The DNA sequence and biological annotation of human chromosome 1

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

The genomic sequence and analysis of the swine major histocompatibility complex

We describe the generation and analysis of an integrated sequence map of a 2.4-Mb region of pig chromosome 7, comprising the classical class I region, the extended and classical class II regions, and the class III region of the major histocompatibility complex (MHC), also known as swine leukocyte antigen (SLA) complex. We have identified and manually annotated 151 loci, of which 121 are known genes (predicted to be functional), 18 are pseudogenes, 8 are novel CDS loci, 3 are novel transcripts, and 1 is a putative gene. Nearly all of these loci have homologues in other mammalian genomes but orthologues could be identified with confidence for only 123 genes. The 28 genes (including all the SLA class I genes) for which unambiguous orthology to genes within the human reference MHC could not be established are of particular interest with respect to porcine-specific MHC function and evolution. We have compared the porcine MHC to other mammalian MHC regions and identified the differences between them. In comparison to the human MHC, the main differences include the absence of HLA-A and other class I-like loci, the absence of HLA-DP-like loci, and the separation of the extended and classical class II regions from the rest of the MHC by insertion of the centromere. We show that the centromere insertion has occurred within a cluster of BTNL genes located at the boundary of the class II and III regions, which might have resulted in the loss of an orthologue to human C6orf10 from this region.

Analysis of the genomic region containing the tammar wallaby (Macropus eugenii) orthologues of MHC class III genes

Major histocompatibility complex (MHC) molecules are central to development and regulation of the immune system in all jawed vertebrates. MHC class III cytokine genes from the tumor necrosis factor core family, including tumor necrosis factor (TNF) and lymphotoxin alpha and beta (LTA, LTB), are well studied in human and mouse. Orthologues have been identified in several other eutherian species and the cDNA sequences have been reported for a model marsupial, the tammar wallaby. Comparative genomics can help to determine gene function, to understand the evolution of a gene or gene family, and to identify potential regulatory regions. We therefore cloned the genomic region containing the tammar LTB, TNF, and LTA orthologues by "genome walking", using primers designed from known tammar sequences and regions conserved in other species. We isolated two tammar BAC clones containing all three genes. These tammar genes show similar intergenic distances and the same transcriptional orientation as in human and mouse. Gene structures and sequences are also very conserved. By comparing the tammar, human and mouse genomic sequences we were able to identify candidate regulatory regions for these genes in mammals. Full length sequencing of BACs containing the three genes has been partially completed, and reveals the presence of a number of other tammar MHC III orthologues in this region.

Decreased internalisation of ErbB1 mutants in lung cancer is linked with a mechanism conferring sensitivity to gefitinib

A majority of gefitinib (IRESSA)-responsive tumours in non-small cell lung cancer have been found to carry mutations in ErbB1. Previously, it has been observed that internalisation-deficient ErbB1 receptors are strong drivers of oncogenesis. Using a computational model of ErbB1 trafficking and signalling, it is found that a deficiency in ErbB1 internalisation is sufficient to explain the observed signalling phenotype of these gefitinib-responsive ErbB1 mutants in lung cancer cell lines. Experimental tests confirm that gefitinib-sensitive cell lines with and without ErbB1 mutations exhibit markedly slower internalisation rates than gefitinib-insensitive cell lines. Moreover, the computational model demonstrates that reduced ErbB1 internalisation rates are mechanistically linked to upregulated AKT signalling. Experimentally it is confirmed that impaired internalisation of ErbB1 is associated with increased AKT activity, which can be blocked by gefitinib. On the basis of these experimental and computational results, it is surmised that gefitinib sensitivity is a marker of a reliance on AKT signalling for cell survival that may be brought about by impaired ErbB1 internalisation.

Transcriptional Activity of the Host-Interaction Locus and a Putative Pilin Gene of Bdellovibrio bacteriovorus in the Predatory Life Cycle

Bdellovibrio bacteriovorus is a predatory bacterium that grows and replicates within the periplasm of a large variety of Gram-negative bacteria. So far, the host-interaction locus (hit locus) is the only genetic locus that is implicated in the obligate predatory lifestyle. Sequence analysis revealed that upstream of the hit locus, the genomic regions of the two obligate predatory B. bacteriovorus-type strains HD100 and HD114 encode genes for pilus formation. As pili might be involved in the invasion process, the transcriptional activity of the hit locus and of a putative pilin gene (flp1) of the pilus cluster were studied in synchronized cultures of B. bacteriovorus with Escherichia coli K-12 as prey bacteria. Stages of the life cycle were monitored with scanning electronic microscopy and transcriptional analyses were performed by quantitative reverse transcription polymerase chain reaction. Our study revealed an increased expression level of the putative hit and flp1 genes in the attack phase of B. bacteriovorus, whereas the transcriptional activity significantly decreased during the intracellular replication phase.

