DNA sequence and analysis of human chromosome 8.

The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.

Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.

BACKGROUND: Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis. RESULTS: The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype. CONCLUSIONS: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.

Genome sequence of the polysaccharide-degrading, thermophilic anaerobe Spirochaeta thermophila DSM 6192.

Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade various α- and ß-linked sugar polymers, including cellulose. We report here the complete genome sequence of S. thermophila DSM 6192, which is the first genome sequence of a thermophilic, free-living member of the Spirochaetes phylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.

Epigenetic mechanisms mediate the experimental evolution of resistance against parasitic fungi in the greater wax moth Galleria mellonella.

Recent concepts in evolutionary biology suggest that epigenetic mechanisms can translate environmental selection pressures into heritable changes in phenotype. To determine whether experimental selection for a complex trait in insects involves epigenetic modifications, we carried out a generation-spanning experiment using larvae of the greater wax moth Galleria mellonella as a model host to investigate the role of epigenetics in the heritability of resistance against the parasitic fungus Metarhizium robertsii. We investigated differences in DNA methylation, histone acetylation and microRNA (miRNA) expression between an experimentally resistant population and an unselected, susceptible line, revealing that the survival of G. mellonella larvae infected with M. robertsii correlates with tissue-specific changes in DNA methylation and histone modification and the modulation of genes encoding the corresponding enzymes. We also identified miRNAs differentially expressed between resistant and susceptible larvae and showed that these regulatory molecules target genes encoding proteinases and proteinase inhibitors, as well as genes related to cuticle composition, innate immunity and metabolism. These results support our hypothesis that epigenetic mechanisms facilitate, at least in part, the heritable manifestation of parasite resistance in insects. The reciprocal adaptations underlying host-parasite coevolution therefore extend beyond the genetic level to encompass epigenetic modifications.

Urate Oxidase produced by Lucilia sericata medical maggots is localized in Malpighian tubes and facilitates allantoin production.

Lucilia sericata maggots are the only species currently approved for maggot debridement therapy (MDT), an alternative treatment for chronic and recalcitrant wounds. Maggots promote wound debridement, disinfection and healing by producing a complex mixture of proteins, peptides and low-molecular-weight compounds in their secretions and excretions, but the individual components are not well characterized at the molecular level. Here we investigated the purine catabolism pathway in L. sericata, focusing on the production of allantoin by Urate Oxidase (UO), which is thought to promote wound healing. We produced recombinant L. sericata UO in Escherichia coli, and characterized the properties of the pure enzyme in terms of the optimum pH (7-10) and temperature (20-25 °C), its stability, sensitivity to inhibition and ion dependency. We used quantitative RT-PCR and RNA in situ hybridization to monitor the expression of the UO gene, and we used a guinea pig anti-UO antibody to detect the native enzyme by western blot and by florescence immunohistochemistry in larval tissues. We found that L. sericata UO is exclusively present in the larval excretion organ (the Malpighian tubes) and is freely available in the cytoplasm rather than restricted to a specific subcellular compartment. Allantoin is a final product of L. sericata purine catabolism. It is produced by UO in the Malpighian tubes to remove uric acid from the hemolymph and is consequently excreted via the hindgut. Our findings confirm the hypothesis that both actively secreted molecules and excretion products contribute to the beneficial effects of MDT.

Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots.

Lucilia sericata larvae are used as an alternative treatment for recalcitrant and chronic wounds. Their excretions/secretions contain molecules that facilitate tissue debridement, disinfect, or accelerate wound healing and have therefore been recognized as a potential source of novel therapeutic compounds. Among the substances present in excretions/secretions various peptidase activities promoting the wound healing processes have been detected but the peptidases responsible for these activities remain mostly unidentified. To explore these enzymes we applied next generation sequencing to analyze the transcriptomes of different maggot tissues (salivary glands, gut, and crop) associated with the production of excretions/secretions and/or with digestion as well as the rest of the larval body. As a result we obtained more than 123.8 million paired-end reads, which were assembled de novo using Trinity and Oases assemblers, yielding 41,421 contigs with an N50 contig length of 2.22 kb and a total length of 67.79 Mb. BLASTp analysis against the MEROPS database identified 1729 contigs in 577 clusters encoding five peptidase classes (serine, cysteine, aspartic, threonine, and metallopeptidases), which were assigned to 26 clans, 48 families, and 185 peptidase species. The individual enzymes were differentially expressed among maggot tissues and included peptidase activities related to the therapeutic effects of maggot excretions/secretions.

Selection and Evaluation of Tissue Specific Reference Genes in Lucilia sericata during an Immune Challenge.

