The Ensembl genome database project

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

RANK is essential for osteoclast and lymph node development

The physiological role of the TNF receptor (TNFR) family member, RANK, was investigated by generating RANK-deficient mice. RANK(-/-) mice were characterized by profound osteopetrosis resulting from an apparent block in osteoclast differentiation. RANK expression was not required for the commitment, differentiation, and functional maturation of macrophages and dendritic cells from their myeloid precursors but provided a necessary and specific signal for the differentiation of myeloid-derived osteoclasts. RANK(-/-) mice also exhibited a marked deficiency of B cells in the spleen. RANK(-/-) mice retained mucosal-associated lymphoid tissues including Peyer's patches but completely lacked all other peripheral lymph nodes, highlighting an additional major role for RANK in lymph node formation. These experiments reveal that RANK provides critical signals necessary for lymph node organogenesis and osteoclast differentiation.

Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States

In late summer 1999, an outbreak of human encephalitis occurred in the northeastern United States that was concurrent with extensive mortality in crows (Corvus species) as well as the deaths of several exotic birds at a zoological park in the same area. Complete genome sequencing of a flavivirus isolated from the brain of a dead Chilean flamingo (Phoenicopterus chilensis), together with partial sequence analysis of envelope glycoprotein (E-glycoprotein) genes amplified from several other species including mosquitoes and two fatal human cases, revealed that West Nile (WN) virus circulated in natural transmission cycles and was responsible for the human disease. Antigenic mapping with E-glycoprotein-specific monoclonal antibodies and E-glycoprotein phylogenetic analysis confirmed these viruses as WN. This North American WN virus was most closely related to a WN virus isolated from a dead goose in Israel in 1998.

The Social Functioning Scale. The development and validation of a new scale of social adjustment for use in family intervention programmes with schizophrenic patients

Social functioning as an outcome variable in family interventions with schizophrenic patients has been a relatively neglected area. The requirements of a scale of social functioning to measure the efficacy of family interventions include: the measurement of skill/behaviour relevant to the impairments and the demography of this group; the ability to yield considerable information with an economy of clinical time; and the establishment of 'comparative' need through comparison between subscales and with appropriate reference groups. Results from three samples show that the Social Functioning Scale is reliable, valid, sensitive and responsive to change.

Ensembl 2007

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Ensembl 2009

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

Rating the burn scar

A reliable, objective, and universal method of assessing burn scars does not exist in today's burn literature. Such a method is necessary to provide a descriptive terminology for the comparison of burn scars and the results of treatment. The method should be applicable to patients both within an institution and between burn centers. A burn scar assessment has been devised based on physical parameters. These relate to the healing and maturation of wounds, cosmetic appearance, and the function of the healed skin. Pigmentation, vascularity, pliability, and scar height are assessed independently, with increasing score being assigned to the greater pathologic condition. Normal skin has a score of 0. Seventy-three patients were assessed by three separate occupational therapists and the findings subjected to statistical analysis for interrater reliability. For each parameter a Cohen's kappa statistic of approximately 0.5 +/- 0.1 indicates a statistically significant agreement between observers. These values were found to improve with time. This appears to be a useful tool for the assessment of burn scars, allowing objective comparison of the same scar by different observers.

Measurement of muscle mass in humans: validity of the 24-hour urinary creatinine method

Measuring muscle mass is an important component of the nutritional assessment examination and a suggested index of this body space is the 24-h urinary excretion of creatinine. The method originated from studies in a variety of animal species in whom early workers found a parallelism between total body creatine and urinary excretion of creatinine. Assuming that nearly all creatine was within muscle tissue, that muscle creatine content remained constant and that creatinine was excreted at a uniform rate, an obvious "corollary" was that urinary creatinine was proportional to muscle mass. The so-called "creatinine equivalence" (kg muscle mass/g urinary creatinine) ranged experimentally from 17 to 22. One of the limiting factors in firmly establishing this constant and its associated variability was (and is) the lack of another totally acceptable noninvasive technique of measuring muscle mass to which the creatinine method could (or would) be compared. An improved understanding of creatine metabolism and a variety of clinical studies in recent years has tended to support the general validity of this approach. However, specific conditions have also been established in which the method becomes either inaccurate or invalid. While creatinine excretion may serve as a useful approximation of muscle mass in carefully selected subjects, there remains a need for accurate and practical indices of muscle mass for use in the individuals in whom the method cannot be reliably applied.

