The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers

Antarctic krill (Euphausia superba) is a crucial component of the Southern Ocean ecosystem, acting as the major link between primary production and higher trophic levels with an annual predator demand of up to 470 million tonnes. It also acts as an ecosystem engineer, affecting carbon sequestration and recycling iron and nitrogen, and has increasing importance as a commercial product in the aquaculture and health industries. Here we describe the creation of a de novo assembled head transcriptome for E. superba. As an example of its potential as a molecular resource, we relate its exploitation in identifying and characterizing numerous genes related to the circadian clock in E. superba, including the major components of the central feedback loop. We have made the transcriptome openly accessible for a wider audience of ecologists, molecular biologists, evolutionary geneticists, and others in a user-friendly format at SuperbaSE, hosted at www.krill.le.ac.uk

A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray

The origins, design, fabrication and performance of an Atlantic salmon microarray are described. The microarray comprises 16 950 Atlantic salmon-derived cDNA features, printed in duplicate and mostly sourced from pre-existing expressed sequence tag (EST) collections [SALGENE and salmon genome project (SGP)] but also supplemented with cDNAs from suppression subtractive hybridization libraries and candidate genes involved in immune response, protein catabolism, lipid metabolism and the parr–smolt transformation. A preliminary analysis of a dietary lipid experiment identified a number of genes known to be involved in lipid metabolism. Significant fold change differences (as low as 1.2x) were apparent from the microarray analysis and were confirmed by quantitative real-time polymerase chain reaction analysis. The study also highlighted the potential for obtaining artefactual expression patterns as a result of cross-hybridization of similar transcripts. Examination of the robustness and sensitivity of the experimental design employed demonstrated the greater importance of biological replication over technical (dye flip) replication for identification of a limited number of key genes in the studied system. The TRAITS (TRanscriptome Analysis of Important Traits of Salmon)–salmon genome project microarray has been proven, in a number of studies, to be a powerful tool for the study of key traits of Atlantic salmon biology. It is now available for use by researchers in the wider scientific community

Neki aspekti proizvodnje Kačkavalja

U ovom izlaganju želimo da istaknemo značaj kačkavalja za naše sirarstvo. Istovremeno namjeravamo da ukažemo na neka pitanja na koja treba da usmjerimo našu pažnju u daljem radu

New Australian guidelines for the treatment of alcohol problems: an overview of recommendations

