Climate change,mean sea levels,wetland decline and the survival of the critically endangered Capricorn Yellow Chat

An isolated population of ~30 Capricorn Yellow Chats (Epthianura crocea macgregori) (Aves: Meliphagidae) occurs on a grassy marine plain (~4000 ha) with complex fresh to hypersaline wetlands bordering unvegetated salt flats and mangroves, the majority less than 2 m above mean sea level (MSL). While there are several species of sedge on the marine plain, only one, a tall salt‐tolerant sedge, Schoenoplectus subulatus, regularly provides tall cover and nesting habitat on the marine plain. Comparison of vegetation data between 2002 and 2018 at four breeding sites showed a loss of S. subulatus at two of the sites in conjunction with persistent extreme hypersalinity. In contrast, sites where S. subulatus recovered had elevated salinity levels coinciding with a drought in 2005–2008, but subsequently returning to pre‐drought levels. Concomitant with the loss of S. subulatus was a substantial decline in Capricorn Yellow Chat abundance. Possible drivers of persistent hypersalinity were an increase in sea level and consequent greater tidal ingress. The two most severely affected sites were relatively close to tidal influence and low points in the landscape. Evaluation of MSL data showed that habitat decline from 2002 to 2018 occurred over a period in which sea level rose by ~80 mm. While it is recognised that other variables are important, this study indicates that if sea‐level rise continues at the 2011–2017 rate of ~8.3 mm per annum, the Curtis Island marine plain will become unsuitable for Capricorn Yellow Chats in the next 60 years or less. Sixty years is likely to be a conservative estimate given that sea‐level rise rates are projected to increase further, as are the influence of more extreme weather events such as drought and storm surges on persistence of key vegetation. Ramifications for other Capricorn Yellow Chat sites and marine plain‐dependent fauna such as shorebirds also need consideration.     

Combined analysis of genome-wide association studies for Crohn disease and psoriasis identifies seven shared susceptibility loci

Psoriasis (PS) and Crohn disease (CD) have been shown to be epidemiologically, pathologically, and therapeutically connected, but little is known about their shared genetic causes. We performed meta-analyses of five published genome-wide association studies on PS (2,529 cases and 4,955 controls) and CD (2,142 cases and 5,505 controls), followed up 20 loci that showed strongest evidence for shared disease association and, furthermore, tested cross-disease associations for previously reported PS and CD risk alleles in additional 6,115 PS cases, 4,073 CD cases, and 10,100 controls. We identified seven susceptibility loci outside the human leukocyte antigen region (9p24 near JAK2, 10q22 at ZMIZ1, 11q13 near PRDX5, 16p13 near SOCS1, 17q21 at STAT3, 19p13 near FUT2, and 22q11 at YDJC) shared between PS and CD with genome-wide significance (p < 5 × 10⁻⁸) and confirmed four already established PS and CD risk loci (IL23R, IL12B, REL, and TYK2). Three of the shared loci are also genome-wide significantly associated with PS alone (10q22 at ZMIZ1, p_rs1250544 = 3.53 × 10⁻⁸, 11q13 near PRDX5, p_rs694739 = 3.71 × 10⁻⁰⁹, 22q11 at YDJC, p_rs181359 = 8.02 × 10⁻¹⁰). In addition, we identified one susceptibility locus for CD (16p13 near SOCS1, p_rs4780355 = 4.99 × 10⁻⁸). Refinement of association signals identified shared genome-wide significant associations for exonic SNPs at 10q22 (ZMIZ1) and in silico expression quantitative trait locus analyses revealed that the associations at ZMIZ1 and near SOCS1 have a potential functional effect on gene expression. Our results show the usefulness of joint analyses of clinically distinct immune-mediated diseases and enlarge the map of shared genetic risk loci.     

Lung injury in acute pancreatitis: mechanisms underlying augmented secondary injury

Acute lung injury (ALI) and its more severe form, the acute respiratory distress syndrome (ARDS), are common complications of acute pancreatitis (AP). ALI/ARDS contribute to the majority of AP-associated deaths, particularly in the setting of secondary infection. Following secondary pulmonary infection there can be an exacerbation of AP-associated lung injury, greater than the sum of the individual injuries alone. The precise mechanisms underlying this synergism, however, are not known. In this review we discuss the main factors contributing to the development of augmented lung injury following secondary infection during AP and review the established models of AP in regard to the development of associated ALI.     

