Awareness and acceptability of HIV pre-exposure prophylaxis (PrEP) among students at two historically Black universities (HBCU): a cross-sectional survey.

BACKGROUND: Despite young African American adults (ages 18-24) being among the highest risk groups for HIV infection, little is known about their awareness of HIV pre-exposure prophylaxis (PrEP) - a once daily pill shown to be > 90% effective in preventing HIV. To explore awareness and acceptability of PrEP among college students in this demographic, we conducted a survey of attendees at two large historically Black universities (HBCU) in North Carolina. METHODS: We administered a 14-item questionnaire to students at two HBCUs in North Carolina between February and April 2018. Questions were formatted in a yes/no or multiple choice format. Questionnaire items specifically addressed PrEP awareness and acceptability. Surveys were administered to students at a campus health fair and while transiting the campus student union via iPad. Response to all questions was optional. We fit a logistic regression model to determine association of key demographic determinants with PrEP acceptability and awareness. Statistical analyses were conducted using SAS 9.4 (SAS, Cary, NC). RESULTS: Overall, 210 students participated in the survey, of which 60 completed all survey items as presented. The survey cohort was 75% female, 89% heterosexual and 39% freshmen. The mean age of respondents was 19.8 years (SD: 1.8). Fifty-two percent of survey respondents reported that they were aware of PrEP prior to the time of survey administration. Only 3% of respondents reported that they were on PrEP. The most common sources of information on PrEP were campus health services (24%) and non-social media advertising (15%). Of respondents who were aware of PrEP, 61% reported that they had heard about in the 6 months prior to survey administration, while only 19% say they were aware of it for more than a year. Regarding acceptability of PrEP, 58% of respondents reported that they would take a once a day pill for HIV if they were at risk. Our logistic regression analysis found no statistically significant associations between key demographic factors and PrEP awareness. However, persons who perceived themselves to be at risk for HIV acquisition were more likely to find once daily oral PrEP (relative risk 2.66 (95% CI 1.31-5.42)) as an acceptable prevention strategy than the rest of the survey cohort. CONCLUSIONS: African American HBCU students are becoming aware of PrEP, and generally perceive the intervention as acceptable and worth consideration.

Mapping and Expression of Candidate Genes for Development Rate in Rainbow Trout (Oncorhynchus mykiss).

Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life-history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a quantitative trait locus for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression, and quantitative genetic methods to further identify the genetic basis of embryonic developmental rate in O. mykiss Among the genes located in the region of the major development rate quantitative trait locus (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in embryonic development (fertilization through hatch), but none were differentially expressed between individuals with the fast- or slow-developing alleles for a major embryonic development rate quantitative trait locus. In a follow-up study of migratory and resident rainbow trout from natural populations in Alaska, we found significant additive variation in development rate and, moreover, found associations between development rate and allelic variation in all 3 candidate genes within the quantitative trait locus for embryonic development. The mapping of these genes to this region and associations in multiple populations provide positional candidates for further study of their roles in growth, development, and life-history diversity in this model salmonid.

Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication.

BACKGROUND: The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention complicates efforts to detect allelic variation in salmonid fishes. Specifically, single nucleotide polymorphism (SNP) detection is problematic because nucleotide variation can be found between the duplicate copies (paralogs) of a gene as well as between alleles. RESULTS: We present a method of differentiating between allelic and paralogous (gene copy) sequence variants, allowing identification of SNPs in organisms with multiple copies of a gene or set of genes. The basic strategy is to: 1) identify windows of unique cDNA sequences with homology to each other, 2) compare these unique cDNAs if they are not shared between individuals (i.e. the cDNA is homozygous in one individual and homozygous for another cDNA in the other individual), and 3) give a "SNP score" value between zero and one to each candidate sequence variant based on six criteria. Using this strategy we were able to detect about seven thousand potential SNPs from the transcriptomes of several clonal lines of rainbow trout. When directly compared to a pre-validated set of SNPs in polyploid wheat, we were also able to estimate the false-positive rate of this strategy as 0 to 28% depending on parameters used. CONCLUSIONS: This strategy has an advantage over traditional techniques of SNP identification because another dimension of sequencing information is utilized. This method is especially well suited for identifying SNPs in polyploids, both outbred and inbred, but would tend to be conservative for diploid organisms.