Summary of recommendations and levels of evidence Chapter 2: Screening and assessment for unhealthy alcohol use Screening Screening for unhealthy alcohol use and appropriate interventions should be implemented in general practice (Level A), hospitals (Level B), emergency departments and community health and welfare settings (Level C). Quantity–frequency measures can detect consumption that exceeds levels in the current Australian guidelines (Level B). The Alcohol Use Disorders Identification Test (AUDIT) is the most effective screening tool and is recommended for use in primary care and hospital settings. For screening in the general community, the AUDIT-C is a suitable alternative (Level A). Indirect biological markers should be used as an adjunct to screening (Level A), and direct measures of alcohol in breath and/or blood can be useful markers of recent use (Level B). Assessment Assessment should include evaluation of alcohol use and its effects, physical examination, clinical investigations and collateral history taking (Level C). Assessment for alcohol-related physical problems, mental health problems and social support should be undertaken routinely (GPP). Where there are concerns regarding the safety of the patient or others, specialist consultation is recommended (Level C). Assessment should lead to a clear, mutually acceptable treatment plan which specifies interventions to meet the patient’s needs (Level D). Sustained abstinence is the optimal outcome for most patients with alcohol dependence (Level C). Chapter 3: Caring for and managing patients with alcohol problems: interventions, treatments, relapse prevention, aftercare, and long term follow-up Brief interventions Brief motivational interviewing interventions are more effective than no treatment for people who consume alcohol at risky levels (Level A). Their effectiveness compared with standard care or alternative psychosocial interventions varies by treatment setting. They are most effective in primary care settings (Level A). Psychosocial interventions Cognitive behaviour therapy should be a first-line psychosocial intervention for alcohol dependence. Its clinical benefit is enhanced when it is combined with pharmacotherapy for alcohol dependence or an additional psychosocial intervention (eg, motivational interviewing) (Level A). Motivational interviewing is effective in the short term and in patients with less severe alcohol dependence (Level A). Residential rehabilitation may be of benefit to patients who have moderate-to-severe alcohol dependence and require a structured residential treatment setting (Level D). Alcohol withdrawal management Most cases of withdrawal can be managed in an ambulatory setting with appropriate support (Level B). Tapering diazepam regimens (Level A) with daily staged supply from a pharmacy or clinic are recommended (GPP). Pharmacotherapies for alcohol dependence Acamprosate is recommended to help maintain abstinence from alcohol (Level A). Naltrexone is recommended for prevention of relapse to heavy drinking (Level A). Disulfiram is only recommended in close supervision settings where patients are motivated for abstinence (Level A). Some evidence for off-label therapies baclofen and topiramate exists, but their side effect profiles are complex and neither should be a first-line medication (Level B). Peer support programs Peer-led support programs such as Alcoholics Anonymous and SMART Recovery are effective at maintaining abstinence or reductions in drinking (Level A). Relapse prevention, aftercare and long-term follow-up Return to problematic drinking is common and aftercare should focus on addressing factors that contribute to relapse (GPP). A harm-minimisation approach should be considered for patients who are unable to reduce their drinking (GPP). Chapter 4: Providing appropriate treatment and care to people with alcohol problems: a summary for key specific populations Gender-specific issues Screen women and men for domestic abuse (Level C). Consider child protection assessments for caregivers with alcohol use disorder (GPP). Explore contraceptive options with women of reproductive age who regularly consume alcohol (Level B). Pregnant and breastfeeding women Advise pregnant and breastfeeding women that there is no safe level of alcohol consumption (Level B). Pregnant women who are alcohol dependent should be admitted to hospital for treatment in an appropriate maternity unit that has an addiction specialist (GPP). Young people Perform a comprehensive HEEADSSS assessment for young people with alcohol problems (Level B). Treatment should focus on tangible benefits of reducing drinking through psychotherapy and engagement of family and peer networks (Level B). Aboriginal and Torres Strait Islander peoples Collaborate with Aboriginal or Torres Strait Islander health workers, organisations and communities, and seek guidance on patient engagement approaches (GPP). Use validated screening tools and consider integrated mainstream and Aboriginal or Torres Strait Islander-specific approaches to care (Level B). Culturally and linguistically diverse groups Use an appropriate method, such as the “teach-back” technique, to assess the need for language and health literacy support (Level C). Engage with culture-specific agencies as this can improve treatment access and success (Level C). Sexually diverse and gender diverse populations Be mindful that sexually diverse and gender diverse populations experience lower levels of satisfaction, connection and treatment completion (Level C). Seek to incorporate LGBTQ-specific treatment and agencies (Level C). Older people All new patients aged over 50 years should be screened for harmful alcohol use (Level D). Consider alcohol as a possible cause for older patients presenting with unexplained physical or psychological symptoms (Level D). Consider shorter acting benzodiazepines for withdrawal management (Level D). Cognitive impairment Cognitive impairment may impair engagement with treatment (Level A). Perform cognitive screening for patients who have alcohol problems and refer them for neuropsychological assessment if significant impairment is suspected (Level A). Summary of key recommendations and levels of evidence Chapter 5: Understanding and managing comorbidities for people with alcohol problems: polydrug use and dependence, co-occurring mental disorders, and physical comorbidities Polydrug use and dependence Active alcohol use disorder, including dependence, significantly increases the risk of overdose associated with the administration of opioid drugs. Specialist advice is recommended before treatment of people dependent on both alcohol and opioid drugs (GPP). Older patients requiring management of alcohol withdrawal should have their use of pharmaceutical medications reviewed, given the prevalence of polypharmacy in this age group (GPP). Smoking cessation can be undertaken in patients with alcohol dependence and/or polydrug use problems; some evidence suggests varenicline may help support reduction of both tobacco and alcohol consumption (Level C). Co-occurring mental disorders More intensive interventions are needed for people with comorbid conditions, as this population tends to have more severe problems and carries a worse prognosis than those with single pathology (GPP). The Kessler Psychological Distress Scale (K10 or K6) is recommended for screening for comorbid mental disorders in people presenting for alcohol use disorders (Level A). People with alcohol use disorder and comorbid mental disorders should be offered treatment for both disorders; care should be taken to coordinate intervention (Level C). Physical comorbidities Patients should be advised that alcohol use has no beneficial health effects. There is no clear risk-free threshold for alcohol intake. The safe dose for alcohol intake is dependent on many factors such as underlying liver disease, comorbidities, age and sex (Level A). In patients with alcohol use disorder, early recognition of the risk for liver cirrhosis is critical. Patients with cirrhosis should abstain from alcohol and should be offered referral to a hepatologist for liver disease management and to an addiction physician for management of alcohol use disorder (Level A). Alcohol abstinence reduces the risk of cancer and improves outcomes after a diagnosis of cancer (Level A)

