Routes for breaching and protecting genetic privacy

We are entering the era of ubiquitous genetic information for research, clinical care, and personal curiosity. Sharing these datasets is vital for rapid progress in understanding the genetic basis of human diseases. However, one growing concern is the ability to protect the genetic privacy of the data originators. Here, we technically map threats to genetic privacy and discuss potential mitigation strategies for privacy-preserving dissemination of genetic data.Comment: Draft for comment

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Housing system and herd size interactions in Norwegian dairy herds; associations with performance and disease incidence

<p>Abstract</p> <p>Background</p> <p>According to the Norwegian animal welfare regulations, it has been forbidden to build new tie-stall barns since the end of 2004. Previous studies have shown that cow performance and health differ between housing systems. The interaction between housing system and herd size with respect to performance and disease incidence has not been evaluated.</p> <p>Methods</p> <p>Cow performance and health in 620 herds housed in free-stall barns were compared with in 192 herds housed in tie-stall barns based on a mail survey and data from the Norwegian Dairy Herd Recording and Cattle Health Systems. The housing systems herds were comparable with respect to herd size (15-55 cows). Associations between performance/disease incidence and housing system, herd size and year of building the cow barn were tested in general linear models, and values for fixed herd size of 20 and 50 cows were calculated. On the individual cow level mixed models were run to test the effect of among others housing system and herd size on test-day milk yield, and to evaluate lactation curves in different parities. All cows were of the Norwegian Red Breed.</p> <p>Results</p> <p>Average milk production per cow-year was 134 kg lower in free-stall herd than in tie-stall herds, but in the range 27-45 cows there was no significant difference in yields between the herd categories. In herds with less than 27 cows there were increasingly lower yields in free-stalls, particularly in first parity, whereas the yields were increasingly higher in free-stalls with more than 45 cows.</p> <p>In free-stalls fertility was better, calving interval shorter, and the incidence rate of teat injuries, ketosis, indigestions, anoestrus and cystic ovaries was lower than in tie-stalls. All of these factors were more favourable in estimated 50-cow herds as compared to 20-cow herds. In the larger herd category, bulk milk somatic cell counts were higher, and the incidence rate of mastitis (all cases) and all diseases was lower.</p> <p>Conclusion</p> <p>This study has shown that there is an interaction between housing system and herd size, and that performance and health is not universally better in small free-stalls than in tie-stalls.</p

Personality preference influences medical student use of specific computer-aided instruction (CAI)

BACKGROUND: The objective of this study was to test the hypothesis that personality preference, which can be related to learning style, influences individual utilization of CAI applications developed specifically for the undergraduate medical curriculum. METHODS: Personality preferences of students were obtained using the Myers-Briggs Type Indicator (MBTI) test. CAI utilization for individual students was collected from entry logs for two different web-based applications (a discussion forum and a tutorial) used in the basic science course on human anatomy. Individual login data were sorted by personality preference and the data statistically analyzed by 2-way mixed ANOVA and correlation. RESULTS: There was a wide discrepancy in the level and pattern of student use of both CAI. Although individual use of both CAI was positively correlated irrespective of MBTI preference, students with a "Sensing" preference tended to use both CAI applications more than the "iNtuitives". Differences in the level of use of these CAI applications (i.e., higher use of discussion forum vs. a tutorial) were also found for the "Perceiving/Judging" dimension. CONCLUSION: We conclude that personality/learning preferences of individual students influence their use of CAI in the medical curriculum

Measurements of neutrino oscillation in appearance and disappearance channels by the T2K experiment with 6.6 x 10(20) protons on target

111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee comments111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee comments111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee commentsWe thank the J-PARC staff for superb accelerator performance and the CERN NA61/SHINE Collaboration for providing valuable particle production data. We acknowledge the support of MEXT, Japan; NSERC, NRC, and CFI, Canada; CEA and CNRS/IN2P3, France; DFG, Germany; INFN, Italy; National Science Centre (NCN), Poland; RSF, RFBR and MES, Russia; MINECO and ERDF funds, Spain; SNSF and SER, Switzerland; STFC, UK; and the U. S. Deparment of Energy, USA. We also thank CERN for the UA1/NOMAD magnet, DESY for the HERA-B magnet mover system, NII for SINET4, the WestGrid and SciNet consortia in Compute Canada, GridPP, UK, and the Emerald High Performance Computing facility in the Centre for Innovation, UK. In addition, participation of individual researchers and institutions has been further supported by funds from ERC (FP7), EU; JSPS, Japan; Royal Society, UK; and DOE Early Career program, USA

Measurement of the electron neutrino charged-current interaction rate on water with the T2K ND280 pi(0) detector