Phosphorus-31 MAS NMR investigations of pyridine stabilized dithiomonometaphosphoryl halides

Phosphorus-31 magic-angle spinning NMR spectroscopy was chosen in order to study a series of N-donor stabilized dithiomonometaphosphoryl halides (F, Cl, and Br) and to extract structural and bonding information from their spectra. Additionally, an unusual line splitting was observed in the 31P MAS NMR spectra of pyridine dithiomonometaphosphoryl chloride (Py-->PS2Cl) and the analogous bromide (Py-->PS2Br). It is shown that this effect is due to a residual dipolar coupling between phosphorus and chlorine or bromine, respectively. This work is to our knowledge the first observation of this effect between P and Br in 31P MAS NMR spectra.

Mass spectrometric decompositions of cationized β-cyclodextrin

The mass spectrometric decompositions of beta-cyclodextrin (beta-CD) complexed with a number of common divalent metal cations (Mg, Ca, Cd, Cu, Co and Pb), obtained under electrospray ionization conditions, are reported. The main fragmentation pathways of [beta-CD+Cat](2+) ions studied (Cat stands for divalent cation) consist of consecutive losses of sugar units. The rupture of C-C bond in sugar units, which occurs via hydrogen atom transfer from the fragment ion formed to the eliminated species, was also observed. Isotope labelling consisting of the exchange of all hydroxyl hydrogens for deuteriums, has been applied in order to understand better the formation of fragment ions. It was found that C-H hydrogen transfer proceeds only during fragmentation across C-C bonds.

New Alström syndrome phenotypes based on the evaluation of 182 cases

BACKGROUND

Alström syndrome is a recessively inherited genetic disorder characterized by congenital retinal dystrophy that leads to blindness, hearing impairment, childhood obesity, insulin resistance, and type 2 diabetes mellitus. We provide new details on cardiologic, hepatic, gastrointestinal, urologic, pulmonary, and neurobehavioral phenotypes in Alström syndrome and describe the histopathologic findings in 5 individuals.

METHODS

We obtained data on 182 patients from clinical examinations, medical record reviews, standardized questionnaires, and personal interviews with physicians and parents.

RESULTS

Dilated cardiomyopathy occurred in 60% of patients. Age at onset was either during infancy, often before vision disturbances were noted, or in adolescence or adulthood. There is a risk of recurrence of infantile cardiomyopathy. Hyperinsulinemia (92%) developed in early childhood and progressed to type 2 diabetes mellitus in 82% of those older than 16 years. Hypertriglyceridemia (54%) precipitated pancreatitis in 8 patients. Urologic dysfunction and gastrointestinal disturbances occurred in 48% and 35% of patients, respectively. Fifty-three percent of patients had persistent pulmonary symptoms. Neurologic symptoms in 20% of patients included clonic tic and absence seizures. Developmental motor or language delays were observed in 46% of patients. Fibrotic infiltrations of multiple organs, that is, kidney, heart, liver, lung, urinary bladder, gonads, and pancreas, were observed.

CONCLUSIONS

The wide-ranging and complex spectrum of phenotypes reported herein broadens those previously described for Alström syndrome. These findings will aid physicians in making an early and accurate diagnosis and will help effect appropriate monitoring and treatment.

Metallkomplexe von 2,2’-Dipyridyldisulfid mit Quecksilber(II)-, Cadmium(II)- und Zink(II)-Halogeniden und mit Cadmium(II)- Trifluormethansulfonat / Metal Complexes of 2,2’-Dipyridyldisulfide with Mercury(II), Cadmium(II), and Zinc(II) Halides and with Cadmium(II) Trifluoromethanesulfonate

Crystals of diiodo-2,2’-dipyridyldisulfide mercury(II) [HgI2(C5H4N)2S2], dichloro-2,2’-dipyridyldisulfide zinc(II) [ZnCl2(C5H4N)2S2], dibromo-2,2’-dipyridyldisulfide cadmium(II) [CdBr2 (C5H4N)2S2], diiodo-2,2’-dipyridyldisulfide cadmium(II) [CdI2(C5H4N)2S2], and diaquo 2,2’-dipyridyldisulfide cadmium(II) trifluoromethanesulfonate [Cd(H2O)2(C5H4N)2S2](CF3SO3)2, were obtained by evaporation of solutions of the ligand and the appropriate metal salts, and their X-ray crystal structures determined