The larvae of the common green bottle fly Lucilia sericata (Diptera: Calliphoridae) have been used for centuries to promote wound healing, but the molecular basis of their antimicrobial, debridement and healing functions remains largely unknown. The analysis of differential gene expression in specific larval tissues before and after immune challenge could be used to identify key molecular factors, but the most sensitive and reproducible method qRT-PCR requires validated reference genes. We therefore selected 10 candidate reference genes encoding products from different functional classes (18S rRNA, 28S rRNA, actin, ß-tubulin, RPS3, RPLP0, EF1α, PKA, GAPDH and GST1). Two widely applied algorithms (GeNorm and Normfinder) were used to analyze reference gene candidates in different larval tissues associated with secretion, digestion, and antimicrobial activity (midgut, hindgut, salivary glands, crop and fat body). The Gram-negative bacterium Pseudomonas aeruginosa was then used to boost the larval immune system and the stability of reference gene expression was tested in comparison to three immune genes (lucimycin, defensin-1 and attacin-2), which target different pathogen classes. We observed no differential expression of the antifungal peptide lucimycin, whereas the representative targeting Gram-positive bacteria (defensin-1) was upregulated in salivary glands, crop, nerve ganglion and reached its maximum in fat body (up to 300-fold). The strongest upregulation in all immune challenged tissues (over 50,000-fold induction in the fat body) was monitored for attacin-2, the representative targeting Gram-negative bacteria. Here we identified and validated a set of reference genes that allows the accurate normalization of gene expression in specific tissues of L. sericata after immune challenge.

MR imaging features in Marinesco-Sjögren syndrome: severe cerebellar atrophy is not an obligatory finding.

BACKGROUND AND PURPOSE: Cerebellar atrophy is considered the most prominent neuroradiologic finding in Marinesco-Sjögren syndrome (MSS). Our purpose was to investigate this neuroradiologic feature in a series of patients with MSS. METHODS: Five patients with MSS (age range, 5-19 years) underwent native MR imaging of the brain. The findings were assessed with particular attention to the cerebellum and the supratentorial structures. RESULTS: Only two patients had slight cerebellar atrophy; the cerebellum was normal in size and configuration in the other patients. Additional supratentorial findings were present in some of the patients, with an apparently small anterior pituitary gland in two and the absence of the posterior pituitary bright spot in three of the patients. CONCLUSION: Cerebellar atrophy is not an obligatory finding in MSS, and almost normal cranial MR imaging results are compatible with the diagnosis. Morphologic changes of the pituitary gland seem to be common in patients with MSS and are not associated with endocrine dysfunction.

Doppler sonographic evaluation of shunts in patients with dural arteriovenous fistulas.

BACKGROUND AND PURPOSE: Doppler sonography has been used to assess global cerebral circulation time (CCT) in healthy volunteers and a small number of patients with cerebral arteriovenous malformations. We evaluated the effect of arteriovenous shunts on global CCT in patients with dural arteriovenous fistulas (DAVFs) by using this Doppler echo contrast-bolus tracking test. METHODS: We measured CCT as the time delay in a contrast bolus to the internal carotid artery (ICA) and internal jugular vein (IJV) in 13 patients with DAVF and 30 age-matched control subjects. Mean CCT and mean arterial and venous rise times (Delta t = 80% of total signal-intensity increase) were compared. Posttreatment follow-up measurements were performed in five patients. RESULTS: Mean CCT and venous Delta t were significantly different between patients and controls (CCT, 1.1 +/- 0.9 vs 6.9 +/- 1.2 seconds, P <.0001; venous Delta t, 5.2 +/- 2.0 vs 7.0 +/- 2.6 seconds, P =.024), but arterial Delta t values were not (4.4 +/- 1.8 vs 4.7 +/- 2.0 seconds). Posttreatment follow-up of two occluded fistulas showed CCT normalization. One near-occlusion showed a two-step increase in signal intensity, and incomplete occlusion in two patients left the CCT unchanged. One patient with an extracranial, highly vascularized glomus tumor draining into the IJV had a CCT of 1.8 seconds. CONCLUSION: In DAVF patients, sonographic CCT is significantly shortened. Our test is highly sensitive for arteriovenous shunts but not specific for DAVF alone. Follow-up measurements in DAVF patients are well correlated with results of angiographic treatment. CCT assessment might become an additional tool for evaluating these patients and monitoring their treatment.

Three-dimensional imaging of the inner ear by volume-rendered reconstructions of magnetic resonance data.