Anthropometric measurement of muscle mass: revised equations for calculating bone-free arm muscle area

Arm muscle area (AMA, cm2) is currently calculated from triceps skinfold thickness (TSF, cm), and midarm circumference (MAC, cm). In assessing the accuracy of the current equation by comparison to AMA measured by computerized axial tomography, error in each of the four approximations made was found to result in a 20 to 25% overestimate of AMA. Two correctible error sources were: a 10 to 15% overestimation caused by assuming a circular midarm muscle compartment and a 5 to 10% overestimation due to inclusion of midarm cross-sectional bone area. Corrected AMA equations for men and women were respectively: [(MAC - pi x TSF)2/4 pi] - 10, and [MAC - pi x TSF)2/4 pip] - 6.5. With two additional study groups, the overall improved accuracy of the new equations was confirmed, although the average error for a given patient was 7 to 8%; the relationship between corrected AMA and total body muscle mass was established [muscle mass (kg) = (ht, cm2) (0.0264 + 0.0029 x corrected AMA)]; and the minimal range of corrected AMA values compatible with survival (9 to 11 cm2) was defined. Bedside estimates of undernutrition severity and prognosis can therefore be calculated from two simple measurements, TSF and MAC.

A self-report Insight Scale for psychosis: reliability, validity and sensitivity to change

Lack of insight is a frequent concomitant of psychosis and has traditionally been viewed as a binary, all or none phenomenon. Recent conceptualization has formulated insight as a continuum representing the juxtaposition of 3 factors--awareness of illness, need for treatment and attribution of symptoms. Measurement of insight has been exclusively based on interview; this method does not easily lend itself to frequent repeated measurement and requires interrater reliability to be established. A self-report Insight Scale is presented, and evidence in support of its reliability, validity and sensitivity is provided that includes a sample of 30 patients monitored during recovery from an acute psychosis. The scale is a quick and acceptable measure that may find application in investigations of acute care, cognitive therapy of psychotic symptoms and as a method of augmenting clinical judgements of insight.

Stimulation of homologous recombination through targeted cleavage by chimeric nucleases

Chimeric nucleases that are hybrids between a nonspecific DNA cleavage domain and a zinc finger DNA recognition domain were tested for their ability to find and cleave their target sites in living cells. Both engineered DNA substrates and the nucleases were injected into Xenopus laevis oocyte nuclei, in which DNA cleavage and subsequent homologous recombination were observed. Specific cleavage required two inverted copies of the zinc finger recognition site in close proximity, reflecting the need for dimerization of the cleavage domain. Cleaved DNA molecules were activated for homologous recombination; in optimum conditions, essentially 100% of the substrate recombined, even though the DNA was assembled into chromatin. The original nuclease has an 18-amino-acid linker between the zinc finger and cleavage domains, and this enzyme cleaved in oocytes at paired sites separated by spacers in the range of 6 to 18 bp, with a rather sharp optimum at 8 bp. By shortening the linker, we found that the range of effective site separations could be narrowed significantly. With no intentional linker between the binding and cleavage domains, only binding sites exactly 6 bp apart supported efficient cleavage in oocytes. We also showed that two chimeric enzymes with different binding specificities could collaborate to stimulate recombination when their individual sites were appropriately placed. Because the recognition specificity of zinc fingers can be altered experimentally, this approach holds great promise for inducing targeted recombination in a variety of organisms.

Structured exercise improves physical functioning in women with stages I and II breast cancer: results of a randomized controlled trial

PURPOSE

Self-directed and supervised exercise were compared with usual care in a clinical trial designed to evaluate the effect of structured exercise on physical functioning and other dimensions of health-related quality of life in women with stages I and II breast cancer.

