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PubMed2006

EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon.

Brachypodium distachyon (Brachypodium) is a temperate grass with the physical and genomic attributes necessary for a model system (small size, rapid generation time, self-fertile, small genome size, diploidy in some accessions). To increase the utility of Brachypodium as a model grass, we sequenced 20,440 expressed sequence tags (ESTs) from five cDNA libraries made from leaves, stems plus leaf sheaths, roots, callus and developing seed heads. The ESTs had an average trimmed length of 650 bp. Blast nucleotide alignments against SwissProt and GenBank non-redundant databases were performed and a total of 99.9% of the ESTs were found to have some similarity to existing protein or nucleotide sequences. Tentative functional classification of 77% of the sequences was possible by association with gene ontology or clusters of orthologous group's index descriptors. To demonstrate the utility of this EST collection for studying cell wall composition, we identified homologs for the genes involved in the biosynthesis of lignin subunits. A subset of the ESTs was used for phylogenetic analysis that reinforced the close relationship of Brachypodium to wheat and barley.

DNA, Complementary↗
PubMed2005

GENII-LIN: a new object-oriented interface for the GENII code.

GENII-LIN is a new object-oriented interface for GENII, a well-known analysis tool for the health impact evaluation of accidental or chronic release of radionuclides to the environment. GENII-LIN has been developed under the Linux OS, chosen because it is a stable, reliable and open source. The suite codes that constitute the original GENII simulation kernel have been re-implemented and built, using the G77, the Fortran 77 module of the GCC collection. The code modules and the flow of data among them are at present fully controlled by a management interface written in C++, which is the core of the package. GENII-LIN comes with a new graphical user interface (GUI), built using the QT libraries by Trolltech. Through the wizard-like GUI, the user has full control over the code and can easily handle both the input and the output files.

Body Burden↗
PubMed1999

Expression of the MUC 6 mucin gene in development of the human kidney and male genital ducts.

The MUC 6 mucin cDNA was isolated from a human stomach cDNA library and has been shown to be expressed in a number of other tissues in the gastrointestinal tract, including the gallbladder, pancreas, and parts of the ileum and colon. Here we establish that MUC 6 is expressed transiently in the nephrogenic zone of the kidney in the early mid-trimester of development. MUC 6 transcripts were detected in the epithelium of ureteric buds at 13 weeks and at lower levels from 17 to 23 weeks of gestation. Traces of MUC 6 mRNA were seen in the collecting ducts but not elsewhere in the developing kidney, and MUC 6 glycoprotein was detected in the epithelium of ureteric buds and collecting ducts. MUC 6 transcripts were absent from adult kidney. This pattern of expression of MUC 6 in the developing kidney suggests a role in epithelial organogenesis. MUC 6 transcripts were also present at low levels in mid-trimester epididymal epithelium.

Epididymis↗
PubMed1995

Evaluation of Community Care Network (CCN) system in a rural health care setting.

Concurrent Engineering Research Center (CERC), under the sponsorship of NLM (National Library of Medicine) is in the process of developing a computerized patient record system for a clinical environment distributed in rural West Virginia. This realization of the CCN (Community Care Network), besides providing computer-based patient records accessible from a chain of clinics and one hospital, supports collaborative health care processes like referral and consulting. To evaluate the effectiveness of the system, a study was designed and is in the process of being executed. Three surveys were designed to provide subjective measures, and four experiments for collecting objective data. Data collection is taking place in several phases: baseline data are collected before the system is deployed; the process is repeated with minimal changes three, then six months later or as often as new versions of the system are installed. Results are then to be compared, using whenever possible matching techniques (i.e. the preliminary data collected on a provider will be matched with the data collected later on the same provider). Surveys are conducted through questionnaires distributed to providers and nurses and person-to-person interviews of the patients. The time spent on patient-chart related activities is measured by work-sampling, aided by a computer application running on a laptop PC. Information about missing patient record parts is collected by the providers, the frequency by which new features of the computerized system are used will be logged by the system itself and clinical outcome measures will be studied from the results of the clinics' own patient chart audits. Preliminary results of the surveys and plans for the immediate and distant future are discussed at the end of the paper.

Attitude to Computers↗
PubMed2002

Surgical interventions for age-related cataract.

BACKGROUND: Cataract is the major cause of global blindness, accounting for 40 to 80% of all blindness in developing countries. The number of people blind from cataract is expected to rise due to the changing age distribution and increasing life expectancy. There is currently no proven intervention to prevent cataract and surgery is the only form of treatment. OBJECTIVES: The objective of this review is to compare the effects of different surgical interventions for age-related cataract. SEARCH STRATEGY: We searched the Cochrane Controlled Trials Register - CENTRAL/CCTR, which contains the Cochrane Eyes and Vision Group specialised register (Cochrane Library Issue 3 2001), MEDLINE (1966 to August 2001), EMBASE (1980 to September 2001), the reference lists of identified trials, and we contacted investigators and experts in the field for details of published and unpublished trials. SELECTION CRITERIA: We included randomised controlled trials evaluating surgical treatment for people with age-related cataract. DATA COLLECTION AND ANALYSIS: Two reviewers independently extracted data and discrepancies were resolved by discussion. Where appropriate, relative risks, odds ratios and weighted mean differences were summarised after assessing heterogeneity between the studies. We used a fixed effect model due to the low number of trials in each comparison. MAIN RESULTS: We identified six trials that randomised a total of 7828 people. Phacoemulsification gave a better visual outcome than extracapsular surgery and gave a similar average cost per procedure in one trial conducted in the UK. Extracapsular surgery with posterior chamber lens implant and intracapsular surgery with or without an anterior chamber intraocular lens implant gave acceptable visual outcomes at 12 to 24 months after surgery. In three large trials in south Asia, best-corrected visual acuity of less than 6/60 ranged from 0.5 to 4%. Higher rates of poor outcome were observed in a multicentre study with 19 surgeons compared to a single-centre study with two surgeons. REVIEWER'S CONCLUSIONS: This review provides evidence from one randomised controlled trial that phacoemulsification gives a better visual outcome than extracapsular extraction with sutures. However, this trial was conducted in a developed country specialised hospital setting and extrapolation to other settings must be made with caution. This review also found evidence that extracapsular cataract extraction with a posterior chamber lens implant provides better visual outcome than intracapsular extraction with aphakic glasses. This finding is also based on the results of a single trial. The long term effects of posterior capsular opacification need to be assessed in larger populations. The data in the review suggest that intracapsular extraction with an anterior chamber lens implant is an effective alternative to intracapsular extraction with aphakic glasses, with similar safety. Further data from developing regions are needed to compare all aspects of intraocular lens surgery with the three main surgical procedures - intracapsular extraction with an anterior chamber lens, extracapsular surgery with a posterior chamber lens with or without sutures.

Age Factors↗
PubMed1999

A generic particle-based nonradioactive homogeneous multiplex method for high-throughput screening using microvolume fluorimetry.

We have developed a novel fluorescence-based homogeneous binding assay for high-throughput screening of chemical compounds. In this assay, a Cy5- or Cy5.5-labeled ligand binds to receptor immobilized on a particle, either a bead or a cell. The resulting localized signal can be detected by a modified microvolume fluorimeter (MVF). When a molecule which competes with the labeled ligand is present, the localized fluorescence on cells or beads is reduced. Image processing software enumerates events and analyzes fluorescence intensity. We describe MVF assays for the IL-1 and IL-5 receptors. Using synthetic peptides with a range of affinities for the IL-1 receptor, we obtained IC(50) data consistent with those determined by radioligand binding assays. Because the image processing software can discriminate among events with different diameters, we were able to develop a multiplex assay, in which the IL-1R and IL-5R assays were carried out in the same well with each receptor immobilized on a different size of bead. IC(50) values generated in the multiplex assay for ligands specific to each receptor were comparable to those determined independently. Finally, similar IC(50) values were obtained in a 16-microl volume in an 864-well plate. This homogeneous, nonradioactive, miniaturizable, and multiplex-capable assay holds much promise for screening of combinatorial libraries and compound collections.

