Movement of Red Snapper, Lutjanus campechanus, in the North Central Gulf of Mexico: Potential Effects of Hurricanes

Site fidelity and movement of red snapper, Lutjanus campechanus, were estimated from a tagging study conducted off the coast of Alabama from March 1995 to January 1997. Red snapper were caught using rod and reel over nine artificial reef sites, with three reefs each located at 21-m, 27-m, and 32-m depths. During the study, 1,604 fish were tagged, and 174 recaptures were made of 167 individuals. On 4 October 1995, the eye of Hurricane Opal passed within 40 km of the artificial reef sites. When recaptures were stratified according to whether or not they were at liberty during Opal, storm effect was the most significant factor in predicting the likelihood of movement and magnitude of movement by tagged red snapper. Eighty percent of recaptured red snapper that were not at liberty during Opal were recaptured at their site of release. Fish that were at liberty during Opal, however, had a significantly higher likelihood of movement away from their site of release (P \u3c 0.001). These fish also moved significantly further than those that were not at liberty during Opal (P \u3c 0.001). Fish that were at liberty during Opal moved a mean distance (± SE) of 32.6 km (± 6.81), compared to a mean distance (± SE) of 2.5 km (± 1.10) for fish that were tagged and recaptured before Opal, and a mean distance (± SE) of 1.7 km (± 0.43) for fish that were tagged and recaptured after Opal. Heretofore, it has generally been accepted that adult red snapper demonstrate strong site fidelity and genetic homogeneity in the stock was hypothesized to result from larval drift or due to historic mixing on longer time scales. This study documents movement of adult red snapper on spatial scales that would facilitate stock mixing and implicates large-scale climatic events, such as hurricanes, as important factors in stock mixing dynamics

Physical Guidance of Cultured Retinal Neurons Using Zig-zag Surface Patterns

3 pagesThe use of physical cues to control and guide various types of cells in vitro, especially neurons and their processes, has been the focus of a large amount of research. The response of neuronal processes to artificial surfaces depends on a number of factors including the cell type, the surface chemistry of the material, and the surface’s topological features [1,2]. In this Opinion piece, we investigate the extent to which retinal neuronal processes can be made to follow straight lines patterned into a surface. We show they can follow lines with relatively shallow heights of 2 μm and be made to undergo directional changes as great as 50°. However, some processes leave the lines and assume a weaving trajectory as they grow into the surface’s unpatterned regions. Based on these findings, we propose that neuronal processes will follow lines more closely if their shapes mimic the fractal weave patterns of unrestricted neurons. In addition to exploring the fundamental behavior of neurons interacting with artificial surfaces, the results inform the design of bio-inspired electrodes for human implants.RPT is a Cottrell Scholar of the Research Council for Science Advancement. This research is supported by the WM Keck Foundation (RPT) and The Swedish Research Council (M.-T.P.: 2016-03757), Crown Princess Margareta’s Committee for the Blind, Stiftelse för Synskadade i fd Malmöhus Län and the Crafoordska Stiftelsen

Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis

Rapid antibiotic susceptibility testing of Mycobacterium tuberculosis is of paramount importance as multiple- and extensively- drug resistant strains of M. tuberculosis emerge and spread. We describe here a virus-based assay in which fluoromycobacteriophages are used to deliver a GFP or ZsYellow fluorescent marker gene to M. tuberculosis, which can then be monitored by fluorescent detection approaches including fluorescent microscopy and flow cytometry. Pre-clinical evaluations show that addition of either Rifampicin or Streptomycin at the time of phage addition obliterates fluorescence in susceptible cells but not in isogenic resistant bacteria enabling drug sensitivity determination in less than 24 hours. Detection requires no substrate addition, fewer than 100 cells can be identified, and resistant bacteria can be detected within mixed populations. Fluorescence withstands fixation by paraformaldehyde providing enhanced biosafety for testing MDR-TB and XDR-TB infections. © 2009 Piuri et al

Options for Producing a Warm-Water Fish in the UK: limits to "Green-Growth"?

