An emerging consensus in the evolution, phylogeny, and systematics of marsupials and their fossil relatives (Metatheria)

Marsupials and their fossil relatives, which collectively comprise Metatheria, have been of scientific interest for centuries, with many aspects of their evolution and systematics subject to intense research and debate. Here, we review progress over the last 25 years, which has included the description of many new species (modern and fossil), and major improvements in understanding of their phylogenetic relationships, as well as the overall evolutionary history and biogeography of Marsupialia (crown-clade) and Metatheria (total-clade). Significant advances have included the deployment of increasingly sophisticated molecular, morphological, and total evidence analyses, which have resolved most previously disputed relationships among and within the modern marsupial orders. A broad systematic consensus is now emerging, although several major areas of contention remain, particularly among fossil metatherians. New modern species continue to be described at an impressive rate, with almost 50 named in the last 25 years, and many more await discovery. There has also been an explosion in the discovery and description of fossil marsupials and non-marsupial metatherians (~270 species), principally from Australasia and the Americas but also from Antarctica, Europe, and Asia. Most are represented by dental specimens only, but some consist of complete and well-preserved material, which has led to major improvements in our understanding of the evolution of cranial and postcranial morphology. Improvements in the fossil record and advances in methods for inferring divergence times have helped clarify when and where key events occurred in metatherian evolution, and the patterns of subclade diversification. We also have improved understanding of biogeographical relationships among metatherians on different landmasses. Despite enormous progress, numerous key uncertainties remain due to major gaps in the fossil record (e.g., Antarctica, Late Cretaceous, and early Paleogene of Australia) and a comparative lack of studies that directly combine molecular and fossil data. Future advances will largely depend on improvements in the fossil record and studies that better integrate neontological and paleontological evidence

Stage-Specific Inhibition of MHC Class I Presentation by the Epstein-Barr Virus BNLF2a Protein during Virus Lytic Cycle

gamma-herpesvirus Epstein-Barr virus (EBV) persists for life in infected individuals despite the presence of a strong immune response. During the lytic cycle of EBV many viral proteins are expressed, potentially allowing virally infected cells to be recognized and eliminated by CD8+ T cells. We have recently identified an immune evasion protein encoded by EBV, BNLF2a, which is expressed in early phase lytic replication and inhibits peptide- and ATP-binding functions of the transporter associated with antigen processing. Ectopic expression of BNLF2a causes decreased surface MHC class I expression and inhibits the presentation of indicator antigens to CD8+ T cells. Here we sought to examine the influence of BNLF2a when expressed naturally during EBV lytic replication. We generated a BNLF2a-deleted recombinant EBV (ΔBNLF2a) and compared the ability of ΔBNLF2a and wild-type EBV-transformed B cell lines to be recognized by CD8+ T cell clones specific for EBV-encoded immediate early, early and late lytic antigens. Epitopes derived from immediate early and early expressed proteins were better recognized when presented by ΔBNLF2a transformed cells compared to wild-type virus transformants. However, recognition of late antigens by CD8+ T cells remained equally poor when presented by both wild-type and ΔBNLF2a cell targets. Analysis of BNLF2a and target protein expression kinetics showed that although BNLF2a is expressed during early phase replication, it is expressed at a time when there is an upregulation of immediate early proteins and initiation of early protein synthesis. Interestingly, BNLF2a protein expression was found to be lost by late lytic cycle yet ΔBNLF2a-transformed cells in late stage replication downregulated surface MHC class I to a similar extent as wild-type EBV-transformed cells. These data show that BNLF2a-mediated expression is stage-specific, affecting presentation of immediate early and early proteins, and that other evasion mechanisms operate later in the lytic cycle

The method of educational assessment affects children’s neural processing and performance: behavioural and fMRI Evidence.