Animals↗
PubMed2004

Antiplatelet agents for preventing pre-eclampsia and its complications.

BACKGROUND: Pre-eclampsia is associated with deficient intravascular production of prostacyclin, a vasodilator, and excessive production of thromboxane, a platelet-derived vasoconstrictor and stimulant of platelet aggregation. These observations led to the hypotheses that antiplatelet agents, low-dose aspirin in particular, might prevent or delay the development of pre-eclampsia. OBJECTIVES: To assess the effectiveness and safety of antiplatelet agents when given to women at risk of developing pre-eclampsia. SEARCH STRATEGY: We searched the Cochrane Pregnancy and Childbirth Group trials register (September 2003), the Cochrane Central Register of Controlled Trials (The Cochrane Library, Issue 2, 2003), EMBASE (1994 to 2003) and we handsearched the congress proceedings of the International and European Societies for the Study of Hypertension in Pregnancy. SELECTION CRITERIA: All randomised trials comparing antiplatelet agents with either placebo or no antiplatelet agent during pregnancy. Quasi-random study designs were excluded. Participants were pregnant women considered to be at risk of developing pre-eclampsia. Interventions were any comparisons of an antiplatelet agent (such as low-dose aspirin or dipyridamole) with either placebo or no antiplatelet agent. DATA COLLECTION AND ANALYSIS: Two reviewers assessed trials for inclusion in the review and extracted data. We entered data into the Review Manager software and double checked. MAIN RESULTS: Fifty-one trials involving 36,500 women are included in this review. There is a 19% reduction in the risk of pre-eclampsia associated with the use of antiplatelet agents ((43 trials, 33,439 women; relative risk (RR) 0.81, 95% confidence interval (CI) 0.75 to 0.88); number needed to treat (NNT) 69 (51, 109)).Twenty-eight trials (31,845 women) reported preterm birth. There is a small (7%) reduction in the risk of delivery before 37 completed weeks ((RR 0.93, 95% CI 0.89 to 0.98); NNT 83 (50, 238)). Fetal or neonatal deaths were reported in 38 trials (34,010 women). Overall there is a 16% reduction in baby deaths in the antiplatelet group (RR 0.84, 95% CI 0.74 to 0.96); NNT 227 (128, 909)). Small-for-gestational age babies were reported in 32 trials (24,310 women), with an 8% reduction in risk (RR 0.92, 95% CI 0.85 to 1.00). There were no significant differences between treatment and control groups in any other measures of outcome. REVIEWER'S CONCLUSIONS: Antiplatelet agents, in this review largely low-dose aspirin, have small-moderate benefits when used for prevention of pre-eclampsia. Further information is required to assess which women are most likely to benefit, when treatment is best started, and at what dose.

Female↗
PubMed1985

A highly polymorphic locus in human DNA revealed by cosmid-derived probes.

Human gene mapping would be greatly facilitated if marker loci with sufficient heterozygosity were generally available. As a source of such markers, we have used cosmids from a human genomic library. We have developed a rapid method for screening random cosmids to identify those that are homologous to genomic regions especially rich in restriction fragment length polymorphisms. This method allows whole cosmids to be used as probes against Southern transfers of genomic DNA; regions of cosmid probes homologous to repeated genomic sequences are rendered unable to hybridize with Southern transfers by prehybridization of the probes with a vast excess of nonradioactive genomic DNA. From one cosmid identified by this procedure, we have isolated three single-copy probes that collectively identify seven polymorphic loci. Of 56 unrelated individuals, 52 were heterozygous at one or more of these marker loci.

Chromosome Mapping↗
PubMed1988

Molecular cloning and temporal expression during pregnancy of the messenger ribonucleic acid encoding uteroferrin, a progesterone-induced uterine secretory protein.

