Current methods for automated annotation of protein-coding genes.

We review software tools for gene prediction - the identification of protein-coding genes and their structure in genome sequences. The discussed approaches include methods based on RNA-Seq and current methods based on homology - comparative gene prediction and protein spliced alignments. Many methods require that their parameters are adjusted to the target species or its broader clade. These include ab initio gene finders, integrated approaches with ab initio components and some aligners. We also review current automatic methods for training for the common case that a bona fide training set of gene structures is not available before annotation.

Flavonoid production in transgenic hop (Humulus lupulus L.) altered by PAP1/MYB75 from Arabidopsis thaliana L.

Hop is an important source of secondary metabolites, such as flavonoids. Some of these are pharmacologically active. Nevertheless, the concentration of some classes as flavonoids in wild-type plants is rather low. To enhance the production in hop, it would be interesting to modify the regulation of genes in the flavonoid biosynthetic pathway. For this purpose, the regulatory factor PAP1/AtMYB75 from Arabidopsis thaliana L. was introduced into hop plants cv. Tettnanger by Agrobacterium-mediated genetic transformation. Twenty kanamycin-resistant transgenic plants were obtained. It was shown that PAP1/AtMYB75 was stably incorporated and expressed in the hop genome. In comparison to the wild-type plants, the color of female flowers and cones of transgenic plants was reddish to pink. Chemical analysis revealed higher levels of anthocyanins, rutin, isoquercitin, kaempferol-glucoside, kaempferol-glucoside-malonate, desmethylxanthohumol, xanthohumol, α-acids and ß-acids in transgenic plants compared to wild-type plants.

Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias.

Using bioinformatics methods, we identified a total of 221 and 199 tRNA genes in the nuclear genomes of Nasonia vitripennis and honey bee (Apis mellifera), respectively. We performed comparative analyses of Nasonia tRNA genes with honey bee and other selected insects to understand genomic distribution, sequence evolution and relationship of tRNA copy number with codon usage patterns. Many tRNA genes are located physically close to each other in the form of small clusters in the Nasonia genome. However, the number of clusters and the tRNA genes that form such clusters vary from species to species. In particular, the Ala-, Pro-, Tyr- and His-tRNA genes tend to accumulate in clusters in Nasonia but not in honey bee, whereas the bee contains a long cluster of 15 tRNA genes (of which 13 are Gln-tRNAs) that is absent in Nasonia. Though tRNA genes are highly conserved, contrasting patterns of nucleotide diversity are observed among the arm and loop regions of tRNAs between Nasonia and honey bee. Also, the sequence convergence between the reconstructed ancestral tRNAs and the present day tRNAs suggests a common ancestral origin of Nasonia and honey bee tRNAs. Furthermore, we also present evidence that the copy number of isoacceptor tRNAs (those having a different anticodon but charge the same amino acid) is correlated with codon usage patterns of highly expressed genes in Nasonia.

Incremental build-up food challenge--a new diagnostic approach to evaluate pseudoallergic reactions in chronic urticaria: a pilot study: stepwise food challenge in chronic urticaria.

BACKGROUND: The remission rate of patients with chronic urticaria (CU) due to elimination diets varies between 31% and 71%. However, the diagnostic value of subsequent traditional oral provocation tests with food additives in capsules remains unsatisfactory. OBJECTIVES: A newly incremental build-up food challenge (IBUF) for patients with CU was designed and implemented in an open pilot study. Primary endpoint was the percentage of patients developing urticaria during at least one step of IBUF after an initial complete remission due to a pseudoallergen-free elimination diet. METHODS: In total, 153 patients with CU were submitted for 5 weeks to a pseudoallergen-free diet. All patients with remission were included to the 6-week IBUF protocol, containing pseudoallergen-rich foods in a systematic and additive manner. The recurrence and severity of CU was evaluated by urticaria score. Subjective disturbance and quality of life were evaluated by patients' diary, visual analogue scale and quality of life questionnaire (CU-Q2oL). Subsequently, patients were followed up for 3-24 months after IBUF by a telephone interview. RESULTS: A total of 104 patients completed the pseudoallergen-free diet, whereby 51% reported partial, 17% complete and 32% no remission due to the diet. All diet responders showed a decrease in subjective impairment, urticaria and quality of life score (P<0.001 each). Eighty-six percent (12/14) of the patients reaching complete remission, showed a recurrence of urticaria symptoms during the IBUF protocol. Fifty-eight percent (7/12) of these patients still remained free of symptoms due to avoidance of IBUF-identified foods at telephone follow-up. In patients with partial remission to pseudoallergen-free diet, however, IBUF did not provide information about the cause of urticaria symptoms. CONCLUSIONS: The newly developed IBUF protocol seemed to be a promising method for identifying individually incompatible foods in some CU patients. IBUF should be verified by randomized controlled trials to gain additional evidence for its diagnostic value.