Standardised educational assessments are now widespread, yet their development has given comparatively more consideration to what to assess than how to optimally assess students’ competencies. Existing evidence from behavioural studies with children and neuroscience studies with adults suggest that the method of assessment may affect neural processing and performance, but current evidence remains limited. To investigate the impact of assessment methods on neural processing and performance in young children, we used functional magnetic resonance imaging to identify and quantify the neural correlates during performance across a range of current approaches to standardised spelling assessment. Results indicated that children’s test performance declined as the cognitive load of assessment method increased. Activation of neural nodes associated with working memory further suggests that this performance decline may be a consequence of a higher cognitive load, rather than the complexity of the content. These findings provide insights into principles of assessment (re)design, to ensure assessment results are an accurate reflection of students’ true levels of competency

Advancing Drug Innovation for Neglected Diseases—Criteria for Lead Progression

The current drug R&D pipeline for most neglected diseases remains weak, and unlikely to support registration of novel drug classes that meet desired target product profiles in the short term. This calls for sustained investment as well as greater emphasis in the risky upstream drug discovery. Access to technologies, resources, and strong management as well as clear compound progression criteria are factors in the successful implementation of any collaborative drug discovery effort. We discuss how some of these factors have impacted drug discovery for tropical diseases within the past four decades, and highlight new opportunities and challenges through the virtual North–South drug discovery network as well as the rationale for greater participation of institutions in developing countries in product innovation. A set of criteria designed to facilitate compound progression from screening hits to drug candidate selection is presented to guide ongoing efforts

Antimonial Resistance in Leishmania donovani Is Associated with Increased In Vivo Parasite Burden

Leishmania donovani is an intracellular protozoan parasite that causes visceral leishmaniasis (VL). Antimonials (SSG) have long been the first-line treatment against VL, but have now been replaced by miltefosine (MIL) in the Indian subcontinent due to the emergence of SSG-resistance. Our previous study hypothesised that SSG-resistant L. donovani might have increased in vivo survival skills which could affect the efficacy of other treatments such as MIL. The present study attempts to validate these hypotheses. Fourteen strains derived from Nepalese clinical isolates with documented SSG-susceptibility were infected in BALB/c mice to study their survival capacity in drug free conditions (non-treated mice) and in MIL-treated mice. SSG-resistant parasites caused a significant higher in vivo parasite load compared to SSG-sensitive parasites. However, this did not seem to affect the strains' response to MIL-treatment since parasites from both phenotypes responded equally well to in vivo MIL exposure. We conclude that there is a positive association between SSG-resistance and in vivo survival skills in our sample of L. donovani strains which could suggest a higher virulence of SSG-R strains compared to SSG-S strains. These greater in vivo survival skills of SSG-R parasites do not seem to directly affect their susceptibility to MIL. However, it cannot be excluded that repeated MIL exposure will elicit different adaptations in these SSG-R parasites with superior survival skills compared to the SSG-S parasites. Our results therefore highlight the need to closely monitor drug efficacy in the field, especially in the context of the Kala-azar elimination programme ongoing in the Indian subcontinent

A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

BACKGROUND: An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing only occurs under specific biological conditions. Non-expression based computational methods support identification of rarely expressed transcripts. RESULTS: A non-expression based statistical method is presented to annotate alternatively spliced exons using a single genome sequence and evidence from cross-species sequence conservation. The computational method is implemented in the program ExAlt and an analysis of prediction accuracy is given for Drosophila melanogaster. CONCLUSION: ExAlt identifies the structure of most alternatively spliced exons in the test set and cross-species sequence conservation is shown to improve the precision of predictions. The software package is available to run on Drosophila genomes to search for new cases of alternative splicing

The Murchison Widefield Array Transients Survey (MWATS). A search for low-frequency variability in a bright Southern hemisphere sample