A lambda gt11 expression library containing cDNA inserts prepared from porcine endometrial mRNA was immunologically screened by using an antiserum developed against porcine uteroferrin (Uf), a glycoprotein that has been strongly implicated in transplacental iron transport in the pregnant pig. Antibody reactive clones (lambda 4a3, 13.1, and 2.2) were isolated after screening 1.5 x 10(5) recombinant phages. Clones 4a3 and 13.1 expressed Uf antigenic determinants in beta-galactosidase fusion proteins and specifically selected antibody which reacted with Uf in immunoblots prepared from uterine cytosolic extracts. In addition, all three cDNA clones collectively contained DNA sequences that encoded an 85-amino acid peptide which corresponded to a region within the carboxyterminal portion of the Uf protein. Northern blot hybridization of these cDNAs to RNAs extracted from whole uterine tissue of pregnant pigs revealed a single uterine poly(A)+ RNA of approximately 1.7 kilobases in length, which was not found in liver and mammary tissue RNAs. The concentration of the Uf mRNA changed in a temporal fashion during pregnancy in a manner that was distinct from that of the progesterone receptor mRNAs. Highest levels of Uf mRNA were found at mid and late pregnancy (days 45-110) and were about 50-fold greater than at day 30 of pregnancy. By contrast, RIA analysis of the uterine tissue extracts showed that maximum amounts of Uf were present at day 60 and then declined sharply. Thus the pattern of Uf mRNA present in the uterus did not parallel the amount of Uf polypeptide that could be recovered from the tissue. The tissue specific and temporal regulation of Uf gene expression emphasizes that the protein plays an important role in uterine activity and/or fetal development.

Acid Phosphatase↗
PubMed2000

Interventions for early stage Hodgkin's disease in children.

BACKGROUND: Hodgkin's Disease is one of the most curable cancers in children, particularly at the early stages. The debate rests now more with retention of high cures and eliminating treatment sequelae. OBJECTIVES: To assess relapse free survival and overall survival rates in children with Stage l-llA Hodgkin's Disease treated with radiotherapy, chemotherapy or a combination of the two treatments. SEARCH STRATEGY: MEDLINE, EMBASE, CINAHL, Cancer-CD and the Cochrane Library were searched for randomised controlled trials. Key words included 'Hodgkin's Disease', 'Reed-Sternberg cells' and variations of 'child'. SELECTION CRITERIA: Treatments with a combination of the following therapies; involved field radiotherapy, extended field radiotherapy, anthracycline based chemotherapy regimens, or alkylating chemotherapy agents. Patients included children to 19 years of age. DATA COLLECTION AND ANALYSIS: Seven papers were identified as meeting the selection criteria. Of these four were usable, though one only covered a small section of the paper. It was not possible to combine the outcomes as they covered different treatment regimens and the numbers in one study were inaccurate. MAIN RESULTS: The results comparing IF with EF radiotherapy for children are based on one large multi-centred trial. Although the study is substantial and methodologically rigorous, the evidence for efficacy rests simply on this one trial. The results from the other three studies are not generalizable. The outcomes could not be combined as the studies assessed different treatment regimens. In addition there is little evidence to suggest that the methodological quality, particularly in terms of randomisation and simple arithmetic, is of a sufficiently robust nature in two of the studies. REVIEWER'S CONCLUSIONS: The treatment of Hodgkin's Disease Stage l -llA for children has undergone considerable evolution and development in the previous three decades with the introduction and refinement of combined modality treatments. There is now overall consensus that the prognosis for these patients following a short course of chemotherapy and low dose local radiotherapy is very good with a large percentage achieving long-term survival or relapse free survival. The main issues and problems facing practitioners in the field is the reduction and management of late effects and sequelae of treatment. The evidence for this overall agreement is based on a mass of cohort studies that have influenced changes in practice and significantly improved outcomes. However, apart from the collaborative study looking at radiotherapy alone, there is little evidence from randomised controlled trials to support this consensus.

Antineoplastic Agents↗
PubMed2006

Vaccines for preventing malaria (blood-stage).

