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PubMed1993

Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes form unique lineages related to the genus Vibrio.

Bioluminescent symbioses range from facultative associations to highly adapted, apparently obligate ones. The family Anomalopidae (flashlight fishes) encompasses five genera of tropical reef fishes that have large suborbital light organs. The suborder Ceratioidei (deep-sea anglerfishes) contains 11 families. In nine of these, females have a bioluminescent lure that contains bacterial symbionts. In all other fish light-organ symbioses (occurring in 10 families in 5 orders), the symbionts belong to three Photobacterium species; nonsymbiotic luminous bacteria are Vibrio species. The bacteria are extracellular and tightly packed in tubules that communicate with the exterior, releasing bacteria into the gut of the host or the surrounding sea water. The released bacteria are usually cultivable and can contribute to planktonic populations. Although anomalopids release bacteria and ceratioids have pores that would allow release, the fate of these bacteria is unknown and they cannot be cultured by standard isolation techniques. We report here phylogenetic analysis of 16S ribosomal RNA gene sequences from light organs that show that anomalopid and ceratioid symbionts are not known luminous bacteria, but are new groups related to Vibrio spp. They are characterized by host specificity, deep divergence between symbionts from different genera (anomalopids) or families (ceratioids) and, possibly, parallel divergence of hosts and symbionts.

Animals↗
PubMed2004

[Laparoscopic and general surgery guided by open interventional magnetic resonance].

Interventional magnetic resonance (IMR) machines have produced unique opportunity for image-guided surgery. The open configuration design and fast pulse sequence allow virtual real time intraoperative scanning to monitor the progress of a procedure, with new images produced every 1.5 sec. This may give greater appreciation of anatomy, especially deep to the 2-dimensional laparoscopic image, and hence increase safety, reduce procedure magnitude and increase confidence in tumour resection surgery. The aim of this paper was to investigate the feasibility of performing IMR-image-guided general surgery, especially in neoplastic and laparoscopic field, reporting a single center -- St. Mary's Hospital (London, UK) -- experience. Procedures were carried out in a Signa 0.5 T General Elettric SP10 Interventional MR (General Electric Medical Systems, Milwaukee, WI, USA) with magnet-compatible instruments (titanium alloy instruments, plastic retractors and ultrasonic driven scalpel) and under general anesthesia. There were performed 10 excision biopsies of palpable benign breast tumors (on female patients), 3 excisions of skin sarcoma (dermatofibrosarcoma protuberans), 1 right hemicolectomy and 2 laparoscopic cholecystectomies. The breast lesions were localized with pre- and postcontrast (intravenous gadolinium DPTA) sagittal and axial fast multiplanar spoiled gradient recalled conventional Signa sequences; preoperative real time fast gradient recalled sequences were also obtained using the flashpoint tracking device. During right hemicolectomy intraoperative single shot fast spin echo (SSFSE) and fast spoiled gradient recalled (FSPGR) imaging of right colon were performed after installation of 150 cc of water or 1% gadolinium solution, respectively, through a Foley catheter; imaging was also obtained in an attempt to identify mesenteric lymph nodes intraoperatively. Concerning laparoscopic procedures, magnetic devices (insufflator, light source) were positioned outside scan room, the tubing and light head being passed through penetration panels. Intraoperative MR-cholangiography was performed using fast spin echo (SSFSE) techniques with minimal intensity projection 3-dimensional reconstruction. About skin sarcomas, 2 of them were skin recurrences of previously surgically treated sarcomas (all of them received preoperative biopsy) and the extent of the lesion was then determined using short tau inversion recovery (STIR) sequence. The skin was closed in each case without need for any plastic reconstruction. The breast lesions were visualized with both Signa and real-time imaging and all enhanced with contrast: 2 (20%) were visualized only after contrast enhancement; intraoperative real time imaging clearly demonstrated a resection margin in all cases. Maximum dimensions of breast specimens (range 8-50 mm, median 24.5 mm) were not significantly different from those measured by Signa (p>0.17, Student's paired t-test) or real time images (p>0.4): also there was no significant difference in lesion size between Signa and real time images (p>0.25). All postprocedure scans clearly demonstrated complete excision. The extent of the tumor at MR imaging was greater in each case than suggested by clinical examination. Adequate resection margins were planned using STIR sequences. Histological examination confirmed clear surgical margins of at least 1 cm in each case. During right hemicolectomy, both intraoperative SSFSE and FSPGR contrast imaging revealed the lesion and details of the colonic surface; imaging of the lymph node draining right colon was only partially successful, due to movement artifact. Concerning laparoscopic procedures, both FSE and SSFSE techniques produced reasonable images of the gallbladder and intrahepatic ducts, but the FSE imaging was of poor quality due to respiration artifact; however, SSFSE allowed visualization of the gallbladder and part of the common bile duct. About skin sarcomas, the extent of the tumor at MR imaging was greater in each case than suggested by clinical examination and in each case the complete tumor excision was confirmed. Histological examination confirmed clear surgical margins of at least 1 cm in each case. Intraoperative MR scanning reliably identifies palpable breast tumours and skin sarcomas and is sufficiently accurate to guide their surgical excision. Further work may be done to develop laparoscopic and open abdominal surgery as well.

