The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

DNA methylation patterns in hereditary human cancers mimic sporadic tumorigenesis

Cancer cells have aberrant patterns of DNA methylation including hypermethylation of gene promoter CpG islands and global demethylation of the genome. Genes that cause familial cancer, as well as other genes, can be silenced by promoter hypermethylation in sporadic tumors, but the methylation of these genes in tumors from kindreds with inherited cancer syndromes has not been well characterized. Here, we examine CpG island methylation of 10 genes (hMLH1, BRCA1, APC, LKB1, CDH1, p16(INK4a), p14(ARF), MGMT, GSTP1 and RARbeta2) and 5-methylcytosine DNA content, in inherited (n = 342) and non-inherited (n = 215) breast and colorectal cancers. Our results show that singly retained alleles of germline mutated genes are never hypermethylated in inherited tumors. However, this epigenetic change is a frequent second "hit", associated with the wild-type copy of these genes in inherited tumors where both alleles are retained. Global hypomethylation was similar between sporadic and hereditary cases, but distinct differences existed in patterns of methylation at non-familial genes. This study demonstrates that hereditary cancers "mimic" the DNA methylation patterns present in the sporadic tumors.

Beta(1,2)-xylose and alpha(1,3)-fucose residues have a strong contribution in IgE binding to plant glycoallergens

Primary structures of the N-glycans of two major pollen allergens (Lol p 11 and Ole e 1) and a major peanut allergen (Ara h 1) were determined. Ole e 1 and Ara h 1 carried high mannose and complex N-glycans, whereas Lol p 11 carried only the complex. The complex structures all had a beta(1,2)-xylose linked to the core mannose. Substitution of the proximal N-acetylglucosamine with an alpha(1, 3)-fucose was observed on Lol p 11 and a minor fraction of Ole e 1 but not on Ara h 1. To elucidate the structural basis for IgE recognition of plant N-glycans, radioallergosorbent test analysis with protease digests of the three allergens and a panel of glycoproteins with known N-glycan structures was performed. It was demonstrated that both alpha(1,3)-fucose and beta(1,2)-xylose are involved in IgE binding. Surprisingly, xylose-specific IgE antibodies that bound to Lol p 11 and bromelain did not recognize closely related xylose-containing structures on horseradish peroxidase, phytohemeagglutinin, Ole e 1, and Ara h 1. On Lol p 11 and bromelain, the core beta-mannose is substituted with just an alpha(1,6)-mannose. On the other xylose-containing N-glycans, an additional alpha(1,3)-mannose is present. These observations indicate that IgE binding to xylose is sterically hampered by the presence of an alpha(1,3)-antenna.

Aspiration and swallowing in Parkinson disease and rehabilitation with EMST: a randomized trial

OBJECTIVE

Dysphagia is the main cause of aspiration pneumonia and death in Parkinson disease (PD) with no established restorative behavioral treatment to date. Reduced swallow safety may be related to decreased elevation and excursion of the hyolaryngeal complex. Increased submental muscle force generation has been associated with expiratory muscle strength training (EMST) and subsequent increases in hyolaryngeal complex movement provide a strong rationale for its use as a dysphagia treatment. The current study's objective was to test the treatment outcome of a 4-week device-driven EMST program on swallow safety and define the physiologic mechanisms through measures of swallow timing and hyoid displacement.

METHODS

This was a randomized, blinded, sham-controlled EMST trial performed at an academic center. Sixty participants with PD completed EMST, 4 weeks, 5 days per week, for 20 minutes per day, using a calibrated or sham, handheld device. Measures of swallow function including judgments of swallow safety (penetration-aspiration [PA] scale scores), swallow timing, and hyoid movement were made from videofluoroscopic images.

RESULTS

No pretreatment group differences existed. The active treatment (EMST) group demonstrated improved swallow safety compared to the sham group as evidenced by improved PA scores. The EMST group demonstrated improvement of hyolaryngeal function during swallowing, findings not evident for the sham group.

CONCLUSIONS

EMST may be a restorative treatment for dysphagia in those with PD. The mechanism may be explained by improved hyolaryngeal complex movement.

CLASSIFICATION OF EVIDENCE

This intervention study provides Class I evidence that swallow safety as defined by PA score improved post EMST.

