The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to ...assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset.
Background and aims The Tehuacán-Cuitcatlán reserve is an area of unique plant biodiversity mostly in the form of xerophytes, with exceptionally high numbers of rare and endemic species. This ...endemism results partly from the characteristics of the climate of this area, with two distinct seasons: rainy and dry seasons. Although rhizosphere communities must be critical in the function of this ecosystem, understanding the structure of these communities is currently limited. This is the first molecular study of the microbial diversity present in the rhizosphere of Mamillaria carnea. Methods Total DNA was obtained from soil and rhizosphere samples at three locations in the Tehuacán Cuicatlán Reserve, during dry and rainy seasons. Temperature gradient gel electrophoresisis (TGGE) fingerprinting, 16S rRNA gene libraries and pyrosequencing were used to investigate bacterial diversity in the rhizosphere of Mammillaria carnea and changes in the microbial community between seasons. Results Deep sequencing data reveal a higher level of biodiversity in the dry season. Statistical analyses based on these data indicates that the composition of the bacterial community differed between both seasons affecting to members of the phyla Acidobacteria, Cyanobacteria, Gemmatimonadetes, Plantomycetes, Actinobacteria and Firmicutes. In addition, the depth of sequencing performed (>24,000 reads) enables detection of changes in the relative abundance of lower bacterial taxa (novel bacterial phylotypes) indicative of the increase of specific bacterial populations due to the season. Conclusions This study states the basis of the bacterial diversity in the rhizosphere of cacti in semi-arid environments and it is a sequence-based demonstration of community shifts in different seasons.
Group II introns in the bacterial world Martínez‐Abarca, Francisco; Toro, Nicolás
Molecular microbiology,
December 2000, Letnik:
38, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Group II introns are large catalytic RNA molecules that act as mobile genetic elements. They were initially identified in the organelle genomes of lower eukaryotes and plants, and it has been ...suggested that they are the progenitors of nuclear spliceosomal introns. Group II self‐splicing introns were shown to be present in bacteria in 1993, since when the various bacterial genome sequencing projects have led to a significant increase in the number of group II intron sequences present in databases. However, few of these introns have been characterized, and most were identified on the basis of their intron‐encoded protein (IEP), with little data available concerning their ribozyme/RNA structure. Their frequency in prokaryotes is also unknown. We attempt here to provide a first comprehensive review of bacterial group II introns based on recent genome sequencing data and mechanistic studies.
•Sustainable tailings management strategies are needed to address mining waste.•Secondary mining of tailings for industrial materials is a viable remediation option.•DES is a powerful tool to assess ...and mitigate operational risk in mining systems.•Alternate modes of operation are critical to developing effective DES frameworks.•Geostatistical heterogeneity can be suitably integrated into geometallurgy via DES.
Discrete event simulation (DES) is a computational tool capable of simulating the interplay of important variables and processes within complex mining systems that are subject to geological uncertainty. Alternate modes of operation are fundamental to the development of effective DES frameworks to model and monitor system performance in response to unexpected changes (e.g. ore feed attributes). The decision to switch between modes is governed by operational policy and is triggered as critical thresholds are crossed. Hundreds of operating days can be simulated to identify potential deficiencies, bottlenecks, or other operational risks. DES is thus useful to support strategic decision-making in the design, development and sustained operation of any mining system. Based on current mining trends, tailings storage facilities are growing in both size and number, resulting in alarming tailings accumulations worldwide. Coupled with a large number of abandoned legacy mines and artisanal mining operations, tailings and other waste materials pose a significant threat to human health and safety, as well as the environment. Cost-effective tailings management strategies to mitigate these risks through site remediation are required. Research on potential uses for discarded tailings is divided between secondary metallurgical processing for extractive purposes, and incorporation into industrial materials. The current framework has been adapted to integrate geostatistical variability into DES in order to assess the potential operational risks related to secondary mining of tailings for a conceptual cement production operation. A case study loosely based on data from a tailings dam in Taltal, northern Chile, is presented. Sample calculations are provided that demonstrate the framework as a valuable tool to evaluate and mitigate potential risk factors in the development of tailings retreatment applications.
In the original HTML version of this Article, the order of authors within the author list was incorrect. The IMEx Consortium contributing authors were incorrectly listed as the last author and should ...have been listed as the first author. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.