Anesthesia, General↗
PubMed2003

Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia.

Ramlibacter gen. nov. is proposed for two aerobic, chemo-organotrophic, cyst-producing soil bacterial strains. These bacteria are Gram-negative, non-flagellated rods or cysts, isolated from subdesert soil in Tataouine, Tunisia. Phylogenetic analyses of the rrs sequences of the two strains showed that they do not constitute a robust clade at the genus level with any previously described bacteria and that they are a deep branch of a clade also grouping the genera Acidovorax and Hydrogenophaga within the beta-Proteobacteria. They belong to two different species, as verified by DNA-DNA hybridization (23.5% reassociation). The type species of the genus is Ramlibacter tataouinensis sp. nov., with the type strain TTB310T (=DSM 14655T =ATCC BAA-407T =LMG 21543T). The second species is Ramlibacter henchirensis sp. nov., with the type strain TMB834T (=DSM 14656T =ATCC BAA-408T =LMG 21542T). The G + C contents of R. tataouinensis and R. henchirensis are 69.6 and 66.6 mol%, respectively.

Betaproteobacteria↗
PubMed1993

Monoclonal antibody 2B5 defines a truncated O-glycan, GlcNAc beta 1-3Gal beta 1-4GlcNAc beta 1-6 (GalNAc), on mucins from deep gastric and duodenal glands as well as metaplasia and neoplasia of gastric differentiation.

Monoclonal antibody (MAb) 2B5 previously generated in BALB/c mice using gastric mucosa of the corpus as immunogen was characterized with regard to its binding epitope. Binding assays on structurally defined neoglycolipids from mucin glycans revealed that MAb 2B5 recognizes a carbohydrate epitope on a neutral O-glycan sequence from gastric mucins. This oligosaccharide chain has been characterized by mass spectrometry and methylation analysis and sequential exoglycosidase treatment of the derived neoglycolipid as GlcNAc beta 1-3Gal beta 1-4GlcNAc beta 1-6OY (where 6OY corresponds to the GalNAc-ol fragment--O--(CH2)2 conjugated to dipalmitoylphosphatidylethanolamine). The selective binding of MAb 2B5 to mucus from deep gastric and duodenal glands, to gastric metaplasia or neoplasia with gastric differentiation may imply that mucin glycosylation in the respective cells is incomplete resulting in the accumulation of truncated blood group precursor chains. MAb 2B5 is the first monoclonal antibody which defines an epitope on M2-type antigens and may substitute, accordingly, for the inconvenient "paradoxical concanavalin A-horseradish peroxidase method" in histochemistry.

Animals↗
PubMed2002

The promoter analysis of the human C17orf25 gene, a novel chromosome 17p13.3 gene.

The human C17orf25 gene (Accession No. AF177342) is one of thirteen genes cloned from a region displaying a high score of loss of heterozygosity within chromosome 17p13.3 in human hepatocellular carcinoma in China. To unveil the underlying mechanisms for the transcription regulation of this gene and understand its implication to the hepatocellular carcinogenesis, we looked into the relevant aspects by both bioinformatic and experimental executions. We found: 1, The abundant expression of the C17orf25 gene was evident in all the cell lines and tissue samples tested, showing little hepatoma-selectivity; 2, Its transcription starts at a single site, locating at -60 from the translation initiation codon; 3, A 58 bp fragment containing the transcription start, extending from -112 to -55, represents the minimal promoter; 4, The consensus sequence within this fragment recognized by SP1 contributes predominantly to the activity of the minimal promoter; 5, The bioinformatic analysis suggests that the C17orf25 gene may encode a protein in the family of the glyoxalase. Our data has provided some deep insight into both function and regulation of the C17orf25 gene in the context of the normal liver and hepatocellular carcinoma.

5' Flanking Region↗
PubMed2026

Cryptic serpentine divergence and substrate adaptation of Cardamine glauca in the Balkan Peninsula.

BACKGROUND AND AIMS: Serpentine soils represent one of the most challenging substrates for plant life due to skewed ratios of essential nutrients and toxic concentrations of metals. Plant adaptation to such conditions may lead to locally adapted edaphic ecotypes or, when reproductive barriers evolve, to distinct serpentine endemics. However, a third scenario may occur: cryptic edaphic divergence, where phenotypically similar lineages adapted to contrasting substrates exhibit deep genetic divergence. Here, we tested whether substrate-associated divergence reflects repeated serpentine adaptation or cryptic edaphic lineage divergence in Cardamine glauca (Brassicaceae) in Balkan peninsula - a hotspot of serpentine endemism in Europe. METHODS: We sampled and sequenced genomes of 43 individuals of C. glauca together with four individuals representing closely related taxa, C. plumieri and C. pancicii, from variable substrates across the Balkans. We combined phylogenomics, population genomic analyses of selection and a reciprocal transplant experiment to infer the most likely evolutionary scenario. KEY RESULTS: Phylogenomic analysis of 941 loci confirmed monophyly of C. glauca, including the local endemic C. pancicii, but revealed deep splits (∼2.2-3.2 Mya) between co-occurring serpentine and non-serpentine lineages. Population genomic analyses of replicated geographically proximate serpentine-non-serpentine population pairs demonstrated strong genome-wide differentiation and limited gene flow between edaphic types. Window-based analyses of local genomic divergence and tests for positive selection revealed candidate genes involved in ion transport, membrane transporter activity and metal homeostasis, consistent with the hypothesis of substrate-driven ecological adaptation. This was further supported by a significant substrate-of-origin fitness advantage in a reciprocal transplant experiment. CONCLUSIONS: Altogether, our results demonstrate that edaphic preferences may correspond with deep genetic divergence between similar-looking yet differently adapted lineages. The presence of cryptic edaphic lineages suggests that plant diversity may still be underestimated in genomically underexplored but edaphically diverse hotspots such as the Balkans.

Cardamine glauca↗
PubMed1995

The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species.

The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, beta, gamma, delta, epsilon proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.

Amino Acid Sequence↗
PubMed1996

MR relaxation times in human brain: measurement at 4 T.

PURPOSE: To determine the values for relaxation times in human brain for magnetic resonance (MR) imaging at 4 T. MATERIALS AND METHODS: T1 measurements were made with a progressive saturation sequence, an implementation of the Look-Locker sequence, and an inversion-recovery (IR) interleaved echo-planar imaging (IEPI) sequence. T2 measurements were made with a standard spin-echo (SE) sequence and an SE IEPI sequence. RESULTS: The T1 measurements yielded values of 1,724 msec +/- 51 for gray matter, 1,043 msec +/- 27 for white matter, and 4,550 msec +/- 800 msec for cerebrospinal fluid. The deep gray matter regions had T1 values of 1,458 +/- 38 (caudate nucleus) and 1,372 +/- 60 (putamen). The T2 measurements yielded results of 63 msec +/- 6.2 for gray matter and 49.8 msec +/- 2.2 for white matter. CONCLUSION: The T1 values measured at 4 T show a higher value than predicted from extrapolation at lower field strengths. The T2 measurements showed a slight decrease in values over those measured at lower-field strength. The gain in signal-to-noise ratio from the higher field strength may be substantially offset by these altered relaxation time values to a degree that is sequence dependent.

Adult↗
PubMed1990

Compositional statistics: an improvement of evolutionary parsimony and its application to deep branches in the tree of life.

We present compositional statistics, a new method of phylogenetic inference, which is an extension of evolutionary parsimony. Compositional statistics takes account of the base composition of the compared sequences by using nucleotide positions that evolutionary parsimony ignores. It shares with evolutionary parsimony the features of rate invariance and the fundamental distinction between transitions and transversions. Of the presently available methods of phylogenetic inference, compositional statistics is based on the fewest and mildest assumptions about the mode of DNA sequence evolution. It is therefore applicable to phylogenetic studies of the most distantly related organisms or molecules. This was illustrated by analyzing conservative positions in the DNA sequences of the large subunit of RNA polymerase from three archaebacterial groups, a eubacterium, a chloroplast, and the three eukaryotic polymerases. Internally consistent results, which are in accord with our knowledge of organelle origin and archaebacterial physiology, were achieved.

Amino Acid Sequence↗
PubMed2004

Phylogenetic and ecological analysis of novel marine stramenopiles.

Culture-independent molecular analyses of open-sea microorganisms have revealed the existence and apparent abundance of novel eukaryotic lineages, opening new avenues for phylogenetic, evolutionary, and ecological research. Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, constituted one of the most important novel lineages in these open-sea samples. Here we carry out a comparative analysis of novel stramenopiles, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites. Novel stramenopiles were found in all major habitats, generally accounting for a significant proportion of clones in genetic libraries. Phylogenetic analyses indicated the existence of 12 independent clusters. Some of these were restricted to anoxic or deep-sea environments, but the majority were typical components of coastal and open-sea waters. We specifically identified four clusters that were well represented in most marine surface waters (together they accounted for 74% of the novel stramenopile clones) and are the obvious targets for future research. Many sequences were retrieved from geographically distant regions, indicating that some organisms were cosmopolitan. Our study expands our knowledge on the phylogenetic diversity and distribution of novel marine stramenopiles and confirms that they are fundamental members of the marine eukaryotic picoplankton.

Animals↗
PubMed2005

NADPH oxidases in Eukaryotes: red algae provide new hints!

The red macro-alga Chondrus crispus is known to produce superoxide radicals in response to cell-free extracts of its green algal pathogenic endophyte Acrochaete operculata. So far, no enzymes involved in this metabolism have been isolated from red algae. We report here the isolation of a gene encoding a homologue of the respiratory burst oxidase gp91(phox) in C. crispus, named Ccrboh. This single copy gene encodes a polypeptide of 825 amino acids. Search performed in available genome and EST algal databases identified sequences showing common features of NADPH oxidases in other algae such as the red unicellular Cyanidioschyzon merolae, the economically valuable red macro-alga Porphyra yezoensis and the two diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Domain organization and phylogenetic relationships with plant, animal, fungal and algal NADPH oxidase homologues were analyzed. Transcription analysis of the C. crispus gene revealed that it was over-transcribed during infection of C. crispus gametophyte by the endophyte A. operculata, and after incubation in presence of atrazine, methyl jasmonate and hydroxyperoxides derived from C20 polyunsaturated fatty acids (PUFAs). These results also illustrate the interest of exploring the red algal lineage for gaining insight into the deep evolution of NADPH oxidases in Eukaryotes.

Algal Proteins↗
PubMed1995

Photoaffinity-labeled ligand binding domains on dopamine transporters identified by peptide mapping.

Binding domains on rat dopamine transporters for cocaine and 1-(2-diphenylmethoxy)ethyl-4-(3-phenylpropyl)piperazine compounds were identified using controlled proteolysis of photoaffinity-labeled protein and epitope-specific immunoprecipitation of the labeled fragments. Rat dopamine transporters were photoaffinity labeled with 1-[2-(diphenylmethoxy)ethyl]-4-[2-(4-azido- 3-[125I]iodophenyl)ethyl]piperazine ([125I]DEEP) [a 1-(2-di- phenylmethoxy)ethyl-4-(3-phenylpropyl)piperazine analog] or 3 beta-(p-chlorophenyl)tropane-2 beta-carboxylic acid, 4'-azido-3'- [125I]iodophenylethyl ester ([125I]RTI 82) (a cocaine analog) and were gel purified to remove contaminating radioactivity. The resulting samples were treated with V8 protease or trypsin and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The peptide maps generated with each enzyme were different for each of the ligands, suggesting that the ligands were incorporated into different regions of the protein. Identical peptide maps were generated from striatum- and nucleus accumbens-derived transporters, indicating that these polypeptides are highly similar in primary sequence. The proteolytic fragments generated by V8 protease were localized to specific domains of the protein using antipeptide antibodies corresponding to five different regions of the transporter. Fragments of 10 and 7 kDa from [125I]DEEP-labeled transporters were specifically immunoprecipitated with an antibody generated against amino acids 42-59 (near the first putative trans-membrane domain), whereas a 34-kDa fragment from [125I]RTI 82-labeled transporters was precipitated with three different sera corresponding to regions in the carboxyl-terminal two thirds of the protein. None of the V8 fragments smaller than 45 kDa, containing either photolabel, was altered in molecular mass by N-deglycosylation. The results indicate that photoincorporation of [125I]DEEP occurs in the amino half of the dopamine transporter, near the first two transmembrane helices, whereas [125I]RTI 82 labels the carboxyl-terminal region of the protein, between transmembrane domains 4 and 12.