Characterization of outer membrane protein fractions ofBdellovibrionales

Bdellovibrio-and-like organisms (BALOs) are predatory bacteria that prey upon Gram-negative bacteria and are taxonomically subsumed in the order Bdellovibrionales. Despite their unique lifestyle, these bacteria show remarkable genotypic diversities. The outer membrane of the predators is likely to play an important role during the recognition and invasion stage, as well as in the intraperiplasmic growth phase. In this study, the outer membrane protein fractions of type strains of Bdellovibrio, Bacteriovorax and Peredibacter were investigated, revealing the presence of outer membrane proteins (Omps) similar to the major Omps of Bdellovibrio bacteriovorus. The primary structures of these Omps of Bdellovibrio sp. W, Bacteriovorax stolpii and Peredibacter starrii were elucidated by a combined mass spectrometric-reverse genetic approach. The similarity between the analyzed Omps of the investigated BALOs ranges from 32% to 89% showing conserved amino acid regions in their primary structure.

Electrospray ionization mass spectrometric study of purine base-cisplatin complexes

By mixing cisplatin (cis-diamminedichloroplatinum(II)) with purine base the following ions have been obtained under electrospray ionization conditions: [A+Pt(NH3)2 Cl]+, [A+PtNH3Cl]+, [G+Pt(NH3)2 Cl]+ and [G+PtNH3)Cl]+. Their collision-induced dissociation led to the loss of NH3 and HCl and formation of the protonated base. The last process is strongly favoured for adenine over guanine. It confirms that, analogously as for DNA, formation of the guanine-cisplatin complex is favoured over that of the adenine complex and, as a consequence, it suggests that the mass spectrometric study of nucleic base complexes with platinum may provide some information on the interactions of DNA with other platinum drugs. The loss of NH3 accompanied by that of CO from the guanine ring has experimentally confirmed the presence of a strong hydrogen bond between the NH3 molecule and the O=C6 moiety of guanine found by theoretical calculations.

Quantitative methods for the analysis of CFTR transcripts/splicing variants

In cystic fibrosis (CF), transcript analysis and quantification are important for diagnosis, prognosis and also as surrogate markers for some therapies including gene therapy. Classical RNA-based methods require significant expression levels in target samples for appropriate analysis, thus PCR-based methods are evolving towards reliable quantification. Various protocols for the quantitative analysis of CFTR transcripts (including those resulting from splicing variants) are described and discussed here.

Methods for RNA extraction, cDNA preparation and analysis of CFTR transcripts

The scope of this article is to outline some of the basic methods for good quality RNA preparation from mammalian tissues and cells (including epithelial cells). Additionally, we give an outline of common techniques of measuring CFTR gene expression such as quantitative and semi-quantitative reverse transcription (RT) PCR and ribonuclease protection assay (RPA). These methods are designed to detect low abundance transcripts, which apply to CFTR mRNA in most cell types and tissues.

DNA sequence and analysis of human chromosome 9

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Bdellovibrio bacteriovorus strains produce a novel major outer membrane protein during predacious growth in the periplasm of prey bacteria

Bdellovibrio bacteriovorus is a predatory bacterium that is capable of invading a number of gram-negative bacteria. The life cycle of this predator can be divided into a nonreproductive phase outside the prey bacteria and a multiplication phase in their periplasm. It was suggested that during the reproduction phase, B. bacteriovorus reutilizes unmodified components of the prey's cell wall. We therefore examined the outer membranes of B. bacteriovorus strains HD100 (DSM 50701) and HD114 (DSM 50705) by using Escherichia coli, Yersinia enterocolitica, and Pseudomonas putida as prey organisms. The combined sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometric analyses revealed novel and innate major outer membrane proteins (OMPs) of B. bacteriovorus strains. An incorporation of prey-derived proteins into the cell wall of B. bacteriovorus was not observed. The corresponding genes of the B. bacteriovorus strains were elucidated by a reverse-genetics approach, and a leader peptide was deduced from the gene sequence and confirmed by Edman degradation. The host-independent mutant strain B. bacteriovorus HI100 (DSM 12732) growing in the absence of prey organisms possesses an OMP similar to the major OMPs of the host-dependent strains. The similarity of the primary structure of the OMPs produced by the three Bdellovibrio strains is between 67 and 89%. The leader peptides of all OMPs have a length of 20 amino acids and are highly conserved. The molecular sizes of the mature proteins range from 34.9 to 37.6 kDa. Secondary-structure predictions indicate preferential alpha-helices and little beta-barrel structures.