[Metastases from a malignant melanoma as extensive, space-occupying lesion in the trachea]. / Metastasen eines malignen Melanoms als ausgedehnte Raumforderung in der Trachea.

We report the case of a 71-year-old man, who was transferred to our clinic with rapidly increasing dyspnea. On examination by flexible bronchoscopy the trachea was found to be almost completely obstructed by metastatic masses of a malignant melanoma. After endoscopic removal of the obstruction, we inserted a covered nitinol stent which led to instantaneous relief of symptoms. Chemotherapy and local radiotherapy were instituted. During the next 9 months there were no signs of recurrence of the tumour in regular pneumological control exams.

The UCSC Genome Browser Database: 2008 update.

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

The genome of the thermoacidophilic red microalga Galdieria sulphuraria encodes a small family of secreted class III peroxidases that might be involved in cell wall modification.

We report the identification of a small family of secreted class III plant peroxidases (Prx) from the genome of the unicellular thermoacidophilic red alga Galdieria sulphuraria (Cyanidiaceae). Apart from two class I ascorbate peroxidases and one cytochrome c peroxidase, the red algal genome encodes four class III plant peroxidases, thus complementing the short list of algal cell wall peroxidases (Passardi et al. in Genomics 89:567-579, 2007). We have characterized the family gene structure, analyzed the extracellular space and cell wall fraction of G. sulphuraria for the presence of peroxidase activity and used shotgun proteomics to identify candidate extracellular peroxidases. For a detailed enzymatic characterization, we have purified a secreted peroxidase (GsPrx04) from the cell-free medium using hydrophobic interaction chromatography. The enzyme proved heat and acid-stable and exhibited an apparent molecular mass of 40 kDa. Comparative genomics between endolithically growing G. sulphuraria and a close relative, the obligatory aquatic, cell wall-less Cyanidioschyzon merolae, revealed that class III peroxidases only occur in the terrestrial microalga, thus supporting the key function of these enzymes in the process of land colonization.

The UCSC genome browser database: update 2007.

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

[Thrombosis in geriatric patients]. / Thrombosen bei geriatrischen Patienten.

BACKGROUND AND OBJECTIVE: There are only a few data on the circumstances and incidence of deep vein thrombosis (DVT) in the elderly, although they are generally considered at risk of it. Classical signs of DVT are atypical or not present. Isolated leg swelling also frequently occurs postoperatively or in the course of a cerebrovascular accident. In this prospective study patient characteristics and associated circumstances pointing to the risk of DVT or an existing DVT were systematically investigated. This was to facilitate rational referral for further tests. PATIENTS AND METHODS: From March 1999 for a total of 13 weeks all new admissions to the specialist geriatric clinic Bad Salzdetfurth, 101 women and 46 men (48-94 years, average 76.6 years) underwent thrombosis screening with duplex sonography of both legs within the first 24 hours after admission. In addition the results of laboratory tests, ECG and medical-geriatric examinations were evaluated and age, sex, duration of stay at an acute hospital, main and subsidiary diagnosis, Barthel index and current medication were recorded. RESULTS: 35 not previously diagnosed DVT were found in 30 of the 101 patients. Independent variables that were significantly more frequent associated with DVT were previous long hospital stay, female sex and higher heart rate in the admission ECG. Neither main and additional diagnosis, age, previous medication, Barthel index, haemoglobin concentration, previous thrombosis nor previous stress on a not yet stable fracture and previous clinical suspicion of DVT were statistically significant risk factors for DVT. CONCLUSIONS: Purely clinical investigation is not suitable for confirming or excluding DVT in elderly patients. It was possible to define a constellation of risks for DVT by combining data from previous examinations with those of routine medical diagnosis.

BMP growth factors and Phox2 transcription factors can induce synaptotagmin I and neurexin I during sympathetic neuron development.

