Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation

GermOnline is a web-accessible relational database that enables life scientists to make a significant and sustained contribution to the annotation of genes relevant for the fields of mitosis, meiosis, germ line development and gametogenesis across species. This novel approach to genome annotation includes a platform for knowledge submission and curation as well as microarray data storage and visualization hosted by a global network of servers. AVAILABILITY: The database is accessible at http://www.germonline.org/. For convenient world-wide access we have set up a network of servers in Europe (http://germonline.unibas.ch/; http://germonline.igh.cnrs.fr/), Japan (http://germonline.biochem.s.u-tokyo.ac.jp/) and USA (http://germonline.yeastgenome.org/). SUPPLEMENTARY INFORMATION: Extended documentation of the database is available through the link 'About GermOnline' at the websites.     

Larvae and a new species of Ancyronyx Erichson, 1847 (Insecta, Coleoptera, Elmidae) from Palawan, Philippines, using DNA sequences for the assignment of the developmental stages

Ancyronyx montanussp. n. is described based on adults and larvae, matched using their cox1 DNA sequence data. Larvae of six additional species of Ancyronyx Erichson, 1847 were also described here for the first time, aided by cox1 or cob data: Ancyronyx helgeschneideri Freitag & J?ch, 2007, Ancyronyx minerva Freitag & J?ch, 2007, Ancyronyx patrolus Freitag & J?ch, 2007, Ancyronyx procerus J?ch, 1994, Ancyronyx punkti Freitag & J?ch, 2007, Ancyronyx pseudopatrolus Freitag & J?ch, 2007. Ancyronyx procerus is newly recorded from the Philippines by a larval specimen from Busuanga island. The new species and larval stages are described in detail and illustrated by digital and SEM images. A key to the Ancyronyx larvae of Palawan and an updated checklist of Philippine Ancyronyx is provided.     

mmsearch: a motif arrangement language and search program.

This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins. AVAILABILITY: The program can be tested online at http://hits.isb-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz CONTACT: Thomas.Junier@isrec.unil.ch SUPPLEMENTARY INFORMATION: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc.     

Ch14.18 antibody produced in CHO cells in relapsed or refractory Stage 4 neuroblastoma patients

Purpose: This study aimed to assess the safety, pharmacokinetic and activity profiles of the human-mouse chimeric monoclonal anti-disialoganglioside GD2 antibody ch14.18 produced in Chinese hamster ovary (CHO) cells (ch14.18/CHO).

Methods: Sixteen children with recurrent/refractory neuroblastoma (median age 7.6 y) were enrolled in this Phase 1 dose-finding study. Patients received ch14.18/CHO courses of 10, 20 or 30 mg/m²/day as an eight-hour infusion over five consecutive days. Three courses at the same dose level were allowed unless disease progressed. Clearance and biodistribution of radiolabelled ch14.18/CHO in Balb/c and A/J mice were analyzed.

Results: A total of 41 ch14.18/CHO courses were given (10 × 3 courses, 5 × 2 courses, 1 × 1 course). Side effects were similar in expectedness, frequency and magnitude to those reported for ch14.18/SP2/0. The dose level of 20 mg/m²/day was confirmed. Toxicity was reversible and no treatment-related deaths occurred. In children, the peak plasma concentration was 16.51 µg/ml ± 5.9 µg/ml and the half-life was 76.91 h ± 52.5 h. A partial response following ch14.18/CHO was observed in 2/7 patients with residual disease. In mice, the half-lives were 22.7 h ± 1.9h for ch14.18/CHO and 25.0 h ± 1.9 h for ch14.18/SP2/0. The biodistribution of ¹²⁵I-ch14.18/CHO in mice with neuroblastoma was identical to ¹²⁵I-ch14.18/SP2/0, indicating GD₂ targeting activity in vivo.

Ch14.18 produced in CHO cells showed an unchanged toxicity profile and pharmacokinetics in neuroblastoma patients compared with ch14.18 produced in SP2/0 cells, and evidence of clinical activity was observed. In mice, analysis of pharmacokinetics and biodistribution showed comparable results between ch14.18/CHO and ch14.18/SP2/0. Based on these results, ch14.18/CHO was accepted for prospective clinical evaluation.     

GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

We live in an age of access to more information than ever before. This can be a double-edged sword. Increased access to information allows for more informed and empowered researchers, while information overload becomes an increasingly serious risk. Thus, there is a need for intelligent information retrieval systems that can summarize relevant and reliable textual sources to satisfy a user's query. Question answering is a specialized type of information retrieval with the aim of returning precise short answers to queries posed as natural language questions. We present a review and comparison of three biomedical question answering systems: askHERMES (http://www.askhermes.org/), EAGLi (http://eagl.unige.ch/EAGLi/), and HONQA (http://services.hon.ch/cgi-bin/QA10/qa.pl).     

