Diseño y programación de un software de transformación de matrices para el análisis de redes

For many professionals linked to Social Network Analysis (SNA), it is important to transform their data for further studies. Often, the data of systems where exist ties are stored in elementary matrices, and not in full matrices, frequently used in SNA software. The objective of this paper was to design and program a modifiable software with the potential to transform three columns matrices [A (group 1), B (group 2) and C (ties between groups nodes)] to full and symmetric matrices, and to analyze the advantages of software regarding storage and data processing problems. To perform the necessary operations was developed a transformation matrix method and an algorithm (pseudocode) of this method. The algorithm was programmed in wxBasic to improve the compatibility between operating systems and to make the user modification easier, obtaining stable and easy-to-use software.Para muchos profesionales vinculados al Análisis de Redes Sociales (ARS), es de importancia transformar sus datos para realizar estudios posteriores. Es frecuente que los datos de sistemas donde intervienen conexiones se almacenen en matrices más elementales que las matrices completas o “full matrix”, frecuentemente utilizadas en programas de ARS. El objetivo principal de este trabajo fue diseñar y programar un software modificable para transformar matrices de tres columnas [A (grupo 1), B (grupo 2) y C (conexiones entre nodos de ambos grupos)] a matrices completas y simétricas, y analizar las ventajas del software con respecto a los problemas de almacenamiento y transformación de datos. Para ello se desarrolló un método de transformación de matrices y se diseñó un algoritmo (pseudocódigo) para realizar las operaciones necesarias. El algoritmo fue programado usando el lenguaje wxBasic para aumentar la compatibilidad entre sistemas operativos y facilitar su modificación por el usuario, obteniéndose un software estable y de fácil uso

CD8α is expressed by human monocytes and enhances FcγR-dependent responses

Abstract Background CD8α enhances the responses of antigen-specific CTL activated through TCR through binding MHC class I, favoring lipid raft partitioning of TCR, and inducing intracellular signaling. CD8α is also found on dendritic cells and rat macrophages, but whether CD8α enhances responses of a partner receptor, like TCR, to activate these cells is not known. TCR and FcR, use analogous or occasionally interchangeable signaling mechanisms suggesting the possibility that CD8α co-activates FcR responses. Interestingly, CD8α+ monocytes are often associated with rat models of disease involving immune-complex deposition and FcR-mediated pathology, such as arthritis, glomerulonephritis, ischaemia, and tumors. While rat macrophages have been shown to express CD8α evidence for CD8α expression by mouse or human monocytes or macrophages was incomplete. Results We detected CD8α, but not CD8β on human monocytes and the monocytic cell line THP-1 by flow cytometry. Reactivity of anti-CD8α mAb with monocytes is at least partly independent of FcR as anti-CD8α mAb detect CD8α by western blot and inhibit binding of MHC class I tetramers. CD8α mRNA is also found in monocytes and THP-1 suggesting CD8α is synthesized by monocytes and not acquired from other CD8α+ cell types. Interestingly, CD8α from monocytes and blood T cells presented distinguishable patterns by 2-D electrophoresis. Anti-CD8α mAb alone did not activate monocyte TNF release. In comparison, TNF release by human monocytes stimulated in a FcR-dependent manner with immune-complexes was enhanced by inclusion of anti-CD8α mAb in immune-complexes. Conclusion Human monocytes express CD8α. Co-engagement of CD8α and FcR enhances monocyte TNF release, suggesting FcR may be a novel partner receptor for CD8α on innate immune cells.</p

Identification of potential novel proteomic markers of Leishmania spp.-derived exosomes

IntroductionExtracellular vesicles (EVs) are heterogenous cell-derived membrane-bound structures which can be subdivided into three distinct classes according to distinct morphological characteristics, cellular origins, and functions. Small EVs, or exosomes, can be produced by the protozoan parasite Leishmania through the evolutionarily conserved ESCRT pathway, and act as effectors of virulence and drivers of pathogenesis within mammalian hosts. Techniques for the identification of EVs of non-mammalian origin, however, remain inaccurate in comparison to their well-characterized mammalian counterparts. Thus, we still lack reliable and specific markers for Leishmania-derived exosomes, which poses a significant challenge to the field.MethodsHerein, we utilized serial differential ultracentrifugation to separate Leishmania-derived EV populations into three distinct fractions. Nanoparticle tracking analysis and transmission electron microscopy were used to validate their morphological characteristics, and bioinformatic analysis of LC-MS/MS proteomics corroborated cellular origins and function.DiscussionProteomic data indicated potential novel proteic markers of Leishmania-derived exosomes, including proteins involved in endosomal machinery and the ESCRT pathway, as well as the parasitic phosphatase PRL-1. Further investigation is required to determine the specificity and sensitivity of these markers

Diseño y programación de un software de transformación de matrices para el análisis de redes

