Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology.

Increasing evidence suggests that alternative splicing plays an important role in Alzheimer's disease (AD) pathology. We used long-read sequencing in combination with a novel bioinformatics tool (FICLE) to profile transcript diversity in the entorhinal cortex of female transgenic (TG) mice harboring a mutant form of human tau. Our analyses revealed hundreds of novel isoforms and identified differentially expressed transcripts - including specific isoforms of Apoe, App, Cd33, Clu, Fyn and Trem2 - associated with the development of tau pathology in TG mice. Subsequent profiling of the human cortex from AD individuals and controls revealed similar patterns of transcript diversity, including the upregulation of the dominant TREM2 isoform in AD paralleling the increased expression of the homologous transcript in TG mice. Our results highlight the importance of differential transcript usage, even in the absence of gene-level expression alterations, as a mechanism underpinning gene regulation in the development of AD neuropathology.

Teaching Disaster Nursing Competencies: Strategies to Succeed.

BACKGROUND: Disaster education for nurses at all levels is imperative to improve the ability for communities to be prepared to respond and recover from disasters and public health emergencies. A variety of educational strategies are available to deliver this vital content. METHOD: A variety of strategies to deliver necessary disaster nursing education are discussed. The development of online disaster response modules for nurses at all levels from nursing student through advanced practice, delivered via a learning management system is described along with standard approaches to disaster content delivery. RESULTS: All methods of teaching disaster nursing competencies are valued. CONCLUSION: Through the effective online approach, nurses can receive disaster management training at the time and location that is most comfortable and convenient for them, thus increasing the potential to train more nurses in this important content area. [J Nurs Educ. 2024;63(X):XXX-XXX.].

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.

Impact of storm events on disinfection byproduct precursors in a drinking water source in the Northeastern United States.

Storm events play a crucial role in organic matter transport within watersheds and can increase the concentration and alter the composition of NOMs and DBP formation potential. To assess the impact that storm events can have on drinking water quality, samples were collected and analyzed across four storm events in the Neversink River, Catskill region, New York in 2019 and 2022. Source water natural organic matter (NOM) was characterized, and the change of NOM quality was evaluated due to storm impacts. During storm events, a high level of NOM mobilization is initiated by heavy precipitation causing overland flow and a rise in the water table. In this way, storms result in increased access to stored NOM pools that are generated during inter-storm periods. A significant correlation was observed between several organic water quality parameters such as UV absorbance (UV254), dissolved organic carbon (DOC) and chlorine demand. Precursors for the total trihalomethanes (TTHM), dichloroacetic acid (DCAA) and trichloroacetic acid (TCAA) exhibited comparable patterns with UV254, DOC, and chlorine demand for four storms. Despite the potential for increased dilution resulting from higher discharges, all organic water quality parameters, including yields of disinfection byproducts (i.e., DBP precursors), exhibited elevated concentrations during periods of higher flows. Three of the four storms showed hysteresis patterns with higher observed concentrations of organic constituents in the falling limb of the hydrographs. Precursors for the nitrogenous DBPs (N-DBPs) were proportional to the DOC for all four storms. The coefficient of determination (R2) for TTHM, DCAA, TCAA with UV254 is higher (R2 0.92-0.98) than corresponding correlations with DOC (R2 0.89-0.92). The R2 for UV254 showed the following hierarchy: DCAA≈TCAA>TTHM. Additionally, the R2 for DOC and specific ultraviolet absorbance (SUVA) had the following hierarchy: DCAA>TCAA>TTHM and TCAA>DCAA>TTHM respectively. A significant correlation between UV254 and DOC (R = 0.99) for all storms was observed. Chlorine demand also yielded a strong correlation (R = 0.91∼0.98) with UV254 and DOC. This research indicates that a significant and disproportionate export of NOM to source waters occurs during storm events compared to baseflow conditions. Consequently, it is recommended for drinking water treatment facilities to reassess chlorine dosages during these events. Treatment plants can employ UV254 as a tool to determine appropriate chlorine dosages, aiming to mitigate DBP formation in treated waters.