OBJECTIVE: To evaluate 3-dimensional inner ear visualization by volume rendering of high-resolution magnetic resonance data in patients with clinically suspected inner ear abnormality. DESIGN: Prospective comparative study of different postprocessing techniques, based on blinded film readings. SETTING: Tertiary referral hospital. SUBJECTS: Fifty patients (17 females and 33 males) aged 1 to 77 years (average age, 42 years) with sensorineural hearing loss, vertigo, and/or tinnitus. INTERVENTION: Postprocessing of magnetic resonance data to inner ear reconstructions by the use of volume rendering as well as maximum-intensity projection; caloric testing by electronystagmography. MAIN OUTCOME MEASURES: Film was read blindly by 4 radiologists using a 5-point parameter scale for image quality and diagnostic value. The assessibility of inner ear subsegments was evaluated. The specificity of volume-rendered reconstructions for detecting semicircular canal obliterations was assessed in a subgroup of 9 patients by caloric testing. The time required for data postprocessing as well as film reading was recorded by means of a stopwatch. RESULTS: Volume-rendered inner ear reconstructions were superior in image quality (P<.001), diagnostic value (P<.001), subsegment inner ear assessment (P<.01 to P<.001), and film reading time (P<.001) compared with maximum-intensity projections. The data postprocessing time was comparable for both techniques. Caloric weakness was noted in all patients assessed by electronystagmography. CONCLUSION: Volume rendering is the postprocessing technique of choice for 3-dimensional inner ear visualization, performing better than maximum-intensity projections with respect to various parameters.

Multislice computed tomographic imaging in temporal bone dysplasia.

OBJECTIVES: To evaluate the impact of multislice computed tomographic (MSCT) imaging, a recently developed computed tomographic technique, on imaging of temporal bone malformations. STUDY DESIGN: Retrospective case review. SETTING: The study was performed at a tertiary referral center. PATIENTS: High-resolution temporal bone studies of 168 consecutive patients were reviewed for various temporal bone malformations. MAIN OUTCOME MEASURES: Visualization of various dysplastic conditions of the temporal bone without the need for supplementary scan procedures or additional imaging techniques. INTERVENTION: MSCT imaging was performed on a scanner with four detector rows by using the following parameters: 120 kV, 50 mA/s, 0.5-mm slice thickness, 0.2-mm reconstruction increment, pitch factor of 0.75, and a field of view of 160 mm. Two-dimensional and three-dimensional image reconstructions were performed subsequent to data transfer to a workstation. In one patient suspected of having a vascular dysplasia, high-resolution MSCT imaging was supplemented by multislice computed tomographic angiography. RESULTS Temporal bone dysplasias were encountered in 28 patients (16.7%), affecting the external auditory canal (n = 15), the middle ear (n = 18), the inner ear (n = 5), and the vascular system (n = 3). All temporal bone dysplasias were visualized by two-dimensional and three-dimensional images of excellent detail resolution. In none of the patients were supplementary computed tomographic scans necessary, except for one patient with evidence of an aberrant course of the internal carotid artery. Multislice computed tomographic angiography obviated the need for invasive diagnostic procedures. CONCLUSION: MSCT imaging of the temporal bone allows for comprehensively assessing various dysplasias through high-quality two-dimensional and three-dimensional image reconstructions.

Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics.

The two closely related deep-sea tubeworms Riftia pachyptila and Tevnia jerichonana both rely exclusively on a single species of sulfide-oxidizing endosymbiotic bacteria for their nutrition. They do, however, thrive in markedly different geochemical conditions. A detailed proteogenomic comparison of the endosymbionts coupled with an in situ characterization of the geochemical environment was performed to investigate their roles and expression profiles in the two respective hosts. The metagenomes indicated that the endosymbionts are genotypically highly homogeneous. Gene sequences coding for enzymes of selected key metabolic functions were found to be 99.9% identical. On the proteomic level, the symbionts showed very consistent metabolic profiles, despite distinctly different geochemical conditions at the plume level of the respective hosts. Only a few minor variations were observed in the expression of symbiont enzymes involved in sulfur metabolism, carbon fixation and in the response to oxidative stress. Although these changes correspond to the prevailing environmental situation experienced by each host, our data strongly suggest that the two tubeworm species are able to effectively attenuate differences in habitat conditions, and thus to provide their symbionts with similar micro-environments.

GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.

SUMMARY: GenColors is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes, considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. The genome comparison tools determine, for example, best-bidirectional hits, gene conservation, syntenies and gene core sets. Swiss-Prot/TrEMBL hits allow annotations in an effective manner. To further support the annotation base-specific quality data can also be displayed if available. With GenColors dedicated genome browsers containing a group of related genomes can be easily set up and maintained. It has been efficiently used for Borrelia garinii and is currently applied to various ongoing genome projects. AVAILABILITY: Detailed information on GenColors is available at http://gencolors.imb-jena.de. Online usage of GenColors-based genome browsers is the preferred application mode. The system is also available upon request for local installation.