Y chromosome phylogeny for cutthroat trout (Oncorhynchus clarkii) subspecies is generally concordant with those of other markers.

Sequence divergence was evaluated in the non-recombining, male-specific OmyY1 region of the Y chromosome among the subspecies of cutthroat trout (Oncorhynchus clarkii) in the western United States. This evaluation identified subspecies-discriminating OmyY1-haplotypes within a ∼1200bp region of the OmyY1 locus and localized the region to the end of the Y chromosome by FISH analysis. OmyY1 sequences were aligned and used to reconstruct a phylogeny of the cutthroat trout subspecies and related species via maximum-parsimony and Bayesian analyses. In the Y-haplotype phylogeny, clade distributions generally corresponded to the geographic distributions of the recognized subspecies. This phylogeny generally corresponded to a mitochondrial tree obtained for these subspecies in a previous study. Both support a clade of trout vs. Pacific salmon, of rainbow trout, and of a Yellowstone cutthroat group within the cutthroat trout. In our OmyY1 tree, however, the cutthroat "clade", although present topologically, was not statistically significant. Some key differences were found between trees obtained from the paternally-inherited OmyY1 vs. maternally-inherited mitochondrial haplotypes in cutthroat trout compared to rainbow trout. Other findings are: The trout OmyY1 region evolves between 3 and 13 times slower than the trout mitochondrial regions that have been studied. The Lahontan cutthroat trout had a fixed OmyY1 sequence throughout ten separate populations, suggesting this subspecies underwent a severe population bottleneck prior to its current dispersal throughout the Great Basin during the pluvial phase of the last ice age. The Yellowstone group is the most derived among the cutthroat trout and consists of the Yellowstone, Bonneville, Colorado, Rio Grande and greenback subspecies. Identification of subspecies and sex with this Y-chromosome marker may prove useful in conservation efforts.

Risk factors of food insecurity among students at diverse post-secondary education institutions: a cross-sectional examination.

OBJECTIVE: Identify the prevalence of food insecurity (FI) and compare sociodemographic, mental, physical, behavioral, and environmental risk factors for FI among students at a private university, community college, and historically black college or university (HBCU). PARTICIPANTS: Adult students attending a private university, community college, or HBCU (n = 4,140) located within the southeastern United States. METHODS: Using an online survey (2017-2019), FI, sociodemographic, mental, physical, behavioral, and environmental data were collected to understand their association with FI. RESULTS: Up to 37.1% of students experienced FI. Identifying as black, other/multi-racial, having poor sleep, federal loans, depressive symptoms, high stress, social isolation, or a chronic condition were associated with FI. These associations varied by institution. CONCLUSIONS: FI is prevalent within diverse post-secondary institutions that serve traditional and nontraditional students with risk factors varying between institutions. The prevalence of FI and risk factors can inform institutional policy responses to ameliorate the effects of FI.

A reconnaissance survey of channel bank particulate phosphorus concentrations, controls and estimated contributions to riverine loads across England.

Channel banks can contribute a significant proportion of fine-grained (<63 µm) sediment to rivers, thereby also contributing to riverine total particulate phosphorus loads. Improving water quality through better agricultural practices alone can be difficult since the contributions from non-agricultural sources, including channel banks, can generate a 'spatial mismatch' between the efficacy of best management applied on farms and the likelihood of meeting environmental objectives. Our study undertook a reconnaissance survey (n = 76 sites each with 3 profiles sampled) to determine the total phosphorus (TP) concentrations of channel banks across England and to determine if TP content can be predicted using readily accessible secondary data. TP concentrations in adjacent field topsoils, local soil soil type/texture and geological parent material were examined as potential predictors of bank TP. Carbon and nitrogen content were also analysed to explore the impacts of organic matter content on measured TP concentrations. The results suggest that channel bank TP concentrations are primarily controlled by parent material rather than P additions to adjacent topsoils through fertilizer and organic matter inputs, but significant local variability in concentrations prevents the prediction of bank TP content using mapped soil type or geology. A median TP concentration of 873 mg kg-1 was calculated for the middle section of the sampled channel bank profiles, with a 25th percentile of 675 mg kg-1, and 75th percentile of 1159 mg kg-1. Using these concentrations and, in comparison with previously published estimates, the estimated number of inland WFD waterbodies in England for which channel bank erosion contributes >20% of the riverine total PP load increased from 15 to 25 (corresponding range of 17-35 using the 25th and 75th percentiles of measured TP concentrations). Collectively, these 25 waterbodies account for 0.2% of the total inland WFD waterbody area comprising England.