Optimism, coping, psychological distress, and high-risk sexual behavior among men at risk for acquired immunodeficiency syndrome (AIDS)

In a cohort of gay men responding to the threat of acquired immunodeficiency syndrome (AIDS), dispositional optimism was associated with less distress, less avoidant coping, positive attitudes as a coping strategy, and fewer AIDS-related concerns. Men who knew they were seropositive for human immunodeficiency virus (HIV) were significantly more optimistic about not developing AIDS than men who knew they were seronegative for HIV. This AIDS-specific optimism was related to higher perceived control over AIDS and to active coping among seropositive men only and to health behaviors in both serostatus groups. There was no relation of optimism to risk-related sexual behavior. It is concluded that optimism is psychologically adaptive without necessarily compromising health behavior. It is also concluded that it is useful to distinguish between event-based optimistic expectations and dispositional optimism.

Homology modeling, model and software evaluation: three related resources

MOTIVATION

Homology modeling is rapidly becoming the method of choice for obtaining three-dimensional coordinates for proteins because genome projects produce sequences at a much higher rate than NMR and X-ray laboratories can solve the three-dimensional structures. The quality of protein models will not be immediately clear to novices and support with the evaluation seems to be needed. Expert users are sometimes interested in evaluating the quality of modeling programs rather than the quality of the models themselves.

RESULTS

Three servers have been made available to the scientific community: a homology modeling server, a model quality evaluation server and a server that evaluates models built of proteins for which the structure is already known, thereby implicitly evaluating the quality of the modeling program.

AVAILABILITY

The modeling-related servers and several structure analysis servers are freely available at http://swift.embl-heidelberg.de/servers/

CONTACT

gert.vriend@embl-heidelberg.de

Association between serum ferritin and measures of inflammation, nutrition and iron in haemodialysis patients

BACKGROUND

Serum ferritin is a frequently used marker of iron status in dialysis patients. Iron administration is to be withheld for ferritin values >800 ng/ml according to K/DOQI guidelines. We hypothesized that such non-iron-related factors as elements of the malnutrition-inflammation complex syndrome (MICS) may increase serum ferritin concentration independently of iron status.

METHODS

We studied 82 prevalent maintenance haemodialysis (MHD) patients (including 43 men), aged 55.7 +/- 15.3 years. The inflammatory and nutritional status was evaluated by serum C-reactive protein (CRP), Subjective Global Assessment (SGA) and its newer, fully quantitative versions, i.e. Dialysis Malnutrition Score (DMS) and Malnutrition-Inflammation Score (MIS).

RESULTS

All but six patients had been on maintenance doses of intravenous iron dextran (between 100 and 200 mg/month) during the 10 weeks prior to the measurements. Serum ferritin levels were increased across SGA categories: (ANOVA P-value 0.03). Both unadjusted and multivariate adjusted correlation coefficients (r) for serum ferritin and CRP vs pertinent values were statistically significant for DMS and MIS and some other measures of nutritional status and iron indices. After deleting 10 MHD patients with either iron deficiency (ferritin <200 ng/ml) or iron overload (ferritin >2000 ng/ml), in the remaining 72 MHD patients both bivariate and multivariate correlations were much stronger and statistically significant (r = -0.33 and -0.29, respectively, P < 0.01). A multivariate model showed simultaneous, significant correlations between serum ferritin and both markers of inflammation and iron status independent of each other. After dividing the 72 MHD patients into two groups of serum ferritin based on a K/DOQI recommended serum ferritin cut-off of 800 ng/ml, the MIS and logarithm of serum CRP were significantly higher in the higher ferritin group.

CONCLUSIONS

Serum ferritin values in the range of 200-2000 ng/ml may be increased due to non-iron-related factors including elements of MICS.

Effects of accidental trauma on cytokine and endotoxin production

OBJECTIVE

To determine the effects of accidental injury of varying severity on interleukin (IL)-1 alpha, IL-6, IL-8, tumor necrosis factor-alpha (TNF-alpha), and endotoxin release.

DESIGN

Prospective, multi-unit, longitudinal study.

SETTING

Emergency Departments and intensive care units of two university hospitals.

PATIENTS

Trauma patients after mild, moderate, and severe injury (Injury Severity Score of < or = 10, 11 to 24, and > or = 25, respectively).

