The in vacuo release of Ar from minerals: 2. The role of structural modifications of K-feldspar during heating revealed by Raman microprobe analyses

The release of Ar during stepwise heating 39Ar-40Ar dating experiments may be controlled by Fick's Law diffusion in an inert matrix, and/or by structural modifications of the host mineral. A ca. 1 mm3 irradiated cleavage fragment of a low sanidine crystal from Itrongay, Madagascar was degassed isothermally at 888 ± 2 °C for 264 h, acquiring 67 stepwise 39Ar release data. The 39Ar release was observed to follow a smooth sigmoid curve and not a line as would be predicted by Fick's Law. If the 39Ar release is controlled by crystallographic changes, the implication is that these changes undergo time-dependent variations. The long-term bulk degassing, being the sum of various structural modifications, approximates a Fickian behavior that is not verified in detail in short-term experiments, as it averages over different 39Ar release regimes. This would make the downslope extrapolation of laboratory data to geological conditions highly underconstrained. In order to constrain the behavior of the crystal structure of K-feldspar during laboratory heating, we measured the Raman spectra of a different, ca. 1 mm3 cleavage fragment of the same irradiated sanidine crystal. The sample was heated in air in a Linkam heating stage, and Raman spectra were acquired at temperatures increasing from 300 to 1000 °C, including a 6-hour isothermal run at 900 ± 1 °C. Raman modes between 50 and 1200 cm-1 were observed to record two kinds of change, defining robust trends. The positions of most peaks were shifted towards lower wavenumbers (lower energies) and broadened; in addition, the relative heights of different peaks showed robust variation trends. The larger changes coincide with discrete temperature increases, but all changes also progressed over time at constant temperature. These peaks mirror the excitation of phonon modes, which are associated with interatomic bond stretching and deformation, with Si,Al ordering and with deformation and rotation of SiO2 tetrahedra. Most, but by far not all, of the change is reversible (such as e.g. the differential activation of phonon modes), but irreversible structure modifications (such as e.g. Al,Si disordering) are also recorded. We conclude that the K-feldspar structure violates mathematical requirements of matrix inertness during laboratory heating

Sex trafficking : an exploration of clinician perspectives of the type and efficacy of treatment interventions

This qualitative study investigates clinician perspectives on the type of clinical interventions used in therapy with sex trafficking survivors. Due to the absence of systematic evaluation of mental health treatment for this population, the limited current research recommends interventions that are used for victims of domestic violence and sexual assault. This study\u27s main research question is: what are the perspectives of clinicians who provide therapy for trafficking survivors on the type and usefulness of their treatment interventions? This study interviewed 11 clinicians who provided therapy for sex trafficking survivors. The major findings of this study show that the most commonly used interventions were trauma informed care and cognitive behavioral therapy. Overall, participants used similar interventions with sex trafficked clients as with domestic violence and sexual assault clients. The clinicians interviewed reported that the interventions helped sex trafficking survivors improve self-concept, increase self-awareness, make healthy connections, and develop life skills. Further research needs to be conducted to systematically evaluate the effectiveness of these interventions

A Large Volume Multi-Anvil Apparatus for the Earth Sciences Community in Taiwan

A modified DIA type multi-anvil apparatus was installed in the Department of Earth Sciences, National Cheng Kung University, Taiwan. This modified DIA multi-anvil system is used with a hydraulic press that generates loads of up to 1000 tons and is the first multi-anvil press installed for geoscience research in Taiwan. In this paper, the geometry of the high-pressure apparatus is briefly described and the pressure calibration performed in the press is reported. The thermal behaviors of various pressure mediums, boron-epoxy, zirconia, and mullite, are also compared. Pressure calibrations at room temperature were performed with different cell designs, paying special attention to the so called ¡§D¡¨ factor, which is defined as the ratio of diagonal length of the cell assembly cube to the diameter of the cavity hole. For a given cell design, the sample-pressure efficiency for the three materials examined was similar. Calibrations with different cell designs showed that increasing the ¡§D¡¨ value results in greater pressure generation efficiency. By comparing the deformation behavior at high temperatures (up to 1200°C), the semi-sintered mullite and zirconia appeared to be better pressure mediums compared to boron-epoxy

Skeletal disproportion in glucocorticoid-treated boys with Duchenne muscular dystrophy

