Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “systematic analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50Linked to original sources
PubMed2006

Traction for low back pain with or without sciatica: an updated systematic review within the framework of the Cochrane collaboration.

STUDY DESIGN: Systematic review. OBJECTIVE: To determine if traction is more effective than reference treatments, placebo/sham traction, or no treatment for low back pain (LBP). SUMMARY OF BACKGROUND DATA: Various types of traction are used in the treatment of LBP, often in conjunction with other treatments. METHODS: We searched MEDLINE, EMBASE, and CINAHL to November 2004, and screened the latest issue of the Cochrane Library (2004, issue 4) and references in relevant reviews and our personal files. We selected randomized controlled trials (RCTs) involving any type of traction for the treatment of acute (less than 4 weeks duration), subacute (4-12 weeks), or chronic (more than 12 weeks) nonspecific LBP with or without sciatica. Sets of 2 reviewers independently performed study selection, methodological quality assessment, and data extraction. Because available studies did not provide sufficient data for statistical pooling, we performed a qualitative "levels of evidence" analysis, systematically estimating the strength of the cumulative evidence on the difference/lack of difference observed in trial outcomes. RESULTS: A total of 24 RCTs (2177 patients) were included. There were 5 trials considered high quality. For mixed groups of patients with LBP with and without sciatica, we found: (1) strong evidence that there is no statistically significant difference in short or long-term outcomes between traction as a single treatment, (continuous or intermittent) and placebo, sham, or no treatment; (2) moderate evidence that traction as a single treatment is no more effective than other treatments; and (3) limited evidence that adding traction to a standard physiotherapy program does not result in significantly different outcomes. For LBP with sciatica, we found conflicting evidence in several of the comparisons: autotraction compared to placebo, sham, or no treatment; other forms of traction compared to other treatments; and different forms of traction. In the remaining comparisons, there were no statistically significant differences; level of evidence is moderate regarding continuous or intermittent traction compared to placebo, sham, or no treatment, and is limited regarding different forms of traction. CONCLUSION: Based on the current evidence, intermittent or continuous traction as a single treatment for LBP cannot be recommended for mixed groups of patients with LBP with and without sciatica. Neither can traction be recommended for patients with sciatica because of inconsistent results and methodological problems in most of the studies involved. However, because high-quality studies within the field are scarce, because many are underpowered, and because traction often is supplied in combination with other treatment modalities, the literature allows no firm negative conclusion that traction, in a generalized sense, is not an effective treatment for patients with LBP.

Humans↗
PubMed2005

A lipidomic study of the effects of N-methyl-N'-nitro-N-nitrosoguanidine on sphingomyelin metabolism.

Systems biology is a new and rapidly developing research area in which, by quantitatively describing the interaction among all the individual components of a cell, a systems-level understanding of a biological response can be achieved. Therefore, it requires high-throughput measurement technologies for biological molecules, such as genomic and proteomic approaches for DNA/RNA and protein, respectively. Recently, a new concept, lipidomics, which utilizes the mass spectrometry (MS) method for lipid analysis, has been proposed. Using this lipidomic approach, the effects of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) on sphingomyelin metabolism, a major class of sphingolipids, were evaluated. Sphingomyelin molecules were extracted from cells and analyzed by matrix-assisted laser desorption ionization-time of flight MS. It was found that MNNG induced profound changes in sphingomyelin metabolism, including the appearance of some new sphingomyelin species and the disappearance of some others, and the concentrations of several sphingomyelin species also changed. This was accompanied by the redistribution of acid sphingomyelinase (ASM), a key player in sphingomyelin metabolism. On the other hand, imipramine, an inhibitor of ASM, caused the accumulation of sphingomyelin. It also prevented some of the effects of MNNG, as well as the redistribution of ASM. Taken together, these data suggested that the lipidomic approach is highly effective for the systematic analysis of cellular lipids metabolism.

Amnion↗
PubMed2003

Analysis of C5a-mediated chemotaxis by lentiviral delivery of small interfering RNA.

