Molecular detection of intra-population structure in a threatened potoroid,Potorous tridactylus: conservation management and sampling implications

Fine-scale genetic structure was investigated in three regional populations of the long-nosed potoroo (Potorous tridactylus) a threatened endemic marsupial. Two populations were from the Australian mainland and one from an island. Populations were sub-sampled at two sites, 6–8 km apart, connected by suitable habitat for dispersal. Factors influencing fine-scale structure were investigated by genotyping 157 individuals at 10 microsatellite loci and sequencing a ~621 bp region of the mtDNA control region. Results indicated that P. tridactylus populations exhibit significant intra-population structure, with significant F _ST and Φ _ST values recorded between subpopulations. This structure appeared mediated by small neighbourhood size, female philopatry and limited dispersal over 6–8 km, predominantly by males. Results highlighted several important features of P. tridactylus populations that have implications for conservation. Firstly, the small neighbourhood size suggests any investigations of intra-population structure should be conducted on a finer scale (e.g. 25–50 m) than many current monitoring programs. Secondly, the island populations were genetically depauperate, which may reflect processes occurring in many isolated ‘mainland island’ populations. Thirdly, the lower gene flow identified between populations separated by anthropogenically modified habitat suggests P. tridactylus is sensitive to changes in habitat configuration.     

Increased WD-repeat containing protein 1 in interstitial fluid from ovarian carcinomas shown by comparative proteomic analysis of malignant and healthy gynecological tissue

We aimed to identify differentially expressed proteins in interstitial fluid from ovarian cancer employing multiple fractioning and high resolution mass spectrometry-based proteomic analysis, and asked whether specific proteins that may serve as biomarker candidates or therapeutic targets could be identified. High throughput proteomics was conducted on immunodepleted and fractioned interstitial fluid from pooled samples of ovarian carcinomas, using endometrial carcinomas and healthy ovarian tissue as controls. Differential analysis revealed the up-regulation of extracellular proteasomes in tumor interstitial fluid compared to the healthy control. Moreover, a number of differentially expressed proteins in interstitial fluid from ovarian carcinomas compared with control tissues were identified. Detection of proteasome 20S related proteins in TIF compared to IF from healthy tissue indicates that the 20S proteasome can have a role in the tumor microenvironment. Six selected proteins, CEACAM5, FREM2, MUC5AC, TFF3, PYCARD and WDR1, were independently validated in individual tumor lysates from ovarian carcinomas by multiple reaction monitoring initiated detection and sequence analysis, Western blot and/or selected reaction monitoring. Quantification of specific proteins revealed substantial heterogeneity between individual samples. Nevertheless, WD repeat-containing protein 1 was confirmed as being significantly overexpressed in interstitial fluid from ovarian carcinomas compared to healthy ovarian tissue by Orbitrap analysis of individual native interstitial fluid from ovarian and endometrial carcinomas and healthy ovarian tissue. We suggest that this protein should be explored as a therapeutic target in ovarian carcinomas. This article is part of a Special Issue entitled: An Updated Secretome.     

Growth, seed development and genetic analysis in wild type and Def mutant of Pisum sativum L

Background

Dementia and cognitive impairment associated with aging are a major medical and social concern. Neuropsychological testing is a key element in the diagnostic procedures of Mild Cognitive Impairment (MCI), but has presently a limited value in the prediction of progression to dementia. We advance the hypothesis that newer statistical classification methods derived from data mining and machine learning methods like Neural Networks, Support Vector Machines and Random Forests can improve accuracy, sensitivity and specificity of predictions obtained from neuropsychological testing. Seven non parametric classifiers derived from data mining methods (Multilayer Perceptrons Neural Networks, Radial Basis Function Neural Networks, Support Vector Machines, CART, CHAID and QUEST Classification Trees and Random Forests) were compared to three traditional classifiers (Linear Discriminant Analysis, Quadratic Discriminant Analysis and Logistic Regression) in terms of overall classification accuracy, specificity, sensitivity, Area under the ROC curve and Press'Q. Model predictors were 10 neuropsychological tests currently used in the diagnosis of dementia. Statistical distributions of classification parameters obtained from a 5-fold cross-validation were compared using the Friedman's nonparametric test.

Results

Press' Q test showed that all classifiers performed better than chance alone (p < 0.05). Support Vector Machines showed the larger overall classification accuracy (Median (Me) = 0.76) an area under the ROC (Me = 0.90). However this method showed high specificity (Me = 1.0) but low sensitivity (Me = 0.3). Random Forest ranked second in overall accuracy (Me = 0.73) with high area under the ROC (Me = 0.73) specificity (Me = 0.73) and sensitivity (Me = 0.64). Linear Discriminant Analysis also showed acceptable overall accuracy (Me = 0.66), with acceptable area under the ROC (Me = 0.72) specificity (Me = 0.66) and sensitivity (Me = 0.64). The remaining classifiers showed overall classification accuracy above a median value of 0.63, but for most sensitivity was around or even lower than a median value of 0.5.