Regulation and expression of sexual differentiation factors in embryonic and extragonadal tissues of Atlantic salmon.

BACKGROUND: The products of cyp19, dax, foxl2, mis, sf1 and sox9 have each been associated with sex-determining processes among vertebrates. We provide evidence for expression of these regulators very early in salmonid development and in tissues outside of the hypothalamic-pituitary-adrenal/gonadal (HPAG) axis. Although the function of these factors in sexual differentiation have been defined, their roles in early development before sexual fate decisions and in tissues beyond the brain or gonad are essentially unknown. RESULTS: Bacterial artificial chromosomes containing salmon dax1 and dax2, foxl2b and mis were isolated and the regulatory regions that control their expression were characterized. Transposon integrations are implicated in the shaping of the dax and foxl2 loci. Splice variants for cyp19b1 and mis in both embryonic and adult tissues were detected and characterized. We found that cyp19b1 transcripts are generated that contain 5'-untranslated regions of different lengths due to cryptic splicing of the 3'-end of intron 1. We also demonstrate that salmon mis transcripts can encode prodomain products that present different C-termini and terminate before translation of the MIS hormone. Regulatory differences in the expression of two distinct aromatases cyp19a and cyp19b1 are exerted, despite transcription of their transactivators (ie; dax1, foxl2, sf1) occurring much earlier during embryonic development. CONCLUSIONS: We report the embryonic and extragonadal expression of dax, foxl2, mis and other differentiation factors that indicate that they have functions that are more general and not restricted to steroidogenesis and gonadogenesis. Spliced cyp19b1 and mis transcripts are generated that may provide regulatory controls for tissue- or development-specific activities. Selection of cyp19b1 transcripts may be regulated by DAX-1, FOXL2 and SF-1 complexes that bind motifs in intron 1, or by signals within exon 2 that recruit splicing factors, or both. The potential translation of proteins bearing only the N-terminal MIS prodomain may modulate the functions of other TGF ß family members in different tissues. The expression patterns of dax1 early in salmon embryogenesis implicate its role as a lineage determination factor. Other roles for these factors during embryogenesis and outside the HPAG axis are discussed.

Recruiting intergenerational African American males for biomedical research Studies: a major research challenge.

The health and well-being of all individuals, independent of race, ethnicity, or gender, is a significant public health concern. Despite many improvements in the status of minority health, African American males continue to have the highest age-adjusted mortality rate of any race-sex group in the United States. Such disparities are accounted for by deaths from a number of diseases such as diabetes, human immunodeficiency virus (HIV), cancer, and cardiovascular disease, as well as by many historical and present social and cultural constructs that present as obstacles to better health outcomes. Distrust of the medical community, inadequate education, low socioeconomic status, social deprivation, and underutilized primary health care services all contribute to disproportionate health and health care outcomes among African Americans compared to their Caucasian counterparts. Results of clinical research on diseases that disproportionately affect African American males are often limited in their reliability due to common sampling errors existing in the majority of biomedical research studies and clinical trials. There are many reasons for underrepresentation of African American males in clinical trials, including their common recollection and interpretation of relevant historical of biomedical events where minorities were abused or exposed to racial discrimination or racist provocation. In addition, African American males continue to be less educated and more disenfranchised from the majority in society than Caucasian males and females and their African American female counterparts. As such, understanding their perceptions, even in early developmental years, about health and obstacles to involvement in research is important. In an effort to understand perspectives about their level of participation, motivation for participation, impact of education, and engagement in research, this study was designed to explore factors that impact their willingness to participate. Our research suggests that: (1) African American males across all ages are willing to participate in several types of research studies, even those that require human samples; (2) their level of participation is significantly influenced by education level; and (3) their decision to participate in research studies is motivated by civic duty, monetary compensation, and whether they or a relative has had the disease of interest. However, African American males, across all age groups, continue to report a lack of trust as a primary reason for their unwillingness to participate in biomedical research. There is an ongoing need to continue to seek advice, improve communication, and design research studies that garner trust and improve participation among African American males as a targeted underrepresented population. Such communication and dialogues should occur at all age levels of research development to assess. current attitudes and behaviors of African American males around participation.