Ultimate drivers of forced extra-pair copulations in birds lacking a penis: jackdaws as a case-study.

Forced copulation is common, presumably because it can increase male reproductive success. Forced extra-pair copulation (FEPC) occurs in birds, even though most species lack a penis and are widely thought to require female cooperation for fertilization. How FEPC persists, despite a presumed lack of siring success and likely non-negligible costs to the male, is unknown. Using the jackdaw (Corvus monedula) as a case study, we use SNPs to quantify the extra-pair paternity rate through FEPC and evaluate explanations for the persistence of FEPC in species without a penis. We then collate evidence for FEPC across penis-lacking birds. Combining genetic and behavioural analyses, our study suggests that the most likely explanations for the maintenance of FEPC in jackdaws are that it provides a selective advantage to males or it is a relic. Our literature review shows that across birds lacking a penis, FEPC is taxonomically widespread, and yet, little is known about its evolution. A broader implementation of the approach used here, combining both genetic and behavioural data, may shed light on why this widespread sexual behaviour persists. Additional work is necessary to understand whether a penis is needed for paternity through forced copulation and to quantify the costs of FEPC.

Transcriptomic Responses to Koi Herpesvirus in Isolated Blood Leukocytes from Infected Common Carp.

Koi herpesvirus (KHV, CyHV-3) causes severe economic losses in carp farms. Its eradication is challenging due to the establishment of latency in blood leukocytes and other tissues. To understand the molecular mechanisms leading to KHV infection in leukocytes, common carp were bath-exposed to KHV at 17 °C. After confirming the presence of viral transcripts in blood leukocytes at ten days post infection, RNA-Seq was performed on peripheral blood leukocytes on the Illumina NovaSeq. KHV infection triggered a robust immune response mediated by pattern recognition receptors, mainly toll-like receptors (tlr2, tlr5, tlr7, and tlr13), urokinase plasminogen activator surface receptor-like, galectin proteins, and lipid mediators such as leukotriene B4 receptor 1. Enriched pathways showed increased mitochondria oxidative phosphorylation and the activation of signalling pathways such as mitogen-activated protein kinases (MAPKs) and vascular endothelial growth factor (VEGF). KHV-infected leukocytes showed low production of reactive oxygen species (ROS) and glutathione metabolism, high iron export and phagocytosis activity, and low autophagy. Macrophage polarization was deduced from the up-regulation of genes such as arginase non-hepatic 1-like, macrophage mannose receptor-1, crem, il-10, and il-13 receptors, while markers for cytotoxic T cells were observed to be down-regulated. Further work is required to characterise these leukocyte subsets and the molecular events leading to KHV latency in blood leukocytes.

The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK.

Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.

Connecting patients notified with hepatitis C to treatment (CONNECT Study): A randomized controlled trial of active case management by a health department to support primary care practitioners.

BACKGROUND: Despite subsidised access to direct-acting antivirals (DAAs), hepatitis C (HCV) treatment uptake in Australia is declining. Interventions are needed to link people living with HCV to care and treatment. We implemented and measured effectiveness of a state-wide, health department-led, enhanced case management through the primary care practitioner for all HCV notifications, aiming to encourage and support treatment commencement. METHODS: A randomised controlled trial compared enhanced case management, delivered by the health department to diagnosing clinicians, with standard of care using notifiable disease systems in Tasmania, Australia (2020-21). The intervention involved a nurse specialist contacting and providing support by telephone to primary care practitioners making an HCV notification. The primary outcome was the proportion of cases notified with chronic hepatitis C who commenced treatment within 12 weeks of notification. We allowed a 12-week extended follow-up period at the end of the study for participants with no outcomes. RESULTS: Eighty-five primary care practitioners randomised to the intervention and 86 to standard of care arms notified 111 and 115 HCV cases, respectively. The proportion of cases notified with chronic hepatitis (HCV RNA detected) commencing treatment within 12 weeks was similar between study arms (41% vs 33%; p=0·51) and after extended study follow-up (65% vs 48%; p=0·18). RNA test completion was higher in the intervention than in standard of care arm (89% vs. 78%; p=0·03), while completing pre-treatment workup for chronic patients (65% vs. 64%; p=0·93) was similar. CONCLUSION: This was the first prospective randomised study of the utility of immediate HCV notification follow-up of primary care practitioners to enhance treatment uptake using disease notification surveillance data. We demonstrated improvement in HCV RNA testing and trend toward better engagement in care, but no significant increase in treatment uptake.

