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/).
Nuclear clusterin (nCLU) is an ionizing radiation (IR)-inducible protein that binds Ku70, and triggers apoptosis when overexpressed
in MCF-7 cells. We demonstrate that endogenous nCLU synthesis is a ...product of alternative splicing. Reverse transcriptase-PCR
analyses revealed that exon II, containing the first AUG and encoding the endoplasmic reticulum-targeting peptide, was omitted.
Exons I and III are spliced together placing a downstream AUG in exon III as the first available translation start site. This
shorter mRNA produces the 49-kDa precursor nCLU protein. Ku70 binding activity was localized to the C-terminal coiled-coil
domain of nCLU. Leucine residues 357, 358, and 361 of nCLU were necessary for Ku70-nCLU interaction. The N- and C-terminal
coiled-coil domains of nCLU interacted with each other, suggesting that the protein could dimerize or fold. Mutation analyses
indicate that the C-terminal NLS was functional in nCLU with the same contribution from N-terminal NLS. The C-terminal coiled-coil
domain of nCLU was the minimal region required for Ku binding and apoptosis. MCF-7 cells show nuclear as well as cytoplasmic
expression of GFP-nCLU in apoptotic cells. Cytosolic aggregation of GFP-nCLU was found in viable cells. These results indicate
that an inactive precursor of nCLU exists in the cytoplasm of non-irradiated MCF-7 cells, translocates into the nucleus following
IR, and induces apoptosis.
Persistent pulmonary hypertension is common in neonates with respiratory failure.
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It is characterized by pulmonary hypertension and extrapulmonary right-to-left shunting across the foramen ...ovale and ductus arteriosus. In many cases, the disease progressively worsens, becoming refractory to treatment.
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When other therapies fail, neonates are treated with extracorporeal membrane oxygenation.
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This therapy improves survival in neonates with respiratory failure,
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but its administration is labor-intensive and costly and necessitates large amounts of blood products. The mortality rate in neonates treated with extracorporeal membrane oxygenation is 15 to 20 percent, and 10 to 20 percent of the neonates who . . .
DNA mismatch repair (MMR) is an efficient system for the detection and repair of mismatched and unpaired bases in DNA. Deficiencies in MMR are commonly found in both hereditary and sporadic ...colorectal cancers, as well as in cancers of other tissues. Because fluorinated thymidine analogues (which through their actions might generate lesions recognizable by MMR) are widely used in the treatment of colorectal cancer, we investigated the role of MMR in cellular responses to 5-fluorouracil and 5-fluoro-2'-deoxyuridine (FdUrd). Human MLH1(-) and MMR-deficient HCT116 colon cancer cells were 18-fold more resistant to 7.5 microM 5-fluorouracil (continuous treatment) and 17-fold more resistant to 7.5 microM FdUrd in clonogenic survival assays compared with genetically matched, MLH1(+) and MMR-proficient HCT116 3-6 cells. Likewise, murine MLH1(-) and MMR-deficient CT-5 cells were 3-fold more resistant to a 2-h pulse of 10 microM FdUrd than their MLH1(+) and MMR-proficient ME-10 counterparts. Decreased cytotoxicity in MMR-deficient cells after treatment with various methylating agents and other base analogues has been well reported and is believed to reflect a tolerance to DNA damage. Synchronized HCT116 3-6 cells treated with a low dose of FdUrd had a 2-fold greater G(2) cell cycle arrest compared with MMR-deficient HCT116 cells, and asynchronous ME-10 cells demonstrated a 4-fold greater G(2) arrest after FdUrd treatment compared with CT-5 cells. Enhanced G(2) arrest in MMR-proficient cells in response to other agents has been reported and is believed to allow time for DNA repair. G(2) cell cycle arrest as determined by propidium iodide staining was not a result of mitotic arrest, but rather a true G(2) arrest, as indicated by elevated cyclin B1 levels and a lack of staining with mitotic protein monoclonal antibody 2. Additionally, p53 and GADD45 levels were induced in FdUrd-treated HCT116 3-6 cells. DNA double-strand break (DSB) formation was 2-fold higher in MMR-proficient HCT116 3-6 cells after FdUrd treatment, as determined by pulsed-field gel electrophoresis. The formation of DSBs was not the result of enhanced apoptosis in MMR-proficient cells. FdUrd-mediated cytotoxicity was caused by DNA-directed and not RNA-directed effects, because administration of excess thymidine (and not uridine) prevented cytotoxicity, cell cycle arrest, and DSB formation. hMLH1-dependent responses to fluoropyrimidine treatment, which may involve the action of p53 and the formation of DSBs, clearly have clinical relevance for the use of this class of drugs in the treatment of tumors with MMR deficiencies.
