Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi, Lates calcarifer

[Extract] Source description: Barramundi, Lates calcarifer, is a commercially important fish farmed throughout Australia and South-East Asia. Despite an increasing availability of genetic resources for the species (e.g. microsatellite and SNP markers, linkage and BAC-based maps and transcriptomic assemblies), the complete characterization of genes is still reliant on laborious molecular methods (e.g. genome walking/RACE PCR cloning/Sanger sequencing)

Estimating mass of harvested Asian seabass Lates calcarifer from images

Total of 1072 Asian seabass or barramundi (Lates calcarifer) were harvested at two different locations in Queensland, Australia. Each fish was digitally photographed and weighed. A subsample of 200 images (100 from each location) were manually segmented to extract the fish-body area (S in cm2), excluding all fins. After scaling the segmented images to 1mm per pixel, the fish mass values (M in grams) were fitted by a single-factor model ( M=aS1.5 , a=0.1695 ) achieving the coefficient of determination (R2) and the Mean Absolute Relative Error (MARE) of R2=0.9819 and MARE=5.1% , respectively. A segmentation Convolutional Neural Network (CNN) was trained on the 200 hand-segmented images, and then applied to the rest of the available images. The CNN predicted fish-body areas were used to fit the mass-area estimation models: the single-factor model, M=aS1.5 , a=0.170 , R2=0.9819 , MARE=5.1% ; and the two-factor model, M=aSb , a=0.124 , b=0.155 , R2=0.9834 , MARE=4.5

Comparative gonad transcriptome analysis in cobia (Rachycentron canadum)

Background: Cobia (Rachycentron canadum) is a species of fish with high commercial potential particularly due to fast growth rates. The evidence of sexual size dimorphism favoring females indicate potential benefits in having a monosex culture. However, the involvement of genetic factors responsible for sexual development and gonadal maintenance that produces phenotypic sex in cobia is largely unknown.Methods: In the present study, we performed transcriptome sequencing of cobia to identify sex-biased significantly differentially expressed genes (DEGs) in testes and ovaries. The reliability of the gonad transcriptome data was validated by qPCR analysis of eight selected significantly differential expressed sex-related candidate genes.Results: This comparative gonad transcriptomic analysis revealed that 7,120 and 4,628 DEGs are up-regulated in testes or ovaries, respectively. Further functional annotation analyses identified 76 important candidate genes involved in sex determination cascades or sex differentiation, including 42 known testis-biased DEGs (dmrt1, amh and sox9 etc.), and 34 known ovary-biased DEGs (foxl2, sox3 and cyp19a etc.). Moreover, eleven significantly enriched pathways functionally related to sex determination and sex differentiation were identified, including Wnt signaling pathway, oocyte meiosis, the TGF-beta signaling pathway and MAPK signaling pathway.Conclusion: This work represents the first comparative gonad transcriptome study in cobia. The putative sex-associated DEGs and pathways provide an important molecular basis for further investigation of cobia’s sex determination, gonadal development as well as potential control breeding of monosex female populations for a possible aquaculture setting

Digital droplet PCR-based environmental DNA tool for monitoring Cryptocaryon irritans in a marine fish farm from Hong Kong

The adoption of new investigative strategies based on environmental DNA (eDNA) can be used to monitor parasites, associated bacterial microbiomes, and physical-chemical parameters in fish farms. In this study, we used the economically important and globally distributed fish ciliate parasite Cryptocaryon irritans as a model to understand the parasite abundance and potential drivers of its presence in marine fish farms. Environmental (rainfall) and physical-chemical (temperature, oxygen, salinity, pH) data collected from a marine fish farm in Hong Kong were analyzed together with the eDNA approach targeting C. irritans abundance based on digital droplet PCR and 16S metagenomics to determine associations and triggers between parasites and specific bacterial groups. Rainfall and temperature demonstrated positive associations with high abundance of C. irritans (eDNA) at the studied marine fish cage farm. However, rainfall was the only parameter tested that demonstrated a significant association with parasite eDNA, indicating that the raining season is a risky period for fish farmers in Hong Kong. Coraliomargarita was the bacterial genus with the most significant relationship with low abundance of C. irritans in water. Understanding the environmental triggers of ciliate parasites propagation and associated bacterial microbiome could elucidate new insights into environmental control, microbial management, and promote the reduction of chemical use in marine fish farms

Control of Vibrio parahaemolyticus (AHPND strain) and improvement of water quality using nanobubble technology