The Journey Toward Inclusive Excellence.

BACKGROUND: Several national organizations have issued calls for academic nursing to create inclusive environments. Inclusive environments are needed given the vast inequities that plague the demography of nursing coupled with the need to serve diverse populations. METHOD: This article describes one school's journey toward inclusive excellence. A framework and infrastructure were developed detailing the strategy to enable the school to move toward an environment that supports inclusive excellence. RESULTS: The framework identified five priority areas to mobilize change: leadership for inclusive excellence, student service delivery and engagement, recruitment retention and advancement, community engagement, and research and scholarship in health equity, along with metrics and measures to monitor progress. CONCLUSION: Inclusive excellence is an ongoing journey rather than a destination that requires leadership commitment as well as faculty, staff, and student involvement to create a diverse environment where all individuals feel valued and respected. [J Nurs Educ. 2023;62(4):225-232.].

Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing.

Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals.

From "crisis to recovery": A complete insight into the mechanisms of chlorine injury in the lung.

Chlorine (Cl2) gas is a toxic industrial chemical (TIC) that poses a hazard to human health following accidental and/or intentional (e.g. terrorist) release. By using a murine model of sub-lethal Cl2 exposure we have examined the airway hyper responsiveness, cellular infiltrates, transcriptomic and proteomic responses of the lung. In the "crisis" phase at 2 h and 6 h there is a significant decreases in leukocytes within bronchoalveolar lavage fluid accompanied by an upregulation within the proteome of immune pathways ultimately resulting in neutrophil influx at 24 h. A flip towards "repair" in the transcriptome and proteome occurs at 24 h, neutrophil influx and an associated drop in the lung function persisting until 14 d post-exposure and subsequent "recovery" after 28 days. Collectively, this research provides new insights into the mechanisms of damage, early global responses and processes of repair induced in the lung following the inhalation of Cl2.

Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells.

The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.

Randomised controlled trial of active case management to link hepatitis C notifications to treatment in Tasmania, Australia: a study protocol.

INTRODUCTION: By subsidising access to direct acting antivirals (DAAs) for all people living with hepatitis C (HCV) in 2016, Australia is positioned to eliminate HCV as a public health threat. However, uptake of DAAs has declined over recent years and new initiatives are needed to engage people living with HCV in care. Active follow-up of HCV notifications by the health department to the notifying general practitioner (GP) may increase treatment uptake. In this study, we explore the impact of using hepatitis C notifications systems to engage diagnosing GPs and improve patient access to treatment. METHODS AND ANALYSIS: This study is a randomised controlled trial comparing enhanced case management of HCV notifications with standard of care. The intervention includes phone calls from a department of health (DoH) specialist HCV nurse to notifying GPs and offering HCV management support. The level of support requested by the GP was graded in complexity: level 1: HCV information only; level 2: follow-up testing advice; level 3: prescription support including linkage to specialist clinicians and level 4: direct patient contact. The study population includes all GPs in Tasmania who notified HCV diagnosis to the DoH between September 2020 and December 2021. The primary outcome is proportion of HCV cases who initiate DAAs after 12 weeks of HCV notification to the health department. Secondary outcomes are proportion of HCV notifications that complete HCV RNA testing, treatment workup and treatment completion. Multiple logistic regression modelling will explore factors associated with the primary and secondary outcomes. The sample size required to detect a significant difference for the primary outcome is 85 GPs in each arm with a two-sided alpha of 0.05% and 80% power. ETHICS AND DISSEMINATION: The study was approved by University of Tasmania's Human Research Ethics Committee (Protocol ID: 18418) on 17 December 2019. Results of the project will be presented in scientific meetings and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER: NCT04510246. TRIAL PROGRESSION: The study commenced recruitment in September 2020 and end of study expected December 2021.