BACKGROUND: A malaria vaccine is needed because of the heavy burden of mortality and morbidity due to this disease. This review describes the results of trials of blood (asexual)-stage vaccines. Several are under development, but only one (MSP/RESA, also known as Combination B) has been tested in randomized controlled trials. OBJECTIVES: To assess the effect of blood-stage malaria vaccines in preventing infection, disease, and death. SEARCH STRATEGY: In March 2006, we searched the Cochrane Infectious Diseases Group Specialized Register, CENTRAL (The Cochrane Library 2006, Issue 1), MEDLINE, EMBASE, LILACS, and the Science Citation Index. We also searched conference proceedings and reference lists of articles, and contacted organizations and researchers in the field. SELECTION CRITERIA: Randomized controlled trials comparing blood-stage vaccines (other than SPf66) against P. falciparum, P. vivax, P. malariae, or P. ovale with placebo, control vaccine, or routine antimalarial control measures in people of any age receiving a challenge malaria infection. DATA COLLECTION AND ANALYSIS: Both authors independently assessed trial quality and extracted data. Results for dichotomous data were expressed as relative risks (RR) with 95% confidence intervals (CI). MAIN RESULTS: Five trials of MSP/RESA vaccine with 217 participants were included; all five reported on safety, and two on efficacy. No severe or systemic adverse effects were reported at doses of 13 to 15 microg of each antigen (39 to 45 microg total). One small efficacy trial with 17 non-immune participants with blood-stage parasites showed no reduction or delay in parasite growth rates after artificial challenge. In the second efficacy trial in 120 children aged five to nine years in Papua New Guinea, episodes of clinical malaria were not reduced, but MSP/RESA significantly reduced parasite density only in children who had not been pretreated with an antimalarial drug (sulfadoxine-pyrimethamine). Infections with the 3D7 parasite subtype of MSP2 (the variant included in the vaccine) were reduced (RR 0.38, 95% CI 0.26 to 0.57; 719 participants) while those with the other main subtype, FC27, were not (720 participants). AUTHORS' CONCLUSIONS: The MSP/RESA (Combination B) vaccine shows promise as a way to reduce the severity of malaria episodes, but the effect of the vaccine is MSP2 variant-specific. Pretreatment for malaria during a vaccine trial makes the results difficult to interpret, particularly with the relatively small sample sizes of early trials. The results show that blood-stage vaccines may play a role and merit further development.

Antigens, Protozoan↗
PubMed2003

Antibiotic therapy for prophylaxis against infection of pancreatic necrosis in acute pancreatitis.

