This is a presentation based off of an article by Garr Reynolds called "Top Ten Slide Tips". As you go through this presentation, you will see some of the wrongs and rights of creating an effective powerpoint presentation.
Comet speeds close to Mars on Oct. 19, 2014. CRISM recorded imaging data in 107 different wavelengths, showing the inner part of the cloud of dust, called the coma, surrounding the comet's nucleus.
Evolutionary relationship between diverse protein with similar domainjj_zein
This document discusses protein domains and their evolutionary relationship between diverse proteins. Protein domains are conserved parts of a protein sequence that determine structure and function. Domains act as compact, independently folding modules that provide specific catalytic and binding sites and serve as building blocks for large protein assemblies. Domains are found across different proteins and have been adapted through evolution, with some folds favored over others as they represent stable arrangements. Bioinformatics approaches like the Protein Data Bank and CATH classify protein structures into families and domains to better understand evolutionary relationships and comparisons between proteins.
El documento describe varios instrumentos de financiación de la I+D+i ofrecidos por el CDTI, incluyendo préstamos, subvenciones y programas internacionales. El CDTI ha apoyado a más de 14.500 empresas con 13.158 millones de euros comprometidos. Los instrumentos incluyen proyectos de I+D, la línea directa de innovación, y programas para la internacionalización de la I+D+i.
Requiem For A Blue Fin Tuna, An International Trade Analysis (1998 2009)RobertoMielgo
This document summarizes an analysis of international trade data related to Atlantic bluefin tuna from 1998 to 2009. It finds that bluefin tuna stocks have collapsed due to relentless overfishing fueled by an insatiable global tuna industry. Fishing capacity and frozen tuna holdings have greatly increased while reported catches have been systematically underreported. This mismanagement has led to billions of euros in illegal, unreported, and unregulated fishing despite the failure of management organizations to curb overfishing or tackle a business that has prioritized short-term profits over long-term sustainability. Experts warn that a total fishing ban in the Mediterranean is needed to have any chance of rebuilding depleted bluefin tuna populations.
Este documento describe un estudio presentado en el 2o Congreso Argentino de Bioinformática y Biología Computacional en la Universidad Católica de Córdoba entre el 11 y 13 de mayo de 2011. El estudio desarrolló nuevos descriptores y un modelo QSPR utilizando redes neuronales artificiales para predecir la temperatura de transición vítrea molar de polímeros. El modelo se basó en cuatro descriptores relacionados con las áreas superficiales y enlaces rotatorios de las cadenas laterales y principales de la unidad repetitiva promedio
This is a presentation based off of an article by Garr Reynolds called "Top Ten Slide Tips". As you go through this presentation, you will see some of the wrongs and rights of creating an effective powerpoint presentation.
Comet speeds close to Mars on Oct. 19, 2014. CRISM recorded imaging data in 107 different wavelengths, showing the inner part of the cloud of dust, called the coma, surrounding the comet's nucleus.
Evolutionary relationship between diverse protein with similar domainjj_zein
This document discusses protein domains and their evolutionary relationship between diverse proteins. Protein domains are conserved parts of a protein sequence that determine structure and function. Domains act as compact, independently folding modules that provide specific catalytic and binding sites and serve as building blocks for large protein assemblies. Domains are found across different proteins and have been adapted through evolution, with some folds favored over others as they represent stable arrangements. Bioinformatics approaches like the Protein Data Bank and CATH classify protein structures into families and domains to better understand evolutionary relationships and comparisons between proteins.
El documento describe varios instrumentos de financiación de la I+D+i ofrecidos por el CDTI, incluyendo préstamos, subvenciones y programas internacionales. El CDTI ha apoyado a más de 14.500 empresas con 13.158 millones de euros comprometidos. Los instrumentos incluyen proyectos de I+D, la línea directa de innovación, y programas para la internacionalización de la I+D+i.