Estimating population sensitivity and confidence of freedom from highly pathogenic avian influenza in the Victorian poultry industry using passive surveillance.

Highly pathogenic avian influenza (HPAI) is a serious disease affecting multiple organ systems and resulting in high levels of mortality in domestic poultry and may also be a serious zoonotic condition. In July-August 2020, HPAI was confirmed on 3 egg-laying chicken farms in Victoria, Australia, while a further two turkey farms and one emu farm were diagnosed with low pathogenicity viruses. All six farms were depopulated and decontaminated by 26 November 2020 and Australia declared regained freedom from HPAI on 26 February 2021. As part of the follow-up surveillance in support of claiming HPAI freedom, a scenario-tree model was developed to estimate the population sensitivity of passive surveillance for the detection of HPAI in the Victorian commercial poultry industry, and to also estimate the confidence of freedom from HPAI provided by passive surveillance, predicted over a 2-year period. Risk factors included in the model were industry sector (breeder, broiler, layer and other), flock size: small commercial (50 ≤ 5000 birds) or large commercial (> 5000 birds) and housing type (cage, barn or free-range). A detection cascade was also modelled, with probabilities allocated, to estimate the flock sensitivity for flocks in each risk stratum. System sensitivity and confidence of freedom were then estimated across all flocks in the industry. Design prevalence was set at 1, 2, 5 or 10 infected flocks and prior confidence of freedom at 0.5. Other model inputs were entered as probability distributions and the model was simulated for 10,000 iterations. Outputs were expressed as median and 95% probability intervals (PI), with the time period for analysis set at 1 month. Median system sensitivity was 0.58 (95% PI: 0.47-0.69) per time period for a single infected flock, increasing to 0.81, 0.985 and 0.9998 for 2, 5 and 10 infected flocks respectively. Median confidence of freedom was > 0.7 (95% PI: 0.65-0.76) after one time period and exceeded 0.95 and 0.99 after 4 and 7 months, respectively for one infected flock and 2 and 3 months respectively for 2 infected flocks. These results support the conclusion that passive surveillance is a highly effective tool for the detection of HPAI in commercial poultry and add further weight to evidence that HPAI has been successfully eradicated from the Victorian poultry industry and that the industry has regained HPAI free status.

Global emotional and spiritual well-being and resilience of Advanced Practice Nurses during the COVID-19 pandemic: A cross-sectional study.

AIM: To evaluate the impact of the COVID-19 pandemic on the emotional and spiritual well-being and resilience of a global sample of Advanced Practice Nurses. DESIGN: A web-based cross-sectional mixed methods study. Survey data were collected from Advanced Practice Nurses globally over a 2-month period ending on 31 August 2020. METHODS: The Warwick-Edinburgh Mental Well-being Scale, FACIT-12 Spiritual Well-being Scale and Connor-Davidson Resilience Scale 10 were used to quantify emotional and spiritual well-being and resilience of Advanced Practice Nurses' globally. The survey was distributed internationally using snowball sampling via a secure platform (Qualtrics). Results were analysed using various bivariate tests for associations and group differences. RESULTS: Nine hundred and twenty-eight Advanced Practice Nurses from 53 countries participated in the study. Study participants reported meaningfully lower scores in resilience and emotional well-being compared with non-pandemic scores. Participants from countries with well-developed Advanced Practice Nurses roles reported lower resilience and well-being scores compared with those from countries where Advanced Practice Nurses roles are still being developed. Each scale revealed significant positive associations with the other scales. CONCLUSIONS: Emotional and spiritual well-being and resilience of Advance Practice Nurses has been significantly impacted during the COVID-19 pandemic. Regardless of their work location, work hours, credential or demographics, the APNs in our study reported lower levels of resilience and mental well-being compared with typical scores on the instruments.

Resistance to white spot syndrome virus in the European shore crab is associated with suppressed virion trafficking and heightened immune responses.