BACKGROUND: Acute pancreatitis is a common acute abdominal emergency which lacks specific therapy. In severe attacks, areas of the pancreas may become necrotic. The mortality risk rises to >40% if sterile necrosis becomes superinfected, usually with gut derived aerobic organisms. Experimental and clinical studies indicate a window of opportunity of 1-2 weeks, when superinfection, and thus high-risk surgical debridement, may be prevented by administering systemic antibiotics to 'sterilise' tissues adjacent to necrotic areas. There are theoretical risks of encouraging antibacterial resistance and opportunistic fungal infections. OBJECTIVES: To determine the effectiveness and safety of prophylactic antibiotic therapy in patients with severe acute pancreatitis who have developed pancreatic necrosis. SEARCH STRATEGY: MEDLINE, EMBASE, and the Cochrane Library were searched. We also examined other sources including Conference Abstracts (published and unpublished data). SELECTION CRITERIA: Randomised controlled trials (RCT) were sought using the search strategy detailed below. No linguistic limitations were applied. RCTs were selected in which antibacterial therapy was evaluated in patients with severe acute pancreatitis associated with pancreatic necrosis proven by intravenous contrast-enhanced computed tomography (CT). No linguistic limitations were applied. Searching was undertaken initially in November 2001 and updated in March 2003. DATA COLLECTION AND ANALYSIS: Two reviewers extracted data from trial publications independently, concerning rates for the primary end-points: with respect to: all cause mortality and rates of infection of pancreatic necrosis (proven by microbiological examination of fine needle aspirate or operative specimens). In addition, secondary end-points included peri-pancreatic sepsis, remote sepsis (respiratory, urinary, central venous line sources), operative rates, length of hospital stay, adverse events including the incidence of drug resistant microorganisms and opportunistic fungal infection. MAIN RESULTS: It was possible to evaluate mortality in all four included studies, and it demonstrated a survival advantage for antibiotic therapy (Odds ratio 0.32, p=0.02). Pancreatic sepsis (infected necrosis) was also measurable in all four studies and showed an advantage for therapy (Odds ratio 0.51, p=0.04). Extra-pancreatic infection could be evaluated in three studies, but showed no significant advantage for therapy (Odds ratio 0.47, p=0.05).Operative treatment data was available in three studies, but surgery rates were not significantly reduced (Odds ratio 0.55, p=0.08). Fungal infections showed no strongly increased preponderance with therapy (Odds ratio 0.83, p=0.7), but there were no data on infection with resistant organisms. Length of hospital stay could only be evaluated in two studies and was not significantly different. Sub-group analyses planned for the influence on outcome measures of the antibiotic regimen, the time of commencement of therapy in relation to symptom onset and/or hospitalisation, duration of therapy, and aetiology could not be performed as no data were available. REVIEWER'S CONCLUSIONS: Despite variations in drug agent, case mix, duration of treatment and methodological quality (especially the lack of double blinded studies), there was strong evidence that intravenous antibiotic prophylactic therapy for 10 to 14 days decreased the risk of superinfection of necrotic tissue and mortality in patients with severe acute pancreatitis with proven pancreatic necrosis at CT. Further studies are required to confirm all of the benefits suggested (in particular the need for operative debridement), to provide more adequate data on adverse effects, to address the choice of antibacterial agents and effects of varying duration of therapy, and whether outcome is related to aetiology.

Acute Disease↗
PubMed2005

Additional anti-Gram-positive antibiotic treatment for febrile neutropenic cancer patients.

BACKGROUND: The pattern of infections among neutropenic cancer patients has shifted in the last decades to a predominance of Gram-positive infections. Some of these Gram-positive bacteria are increasingly resistant to beta-lactams and necessitate specific antibiotic treatment. OBJECTIVES: To assess the effectiveness of empirical anti-Gram-positive (antiGP) antibiotic treatment for febrile neutropenic cancer patients in terms of mortality and treatment failure. To assess the rate of resistance development, further infections and adverse events associated with additional antiGP treatment. SEARCH STRATEGY: We searched The Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library Issue 4, 2004), MEDLINE (1966 to 2004), EMBASE (January 1980 to 2004), LILACS (1982 to 2004), conference proceedings, and all references of included studies. First authors of all included and potentially relevant trials were contacted. SELECTION CRITERIA: Randomised controlled trials comparing one antibiotic regimen to the same regimen with the addition of an antiGP antibiotic for the treatment of febrile neutropenic cancer patients. DATA COLLECTION AND ANALYSIS: Two reviewers independently assessed trial eligibility, methodological quality and extracted all data. Relative risks (RR) with 95% confidence intervals (CI) were calculated. A random effects model was used for all comparisons showing substantial heterogeneity (I(2 )> 50%). Outcomes were extracted by intention-to-treat and the analysis was patient-based whenever possible. MAIN RESULTS: Thirteen trials and 2392 patients or episodes were included. Empirical antiGP antibiotics were tested at the onset of treatment in eleven studies and for persistent fever in two studies. The antiGP treatment was a glycopeptide in nine trials. Seven studies were assessed in the overall mortality comparison and no significant difference between the comparator arms was seen, RR 0.82 (95% CI 0.56 to 1.20, 852 patients). Ten trials assessed failure including modifications as failures, while six assessed overall failure, disregarding treatment modifications. Failure with modifications was significantly reduced, RR 0.76 (95% CI 0.68 to 0.85, 1779 patients) while overall failure was equal, RR 1.00, 95% CI (0.79 to 1.27, 943 patients). Both mortality and failure did not differ significantly among patients with Gram-positive infections, but comparisons were small. Data regarding other patient subgroups likely to benefit from antiGP treatment were not available. Glycopeptides did not increase fungal superinfection rates, and were associated with a reduction in documented Gram-positive superinfections. Resistant colonisation was not documented in the studies. AUTHORS' CONCLUSIONS: Current evidence shows that the addition of antiGP treatment, namely glycopeptides, prior to documentation of a Gram-positive infection does not improve outcomes.