Phase I trial of combined treatment with ch14.18 and R24 monoclonal antibodies and interleukin-2 for patients with melanoma or sarcoma

Purpose: We conducted a phase I trial of interleukin 2 (IL-2) in combination with chimeric 14.18 (ch14.18) and murine R24 antibodies to determine the maximal tolerated dose (MTD), immunological effects, and toxicity of this treatment combination. Experimental Design: Twenty-seven patients with either melanoma (23 patients) or sarcoma (4 patients) were enrolled to receive a combination therapy with ch14.18 and R24 antibodies together with continuous infusion of Roche IL-2 (1.5×10⁶ U/m²/day, 26 patients) or Chiron IL-2 (4.5×10⁶ U/m²/day, 1 patient) given 4 days/week for 3 weeks. The antibodies ch14.18 (2–7.5 mg/m²/day) and R24 (1–10 mg/m²/day) were scheduled to be administered for 5 days during the second week of IL-2 therapy. Results: When given in combination in this study, the MTD for ch14.18 was 5 mg/m²/day and the MTD for R24 was 5 mg/m²/day. Dose-limiting toxicities were severe allergic reactions to both ch14.18 and R24 as well as pain related to ch14.18. This ch14.18 MTD was lower than the 7.5 mg/m²/day MTD previously determined for ch14.18 given alone with the same dose and schedule of IL-2. Immunological effects included the induction of lymphokine-activated killer (LAK) activity and antibody-dependent cell-mediated cytoxicity (ADCC). Anti-idiotype response to ch14.18 was seen in six patients, including two melanoma patients who had a partial response to treatment. In addition to two partial responses, four patients had a stable disease and one patient remained without any evidence of disease. Conclusions: Immunotherapy with IL-2 in combination with ch14.18 and R24 antibodies augments LAK function and ADCC measured in vitro in all patients. While there exist theoretical advantages of combining these two antibodies, the MTD of ch14.18 and of R24 were lower than the MTD of each antibody in prior studies evaluating single antibody therapy with IL-2. As such, the combination of these two antibodies together with IL-2 therapy appeared to influence the MTD and toxicity of each of the administered antibodies. This work is supported by NIH grants M01-RR03186, R01-CA32685, and P30-CA14520     

Dotlet: diagonal plots in a web browser

SUMMARY: Dotlet is a program for comparing sequences by the diagonal plot method. It is designed to be platform-independent and to run in a Web browser, thus enabling the majority of researchers to use it. AVAILABILITY: The applet can be tested at http://www.isrec.isb-sib.ch/java/dotlet/ Dotlet.html, and the source code is available upon request. CONTACT: Thomas.Junier Marco.Pagni @isrec.unil.ch SUPPLEMENTARY: The full documentation about d o t l e t is available from the above URL.     

Compilation of tRNA sequences and sequences of tRNA genes.

Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth. de/departments/biochemie/trna/     

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits. isb-sib.ch).     

Arabidopsis consensus intron sequences

We have analysed 998 Arabidopsis intron sequences in the EMBL database. All Arabidopsis introns to adhere to the :GU...AG: rule with the exception of 1% of introns with :GC at their 5 ends. Virtually all of the introns contained a putative branchpoint sequence (YUNAN) 18 to 60 nt upstream of the 3 splice site. Although a polypyrimidine tract was much less apparent than in vertebrate introns, the most common nucleotide in the region upstream of the 3 splice site was uridine. Consensus sequences for 5 and 3 splice sites and branchpoint sequences for Arabidopsis introns are presented.     

The demography of slow aging in male and female Drosophila mutant for the insulin-receptor substrate homologue chico

Hypomorphic mutants affecting the Drosophila insulin/IGF signal pathway are reported to increase longevity in females but not in males. To understand this sex-difference, we conducted a large-scale demographic study with three new isogenic strains of alleles at chico, the insulin-receptor substrate homologue. We verify that female dwarf homozygotes (ch1/ch1) and normal-sized heterozygotes (ch1/+) are long-lived, as originally reported. We find for the first time that male heterozygotes are long-lived relative to wildtype, by about 50%. The life span of male ch1/ch1 is similar to that of wildtype but these dwarf males age at a slow demographic rate. The levels of demographic frailty and of age-independent mortality are elevated in ch1/ch1 males, counteracting the effect of slow aging upon life expectancy. Mortality deceleration occurs amongst the oldest-old wildtype adults, as seen in many organisms. Remarkably, in similarly sized cohorts of male and female ch1/ch1 and of male ch1/+ mortality deceleration is absent. Mortality deceleration is a phenotype of chico.     

