Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby

Background: The thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have multiple thymuses. The tammar wallaby has two thymuses: a thoracic thymus (typically found in all mammals) and a dominant cervical thymus. Researchers have known about the presence of the two wallaby thymuses since the 1800s, but no genome-wide research has been carried out into possible functional differences between the two thymic tissues. Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby.Results: We show that both the tammar thoracic and the cervical thymuses displayed gene expression profiles consistent with roles in T-cell development. Both thymuses expressed genes that mediate distinct phases of T-cells differentiation, including the initial commitment of blood stem cells to the T-lineage, the generation of T-cell receptor diversity and development of thymic epithelial cells. Crucial immune genes, such as chemokines were also present. Comparable patterns of expression of non-coding RNAs were seen. 67 genes differentially expressed between the two thymuses were detected, and the possible significance of these results are discussed.Conclusion: This is the first study comparing the transcriptomes of two thymuses from a single individual. Our finding supports that both thymuses are functionally equivalent and drive T-cell development. These results are an important first step in the understanding of the genetic processes that govern marsupial immunity, and also allow us to begin to trace the evolution of the mammalian immune system

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Intermittent Intense Turbulent Mixing under Ice in the Laptev Sea Continental Shelf

Vertical mixing in the bottom boundary layer and pycnocline of the Laptev Sea is evaluated from a rapidly sampled 12-h time series of microstructure temperature, conductivity, and shear observations collected under 100% sea ice during October 2008. The bottom boundary turbulent kinetic energy dissipation was observed to be enhanced (? 10?4 W m?3) beyond background levels (? 10?6 W m?3), extending up to 10 m above the seabed when simulated tidal currents were directed on slope. Upward heat fluxes into the halocline-class waters along the Laptev Sea seabed peaked at 4–8 W m?2, averaging out to 2 W m?2 over the 12-h sampling period. In the Laptev Sea pycnocline, an isolated 2-h episode of intense dissipation (? 10?3 W m?3) and vertical diffusivities was observed that was not due to a localized wind event. Observations from an acoustic Doppler current meter moored in the central Laptev Sea near the M2 critical latitude are consistent with a previous model in which mixing episodes are driven by an enhancement of the pycnocline shear resulting from the alignment of the rotating pycnocline shear vector with the under-ice stress vector. Upward cross-pycnocline heat fluxes from the Arctic halocline peaked at 54 W m?2, resulting in a 12-h average of 12 W m?2. These results highlight the intermittent nature of Arctic shelf sea mixing processes and how these processes can impact the transformation of Arctic Ocean water masses. The observations also clearly demonstrate that absence or presence of sea ice profoundly affects the availability of near-inertial kinetic energy to drive vertical mixing on the Arctic shelves

The GOGREEN and GCLASS surveys : first data release

We present the first public data release of the GOGREEN (Gemini Observations of Galaxies in Rich Early Environments) and GCLASS (Gemini CLuster Astrophysics Spectroscopic Survey) surveys of galaxies in dense environments, spanning a redshift range 0.8 <z <1.5. The surveys consist of deep, multiwavelength photometry and extensive Gemini GMOS spectroscopy of galaxies in 26 overdense systems ranging in halo mass from small groups to the most massive clusters. The objective of both projects was primarily to understand how the evolution of galaxies is affected by their environment, and to determine the physical processes that lead to the quenching of star formation. There was an emphasis on obtaining unbiased spectroscopy over a wide stellar mass range (M greater than or similar to 2 x 10(10) M-circle dot), throughout and beyond the cluster virialized regions. The final spectroscopic sample includes 2771 unique objects, of which 2257 have reliable spectroscopic redshifts. Of these, 1704 have redshifts in the range 0.8 <z <1.5, and nearly 800 are confirmed cluster members. Imaging spans the full optical and near-infrared wavelength range, at depths comparable to the UltraVISTA survey, and includes Hubble Space Telescope/Wide Field Camera 3 F160W (GOGREEN) and F140W (GCLASS). This data release includes fully reduced images and spectra, with catalogues of advanced data products including redshifts, line strengths, star formation rates, stellar masses, and rest-frame colours. Here, we present an overview of the data, including an analysis of the spectroscopic completeness and redshift quality.Peer reviewe

Genome Sequence of the Brown Norway Rat Yields Insights Into Mammalian Evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution