Assessing computational methods and science policy in systems biology

Thesis (S.M. in Technology and Policy)--Massachusetts Institute of Technology, Engineering Systems Division, Technology and Policy Program, 2009.Includes bibliographical references (p. 109-112).In this thesis, I discuss the development of systems biology and issues in the progression of this science discipline. Traditional molecular biology has been driven by reductionism with the belief that breaking down a biological system into the fundamental biomolecular components will elucidate such phenomena. We have reached limitations with this approach due to the complex and dynamical nature of life and our inability to intuit biological behavior from a modular perspective [37]. Mathematical modeling has been integral to current system biology endeavors since detailed analysis would be invasive if performed on humans experimentally or in clinical trials [17]. The interspecies commonalities in systemic properties and molecular mechanisms suggests that certain behaviors transcend specie differentiation and therefore easily lend to generalizing from simpler organisms to more complex organisms such as humans [7, 17]. Current methodologies in mathematical modeling and analysis have been diverse and numerous, with no standardization to progress the discipline in a collaborative manner. Without collaboration during this formative period, successful development and application of systems biology for societal welfare may be at risk. Furthermore, such collaboration has to be standardized in a fundamental approach to discover generic principles, in the manner of preceding long-standing science disciplines. This study effectively implements and analyzes a mathematical model of a three-protein biochemical network, the Synechococcus elongatus circadian clock.(cont.) I use mass action theory expressed in kronecker products to exploit the ability to apply numerical methods-including sensitivity analysis via boundary value formulation (BVP) and trapiezoidal integration rule-and experimental techniques-including partial reaction fitting and enzyme-driven activations-when mathematically modeling large-scale biochemical networks. Amidst other applicable methodologies, my approach is grounded in the law of mass action because it is based in experimental data and biomolecular mechanistic properties, yet provides predictive power in the complete delineation of the biological system dynamics for all future time points. The results of my research demonstrate the holistic approach that mass action method-ologies have in determining emergent properties of biological systems. I further stress the necessity to enforce collaboration and standardization in future policymaking, with reconsiderations on current stakeholder incentive to redirect academia and industry focus from new molecular entities to interests in holistic understanding of the complexities and dynamics of life entities. Such redirection away from reductionism could further progress basic and applied scientific research to embetter our circumstances through new treatments and preventive measures for health, and development of new strains and disease control in agriculture and ecology [13].by Andrea R. Castillo.S.M.in Technology and Polic

Overexpressing Two Helicobacter pylori Small RNAs from a Bacterial Pathogenicity-related Chromosomal Region to Investigate Their Regulation of Virulence Genes

The bacterial pathogen Helicobacter pylori infects the stomachs of approximately 50% of humanity, causing symptomatic disease (e.g., stomach ulcers, gastric cancer, and MALT lymphoma) in 10-15% of the infected. Colonizing the acidic, inhospitable stomach requires H. pylori to tightly regulate gene expression despite lacking many common bacterial genetic regulatory elements. The pathogen may compensate by using abundant non-protein-coding small RNAs (sRNAs) to regulate gene expression, including of infection-intensifying virulence genes. Additionally, severe disease and cancer correlate with infection by H. pylori strains that contain a nonessential chromosomal region, the cytotoxin-associated gene pathogenicity island (cagPAI). This encodes powerful virulence factors that include a mechanism for injecting a cancer-promoting protein (CagA) into host cells. Despite identification of multiple cagPAI sRNAs, regulatory effects of only one have been characterized. To investigate potential sRNA-mediated regulation of RNA gene expression in the cagPAI and other virulence genes, we are developing strains overexpressing (abundantly producing) two promising cagPAI sRNAs. We cloned experimental plasmids (circular DNA molecules) to contain an overexpression promoter element and the relevant sRNA. Subsequently, we will introduce these plasmids into H. pylori to generate two sRNA-overexpressing strains. Finally, we will compare total RNA harvested from these two strains and the unmodified strain using RNA sequencing and reverse transcription quantitative polymerase chain reaction (RT-qPCR). The resulting identification/quantification of any significant regulation by these two H. pylori cagPAI sRNAs could illuminate aspects of sRNA regulation of the cancer-associated cagPAI region and other virulence genes

The yeast protein kinase Mps1p is required for assembly of the integral spindle pole body component Spc42p

Saccharomyces cerevisiae MPS1 encodes an essential protein kinase that has roles in spindle pole body (SPB) duplication and the spindle checkpoint. Previously characterized MPS1 mutants fail in both functions, leading to aberrant DNA segregation with lethal consequences. Here, we report the identification of a unique conditional allele, mps1–8, that is defective in SPB duplication but not the spindle checkpoint. The mutations in mps1-8 are in the noncatalytic region of MPS1, and analysis of the mutant protein indicates that Mps1-8p has wild-type kinase activity in vitro. A screen for dosage suppressors of the mps1-8 conditional growth phenotype identified the gene encoding the integral SPB component SPC42. Additional analysis revealed that mps1-8 exhibits synthetic growth defects when combined with certain mutant alleles of SPC42. An epitope-tagged version of Mps1p (Mps1p-myc) localizes to SPBs and kinetochores by immunofluorescence microscopy and immuno-EM analysis. This is consistent with the physical interaction we detect between Mps1p and Spc42p by coimmunoprecipitation. Spc42p is a substrate for Mps1p phosphorylation in vitro, and Spc42p phosphorylation is dependent on Mps1p in vivo. Finally, Spc42p assembly is abnormal in a mps1-1 mutant strain. We conclude that Mps1p regulates assembly of the integral SPB component Spc42p during SPB duplication

Métodos moleculares para diagnóstico de niños con tuberculosis en países de Latinoamérica

The diagnosis of tuberculosis in the childhood population represents a major obstacle to the health system because the pediatric patient is paucibacillary. This is done by four classic criteria: epidemiological, tuberculinic, radiological and clinical; however, this method has an approximate sensitivity of 50%. On the other hand, molecular tests are new methods for the diagnosis and treatment of these infections, due to the rapidity of the result, high sensitivity, specificity and also, it reports resistance to antituberculosis drugs. Therefore, the objective of the review is to investigate the diagnosis of molecular methods in pediatric tuberculosis, since it is considered a vulnerable population, with more probability of disease progression, diagnostic problems due to the condition of being pediatric patients, the difficult microbiological isolation and therapeutic difficulties. Objective: describe the evidence on the use of molecular tests in the diagnosis of childhood tuberculosis in Latin American countries reported in the scientific literature. Materials and methods: a narrative review of the literature was performed. The selection criteria were articles that evaluated molecular tests in pediatric patients up to 18 years with a diagnosis of tuberculosis in Latin American countries. A structured search was conducted in Medline via OVID and Embase using the keywords “tuberculosis”, “pediatric”, “children”, “diagnosis” and “molecular”. The language was limited to English and Spanish, but there was no date limit. Results: 1050 articles were found, of which 751 articles were removed by the selection criteria in the title / summary and 95 articles in the full text. A qualitative analysis was performed with the 8 selected articles, which were published between 2003 and 2018, in addition 50 % of the articles were made in Peru. It was also found that the nested PCR test was implemented in 87.5 % of the studies and only 12.5 % used the GeneXpert MTB / RIF test. Most of the articles showed that nPCR has high specificity, but low sensitivity compared to liquid cultures. The nPCR has a tendency to have more false positives. Conclusions: although there are multiple molecular tests, only the report of the nested PCR test and GeneXpert MTB / RIF was found in the articles. There is little literature reported on the application of molecular diagnostic methods in the pediatric population for Latin America.PublishedEl diagnóstico de tuberculosis en la población infantil representa un gran obstáculo para el sistema de salud porque el paciente pediátrico es paucibacilar. Este se realiza mediante cuatro criterios clásicos: epidemiológico, tuberculínico, radiológico y clínico; sin embargo, este método tiene una sensibilidad aproximada del 50 %. Por otro lado, las pruebas moleculares son métodos nuevos para el diagnóstico de estas infecciones, por la rapidez del resultado, una alta sensibilidad, especificidad y además, reporta la resistencia a los fármacos antituberculosos. Por lo anterior el objetivo de la revisión es investigar acerca del diagnóstico de métodos moleculares en tuberculosis pediátrica, ya que se considera que esta es una población vulnerable, teniendo más probabilidad de progresión de la enfermedad, problemas en el diagnóstico por la dificultad en la toma de los exámenes, la dificultad del aislamiento microbiológico y las dificultades terapéuticas. Objetivo: describir la evidencia sobre el uso de pruebas moleculares en el diagnóstico de tuberculosis infantil en países de Latinoamérica reportadas en la literatura científica. Materiales y métodos: se realizó una revisión narrativa de la literatura. Los criterios de selección fueron artículos que evaluaran pruebas moleculares en pacientes pediátricos hasta los 18 años con diagnóstico de tuberculosis en países de Latinoamérica. Se realizó una búsqueda estructurada en Medline vía OVID y Embase utilizando las palabras clave “tuberculosis”, “pediatric”, “children”, “diagnosis” y “molecular”. Se limitó el lenguaje al inglés y español, pero no se tuvo límite de fecha. Resultados: se encontraron 1050 artículos, de los cuales se eliminaron 751 artículos por los criterios de selección en el título/resumen y 95 artículos en el texto completo. Se realizó un análisis cualitativo con los ocho artículos seleccionados, los cuales fueron publicados entre el 2003 y 2018; además el 50 % de los artículos se realizaron en Perú. También se encontró que en el 87.5 % de los estudios se implementó la prueba PCR anidada y solo el 12.5 % utilizó la prueba GeneXpert MTB/RIF. La mayor parte de los artículos mostraron que la PCR anidada tiene alta especificidad, pero baja sensibilidad comparada con los cultivos líquidos. La nPCR tiene tendencia a tener más falsos positivos. Conclusiones: aunque existen múltiples pruebas moleculares, en los artículos solo se encontró el reporte de la prueba PCR anidada y GeneXpert MTB/RIF. Existe poca literatura reportada de la aplicación de los métodos diagnósticos moleculares en población pediátrica para Latinoamérica

Oxidative Cleavage of Cellobiose by Lytic Polysaccharide Monooxygenase (LPMO)-Inspired Copper Complexes

Correction published on October 23, 2020 https://doi.org/10.1021/acsomega.0c04910The potentially tridentate ligand bis[(1-methyl-2-benzimidazolyl)ethyl]amine (2BB) was employed to prepare copper complexes [(2BB)CuI]OTf and [(2BB)CuII(H2O)2](OTf)2 as bioinspired models of lytic polysaccharide copper-dependent monooxygenase (LPMO) enzymes. Solid-state characterization of [(2BB)CuI]OTf revealed a Cu(I) center with a T-shaped coordination environment and metric parameters in the range of those observed in reduced LPMOs. Solution characterization of [(2BB)CuII(H2O)2](OTf)2 indicates that [(2BB)CuII(H2O)2]2+ is the main species from pH 4 to 7.5; above pH 7.5, the hydroxo-bridged species [{(2BB)CuII(H2O)x}2(μ-OH)2]2+ is also present, on the basis of cyclic voltammetry and mass spectrometry. These observations imply that deprotonation of the central amine of Cu(II)-coordinated 2BB is precluded, and by extension, amine deprotonation in the histidine brace of LPMOs appears unlikely at neutral pH. The complexes [(2BB)CuI]OTf and [(2BB)CuII(H2O)2](OTf)2 act as precursors for the oxidative degradation of cellobiose as a cellulose model substrate. Spectroscopic and reactivity studies indicate that a dicopper(II) side-on peroxide complex generated from [(2BB)CuI]OTf/O2 or [(2BB)CuII(H2O)2](OTf)2/H2O2/NEt3 oxidizes cellobiose both in acetonitrile and aqueous phosphate buffer solutions, as evidenced from product analysis by high-performance liquid chromatography-mass spectrometry. The mixture of [(2BB)CuII(H2O)2](OTf)2/H2O2/NEt3 results in more extensive cellobiose degradation. Likewise, the use of both [(2BB)CuI]OTf and [(2BB)CuII(H2O)2](OTf)2 with KO2 afforded cellobiose oxidation products. In all cases, a common Cu(II) complex formulated as [(2BB)CuII(OH)(H2O)]+ was detected by mass spectrometry as the final form of the complex

Aging dynamics of heterogeneous spin models

We investigate numerically the dynamics of three different spin models in the aging regime. Each of these models is meant to be representative of a distinct class of aging behavior: coarsening systems, discontinuous spin glasses, and continuous spin glasses. In order to study dynamic heterogeneities induced by quenched disorder, we consider single-spin observables for a given disorder realization. In some simple cases we are able to provide analytical predictions for single-spin response and correlation functions. The results strongly depend upon the model considered. It turns out that, by comparing the slow evolution of a few different degrees of freedom, one can distinguish between different dynamic classes. As a conclusion we present the general properties which can be induced from our results, and discuss their relation with thermometric arguments.Comment: 39 pages, 36 figure

TOROS optical follow-up of the advanced LIGO–VIRGO O2 second observational campaign

We present themethods and results of the optical follow-up, conducted by the Transient Optical Robotic Observatory of the South Collaboration, of gravitational wave events detected during the Advanced LIGO–Virgo second observing run (2016 November–2017 August). Given the limited field of view (∼100 arcmin) of our observational instrumentation, we targeted galaxies within the area of high localization probability that were observable from our sites. We analysed the observations using difference imaging, followed by a random forest algorithm to discriminate between real and spurious transients. Our observations were conducted using telescopes at Estacion Astrofısica de Bosque Alegre, Cerro Tololo Inter-American Observatory, the Dr. Cristina V. Torres Memorial Astronomical Observatory, and an observing station in Salta, Argentina

Influence of the activation time on the development of the porosity of physically activated carbons

En este trabajo se estudia la influencia en la porosidad de carbones activados mediante una mezcla de vapor de agua y nitrógeno, en función del tiempo de activación. Este estudio se basa en la aplicación de tres métodos de análisis distintos: el conocido método DFT, un método analítico basado en una combinación de las ecuaciones de BET y de Kelvin, y un método de simulación de Monte Carlo. Dichos métodos son aplicados sobre los datos obtenidos de las isotermas de adsorción de nitrógeno a 77K sobre una serie de muestras de carbón activado obtenidas bajo condiciones cuidadosamente controladas. Los resultados obtenidos son consistentes para los tres métodos, lo que permite extraer conclusiones confiables sobre la influencia del tiempo de activación en las características de los carbones obtenidos.In this work, the influence of the activation time on the development of the porosity is studied for carbons activated by means of a mixture of water vapor and nitrogen. The study is based on the application of three different methods of analysis: the well known DFT method, an analytical method base don a combination of the BET and Kelvin equations, and a Monte Carlo simulation method. These methods are applied to experimental data of nitrogen adsorption isotherms at 77K for a series of activated carbons obtained under carefully controlled conditions. Results turn out to be consistent among the three methods, leading to reliable conclusions about the influence of the activation time on the characteristics of the obtained carbons.Fil: Toso, Juan Pablo. Universidad Nacional de San Luis. Facultad de Ciencias Fisico Matematicas y Naturales. Departamento de Fisica. Laboratorio de Ciencias de Superficies y Medios Porosos; ArgentinaFil: Aja Muñiz, R.. Centro de Investigación para la Industria Minero ; CubaFil: Vallone, Andrea Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Fernández Rodriguez, A.. Centro de Investigación para la Industria Minero ; CubaFil: Castillo, C.R.. Centro de Investigación para la Industria Minero ; CubaFil: Sapag, Manuel Karim. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Zgrablich, Jorge Andres. Universidad Nacional de San Luis. Facultad de Ciencias Fisico Matematicas y Naturales. Departamento de Fisica. Laboratorio de Ciencias de Superficies y Medios Porosos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis; Argentin

Cribado de Citomegalovirus en mujeres embarazadas

Introduction: Cytomegalovirus (CMV) is a DNA virus of the family Herpesviridae, constitutes one of the main causes of congenital infections in the world, the overall prevalence of births in developed countries is 0.64% and the incidence of 1% -7%. The rate of acquisition of CMV in pregnant women is 2% per year, in the medium-high socioeconomic level and 6% at lower levels. The susceptibility is greater in African-American and Hispanic women. The risk ofmaternal-fetal transmission increases with advancing gestational age, also (30-40%) depends on maternal primary infection both seroconversion and in the revival (1-2%), highlighting that the pre-existing maternal immunity not prevent intrauterine transmission or the development of the disease. Objective: To evaluate the frequency of Cytomegalovirus infection in pregnant women. Material and methods: a study of non-experimental, observational -cross in the pro-life basic Hospital, of the city of Latacunga,Ecuador. Analyzed 981 results of screening for IgG and IgM for CMV, pregnant womages between 14 and 45 years who were enrolled in the first trimester of pregnancy, the period between January 1, 2013 to December 31, 2016. Descriptive statistical methods were used. Results: IgG positive was 95.7% and no positive result for IgM. Conclusions: We cannot support universal screening for CMV, by the low prevalence of infection.Introducción: El citomegalovirus(CMV)es un ADN virus, de la familia Herpesviridae, constituye una de las principales causas de infecciones congénitas en el mundo, la prevalencia general de nacimientos en países desarrollados es de 0,64% y la incidencia del 1% -7%. La tasa de adquisición de CMV en mujeres embarazadas es de 2% anual,en el nivel socioeconómico medio-alto y 6% en niveles más bajos. La susceptibilidad es mayor en mujeres afroamericanas e hispanas. El riesgo de transmisión materno-fetalseincrementa con el avance de la edad gestacional, además depende de la seroconversión materna tanto en la primoinfección (30-40%) como en la reactivación (1-2%), poniendo en evidencia que la inmunidad materna preexistente no previene la transmisión intrauterina o el desarrollo de la enfermedad. Objetivo: Evaluar la frecuencia deinfección por Citomegalovirus en mujeres embarazadas. Material y métodos: Se realizó un estudio no experimental, observacional –transversal en el Hospital Básico PROVIDA, de la cuidad de Latacunga, Ecuador. Se analizaron 981 resultados de screening de IgG e IgM para CMV, de mujeres gestantes en edades entre 14 y 45 años que cursaban el primer trimestre de embarazo, del periodo comprendido entre el 1 de enero de 2013 al 31 de diciembre de 2016.Se utilizaron métodos estadísticos descriptivos. Resultados: La IgG fue positiva el 95,7% y ningún resultado positivo para IgM. Conclusiones: No podemos apoyar el cribado universal de CMV, por la baja prevalencia de primoinfeccion