Immune cells respond to chemotactic signals by means of G protein-coupled receptors. Attempts to elucidate the function of specific G protein family members in these responses is complicated by redundancy among the different G protein isoforms. We have used lentiviral-based RNA interference to eliminate expression of specific G protein subunits selectively in J774A.1 mouse macrophages. The chemotactic response to the complement factors C5a and C3a is ablated in cells lacking G beta(2) but is unaffected in cells lacking G beta(1), G alpha i(2), or G alpha i(3). Similarly, the C5a-mediated calcium response of single cells is either absent or significantly delayed and weakened by G beta(2) knockdown. Assessment of Akt1 phosphorylation levels in response to C5a shows rapid and sustained phosphorylation in both wild-type cells and cells lacking G beta(1). Cells lacking G beta(2) retain the rapid response but cannot sustain phospho-Akt1 levels. The phenotype of cells lacking G beta(2) can be reversed by overexpression of either human G beta(2) or mouse G beta(1). These data demonstrate the usefulness of lentiviral-based RNA interference in the systematic analysis of a signaling pathway, and they suggest that in J774A.1 cells, G beta(2)-derived G beta gamma is the most effective mediator of chemotaxis to C5a.

Animals↗
PubMed2000

Analysis of drug interactions in combined drug therapy by reflection method.

AIM: To set up a new method to analyze multidrug interaction in combined drug therapy. METHODS: Based on a dose-effect curve of the combined drugs and the equieffective test, a new mathematical model was set as Q = (Eo - Et)/L (-1 < Q < 1 addition, Q < or = 1 antagonism, Q > or = 1 synergism) where Eo = an observed value (or its fitted value) of combined effect, Et = an expected value of combined effect, and L = an equieffective cutoff between Eo and Et, decided by the equieffective criterion of a special field, the number of data points, and the experimental error. The different types of experimental data were analyzed by the new model. RESULTS: This reflection method could deal with data in combined drug therapy, unnecessary to distinguish between independent and similar action, or exclusive and non-exclusive case among drugs. The number of drugs for combination did not need to be limited. But the experimental data should be enough to fit a dose-effect curve of drugs in combination. If every dose-effect curve of drugs for combination was made, a series of Q values was obtained from all levels of dose-effect for a systematic analysis. To large animal or human experiment, the points of dose-effect of each drug used alone could be reduced to even 1 point. The results of analysis took the criterion of a special field and laboratory error into account in this method. CONCLUSION: The reflection method is an effective method for analysis of multidrug interaction in combined drug therapy.

Animals↗
PubMed2005

Signal identification in NMR spectra with coupled evolution periods.

Novel multidimensional NMR experiments rely on modified time-domain sampling schemes to provide significant savings of experimental time. Several approaches are based on the coupling of evolution times resulting in a reduction of the dimensionality of the recorded spectra, and a concomitant saving of experimental time. We present a consistent and general tool, called EVOCOUP, for the analysis of these reduced dimensionality spectra. The approach is flexible in the sense that the input can consist of various forms of reduced dimensionality spectra, that any piece of information can be removed (provided enough information is left), e.g., signals undetectable due to poor signal-to-noise or covered by artifacts, and that it can be applied to spectra involving any number of nuclei. The use of a general optimization procedure and an appropriate target function provides for a robust approach with well-defined results and ensures optimal use of redundant information normally present in the input. Spectral overlap in the directly detected dimension is resolved in a fully automated manner, avoiding the assessment of signal quality and its use in combinatorial trials. The positions of all peaks in a corresponding full-dimensional spectrum are obtained without need for reconstruction of this spectrum. In a systematic analysis of a complete spectrum recorded for the 14 kDa protein azurin and involving five different nuclei, only four spin systems were missed and no false spins systems were detected.

Artifacts↗
PubMed2003

Hypothesis testing I: proportions.