We aimed to compare body segment and bone lengths in glucocorticoid-treated boys with Duchenne muscular dystrophy (DMD) with healthy controls using dual-energy absorptiometry (DXA) images. Total height (Ht), sitting height (SH), leg length (LL) and bone lengths (femur, tibia) in boys with DMD and age-matched control boys were measured using DXA. Thirty boys with DMD (median age 10.0 years (6.1, 16.8)) were compared with 30 controls. SH in DMD was 3.3 cm lower (95% CI − 6.1, − 0.66; p = 0.016). LL in DMD was 7.3 cm lower (95% CI − 11.2, − 3.4; p < 0.0001). SH:LL of boys with DMD was higher by 0.08 (95% CI 0.04, 0.12; p < 0.0001). Femur length in DMD was 2.4 cm lower (95% CI − 4.6, − 0.12; p = 0.04), whereas tibial length in DMD was 4.8 cm lower (95% CI − 6.7, − 2.9; p < 0.0001). SH:LL was not associated with duration of glucocorticoid use (SH:LL β = 0.003, 95% CI − 0.01 to 0.002, p = 0.72). Conclusion: Glucocorticoid-treated boys with DMD exhibit skeletal disproportion with relatively shorter leg length and more marked reduction of distal long bones. As glucocorticoid excess is not associated with such disproportion, our findings raise the possibility of an intrinsic disorder of growth in DMD

Australian bat lyssavirus infection in two horses

In May 2013, the first cases of Australian bat lyssavirus infections in domestic animals were identified in Australia. Two horses (filly-H1 and gelding-H2) were infected with the Yellow-bellied sheathtail bat (YBST) variant of Australian bat lyssavirus (ABLV). The horses presented with neurological signs, pyrexia and progressing ataxia. Intra-cytoplasmic inclusion bodies (Negri bodies) were detected in some Purkinje neurons in haematoxylin and eosin (H&E) stained sections from the brain of one of the two infected horses (H2) by histological examination. A morphological diagnosis of sub-acute moderate non-suppurative, predominantly angiocentric, meningo-encephalomyelitis of viral aetiology was made. The presumptive diagnosis of ABLV infection was confirmed by the positive testing of the affected brain tissue from (H2) in a range of laboratory tests including fluorescent antibody test (FAT) and real-time PCR targeting the nucleocapsid (N) gene. Retrospective testing of the oral swab from (H1) in the real-time PCR also returned a positive result. The FAT and immunohistochemistry (IHC) revealed an abundance of ABLV antigen throughout the examined brain sections. ABLV was isolated from the brain (H2) and oral swab/saliva (H1) in the neuroblastoma cell line (MNA). Alignment of the genome sequence revealed a 97.7% identity with the YBST ABLV strain

Sec24p and Sec16p cooperate to regulate the GTP cycle of the COPII coat

Vesicle budding from the endoplasmic reticulum (ER) employs a cycle of GTP binding and hydrolysis to regulate assembly of the COPII coat. We have identified a novel mutation (sec24‐m11) in the cargo‐binding subunit, Sec24p, that specifically impacts the GTP‐dependent generation of vesicles in vitro. Using a high‐throughput approach, we defined genetic interactions between sec24‐m11 and a variety of trafficking components of the early secretory pathway, including the candidate COPII regulators, Sed4p and Sec16p. We defined a fragment of Sec16p that markedly inhibits the Sec23p‐ and Sec31p‐stimulated GTPase activity of Sar1p, and demonstrated that the Sec24p‐m11 mutation diminished this inhibitory activity, likely by perturbing the interaction of Sec24p with Sec16p. The consequence of the heightened GTPase activity when Sec24p‐m11 is present is the generation of smaller vesicles, leading to accumulation of ER membranes and more stable ER exit sites. We propose that association of Sec24p with Sec16p creates a novel regulatory complex that retards the GTPase activity of the COPII coat to prevent premature vesicle scission, pointing to a fundamental role for GTP hydrolysis in vesicle release rather than in coat assembly/disassembly

GENCODE: producing a reference annotation for ENCODE

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation

Identifying Hendra Virus Diversity in Pteropid Bats

Hendra virus (HeV) causes a zoonotic disease with high mortality that is transmitted to humans from bats of the genus Pteropus (flying foxes) via an intermediary equine host. Factors promoting spillover from bats to horses are uncertain at this time, but plausibly encompass host and/or agent and/or environmental factors. There is a lack of HeV sequence information derived from the natural bat host, as previously sequences have only been obtained from horses or humans following spillover events. In order to obtain an insight into possible variants of HeV circulating in flying foxes, collection of urine was undertaken in multiple flying fox roosts in Queensland, Australia. HeV was found to be geographically widespread in flying foxes with a number of HeV variants circulating at the one time at multiple locations, while at times the same variant was found circulating at disparate locations. Sequence diversity within variants allowed differentiation on the basis of nucleotide changes, and hypervariable regions in the genome were identified that could be used to differentiate circulating variants. Further, during the study, HeV was isolated from the urine of flying foxes on four occasions from three different locations. The data indicates that spillover events do not correlate with particular HeV isolates, suggesting that host and/or environmental factors are the primary determinants of bat-horse spillover. Thus future spillover events are likely to occur, and there is an on-going need for effective risk management strategies for both human and animal health