People, Pulpits and Non-Profits: Outlining A Model for Collaboration Near the Origins of the HIV Epidemic.

A collaborative HIV health promotion program was implemented in Durham, North Carolina to aid in mitigating the deleterious impact of HIV in the African American community. This equity-centered program produced engagement and action at the community, organizational and individual socio-ecological levels. A variety of organizations successfully collaborated in this effort. This cooperative act details the collective power of community members, Black faith-based organizations, a local health department and two community-based non-profit organizations to actualize solutions regarding the HIV epidemic. Health equity and social justice were promoted as a result of this successful initiative.

Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire.

BACKGROUND: The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and ß hemoglobin genes is of great interest. RESULTS: We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and ß hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and ß hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr ß globin genes, than the genomes of other teleosts that have been sequenced. CONCLUSIONS: We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster after the whole genome duplication (WGD) at the base of the teleost radiation but prior to the salmonid-specific WGD, which then produced the duplicated copies seen today. We also propose that the relatively high number of hemoglobin genes as well as the presence of non-Bohr ß hemoglobin genes may be due to the dynamic life history of salmon and the diverse environmental conditions that the species encounters.Data deposition: BACs S0155C07 and S0079J05 (fps135): GenBank GQ898924; BACs S0055H05 and S0014B03 (fps1046): GenBank GQ898925.

Genomic organization and evolution of the vomeronasal type 2 receptor-like (OlfC) gene clusters in Atlantic salmon, Salmo salar.

There are three major multigene superfamilies of olfactory receptors (OR, V1R, and V2R) in mammals. The ORs are expressed in the main olfactory organ, whereas the V1Rs and V2Rs are located in the vomeronasal organ. Fish only possess one olfactory organ in each nasal cavity, the olfactory rosette; therefore, it has been proposed that their V2R-like genes be classified as olfactory C family G protein-coupled receptors (OlfC). There are large variations in the sizes of OR gene repertoires. Previous studies have shown that fish have between 12 and 46 functional V2R-like genes, whereas humans have lost all functional V2Rs, and frog sp. have more than 240. Pseudogenization of V2R genes is a prevalent event across species. In the mouse and frog genomes, there are approximately double the number of pseudogenes compared with functional genes. An oligonucleotide probe was designed from a conserved sequence from four Atlantic salmon OlfC genes and used to screen the Atlantic salmon bacterial artificial chromosome (BAC) library. Hybridization-positive BACs were matched to fingerprint contigs, and representative BACs were shotgun cloned and sequenced. We identified 55 OlfC genes. Twenty-nine of the OlfC genes are classified as putatively functional genes and 26 as pseudogenes. The OlfC genes are found in two genomic clusters on chromosomes 9 and 20. Phylogenetic analysis revealed that the OlfC genes could be divided into 10 subfamilies, with nine of these subfamilies corresponding to subfamilies found in other teleosts and one being salmon specific. There is also a large expansion in the number of OlfC genes in one subfamily in Atlantic salmon. Subfamily gene expansions have been identified in other teleosts, and these differences in gene number reflect species-specific evolutionary requirements for olfaction. Total RNA was isolated from the olfactory epithelium and other tissues from a presmolt to examine the expression of the odorant genes. Several of the putative OlfC genes that we identified are expressed only in the olfactory epithelium, consistent with these genes encoding odorant receptors.

Integration of growth hormone gene constructs in transgenic strains of coho salmon (Oncorhynchus kisutch) at centromeric or telomeric sites.