Anti-Bacterial Agents↗
PubMed2004

A structural pattern-based method for protein fold recognition.

A method (SPREK) was developed to evaluate the register of a sequence on a structure based on the matching of structural patterns against a library derived from the protein structure databank. The scores obtained were normalized against random background distributions derived from sequence shuffling and permutation methods. 'Random' structures were also used to evaluate the effectiveness of the method. These were generated by a simple random-walk and a more sophisticated structure prediction method that produced protein-like folds. For comparison with other methods, the performance of the method was assessed using collections of models including decoys and models from the CASP-5 exercise. The performance of SPREK on the decoy models was equivalent to (and sometimes better than) those obtained with more complex approaches. An exception was the two smallest proteins, for which SPREK did not perform well due to a lack of patterns. Using the best parameter combination from trials on decoy models, the CASP models of intermediate difficulty were evaluated by SPREK and the quality of the top scoring model was evaluated by its CASP ranking. Of the 14 targets in this class, half lie in the top 10% (out of around 140 models for each target). The two worst rankings resulted from the selection by our method of a well-packed model that was based on the wrong fold. Of the other poor rankings, one was the smallest protein and the others were the four largest (all over 250 residues).

Algorithms↗
PubMed2005

Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings.

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions-deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.

Computational Biology↗
PubMed2005

libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.

BACKGROUND: An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. RESULTS: The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. CONCLUSION: Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

Algorithms↗
PubMed1998

Single nucleotide polymorphism hunting in cyberspace.

Large-scale sequencing of human cDNA and genomic DNA libraries has produced a large collection of sequence data in public databases. To date, >900,000 human expressed sequence tag (EST) sequences and >80,000,000 bases of genomic DNA sequence have been deposited in Genbank. This ever-expanding data set is a rich source of gene-associated and anonymous single nucleotide polymorphisms (SNPs). DNA sequence variations can be found by comparing the sequences of redundant ESTs and by comparing sequences from overlapping genomic clones. Initial studies have shown that, with proper computer screening, informative SNP markers can be developed from these DNA databases in an efficient and cost-effective manner. Complete public access to these databases will allow individual investigators to add biological value to the human sequence data generated by large-scale sequencing centers.

DNA↗
PubMed2000

An algorithm for automated bacterial identification using matrix-assisted laser desorption/ionization mass spectrometry.

An algorithm for bacterial identification using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is being developed. This mass spectral fingerprint comparison algorithm is fully automated and statistically based, providing objective analysis of samples to be identified. Based on extraction of reference fingerprint ions from test spectra, this approach should lend itself well to real-world applications where samples are likely to be impure. This algorithm is illustrated using a blind study. In the study, MALDI-MS fingerprints for Bacillus atrophaeus ATCC 49337, Bacillus cereus ATCC 14579T, Escherichia coli ATCC 33694, Pantoea agglomerans ATCC 33243, and Pseudomonas putida F1 are collected and form a reference library. The identification of test samples containing one or more reference bacteria, potentially mixed with one species not in the library (Shewanella alga BrY), is performed by comparison to the reference library with a calculated degree of association. Out of 60 samples, no false positives are present, and the correct identification rate is 75%. Missed identifications are largely due to a weak B. cereus signal in the bacterial mixtures. Potential modifications to the algorithm are presented and result in a higher than 90% correct identification rate for the blind study data, suggesting that this approach has the potential for reliable and accurate automated data analysis of MALDI-MS.

Algorithms↗