Smell of Infection:a novel, non-invasive method for detection of fish excretory- secretory proteins

Chemical signals are produced by aquatic organisms following predatory attacks or perturbations such as parasitic infection. Ectoparasites feeding on fish hosts are likely to cause release of similar alarm cues into the environment due to the stress, wounding, and immune response stimulated upon infection. Alarm cues are often released in the form of proteins, antimicrobial peptides, and immunoglobulins that provide important insights into bodily function and infection status. Here we outline a noninvasive method to identify potential chemical cues associated with infection in fish by extracting, purifying, and characterizing proteins from water samples from cultured fish. Gel free proteomic methods were deemed the most suitable for protein detection in saline water samples. It was confirmed that teleost proteins can be characterized from water and that variation in protein profiles could be detected between infected and uninfected individuals and fish and parasite only water samples. Our novel assay provides a noninvasive method for assessing the health condition of both wild and farmed aquatic organisms. Similar to environmental DNA monitoring methods, these proteomic techniques could provide an important tool in applied ecology and aquatic biology

stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences.

The enzyme Dicer is a component of many small RNA (sRNA) pathways involved in RNA processing for post-transcriptional regulation, anti-viral response and control of transposable elements. Cleavage of double-stranded RNA by Dicer produces a signature overhanging sequence at the 3' end of the sRNA sequence relative to a complementary passenger strand in a RNA duplex. There is a need for reliable tools to computationally search for Dicer cleavage signatures to help characterise families of sRNAs. This is increasingly important due to the rising popularity of sRNA sequencing, especially in non-model organisms. Here, we present stepRNA, a fast, local tool that identifies (i) overhang signatures strongly indicative of Dicer cleavage in RNA sequences, and (ii) the length of the passenger strand in sRNAs duplexes. We demonstrate the use of stepRNA with simulated and biological datasets to detect Dicer cleavage signatures in experimentally validated examples. Compared to currently available tools, stepRNA is more accurate, requires only sRNA sequence data rather than a reference genome, and provides information about other important features such as passenger strand length. stepRNA is freely available at https://github.com/Vicky-Hunt-Lab/stepRNA and is easily installable

Host size constrains growth patterns in both female and male Ceratothoa italica, a mouth-dwelling isopod

Host–parasite associations are among the primary drivers of evolutionary diversification, and hold considerable importance for understanding ecological equilibria. In particular, crustacean ectoparasites are typically associated with many fish families, and may, under certain conditions, pose threats to fisheries and aquaculture. Cymothoid isopods include blood-feeding genera that inhabit the mouth of their host, and whose variation in life-history strategies remains largely unexplored. Here we investigate the size relationship between the highly prevalent Ceratothoa italica and its main natural host, the striped sea bream, Lithognathus mormyrus. We found significant correlation between host size and that of both female and male parasites. Although the generality of a host–female size association in mouth-dwelling cymothoids had been widely recognised for some time, here we provide the first robust support for the occurrence of this size association also in mouth-dwelling male parasites. The potential underlying biological causes of the patterns are discussed, contributing to the debate on the evolution of host–parasite interactions, and the adaptive radiation of this family of parasitic isopods

CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms

Genetic manipulation of microorganisms has been crucial in understanding their biology, yet for many microbial species, robust tools for comprehensive genetic analysis were lacking until the advent of CRISPR–Cas-based gene editing techniques. In this Progress article, we discuss advances in CRISPR-based techniques for the genetic analysis of genetically intractable microorganisms, with an emphasis on mycobacteria, fungi and parasites. We discuss how CRISPR-based analyses in these organisms have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors