42 research outputs found
Polyketide Synthase III isolated from uncultured deep-sea Proteobacterium from the Red Sea- functional and evolutionary characterization
No full textNatural polyketide products are one of the major secondary metabolites produced among bacteria, fungi, and plants. They vary from flavonoids, pyrones, and stilbenes to phloroglucinols and resorcinols that are involved in important functions as antimicrobial activity, defense mechanisms and pigmentation. They are biosynthesized from acyl-CoA precursors by polyketides synthases (PKSs) that are categorized into 3 types: I, II and III. PKS type III is considered the simplest in its structure. It was believed that PKS type III was exclusively encoded by higher plants until the enduring efforts of bacterial genomes sequencing revealed the presence of more and more PKSs type III among them. There is an urge to investigate novel PKSs type III due to their promising polyketides of great biological and pharmaceutical advantages. This allowed metagenomic approaches to be a valuable tool to explore diverse environments for PKSs type III. Extreme environments as deep sea brine pools could probe unique natural polyketides capable of functioning in such conditions with valuable biotechnological and pharmaceutical applications. In this study, screening of the Lower Convective Layer (LCL) of Atlantis II (ATII) deep brine pool in the Red Sea was done. It identified sequences belonging to bacterial PKSs type III. A candidate encoding sequence was amplified from the environmental DNA. Functional annotations were assigned to the translated open reading frame including the conserved catalytic triad, domains, motifs and 3D modelling. Preliminary structural analysis showed well-fitted superimposition with the flowering plant Medicago sativa PKS type III crystal structure and predicted the interaction of the catalytic triad with the most common substrate malonyl-CoA. Further optimization of heterologous expression is required to investigate this isolated PKS type III functional activity. In an approach to gain better insights into the enzyme’s unresolved evolutionary origin, a comprehensive phylogenetic analysis was conducted. The analysis pinpoints the possible involvement of symbiotic bacterium Parachlamydia acanthamoebae in horizontal gene transfer events to eukaryotes. On the other hand, the sequence isolated from ATII brine pool was clustered in a clade with related PKSs type III sequences belonging to alpha-proteobacteria. Environmental assessment of PKSs type III abundance in ATII and nearby Discovery Deep (DD) brine pool revealed the presence of PKSs type III in ATII only, where most sequences were located in the LCL. This could be attributed to the high aromatic content within the brine as possible substrates for the enzyme. Based on these analyses, we could propose ATII microbial community as a unique source for natural polyketides
Eco-conscious upcycling of sugarcane bagasse into flexible polyurethane foam for mechanical & acoustic relevance
No full textThis study explores the use of sugarcane bagasse (SCB), a byproduct of sugarcane processing, as a bio-filler in the production of flexible polyurethane foam (FPU), focusing on its benefits for both the environment and the economy. By varying the inclusion of SCB waste from 1 to 6 wt%, the research aims to enhance the FPU's mechanical and acoustic characteristics. Techniques such as Fourier transform infrared (FTIR) spectroscopy and field emission scanning electron microscopy (FESEM) were utilized to analyze the chemical structure and surface characteristics of both SCB and the FPU/SCB composites. Additionally, tests on gel fraction, density, and mechanical properties were conducted. The results indicate that adding 4 wt% SCB to FPU considerably improved the foam's properties. This modification resulted in a 148.63% increase in apparent density, a 228.47% rise in compressive strength, and a 116.24% boost in tensile strength. Furthermore, sound absorption across various frequency ranges was enhanced compared to the control foam. Additionally, the findings show that SCB effectively shifts sound absorption characteristics to lower frequencies. Specifically, at a low frequency of 500 Hz, the sound absorption coefficient increased to 0.4 with a foam thickness of 20 mm. This demonstrates that SCB can significantly improve FPU's performance, making it an attractive option for applications requiring noise mitigation, such as in the automotive and construction industries, thereby offering a sustainable solution to waste management and materials innovation.This article is published as El-Metwaly, Esraa A., Hadeel E. Mohamed, Tarek M. El-Basheer, Manal TH Moselhy, Sonia Zulfiqar, Eric W. Cochran, and Ahmed Abdelhamid Maamoun. "Eco-conscious upcycling of sugarcane bagasse into flexible polyurethane foam for mechanical & acoustic relevance." RSC advances 14, no. 33 (2024): 23683-23692.
doi: https://doi.org/10.1039/D4RA04025B. © 2024 The Author(s). This Open Access Article is licensed under a Creative Commons Attribution-Non Commercial 3.0 Unported Licence
Caries, oral hygiene status and dates consumption among Saudi female university students
No full textAuthors: Al Essa, Noura A., Al Mutairi, Manal A., Al Ohali, Hadeel M. From
Intern, King Saud University College of Dentistry
Authors: El Hejazi, Ahmed, Associate Professor, RDS Department, Operative Dentistry Division, King Saud University
College of Dentistry, Riyadh.
Author: Chohan, Arham, Lecturer, PDS Department, Pediatric Dentistry Division, King Saud University College of
Dentistry, RiyadhThe objectives of the present study were to determine the caries experience, oral hygiene
status and consumption of dates among Saudi female University students. A total of 406
female University students were examined for dental caries and oral hygiene. The information
about oral hygiene practices and consumption of dates was obtained through a selfadministered
questionnaire. The mean DMFT was 10.01 (SD 4.71) with a decay (D)
component of 5.87 (SD 4.28), missing (M) component of 0.83 (SD 1.44) and filled
component of 3.31 (SD 3.92). There was significant (p< .05) difference observed between the
mean DMFT scores of the students from various age groups. Only one-fourth (25.6%) of the
students had good oral hygiene. A positive correlation (p< .0001) was exhibited between the
mean DMFT scores and oral hygiene. Almost all (98.0%) students used brush to clean their
teeth. A majority of the students were cleaning their teeth twice (47.0%) or thrice (22.4%)
daily and only about one in ten (12.3%) students’ used miswak to clean their teeth. More than
three-fourth (81.0%) students were eating dates and about one-fourth (24.4%) of the students
were eating 5-10 dates per day. No significant (p> .05) correlation was observed between
caries and dates consumption. It was concluded that the caries prevalence and severity was
very high. Only small percentage of the students had good oral hygiene and eight in every ten
students was eating dates daily
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacterium from the Red Sea – Functional and Evolutionary Characterization
No full text<p>Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool in the Red Sea using a metagenomic approach and gaining deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes</p
The effect of increased lipoproteins levels on the disposition of vincristine in rat
No full textBackground: Vincristine (VCR), an antineoplastic agent, is a key component in the treatment of acute lymphoblastic leukemia, lymphomas, rhabdomyosarcoma, neuroblastoma, and Wilms' tumor diseases. Recently, high incidence of hyperlipidemia was reported to be associated with allogenic hematopoietic stem cell transplantation and VCR/L-asparaginase therapy. The aim of this study is to test the effects of incremental increase in lipoproteins levels on vincristine disposition in rat. Method: To study VCR pharmacokinetics and protein binding, rats (n = 25) were assigned to three groups, normal lipidemic (NL), intermediate (IHL) and extreme hyperlipidemic (HL). Hyperlipidemia was induced by ip injection of (1 g/Kg) poloxamer 407 in rats. Serial blood samples were collected using the pre-inserted jugular vein cannula for 72 h post VCR (0.15 mg/Kg) i.v. dose. VCR unbound fractions in NL, IHL and HL plasma were determined using ultrafiltration kits. Results: VCR demonstrated a rapid distribution phase (6-8 h) followed by a slower elimination phase with a mean elimination t of ~ 14 h. VCR exhibited moderate binding to plasma proteins ~ 83 %. It showed a relatively small Vc (~0.17 L/Kg) and a larger Vβ (1.53 L/Kg) indicating good tissue distribution. As the lipoproteins levels were increased, no significant changes were noted in VCR unbound fraction, plasma concentration, or volume of distribution indicating low affinity to lipoprotein binding. Induced HL also did not affect VCR elimination where similar VCR AUC0-∞, Cl and elimination phase t were reported along the different lipemic groups. Conclusion: Incremental increase in lipoprotein levels resulted in no significant effect on VCR disposition as such ALL malignant lymphoma and allogenic hematopoietic stem cell transplantation patients need not to worry about HL-VCR interaction. Whether, HL can potentiate another drug-drug or drug-disease interaction involving VCR warrants further studying and monitoring to ensure therapeutic safety and efficiency. © 2016 The Author(s)
From deterministic methods to a Bayesian approximation: towards reliable segmentation of multiple sclerosis Lesions in magnetic resonance imaging
No full textEn este trabajo, se presenta una metodología para la segmentación de lesiones de esclerosis múltiple (EM) en imágenes de resonancia magnética (IRM) que aborda las limitaciones de los modelos deterministas mediante la incorporación de la estimación de incertidumbre. Se compara una arquitectura U-Net 3D determinista con una versión modificada que emplea una aproximación bayesiana con Monte Carlo Dropout (MCD) para cuantificar la incertidumbre epistémica. Los resultados demuestran que, si bien ambos modelos alcanzan un rendimiento competitivo en términos de las métricas estándar de segmentación de imágenes médicas, la estimación de incertidumbre proporciona información valiosa sobre la fiabilidad de las predicciones, especialmente en regiones desafiantes como los bordes de las lesiones. Esto tiene el potencial de mejorar la aplicabilidad clínica de la segmentación automática al permitir a los usuarios médicos evaluar la confianza en los resultados y enfocar su revisión en áreas de mayor incertidumbre.In this work, we present a methodology for the segmentation of multiple sclerosis (MS) lesions in magnetic resonance imaging (MRI) that addresses the limitations of deterministic models by incorporating uncertainty estimation. We compare a deterministic 3D U-Net architecture with a modified version that employs a Bayesian approximation with Monte Carlo Dropout (MCD) to quantify epistemic uncertainty. The results demonstrate that while both models achieve competitive performance in terms of standard medical image segmentation metrics, the uncertainty estimation provides valuable information on the reliability of the predictions, especially in challenging regions such as lesion borders. This has the potential to improve the clinical applicability of automatic segmentation by allowing medical users to assess confidence in the results and focus their review on areas of higher uncertainty