Gene organization features in A/T-rich organisms.

Several species have genomes in which the four nucleotides are not equally represented (Glöckner 2000). Interestingly, shifts to very high A/T or G/C levels can occur in several distinct branches of the tree of life. The underlying reasons for these shifts therefore may be of different origin. Now entire chromosome sequences from two different A/T-rich genomes, Dictyostelium discoideum and Plasmodium falciparum, are available (Bowman et al. 1999; Gardner et al. 2002; Glöckner et al. 2002). This gives us the opportunity to investigate how a high A/T content may influence the signals that are the landmarks for gene specification. We found that, in contrast with most known metazoan and plant genomes, splice signals contain, little information other than the canonical GT-AG dinucleotides. Intron lengths in A/T rich organisms, on the other hand, are comparable to those of other lower eukaryotes. Intergenic regions show, dependent on the orientation of adjacent genes, a size pattern with a ratio of 1 (3'-3') to 2 (3'-5') to 3 (5'-5'). Overall, gene organization patterns seem not to be influenced by the A/T bias. Surprisingly, the slightly higher A/T content of the P. falciparum genome compared to that of D. discoideum (80.1 versus 77.4%) is not achieved by increased A/T richness in intergenic regions. Instead both the shift of the nucleotide usage in coding regions to A/T-rich codons and the longer intergenic regions make an equal contribution to the higher A/T content in this organism.

DictyMOLD-a Dictyostelium discoideum genome browser database.

UNLABELLED: With the Dictyostelium Genome Project nearing completion, we initiated the construction of a data repository for all Dictyostelium discoideum genomic data. Up to now this database, called DictyMOLD (Dicty Map Of Linked Data), incorporates the recently completed D.discoideum chromosomes 1 and 2 sequences together with related annotations. To visualise maps, sequences and annotations and to provide access for the scientific community a perl-based browser was developed. AVAILABILITY: The DictyMOLD database is freely accessible via http://genome.imb-jena.de/dictyostelium/ CONTACT: gernot@imb-jena.de.

Neurofibroma in the mastoid segment of the facial canal.

Neural tissue-derived facial nerve tumours usually present as neurinomas. We describe the extremely rare occurrence of a histologically verified neurofibroma primarily arising in the mastoid segment of the facial canal in a patient not fulfilling diagnostic criteria for neurofibromatosis. The tumour showed evidence of perineural growth into the jugular foramen, as suggested by cross-sectional imaging and intraoperative findings.

Two brothers with findings resembling congenital intrauterine infection-like syndrome (pseudo-TORCH syndrome).

Clinical, pathological, and X-ray findings of two brothers with features resembling congenital intrauterine infection-like syndrome are presented. Extensive screening for intrauterine infection was performed. Nevertheless all confirmatory tests were normal. Both brothers showed extensive intra- and extra-cranial calcifications, thrombocytopenia, a septum pellucidum cyst, one-sided paresis of the diaphragm, and metaphyseal changes on X-ray scans resembling intrauterine infection. Within the first days of life, they developed seizures and died from severe cerebral hemorrhage. The MRI scan of the brain showed cerebellar hypoplasia in one of the boys, while the cerebellum had normal size in the other. No indication of a metabolic disorder, especially in calcium metabolism, was identified. Due to the clinical overlap with Hoyeraal-Hreidarsson syndrome, mutations in the DKC1 gene (Xq28) and the hTR gene (RNA component of telomerase on chromosome 3q) have been excluded. The parents are non-consanguineous and further family history was unremarkable. The findings in these boys overlap with features described in congenital intrauterine infection-like syndrome (pseudo-TORCH syndrome).

Sequence and analysis of chromosome 2 of Dictyostelium discoideum.

The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despite an A + T content of nearly 80%, the chromosome codes for 2,799 predicted protein coding genes and 73 transfer RNA genes. This gene density, about 1 gene per 2.6 kilobases (kb), is surpassed only by Saccharomyces cerevisiae (one per 2 kb) and is similar to that of Schizosaccharomyces pombe (one per 2.5 kb). If we assume that the other chromosomes have a similar gene density, we can expect around 11,000 genes in the D. discoideum genome. A significant number of the genes show higher similarities to genes of vertebrates than to those of other fully sequenced eukaryotes. This analysis strengthens the view that the evolutionary position of D. discoideum is located before the branching of metazoa and fungi but after the divergence of the plant kingdom, placing it close to the base of metazoan evolution.