The DNA sequence and comparative analysis of human chromosome 10

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

The DNA sequence and analysis of human chromosome 13

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

The DNA sequence and analysis of human chromosome 6

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

Sequence analysis of the genome of the temperate Yersinia enterocolitica phage PY54

The temperate Yersinia phage PY54 belongs to the unusual group of phages that replicate as linear plasmids with covalently closed ends. Besides Escherichia coli phage N15, PY54 is the only member of this group to be identified. We have determined the complete sequence (46,339 bp) of the PY54 genome. Bioinformatic analyses revealed 67 open reading frames (ORFs) with good coding potential located on both DNA strands. The comparison of the deduced PY54 gene products with known proteins encoded by other phages and bacteria along with functional studies have enabled us to assign the possible functions of 25 ORFs. In the left arm of the PY54 genome, we identified a number of ORFs that obviously code for head and tail proteins. Furthermore, this part of the phage genome contains genes probably involved in plasmid partitioning. Regarding the predicted gene functions and gene order, the PY54 and N15 left arms are similar. However, there are only weak DNA homologies and, in contrast to N15, the Yersinia phage harbours only a few ORFs related to genes found in lambdoid phages. The PY54 right arm comprises mainly regulatory genes as well as genes important for plasmid replication, DNA methylation, and host cell lysis. Out of 36 deduced products of the right arm, 13 revealed strongest database homologies to N15 proteins, of which the protelomerase and the Rep protein are exclusively homologous to their N15 counterparts. A number of PY54 genes essential for the lytic or lysogenic cycle were identified by functional analysis and characterization of phage mutants. In order to study transcription during the lytic and lysogenic stage, we analysed 34 PY54 ORFs by reverse transcriptase (RT)-PCR. The phage transcription patterns in lysogenic bacteria and at the late lytic stage of infection are nearly identical. The reasons for this finding are spontaneous release of phages during lysogeny and a high rate of phages that lysogenize their Yersinia host upon infection.

Peritumoral CpG DNA elicits a coordinated response of CD8 T cells and innate effectors to cure established tumors in a murine colon carcinoma model

The immune system of vertebrates is able to detect bacterial DNA based on the presence of unmethylated CpG motifs. We examined the therapeutic potential of oligodeoxynucleotides with CpG motifs (CpG ODN) in a colon carcinoma model in BALB/c mice. Tumors were induced by s.c. injection of syngeneic C26 cells or Renca kidney cancer cells as a control. Injection of CpG ODN alone or in combination with irradiated tumor cells did not protect mice against subsequent tumor challenge. In contrast, weekly injections of CpG ODN into the margin of already established tumors resulted in regression of tumors and complete cure of mice. The injection site was critical, since injection of CpG ODN at distant sites was not effective. Mice with two bilateral C26 tumors rejected both tumors upon peritumoral injection of one tumor, indicating the development of a systemic immune response. The tumor specificity of the immune response was demonstrated in mice bearing a C26 tumor and a Renca tumor at the same time. Mice that rejected a tumor upon peritumoral CpG treatment remained tumor free and were protected against rechallenge with the same tumor cells, but not with the other tumor, demonstrating long term memory. Tumor-specific CD8 T cells as well as innate effector cells contributed to the antitumor activity of treatment. In conclusion, peritumoral CpG ODN monotherapy elicits a strong CD8 T cell response and innate effector mechanisms that seem to act in concert to overcome unresponsiveness of the immune system toward a growing tumor.

Combined dendritic cell- and CpG oligonucleotide-based immune therapy cures large murine tumors that resist chemotherapy

The use of dendritic cells (DC) loaded with tumor antigen is one of the most advanced approaches in cancer immunotherapy. CpG motifs within microbial DNA detected by toll-like receptor 9 are responsible for the favorable properties of CpG oligodeoxynucleotides (ODN) as immune modulators. In this study, mature antigen-pulsed DC or peritumoral injections of CpG ODN, both effective for the treatment of small established tumors, were almost ineffective against large established tumors (1-cm diameter) in a syngeneic murine colon carcinoma model. For large tumors, the antitumor activity of mature antigen-pulsed DC was strongly increased by coinjection of CpG ODN, resulting in a transient control of tumor growth. Rejection of large tumors and long-term cure of mice was achieved by combining injection of antigen-pulsed DC plus CpG ODN at a site distant to the tumor with peritumoral injections of CpG ODN. Depletion of CD8 T cells abrogated the therapeutic activity. Large numbers of DEC-205-positive DC infiltrated the tumor in treated mice. Therapy with 5-fluorouracil and leucovorin was unable to control tumors of the same size. In conclusion, we demonstrate that the immune system, provided that appropriate stimulation with DC and CpG ODN is given, has the potential to cure animals of large solid tumors in situations where even chemotherapy is not efficient.