Statistical inference involves two analysis methods: estimation and hypothesis testing, the latter of which is the subject of this article. Specifically, Z tests of proportion are highlighted and illustrated with imaging data from two previously published clinical studies. First, to evaluate the relationship between nonenhanced computed tomographic (CT) findings and clinical outcome, the authors demonstrate the use of the one-sample Z test in a retrospective study performed with patients who had ureteral calculi. Second, the authors use the two-sample Z test to differentiate between primary and metastatic ovarian neoplasms in the diagnosis and staging of ovarian cancer. These data are based on a subset of cases from a multiinstitutional ovarian cancer trial conducted by the Radiologic Diagnostic Oncology Group, in which the roles of CT, magnetic resonance imaging, and ultrasonography (US) were evaluated. The statistical formulas used for these analyses are explained and demonstrated. These methods may enable systematic analysis of proportions and may be applied to many other radiologic investigations.

Diagnostic Imaging↗
PubMed2003

Approaches for a sustainable use of the bioactive potential in sponges: analysis of gene clusters, differential display of mRNA and DNA chips.

In recent years, analyses of the genome organization of marine sponges have begun that have led to the elucidation of selected genes and gene arrangements that exist in gene clusters (e.g. the receptor tyrosine kinase cluster and the allograft inflammatory factor cluster). Most of these studies were performed with the demosponge Suberites domuncula; but Geodia cydonium (Demospongiae), Aphrocallistes vastus (Hexactinellida) and Sycon raphanus (Calcarea) were also investigated. Both S. domuncula and G. cydonium possess a surprisingly large genome of approximately 1.7 pg DNA per haploid set. Taking the high gene density in these sponges into account and considering that predominantly single-copy DNA exists, the gene number of S. domuncula and G. cydonium was estimated to be approximately 300,000. Presumably, the large gene number in the sponge genome is due to regional gene duplication; so far evidence for a transposition in sponges has been presented. Data indicate that only 0.25 % of the total sponge genome comprises CA/TG microsatellites, and until now also no SINEs/transposable elements have been identified. Due to the rapid progress in the field of molecular biology of sponges the application of sponge genes for expression studies by DNA-array techniques (microarray) has become possible. These achievements will be further supported by the systematic analysis of the expressed genome of sponges; the results will be (partially) released (http://spongebase.uni-mainz.de/cgi-bin/blast/blastserver.cgi). In our efforts employing the results from the analysis of the genome to molecular biotechnology, we applied the technique of differential display of mRNA. One example, the effect of silicate on gene expression in S. domuncula, is outlined here. Future results will allow the identification of the genes involved in the synthesis of bioactive compounds from sponges [Porifera]. This progress will contribute considerably to a fruitful and fast development in the field of molecular marine biotechnology.

Amino Acid Sequence↗
PubMed1990

Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data.

A total of 3430 polypeptides (2592 cellular; 838 secreted) from transformed human amnion cells (AMA) labeled with [35S]methionine were separated and recorded using computer-aided two-dimensional (2-D) gel electrophoresis. A master 2-D gel database of cellular protein information that includes both qualitative and quantitative annotations has been established. The protein numbers in this database differ from those reported in an earlier version (Celis et al. Leukemia 1988, 2,561-602) as a result of changes in the scanning hardware. The reported information includes: percentage of total radioactivity recovered from the gels (based on quantitations of polypeptides labeled with a mixture of 16 14C-amino acids), protein name (including credit to investigators that aided identification), antibody against protein, cellular localization, (nuclear, 40S hnRNP, 20S snRNP U5, proteasomes, endoplasmic reticulum, mitochondria, Golgi, ribosomes, intermediate filaments, microfilaments and microtubules), levels in fetal human tissues, partial protein sequences (containing information on 48 human proteins microsequenced so far), cell cycle-regulated proteins, proteins sensitive to interferons alpha, beta, and gamma, heat shock proteins, annexins and phosphorylated proteins. The results presented should be considered as the initial phase of a joint effort between our laboratories to undertake a general and systematic analysis of human proteins. Using this integrated approach it will be possible to identify phenotype-specific proteins, to microsequence them and store the information in the database, to identify the corresponding genes, to search for homology with previously characterized proteins and to study the function of groups of proteins (pathways, organelles, etc.) that exhibit interesting regulatory properties. In particular, the 2-D gel protein database may become increasingly important in view of the concerted effort to map and sequence the entire human genome.