Very little information is currently available regarding the sites of integration of transgenes in genetically engineered fish. We examined the chromosomal location of growth hormone gene constructs containing GH1 in three different strains of transgenic coho salmon produced by microinjection into pronuclei of fertilized eggs. The constructs were labeled and used as probes in fluorescence in situ hybridization experiments on chromosome preparations from the M77, MT5750A, and H3D0474 strains of transgenic coho salmon. The constructs were localized at 1-3 different sites in different strains. In the M77 strain the construct was found at a single centromeric site on a medium-sized metacentric chromosome, while in the MT5750A strain, the construct was found at a single telomeric site on the short arm of chromosome pair 21, a subtelocentric chromosome with a large band of repetitive DNA on the short arm. In the H3D0474 strain, the construct was found at telomeric sites on the long arms of three metacentric chromosomes that appear to represent one pair of homologous chromosomes and one chromosome containing the homeologous long arm (recently duplicated chromosome arm) corresponding to the long arm of the first pair. This suggests transfer of the construct may have occurred by homologous and homeologous crossing over. All of the constructs incorporated at restricted sites characterized by the presence of tandem DNA repeats.

Student-Scientist Curriculum: Integrating Inquiry-Based Research Experiences and Professional Development Activities into an Introductory Biology Laboratory Course.

We designed a 16-week scaffolded student-scientist curriculum using inquiry-based research experiences integrated with professional development activities. This curriculum was implemented to teach undergraduate students enrolled in an introduction to biology course about enzyme activity, biochemical reactions, and alcohol fermentation. While working through the curriculum, students completed the entire scientific process by planning experiments, maintaining laboratory journals, analyzing and interpreting data, peer-reviewing research proposals, and producing and presenting a poster. The overall outcome was for students to complete a multiweek, collaborative, student-scientist project using Saccharomyces cerevisiae as the model organism. Student learning outcomes were evaluated using formative assessments (post-Research on the Integrated Science Curriculum survey and peer- and self-reflection worksheets) and summative assessments (pre/post assessments and assignment grades). Results indicated that more than 50% of the students scored 70% or higher on the collaborative student-scientist project, demonstrated several self-reported learning gains in scientific concepts and skills, and reported they would recommend this laboratory course to their peers. By providing the opportunity for students to carry out the entire scientific process, this curriculum enhanced their technical, analytical, and communication skills.

Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss).

BACKGROUND: Most teleost species, especially freshwater groups such as the Esocidae which are the closest relatives of salmonids, have a karyotype comprising 25 pairs of acrocentric chromosomes and 48-52 chromosome arms. After the common ancestor of salmonids underwent a whole genome duplication, its karyotype would have 100 chromosome arms, and this is reflected in the modal range of 96-104 seen in extant salmonids (e.g., rainbow trout). The Atlantic salmon is an exception among the salmonids as it has 72-74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, which appear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon's linkage map and karyotype and to compare the chromosome map with that of rainbow trout. RESULTS: The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in the European subspecies using fluorescence in situ hybridization with BAC probes containing genetic markers mapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomes compared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosome map with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in these species, corresponding to entire chromosome arms in the rainbow trout. CONCLUSION: It had been suggested that some of the large acrocentric chromosomes in Atlantic salmon are the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the arms represent the sites of chromosome fusions. The finding that the chromosomal regions on either side of the blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbow trout chromosome arms provides support for this hypothesis.

Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon).