Actigraphic sleep and developmental progress of one-year-old infants

The aims of this study were to pilot methods to monitor the sleep of infants, as well as explore the relationships between infant sleep and physical, cognitive and motor development. Fifty-two one-year-old infants and their parents participated in the study. Infant sleep was assessed by one week’s actigraphy, sleep diaries and by the Brief Infant Sleep Questionnaire. Parents also completed a background questionnaire and the Ages and Stages Questionnaire to measure stages of development across five domains. Infant’s weight and length were measured by the researcher at study onset and Body Mass Index (BMI) scores were calculated. Sleep efficiency, and having a higher proportion of total sleep at night, were significantly correlated with age as well as stages of cognitive and motor development. However, sleep measures were not correlated with infant BMI. These findings support increasing evidence that sleep matures quickly around the age of one year and is related to other stages of development. Further research is required to confirm whether links between sleep and development are simply a marker of maturation, or if sleep per se plays a specific role in infant cognitive and motor development. Sleep and physical growth at this age need further investigation with a more representative sample including short-sleeping and overweight infants.

     

Direct seeding to restore tropical seasonal forests: effects of green manure and hydrogel amendment on tree species performances and weed infestation

Although direct tree seeding may be a potentially useful restoration practice, many biotic and abiotic barriers prevent seedling emergence and early development, reducing its success and applicability. To overcome these barriers, we undertook a field experiment to test the effects of using green manure and hydrogel alone, or in combination, on seedling performances of 14 native tree species that were planted by direct seeding in a deforested tropical seasonal forest area in southern Brazil and to examine how green manure affected the initial weed coverage in the study plots. We evaluated competing vegetation coverage and tree seedling emergence and early development for 2 years after sowing. Weed infestation was significantly higher in the experimental plots with no green manure; however, neither green manure nor hydrogel improved tree seedling emergence and early development at any time of measurement. Our results suggest that the use of green manure and hydrogel alone, or in combination, were not effective in guaranteeing direct seeding success; however, green manure can be an effective method to reduce weed infestation. Direct seeding techniques for tree species still need to be improved in order to restore tropical seasonal forests on a larger scale.     

Changes in the gene expression profiles of the brains of male European eels (Anguilla anguilla) during sexual maturation

Background

The vertebrate brain plays a critical role in the regulation of sexual maturation and reproduction by integrating environmental information with developmental and endocrine status. The European eel Anguilla anguilla is an important species in which to better understand the neuroendocrine factors that control reproduction because it is an endangered species, has a complex life cycle that includes two extreme long distance migrations with both freshwater and seawater stages and because it occupies a key position within the teleost phylogeny. At present, mature eels have never been caught in the wild and little is known about most aspects of reproduction in A. anguilla. The goal of this study was to identify genes that may be involved in sexual maturation in experimentally matured eels. For this, we used microarrays to compare the gene expression profiles of sexually mature to immature males.

Results

Using a false discovery rate of 0.05, a total of 1,497 differentially expressed genes were identified. Of this set, 991 were expressed at higher levels in brains (forebrain and midbrain) of mature males while 506 were expressed at lower levels relative to brains of immature males. The set of up-regulated genes includes genes involved in neuroendocrine processes, cell-cell signaling, neurogenesis and development. Interestingly, while genes involved in immune system function were down-regulated in the brains of mature males, changes in the expression levels of several receptors and channels were observed suggesting that some rewiring is occurring in the brain at sexual maturity.

Conclusions

This study shows that the brains of eels undergo major changes at the molecular level at sexual maturity that may include re-organization at the cellular level. Here, we have defined a set of genes that help to understand the molecular mechanisms controlling reproduction in eels. Some of these genes have previously described functions while many others have roles that have yet to be characterized in a reproductive context. Since most of the genes examined here have orthologs in other vertebrates, the results of this study will contribute to the body of knowledge concerning reproduction in vertebrates as well as to an improved understanding of eel biology.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-799) contains supplementary material, which is available to authorized users.     