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Plasma cytokine and endotoxin concentrations were measured over a 5-day period, starting within 2 hrs of accidental injury. An enzyme-linked immunosorbent assay was used to determine plasma concentrations of IL-1 alpha, IL-6, IL-8, and TNF-alpha. Plasma endotoxin concentrations were measured using a chromogenic limulus amebocyte assay. Preresuscitation samples obtained immediately on arrival in the Emergency Department, and within 2 hrs of injury, demonstrated significant increases of IL-6 and IL-8 concentrations in the severe injury group, in contrast to minimal increases seen after mild or moderate injury. Analysis of serial postresuscitation samples demonstrated rapid increases in IL-6 and IL-8 concentrations within 12 hrs of injury. IL-6 and IL-8 remained increased for 24 hrs after injury, then decreased markedly from their peak values during the next 24 hrs. Increased circulating concentrations of these cytokines continued to be present for > 5 days in the severely injured patients. IL-6 and IL-8 concentrations were only minimally increased in patients 8 and 24 hrs after moderate injury. Endotoxin and IL-1 alpha were not found in any samples, including those samples obtained serially from severely injured patients. No patient at any time point had TNF-alpha concentrations of > 35 pg/mL.

CONCLUSIONS

These results demonstrate that severe injury produces rapid, large increases in circulating concentrations of IL-6 and IL-8 that may contribute to the frequent development of the adult respiratory distress syndrome and multiple organ system failure in this clinical setting.

The progesterone receptor stimulates cell-free transcription by enhancing the formation of a stable preinitiation complex

Highly purified chicken progesterone receptor (cPR) is shown to stimulate RNA synthesis directly in an in vitro transcription assay. Stimulation of transcription by cPR requires the presence of progesterone response elements (PREs) in the template and can be specifically inhibited by addition of competitor oligonucleotides containing PREs. Binding of receptor to two PREs is cooperative and leads to synergistic (27-fold) stimulation of transcription. A purified fusion protein containing the DNA binding domain of cPR linked to yeast ubiquitin was produced in E. coli and also functions in the transcription assay. Using this in vitro transcription system, we demonstrate that hormone-free cPR activated by salt treatment induces transcription of a test gene in a hormone-independent manner. Finally, we present evidence that the progesterone receptor acts by facilitating the formation of a stable preinitiation complex at the target gene promoter and thus augments the initiation of transcription by RNA polymerase II.

Trajectories of kidney function decline in the 2 years before initiation of long-term dialysis

BACKGROUND

Little is known about patterns of kidney function decline leading up to the initiation of long-term dialysis.

STUDY DESIGN

Retrospective cohort study.

SETTING & PARTICIPANTS

5,606 Veterans Affairs patients who initiated long-term dialysis in 2001-2003.

PREDICTOR

Trajectory of estimated glomerular filtration rate (eGFR) during the 2-year period before initiation of long-term dialysis.

OUTCOMES & MEASUREMENTS

Patient characteristics and care practices before and at the time of dialysis initiation and survival after initiation.

RESULTS

We identified 4 distinct trajectories of eGFR during the 2-year period before dialysis initiation: 62.8% of patients had persistently low level of eGFR < 30 mL/min/1.73 m2 (mean eGFR slope, 7.7 ± 4.7 [SD] mL/min/1.73 m2 per year), 24.6% had progressive loss of eGFR from levels of approximately 30-59 ml/min/1.73 m2 (mean eGFR slope, 16.3 ± 7.6 mL/min/1.73 m2 per year), 9.5% had accelerated loss of eGFR from levels > 60 mL/min/1.73 m2 (mean eGFR slope, 32.3 ± 13.4 mL/min/1.73 m2 per year), and 3.1% experienced catastrophic loss of eGFR from levels > 60 mL/min/1.73 m2 within 6 months or less. Patients with steeper eGFR trajectories were more likely to have been hospitalized and have an inpatient diagnosis of acute kidney injury. They were less likely to have received recommended predialysis care and had a higher risk of death in the first year after dialysis initiation.

CONCLUSIONS

There is substantial heterogeneity in patterns of kidney function loss leading up to the initiation of long-term dialysis perhaps calling for a more flexible approach toward preparing for end-stage renal disease.

Microsurgical anatomy of the superficial veins of the cerebrum

The microsurgical anatomy of the superficial cortical veins was examined in 20 cerebral hemispheres. The superficial cortical veins are divided into three groups based on whether they drain the lateral, medial, or inferior surface of the hemisphere. The veins on the three surfaces are further subdivided on the basis of the lobe and cortical area that they drain. The superficial cerebral veins collect into four groups of bridging veins: a superior sagittal group, which drains into the superior sagittal sinus; a sphenoidal group, which drains into the sphenoparietal and cavernous sinuses on the inner surface of the sphenoid bone; a tentorial group, which converges on the sinuses in the tentorium; and a falcine group, which empties into the inferior sagittal or straight sinus or their tributaries. The superior sagittal group drains the superior part of the medial and lateral surfaces of the frontal, parietal, and occipital lobes and the anterior part of the basal surface of the frontal lobe. The sphenoidal group drains the parts of the frontal, temporal, and parietal lobes adjoining the sylvian fissure. The tentorial group drains the lateral surface of the temporal lobe and the basal surface of the temporal and occipital lobes. The falcine group drains an area that includes the cingulate and parahippocampal gyri and approximates the cortical parts of the limbic lobe of the brain. The relationship of these veins to the venous lacunae was also examined.

Geography matters: relationships among urban residential segregation, dialysis facilities, and patient outcomes

BACKGROUND

End-stage renal disease disproportionately affects black Americans. However, the impact of residential segregation by race-a prominent feature of many U.S. cities--on outcomes of patients receiving dialysis and on facility performance has not been evaluated.

OBJECTIVE

To examine the relationship among racial composition of ZIP codes in metropolitan areas, outcomes of patients receiving dialysis, and characteristics of dialysis facilities.

DESIGN

Retrospective cohort study of patients receiving dialysis and cross-sectional study of dialysis facilities.

SETTING

U.S. metropolitan ZIP codes with differing percentages of black residents.

PATIENTS

Black and non-Hispanic white patients who initiated long-term dialysis between 1 January 1995 and 31 December 2002 (n = 399,424) and dialysis facilities in operation in December 2004 (n = 3244).

MEASUREMENTS

Mortality and time to transplantation among patients receiving dialysis, and performance of dialysis facilities on the basis of quality indicators (anemia management, dialysis adequacy, and facility-level mortality rates).

RESULTS

Most black patients (50.3%) but few white patients (5%) lived in the 3% (n = 769) of ZIP codes in which most residents were black. In analyses adjusted for patient and ZIP code characteristics, mortality rates were higher among white patients but not among black patients living in areas with a higher percentage of black residents (adjusted hazard ratio for ZIP codes with > or =75% black residents vs. <10% black residents, 1.14 [95% CI, 1.07 to 1.21] for white patients and 1.02 [CI, 0.99 to 1.06] for black patients). Time to transplantation was longer among both black and white patients (adjusted hazard ratio for ZIP codes with > or =75% black residents vs. <10% black residents, 0.84 [CI, 0.78 to 0.92] and 0.63 [CI, 0.57 to 0.71] for black patients and white patients, respectively). Dialysis facilities located in areas with a higher percentage of black residents were more likely to have higher-than-expected mortality rates and were less likely to meet performance targets.

LIMITATIONS

Patient-level analyses were restricted to black and non-Hispanic white patients. Patient-level and facility-level analyses focused only on the percentage of black residents in each ZIP code.

CONCLUSIONS

The racial composition of urban residential areas is associated with time to transplantation and dialysis facility performance on standard quality measures. Closer scrutiny of care provided to patients receiving dialysis who live in predominantly black residential areas and to dialysis facilities operating in these areas may be warranted.

Vinorelbine as first-line chemotherapy for metastatic breast carcinoma

PURPOSE

A phase II trial was performed to evaluate the efficacy and toxicity of vinorelbine (VNB) as first-line chemotherapy for metastatic breast carcinoma.

PATIENTS AND METHODS

Between August 1991 and February 1993, 45 patients with metastatic breast cancer were entered onto the study. Therapy consisted of VNB 30 mg/m2 diluted in 500 mL of normal saline administered as a 1-hour intravenous infusion. Injections were repeated weekly until evidence of progressive disease (PD) or severe toxicity developed.

RESULTS

One patient was considered not assessable for response. An objective response (OR) was observed in 18 of 44 patients (41%; 95% confidence interval, 26% to 56%). Three patients (7%) had a complete response (CR) and 15 (34%) had a partial response (PR). The median time to treatment failure for the entire group was 6 months (range, 1 to 15), and the median duration of response was 9 months (range, 1 to 15). The median survival duration has not been reached yet. There were no treatment-related deaths. The dose-limiting toxicity was myelosuppression. Leukopenia occurred in 35 patients (78%) and was grade 3 or 4 in 16 (36%). Phlebitis was observed in 19 of 29 patients (66%) who did not have central implantable venous systems. Fifteen patients (33%) developed peripheral neurotoxicity. Myalgia occurred in 20 patients (44%).