Amnion↗
PubMed2005

Differences in gene expression profiles in dermal fibroblasts from control and patients with age-related macular degeneration elicited by oxidative injury.

The pathogenesis of age-related macular degeneration (AMD) is still unknown but there is growing evidence that a combination of both oxidative injury and genetic factors may play a role. One particle hypothesis proposes that dysregulation of multiple genes in response to an oxidative injury could contribute to the development of AMD. While direct examination of ocular cells from AMD patients is difficult, AMD also appears to have a systemic component. Therefore, as is the case with other central nervous diseases, peripheral sites may also manifest any underlying genetic abnormalities. For the present study, biopsy-derived fibroblasts from 4 patients with the early form and 4 patients with the late form of AMD and 3 age-matched control patients were grown in culture and treated with a nonlethal dose of the oxidative stimulus menadione. Gene expression patterns were quantitatively and qualitatively examined using Human Genome U95A GeneChips (Affymetrix) and verified by real-time PCR analysis. In response to the oxidative injury 755 genes were found to be upregulated at least twofold in one of the patients groups. Cluster analysis of expression profiles detected six patterns of dysregulation initiated by oxidative injury specific for the disease groups (98 genes total). Clusters of genes dysregulated by the sublethal oxidative injury in either early and/or late AMD groups were further categorized by overrepresentation of GO "biological process" categories using Expression Analysis Systematic Explorer (EASE) software. This approach demonstrated that four major functional gene groups including inflammatory/innate immune response, transcriptional regulation, cell cycle, and proliferation were significantly overrepresented (Fisher test ranging from 0.0393 to 0.00018) in both AMD patients groups in response to the oxidative injury. Despite the small number of patients in the study, specific biological and statistical differences in gene expression profiles between control and AMD patients were identified but only in the presence of an environmental stimulus.

Aged↗
PubMed2000

Mining for putative regulatory elements in the yeast genome using gene expression data.

We have developed a set of methods and tools for automatic discovery of putative regulatory signals in genome sequences. The analysis pipeline consists of gene expression data clustering, sequence pattern discovery from upstream sequences of genes, a control experiment for pattern significance threshold limit detection, selection of interesting patterns, grouping of these patterns, representing the pattern groups in a concise form and evaluating the discovered putative signals against existing databases of regulatory signals. The pattern discovery is computationally the most expensive and crucial step. Our tool performs a rapid exhaustive search for a priori unknown statistically significant sequence patterns of unrestricted length. The statistical significance is determined for a set of sequences in each cluster with respect to a set of background sequences allowing the detection of subtle regulatory signals specific for each cluster. The potentially large number of significant patterns is reduced to a small number of groups by clustering them by mutual similarity. Automatically derived consensus patterns of these groups represent the results in a comprehensive way for a human investigator. We have performed a systematic analysis for the yeast Saccharomyces cerevisiae. We created a large number of independent clusterings of expression data simultaneously assessing the "goodness" of each cluster. For each of the over 52,000 clusters acquired in this way we discovered significant patterns in the upstream sequences of respective genes. We selected nearly 1,500 significant patterns by formal criteria and matched them against the experimentally mapped transcription factor binding sites in the SCPD database. We clustered the 1,500 patterns to 62 groups for which we derived automatically alignments and consensus patterns. Of these 62 groups 48 had patterns that have matching sites in SCPD database.

Gene Expression Profiling↗
PubMed1989

Efficient mapping and characterization of a T cell epitope by the simultaneous synthesis of multiple peptides.