Requiem For A Blue Fin Tuna, An International Trade Analysis (1998 2009)RobertoMielgo
This document summarizes an analysis of international trade data related to Atlantic bluefin tuna from 1998 to 2009. It finds that bluefin tuna stocks have collapsed due to relentless overfishing fueled by an insatiable global tuna industry. Fishing capacity and frozen tuna holdings have greatly increased while reported catches have been systematically underreported. This mismanagement has led to billions of euros in illegal, unreported, and unregulated fishing despite the failure of management organizations to curb overfishing or tackle a business that has prioritized short-term profits over long-term sustainability. Experts warn that a total fishing ban in the Mediterranean is needed to have any chance of rebuilding depleted bluefin tuna populations.
Este documento describe un estudio presentado en el 2o Congreso Argentino de Bioinformática y Biología Computacional en la Universidad Católica de Córdoba entre el 11 y 13 de mayo de 2011. El estudio desarrolló nuevos descriptores y un modelo QSPR utilizando redes neuronales artificiales para predecir la temperatura de transición vítrea molar de polímeros. El modelo se basó en cuatro descriptores relacionados con las áreas superficiales y enlaces rotatorios de las cadenas laterales y principales de la unidad repetitiva promedio
Este documento describe las actividades de la Unidad de Bioinformática del INTA en Argentina. En 3 oraciones o menos:
La Unidad de Bioinformática del INTA ha realizado estudios genómicos limitados en girasol y ha desarrollado herramientas bioinformáticas para analizar secuencias moleculares. Han colaborado con otras instituciones para crear una base de datos y han formado recursos humanos a través de cursos y pasantías para aplicar tecnología informática a preguntas biológicas. El objetivo es responder preguntas biol
This document analyzes the sequence and functional evolution of the E7 protein in papillomaviruses using 210 natural sequences. It finds that:
1) The intrinsically disordered N-terminal domain (E7N) and globular C-terminal domain (E7C) are both highly conserved, despite E7N lacking a stable structure.
2) Key linear motifs in E7N, like the LxCxE Rb-binding site and CKII phosphorylation site, have coevolved and suggest a functional relationship.
3) The C-terminal domain is also highly conserved, retaining zinc-binding cysteines and residues important for dimerization and interactions with cellular targets.
The algorithm discovers novel functional linear motifs within sets of unaligned protein sequences using a greedy approach. It identifies overrepresented short sequences or "motifs" that may mediate protein-protein interactions. The algorithm is tested on known motifs from databases, showing it can correctly identify several known motifs. As a case study, the algorithm extracts a putative nucleolar localization motif present in nucleolar proteins including the N-terminus of protein MAGE-B2, explaining its nucleolar localization.
Este documento describe un modelo estocástico para la regulación de la expresión génica que incluye múltiples sitios de unión para factores de transcripción en el sistema regulatorio cis. El modelo predice que la cooperatividad y el nivel de ruido aumentan con la energía de interacción entre los factores de transcripción. El modelo también distingue entre dos mecanismos de unión cooperativa que resultan en diferentes niveles de ruido aunque la expresión media sea la misma. El documento analiza el diagrama de fases para determinar las regiones donde
This document describes a computational study that aimed to predict heparin binding sites on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) using molecular docking simulations. The researchers developed a docking protocol that successfully identified heparin binding sites on other proteins. Applying this protocol, they predicted that positively charged residues on GAPDH interact with the negatively charged sulfate and carboxylate groups on heparin. The results provide insight into how protein-glycosaminoglycan interactions may contribute to amyloid formation associated with neurodegenerative diseases.
This document summarizes a study that analyzed three major evolutionary signals in protein sequences: conservation, specificity determining positions (SDPs), and coevolution between residues. These signals result from different evolutionary mechanisms and have been used by bioinformatics methods to predict functionally important sites. The study evaluated several methods for predicting conserved residues, SDPs, and coevolving positions using a dataset of 434 protein families. It found that the methods capture different information and identify different top-scoring residues. Conservation and mutual information scores performed best at detecting catalytic residues, but combining scores could improve predictions. SDP prediction remains challenging due to limited data and methods detecting conserved residues may miss SDPs until more sequences are available.
The document discusses predicting peptide interactions with MHC molecules to identify epitopes for vaccine design and diagnosis. It notes the challenges of identifying epitopes within pathogen genomes and accounting for human HLA diversity. It presents data on experimentally validating bioinformatics predictions of peptide-MHC binding, and discusses strategies for covering common HLA alleles based on clustering and representative alleles from different supertypes.