Introduction: All decapod crustaceans are considered potentially susceptible to White Spot Syndrome Virus (WSSV) infection, but the degree of White Spot Disease (WSD) susceptibility varies widely between species. The European shore crab Carcinus maenas can be infected with the virus for long periods of time without signs of disease. Given the high mortality rate of susceptible species, the differential susceptibility of these resistant hosts offers an opportunity to investigate mechanisms of disease resistance. Methods: Here, the temporal transcriptional responses (mRNA and miRNA) of C. maenas following WSSV injection were analysed and compared to a previously published dataset for the highly WSSV susceptible Penaeus vannamei to identify key genes, processes and pathways contributing to increased WSD resistance. Results: We show that, in contrast to P. vannamei, the transcriptional response during the first 2 days following WSSV injection in C. maenas is limited. During the later time points (7 days onwards), two groups of crabs were identified, a recalcitrant group where no replication of the virus occurred, and a group where significant viral replication occurred, with the transcriptional profiles of the latter group resembling those of WSSV-susceptible species. We identify key differences in the molecular responses of these groups to WSSV injection. Discussion: We propose that increased WSD resistance in C. maenas may result from impaired WSSV endocytosis due to the inhibition of internal vesicle budding by dynamin-1, and a delay in movement to the nucleus caused by the downregulation of cytoskeletal transcripts required for WSSV cytoskeleton docking, during early stages of the infection. This response allows resistant hosts greater time to fine-tune immune responses associated with miRNA expression, apoptosis and the melanisation cascade to defend against, and clear, invading WSSV. These findings suggest that the initial stages of infection are key to resistance to WSSV in the crab and highlight possible pathways that could be targeted in farmed crustacean to enhance resistance to WSD.

Genome-wide characterization of mitochondrial DNA methylation in human brain.

Background: There is growing interest in the role of DNA methylation in regulating the transcription of mitochondrial genes, particularly in brain disorders characterized by mitochondrial dysfunction. Here, we present a novel approach to interrogate the mitochondrial DNA methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors. Results: We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation at several sites, such as within the D-LOOP and the genes MT-ND2, MT-ATP6, MT-ND4, MT-ND5 and MT-ND6, predominantly in a non-CpG context. The elevated DNA methylation we observe in the D-LOOP we validate using pyrosequencing. We identify loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally, we replicate previously reported differentially methylated regions between brain regions from a methylated DNA immunoprecipitation sequencing study. Conclusions: We have annotated patterns of DNA methylation at single base resolution across the mitochondrial genome in human brain samples. Looking to the future this approach could be utilized to investigate the role of mitochondrial epigenetic mechanisms in disorders that display mitochondrial dysfunction.

Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing.

Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community.

The complete mitochondrial genome of the pink sea fan, Eunicella verrucosa (Pallas, 1766).

The pink sea fan, Eunicella verrucosa (Pallas, 1766), inhabits rocky substrates across the northeast Atlantic and the western Mediterranean. Across much of its range it has been detrimentally affected by fishing. DNA from 17 E. verrucosa specimens was amplified by phi29-induced rolling circle amplification. Following purification by sodium acetate-ethanol precipitation, the circular genomic DNA was sequenced on an Illumina MiSeq v2. Specimens originated from sites along the west coast of Ireland, southwest Wales, southwest/southern England, northwest France, southern Portugal, and the Mediterranean coast of northeast Spain. All samples had identical mitochondrial genome sequences of 19,267 bp and included 14 protein-coding genes (including the mutS gene), two ribosomal RNA subunits (12S and 16S) and one methionine tRNA gene. Two genes (nad2 and nad5) overlapped by 13 bp; all other genes were separated by non-coding intergenic regions. All protein-coding genes had the same start codon (ATG) and a TAA or TAG stop codon, except for cox1 that terminated with the incomplete stop codon T--. The mitochondrial genome of E. verrucosa (MW588805) showed 99.72% similarity with that of a related sea fan species, Eunicella cavolini, with six SNPs and a 49 bp deletion between nad5 and nad4 in E. verrucosa distinguishing the two.

Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp.

White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed-with limited differential expression from 3-12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.