Conclusions

When taking into account sensitivity, specificity and overall classification accuracy Random Forests and Linear Discriminant analysis rank first among all the classifiers tested in prediction of dementia using several neuropsychological tests. These methods may be used to improve accuracy, sensitivity and specificity of Dementia predictions from neuropsychological testing.     

Plastid division control: the PDV proteins regulate DRP5B dynamin activity

Chloroplast division represents a fundamental but complex biological process involving remnants of the ancestral bacterial division machinery and proteins of eukaryotic origin. Moreover, the chloroplast division machinery is divided into stromal and cytosolic sub machineries, which coordinate and control their activities to ensure appropriate division initiation and progression. Dynamin related protein 5B (DRP5B) and plastid division protein 1 and 2 (PDV1 and PDV2) are all plant-derived proteins and represent components of the cytosolic division machinery, where DRP5B is thought to exert constrictional force during division. However, the direct relationship between PDV1, PDV2 and DRP5B, and moreover how DRP5B is regulated during plastid constriction remains unclear. In this study we show that PDV1 and PDV2 can interact with themselves and with each other through their cytosolic domains. We demonstrate that DRP5B interacts with itself and with the cytosolic region of PDV1 and that the two functional isoforms of DRP5B have highly overlapping functions. We further show that DRP5B harbors GTPase activity and moreover that PDV1 and PDV2 inhibits DRP5B-mediated GTP hydrolysis in a ratio dependent manner. Our data suggest that the PDV proteins contribute to the regulation of DRP5B activity thereby enforcing control over the division process during early constriction.     

Protein Interaction Screening for the Ankyrin Repeats and Suppressor of Cytokine Signaling (SOCS) Box (ASB) Family Identify Asb11 as a Novel Endoplasmic Reticulum Resident Ubiquitin Ligase

The ankyrin and SOCS (suppressor of cytokine signaling) box (ASB) family of proteins function as the substrate recognition subunit in a subset of Elongin-Cullin-SOCS (ECS) E3 ubiquitin ligases. Despite counting 18 members in humans, the identity of the physiological targets of the Asb proteins remains largely unexplored. To increase our understanding of the function of ASB proteins, we conducted a family-wide SILAC (stable isotope labeling by amino acids in cell culture)-based protein/protein interaction analysis. This investigation led to the identification of novel as well as known ASB-associated proteins like Cullin 5 and Elongins B/C. We observed that several proteins can be bound by more than one Asb protein. The additional exploration of this phenomenon demonstrated that ASB-Cullin 5 complexes can oligomerize and provides evidence that Cullin 5 forms heterodimeric complexes with the Cullin 4a-DDB1 complex. We also demonstrated that ASB11 is a novel endoplasmic reticulum-associated ubiquitin ligase with the ability to interact and promote the ubiquitination of Ribophorin 1, an integral protein of the oligosaccharyltransferase (OST) glycosylation complex. Moreover, expression of ASB11 can increase Ribophorin 1 protein turnover in vivo. In summary, we provide a comprehensive protein/protein interaction data resource that can aid the biological and functional characterization of ASB ubiquitin ligases.     

High Interest in a Long-Acting Injectable Formulation of Pre-Exposure Prophylaxis for HIV in Young Men Who Have Sex with Men in NYC: A P18 Cohort Substudy

Objective

In the context of continued high rates of condomless anal intercourse and HIV-1 infection, young men who have sex with men (YMSM) need additional effective and desirable HIV prevention tools. This study reports on the willingness of a racially-ethnically diverse cohort of YMSM to use a new biomedical prevention approach, a long-acting injectable pre-exposure prophylaxis (LAI-PrEP) agent.

Methods

A cross-sectional study conducted between June-August 2013 recruited participants from an ongoing cohort study of YMSM in NYC. Participants included 197 YMSM, of whom 72.6% (n = 143) identified as men of color. Two outcomes were measured through computer-assisted self-interviews: 1) willingness to use long-acting injectable PrEP and 2) preference for route of administration of PrEP. In addition, concerns about perceived impacts of PrEP on health and risk behavior, access to health services, and stigma were investigated.

Results

Over 80% (n = 159/197, p<0.001) of participants stated they would be willing to use LAI-PrEP. With regards to preference for mode of delivery 79.2% (n = 156/197, p<0.001) stated they would prefer an injection administered every three months over a daily pill or neither one.

Conclusions

This study is the first to explore acceptability of LAI-PrEP in the US. A significant majority of participants expressed willingness to use LAI and the majority preferred LAI-PrEP. LAI-PrEP holds great promise in that it could circumvent the adherence challenges associated with daily dosing, especially if nested within appropriate psycho-behavioral support. Medical providers whose patients include YMSM at high risk for HIV infection should note the positive attitudes toward PrEP, and specifically LAI-PrEP.     