Despite the evidence that diseases have increased in marine taxa, parasites remain underrepresented in studies of marine ecology. Recently, observations of black-spot syndrome (BSS) in Caribbean ...fishes, especially ocean surgeonfishes,
Acanthurus tractus
(Poey, 1860), have been reported, although its cause(s) has remained conjectural. We investigated the etiology of BSS and whether the pathology was functionally and consistently associated with particular infections. By examining the patterns of BSS among reef fishes in Bonaire, we show that observed dermal spots are the encysted stages (metacercariae) of the heterophyid trematode
Scaphanocephalus expansus
(Creplin, 1842). Metacercariae were detected within ten species of fishes, with loads ranging from 1–315 per fish. These represent the first published accounts of the genus
Scaphanocephalus
in the Caribbean and are all new host records. Molecular analysis of sequences identified the infection as a heterophyid, while morphological examinations and comparisons with archival specimens confirmed the species identity as
S. expansus.
Field-based estimates of BSS by scuba divers and subsequent video analysis correlated positively with parasite counts from necropsy. No such correlation was observed between BSS and metacercariae of a second trematode genus,
Bucephalus
. The consistent link between host burdens of
S. expansus
and BSS highlights the potential for low-cost and low-impact assessments in fish populations, including the use of images from citizen scientists and public databases. Taken together, these results help establish the foundation for future investigations into the pathology, geographic distribution, life cycle, and ecological consequences of BSS.
The life history characteristics of hosts often influence patterns of parasite infection either by affecting the likelihood of parasite exposure or the probability of infection after exposure. In ...birds, migratory behavior has been suggested to affect both the composition and abundance of parasites within a host, although whether migratory birds have more or fewer parasites is unclear. To help address these knowledge gaps, we collaborated with airports, animal rescue/rehabilitation centers, and hunter check stations in the San Francisco Bay Area of California to collect 57 raptors, egrets, herons, ducks, and other waterfowl for parasitological analysis. After dissections of the gastrointestinal tract of each host, we identified 64 taxa of parasites: 5 acanthocephalans, 24 nematodes, 8 cestodes, and 27 trematodes. We then used a generalized linear mixed model to determine how life history traits influenced parasite richness among bird hosts, while controlling for host phylogeny. Parasite richness was greater in birds that were migratory with larger clutch sizes and lower in birds that were herbivorous. The effects of clutch size and diet are consistent with previous studies and have been linked to immune function and parasite exposure, respectively, whereas the effect of migration supports the hypothesis of “migratory exposure” rather than that of “migratory escape.”
Clusterin CLU, a.k.a. TRPM-2, SGP-2, or ionizing radiation (IR)-induced protein-8(XIP8) was implicated in apoptosis, tissue injury, and aging. Its function remains elusive. We reisolated CLU/XIP8 by ...yeast two-hybrid analyses using as bait the DNA double-strand break repair protein Ku70. We show that a delayed (2-3 days), low-dose (0.02-10 Gy) IR-inducible nuclear CLU/XIP8 protein coimmunoprecipitated and colocalized (by confocal microscopy) in vivo with Ku70/Ku80, a DNA damage sensor and key double-strand break repair protein, in human MCF-7:WS8 breast cancer cells. Overexpression of nuclear CLU/XIP8 or its minimal Ku70 binding domain (120 aa of CLU/XIP8 C terminus) in nonirradiated MCF-7:WS8 cells dramatically reduced cell growth and colony-forming ability concomitant with increased G1cell cycle check-point arrest and increased cell death. Enhanced expression and accumulation of nuclear CLU/XIP8-Ku70/Ku80 complexes appears to be an important cell death signal after IR exposure.