Glycogen Synthase Kinase 3 Protein Kinase Activity Is Frequently Elevated in Human Non-Small Cell Lung Carcinoma and Supports Tumour Cell Proliferation

Background

Glycogen synthase kinase 3 (GSK3) is a central regulator of cellular metabolism, development and growth. GSK3 activity was thought to oppose tumourigenesis, yet recent studies indicate that it may support tumour growth in some cancer types including in non-small cell lung carcinoma (NSCLC). We examined the undefined role of GSK3 protein kinase activity in tissue from human NSCLC.

Methods

The expression and protein kinase activity of GSK3 was determined in 29 fresh frozen samples of human NSCLC and patient-matched normal lung tissue by quantitative immunoassay and western blotting for the phosphorylation of three distinct GSK3 substrates in situ (glycogen synthase, RelA and CRMP-2). The proliferation and sensitivity to the small-molecule GSK3 inhibitor; CHIR99021, of NSCLC cell lines (Hcc193, H1975, PC9 and A549) and non-neoplastic type II pneumocytes was further assessed in adherent culture.

Results

Expression and protein kinase activity of GSK3 was elevated in 41% of human NSCLC samples when compared to patient-matched control tissue. Phosphorylation of GSK3α/β at the inhibitory S21/9 residue was a poor biomarker for activity in tumour samples. The GSK3 inhibitor, CHIR99021 dose-dependently reduced the proliferation of three NSCLC cell lines yet was ineffective against type II pneumocytes.

Conclusion

NSCLC tumours with elevated GSK3 protein kinase activity may have evolved dependence on the kinase for sustained growth. Our results provide further important rationale for exploring the use of GSK3 inhibitors in treating NSCLC.     

Strengths and Weaknesses of Global Positioning System (GPS) Data-Loggers and Semi-structured Interviews for Capturing Fine-scale Human Mobility: Findings from Iquitos,Peru

Quantifying human mobility has significant consequences for studying physical activity, exposure to pathogens, and generating more realistic infectious disease models. Location-aware technologies such as Global Positioning System (GPS)-enabled devices are used increasingly as a gold standard for mobility research. The main goal of this observational study was to compare and contrast the information obtained through GPS and semi-structured interviews (SSI) to assess issues affecting data quality and, ultimately, our ability to measure fine-scale human mobility. A total of 160 individuals, ages 7 to 74, from Iquitos, Peru, were tracked using GPS data-loggers for 14 days and later interviewed using the SSI about places they visited while tracked. A total of 2,047 and 886 places were reported in the SSI and identified by GPS, respectively. Differences in the concordance between methods occurred by location type, distance threshold (within a given radius to be considered a match) selected, GPS data collection frequency (i.e., 30, 90 or 150 seconds) and number of GPS points near the SSI place considered to define a match. Both methods had perfect concordance identifying each participant''s house, followed by 80–100% concordance for identifying schools and lodgings, and 50–80% concordance for residences and commercial and religious locations. As the distance threshold selected increased, the concordance between SSI and raw GPS data increased (beyond 20 meters most locations reached their maximum concordance). Processing raw GPS data using a signal-clustering algorithm decreased overall concordance to 14.3%. The most common causes of discordance as described by a sub-sample (n = 101) with whom we followed-up were GPS units being accidentally off (30%), forgetting or purposely not taking the units when leaving home (24.8%), possible barriers to the signal (4.7%) and leaving units home to recharge (4.6%). We provide a quantitative assessment of the strengths and weaknesses of both methods for capturing fine-scale human mobility.     

Assessing the contribution of breeds to genetic diversity in conservation schemes

The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the relative contribution of populations to a core set of populations in which the overlap of genetic diversity was minimised. This implies that the mean kinship in the core set should be minimal. The above definition of diversity differs from Weitzman diversity in that it attempts to conserve the founder population (and thus minimises the loss of alleles), whereas Weitzman diversity favours the conservation of many inbred lines. The former is preferred in species where inbred lines suffer from inbreeding depression. The application of the method is illustrated by an example involving 45 Dutch poultry breeds. The calculations used were easy to implement and not computer intensive. The method gave a ranking of breeds according to their contributions to genetic diversity. Losses in genetic diversity ranged from 2.1% to 4.5% for different subsets relative to the entire set of breeds, while the loss of founder genome equivalents ranged from 22.9% to 39.3%.