Affinity Labels↗
PubMed1996

[New mucin core protein genes and their clinical application].

Recent molecular biological approach has revealed the primary structure of some mucin core proteins. Most prominent characteristic is tandemly repeated sequences. cDNA cloning of 8 kinds of mucin core proteins, MUC1-7, have thus been performed. Among them, the entire structure was revealed on MUC1,2 and 7. MUC1 is a type I transmembrane protein with a large number of tandem repeat consisting of 20 amino acids. We have found that mouse MoAb MUSE11 against adenocarcinoma, which detects circulating MUC1 in patients with gastrointestinal and pancreatic cancers, recognizes part of the tandem repeat of MUC1 using synthetic peptides. We have transfected MUC1 cDNA to some cell lines, and they indicated that cell-cell and cell-matrix adhesion, growth rate and reactivity with growth factor were suppressed. To date, some of the MoAbs to adenocarcinoma have been shown to react with PDTRP sequence in the tandem repeat of MUC1 (MUC1 epitope), suggesting that MUC1 epitope could be highly immunogenic in human. Recently, cytotoxic T-cells against MUC1 epitope were established from breast and pancreas cancer patients. We also induce those T-cells from the patient with multiple myeloma. Interestingly, CTL functions in an HLA-unrestricted manner, and may be of use an adoptive immunotherapy. MUC2, a large secretory type mucin, cysteine-rich subdomains located both upstream and downstream of its central repetitive region, and these subdomains have sequence similarity with von Willebrand factor. We have shown that anti MUC2 core-protein MoAb CCP58 reacts intestinal metaplasia and cancer in stomach, but not normal gastric mucous membrane. Recently we established a new monoclonal antibody against purified deglycosylated gastric mucin. This antigen was expressed in the deep portion of metaplastic glands and cancers in the stomach. Two cDNA clones coding for this antigenic molecule were obtained.

Animals↗
PubMed1999

Molecular characterization and in situ localization of a full-length cyclic nucleotide-gated channel in rat brain.

Ion channels gated directly by cyclic nucleotides are required for the transduction of sensory signals in photoreceptor cells and olfactory cells. Cyclic nucleotide-gated (CNG) channels may also be expressed in the central nervous system because partial transcripts that share homology with CNG channels have been found therein. We have now isolated and cloned a full-length CNG channel cDNA from adult rat brain. The sequence is identical to that of the alpha-subunit originally found in the olfactory epithelium (CNCalpha3). In situ hybridization, using probes specific for the CNCalpha3 mRNA, suggest that this channel is expressed widely in the rat brain, albeit mostly at relatively low levels. Certain neuronal populations, however, such as deep cerebellar nuclei, olfactory bulb mitral cells and cerebellar Purkinje neurons, appeared specially enriched. The study demonstrates for the first time that a full-length CNG channel mRNA is expressed in the brain, supporting the possibility that CNG channels are involved in central neural communication and plasticity. The sequence reported in this paper has been deposited in the GenBank data base (accession no. AF126808).

Animals↗
PubMed2003

Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen.

It has long been suggested that the overall shape of the antigen combining site (ACS) of antibodies is correlated with the nature of the antigen. For example, deep pockets are characteristic of antibodies that bind haptens, grooves indicate peptide binders, while antibodies that bind to proteins have relatively flat combining sites. In 1996, MacCallum, Martin and Thornton used a fractal shape descriptor and showed a strong correlation of the shape of the binding region with the general nature of the antigen.However, the shape of the ACS is determined primarily by the lengths of the six complementarity-determining regions (CDRs). Here, we make a direct correlation between the lengths of the CDRs and the nature of the antigen. In addition, we show significant differences in the residue composition of the CDRs of antibodies that bind to different antigen classes. As well as helping us to understand the process of antigen recognition, autoimmune disease and cross-reactivity, these results are of direct application in the design of antibody phage libraries and modification of affinity.

Amino Acids↗
PubMed2001

Phylogeny and origin of 82 zygomycetes from all 54 genera of the Mucorales and Mortierellales based on combined analysis of actin and translation elongation factor EF-1alpha genes.