CONCLUSION

VNB is an active drug against metastatic breast cancer with moderate toxicity, which justifies further evaluation in association with other agents.

Association of hepatitis C seropositivity with increased risk for developing end-stage renal disease

BACKGROUND

Infection with chronic hepatitis C virus (HCV) has been linked to glomerulonephritis. We undertook this study to determine whether having a positive HCV test result was associated with an increased risk for developing treated end-stage renal disease (ESRD).

METHODS

Using data from Medicare, the Department of Veterans Affairs, and the United States Renal Data System, we performed a retrospective cohort study of 474,369 adult veterans who had serum creatinine levels measured between October 1, 2000, and September 30, 2001, and HCV antibody testing within 1 year of creatinine testing. Patients were followed up until October 1, 2004, for the outcome of treated ESRD, defined as the onset of chronic dialysis or renal transplantation. Cox proportional hazards models were used to determine the relative hazard for ESRD associated with HCV, adjusted for other covariates (age, sex, race/ethnicity, and comorbidities).

RESULTS

Of 474,369 patients in the cohort, 52,874 (11.1%) had a positive HCV antibody test result. Patients with HCV were more likely to develop ESRD: the rate per 1000 person-years was 4.26 (95% confidence interval, 3.97-4.57) for HCV-seropositive patients vs 3.05 (95% confidence interval, 2.96-3.14) for HCV-seronegative patients. For patients aged 18 to 70 years with an estimated glomerular filtration rate of at least 30 mL/min per 1.73 m2, HCV seropositivity was associated with a greater than 2-fold risk for developing ESRD (adjusted hazard rate, 2.80; 95% confidence interval, 2.43-3.23).

CONCLUSION

In this large national cohort of adult veterans, patients younger than 70 years with HCV seropositivity were at increased risk for developing ESRD treated with dialysis or transplantation.

Auditory system degeneration in Alzheimer's disease

We observed a highly topographically specific and consistent pattern of degeneration in the auditory system of Alzheimer's disease (AD) patients. Senile plaques (SP) and neurofibrillary tangles (NFT) were distributed throughout the ventral nucleus of the medial geniculate body (MGB) and the central nucleus of the inferior colliculus (IC) in nine of nine AD patients. Adjacent nuclei within the MGB and IC were consistently spared. NFT and SP were also present in the primary auditory and the auditory association cortices. In all control tissues, there were neither SP nor NFT in any of the above sites. The cochlear nuclei were normal in tissues from both AD and control patients. The ventral nucleus of the MGB is the major thalamic relay station for auditory function and receives fibers from neurons of the central nucleus of the IC, with projections arranged tonotopically in a laminar pattern corresponding to a gradient of high-to-low frequency ranges. The degenerative changes distributed throughout these nuclei suggest that neuronal loss may include all frequency ranges in AD. In contrast, the clinical features of presbycusis in elderly patients include only high-frequency loss due to lesions peripherally in the cochlea or auditory nerves, rather than in the central auditory nuclei. These histologic changes in the brains of AD patients may provide an additional basis for altered cognitive function due to primary sensory deafferentation.

MR urography using HASTE imaging in the assessment of ureteric obstruction

OBJECTIVE

The purpose of this study was to evaluate an MR sequence using half-Fourier acquisition single-shot turbo spin-echo (HASTE) imaging in the assessment of ureteric obstruction.

SUBJECTS AND METHODS

We prospectively evaluated 111 kidneys in 56 consecutive patients with HASTE MR urography and compared that imaging technique with excretory urography. The HASTE sequence was used to acquire images in the axial, sagittal, and coronal planes while patients held their breath. Level of obstruction and ureteric diameter were assessed, and the time required to determine the level of obstruction by both techniques was noted.

RESULTS

With HASTE MR urography, we correctly diagnosed obstruction in 41 (100%) of 41 kidneys. Of the obstructed kidneys in which the ureter was shown by both excretory urography and MR urography, agreement was high (kappa = .642) between the two imaging techniques regarding the level of obstruction. HASTE MR urography showed perirenal fluid in 20 (87%) of 23 acutely obstructed kidneys. HASTE MR urography showed the site of obstruction on the first 13-sec scan in 33 (80%) of 41 kidneys.

