Background: Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems.
Description: Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and approximately 67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined.
Conclusion: The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches.
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http://dx.doi.org/10.1186/1471-2164-6-123 | DOI Listing |
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Plastic, Reconstructive, and Aesthetic Surgery Unit, Nantes University Hospital, Nantes, France.
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January 2025
Division of Pulmonary and Critical Care Medicine, Department of Medicine; and Department of Physical Medicine and Rehabilitation. Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Approximately half of critically ill adults experience intensive care unit acquired weakness (ICUAW). Patients who develop ICUAW may have negative outcomes, including longer duration of mechanical ventilation, greater length of stay, and worse mobility, physical functioning, quality of life, and mortality. Early physical rehabilitation interventions have potential for improving ICUAW; however, randomized trials show inconsistent findings on the efficacy of these interventions.
View Article and Find Full Text PDFPlanta Med
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Instituto de Química, Departamento de Productos Naturales, Universidad Nacional Autónoma de México, Mexico City, Mexico.
An approach combining enzymatic inhibition and untargeted metabolomics through molecular networking was employed to search for human recombinant full-length protein tyrosine phosphatase 1B (PTP1 B) inhibitors from a collection of 66 mangrove-associated fungal taxa. This strategy prioritized two strains (IQ-1612, section , and IQ-1620, section ) for further studies. Chemical investigation of strain IQ-1612 resulted in the isolation of a new nonanolide derivative, roseoglobuloside A (1: ), along with two known metabolites (2: and 3: ), whereas strain IQ-1620 led to the isolation of four known naphtho-γ-pyrones and one known diketopiperazine (4: -8: ).
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