In silico inference of immunological relationship between protein antigens based on their cytotoxic T-lymphocyte epitope repertoires

The importance of Cytotoxic T-Cell (CTL) reponses during the course of intracellular infections has received a lot of attention during the past few decades. CTLs respond to epitopes presented by the Major Histocompatibility Complex (MHC) originating from intracellular proteins for which they have an appropriate T-Cell Receptor (TCR) for. This response is crucial for the control of pathogens such as Influenza, Hepatitis, HIV and others by destroying the cell in which the pathogen replicates. Due to the extreme polymorphism of MHC molecules, Computational Immunology techniques have been developed to detect potential MHC ligands and as a consequence, potential CTL epitopes. The polymorphism factor needs to be taken into account especially when concerning the design of vaccines with a CTL response component to maximize population coverage. Tools have been constructed that combine the predictions tools concerning major steps in this pathway, that is, proteasomal cleavage, Transporter associated with Antigen Presentation (TAP) affinity, Major Histocompatibility Complex (MHC) affinity and Immunogenicity. In this study, a novel method is developed to combine the different steps in the pathway, which includes the development of a novel TAP predictor. Furthermore, by using a BLOSUM-based score in conjunction with the epitope prediction results, a novel CTL epitopebased clustering method was developed. Two pathogens with major CTL epitope components, but vastly different mutation rates were chosen to infer whether the aforementioned methods can be used to detect potential CTL epitopes and group sequences together based on shared immunogenicity.Dissertation (MSc)--University of Pretoria, 2011.Bioinformatics and Computational Biology Unitunrestricte

Flora Fanerogâmica do Estado do Paraná, Brasil: Psilochilus Barb.Rodr. (Orchidaceae, Triphorinae)

Flora Fanerogâmica do Estado do Paraná, Brasil: Psilochilus Barb.Rodr. (Orchidaceae, Triphorinae)</htm

Flora Fanerogâmica do Estado do Paraná, Brasil: Psilochilus Barb.Rodr. (Orchidaceae, Triphorinae)

Flora Fanerogâmica do Estado do Paraná, Brasil: Psilochilus Barb.Rodr. (Orchidaceae, Triphorinae)</htm

HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy

Prolonged virologic failure on 2nd-line protease inhibitor (PI)-based antiretroviral therapy (ART) without emergence of major protease mutations is well recognized and provides an opportunity to study within-host evolution in long-term viremic individuals. Using next-generation sequencing and in silico haplotype reconstruction, we analyzed whole-genome sequences from longitudinal plasma samples of eight chronically infected HIV-1-positive individuals failing 2nd-line regimens from the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) trial. On nonsuppressive ART, there were large fluctuations in synonymous and nonsynonymous variant frequencies despite stable viremia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral haplotype competition, during periods of low drug exposure. Drug resistance mutations in reverse transcriptase (RT) were used as markers of viral haplotypes in the reservoir, and their distribution over time indicated recombination. We independently observed linkage disequilibrium decay, indicative of recombination. These data highlight dramatic changes in virus population structure that occur during stable viremia under nonsuppressive ART. IMPORTANCE HIV-1 infections are most commonly initiated with a single founder virus and are characterized by extensive inter- and intraparticipant genetic diversity. However, existing literature on HIV-1 intrahost population dynamics is largely limited to untreated infections, predominantly in subtype B-infected individuals. The manuscript characterizes viral population dynamics in long-term viremic treatment-experienced individuals, which has not been previously characterized. These data are particularly relevant for understanding HIV dynamics but can also be applied to other RNA viruses. With this unique data set we propose that the virus is highly unstable, and we have found compelling evidence of HIV-1 within-host viral diversification, recombination, and haplotype competition during nonsuppressive ART

Reporting Guidelines for Survey Research: An Analysis of Published Guidance and Reporting Practices

Carol Bennett and colleagues review the evidence and find that there is limited guidance and no consensus on the optimal reporting of survey research

Platelet rich plasma injection grafts for musculoskeletal injuries: a review

In Europe and the United States, there is an increasing prevalence of the use of autologous blood products to facilitate healing in a variety of applications. Recently, we have learned more about specific growth factors, which play a crucial role in the healing process. With that knowledge there is abundant enthusiasm in the application of concentrated platelets, which release a supra-maximal quantity of these growth factors to stimulate recovery in non-healing injuries. For 20 years, the application of autologous PRP has been safely used and documented in many fields including; orthopedics, sports medicine, dentistry, ENT, neurosurgery, ophthalmology, urology, wound healing, cosmetic, cardiothoracic, and maxillofacial surgery. This article introduces the reader to PRP therapy and reviews the current literature on this emerging treatment modality. In summary, PRP provides a promising alternative to surgery by promoting safe and natural healing. However, there are few controlled trials, and mostly anecdotal or case reports. Additionally the sample sizes are frequently small, limiting the generalization of the findings. Recently, there is emerging literature on the beneficial effects of PRP for chronic non-healing tendon injuries including lateral epicondylitis and plantar fasciitis and cartilage degeneration (Mishra and Pavelko, The American Journal of Sports Medicine 10(10):1–5, 2006; Barrett and Erredge, Podiatry Today 17:37–42, 2004). However, as clinical use increases, more controlled studies are needed to further understand this treatment

African Linguistics in Central and Eastern Europe, and in the Nordic Countries

Non peer reviewe