fe) deficiency, two major limiting factors for plant productivity. In response to both nutrient deficiencies, white lupin forms cluster roots, bottle-brush-like root structures that aid in P and Fe acquisition from soil. While the cluster root function is well-studied, not much is known about the signaling pathways involved in sensing and responding to a P and Fe deficiency. Sucrose has been identified as a long-distance signal sent in increased concentrations from shoot to root in response to both a P and Fe deficiency. Thus, sucrose plays a dual role both as a signal and as a major source of energy for the root. To unravel the responses to sucrose as a signal, we performed an Illumina paired-end cDNA sequencing of white lupin roots treated with sucrose for 20, 40 or 80 min, compared to untreated controls (0 min). We identified 634 up-regulated and 956 down-regulated genes in response to sucrose. Twenty minutes of sucrose treatment showed the most responses, with the ethylene-activated signaling pathway as the most enriched Gene Ontology (GO) category. The number of up-regulated genes decreased at 40 min and 80 min, and protein dephosphorylation became the most enriched category. Taken together, our findings indicate active responses to sucrose as a signal at 20 min after a sucrose addition, but fewer responses and a potential resetting of signal transduction pathways by the dephosphorylation of proteins at 40 and 80 min

Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus

Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens