Gene content and distribution in the nuclear genome of Fragaria vesca

Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.EEA BalcarceFil: Pontaroli, Ana Clara. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. University of Georgia. Department of Genetics; Estados UnidosFil: Rogers, Rebekah L. Harvard University. Department of Organismic and Evolutionary Biology; Estados Unidos. University of Georgia. Department of Genetics; Estados UnidosFil: Qian, Zhang. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Shields, Melanie E. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Davis, Thomas M. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Folta, Kevin M. University of Florida. Horticultural Sciences Department; Estados UnidosFil: SanMiguel, Phillip. Purdue University. Department of Horticulture and Landscape Architecture; Estados UnidosFil: Bennetzen, Jeffrey L. University of Georgia. Department of Genetics; Estados Unido

An examination of targeted gene neighborhoods in strawberry

<p>Abstract</p> <p>Background</p> <p>Strawberry (<it>Fragaria </it>spp.) is the familiar name of a group of economically important crop plants and wild relatives that also represent an emerging system for the study of gene and genome evolution. Its small stature, rapid seed-to-seed cycle, transformability and miniscule basic genome make strawberry an attractive system to study processes related to plant physiology, development and crop production; yet it lacks substantial genomics-level resources. This report addresses this deficiency by characterizing 0.71 Mbp of gene space from a diploid species (<it>F. vesca</it>). The twenty large genomic tracks (30-52 kb) captured as fosmid inserts comprise gene regions with roles in flowering, disease resistance, and metabolism.</p> <p>Results</p> <p>A detailed description of the studied regions reveals 131 Blastx-supported gene sites and eight additional EST-supported gene sites. Only 15 genes have complete EST coverage, enabling gene modelling, while 76 lack EST support. Instances of microcolinearity with <it>Arabidopsis thaliana </it>were identified in twelve inserts. A relatively high portion (25%) of targeted genes were found in unanticipated tandem duplications. The effectiveness of six FGENESH training models was assessed via comparisons among <it>ab initio </it>predictions and homology-based gene and start/stop codon identifications. Fourteen transposable-element-related sequences and 158 simple sequence repeat loci were delineated.</p> <p>Conclusions</p> <p>This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.</p

Feasibility study of the National Autistic Society EarlyBird parent support programme

The EarlyBird programme is a group-based psychoeducation intervention for parents of young children with autism. Although it is widely used in the United Kingdom, the evidence base for the programme is very limited. Using a mixed method, non-randomised research design, we aimed to test (1) the acceptability of the research procedures (recruitment, retention, suitability of measures), (2) the parental acceptability of EarlyBird (attendance, views of the programme, perceived changes) and (3) the facilitator acceptability of EarlyBird (fidelity, views of the programme, perceived changes). Seventeen families with a 2- to 5-year-old autistic child and 10 EarlyBird facilitators took part. Pre- and post-intervention assessment included measures of the child’s autism characteristics, cognitive ability, adaptive behaviour, emotional and behavioural problems and parent-reported autism knowledge, parenting competence, stress and wellbeing. Semi-structured interviews were completed at post-intervention with parents and facilitators. For those involved in the study, the research procedures were generally acceptable, retention rates were high and the research protocol was administered as planned. Generally, positive views of the intervention were expressed by parents and facilitators. Although the uncontrolled, within-participant design does not allow us to test for efficacy, change in several outcome measures from pre- to post-intervention was in the expected direction. Difficulties were encountered with recruitment (opt-in to the groups was ~56% and opt-in to the research was 63%), and strategies to enhance recruitment need to be built into any future trial. These findings should be used to inform protocols for pragmatic, controlled trials of EarlyBird and other group-based interventions for parents with young autistic children

Evidence of Long-Distance Coastal Sea Migration of Atlantic Salmon, Salmo Salar, Smolts from Northwest England (River Derwent).