This paper explores the development of a sustainable production system for tilapia and the research implications involved with ensuring commercial viability of such a system for UK farmers. The tilapia is a warm water fish with firm texture, white flesh and mild taste quite similar to a cod or haddock. Whilst tropical in origin it is thought to be highly suitable for low cost aquaculture in temperate zones with the potential to be a more sustainable source of food with fewer environmental impacts than other substitutes. Drawing on a literature review and findings from technical trials the paper will review and compare two production systems - novel Activated Suspension Technology (AST) and conventional Recirculating Aquaculture Systems (RAS) - considering their feasibility in terms of potential and financial viability for scaling up to commercial production of tilapia and their environmental and sustainability benefits. The review concludes that AST based only on microbial floc is currently uncompetitive with RAS in a UK context although the approach has benefits that might be incorporated in a new generation of mixed systems. Refinement of such systems needs to occur with potential adopters and could be part of diversification of mixed farms. Such development might further enhance the ethical values of fish produced in small-scale, modular RAS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

<p>Abstract</p> <p>Background</p> <p>Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SNP discovery using this novel sequencing technology provide a set of baseline tools for genome-level research. However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation.</p> <p>Results</p> <p>With the purpose of generating the first broad survey of gene sequences in <it>Eucalyptus grandis</it>, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of <it>Arabidopsis</it> genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta (θ) parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches.</p> <p>Conclusion</p> <p>In providing an abundance of foundational transcript sequences where limited prior genomic information existed, this work created part of the foundation for the annotation of the <it>E. grandis </it>genome that is being sequenced by the US Department of Energy. In addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species.</p

An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway.

In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway

Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster

Tandemly arranged paralogous genes lbe and lbl are members of the Drosophila NK homeobox family. We analyzed population samples of Drosophila melanogaster from Africa, Europe, North and South America, and single strains of D. sechellia, D. simulans, and D. yakuba within two linked regions encompassing partial sequences of lbe and lbl. The evolution of lbe and lbl is highly constrained due to their important regulatory functions. Despite this, a variety of forces have shaped the patterns of variation in lb genes: recombination, intragenic gene conversion and natural selection strongly influence background variation created by linkage disequilibrium and dimorphic haplotype structure. The two genes exhibited similar levels of nucleotide diversity and positive selection was detected in the noncoding regions of both genes. However, synonymous variability was significantly higher for lbe: no nonsynonymous changes were observed in this gene. We argue that balancing selection impacts some synonymous sites of the lbe gene. Stability of mRNA secondary structure was significantly different between the lbe (but not lbl) haplotype groups and may represent a driving force of balancing selection in epistatically interacting synonymous sites. Balancing selection on synonymous sites may be the first, or one of a few such observations, in Drosophila. In contrast, recurrent positive selection on lbl at the protein level influenced evolution at three codon sites. Transcription factor binding-site profiles were different for lbe and lbl, suggesting that their developmental functions are not redundant. Combined with our previous results on nucleotide variation in esterase and other homeobox genes, these results suggest that interplay of balancing and directional selection may be a general feature of molecular evolution in Drosophila and other eukaryote genomes

Modeling the Improved Visual Acuity Using Photodiode Based Retinal Implants Featuring Fractal Electrodes

Electronically restoring vision to patients blinded by severe retinal degenerations is rapidly becoming a realizable feat through retinal implants. Upon receiving an implant, previously blind patients can now detect light, locate objects, and determine object motion direction. However, the restored visual acuity (VA) is still significantly below the legal blindness level (VA &lt; 20/200). The goal of this research is to optimize the inner electrode geometry in photovoltaic subretinal implants in order to restore vision to a VA better than blindness level. We simulated neural stimulation by 20 μm subretinal photovoltaic implants featuring square or fractal inner electrodes by: (1) calculating the voltage generated on the inner electrode based on the amount of light entering the photodiode, (2) mapping how this voltage spreads throughout the extracellular space surrounding retinal bipolar neurons, and (3) determining if these extracellular voltages are sufficient for neural stimulation. By optimizing the fractal inner electrode geometry, we show that all neighboring neurons can be stimulated using an irradiance of 12 mW/mm2, while the optimized square only stimulates ~10% of these neurons at an equivalent irradiance. The 20 μm fractal electrode can thus theoretically restore VA up to 20/80, if other limiting factors common to retinal degenerations, such as glia scarring and rewiring of retinal circuits, could be reduced. For the optimized square to stimulate all neighboring neurons, the irradiance has to be increased by almost 300%, which is very near the maximum permissible exposure safety limit. This demonstration that fractal electrodes can stimulate targeted neurons for long periods using safe irradiance levels highlights the possibility for restoring vision to a VA better than the blindness level using photodiode-based retinal implants