The document describes research to design degenerate primers to amplify a segment of the putative ACE-1 transcription factor gene in Peniophora sp. using bioinformatics tools. Researchers identified a conserved copper-fist DNA binding domain in the ACE-1 protein sequence of Phanerochaete chrysosporium that is about 50 amino acids long and 80-90% similar to other sequences. Degenerate primers targeting this conserved region were designed and analyzed in silico. The results suggest the conserved domain is likely important for function and differences are due to synonymous substitutions, supporting using online tools to accelerate molecular biology research.
Este documento describe el modelado tridimensional de la proteína P35 de Toxoplasma gondii y la predicción de sus epitopes. Los autores modelaron la estructura de P35 usando programas de modelado y evaluaron la calidad del modelo. Luego predijeron los epitopes lineales y estructurales de P35 usando programas de predicción de epitopes. La mayoría de las regiones antigénicas predichas se encuentran en la región media y N-terminal de la proteína. Actualmente están evaluando experimentalmente estas regiones como posibles antígenos
The document discusses balancing data for phenotype classification based on SNPs. It explains that training data often has imbalanced class distributions that do not reflect real-world proportions, affecting classifier design. Techniques are presented to balance discrete SNP data artificially by changing marginal distributions while keeping conditional distributions unchanged. This produces a classifier independent of sample proportions and more robust to incorrect prior assumptions. Balancing allows generating the same optimal classifier from any sample sizes.
The document proposes a new algorithm for gene selection that uses hierarchical clustering and the Silhouette index. Hierarchical clustering is used to group genes with similar expression into clusters. The Silhouette index measures how tightly grouped and separated clusters are. The algorithm ranks gene subsets based on their Silhouette index scores and selects the subsets with the highest scores, providing sets of genes with very similar expression patterns.
Bolstering is an error estimation technique that provides a less biased estimation than resubstitution. While a general bolstering model exists for continuous classification spaces, discrete classifiers present a more complex framework. The paper proposes a bolstering model for discrete classification based on a convolution kernel applied to conditional probabilities. This approach could help infer genetic regulatory functions from microarray data by deducing transcriptional states of genes based on other genes' states.
Biopython is a set of freely available Python tools for bioinformatics and molecular biology. It provides features like parsing bioinformatics files into Python structures, a sequence class to store sequences and features, and interfaces to popular bioinformatics programs. Biopython can be used to address common bioinformatics problems like sequence manipulation, searching for primers, and running BLAST searches. The current version is 1.53 from December 2009 and future plans include updating the multiple sequence alignment object and adding a Bio.Phylo module.
El documento resume los conceptos de estabilidad termodinámica y cinética en proteínas de dos y tres estados. Explica que la estabilidad termodinámica se refiere a la diferencia de energía libre entre los estados plegado y desplegado, mientras que la estabilidad cinética se refiere a las tasas de plegamiento y desplegamiento. Los estudios de mutaciones en múltiples proteínas muestran que el plegamiento se ve afectado negativamente pero el desplegamiento y la estabilidad general se ven afectados
El documento describe métodos para el análisis de vicarianza, un enfoque de biogeografía histórica que utiliza información geográfica directamente en lugar de áreas predefinidas. Se presentan algoritmos para representar distribuciones geográficas como árboles cuadrados y optimizar reconstrucciones biogeográficas mediante criterios que minimizan nodos no vicariantes. También se discuten heurísticas como "subida de colina" para encontrar soluciones óptimas en árboles grandes.
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This document analyzes the sequence and functional evolution of the E7 protein in papillomaviruses using 210 natural sequences. It finds that:
1) The intrinsically disordered N-terminal domain (E7N) and globular C-terminal domain (E7C) are both highly conserved, despite E7N lacking a stable structure.
2) Key linear motifs in E7N, like the LxCxE Rb-binding site and CKII phosphorylation site, have coevolved and suggest a functional relationship.
3) The C-terminal domain is also highly conserved, retaining zinc-binding cysteines and residues important for dimerization and interactions with cellular targets.