10 pages, 6 figures, Submitted to PRDhttp://journals.aps.org/prd/abstract/10.1103/PhysRevD.91.112010© 2015 American Physical Society11 pages, 6 figures, as accepted to PRD11 pages, 6 figures, as accepted to PRD11 pages, 6 figures, as accepted to PR

Antibiotics Threaten Wildlife: Circulating Quinolone Residues and Disease in Avian Scavengers

Antibiotic residues that may be present in carcasses of medicated livestock could pass to and greatly reduce scavenger wildlife populations. We surveyed residues of the quinolones enrofloxacin and its metabolite ciprofloxacin and other antibiotics (amoxicillin and oxytetracycline) in nestling griffon Gyps fulvus, cinereous Aegypius monachus and Egyptian Neophron percnopterus vultures in central Spain. We found high concentrations of antibiotics in the plasma of many nestling cinereous (57%) and Egyptian (40%) vultures. Enrofloxacin and ciprofloxacin were also found in liver samples of all dead cinereous vultures. This is the first report of antibiotic residues in wildlife. We also provide evidence of a direct association between antibiotic residues, primarily quinolones, and severe disease due to bacterial and fungal pathogens. Our results indicate that, by damaging the liver and kidney and through the acquisition and proliferation of pathogens associated with the depletion of lymphoid organs, continuous exposure to antibiotics could increase mortality rates, at least in cinereous vultures. If antibiotics ingested with livestock carrion are clearly implicated in the decline of the vultures in central Spain then it should be considered a primary concern for conservation of their populations

High catechin concentrations detected in Withania somnifera (ashwagandha) by high performance liquid chromatography analysis

<p>Abstract</p> <p>Background</p> <p><it>Withania somnifera </it>is an important medicinal plant traditionally used in the treatment of many diseases. The present study was carried out to characterize the phenolic acids, flavonoids and 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) scavenging activities in methanolic extracts of <it>W. somnifera </it>fruits, roots and leaves (WSFEt, WSREt and WSLEt).</p> <p>Methods</p> <p>WSFEt, WSREt and WSLEt was prepared by using 80% aqueous methanol and total polyphenols, flavonoids as well as DPPH radical scavenging activities were determined by spectrophotometric methods and phenolic acid profiles were determined by HPLC methods.</p> <p>Results</p> <p>High concentrations of both phenolics and flavonoids were detected in all parts of the plant with the former ranging between 17.80 ± 5.80 and 32.58 ± 3.16 mg/g (dry weight) and the latter ranging between 15.49 ± 1.02 and 31.58 ± 5.07 mg/g. All of the three different plant parts showed strong DPPH radical scavenging activities (59.16 ± 1.20 to 91.84 ± 0.38%). Eight polyphenols (gallic, syringic, benzoic, p-coumaric and vanillic acids as well as catechin, kaempferol and naringenin) have been identified by HPLC in parts of the plant as well. Among all the polyphenols, catechin was detected in the highest concentration (13.01 ± 8.93 to 30.61 ± 11.41 mg/g).</p> <p>Conclusion</p> <p>The results indicating that <it>W. somnifera </it>is a plant with strong therapeutic properties thus further supporting its traditional claims. All major parts of <it>W. somnifera </it>such as the roots, fruits and leaves provide potential benefits for human health because of its high content of polyphenols and antioxidant activities with the leaves containing the highest amounts of polyphenols specially catechin with strong antioxidant properties.</p

Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts.

A small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses ($\textit{Rhabdoviridae}$). Here, we report that sigma viruses that infect Mediterranean fruit flies ($\textit{Ceratitis capitata}$), $\textit{Drosophila}$ immigrans, and speckled wood butterflies ($\textit{Pararge aegeria}$) are all vertically transmitted. We find patterns of vertical transmission that are consistent with those seen in $\textit{Drosophila}$ sigma viruses, with high rates of maternal transmission, and lower rates of paternal transmission. This mode of transmission allows them to spread rapidly in populations, and using viral sequence data we found the viruses in $\textit{D. immigrans}$ and $\textit{C. capitata}$ had both recently swept through host populations. The viruses were common in nature, with mean prevalences of 12% in $\textit{C. capitata}$, 38% in $\textit{D. immigrans}$ and 74% in $\textit{P. aegeria}$. We conclude that vertically transmitted rhabdoviruses may be widespread in a broad range of insect taxa, and that these viruses can have dynamic interactions with their hosts.B.L. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant no. 109356/Z/15/Z). B.L. and F.M.J. are supported by an NERC grant no. (NE/L004232/1 http://www.nerc.ac.uk/) and by an ERC grant (281668, DrosophilaInfection, http://erc.europa.eu/). P.T.L., T.C. and L.A.F. are supported by a BBSRC grant no. (BB/K000489/1)