CONCLUSION

HASTE MR urography accurately and rapidly shows the level and degree of ureteric obstruction. It can be used to differentiate between acute and chronic obstruction on the basis of its ability to show perirenal fluid.

Detection of epithelial tumour RNA in the plasma of colon cancer patients is associated with advanced stages and circulating tumour cells

BACKGROUND

Although circulating tumour DNA has been detected in patients with different types of cancer, little is known of free RNA in cancer patients.

AIMS

We investigated the presence of RNA from epithelial tumours in plasma from patients with colorectal carcinomas, and its correlation with tumour characteristics and circulating tumour cells.

METHODS

beta-actin mRNA was analysed to assess the viability of plasma RNA in samples from 53 patients with colonic cancer and 25 controls. Subsequently, nested primers were used to detect the presence of cytokeratin 19 (CK19) and carcinoembryonic antigen (CEA) RNA in the same samples. Nine clinicopathological parameters were studied to correlate the molecular and clinical parameters. Additionally, we investigated for micrometastases in blood in 18 of these patients and in 10 of the controls samples.

RESULTS

All samples had detectable quantities of beta-actin RNA. In the controls, one case (4%) was positive for CEA and five (20%) for CK19 RNA; of the 53 patients, 17 cases (32%) were positive for CEA and 39 (73.6%) for CK19 RNA. This was statistically significant (p=0.000001). Advanced stages (p=0.03) and soluble CEA status (p=0.03) were associated with the presence of CEA, CK19, or both RNAs in plasma. Lymph node metastases (p=0.06) and vascular invasion (p=0.07) were almost significant. On the basis of these results, we examined the possible presence of micrometastases in blood in several of these patients. The presence of plasma tumour RNA was found to be associated with circulating tumour cells in blood (p=0.04).

CONCLUSIONS

Epithelial tumour RNA is detectable in plasma from colon cancer patients. This molecular event is associated with advanced stages and circulating tumour cells. Our results could offer new approaches in the diagnosis and monitoring of colon cancer.

Mesenchymal stem cells and their use as cell replacement therapy and disease modelling tool

Mesenchymal stem cells (MSCs) from adult somatic tissues may differentiate in vitro and in vivo into multiple mesodermal tissues including bone, cartilage, adipose tissue, tendon, ligament or even muscle. MSCs preferentially home to damaged tissues where they exert their therapeutic potential. A striking feature of the MSCs is their low inherent immunogenicity as they induce little, if any, proliferation of allogeneic lymphocytes and antigen-presenting cells. Instead, MSCs appear to be immunosuppressive in vitro. Their multi-lineage differentiation potential coupled to their immuno-privileged properties is being exploited worldwide for both autologous and allo-geneic cell replacement strategies. Here, we introduce the readers to the biology of MSCs and the mechanisms underlying immune tolerance. We then outline potential cell replacement strategies and clinical applications based on the MSCs immunological properties. Ongoing clinical trials for graft-versus-host-disease, haematopoietic recovery after co-transplantation of MSCs along with haematopoietic stem cells and tissue repair are discussed. Finally, we review the emerging area based on the use of MSCs as a target cell subset for either spontaneous or induced neoplastic transformation and, for modelling non-haematological mesenchymal cancers such as sarcomas.

Severe community-acquired pneumonia in the elderly: epidemiology and prognosis. Study Group for Severe Community-Acquired Pneumonia

Ninety-five patients with severe community-acquired pneumonia (SCAP) who were > or = 65 years of age were studied prospectively. A definite pathogen was identified in 37 cases (38.9%) and was most commonly Streptococcus pneumoniae, Haemophilus influenzae, or another gram-negative bacillus. The overall death rate was 40%. Eighty-three patients required mechanical ventilation and 40 needed vasoactive drugs. Multivariate analysis showed that the risk of death was higher in cases involving rapid radiological spread (relative risk [RR] = 6.99; 95% confidence interval (95% CI) = 1.54-31.70), shock (RR = 6.70; 95% CI = 2.13-21.02), previous steroid treatment or immunosuppression (RR = 5.50; 95% CI = 0.77-39.10), acute renal failure (RR = 3.88; 95% CI = 1.30-11.59), or an APACHE II score of > 22 on admission (RR = 2.25; 95% CI = 0.73-6.95). We conclude that SCAP in elderly patients is associated with high mortality, but it is inappropriate to withhold intensive care on account of age. The presence of complications and the severity of illness at initial presentation were the major variables affecting outcome. Except for immunosuppression, comorbidities did not seem to influence outcome. Finally, our data reinforce the current American Thoracic Society guidelines concerning therapy for patients with SCAP.