The algorithm discovers novel functional linear motifs within sets of unaligned protein sequences using a greedy approach. It identifies overrepresented short sequences or "motifs" that may mediate protein-protein interactions. The algorithm is tested on known motifs from databases, showing it can correctly identify several known motifs. As a case study, the algorithm extracts a putative nucleolar localization motif present in nucleolar proteins including the N-terminus of protein MAGE-B2, explaining its nucleolar localization.
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This document describes a computational study that aimed to predict heparin binding sites on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) using molecular docking simulations. The researchers developed a docking protocol that successfully identified heparin binding sites on other proteins. Applying this protocol, they predicted that positively charged residues on GAPDH interact with the negatively charged sulfate and carboxylate groups on heparin. The results provide insight into how protein-glycosaminoglycan interactions may contribute to amyloid formation associated with neurodegenerative diseases.
This document summarizes a study that analyzed three major evolutionary signals in protein sequences: conservation, specificity determining positions (SDPs), and coevolution between residues. These signals result from different evolutionary mechanisms and have been used by bioinformatics methods to predict functionally important sites. The study evaluated several methods for predicting conserved residues, SDPs, and coevolving positions using a dataset of 434 protein families. It found that the methods capture different information and identify different top-scoring residues. Conservation and mutual information scores performed best at detecting catalytic residues, but combining scores could improve predictions. SDP prediction remains challenging due to limited data and methods detecting conserved residues may miss SDPs until more sequences are available.
The document discusses predicting peptide interactions with MHC molecules to identify epitopes for vaccine design and diagnosis. It notes the challenges of identifying epitopes within pathogen genomes and accounting for human HLA diversity. It presents data on experimentally validating bioinformatics predictions of peptide-MHC binding, and discusses strategies for covering common HLA alleles based on clustering and representative alleles from different supertypes.
The document describes research to design degenerate primers to amplify a segment of the putative ACE-1 transcription factor gene in Peniophora sp. using bioinformatics tools. Researchers identified a conserved copper-fist DNA binding domain in the ACE-1 protein sequence of Phanerochaete chrysosporium that is about 50 amino acids long and 80-90% similar to other sequences. Degenerate primers targeting this conserved region were designed and analyzed in silico. The results suggest the conserved domain is likely important for function and differences are due to synonymous substitutions, supporting using online tools to accelerate molecular biology research.
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The document discusses balancing data for phenotype classification based on SNPs. It explains that training data often has imbalanced class distributions that do not reflect real-world proportions, affecting classifier design. Techniques are presented to balance discrete SNP data artificially by changing marginal distributions while keeping conditional distributions unchanged. This produces a classifier independent of sample proportions and more robust to incorrect prior assumptions. Balancing allows generating the same optimal classifier from any sample sizes.
The document proposes a new algorithm for gene selection that uses hierarchical clustering and the Silhouette index. Hierarchical clustering is used to group genes with similar expression into clusters. The Silhouette index measures how tightly grouped and separated clusters are. The algorithm ranks gene subsets based on their Silhouette index scores and selects the subsets with the highest scores, providing sets of genes with very similar expression patterns.
Bolstering is an error estimation technique that provides a less biased estimation than resubstitution. While a general bolstering model exists for continuous classification spaces, discrete classifiers present a more complex framework. The paper proposes a bolstering model for discrete classification based on a convolution kernel applied to conditional probabilities. This approach could help infer genetic regulatory functions from microarray data by deducing transcriptional states of genes based on other genes' states.
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El documento resume los conceptos de estabilidad termodinámica y cinética en proteínas de dos y tres estados. Explica que la estabilidad termodinámica se refiere a la diferencia de energía libre entre los estados plegado y desplegado, mientras que la estabilidad cinética se refiere a las tasas de plegamiento y desplegamiento. Los estudios de mutaciones en múltiples proteínas muestran que el plegamiento se ve afectado negativamente pero el desplegamiento y la estabilidad general se ven afectados
El documento describe métodos para el análisis de vicarianza, un enfoque de biogeografía histórica que utiliza información geográfica directamente en lugar de áreas predefinidas. Se presentan algoritmos para representar distribuciones geográficas como árboles cuadrados y optimizar reconstrucciones biogeográficas mediante criterios que minimizan nodos no vicariantes. También se discuten heurísticas como "subida de colina" para encontrar soluciones óptimas en árboles grandes.
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