Stability of RNA isolated from post-mortem tissues of Atlantic salmon (Salmo salar L.)

Studies of post-mortem interval on the stability of RNA from a number of various mammals have shown RNA to be stable for between 24 and 48 h following death. As yet there have been no studies looking at RNA stability in post-mortem tissues of poikilothermic fish. Brain, kidney, liver and muscle were collected from Atlantic salmon (Salmo salar) parr and samples of each tissue were placed into RNAlater (TM) after 0-24 h post-mortem storage at room temperature. Electrophoretic analysis of the total RNA showed degradation of ribosomal RNA only in muscle from 8 h onwards. Probing of northern blots with beta-actin showed that, in the brain, beta-actin mRNA was stable for 24 h post-mortem but degradation of mRNA was observed after 8 h with the kidney and liver and after 4 h with the muscle. Expression of the weakly expressed thyroid hormone receptor beta (TR beta) was detected by reverse transcriptase polymerase chain reaction (RT-PCR) in all tissues up to 24 h post-mortem although a reduction in PCR product was observed after 8 h with muscle and 24 h with kidney. Analysis with an Agilent 2100 Bioanalyzer showed that the RNA integrity number (RIN) of brain total RNA remained constant for 8 h post-mortem with only a small fall at 24 h post-mortem. The RINs of the remaining tissues indicated degradation at 8 h post-mortem with kidney and muscle and at 24 hours post-mortem with liver. Taken together these findings show that degradation of Atlantic salmon RNA is tissue dependent but stable for at least one hour post-mortem

Variable leucine-rich repeats of tomato disease resistance genes Cf-2 and Cf-5 determine specificity

The tomato Cf-2 and Cf-5 genes confer race specific resistance to infection by the leaf mould pathogen Cladosporium fulvum. The encoded proteins induce a defence response upon recognition of the fungal Avr2 and Avr5 determinants, respectively. Each resistance protein is comprised largely of leucine-rich repeats (LRRs) and the specificity of recognition is thought to occur through a particular domain. We have investigated this further using domain swaps between Cf-2 and Cf-5. Engineered chimeric genes containing portions of Cf-2 and Cf-5 were expressed and shown to be functional. The results clearly show that the specificity for the particular avirulence determinant is restricted to a region of each gene that encodes a subset of LRRs containing the highest level of intergenic variability. In addition, two non-functional mutants of Cf-5 were characterized and their significance discussed