Publication history: Accepted - 10 January 2022; Published online - 26 January 2022Background Combining data from multiple acoustic telemetry studies has revealed that west coast England Atlantic salmon (Salmo salar L.) smolts used a northward migration pathway through the Irish Sea to reach their feeding grounds. Hundred Atlantic salmon smolts were captured and tagged in May 2020 in the River Derwent, northwest England as part of an Environment Agency/Natural England funded project. Results Three tagged smolts were detected on marine acoustic receivers distributed across two separate arrays from different projects in the Irish Sea. One fish had migrated approximately 262 km in 10 days from the river mouth at Workington Harbour, Cumbria to the northernmost receiver array operated by the SeaMonitor project; this is the longest tracked marine migration of an Atlantic salmon smolt migrating from the United Kingdom. This migrating fish displayed behaviours which resulted in fast northward migration. The remaining two fish were detected on a receiver array operated by a third project: the Collaborative Oceanography and Monitoring for Protected Areas and Species (COMPASS). Conclusion These detections further provide evidence that migration to reach marine feeding grounds of at least a proportion of salmon smolts from rivers draining into the Irish Sea is northerly, though without a southern marine array it is impossible to conclude that this is the only route. The pattern of these detections would not have been possible without the collaborative efforts of three distinct and separately funded projects to share data. Further work is required to fully understand migration trajectories in this species on the west coast of the British Isles.The main Funding bodies for this project were the Environment Agency, Cumbria and Natural England, Cumbria. Additional funding was provided by The Derwent Owners Association and Bowland Game: Isel Fishings

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group

Inshore and offshore marine migration pathways of Atlantic salmon post-smolts from multiple rivers in Scotland, England, Northern Ireland and Ireland

The migratory behavior of Atlantic salmon (Salmo salar) post-smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post-smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicle. Migration pathways (defined as the shortest distance between two detections) of up to 575 km and over 100 days at sea were described for all 25 populations. Post-smolts from different rivers, as well as individuals from the same river, used different pathways in coastal waters. Although difficult to generalize to all rivers, at least during the year of this study, no tagged post-smolts from rivers draining into the Irish Sea were detected entering the areas of sea between the Hebrides and mainland Scotland, which is associated with a high density of finfish aquaculture. An important outcome of this study is that a high proportion of post-smolts crossed through multiple legislative jurisdictions and boundaries during their migration. This study provides the basis for spatially explicit assessment of the impact risk of coastal pressures on salmon during their first migration to sea

Формирование эмоциональной культуры как компонента инновационной культуры студентов

Homozygosity has long been associated with rare, often devastating, Mendelian disorders1 and Darwin was one of the first to recognise that inbreeding reduces evolutionary fitness2. However, the effect of the more distant parental relatedness common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity, ROH), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power3,4. Here we use ROH to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts and find statistically significant associations between summed runs of homozygosity (SROH) and four complex traits: height, forced expiratory lung volume in 1 second (FEV1), general cognitive ability (g) and educational attainment (nominal p<1 × 10−300, 2.1 × 10−6, 2.5 × 10−10, 1.8 × 10−10). In each case increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing convincing evidence for the first time that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples5,6, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein (LDL) cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection7, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been

Inshore and offshore marine migration pathways of Atlantic salmon post-smolts from multiple rivers in Scotland, England, Northern Ireland, and Ireland

The migratory behavior of Atlantic salmon (Salmo salar) post-smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post-smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicle. Migration pathways (defined as the shortest distance between two detections) of up to 575 km and over 100 days at sea were described for all 25 populations. Post-smolts from different rivers, as well as individuals from the same river, used different pathways in coastal waters. Although difficult to generalize to all rivers, at least during the year of this study, no tagged post-smolts from rivers draining into the Irish Sea were detected entering the areas of sea between the Hebrides and mainland Scotland, which is associated with a high density of finfish aquaculture. An important outcome of this study is that a high proportion of post-smolts crossed through multiple legislative jurisdictions and boundaries during their migration. This study provides the basis for spatially explicit assessment of the impact risk of coastal pressures on salmon during their first migration to sea