We report on a search for low-frequency radio variability in 944 bright (>4 Jy at 154 MHz) unresolved, extragalactic radio sources monitored monthly for several years with the Murchison Widefield Array. In the majority of sources, we find very low levels of variability with typical modulation indices 2.8 yr) with time-averaged modulation indices M¯¯¯¯¯=3.1−7.1M¯=3.1−7.1 per cent. With 7/15 of these variable sources having peaked spectral energy distributions, and only 5.7 per cent of the overall sample having peaked spectra, we find an increase in the prevalence of variability in this spectral class. We conclude that the variability seen in this survey is most probably a consequence of refractive interstellar scintillation and that these objects must have the majority of their flux density contained within angular diameters less than 50 milliarcsec (which we support with multiwavelength data). At 154 MHz, we demonstrate that interstellar scintillation time-scales become long (∼decades) and have low modulation indices, while synchrotron-driven variability can only produce dynamic changes on time-scales of hundreds of years, with flux density changes less than one milli-jansky (without relativistic boosting). From this work, we infer that the low-frequency extragalactic southern sky, as seen by SKA-Low, will be non-variable on time-scales shorter than 1 yr

The association between hip fracture and hip osteoarthritis: A case-control study

<p>Abstract</p> <p>Background</p> <p>There have been reports both supporting and refuting an inverse relationship between hip fracture and hip osteoarthritis (OA). We explore this relationship using a case-control study design.</p> <p>Methods</p> <p>Exclusion criteria were previous hip fracture (same side or contralateral side), age younger than 60 years, foreign nationality, pathological fracture, rheumatoid arthritis and cases were radiographic examinations were not found in the archives. We studied all subjects with hip fracture that remained after the exclusion process that were treated at Akureyri University Hospital, Iceland 1990-2008, n = 562 (74% women). Hip fracture cases were compared with a cohort of subjects with colon radiographs, n = 803 (54% women) to determine expected population prevalence of hip OA. Presence of radiographic hip OA was defined as a minimum joint space of 2.5 mm or less on an anteroposterior radiograph, or Kellgren and Lawrence grade 2 or higher. Possible causes of secondary osteoporosis were identified by review of medical records.</p> <p>Results</p> <p>The age-adjusted odds ratio (OR) for subjects with hip fracture having radiographic hip OA was 0.30 (95% confidence interval [95% CI] 0.12-0.74) for men and 0.33 (95% CI 0.19-0.58) for women, compared to controls. The probability for subjects with hip fracture and hip OA having a secondary cause of osteoporosis was three times higher than for subjects with hip fracture without hip OA.</p> <p>Conclusion</p> <p>The results of our study support an inverse relationship between hip fractures and hip OA.</p

Range of shoulder motion in patients with adhesive capsulitis; Intra-tester reproducibility is acceptable for group comparisons

<p>Abstract</p> <p>Background</p> <p>Measurements of range of motion play a key role in shoulder research. The purpose of this study is to investigate intra-observer reproducibility of measurements of active and passive range of motion in patients with adhesive capsulitis.</p> <p>Methods</p> <p>The study was carried out in a population consisting of 32 patients with clinical signs of adhesive capsulitis. A specified measurement protocol was used, and range of motion in affected and non-affected shoulders was measured twice for each patient with a one-week interval.</p> <p>Results</p> <p>For most of the investigated individual movements, test-retest differences in range of motion score of more than approximately 15° are not likely to occur as a result of measurement error only. Point-estimates for the intraclass correlation coefficient ranged from 0.61 to 0.93.</p> <p>Conclusion</p> <p>Range of motion of patients with adhesive capsulitis can be measured with acceptable reproducibility in settings where groups are compared. Scores for individual patients should be interpreted with caution.</p

Changes in chromatin structure during processing of wax-embedded tissue sections

The use of immunofluorescence (IF) and fluorescence in situ hybridisation (FISH) underpins much of our understanding of how chromatin is organised in the nucleus. However, there has only recently been an appreciation that these types of study need to move away from cells grown in culture and towards an investigation of nuclear organisation in cells in situ in their normal tissue architecture. Such analyses, however, especially of archival clinical samples, often requires use of formalin-fixed paraffin wax-embedded tissue sections which need addition steps of processing prior to IF or FISH. Here we quantify the changes in nuclear and chromatin structure that may be caused by these additional processing steps. Treatments, especially the microwaving to reverse fixation, do significantly alter nuclear architecture and chromatin texture, and these must be considered when inferring the original organisation of the nucleus from data collected from wax-embedded tissue sections