Background and importance6-mercaptopurine (6-MP) is an anticancer and immunosuppressive agent used as part of the therapeutic strategy in acute lymphoblastic leukaemia (ALL), in the induction, ...consolidation and maintenance phases. However, it may cause life threatening myelotoxicity that is commonly associated with polymorphisms in genes involved in its metabolism (thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15)).Aim and objectivesTo describe the clinical case of a Caucasian girl, aged 2 years, diagnosed with B-ALL (intermediate risk of hyperdiploidy in cytogenetics (DNI index 1.27) and MRD on day +15 of 1.4%, CNS-1) that presented prolonged myelotoxicity under the LAL-SEHOP-PETHEMA-2013 treatment protocol.Material and methodsDuring the induction phase, prolonged spinal cord aplasia occurred with the complication of sepsis due to Staphylococcus epidermidis, which required intensive care unit support. Subsequently, she presented sepsis due to Pseudomonas, a granuloma in the reservoir area that requires channelling of a peripheral access central catheter type PICC. TPMT polymorphisms (*2, *3A, *3B and *3C) were studied without alterations. Therefore, the consolidation phase continued, and she presented with aplasia, febrile neutropenia, respiratory infection and central venous catheter infection. The dose of 6-MP was reduced to 10%. In the reinduction phase she also showed aplasia, febrile neutropenia and mucocutaneous infection by Candida dubliniensis. During maintenance, methotrexate and 6-MP were suspended several times, and 6-MP was resumed at 3% of the dose. She received multiple transfusions of red blood cells and platelets.To understand the toxicity manifested by the patient and considering the update of the pharmacogenetic guide for thiopurines of the Clinical Pharmacogenetics Implementation Consortium, real time PCR genotyping by Taqman was performed for NUDT15-rs116855232 gene polymorphism.ResultsAlthough initial genetic testing revealed that the patient carried the TPMT wild-type allele, the patient had prolonged spinal cord aplasia and multiple infectious complications. Subsequent analysis revealed that the patient carried the rs116855232-TT genotype (frequency in Europeans 0.000004). This polymorphism is associated with potentially fatal myelosuppression (evidence level 1A), which explains the toxicity manifested.Conclusion and relevanceThis case shows the relevance of implementing pharmacogenetics studies (TPMT and NUDT15 gene polymorphisms) in daily clinical practice that allows the early detection of patients treated with 6-MP with a higher risk of myelosuppression.References and/or acknowledgementsConflict of interestNo conflict of interest
En este estudio se identifican las principales necesidades de la comunidad sorda de la ciudad de Medellín (Colombia) en términos de formación educativa. La comunidad sorda se enfrenta a diversas ...dificultades en el ámbito educativo, laboral, cultural y social, lo que afecta su inclusión en la sociedad. La metodología es cualitativa. Se recolecta información mediante entrevistas a 16 sordos y a 4 expertos en el acompañamiento educativo de las personas sordas. Se establecen tres categorías de análisis: necesidades de inserción laboral, alfabetización digital y percepciones sobre MOOC (curso en línea masivo y abierto) para Sordos. Los resultados muestran que los sordos consideran que el MOOC para sordos en lengua de señas es adecuado para el fortalecimiento de sus habilidades y capacidades. Se concluye que los sordos necesitan mayor formación en inserción laboral, aprender a hacer un mayor uso de las TIC (tecnologías de la información y la comunicación) y que se incluya más la lengua de señas en dichas tecnologías.
•Changes of isoflavones in sterilised UHPH soymilks under storage were studied.•Interconversion of isoflavones was slower in UHPH than in UHT treatment.•Similar evolution of protein quality in UHPH ...and UHT soymilks was observed.
The application of ultra high pressure homogenisation (UHPH) treatments is useful to obtain fine and stable soymilk emulsions. Changes of isoflavones, protein digestibility and lysine availability during 4months of storage at 20±2°C in soymilk treated by UHPH (300MPa and 75°C of inlet temperature) were studied in comparison to UHT-sterilised soymilk (142°C, 6s). Results indicated that although there was a significantly higher extractability of isoflavones in UHT (about 38%) than in UHPH-treated samples (about 15%), similar total contents were found at the end of storage. The interconversion of isoflavones into β-glucosides was faster in UHT than in UHPH-treated soymilk. Similar evolution of protein digestibility in both UHPH and UHT-treated soymilks was found, being slightly higher in the initial UHT (88.4%) than in UHPH-treated samples (83.3%). No great differences were observed in the % of blocked lysine among samples after treatments, neither in their evolution throughout storage.
We summarize the ongoing scientific program of the 12 GeV Continuous Electron Beam Accelerator Facility (CEBAF) and give an outlook into future opportunities. The program addresses important topics ...in nuclear, hadronic, and electroweak physics, including nuclear femtography, meson and baryon spectroscopy, quarks and gluons in nuclei, precision tests of the standard model and dark sector searches. Potential upgrades of CEBAF and their impact on scientific reach are discussed, such as higher luminosity, the addition of polarized and unpolarized positron beams, and doubling the beam energy.
Prodiplosis longifila is reported as a pest of a wide range of species cultivated in America, including citrus, solanaceous species and asparagus. This species has different behavioural traits that ...are primarily centred on the oviposition habit and the feeding of larvae, which can change depending on the host. However, scarce information is available on population studies and the natural history of this insect, and uncertainty exists about the taxonomic identity and the geographic distribution of this species. The main objective was to perform a phylogenetic and genetic study of P. longifila populations and to define whether the North American and South American populations belong to the same species or whether a differentiation process had occurred due to geographic distance. A second objective was to determine whether this species showed genetic differentiation by host specialization in South America. The phylogenetic and population analyses based on DNA barcodes (cytochrome oxidase I gene) and a region of the ribosomal DNA (ITS2) revealed divergent clades attributable to geographic distance and host specificity. The North American and South American P. longifila insects were confirmed to be genetically distinct, and the genetic distances exceeded the values expected for intraspecific variation. In South America, the population analysis of P. longifila from tomato, sweet pepper (Solanaceae), Tahiti lime and key lime (Rutaceae) hosts evidenced high genetic differentiation between populations associated with different hosts and an absence of gene flow between these groups, suggesting the corresponding formation of cryptic species.
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