PATIENTS AND METHODS

One hundred twenty-three women with stages I and II breast cancer completed baseline evaluations of generic and disease- and site-specific health-related quality of life, aerobic capacity, and body weight. Participants were randomly allocated to one of three intervention groups: usual care (control group), self-directed exercise, or supervised exercise. Quality of life, aerobic capacity, and body weight measures were repeated at 26 weeks. The primary outcome was the change in the Short Form-36 physical functioning scale between baseline and 26 weeks.

RESULTS

Physical functioning in the control group decreased by 4.1 points, whereas it increased by 5.7 points and 2.2 points in the self-directed and supervised exercise groups, respectively (P =.04). Post hoc analysis showed a moderately large (and clinically important) difference between the self-directed and control groups (9.8 points; P =.01) and a more modest difference between the supervised and control groups (6.3 points; P =.09). No significant differences between groups were observed for changes in quality of life scores. In a secondary analysis of participants stratified by type of adjuvant therapy, supervised exercise improved aerobic capacity (+3.5 mL/kg/min; P =.01) and reduced body weight (-4.8 kg; P <.05) compared with usual care only in participants not receiving chemotherapy.

CONCLUSION

Physical exercise can blunt some of the negative side effects of breast cancer treatment, including reduced physical functioning. Self-directed exercise is an effective way to improve physical functioning compared with usual care. In participants not receiving chemotherapy, supervised exercise may increase aerobic capacity and reduce body weight compared with usual care.

Evidence for a prostate cancer susceptibility locus on the X chromosome

Over 200,000 new prostate cancer cases are diagnosed in the United States each year, accounting for more than 35% of all cancer cases affecting men, and resulting in 40,000 deaths annually. Attempts to characterize genes predisposing to prostate cancer have been hampered by a high phenocopy rate, the late age of onset of the disease and, in the absence of distinguishing clinical features, the inability to stratify patients into subgroups relative to suspected genetic locus heterogeneity. We previously performed a genome-wide search for hereditary prostate cancer (HPC) genes, finding evidence of a prostate cancer susceptibility locus on chromosome 1 (termed HPC1; ref. 2). Here we present evidence for the location of a second prostate cancer susceptibility gene, which by heterogeneity estimates accounts for approximately 16% of HPC cases. This HPC locus resides on the X chromosome (Xq27-28), a finding consistent with results of previous population-based studies suggesting an X-linked mode of HPC inheritance. Linkage to Xq27-28 was observed in a combined study population of 360 prostate cancer families collected at four independent sites in North America, Finland and Sweden. A maximum two-point lod score of 4.60 was observed at DXS1113, theta=0.26, in the combined data set. Parametric multipoint and non-parametric analyses provided results consistent with the two-point analysis. Significant evidence for genetic locus heterogeneity was observed, with similar estimates of the proportion of linked families in each separate family collection. Genetic mapping of the locus represents an important initial step in the identification of an X-linked gene implicated in the aetiology of HPC.

Randomized study of carotid angioplasty and stenting versus carotid endarterectomy: a stopped trial

BACKGROUND

Carotid angioplasty (CA) has been suggested to be a safer and more cost-effective alternative to carotid endarterectomy (CEA) in the management of symptomatic severe internal carotid artery (ICA) disease.

METHODS

The study was conducted as a prospective consecutive randomized trial of CEA versus CA for symptomatic severe ICA disease in a university teaching hospital. All patients were assessed before and after surgery by a neurologist. The study consisted of 23 patients with focal carotid territory symptoms and severe ICA stenosis (> 70%) who were randomized to either CEA or CA. However, only 17 had received their allocated treatment before trial suspension. CEA with patching or CA with stenting were used as interventions. The main outcome measures were death or disabling or nondisabling stroke within 30 days.

RESULTS

All 10 CEA operations proceeded without complication, but 5 of the 7 patients who underwent CA had a stroke (P=.0034), 3 of which were disabling at 30 days.

