NeuriteQuant: An open source toolkit for high content screens of neuronal Morphogenesis

<p>Abstract</p> <p>Background</p> <p>To date, some of the most useful and physiologically relevant neuronal cell culture systems, such as high density co-cultures of astrocytes and primary hippocampal neurons, or differentiated stem cell-derived cultures, are characterized by high cell density and partially overlapping cellular structures. Efficient analytical strategies are required to enable rapid, reliable, quantitative analysis of neuronal morphology in these valuable model systems.</p> <p>Results</p> <p>Here we present the development and validation of a novel bioinformatics pipeline called NeuriteQuant. This tool enables fully automated morphological analysis of large-scale image data from neuronal cultures or brain sections that display a high degree of complexity and overlap of neuronal outgrowths. It also provides an efficient web-based tool to review and evaluate the analysis process. In addition to its built-in functionality, NeuriteQuant can be readily extended based on the rich toolset offered by ImageJ and its associated community of developers. As proof of concept we performed automated screens for modulators of neuronal development in cultures of primary neurons and neuronally differentiated P19 stem cells, which demonstrated specific dose-dependent effects on neuronal morphology.</p> <p>Conclusions</p> <p>NeuriteQuant is a freely available open-source tool for the automated analysis and effective review of large-scale high-content screens. It is especially well suited to quantify the effect of experimental manipulations on physiologically relevant neuronal cultures or brain sections that display a high degree of complexity and overlap among neurites or other cellular structures.</p

A Uniform Genomic Minor Histocompatibility Antigen Typing Methodology and Database Designed to Facilitate Clinical Applications

BACKGROUND: Minor Histocompatibility (H) antigen mismatches significantly influence the outcome of HLA-matched allogeneic stem cell transplantation. The molecular identification of human H antigens is increasing rapidly. In parallel, clinical application of minor H antigen typing has gained interest. So far, relevant and simple tools to analyze the minor H antigens in a quick and reliable way are lacking. METHODOLOGY AND FINDINGS: We developed a uniform PCR with sequence-specific primers (PCR-SSP) for 10 different autosomal minor H antigens and H-Y. This genomic minor H antigen typing methodology allows easy incorporation in the routine HLA typing procedures. DNA from previously typed EBV-LCL was used to validate the methodology. To facilitate easy interpretation for clinical purposes, a minor H database named dbMinor (http://www.lumc.nl/dbminor) was developed. Input of the minor H antigen typing results subsequently provides all relevant information for a given patient/donor pair and additional information on the putative graft-versus-host, graft-versus-tumor and host-versus-graft reactivities. SIGNIFICANCE: A simple, uniform and rapid methodology was developed enabling determination of minor H antigen genotypes of all currently identified minor H antigens. A dbMinor database was developed to interpret the genomic typing for its potential clinical relevance. The combination of the minor H antigen genomic typing methodology with the online dbMinor database and applications facilitates the clinical application of minor H antigens anti-tumor targets after stem cell transplantation

Facility and home based HIV Counseling and Testing: a comparative analysis of uptake of services by rural communities in southwestern Uganda

<p>Abstract</p> <p>Background</p> <p>In Uganda, public human immunodeficiency virus (HIV) Voluntary Counseling and Testing (VCT) services are mainly provided through the facility based model, although the home based approach is being promoted as a strategy for improving access to VCT. However the uptake of VCT varies according to service delivery model and is influenced by a number of factors. The aim of this study therefore, was to compare predictors for uptake of facility and home based VCT in a rural context.</p> <p>Methods</p> <p>A longitudinal study with cross-sectional investigative phases was conducted at two sites (Rugando and Kabingo) in southwestern Uganda between November 2007 (baseline) and March 2008 (follow up). During the baseline visit, facility based VCT was offered at the main health centre in Rugando while home based VCT was offered at the household level in Kabingo and a mixed survey questionnaire administered to the respondents. The results presented in this paper are derived from only the baseline data.</p> <p>Results</p> <p>Nine hundred ninety four (994) respondents were interviewed, of whom 500 received facility based VCT in Rugando and 494 home based VCT in Kabingo during the baseline visit. The respondents had a mean age of 32.2 years (SD 10.9) and were mainly female (68 percent). Clients who received facility based VCT were less likely to be residents of the more rural households (adjusted Odds Ratio (aOR) = 0.14, 95% CI 0.07, 0.22). The clients who received home based VCT were less likely to report having an STI symptom (aOR = 0.63, 95% CI 0.46, 0.86), and more likely to be worried about discrimination if they contracted AIDS (aOR = 1.78, 95% CI 1.22, 2.61).</p> <p>Conclusion</p> <p>The uptake of VCT provided through either the facility or home based models is influenced by client characteristics such as proximity to service delivery points, HIV related symptoms, and fear of discrimination in rural Uganda. Interventions that seek to improve uptake of VCT should provide potential clients with both facility and home based VCT options within a given setting. The clients are then able to select a model for VCT that best fits their characteristics. This is likely to have positive implications for both service coverage and uptake by different sub-groups within particular communities.</p

