Biology subjects

Alvarado, R.

Publications and source records attributed to Alvarado, R..

3 recordsLinked to original sources

bioRxiv2024

Real-time Imaging of Decompression Gas Bubble Growth in the Spinal Cord of Live Rats

1)Structured AbstractO_ST_ABSPurposeC_ST_ABSTo observe the growth and resolution of decompression gas bubbles in the spinal cord of live rats in real time using magnetic resonance imaging (MRI). MethodsWe constructed an MRI-compatible pressure chamber system to visualize gas bubble dynamics in deep tissues in real time. The system pressurizes and depressurizes rodents inside an MRI scanner and monitors their respiratory rate, heart rate, and body temperature while providing gaseous anesthesia under pressure during the experiments. ResultsWe observed the formation of decompression gas bubbles in the spinal cord of rats after compression to 7.1 bar absolute and rapid decompression inside the MRI scanner while maintaining continuous gaseous anesthesia and vital monitoring. ConclusionWe have shown the direct observation of decompression gas bubble formation in real time by MRI in live, anesthetized rats.

bioengineering↗

bioRxiv2019

PATHWAYS ANALYZER: Design of a Tool for the Synthetic Assembly of Escherichia Coli K-12 MG1655 Bacteria for Biofuel Production

SummaryDue to the impact of environmental pollution, the importance of producing high quality biofuels and to leverage organic waste that normally would have no use has increased over time. Through synthetic biology, it is possible to improve existing organisms to process waste that is traditionally not used for biofuel production, such as whey.\n\nWith the redesign of metabolic pathways, it is possible to create connections for the implementation of new organisms that carry out functions that are normally not present in nature.\n\nFrom a computational point of view, metabolic pathways, which can be found in data sources as KEGG, can be converted to a graph data structure. These transformations enable the use of well-known algorithms, which enables the optimization of the analyses required to achieve the assembly of new organisms.\n\nThe present work aims to design a tool for the transformation of metabolic pathways and the development of path finding algorithms that establish relevant links between compounds that are essential to the biofuel production process.\n\nAs a result, a catalog of biobricks is created from the analysis of a subset of paths which can be used in the design stage of the synthetic assembly of the E. coli bacteria. The assemblys structure and functions are characterized according to the pieces used.\n\nFinally, new constructions are visualized with the goal of demonstrating and supporting the analysis processes, thus assisting people that work in the field of Synthetic Biology.\n\nAvailabilityPathways Analyzer is accessible at: https://gitlab.com/lvasquezcr/pathways-analyzer/

synthetic biology↗

bioRxiv2018

Truncated, uncapped mRNA 5’ ends targeted by cytoplasmic recapping cluster at CAGE tags and some transcripts are alternatively spliced

Until cytoplasmic recapping was discovered, decapping was thought to irreversibly destine an mRNA to degradation. Contradicting this idea, we readily observe mRNAs targeted by cytoplasmic capping in uncapped, yet stable forms. 5 RACE shows that nearly all uncapped ends correspond to CAGE tags and that the recapping of ZNF207 mRNA may be restricted to a single splice isoform. A modified RACE approach detected uncapped 5 RNA ends mapping to 46 mRNAs in dominant negative cytoplasmic capping enzyme expressing and normal cells. 11 of 46 cloned mRNAs also contained splice isoform-limiting sequences. Collectively, these data reinforce earlier work and suggest that alternative splicing may play a role in targeting transcripts for- and/or determining the position of- cytoplasmic capping.

molecular biology↗