BACKGROUND: Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12-13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD) in their ancestry (2R duplication). Salmonids have experienced one additional WGD (4R duplication event) compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates. We describe the organization of the 4R chromosomal segments of the proto-ray-finned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes. RESULTS: Evidence is presented for the retention of large whole-arm affinities between the ancestral linkage groups of the ray-finned fishes, and the 50 homeologous chromosomal segments in Atlantic salmon and rainbow trout. In the comparisons between the two salmonid species, there is also evidence for the retention of large whole-arm homeologous affinities that are associated with the retention of duplicated markers. Five of the 7 pairs of chromosomal arm regions expressing the highest level of duplicate gene expression in rainbow trout share homologous synteny to the 5 pairs of homeologs with the greatest duplicate gene expression in Atlantic salmon. These regions are derived from proto-Actinopterygian linkage groups B, C, E, J and K. CONCLUSION: Two chromosome arms in Danio rerio and Oryzias latipes (descendants of the 3R duplication) can, in most instances be related to at least 4 whole or partial chromosomal arms in the salmonid species. Multiple arm assignments in the two salmonid species do not clearly support a 13 proto-linkage group model, and suggest that a 12 proto-linkage group arrangement (i.e., a separate single chromosome duplication and ancestral fusion/fissions/recombination within the putative G/H/I groupings) may have occurred in the more basal soft-rayed fishes. We also found evidence supporting the model that ancestral linkage group M underwent a single chromosome duplication following the 3R duplication. In the salmonids, the M ancestral linkage groups are localized to 5 whole arm, and 3 partial arm regions (i.e., 6 whole arm regions expected). Thus, 3 distinct ancestral linkage groups are postulated to have existed in the G/H and M lineage chromosomes in the ancestor of the salmonids.

Striking antigen recognition diversity in the Atlantic salmon T-cell receptor alpha/delta locus.

The complete TCR alpha/delta locus of Atlantic salmon (Salmo salar) has been characterized and annotated. In the 900 kb TCR alpha/delta locus, 292 Valpha/delta segments and 123 Jalpha/delta segments were identified. Of these, 128 Valpha/delta, 113 Jalpha, and a Jdelta segment appeared to be functional as they lacked frame shifts or stop codons. This represents the largest repertoire of Valpha/delta and Jalpha segments of any organism to date. The 128 functional Valpha/delta segments could be grouped into 29 subgroups based upon 70% nucleotide similarity. Expression data confirmed the usage of the diverse repertoire found at the genomic level. At least 99 Valpha, 13 Vdelta 86 Jalpha, 1 Jdelta, and 2 Ddelta segments were used in TCR alpha or delta transcription, and 652 unique genes were identified from a sample of 759 TCRalpha cDNA clones. Cumulatively, the genomic and expression data suggest that the Atlantic salmon T-cell receptor has enormous capacity to recognize a wide diversity of antigens.

Characterization of a chromosomal rearrangement responsible for producing "apparent" XY-female fall-run Chinook salmon in California.

Fluorescence in situ hybridization (FISH) was used to identify the X and Y chromosomes of offspring produced by normal and "apparent" XY-female fall-run Chinook salmon (Oncorhynchus tshawytscha) from California. FISH experiments were performed using probes to 2 sex-linked loci, growth hormone pseudogene (GH-Psi), and OtY1, as well as a probe to a sex-linked microsatellite (Omy7INRA). Comparison of FISH staining patterns between the offspring produced by normal and apparent XY-females revealed that the apparent XY-female examined transmitted a "Y-like" chromosome with an attenuated OtY1 and GH-Psi signal to half of its offspring. Segregation analysis of microsatellites derived from rainbow trout (Oncorhynchus mykiss) with respect to phenotypic sex was carried out for 2 normal and 2 apparent XY-female Chinook salmon families. Inheritance patterns of Omy7INRA were consistent with this locus being closely linked to GH-Psi in males and in apparent XY-females carrying the Y-like chromosome. Another microsatellite locus (Omm1077) was closely linked to the primary sex-determining locus (SEX) in males but not to GH-Psi/OtY1 in apparent XY-females. The FISH analyses suggest that apparent XY-female fall-run Chinook salmon in California are not the product of a Y chromosome to autosome translocation. Despite the combined FISH and inheritance analyses, we were unable to differentiate between 2 alternative explanations for apparent XY-females, namely, recombination of markers between the sex chromosomes, or a Y chromosome with a dysfunctional or missing sex-determining region.

Technology Applications: Use of Digital Health Technology to Enable Drug Development.