Diversity of soil yeasts isolated from South Victoria Land, Antarctica

Unicellular fungi, commonly referred to as yeasts, were found to be components of the culturable soil fungal population in Taylor Valley, Mt. Discovery, Wright Valley, and two mountain peaks of South Victoria Land, Antarctica. Samples were taken from sites spanning a diversity of soil habitats that were not directly associated with vertebrate activity. A large proportion of yeasts isolated in this study were basidiomycetous species (89%), of which 43% may represent undescribed species, demonstrating that culturable yeasts remain incompletely described in these polar desert soils. Cryptococcus species represented the most often isolated genus (33%) followed by Leucosporidium (22%). Principle component analysis and multiple linear regression using stepwise selection was used to model the relation between abiotic variables (principle component 1 and principle component 2 scores) and yeast biodiversity (the number of species present at a given site). These analyses identified soil pH and electrical conductivity as significant predictors of yeast biodiversity. Species-specific PCR primers were designed to rapidly discriminate among the Dioszegia and Leucosporidium species collected in this study.

Participation of thromboxane and other eicosanoid synthesis in the course of experimental inflammatory colitis

Eicosanoids, as modulators of inflammation, may be involved in the pathogenesis of inflammatory bowel disease. We investigated their potential role in a rat model of chronic granulomatous colonic inflammation induced by trinitrobenzene sulphonic acid. Luminal eicosanoid release was quantified in vivo using a dialysis bag placed into the distal colon. We tested the effect of drugs known to modify inflammatory activity or arachidonic acid metabolism. Three days after intracolonic injection of trinitrobenzene sulphonic acid at different dose levels, the dialysates showed a highly significant increase of prostaglandin E2, 6-keto-prostaglandin F1 alpha, thromboxane B2 (TXB2), and leukotriene B4, compared with levels in controls not subjected to the toxic agent. Remarkably, the release of TXB2 continued to increase during the stage of chronic inflammation (up to day 21), whereas the levels of the remainder eicosanoids declined. Treatment with prednisone or 5-aminosalicylic acid reduced TXB2 levels in the chronic stage of the inflammatory disease and improved the morphological damage as assessed macroscopically and histologically. Moreover, two selective thromboxane synthetase inhibitors, OKY 1581 and R70416, significantly reduced the development of chronic inflammatory lesions in the colon while inhibiting the release of TXB2. Our results indicate that (1) luminal release of thromboxane increases in the chronic stage of colonic inflammation, (2) anti-inflammatory treatment reduces tissue damage and thromboxane release, and (3) selective thromboxane synthetase inhibition improves the course of the disease in our experimental model.

When to refer patients with chronic kidney disease for vascular access surgery: Should age be a consideration?

To determine whether age should inform our approach toward permanent vascular access placement in patients with chronic kidney disease, we conducted a retrospective cohort study among 11 290 non-dialysis patients with an estimated glomerular filtration rate (eGFR) <25 ml/min/1.73 m(2) based on 2000-2001 outpatient creatinine measurements in the Department of Veterans Affairs. For each age group, we examined the percentage of patients that had and had not received a permanent access by 1 year after cohort entry, and the percentage in each of these groups that died, started dialysis, or survived without dialysis. We also modeled the number of unnecessary procedures that would have occurred in theoretical scenarios based on existing vascular access guidelines. The mean eGFR was 17.7 ml/min/1.73 m(2) at cohort entry. Twenty-five percent (n=2870) of patients initiated dialysis within a year of cohort entry. Among these, only 39% (n=1104) had undergone surgery to place a permanent access beforehand. As compared with younger patients, older patients were less likely to undergo permanent access surgery, but also less likely to start dialysis. In all theoretical scenarios examined, older patients would have been more likely than younger patients to receive unnecessary procedures. If all patients had been referred for permanent access surgery at cohort entry, the ratio of unnecessary to necessary procedures after 2 years of follow-up would have been 5:1 for patients aged 85-100 years but only 0.5:1 for those aged 18-44 years. Currently recommended approaches to permanent access placement based on a single threshold level of renal function for patients of all ages are not appropriate.