Exploring intraspecific life history patterns in sharks

Marine ecosystems compose the major source (85%) of world fisheries production (Garcia and Newton, 1997). Although only a few fish species tend to dominate fishery catches (Jennings et al., 2001), a large diversity of fishes representing varied taxonomic levels, ecological guilds, and life histories is commonly taken. Recently, 66% of global marine resources were determined to be either fully, heavily, or over-exploited (Botsford et al., 1997). Considering the current state of many fisheries, the large diversity of species taken globally, and the general lack of resources to adequately assess many stocks, it has become important to develop shortcuts that may provide methods fisheries scientists can use to determine which stocks are in danger of overexploitation and which recovery plans are appropriate when biological data are limited (Stobutzki et al., 2001)

Co-occurrence of bycatch and target species in the groundfish demersal trawl fishery of the U.S. west coast; with special consideration of rebuilding stocks

Bycatch and resultant discard mortality are issues of global concern. The groundfish demersal trawl fishery on the west coast of the United States is a multispecies fishery with significant catch of target and nontarget species. These catches are of particular concern in regard to species that have previously been declared overfished and are currently rebuilding biomass back to target levels. To understand these interactions better, we used data from the West Coast Groundfish Observer Program in a series of cluster analyses to evaluate 3 questions: 1) Are there identifiable associations between species caught in the bottom trawl fishery; 2) Do species that are undergoing population rebuilding toward target biomass levels (“rebuilding species”) cluster with targeted species in a consistent way; 3) Are the relationships between rebuilding bycatch species and target species more resolved at particular spatial scales or are relationships spatially consistent across the whole data set? Two strong species clusters emerged—a deepwater slope cluster and a shelf cluster—neither of which included rebuilding species. The likelihood of encountering rebuilding rockfish species is relatively low. To evaluate whether weak clustering of rebuilding rockfish was attributable to their low rate of occurrence, we specified null models of species occurrence. Results indicated that the ability to predict occurrence of rebuilding rockfish when target species were caught was low. Cluster analyses performed at a variety of spatial scales indicated that the most reliable clustering of rebuilding species was at the spatial scale of individual fishing ports. This finding underscores the value of spatially resolved data for fishery management

Apparatus and method for removal of seed pericarp

Presents an apparatus and method for removing pericarp from a seed, such as a corn kernel. The method includes sonicating the kernel to loosen the pericarp and then separation of the pericarp. One example of separation is by frictional milling. An additional optional aspect of the invention is isolation of the pericarp from the remainder of the seed and/or further cleaning or purification of the pericarp

A gene signature for post-infectious chronic fatigue syndrome

Background: At present, there are no clinically reliable disease markers for chronic fatigue syndrome. DNA chip microarray technology provides a method for examining the differential expression of mRNA from a large number of genes. Our hypothesis was that a gene expression signature, generated by microarray assays, could help identify genes which are dysregulated in patients with post-infectious CFS and so help identify biomarkers for the condition. Methods: Human genome-wide Affymetrix GeneChip arrays (39,000 transcripts derived from 33,000 gene sequences) were used to compare the levels of gene expression in the peripheral blood mononuclear cells of male patients with post-infectious chronic fatigue (n = 8) and male healthy control subjects (n = 7). Results: Patients and healthy subjects differed significantly in the level of expression of 366 genes. Analysis of the differentially expressed genes indicated functional implications in immune modulation, oxidative stress and apoptosis. Prototype biomarkers were identified on the basis of differential levels of gene expression and possible biological significance Conclusion: Differential expression of key genes identified in this study offer an insight into the possible mechanism of chronic fatigue following infection. The representative biomarkers identified in this research appear promising as potential biomarkers for diagnosis and treatment

ESA-listed Puget Sound rockfish: How did we get here and how do we assess progress towards recovery planning goals?

In Puget Sound, WA, rockfish abundance declined significantly over the last 50+ years as a result of fishing pressure, life-history characteristics and the isolated geography of Puget Sound. In 2010, three species of rockfish were listed under the Endangered Species Act (ESA): yelloweye rockfish, canary rockfish and bocaccio. Due to a general lack of data specific to these three species, data from other rockfish species were used to support the listings. Since the listings, targeted research and recovery planning has begun to address major data gaps for these three species. First, cooperative research with the recreational fishing community has revealed that yelloweye rockfish are genetically distinct from coastal populations, whereas canary rockfish are not distinct - which has led to canary rockfish being delisted, the first delisting of a marine fish. Second, an ROV survey has been designed specifically to provide a path forward to estimate changes in abundance of listed rockfish in Puget Sound. Third, the Rockfish Recovery Plan for yelloweye rockfish and bocaccio has been published. This plan provides, and we have begun to address, a list of research activities related to environmental conditions and human activities that might constrain rockfish recovery. Two ongoing studies examine whether specific environmental covariates (e.g. dissolved oxygen) alter the movement and foraging behavior of yelloweye rockfish and whether rockfish bycatch can be reduced in the recreational lingcod fishery by using specific bait types. Finally, we will discuss the criteria to be used for delisting these species under the ESA, including statistical methods and operational challenges