Mycobacterium ulcerans causes minimal pathogenesis and colonization in medaka (Oryzias latipes): an experimental fish model of disease transmission

Mycobacterium ulcerans causes Buruli ulcer in humans, a progressive ulcerative epidermal lesion due to the mycolactone toxin produced by the bacterium. Molecular analysis of M. ulcerans reveals it is closely related to Mycobacterium marinum, a pathogen of both fish and man. Molecular evidence from diagnostic PCR assays for the insertion sequence IS2404 suggests an association of M. ulcerans with fish. However, fish infections by M. ulcerans have not been well documented and IS2404 has been found in other mycobacteria. We have thus, employed two experimental approaches to test for M. ulcerans in fish. We show here for the first time that M. ulcerans with or without the toxin does not mount acute or chronic infections in Japanese Medaka "Oryzias latipes" even at high doses. Moreover, M. ulcerans-infected medaka do not exhibit any visible signs of infection nor disease and the bacteria do not appear to replicate over time. In contrast, similar high doses of the wild-type M. marinum or a mycolactone-producing M. marinum "DL" strain are able to mount an acute disease with mortality in medaka. Although these results would suggest that M. ulcerans does not mount infections in fish we have evidence that CLC macrophages from goldfish are susceptible to mycolactones.     

Factors associated with Danish cancer patients' return to work. A report from the population-based study 'The Cancer Patient's World'

Purpose: If patients facing difficulties in the process of returning to work after treatment of cancer could be identified, these patients could be assisted in the transition. This might help some patients to stay in work. We therefore assessed demographic and clinical factors associated with returning to work after a cancer diagnosis. Materials and methods: In this cross-sectional survey, 1490 cancer patients who had been in contact with a hospital department during the past 12 months in three Danish counties responded to a mailed questionnaire. Factors associated with employment and return to work (i.e., working more than 0 h in the past month) respectively, were assessed in multivariate ordinal logistic regression models. Results: Of the 598 patients below age 65 who were employed at the time of diagnosis, 75% were still employed when answering the questionnaire at a median of 2.8 years after diagnosis and 63% were working. In multivariate analyses, younger and more recently diagnosed patients were more often employed. Patients diagnosed with lung or head and neck cancer were least likely to be employed and having returned to work. Advanced cancer at diagnosis was associated with loss of employment. Advanced cancer and being in active treatment were associated with not having returned to work. Conclusion: A quarter of the patients had lost their employment probably resulting in economic consequences on the individual as well as at the societal level. The highest risk was observed for older patients and those diagnosed with lung or head and neck cancer.     

Diabetic nephropathy, inflammation, hyaluronan and interstitial fibrosis

Hyaluronan (HA) is a ubiquitous connective tissue glycosaminoglycan component of most extracellular matrices and alterations in its synthesis have been suggested to be involved in the glomerular changes of diabetic nephropathy. Similarly it has been suggested that macrophages are involved in the initiation of diabetic glomerular injury. Much less is known regarding the role of the prognostic value of changes in interstitial HA and interstitial inflammatory infiltrate. The aim of this study was to examine the potential association of inflammatory infiltrate, deposition of the matrix component hyaluronan and inter-alpha inhibitor (which is involved in HA assembly) and clinical outcome in diabetic nephropathy. Histological specimens of 40 patients with biopsy proven diabetic nephropathy were examined. Based on the rate of change in estimated GFR (eGFR, abbreviated MDRD formula), patients were defined as late presenters, progressors or non-progressors. The degree of interstitial fibrosis was associated with progression of disease and late presentation. There was a significant greater number of CD68-positive cells in the interstitium of patients who subsequently developed progressive renal disease, or those who presented with advanced disease compared to non-progressors. In contrast, there was significant staining for interstitial HA in all the patient groups. Furthermore there was no correlation between the accumulation of HA and CD68-positive macrophages. In addition all patients with biopsy-proven diabetic nephropathy had significantly greater interstitial IalphaI compared to the normal controls and there was a significant correlation between interstitial HA and IalphaI. Increased HA is seen at all stages of diabetic change in the kidney but is not predictive of progression. Macrophage influx, however, is directly related to the progression of diabetic nephropathy and is not associated with HA accumulation.     

A tool for analyzing information from data storage tags: the continuous wavelet transform (CWT)

Electronic Data Storage Tags (DSTs) have the potential of providing long term, high-resolution observation data of individual fish in the ecosystem. However, traditional time series analysis methods are limited in extracting the required information from DSTs. The continuous wavelet transform (CWT) is a tool for decomposing a time series into instantaneous frequency versus time characteristics. This allows data signals, which are restricted to specific frequencies (localized frequencies), or frequency components, which are restricted to specific time intervals (time localized) to be extracted and displayed in a highly intuitive way. The aim of this short communication is to present the CWT as a tool for extracting information from DST data. In the first case, synthetically generated data is used to demonstrate how the methodology captures different time–frequency dependent patterns in the time series data. The relevance of the methodology to real field data is demonstrated by an analysis of DST depth data from tagged Barents Sea coastal cod. This work has also enjoyed partial funding from the EU-FP5-Q5RS200200813 CODYSSEY project.