Nanobubble technology is used in wastewater treatment, but its disinfectant properties in aquaculture have not been clearly demonstrated. This study investigated the ability of nanobubbles to reduce Vibrio parahaemolyticus (AHPND strain) and to improve water quality. Two laboratory experiments were conducted over a one‐week period, that is (a) assessing the effects of air and oxygen nanobubbles for 60 minutes per day and (b) comparing effects of ozone nanobubble treatments for 2, 4 and 6 minutes per day. Experiments were done in triplicate 100 L tanks with 15‰ saline water, inoculated with an initial bacterial concentration of 106 CFU/ml. At the end of experiment 1, the bacterial concentration of the air and oxygen nanobubble groups was counted for 69% and 46% of the control group respectively. At the end of experiment 2, the bacterial concentration of the 2‐, 4‐ and 6‐minute ozone nanobubble groups were counted for 23%, 2.2% and 0% of the control group respectively. Oxygen and ozone nanobubbles significantly increased oxygen reduction potential and oxygen values. Results indicate that under effective dosages nanobubbles can be used in the production farms to control V.parahaemolyticus and increase oxygen levels

Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) coinfection downregulate immune-relevant pathways and cause splenic and kidney necrosis in barramundi under commercial farming conditions

Marine farming of barramundi (Lates calcarifer) in Southeast Asia is currently severely affected by viral diseases. To better understand the biological implications and gene expression response of barramundi in commercial farming conditions during a disease outbreak, the presence of pathogens, comparative RNAseq, and histopathology targeting multiple organs of clinically “sick” and “healthy” juveniles were investigated. Coinfection of scale drop disease virus (SDDV) and L. calcarifer herpes virus (LCHV) were detected in all sampled fish, with higher SDDV viral loads in sick than in healthy fish. Histopathology showed that livers in sick fish often had moderate to severe abnormal fat accumulation (hepatic lipidosis), whereas the predominant pathology in the kidneys shows moderate to severe inflammation and glomerular necrosis. The spleen was the most severely affected organ, with sick fish presenting severe multifocal and coalescing necrosis. Principal component analysis (PC1 and PC2) explained 70.3% of the observed variance and strongly associated the above histopathological findings with SDDV loads and with the sick phenotypes, supporting a primary diagnosis of the fish being impacted by scale drop disease (SDD). Extracted RNA from kidney and spleen of the sick fish were also severely degraded likely due to severe inflammation and tissue necrosis, indicating failure of these organs in advanced stages of SDD. RNAseq of sick vs. healthy barramundi identified 2,810 and 556 differentially expressed genes (DEGs) in the liver and muscle, respectively. Eleven significantly enriched pathways (e.g., phagosome, cytokine-cytokine-receptor interaction, ECM-receptor interaction, neuroactive ligand-receptor interaction, calcium signaling, MAPK, CAMs, etc.) and gene families (e.g., tool-like receptor, TNF, lectin, complement, interleukin, chemokine, MHC, B and T cells, CD molecules, etc.) relevant to homeostasis and innate and adaptive immunity were mostly downregulated in sick fish. These DEGs and pathways, also previously identified in L. calcarifer as general immune responses to other pathogens and environmental stressors, suggest a failure of the clinically sick fish to cope and overcome the systemic inflammatory responses and tissue degeneration caused by SDD

Species occurrence of ticks in South America, and interactions with biotic and abiotic traits

The datasets of records of the distribution of ticks and their hosts are invaluable tools to understand the phylogenetic patterns of evolution of ticks and the abiotic traits to which they are associated. Such datasets require an exhaustive collection of bibliographical references. In most cases, it is necessary the confirmation of reliable identification of ticks, together with an update of the scientific names of the vertebrate hosts. These data are not easily available, because many records were published in the so-called “grey literature”. Herein, we introduced the Dataset of Ticks in South America, a repository that collates data on 4,764 records of ticks (4,124 geo-referenced) with a special reference to an extra 2,370 records of ticks on cattle, together with a set of abiotic traits, curated from satellite-derived information over the complete target region. The dataset includes details of the phylogenetic relationships of the species of hosts, providing researchers with both biotic and abiotic traits that drive the distribution and evolution of ticks in South America.publishersversionpublishe

Design, Environmental and Sustainability Constraints of new African Observatories: The example of the Mozambique Radio Astronomy Observatory

The Mozambique Radio Astronomy Observatory (MRAO) will be a first milestone towards development of radioastronomy in Mozambique. Development of MRAO will constitute a preparation step towards participation in the upcoming Africa VLBI Network and the Square Kilometer Array project. The MRAO first antenna is planned to serve as a capacitation and training facility and will be installed after the conversion of a 7-meter telecom dish in South Africa. Therefore, this first radiotelescope design has to comply with local spectral and environmental constraints. Furthermore, power availability and long term sustainability with potential inclusion of solar power and control of Radio Frequency Interference are analyzed. Here we outline some of the design, environmental and power sustainability constraints.Comment: 5 pages, 3 Figures; Proceedings of the URSI BEJ Session 'Large Scale Science Projects: Europa-Africa Connects', IEEE Africon 2013 Conference Mauritius (9-12 Sep) 2013, Accepted for Publication at IEEE Xplorer, Nov 201

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18