Data from: The molecular evolution of spiggin nesting glue in sticklebacks

Gene duplication and subsequent divergence can lead to the evolution of new functions and lineage-specific traits. In sticklebacks, the successive duplication of a mucin gene (MUC19) into a tandemly arrayed, multigene family has enabled the production of copious amounts of ‘spiggin’, a secreted adhesive protein essential for nest construction. Here, we examine divergence between spiggin genes among three-spined sticklebacks (Gasterosteus aculeatus) from ancestral marine and derived freshwater populations, and propose underpinning gene duplication mechanisms. Sanger sequencing revealed substantial diversity among spiggin transcripts, including alternatively spliced variants and interchromosomal spiggin chimeric genes. Comparative analysis of the sequenced transcripts and all other spiggin genes in the public domain support the presence of three main spiggin lineages (spiggin A, spiggin B and spiggin C) with further subdivisions within spiggin B (B1, B2) and spiggin C (C1, C2). Spiggin A had diverged least from the ancestral MUC19, while the spiggin C duplicates had diversified most substantially. In silico translations of the spiggin gene open reading frames predicted that spiggins A and B are secreted as long mucin-like polymers, while spiggins C1 and C2 are secreted as short monomers, with putative antimicrobial properties. We propose that diversification of duplicated spiggin genes has facilitated local adaptation of spiggin to a range of aquatic habitats

Data from: The molecular evolution of spiggin nesting glue in sticklebacks

Gene duplication and subsequent divergence can lead to the evolution of new functions and lineage-specific traits. In sticklebacks, the successive duplication of a mucin gene (MUC19) into a tandemly arrayed, multigene family has enabled the production of copious amounts of ‘spiggin’, a secreted adhesive protein essential for nest construction. Here, we examine divergence between spiggin genes among three-spined sticklebacks (Gasterosteus aculeatus) from ancestral marine and derived freshwater populations, and propose underpinning gene duplication mechanisms. Sanger sequencing revealed substantial diversity among spiggin transcripts, including alternatively spliced variants and interchromosomal spiggin chimeric genes. Comparative analysis of the sequenced transcripts and all other spiggin genes in the public domain support the presence of three main spiggin lineages (spiggin A, spiggin B and spiggin C) with further subdivisions within spiggin B (B1, B2) and spiggin C (C1, C2). Spiggin A had diverged least from the ancestral MUC19, while the spiggin C duplicates had diversified most substantially. In silico translations of the spiggin gene open reading frames predicted that spiggins A and B are secreted as long mucin-like polymers, while spiggins C1 and C2 are secreted as short monomers, with putative antimicrobial properties. We propose that diversification of duplicated spiggin genes has facilitated local adaptation of spiggin to a range of aquatic habitats

Seasonal and spatial influences on gene expression in Antarctic krill Euphausia superba

The high latitudes inhabited by Antarctic krill Euphausia superba Dana are characterised by extreme changes in seasonal conditions, with very low food availability, long periods of darkness and a massive expansion of sea ice in autumn and winter. How krill adapt to these conditions has yet to be determined, and it was the purpose of this study to gain more insight by investigating the differences between summer and winter krill populations at the molecular level. To achieve this, we used a cDNA microarray to compare gene expression between female adult krill caught during summer and winter near the Antarctic Peninsula (60° S), and between Peninsula krill and krill caught near South Georgia (54° S) during the same winter. The Peninsula seasonal comparison showed up-regulation in summer krill of genes involved in feeding and digestion, respiration, motor activity and immunity. Summer krill also showed evidence of increased vitellogenesis, with an insulin-related peptide up-regulated and neuroparsin down-regulated. The comparison between the different overwintering locations showed an up-regulation in the South Georgia krill of genes involved in feeding and digestion, and immunity. There was, however, no differential expression of genes involved in respiration, motor activity or vitellogenesis, suggesting that despite the above differences, both populations of overwintering krill were in a quiescent state. This study shows how krill physiology changes seasonally at the molecular level and how these changes are flexible according to the overwintering environment