CONCLUSIONS

After referral, the Data Monitoring Committee invoked the stopping rule and the trial was suspended. The investigators and the Ethics Committee subsequently concluded that the trial could not be restarted--even in an amended format-primarily because of problems with informed consent. We review many of the ethical dilemmas encountered in the performance of this study. If future trials do suggest a selected role for CA, it is essential that both the inclusion and the exclusion criteria are fully documented.

Hyperactivity and delay aversion--I. The effect of delay on choice

Two experiments are reported in which hyperactive and control children repeatedly chose between small immediate and large delayed rewards. In experiment 1, the best choice option was manipulated by varying levels of delay after reward delivery. In experiment 2 it was manipulated by changing the economic constraint (10 minutes or 20 trials). Both groups were equally efficient at earning points under most conditions, but hyperactive children exhibited a maladaptive preference for the small reward under the trials constraint. The results suggest that hyperactive children were more concerned to reduce overall delay levels than either to maximize reward amount or immediacy.

Ensembl 2008

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Activation of the mouse cellular Harvey-ras gene in chemically induced benign skin papillomas

An important feature of the development of many human and animal tumours is the appearance of pre-malignant benign lesions, some of which undergo further changes during progression to malignancy. Many of the currently accepted concepts of multi-stage carcinogenesis have been developed using an experimental model based on the chemical induction of tumours in mouse skin. In this system, many of the premalignant papillomas which arise are promoter-dependent, and appear to regress if promoter treatment is interrupted, whereas others progress to form autonomous benign lesions and, in some cases, malignant carcinomas. Although the number and nature of the events leading to malignancy are not known, DNA transfection experiments have led to the identification of several genes which may be qualitatively altered in tumour cells (see ref. 6 for review). We have previously shown that DNA from transplantable mouse skin carcinomas induced by chemical carcinogens has the ability to transform NIH/3T3 cells, and that the gene responsible for the transformation is an activated form of the mouse cellular Harvey-ras gene (c-rasH). We have now investigated the stage of carcinogenesis at which the proto-oncogene acquires transforming activity. We demonstrate that primary papillomas induced by chemical carcinogens in two different mouse strains have an activated c-rasH gene. This constitutes the first report of a benign tumour which contains DNA with detectable transforming activity. In addition, steady-state levels of c-rasH gene transcripts are elevated in the papillomas as compared with normal epidermis.

Germline mutations in the ribonuclease L gene in families showing linkage with HPC1

Although prostate cancer is the most common non-cutaneous malignancy diagnosed in men in the United States, little is known about inherited factors that influence its genetic predisposition. Here we report that germline mutations in the gene encoding 2'-5'-oligoadenylate(2-5A)-dependent RNase L (RNASEL) segregate in prostate cancer families that show linkage to the HPC1 (hereditary prostate cancer 1) region at 1q24-25 (ref. 9). We identified RNASEL by a positional cloning/candidate gene method, and show that a nonsense mutation and a mutation in an initiation codon of RNASEL segregate independently in two HPC1-linked families. Inactive RNASEL alleles are present at a low frequency in the general population. RNASEL regulates cell proliferation and apoptosis through the interferon-regulated 2-5A pathway and has been suggested to be a candidate tumor suppressor gene. We found that microdissected tumors with a germline mutation showed loss of heterozygosity and loss of RNase L protein, and that RNASEL activity was reduced in lymphoblasts from heterozyogous individuals compared with family members who were homozygous with respect to the wildtype allele. Thus, germline mutations in RNASEL may be of diagnostic value, and the 2-5A pathway might provide opportunities for developing therapies for those with prostate cancer.