Prediction, identification and analysis of T cell epitopes in protein antigens has become a central theme in fundamental and applied immunology. However, while for the characterization of linear B cell epitopes the so-called Pepscan procedure was found to be extremely effective, no such technique has so far been available for T cell studies. Recently, we described the identification and localization of a T cell epitope in a mycobacterial 65-kDa shock protein in the model of adjuvant arthritis. This was done by molecular cloning and conventional solid-phase synthesis techniques. We now show that the delineation of such a T cell epitope and its further characterization can be accomplished in a much more rapid and efficient manner by a modification of the existing Pepscan technique. We show for the first time that several hundreds of peptides, simultaneously synthesized in an automated way on activated polyethylene rods, can be easily recovered from these rods in adequate quantities, enabling a systematic analysis of T cell epitopes. Synthesis of sequentially overlapping peptides along the 65-kDa protein revealed that the adjuvant arthritis T cell clones are fully stimulated by peptides that comprise a minimal sequence of seven residues, corresponding to positions 180-186 in the sequence of the 65-kDa protein of M. bovis Bacillus Calmette Guerin (BCG). Detailed examination of the epitope by peptides containing a single amino acid substitution showed that, apart from one conservative replacement (Glu----Asp), the requirement for the native residue at all positions in peptide 180-186 was absolute for full T cell stimulation. Their indispensability was confirmed with deletion and insertion peptides. It is concluded that the occurrence of indifferent or spacer residues in a minimal stimulatory sequence, as observed by others, is not a general feature of T cell epitopes.

Amino Acid Sequence↗
PubMed2004

A genotype-phenotype correlation for GJB2 (connexin 26) deafness.

INTRODUCTION: Mutations in GJB2 are the most common cause of non-syndromic autosomal recessive hearing impairment, ranging from mild to profound. Mutation analysis of this gene is widely available as a genetic diagnostic test. OBJECTIVE: To assess a possible genotype-phenotype correlation for GJB2. DESIGN: Retrospective analysis of audiometric data from people with hearing impairment, segregating two GJB2 mutations. SUBJECTS: Two hundred and seventy seven unrelated patients with hearing impairment who were seen at the ENT departments of local and university hospitals from Italy, Belgium, Spain, and the United States, and who harboured bi-allelic GJB2 mutations. RESULTS: We found that 35delG homozygotes have significantly more hearing impairment, compared with 35delG/non-35delG compound heterozygotes. People with two non-35delG mutations have even less hearing impairment. We observed a similar gradient of hearing impairment when we categorised mutations as inactivating (that is, stop mutations or frame shifts) or non-inactivating (that is, missense mutations). We demonstrated that certain mutation combinations (including the combination of 35delG with the missense mutations L90P, V37I, or the splice-site mutation IVS1+1G>A, and the V37I/V37I genotype) are associated with significantly less hearing impairment compared with 35delG homozygous genotypes. CONCLUSIONS: This study is the first large systematic analysis indicating that the GJB2 genotype has a major impact on the degree of hearing impairment, and identifying mild genotypes. Furthermore, this study shows that it will be possible to refine this correlation and extend it to additional genotypes. These data will be useful in evaluating habilitation options for people with GJB2 related deafness.

Adolescent↗
PubMed2026

Crosstalk mediators implicated in the Stevens-Johnson Syndrome through gene regulatory network analysis.

Stevens-Johnson syndrome (SJS) is a rare and severe mucocutaneous disorder often triggered by medications or infections. Our previous research identified that four key genes, Ikzf1, Ptger3, Mavs, and Tlr3 are involved in SJS susceptibility and the conjunctival epithelial innate immune response, demonstrating their role in regulating interferon-stimulated genes. However, the interplay among these regulatory factors remains unclear. This study aimed to elucidate the crosstalk mechanisms between the pathways regulated by these four genes in conjunctival epithelial cells. We constructed a comprehensive gene regulatory network using transcriptomic data from murine conjunctival epithelial cells under 16 distinct conditions, including polyI:C stimulation across wild-type, knockout, and transgenic backgrounds for the key genes. A targeted network analysis systematically identified numerous candidate genes mediating the crosstalk between the regulatory pathways initiated by Ikzf1, Ptger3, Mavs, and Tlr3. The identified candidates suggest the involvement of diverse signaling pathways previously unlinked to SJS pathology. Our findings suggest that the pathogenesis of SJS may arise not from the dysfunction of isolated genes but from the disruption of a balance maintained by intricate pathway crosstalk.

Animals↗
PubMedDate not supplied

Ocular abnormalities in transgenic mice harboring mutations in the type II collagen gene.

PURPOSE: To characterize the morphological changes in the eyes of transgenic mice harboring different mutations in type II collagen gene to elucidate the function of this collagen in the eye, and to find out whether these animals could function as models for the human arthro-ophthalmopathies of the Kniest, Stickler and Wagner types. METHODS: Three genetically engineered mouse lines representing two types of mutations in the triple-helical domain of type II collagen and their nontransgenic littermates used as controls were analyzed on day 18.5 embryonic development. After genotyping by polymerase chain reaction (PCR) and Southern hybridization the embryos were prepared for routine histology. Polarization microscopy was done on hyaluronidase-treated sections. RESULTS: Histological analysis revealed several genotype-dependent abnormalities in the eyes of the transgenic mice. Most striking changes were observed in the vitreous architecture; in one line of mice the vitreous was tightly packed in the posterior region of the vitreous space with thick fibrils, empty cavities and dense membrane-like material. The other mutation resulted in reduced filament density of the vitreous. In the most severely affected phenotype the internal limiting membrane was detached from the retinal layers and was markedly thickened, and the posterior lens capsule was thickened. The anterior chamber was shallow or absent in all transgenic lines but was well formed in the normal animals. Changes were also observed in the lens, corneal and scleral structures. CONCLUSIONS: The ocular changes observed in transgenic mice harboring mutations in type II collagen gene show similarities to the human ocular findings in Kniest dysplasia, and in Stickler and Wagner syndromes. We therefore propose that these animals could serve as models for systematic analysis of vitreoretinal degeneration and other abnormalities, as seen in these syndromes.

Abnormalities, Multiple↗
PubMed2000

A structure-function analysis of serine/threonine phosphorylation of the thrombopoietin receptor, c-Mpl.

Thrombopoietin (TPO), the critical regulator of platelet production, acts by binding to its cell surface receptor, c-Mpl. Numerous studies have shown that TPO binding leads to JAK2 kinase activation and Tyr phosphorylation of c-Mpl and several intracellular signaling intermediates, events vital for the biological activity of the hormone. In contrast, virtually nothing is known of the role of Ser or Thr phosphorylation of c-Mpl. By using phosphoamino acid analysis we found that Ser residues of c-Mpl were constitutively phosphorylated in receptor-bearing cells, levels that were increased following exposure of cells to TPO. To identify which residues were modified, and to determine the functional consequences of their phosphorylation, we generated a series of Ser to Ala mutations of a truncated c-Mpl receptor (T69) capable of supporting TPO-induced cell growth. Of the eight Ser within T69 we found that at least four are phosphorylated in TPO-stimulated cells. The mutation of each of these residues alone had minimal effects on TPO-induced proliferation, but substitution of all of the phosphoserine residues with Ala reduced the capacity of the receptor to support cell growth by over 50%. Additionally, the Ser at cytoplasmic position 18 is not detectably phosphorylated. However, the mutation of Ser-18 to Ala nearly abrogates TPO-induced proliferation and co-precipitation of JAK2 with Mpl. This study provides the first systematic analysis of the role of Ser residues in c-Mpl signaling.

Amino Acid Sequence↗
PubMed2000

Systematic review of aetiology and treatment of post-stroke hand oedema and shoulder-hand syndrome.