Employing an open-source tool to assess astrocyte tridimensional structure

Astrocytes display important features that allow them to maintain a close dialog with neurons, ultimately impacting brain function. The complex morphological structure of astrocytes is crucial to the role of astrocytes in brain networks. Therefore, assessing morphologic features of astrocytes will help provide insights into their physiological relevance in healthy and pathological conditions. Currently available tools that allow the tridimensional reconstruction of astrocytes present a number of disadvantages, including the need for advanced computational skills and powerful hardware, and are either time-consuming or costly. In this study, we optimized and validated the FIJI-ImageJ, Simple Neurite Tracer (SNT) plugin, an open-source software that aids in the reconstruction of GFAP-stained structure of astrocytes. We describe (1) the loading of confocal microscopy Z-stacks, (2) the selection criteria, (3) the reconstruction process, and (4) the post-reconstruction analysis of morphological features (process length, number, thickness, and arbor complexity). SNT allows the quantification of astrocyte morphometric parameters in a simple, efficient, and semi-automated manner. While SNT is simple to learn, and does not require advanced computational skills, it provides reproducible results, in different brain regions or pathophysiological states.The authors acknowledge funding from national funds through the FCT—Foundation for Science and Technology—project (PTDC/SAU-NSC/118194/2010) to G.T., V.M.S., S.G.G. and J.F.O., and fellowships (SFRH/BD/89714/2012 to V.M.S., SFRH/BPD/97281/2013 to J.F.O., SFRH/BD/101298/2014 to S.G.G., PD/BD/114120/2015 to S.P.N, and PD/BD/127822/2016 to G.T.); Marie Curie Fellowship FP7-PEOPLE-2010-IEF 273936 and BIAL Foundation Grants and 207/14 to J.F.O.; QREN and FEDER funds through Operational program for competitiveness factors—COMPETE, “ON.2 SR&TD Integrated Program—NORTE-07-0124-FEDER-000021”; National and European funds through FCT, and FEDER through COMPETE (PEst-C/SAU/LA0026/2011 and FCOMP-01-0124-FEDER-022724; PEst-C/SAU/LA0026/2013 and FCOMP-01-0124-FEDER-037298, respectively)info:eu-repo/semantics/publishedVersio

A critical assessment of the WHO responsiveness tool: lessons from voluntary HIV testing and counselling services in Kenya

<p>Abstract</p> <p>Background</p> <p>Health, fair financing and responsiveness to the user's needs and expectations are seen as the essential objectives of health systems. Efforts have been made to conceptualise and measure responsiveness as a basis for evaluating the non-health aspects of health systems performance. This study assesses the applicability of the responsiveness tool developed by WHO when applied in the context of voluntary HIV counselling and testing services (VCT) at a district level in Kenya.</p> <p>Methods</p> <p>A mixed method study was conducted employing a combination of quantitative and qualitative research methods concurrently. The questionnaire proposed by WHO was administered to 328 VCT users and 36 VCT counsellors (health providers). In addition to the questionnaire, qualitative interviews were carried out among a total of 300 participants. Observational field notes were also written.</p> <p>Results</p> <p>A majority of the health providers and users indicated that the responsiveness elements were very important, e.g. confidentiality and autonomy were regarded by most users and health providers as very important and were also reported as being highly observed in the VCT room. However, the qualitative findings revealed other important aspects related to confidentiality, autonomy and other responsiveness elements that were not captured by the WHO tool. Striking examples were inappropriate location of the VCT centre, limited information provided, language problems, and concern about the quality of counselling.</p> <p>Conclusion</p> <p>The results indicate that the WHO developed responsiveness elements are relevant and important in measuring the performance of voluntary HIV counselling and testing. However, the tool needs substantial revision in order to capture other important dimensions or perspectives. The findings also confirm the importance of careful assessment and recognition of locally specific aspects when conducting comparative studies on responsiveness of HIV testing services.</p

Population genomics of speciation and admixture

The application of population genomics to the understanding of speciation has led to the emerging field of speciation genomics. This has brought new insight into how divergence builds up within the genome during speciation and is also revealing the extent to which species can continue to exchange genetic material despite reproductive barriers. It is also providing powerful new approaches for linking genotype to phenotype in admixed populations. In this chapter, we give an overview of some of the methods that have been used and some of the novel insights gained. We also outline some of the pitfalls of the most commonly used methods and possible problems with interpretation of the results

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe and Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy number, and reconstruct Wolbachia and mtDNA genome sequences. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats.Comment: 41 pages, 5 figure

Neurostimulatory and ablative treatment options in major depressive disorder: a systematic review

Introduction Major depressive disorder is one of the most disabling and common diagnoses amongst psychiatric disorders, with a current worldwide prevalence of 5-10% of the general population and up to 20-25% for the lifetime period. Historical perspective Nowadays, conventional treatment includes psychotherapy and pharmacotherapy; however, more than 60% of the treated patients respond unsatisfactorily, and almost one fifth becomes refractory to these therapies at long-term follow-up. Nonpharmacological techniques Growing social incapacity and economic burdens make the medical community strive for better therapies, with fewer complications. Various nonpharmacological techniques like electroconvulsive therapy, vagus nerve stimulation, transcranial magnetic stimulation, lesion surgery, and deep brain stimulation have been developed for this purpose. Discussion We reviewed the literature from the beginning of the twentieth century until July 2009 and described the early clinical effects and main reported complications of these methods. © The Author(s) 2010.Link_to_subscribed_fulltex