Design of an architecture based on Grid Computing for the management of repositories of online learning objects of public access
No full textEste trabajo introduce una arquitectura computacional basada en Grid Computing para el montaje, almacenamiento, y visualización de repositorios de objetos de aprendizaje (OAs) soportado en herramientas de código abierto, i.e., Dspace. La solución, aquí presentada, se ha implementado teniendo en cuenta, la descripción de las especificaciones técnicas y de usuario del repositorio, un cuadro comparativo de los distintos aplicativos de código abierto para la gestión de repositorios educativos/contenido digital publicable; y por último, el diseño de la arquitectura computacional donde opera el repositorio, y se ofrecen servicios. Para validar la solución, se considera un ecosistema digital que opera de manera independiente, i.e., Programa Ondas de Santander; el cual ofrece los actores y medios necesarios para incentivar el trabajo colaborativo y el máximo aprovechamiento de la arquitectura. En síntesis, este documento describe en detalle el diseño de una arquitectura computacional y un repositorio operacional, los cuales pueden aprovechar al máximo los servicios tecnológicos de la Red Nacional Académica de Tecnología Avanzada – RENATA; y de esta manera contribuir al fortalecimiento de la capacidad científica y tecnológica de los sectores estratégicos del Departamento de Santander.INTRODUCCIÓN 18
1. MARCO CONCEPTUAL 26
1.1 GRID DE CÓMPUTO 26
1.2 E-SCIENCE 28
1.3 OBJETO DE APRENDIZAJE 31
1.4 REPOSITORIOS 35
1.5 PLATAFORMA DE SOFTWARE PARA REPOSITORIOS INSTITUCIONALES 38
1.6 SOFTWARE DE UN REPOSITORIO INSTITUCIONAL 42
2. ESTADO DEL ARTE 44
2.1 REFERENTES INTERNACIONALES DE INICIATIVAS DE GRID 44
2.2 PRINCIPALES PROYECTOS INTERNACIONALES Y NACIONALES DE REPOSITORIOS 47
2.3 ARQUITECTURA DEL REPOSITORIO DE LA BIBLIOTECA DIGITAL COLOMBIANA - BDCOL 49
2.4 DESCRIPCIÓN DE PROYECTOS EN LA BIBLIOTECA DIGITAL COLOMBIANA 50
3. PROCESO INVESTIGATIVO 55
3.1 ASPECTOS METODOLÓGICOS 55
3.2 RELACIÓN DE OBJETIVOS CON INDICADORES, ACTIVIDADES Y RESULTADOS 57
4. RESULTADOS 60
4.1 IDENTIFICACIÓN DE LOS ACTORES Y SU GRADO DE PARTICIPACIÓN EN LA ARQUITECTURA DE CÓMPUTO 61
4.2 DEFINICIÓN DE REQUERIMIENTOS FUNCIONALES Y NO FUNCIONALES PARA LA ARQUITECTURA DE CÓMPUTO 77
4.3 SELECCIÓN DEL SOFTWARE DE REPOSITORIO PARA OBJETOS DE APRENDIZAJE 83
4.4 ESPECIFICACIONES TÉCNICAS PARA LA ARQUITECTURA GRID DISEÑADA 91
4.5 DISEÑO DE LA ARQUITECTURA DE CÓMPUTO BASADA EN COMPUTACIÓN GRID 99
4.6 ESPECIFICACIONES TÉCNICAS PARA EL REPOSITORIO 103
4.7 PROTOTIPO DE REPOSITORIO INSTALADO: “REPOSITORIO PARA ONDAS SANTANDER - ENLAZA2” 103
4.8 RESULTADOS DE LA EVALUACIÓN DE LA FUNCIONALIDAD DE LA ARQUITECTURA 111
4.9 RECOMENDACIONES Y PERSPECTIVAS PARA EL REPOSITORIO ENLAZA2 115
5. CONCLUSIONES 116
BIBLIOGRAFÍA 118MaestríaThis work introduces a computational architecture based on Grid Computing for the assembly, storage, and visualization of learning object repositories (OAs) supported by open source tools, i.e., Dspace. The solution, presented here, has been implemented taking into account, the description of the technical and user specifications of the repository, a comparative table of the different open source applications for the management of educational repositories / publishable digital content; and lastly, the design of the computational architecture where the repository operates, and services are offered. To validate the solution, a digital ecosystem that operates independently is considered, i.e., the Ondas de Santander Program; which offers the actors and means necessary to encourage collaborative work and the maximum use of architecture. In summary, this document describes in detail the design of a computational architecture and an operational repository, which can take full advantage of the technological services of the National Academic Network of Advanced Technology - RENATA; and in this way contribute to the strengthening of the scientific and technological capacity of the strategic sectors of the Santander Department.Modalidad Presencia
SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues
No full textVariability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types. © 2021 The Author(s
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.
No full textHost genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights
Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19
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