PURPOSE: This pilot study developed and evaluated the feasibility, usability, and perceived satisfaction with an end-user mobile medical application and provider web portal. The two interfaces allowed for remote monitoring, provided daily guidance in the management of hypertension and diarrhea, and allowed for rapid management of adverse events during a clinical trial of olaparib and cediranib. PATIENTS AND METHODS: eCO (eCediranib/Olaparib) was designed for patient self-reported, real-time management of hypertension and diarrhea using remote monitoring. eCO links to a Bluetooth-enabled blood pressure (BP) monitor and transmits data to a secure provider web portal. eCO use was assessed for suitability, usability, and satisfaction after 4 weeks using a 17-item questionnaire. Metrics regarding patient-reported BP and diarrhea events were analyzed. RESULTS: Sixteen patients enrolled in the pilot. A total of 98.2% of expected BP values were reported: 94.2% via Bluetooth and 5.8% entered manually. Twelve patients experienced 21 BP events (systolic BP > 140 and/or diastolic BP > 90 mmHg on two consecutive readings); data from cycle 1 were comparable to the study database. Thirteen patients reported diarrhea (more than one stool per 24 hours over baseline) categorized as grade 1 or 2, which was comparable to the study database. Survey analysis showed that patients had statistically significant, positive responses to the use of the eCO application. Patients indicated eCO use made them feel more involved in their care and better connected to their health care team. The only aspect of the application that did not show a statistically significant positive response was the process of reporting diarrhea. CONCLUSION: The eCO application was designed to assist in managing acute treatment-related events most often associated with treatment discontinuation, need for drug holidays, or dose interruption. Hypertension and diarrhea events reported via eCO allowed rapid provider response and a positive overall patient experience.

Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar).

BACKGROUND: We have previously identified associations between major histocompatibility complex (MHC) class I and resistance towards bacterial and viral pathogens in Atlantic salmon. To evaluate if only MHC or also closely linked genes contributed to the observed resistance we ventured into sequencing of the duplicated MHC class I regions of Atlantic salmon. RESULTS: Nine BACs covering more than 500 kb of the two duplicated MHC class I regions of Atlantic salmon were sequenced and the gene organizations characterized. Both regions contained the proteasome components PSMB8, PSMB9, PSMB9-like and PSMB10 in addition to the transporter for antigen processing TAP2, as well as genes for KIFC1, ZBTB22, DAXX, TAPBP, BRD2, COL11A2, RXRB and SLC39A7. The IA region contained the recently reported MHC class I Sasa-ULA locus residing approximately 50 kb upstream of the major Sasa-UBA locus. The duplicated class IB region contained an MHC class I locus resembling the rainbow trout UCA locus, but although transcribed it was a pseudogene. No other MHC class I-like genes were detected in the two duplicated regions. Two allelic BACs spanning the UBA locus had 99.2% identity over 125 kb, while the IA region showed 82.5% identity over 136 kb to the IB region. The Atlantic salmon IB region had an insert of 220 kb in comparison to the IA region containing three chitin synthase genes. CONCLUSION: We have characterized the gene organization of more than 500 kb of the two duplicated MHC class I regions in Atlantic salmon. Although Atlantic salmon and rainbow trout are closely related, the gene organization of their IB region has undergone extensive gene rearrangements. The Atlantic salmon has only one class I UCA pseudogene in the IB region while trout contains the four MHC UCA, UDA, UEA and UFA class I loci. The large differences in gene content and most likely function of the salmon and trout class IB region clearly argues that sequencing of salmon will not necessarily provide information relevant for trout and vice versa.

Assignment of rainbow trout linkage groups to specific chromosomes.

The rainbow trout genetic linkage groups have been assigned to specific chromosomes in the OSU (2N=60) strain using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group. There was a rough correlation between chromosome size and size of the genetic linkage map in centimorgans for the genetic maps based on recombination from the female parent. Chromosome size and structure have a major impact on the female:male recombination ratio, which is much higher (up to 10:1 near the centromeres) on the larger metacentric chromosomes compared to smaller acrocentric chromosomes. Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location, suggesting that diploidization resulted in substantial divergence of intergenic regions. The BAC clones that hybridized to both duplicate loci were usually located in the distal portion of the chromosome. Duplicate genes were almost always found at a similar location on the chromosome arm of two different chromosome pairs, suggesting that most of the chromosome rearrangements following tetraploidization were centric fusions and did not involve homeologous chromosomes. The set of BACs compiled for this research will be especially useful in construction of genome maps and identification of QTL for important traits in other salmonid fishes.