Purpose
: Recent randomized trials of selected patients with single brain metastasis comparing resection followed by whole-brain radiotherapy (WBRT) to WBRT alone have shown a statistically ...significant survival advantage for surgery and WBRT. A multiinstitutional retrospective study was performed, which identified comparable patients who were treated with stereotactic radiosurgery (RS) and WBRT.
Methods and Materials
: The RS databases of four institutions were reviewed to identify patients who met the following criteria: single-brain metastasis; no prior cranial surgery or WBRT; age > 18 years; surgically resectable lesion; Karnofsky Performance Status (KPS) ≥ 70 at time of RS; nonradiosensitive histology. One hundred twenty-two patients were identified who met these criteria. Patients were categorized by: (a) status of the primary, (b) status of non-CNS metastasis, (c) age, (d) baseline KPS (from 70–100), (e) histology, (f) time from diagnosis of primary to the detection of the brain metastasis, (g) gender, and (h) tumor volume. RS was performed with a linear accelerator based technique (peripheral dose range was 10–27 Gy, median was 17 Gy). WBRT was performed in all but five patients who refused WBRT (dose range was 25–40 Gy, median was 37.5 Gy).
Results
: The median follow-up for all patients was 123 weeks. The overall local control rate (defined as lack of progression in the RS volume) was 86%. Intracranial recurrence outside of the RS volume was seen in 27 patients (22%). The actuarial median survival from date of RS is 56 weeks, and the 1-year and 2-year actuarial survival rates are 53 and 30%. The median duration of functional independence (sustained KPS ≥ 70) is 44 weeks. Nineteen of 77 deaths were attributed to CNS progression (25% of all deaths). Multivariate analysis revealed the following factors to be statistically significant predictors of survival: baseline KPS (
p < .0001) and absence of other sites of metastasis (
p = 0.008).
Conclusion
: The RS in conjunction with WBRT for single brain metastasis can produce substantial functional survival, especially in patients with good performance status and without extracranial metastasis. These results are comparable to recent randomized trials of resection and WBRT. The advantages of RS over surgery in terms of cost, hospitalization, morbidity, and wider applicability strongly suggest that a randomized trial to compare RS with surgery is warranted.
Purpose
: Proliferation of surviving tumor clonogens during a course of protracted radiation therapy may be a cause of local failure in cervical carcinoma. The effect of total treatment time was ...analyzed retrospectively in relation to pelvic control and overall survival for squamous cell carcinomas of the uterine cervix.
Methods and Materials
: Two hundred and nine patients (Stage IB-IIIB) treated with a combination of external beam and low dose rate intracavitary irradiation were evaluable for study. Multivariate analysis and Kaplan-Meier statistical methods were used to determine the effect of treatment time on pelvic control and survival at 5 years.
Results
: The median treatment duration was 55 days. For all stages combined, the 5-year survival and pelvic control rates were significantly different with treatment times < days vs. ≥ 55 days 65 and 54% (
p = 0.03), 87 and 72% (
p = 0.006), respectively. By stage, a shorter treatment duration (i.e., < 55 days vs. ≥ 55 days) was significant for 5-year overall survival and pelvic control for Stages IB/IIA and III, but not for Stage IIB: Stage IB/IIA (81 and 67%, and 84%), Stage III disease (52 and 42%, 76 and 55%) and Stage IIB (43 and 50%, 74 and 80%, respectively). Survival decreased 0.6%/day and pelvic control decreased 0.7%/day for each additional day of treatment beyond 55 days for all stages of disease. Additionally, significantly late complications were not influenced by treatment time.
Conclusion
: These results that prolongation of treatment time is associated with decreased local control and survival in patients with cervical carcinoma. This is consistent with emerging data from other institutions. Therapeutic implications include avoidance of unnecessary treatment breaks, the design of fractionation schemes that decrease treatment duration, and possibly the use of tumor cytostatic drugs during conventional radiation.
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