Synaptotagmin I and neurexin I mRNAs, coding for proteins involved in neurotransmitter secretion, become detectable in primary sympathetic ganglia shortly after initial induction of the noradrenergic transmitter phenotype. To test whether the induction of these more general neuronal genes is mediated by signals known to initiate noradrenergic differentiation in a neuronal subpopulation, we examined their expression in noradrenergic neurons induced by ectopic overexpression of growth and transcription factors. Overexpression of BMP4 or Phox2a in vivo results in synaptotagmin I and neurexin I expression in ectopically located noradrenergic cells. In vitro, BMP4 initiates synaptotagmin I and neurexin I expression in addition to tyrosine hydroxylase induction. Thus, the induction of synaptotagmin I and neurexin I, which are expressed in a large number of different neuron populations, can be accomplished by growth and transcription factors available only to a subset of neurons. These findings suggest that the initial expression of proteins involved in neurotransmitter secretion is regulated by different signals in different neuron populations.

The transcription factor dHAND is a downstream effector of BMPs in sympathetic neuron specification.

The dHAND basic helix-loop-helix transcription factor is expressed in neurons of sympathetic ganglia and has previously been shown to induce the differentiation of catecholaminergic neurons in avian neural crest cultures. We now demonstrate that dHAND expression is sufficient to elicit the generation of ectopic sympathetic neurons in vivo. The expression of the dHAND gene is controlled by bone morphogenetic proteins (BMPs), as suggested by BMP4 overexpression in vivo and in vitro, and by noggin-mediated inhibition of BMP function in vivo. The timing of dHAND expression in sympathetic ganglion primordia, together with the induction of dHAND expression in response to Phox2b implicate a role for dHAND as transcriptional regulator downstream of Phox2b in BMP-induced sympathetic neuron differentiation.

The early expression of VAChT and VIP in mouse sympathetic ganglia is not induced by cytokines acting through LIFRbeta or CNTFRalpha.

Sympathetic ganglia consist of noradrenergic and cholinergic neurons. The cholinergic marker protein vesicular acetylcholine transporter (VAChT) and the neuropeptide vasoactive intestinal peptide (VIP), co-expressed in mature cholinergic sympathetic neurons, are first detectable during embryonic development of rat sympathetic ganglia. However, the subpopulation of cholinergic sympathetic neurons which innervates sweat glands in mammalian footpads starts to express VAChT and VIP during the first postnatal weeks, under the influence of sweat gland-derived signals. In vitro evidence suggests that the sweat gland-derived cholinergic differentiation factor belongs to a group of neuropoietic cytokines, including LIF, CNTF and CT-1, that act through a LIFRbeta-containing cytokine receptor. To investigate whether the embryonic expression of cholinergic properties is elicited by a related cytokine, the expression of VAChT and VIP was analyzed in stellate ganglia of mice deficient for the cytokine receptor subunits LIFRbeta or CNTFRalpha. The density of VAChT- and VIP-immunoreactive cells in stellate ganglia of new-born animals was not different in LIFRbeta(-/-) and CNTFRalpha(-/-) ganglia as compared to ganglia from wild-type mice. These results demonstrate that the early, embryonic expression of VAChT and VIP is not induced by cytokines acting through LIFRbeta- or CNTFRalpha-containing receptors.

The Phox2 homeodomain proteins are sufficient to promote the development of sympathetic neurons.

The development of sympathetic neurons is controlled by a network of transcriptional regulators, including the paired homeodomain proteins Phox2a and Phox2b. To understand the role of Phox2 proteins in more detail, the effect of Phox2 overexpression was analysed in the avian peripheral nervous system. Phox2a expression in neural crest cultures elicited a strong increase in the number of sympathoadrenergic cells. Expression of Phox2a in the chick embryo promoted the generation of additional neurons expressing the noradrenergic marker genes DBH and TH, pan-neuronal genes SCG10 and NF160 and cholinergic genes ChAT and VAChT. Phox2a-induced neurons were found in ectopic locations such as dorsal root ganglia and peripheral nerve. Sympathoadrenergic development could be elicited in cultures of E5 dorsal root ganglia, demonstrating the presence of Phox2a-responsive cells in non-autonomic peripheral ganglia. Phox2b induced ectopic neurons in the chick embryo in the same way as Phox2a. These results show that Phox2 proteins are sufficient to promote sympathetic neuron generation and control, directly or indirectly, the expression of a large number of genes characteristic for sympathetic neurons.