Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis

BACKGROUND: Recent, rapid growth in the quantity of available genomic data has generated many protein sequences that are not yet biochemically classified. Thus, the prediction of biochemical function based on structural motifs is an important task in post-genomic analysis. The InterPro databases are a major resource for protein function information. For optimal results, these databases should be searched at regular intervals, since they are frequently updated. RESULTS: We describe here a new program JIPS (Java GUI for InterProScan), a tool for tracking and viewing results obtained from repeated InterProScan searches. JIPS stores matches (in a local database) obtained from InterProScan searches performed with multiple versions of the InterPro database and highlights hits that have been added since the last search of the InterPro database. Results are displayed in an easy-to-use tabular format. JIPS also contains tools to assist with ortholog-based comparative studies of protein signatures. CONCLUSION: JIPS is an efficient tool for performing repeated InterProScans on large batches of protein sequences, tracking and viewing search results, and mining the collected data

Scoring Protein Relationships in Functional Interaction Networks Predicted from Sequence Data

The abundance of diverse biological data from various sources constitutes a rich source of knowledge, which has the power to advance our understanding of organisms. This requires computational methods in order to integrate and exploit these data effectively and elucidate local and genome wide functional connections between protein pairs, thus enabling functional inferences for uncharacterized proteins. These biological data are primarily in the form of sequences, which determine functions, although functional properties of a protein can often be predicted from just the domains it contains. Thus, protein sequences and domains can be used to predict protein pair-wise functional relationships, and thus contribute to the function prediction process of uncharacterized proteins in order to ensure that knowledge is gained from sequencing efforts. In this work, we introduce information-theoretic based approaches to score protein-protein functional interaction pairs predicted from protein sequence similarity and conserved protein signature matches. The proposed schemes are effective for data-driven scoring of connections between protein pairs. We applied these schemes to the Mycobacterium tuberculosis proteome to produce a homology-based functional network of the organism with a high confidence and coverage. We use the network for predicting functions of uncharacterised proteins

PET/CT with 89Zr-girentuximab can aid in diagnostic dilemmas of clear cell renal cell carcinoma suspicion

Based on the high expression of Carbonic Anhydrase IX (CAIX) in 95% of clear cell renal cell carcinoma (ccRCC), the anti-CAIX monoclonal antibody girentuximab can be used for the detection of ccRCC. This clinical study explores the value of 89Zr-labeled girentuximab PET/CT imaging in diagnostic challenges regarding ccRCC. PET/CT imaging was performed 4 or 5 days after injection of 89Zr-girentuximab in patients with a primary renal mass (n=16) or a history of ccRCC (n=14). Scans were used for decision making (surgery/active surveillance) in case of indistinct renal masses. All resected PET-positive primary lesions proved to be ccRCC, while no lesion progression was seen in PET-negative masses. In patients suspected of recurrent/metastatic ccRCC, PET/CT with 89Zr-girentuximab was useful to confirm or exclude ccRCC, to evaluate the extent of the disease and to differentiate from other cancers. In this group 89Zr-girentuximab PET/CT resulted in a major change in clinical management in five patients (36%), while in three patients (21%) repeat biopsies could be avoided. We conclude that 89Zr-girentuximab PET/CT is a valuable diagnostic tool that can guide clinical decision making in case of diagnostic dilemmas concerning ccRCC suspicion. Patient summary: 89Zr-girentuximab PET/CT imaging can be a valuable diagnostic tool to identify ccRCC

Functional status of masticatory system, excutive function and episodic memory in older persons.

Findings from human experimental studies suggest that mastication positively influences cognitive function. The participants in those studies were relatively young. The goal of this study was to examine the relationship between the functional status of the masticatory system, episodic memory, and executive functions in elderly people. The participants, elderly people living independently at home, were divided into two groups. One group had a full complement of natural teeth (n = 19) and the other group had full dentures (n = 19). The functional status of the masticatory system was assessed by measuring mandibular excursions (i.e. the distances over which the mandible can move in the open, lateral, and forward directions), bite force, number of occluding pairs and complaints of the masticatory system (facial pain, headaches/migraine). Executive functions and episodic memory were assessed by neuropsychological tests. Backward regression analysis showed that only in the group of elderly people with full dentures, 22% of executive functions were predicted by complaints of the masticatory system and 19.4% of episodic memory was predicted by masticatory performance (composed of mandibular excursions and bite force). The conclusion of this study is that only in older persons with full dentures the relationship between mastication, episodic memory, and executive function becomes evident when the functional status of the masticatory system decreases

Treatment Outcome in Patients Receiving Assertive Community Treatment

In an observational study of severely mentally ill patients treated in assertive community treatment (ACT) teams, we investigated how treatment outcome was associated with demographic factors, clinical factors, and motivation for treatment. To determine psychosocial outcome, patients were routinely assessed using the Health of the Nation Outcome Scales (HoNOS). Trends over time were analyzed using a mixed model with repeated measures. The HoNOS total score was modeled as a function of treatment duration and patient-dependent covariates. Data comprised 637 assessments of 139 patients; mean duration of follow-up was 27.4 months (SD = 5.4). Substance abuse, higher age, problems with motivation, and lower educational level were associated with higher HoNOS total scores (i.e., worse outcome). To improve treatment outcome, we recommend better implementation of ACT, and also the implementation of additional programs targeting subgroups which seem to benefit less from ACT

Phase 2 Study of Lutetium 177-Labeled Anti-Carbonic Anhydrase IX Monoclonal Antibody Girentuximab in Patients with Advanced Renal Cell Carcinoma.