The role of Havana and communities in the manual curation of unfinished vertebrate genomes

Manual annotation‭ (‬the‭ "‬museum‭" ‬model of annotation‭) ‬relies on a small group of specialized curators to catalogue and classify genes according to their functional roles.‭ This‬ is both costly and time consuming and therefore is used only for model organisms with sufficient funding.‭ ‬Smaller research communities often have to rely on other models of annotation,‭ ‬mainly automated annotation‭ (‬the‭ "‬factory‭" ‬model,‭ ‬e.g.‭ ‬Ensembl‭)‬,‭ ‬and the‭ "‬jamboree‭" ‬model‭ (‬in which a group of leading biologists from the community and bioinformaticians come together for a short intensive annotation workshop‭)‬.‭ ‬At the Wellcome Trust Sanger Institute‭ (‬WTSI‭)‬,‭ ‬the Havana team provides high quality manual annotation of finished vertebrate genome sequences,‭ ‬namely human,‭ ‬mouse and zebrafish.‭ ‬We also perform the curation of specific finished regions such as the MHC in dog,‭ ‬cow and pig,‭ ‬whose whole genomes have been‭ ‬assembled from unfinished BACs or from whole genome shotgun sequences.‭ ‬In addition,‭ ‬we at Havana have also hosted annotation jamborees for the cow‭ (‬Bos taurus‭) ‬and pig‭ (‬Sus scrofa‭) ‬genomes.‭ ‬During those sessions,‭ ‬the research community had the opportunity to annotate their genes of interest under expert guidance using the custom written publicly available Otterlace annotation system,‭ ‬and the unified manual annotation guidelines.‭ ‬By making use of the tools and skills acquired during the cow and pig jamborees,‭ ‬the delegates can continue annotating their genomes remotely.‭ ‬For the pig genome,‭ ‬a highly contiguous physical map has been generated by an international effort of four laboratories (available in Pre!Ensembl) and‭ ‬is being used as a substrate for the swine genome sequencing project.‭ ‬Upcoming vertebrate genomes will be sequenced to a high depth coverage with the next generation sequencing technologies‭ (‬e.g.‭ ‬Illumina,‭ ‬454,‭ ‬SOLiD‭) ‬but will have the drawback of not being manually finished.‭ ‬Manual annotation will be more accurate than the automated predictions at coping with any assembly problems derived from these high coverage but unfinished‭ (‬or automatic pre-finished‭) ‬genomes.‭ ‬Once these inherent assembly errors are corrected and the gene structures are accurately identified with manual annotation,‭ ‬the curated genes will be incorporated and merged with the predicted gene models in Ensembl to provide a unified view of the landscape of vertebrate genomes.‭ ‬I will present an introduction to our manual annotation system and our experience using it for annotation jamborees at the WTSI

Protein kinetics of superoxide dismutase-1 in familial and sporadic amyotrophic lateral sclerosis

OBJECTIVE: Accumulation of misfolded superoxide dismutase-1 (SOD1) is a pathological hallmark of SOD1-related amyotrophic lateral sclerosis (ALS) and is observed in sporadic ALS where its role in pathogenesis is controversial. Understanding in vivo protein kinetics may clarify how SOD1 influences neurodegeneration and inform optimal dosing for therapies that lower SOD1 transcripts. METHODS: We employed stable isotope labeling paired with mass spectrometry to evaluate in vivo protein kinetics and concentration of soluble SOD1 in cerebrospinal fluid (CSF) of SOD1 mutation carriers, sporadic ALS participants and controls. A deaminated SOD1 peptide, SDGPVKV, that correlates with protein stability was also measured. RESULTS: In participants with heterozygous SOD1 INTERPRETATION: These results highlight the ability of stable isotope labeling approaches and peptide deamidation to discern the influence of disease mutations on protein kinetics and stability and support implementation of this method to optimize clinical trial design of gene and molecular therapies for neurological disorders. TRIAL REGISTRATION: Clinicaltrials.gov: NCT03449212