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Human anergic/suppressive CD4(+)CD25(+) T cells: a highly differentiated and apoptosis-prone population

Anergic/suppressive CD4(+)CD25(+) T cells exist in animal models but their presence has not yet been demonstrated in humans. We have identified and characterized a human CD4(+)CD25(+) T cell subset, which constitutes 7-10 % of CD4(+) T cells in peripheral blood and tonsil. These cells are a CD45RO(+)CD45RB(low) highly differentiated primed T cell population that is anergic to stimulation. Depletion of this small subset from CD4(+) T cells significantly enhances proliferation by threefold in the remaining CD4(+)CD25(-) T cells, while the addition of isolated CD4(+)CD25(+) T cells to CD4(+)CD25(-) T cells significantly inhibits proliferative activity. Blocking experiments suggest that suppression is not mediated via IL-4, IL-10 or TGF-beta and is cell-contact dependent. Isolated CD4(+)CD25(+) T cells are susceptible to apoptosis that is associated with low Bcl-2 expression, but this death can be prevented by IL-2 or fibroblast-secreted IFN-beta. However, the anergic/suppressive state of these cells is maintained after cytokine rescue. These human regulatory cells are therefore a naturally occurring, highly suppressive, apoptosis-prone population which are at a late stage of differentiation. Further studies into their role in normal and pathological situations in humans are clearly essential.

Prediction of adverse outcomes in children with sickle cell disease

BACKGROUND

The ability to identify infants with sickle cell anemia who are likely to have severe complications later in life would permit accurate prognostication and tailoring of therapy to match disease-related risks and facilitate planning of clinical trials. We attempted to define the features of such babies by following the clinical course of 392 children with sickle cell disease from infancy to about the age of 10 years.

METHODS

We analyzed the records of 392 infants who received the diagnosis of homozygous sickle cell anemia or sickle cell-Beta(0)-thalassemia before the age of six months and for whom comprehensive clinical and laboratory data were recorded prospectively; data were available for a mean (+/-SD) of 10.0+/-4.8 years. Results obtained before the age of two years were evaluated to determine whether they predicted the outcome later in life.

RESULTS

Of the 392 infants in the cohort, 70 (18 percent) subsequently had an adverse outcome, defined as death (18 patients [26 percent]), stroke (25 [36 percent]) frequent pain (17 [24 percent]), or recurrent acute chest syndrome (10 [14 percent]). Using multivariate analysis, we found three statistically significant predictors of an adverse outcome: an episode of dactylitis before the age of one year (relative risk of an adverse outcome, 2.55; 95 percent confidence interval, 1.39 to 4.67), a hemoglobin level of less than 7 g per deciliter (relative risk, 2.47; 95 percent confidence interval, 1.14 to 5.33), and leukocytosis in the absence of infection (relative risk, 1.80; 95 percent confidence interval, 1.05 to 3.09).

CONCLUSIONS

Three easily identifiable manifestations of sickle cell disease that may appear in the first two years of life (dactylitis, severe anemia, and leukocytosis) can help to predict the possibility of severe sickle cell disease later in life.

Ensembl 2006

The Ensembl () project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

The perception of self-produced sensory stimuli in patients with auditory hallucinations and passivity experiences: evidence for a breakdown in self-monitoring

BACKGROUND

To test the hypothesis that certain psychotic symptomatology is due to a defect in self-monitoring, we investigated the ability of groups of psychiatric patients to differentiate perceptually between self-produced and externally produced tactile stimuli.

METHODS

Responses to tactile stimulation were assessed in three groups of subjects: schizophrenic patients; patients with bipolar affective disorder or depression; and normal control subjects. Within the psychiatric groups subjects were divided on the basis of the presence or absence of auditory hallucinations and/or passivity experiences. The subjects were asked to rate the perception of a tactile sensation on the palm of their left hand. The tactile stimulation was either self-produced by movement of the subject's right hand or externally produced by the experimenter.

RESULTS

Normal control subjects and those psychiatric patients with neither auditory hallucinations nor passivity phenomena experienced self-produced stimuli as less intense, tickly and pleasant than identical, externally produced tactile stimuli. In contrast, psychiatric patients with these symptoms did not show a decrease in their perceptual ratings for tactile stimuli produced by themselves as compared with those produced by the experimenter. This failure to show a difference in perception between self-produced and externally produced stimuli appears to relate to the presence of auditory hallucinations and/or passivity experiences rather than to the diagnosis of schizophrenia.

CONCLUSIONS

We propose that auditory hallucinations and passivity experiences are associated with an abnormality in the self-monitoring mechanism that normally allows us to distinguish self-produced from externally produced sensations.