Unlabelled Despite advances in the treatment of metastatic clear cell renal cell carcinoma (ccRCC), there is still an unmet need in the treatment of this disease. A phase 2 radioimmunotherapy (RIT) trial with lutetium 177 ((177)Lu)-girentuximab was initiated to evaluate the efficacy of this approach. In this nonrandomized single-arm trial, patients with progressive metastatic ccRCC who met the inclusion criteria received 2405 MBq/m(2) of (177)Lu-girentuximab intravenously. In the absence of persistent toxicity and progressive disease, patients were eligible for retreatment after 3 mo with 75% of the previous activity dose. A total of 14 patients were included. After the first therapeutic infusion, eight patients (57%) had stable disease (SD) and one (7%) had a partial regression. The treatment was generally well tolerated but resulted in grade 3-4 myelotoxicity in most patients. After the second cycle, continued SD was observed in five of six patients, but none were eligible for retreatment due to prolonged thrombocytopenia. In conclusion, RIT with (177)Lu-girentuximab resulted in disease stabilization in 9 of 14 patients with progressive metastatic ccRCC, but myelotoxicity prevented retreatment in some patients.Patient summary We investigated the efficacy of lutetium 177-girentuximab radioimmunotherapy in patients with metastatic kidney cancer. The treatment resulted in disease stabilization in 9 of 14 patients. The main toxicity was prolonged low blood cell counts.Trial registration ClinicalTrials.gov identifier: NCT02002312 (https://clinicaltrials.gov/ct2/show/NCT02002312)

FastBLAST: Homology Relationships for Millions of Proteins

BackgroundAll-versus-all BLAST, which searches for homologous pairs of sequences in a database of proteins, is used to identify potential orthologs, to find new protein families, and to provide rapid access to these homology relationships. As DNA sequencing accelerates and data sets grow, all-versus-all BLAST has become computationally demanding.Methodology/principal findingsWe present FastBLAST, a heuristic replacement for all-versus-all BLAST that relies on alignments of proteins to known families, obtained from tools such as PSI-BLAST and HMMer. FastBLAST avoids most of the work of all-versus-all BLAST by taking advantage of these alignments and by clustering similar sequences. FastBLAST runs in two stages: the first stage identifies additional families and aligns them, and the second stage quickly identifies the homologs of a query sequence, based on the alignments of the families, before generating pairwise alignments. On 6.53 million proteins from the non-redundant Genbank database ("NR"), FastBLAST identifies new families 25 times faster than all-versus-all BLAST. Once the first stage is completed, FastBLAST identifies homologs for the average query in less than 5 seconds (8.6 times faster than BLAST) and gives nearly identical results. For hits above 70 bits, FastBLAST identifies 98% of the top 3,250 hits per query.Conclusions/significanceFastBLAST enables research groups that do not have supercomputers to analyze large protein sequence data sets. FastBLAST is open source software and is available at http://microbesonline.org/fastblast

Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc Aplysia

<p>Abstract</p> <p>Background</p> <p>Marine molluscs, as is the case with most aquatic animals, rely heavily on olfactory cues for survival. In the mollusc <it>Aplysia californica</it>, mate-attraction is mediated by a blend of water-borne protein pheromones that are detected by sensory structures called rhinophores. The expression of G protein and phospholipase C signaling molecules in this organ is consistent with chemosensory detection being via a G-protein-coupled signaling mechanism.</p> <p>Results</p> <p>Here we show that novel multi-transmembrane proteins with similarity to rhodopsin G-protein coupled receptors are expressed in sensory epithelia microdissected from the <it>Aplysia </it>rhinophore. Analysis of the <it>A. californica </it>genome reveals that these are part of larger multigene families that possess features found in metazoan chemosensory receptor families (that is, these families chiefly consist of single exon genes that are clustered in the genome). Phylogenetic analyses show that the novel <it>Aplysia </it>G-protein coupled receptor-like proteins represent three distinct monophyletic subfamilies. Representatives of each subfamily are restricted to or differentially expressed in the rhinophore and oral tentacles, suggesting that they encode functional chemoreceptors and that these olfactory organs sense different chemicals. Those expressed in rhinophores may sense water-borne pheromones. Secondary signaling component proteins Gα_q, Gα_i, and Gα_oare also expressed in the rhinophore sensory epithelium.</p> <p>Conclusion</p> <p>The novel rhodopsin G-protein coupled receptor-like gene subfamilies identified here do not have closely related identifiable orthologs in other metazoans, suggesting that they arose by a lineage-specific expansion as has been observed in chemosensory receptor families in other bilaterians. These candidate chemosensory receptors are expressed and often restricted to rhinophores and oral tentacles, lending support to the notion that water-borne chemical detection in <it>Aplysia </it>involves species- or lineage-specific families of chemosensory receptors.</p

Prime movers : mechanochemistry of mitotic kinesins

Mitotic spindles are self-organizing protein machines that harness teams of multiple force generators to drive chromosome segregation. Kinesins are key members of these force-generating teams. Different kinesins walk directionally along dynamic microtubules, anchor, crosslink, align and sort microtubules into polarized bundles, and influence microtubule dynamics by interacting with microtubule tips. The mechanochemical mechanisms of these kinesins are specialized to enable each type to make a specific contribution to spindle self-organization and chromosome segregation