True fungi (Eumycota) are heterotrophic eukaryotic microorganisms encompassing ascomycetes, basidiomycetes, chytridiomycetes and zygomycetes. The natural systematics of the latter group, Zygomycota, are very poorly understood due to the lack of distinguishing morphological characters. We have determined sequences for the nuclear-encoded genes actin (act) from 82 zygomycetes representing all 54 currently recognized genera from the two zygomycetous orders Mucorales and Mortierellales. We also determined sequences for translation elongation factor EF-1alpha (tef) from 16 zygomycetes (total of 96,837 bp). Phylogenetic analysis in the context of available sequence data (total 2,062 nucleotide positions per species) revealed that current classification schemes for the mucoralean fungi are highly unnatural at the family and, to a large extent, at the genus level. The data clearly indicate a deep, ancient and distinct dichotomy of the orders Mucorales and Mortierellales, which are recognized only in some zygomycete systems. Yet at the same time the data show that two genera - Umbelopsis and Micromucor - previously placed within the Mortierellales on the basis of their weakly developed columella (a morphological structure of the sporangiophore well-developed within all Mucorales) are in fact members of the Mucorales. Phylogenetic analyses of the encoded amino acid sequences in the context of homologues from eukaryotes and archaebacterial outgroups indicate that the Eumycota studied here are a natural group but provide little or no support for the monophyly of either zygomycetes, ascomycetes or basidiomycetes. The data clearly indicate that a complete revision of zygomycete natural systematics is necessary.

Actins↗
PubMed2004

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.

BACKGROUND: The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation. RESULTS: The GOtcha method was applied to the recently sequenced genome for Plasmodium falciparum and six other genomes. GOtcha was compared quantitatively for retrieval of assigned GO terms against direct transitive assignment from the highest scoring annotated BLAST search hit (TOPBLAST). GOtcha exploits information deep into the 'twilight zone' of similarity search matches, making use of much information that is otherwise discarded by more simplistic approaches. At a P-score cutoff of 50%, GOtcha provided 60% better recovery of annotation terms and 20% higher selectivity than annotation with TOPBLAST at an E-value cutoff of 10(-4). CONCLUSIONS: The GOtcha method is a useful tool for genome annotators. It has identified both errors and omissions in the original Plasmodium falciparum annotation and is being adopted by many other genome sequencing projects.

Animals↗
PubMed2003

Periarticular lesions detected on magnetic resonance imaging: prevalence in knees with and without symptoms.

OBJECTIVE: To evaluate, using magnetic resonance imaging (MRI), the prevalence of periarticular lesions in older persons with or without knee pain, and to assess the association of these lesions with knee pain. METHODS: Subjects ages 45 years and older, with or without knee pain, were recruited from Veterans Affairs medical centers and from the community. Weight-bearing posteroanterior, skyline, and lateral radiographs were obtained in all subjects. Subjects were divided into 3 groups: those with radiographic OA (ROA) and knee pain (n = 376), those with ROA and no knee pain (n = 51), and those with neither ROA nor knee pain (n = 24). A single knee (the more symptomatic one in subjects with knee pain) was imaged with a 1.5T scanner using T1- and T2-weighted and proton-density spin-echo imaging sequences. MRIs were read for the presence of periarticular lesions, which were categorized (according to their general location) as being either peripatellar (prepatellar, superficial infrapatellar, deep infrapatellar) or "other periarticular lesions" (semimembranosus-tibial collateral ligament bursitis, anserine bursitis, iliotibial band syndrome, tibiofibular cyst). RESULTS: Patients with knee pain had more severe radiographic disease than did subjects who were asymptomatic. Peripatellar lesions (prepatellar or superficial infrapatellar) were present in 12.1% of the patients with knee pain and ROA, in 20.5% of the patients with ROA and no knee pain, and in 0% of subjects with neither ROA nor knee pain (P = 0.116). However, other periarticular lesions were present in 14.9% of patients with both ROA and knee pain, in only 3.9% of patients with ROA but no knee pain, and in 0% of the group with no knee pain and no ROA (P = 0.004). CONCLUSION: Although peripatellar lesions are equally common among subjects with knee pain and those without knee pain, other periarticular lesions (including bursitis and iliotibial band syndrome) are significantly more common among subjects with knee pain and may contribute to pain in these individuals.

Aged↗