Vulnerability to climate change of managed stocks in the California Current large marine ecosystem

Introduction: Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. Methods: This study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Results: Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. Discussion: As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore

Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene

The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes

Behavioural and neuroanatomical correlates of auditory speech analysis in primary progressive aphasias

Background Non-verbal auditory impairment is increasingly recognised in the primary progressive aphasias (PPAs) but its relationship to speech processing and brain substrates has not been defined. Here we addressed these issues in patients representing the non-fluent variant (nfvPPA) and semantic variant (svPPA) syndromes of PPA. Methods We studied 19 patients with PPA in relation to 19 healthy older individuals. We manipulated three key auditory parameters—temporal regularity, phonemic spectral structure and prosodic predictability (an index of fundamental information content, or entropy)—in sequences of spoken syllables. The ability of participants to process these parameters was assessed using two-alternative, forced-choice tasks and neuroanatomical associations of task performance were assessed using voxel-based morphometry of patients’ brain magnetic resonance images. Results Relative to healthy controls, both the nfvPPA and svPPA groups had impaired processing of phonemic spectral structure and signal predictability while the nfvPPA group additionally had impaired processing of temporal regularity in speech signals. Task performance correlated with standard disease severity and neurolinguistic measures. Across the patient cohort, performance on the temporal regularity task was associated with grey matter in the left supplementary motor area and right caudate, performance on the phoneme processing task was associated with grey matter in the left supramarginal gyrus, and performance on the prosodic predictability task was associated with grey matter in the right putamen. Conclusions Our findings suggest that PPA syndromes may be underpinned by more generic deficits of auditory signal analysis, with a distributed cortico-subcortical neuraoanatomical substrate extending beyond the canonical language network. This has implications for syndrome classification and biomarker development

Eleventh workshop on the development of quantitative assessment methodologies based on LIFE-history traits, exploitation characteristics, and other relevant parameters for data-limited stocks (WKLIFE XI)

The Workshop on the Development of Quantitative Assessment Methodologies based on Life-history traits, exploitation characteristics, and other relevant parameters for data-limited stocks (WKLIFE XI), chaired by Carl O'Brien (UK), Tobias Mildenberger* (Denmark) and Simon Fischer* (UK) met in Copenhagen, Denmark 16-20 January 2023 (with hybrid meeting access), to further develop methods for stock assessment, stock status, and catch advice for stocks in ICES Categories 2–6, including the clarification of key issues previously raised by the ICES’ Community when implementing methods developed by WKLIFE for use in the ICES’ advice. Intersessional work had taken place ahead of the WKLIFE XI meeting and was presented during the workshop. The presentations defined the work programme for the workshop and the identification of virtual subgroups; eight of which were identified within three Themes – Theme 1 (assessment methods), Theme 2 (challenges independent of assessment method) and Theme 3 (advice for stocks in ICES’ Categories 4-6, model diagnostics, control rules and management strategy evaluation). This workshop report contains detailed responses to collated comments from the ICES’ community on the empirical harvest control rules for Category 3 data-limited stocks and surplus production models for Category 2 stocks; together with further guidance. However, WKLIFE XI decided not to update the ICES technical guidance for harvest control rules and stock assessments for stocks in categories 2 and 3 (published 20 May 2022) at this stage. A draft roadmap was developed during the workshop for future data-limited research, assessment and management advice within ICES. The intended focus will be to make use of the best available science to further improve the provision of data-limited advice within ICES and to review new developments from both inside and outside of ICES; including FAO, RFMOs and scientists outside ICES’ membership. Topics include: data and their preparation, Categories 4-6 stocks including revisiting PSA (Productivity and Susceptibility Analysis), empirical indicators and harvest control rules (HCRs), length-based assessments, surplus production model assessments, data-limited reference points, simulation frameworks, short-lived and fast-growing species, and long-lived and slow-growing species, elasmobranchs, and sensitive and rare species. Timelines for delivery of the activities within the roadmap are to be identified at the next meeting of WKLIFE; together with prioritising tasks

Hearing and dementia

Hearing deficits associated with cognitive impairment have attracted much recent interest, motivated by emerging evidence that impaired hearing is a risk factor for cognitive decline. However, dementia and hearing impairment present immense challenges in their own right, and their intersection in the auditory brain remains poorly understood and difficult to assess. Here, we outline a clinically oriented, symptom-based approach to the assessment of hearing in dementias, informed by recent progress in the clinical auditory neuroscience of these diseases. We consider the significance and interpretation of hearing loss and symptoms that point to a disorder of auditory cognition in patients with dementia. We identify key auditory characteristics of some important dementias and conclude with a bedside approach to assessing and managing auditory dysfunction in dementia