Global diversity of water beetles (Coleoptera) in freshwater

The global diversity of True Water Beetles, False Water Beetles and Phytophilous Water Beetles (sensu Jäch, 1998a. In Jäch &; Ji (eds), Water Beetles of China, Vol. II. Zoologisch-Botanische Gesellschaft in Österreich and Wiener Coleopterologenverein, Wien: 25–42.) is assessed. Facultative Water Beetles, Parasitic Water Beetles and Shore Beetles (sensu Jäch, 1998a. In Jäch &; Ji (eds), Water Beetles of China, Vol. II. Zoologisch-Botanische Gesellschaft in Österreich and Wiener Coleopterologenverein, Wien: 25–42.) are here classified as “paraquatic” and are thus not included in the assessment. It is estimated that about 18,000 species of aquatic Coleoptera are roaming the earth at present. About 12,600 (70%) of these are already described (deadline: October 2005). About 30 beetle families have aquatic representatives, and in 25 of these families at least 50% of the species are to be considered as aquatic. Six families are supposed to include 1,000 or more aquatic species: Dytiscidae (3,908 described species/5,000 estimated), Hydraenidae (1,380/2,500), Hydrophilidae (1,800/2,320), Elmidae (1,330/1,850), Scirtidae (900/1,700) and Gyrinidae (750/1,000). Scirtidae and Hydraenidae are regarded as the least explored families, the number of described species in each of these two families probably will be almost doubled in the future. The Palearctic (ca. 3,350 described species/ca. 3,900 estimated), the Neotropical (2,510/3,900) and the Afrotropical Region (2,700/3,750) harbour almost the same number of water beetle species, followed by the Oriental (2,200/3,580) and the Australian/Pacific Realm (1,340/2,100). The Nearctic (1,420/1,550) is by far the poorest region in terms of water beetle diversity.     

Quality estimation of multiple sequence alignments by Bayesian hypothesis testing

In this work we present a web-based tool for estimating multiple alignment quality using Bayesian hypothesis testing. The proposed method is very simple, easily implemented and not time consuming with a linear complexity. We evaluated method against a series of different alignments (a set of random and biologically derived alignments) and compared the results with tools based on classical statistical methods (such as sFFT and csFFT). Taking correlation coefficient as an objective criterion of the true quality, we found that Bayesian hypothesis testing performed better on average than the classical methods we tested. This approach may be used independently or as a component of any tool in computational biology which is based on the statistical estimation of alignment quality. AVAILABILITY: http://www.fmi.ch/groups/functional.genomics/tool.htm. SUPPLEMENTARY INFORMATION: Supplementary data are available from http://www.fmi.ch/groups/functional.genomics/tool-Supp.htm.     

Genetic mapping of endogenous RD-114 retroviral sequences of domestic cats.

The RD-114 family of endogenous retroviral sequences in domestic cats has been shown to consist of approximately 20 copies of genetically divergent virogenes per haploid genome. The chromosomal localization for four endogenous sequences (RDV1-4) was accomplished by correlating the occurrence of specific feline chromosomes with diagnostic viral DNA fragments in a panel of cat X rodent somatic cell hybrids. Analysis of the hybrid panel revealed that endogenous RD-114 sequences are dispersed on multiple cat chromosomes, that certain proviral segments are polymorphic with respect to the presence or absence of virus, and that a restriction fragment characteristic of inducible RD-114 resides on a single feline chromosome (B3), probably at a single locus.     

Y chromosome--specific DNA sequences in Turner-syndrome mosaicism.

Phenotypic females with Y-chromosomal material in their genome have an increased risk for development of gonadal malignancy. The detection and identification of Y-chromosomal material in these cases can be of critical importance for medical management. Chromosome analysis in four patients with Turner syndrome revealed the characteristic 45,X chromosome complement together with a second cell population containing a small marker chromosome (46,X, + mar). Molecular-hybridization analyses utilizing cloned, Y chromosome-specific DNA sequences were performed to determine whether Y-chromosomal material was present in each patient. Three cases contained some Y chromosome-specific sequences, whereas one case was negative with all four probes that we used. These results were compared with detailed cytogenetic studies--including G-, Q-, and G-11-banding--of the marker chromosomes. In one case in which Y chromosome-specific DNA sequences were demonstrated, the marker chromosome was G-11 negative. These results demonstrate that cytogenetic analysis alone can lead to misidentification of some Y chromosome-derived markers. The combination of cytogenetic and molecular analyses permits a more accurate characterization of anomalous Y chromosomes and in turn provides additional information that can be crucial to the correct medical management of Turner-syndrome patients.     

Probabilistic alignment of motifs with sequences

MOTIVATION: Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.e. functional, biophysical, etc.) characteristics of a signal or pattern to be detected. The results produced are based on the statistical relevance of the alignment. The method was targeted to avoid the problems (i.e. over-fitting, biological interpretation and mathematical soundness) encountered in other methods currently available. RESULTS: The method was tested on lipoprotein signals in B. subtilis yielding stable results. The results of signal prediction were consistent with other methods where literature was available. AVAILABILITY: An implementation of the motif alignment, refining and bootstrapping is available for public use online at http://www.expasy.org/tools/patoseq/     

Study of neuronal gain in a conductance-based leaky integrate-and-fire neuron model with balanced excitatory and inhibitory synaptic input

Neurons receive a continual stream of excitatory and inhibitory synaptic inputs. A conductance-based neuron model is used to investigate how the balanced component of this input modulates the amplitude of neuronal responses. The output spiking rate is well described by a formula involving three parameters: the mean and variance of the membrane potential and the effective membrane time constant _Q. This expression shows that, for sufficiently small _Q, the level of balanced excitatory-inhibitory input has a nonlinear modulatory effect on the neuronal gain.