Para muchos profesionales vinculados al Análisis de Redes Sociales (ARS), es de importancia transformar sus datos para realizar estudios posteriores. Es frecuente que los datos de sistemas donde intervienen conexiones se almacenen en matrices más elementales que las matrices completas o "full matrix", frecuentemente utilizadas en programas de ARS. El objetivo principal de este trabajo fue diseñar y programar un software modificable para transformar matrices de tres columnas [A (grupo 1), B (grupo 2) y C (conexiones entre nodos de ambos grupos)] a matrices completas y simétricas, y analizar las ventajas del software con respecto a los problemas de almacenamiento y transformación de datos. Para ello se desarrolló un método de transformación de matrices y se diseñó un algoritmo (pseudocódigo) para realizar las operaciones necesarias. El algoritmo fue programado usando el lenguaje wxBasic para aumentar la compatibilidad entre sistemas operativos y facilitar su modificación por el usuario, obteniéndose un software estable y de fácil uso.For many professionals linked to Social Network Analysis (SNA), it is important to transform their data for further studies. Often, the data of systems where exist ties are stored in elementary matrices, and not in full matrices, frequently used in SNA software. The objective of this paper was to design and program a modifiable software with the potential to transform three columns matrices [A (group 1), B (group 2) and C (ties between groups nodes)] to full and symmetric matrices, and to analyze the advantages of software regarding storage and data processing problems. To perform the necessary operations was developed a transformation matrix method and an algorithm (pseudocode) of this method. The algorithm was programmed in wxBasic to improve the compatibility between operating systems and to make the user modification easier, obtaining stable and easy-to-use software

Presentation_1_Identification of potential novel proteomic markers of Leishmania spp.-derived exosomes.pdf

IntroductionExtracellular vesicles (EVs) are heterogenous cell-derived membrane-bound structures which can be subdivided into three distinct classes according to distinct morphological characteristics, cellular origins, and functions. Small EVs, or exosomes, can be produced by the protozoan parasite Leishmania through the evolutionarily conserved ESCRT pathway, and act as effectors of virulence and drivers of pathogenesis within mammalian hosts. Techniques for the identification of EVs of non-mammalian origin, however, remain inaccurate in comparison to their well-characterized mammalian counterparts. Thus, we still lack reliable and specific markers for Leishmania-derived exosomes, which poses a significant challenge to the field.MethodsHerein, we utilized serial differential ultracentrifugation to separate Leishmania-derived EV populations into three distinct fractions. Nanoparticle tracking analysis and transmission electron microscopy were used to validate their morphological characteristics, and bioinformatic analysis of LC-MS/MS proteomics corroborated cellular origins and function.DiscussionProteomic data indicated potential novel proteic markers of Leishmania-derived exosomes, including proteins involved in endosomal machinery and the ESCRT pathway, as well as the parasitic phosphatase PRL-1. Further investigation is required to determine the specificity and sensitivity of these markers.</p

Validation of HIV-1 MA Shell Structural Arrangements and Env Protein Interactions Predict a Role of the MA Shell in Viral Maturation

The molecular structure of the type 1 human immunodeficiency virus (HIV-1) is tightly linked to the mechanism of viral entry. The spike envelope (Env) glycoproteins and their interaction with the underlying matrix (MA) shell have emerged as key components of the entry mechanism. Microscopy evidence suggests that the MA shell does not span the entire inner lipid surface of the virus, producing a region of the virus that completely lacks an MA shell. Interestingly, evidence also suggests that Env proteins cluster during viral maturation and, thus, it is likely that this event takes place in the region of the virus that lacks an MA shell. We have previously called this part of the virus a fusion hub to highlight its importance during viral entry. While the structure of the MA shell is in contention due to the unaddressed inconsistencies between its reported hexagonal arrangement and the physical plausibility of such a structure, it is possible that a limited number of MA hexagons could form. In this study, we measured the size of the fusion hub by analysing the cryo-EM maps of eight HIV-1 particles and measured the size of the MA shell gap to be 66.3 nm ± 15.0 nm. We also validated the feasibility of the hexagonal MA shell arrangement in six reported structures and determined the plausible components of these structures that do not violate geometrical limitations. We also examined the cytosolic domain of Env proteins and discovered a possible interaction between adjacent Env proteins that could explain the stability of cluster formation. We present an updated HIV-1 model and postulate novel roles of the MA shell and Env structure

Mathematical determination of the HIV-1 matrix shell structure and its impact on the biology of HIV-1.

Since its discovery in the early 1980s, there has been significant progress in understanding the biology of type 1 human immunodeficiency virus (HIV-1). Structural biologists have made tremendous contributions to this challenge, guiding the development of current therapeutic strategies. Despite our efforts, there are unresolved structural features of the virus and consequently, significant knowledge gaps in our understanding. The superstructure of the HIV-1 matrix (MA) shell has not been elucidated. Evidence by various high-resolution microscopy techniques support a model composed of MA trimers arranged in a hexameric configuration consisting of 6 MA trimers forming a hexagon. In this manuscript we review the mathematical limitations of this model and propose a new model consisting of a 6-lune hosohedra structure, which aligns with available structural evidence. We used geometric and rotational matrix computation methods to construct our model and predict a new mechanism for viral entry that explains the increase in particle size observed during CD4 receptor engagement and the most common HIV-1 ellipsoidal shapes observed in cryo-EM tomograms. A better understanding of the HIV-1 MA shell structure is a key step towards better models for viral assembly, maturation and entry. Our new model will facilitate efforts to improve understanding of the biology of HIV-1

Subtle differences in CD8α between monocytes and lymphocytes detected by 2-D electrophoresis

<p><b>Copyright information:</b></p><p>Taken from "CD8α is expressed by human monocytes and enhances FcγR-dependent responses"</p><p>http://www.biomedcentral.com/1471-2172/8/12</p><p>BMC Immunology 2007;8():12-12.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000912.</p><p></p> , Western blot with a polyclonal anti-CD8α antibody after 2-D electrophoresis of monocytes and lymphocytes. Cell lysates of lymphocytes and monocytes from one donor were separated by adherence, halved and treated (bottom panels) or not treated (top panels) with neuraminidase before analysis. , Western blot with anti-CD8α mAb D9. , Neuraminidase treatment and western blot with D9 of lymphocyte lysate. Results are representative of experiments with three donors