Studies on the aetiology and treatment of post-stroke hand oedema and shoulder-hand syndrome (SHS) published from January 1973 until August 1998 were identified. Eleven studies were included with at least some control for confounding. These were evaluated on 11 methodological criteria and by standardized effect sizes. There were five aetiological studies: four cohort studies and one study consisting of two case series using a within-subjects design. The matters investigated included lymph scintigraphy in hand oedema, bone scintigraphy, putative risk factors and the existence of autonomic dysregulation and peripheral nerve lesions in SHS. There were six therapeutic studies: one randomized controlled trial, one non-randomized controlled trial, one cohort study and three case series, of which two studies used a within-subjects design. These studies investigated continuous passive motion and neuromuscular stimulation in hand oedema as well as oral corticosteroids, intramuscular calcitonin and trauma prevention in SHS. A great diversity of pathophysiological and therapeutic insight was found. Based on systematic analysis of the literature, the following conclusions seem justified: (i) the shoulder is involved in only half of the cases with painful swelling of wrist and hand, suggesting a "wrist-hand syndrome" between simple hand oedema and SHS; (ii) hand oedema is not lymphoedema; (iii) SHS usually coincides with increased arterial blood flow; (iv) trauma causes aseptic joint inflammations in SHS; (v) no specific treatment has yet proven its advantage over other physical methods for reducing hand oedema; and (vi) oral corticosteroids are the most effective treatment for SHS.

Edema↗
PubMed2004

Defining a large set of full-length clones from a Xenopus tropicalis EST project.

Amphibian embryos from the genus Xenopus are among the best species for understanding early vertebrate development and for studying basic cell biological processes. Xenopus, and in particular the diploid Xenopus tropicalis, is also ideal for functional genomics. Understanding the behavior of genes in this accessible model system will have a significant and beneficial impact on the understanding of similar genes in other vertebrate systems. Here we describe the analysis of 219,270 X. tropicalis expressed sequence tags (ESTs) from four early developmental stages. From these, we have deduced a set of unique expressed sequences comprising approximately 20,000 clusters and 16,000 singletons. Furthermore, we developed a computational method to identify clones that contain the complete coding sequence and describe the creation for the first time of a set of approximately 7000 such clones, the full-length (FL) clone set. The entire EST set is cloned in a eukaryotic expression vector and is flanked by bacteriophage promoters for in vitro transcription, allowing functional experiments to be carried out without further subcloning. We have created a publicly available database containing the FL clone set and related clustering data (http://www.gurdon.cam.ac.uk/informatics/Xenopus.html) and we make the FL clone set publicly available as a resource to accelerate the process of gene discovery and function in this model organism. The creation of the unique set of expressed sequences and the FL clone set pave the way toward a large-scale systematic analysis of gene sequence, gene expression, and gene function in this vertebrate species.

Animals↗
PubMed1997

Comparison of the in vitro activities of the echinocandin LY303366, the pneumocandin MK-0991, and fluconazole against Candida species and Cryptococcus neoformans.

Two new glucan synthesis inhibitors, the echinocandin LY303366 and the pneumocandin MK-0991 (formerly L-743,872), were studied for their antifungal activities in vitro in relation to each other and in relation to the activity of the triazole fluconazole. Systematic analysis of broth macrodilution testing by varying the starting inoculum size, medium composition, medium pH, temperature of incubation, length of incubation, or selection of endpoints failed to identify significant differences in antifungal activity for either LY303366 or MK-0991 in comparison to the activity under standard test conditions specified for other antifungal agents in National Committee for Clinical Laboratory Standards (NCCLS) document M27A. Under standardized conditions, both drugs exhibited prominent activity against Candida species including Candida glabrata and Candida krusei but showed little activity against Cryptococcus neoformans. This spectrum of activity differed from that of fluconazole, which exhibited marginal activity against C. glabrata and C. krusei but prominent activity against other Candida species and C. neoformans. For individual strains, broth microdilution MICs of LY303366 and MK-0991 were similar to but frequently higher than broth macrodilution results. In contrast, fluconazole broth microdilution MICs were often lower than broth microdilution results. We conclude that the test conditions specified in NCCLS document M27A are applicable to these two new glucan synthesis inhibitors and that systematic differences between broth microdilution procedures and the broth macrodilution reference standard will need to be addressed before the two test methods can be used interchangeably.

Anidulafungin↗