The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

Background

Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers.

Results

A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats.

Conclusion

The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data.

The gel test: a new way to detect red cell antigen-antibody reactions

A new process for the detection of red cell (RBC) antigen antibody reactions is described. It is applicable to most of the tests performed in blood group serology. The procedures are standardized and easy, and they provide clear and stable reactions that improve the interpretation of results. The process uses special microtubes filled with a mixture of gel, buffer, and reagent. Depending on the test to be carried out, the test uses a neutral gel containing no reagents (reagents are added to top of gel) or a specific gel containing reagents (e.g., antiglobulin serum or anti-A, -B, -D, etc.). A suspension of RBCs (for typing or the direct antiglobulin test) or a mixture of RBCs and serum (for reverse ABO typing or antibody characterization) is centrifuged through the gel under precise conditions. In negative reactions, the RBCs pass through the gel and pellet in the bottom of the tube, whereas, in positive reactions, they are trapped in the gel and the reaction may be read for hours afterwards. The test is easy to perform, sensitive, and reproducible. The antiglobulin tests can be performed without washing of the RBCs. There should be a reduction of risk from biohazardous materials.

Insulin-like growth factors, their binding proteins, and prostate cancer risk: analysis of individual patient data from 12 prospective studies

BACKGROUND

Some, but not all, published results have shown an association between circulating blood levels of some insulin-like growth factors (IGFs) and their binding proteins (IGFBPs) and the subsequent risk for prostate cancer.

PURPOSE

To assess the association between levels of IGFs and IGFBPs and the subsequent risk for prostate cancer.

DATA SOURCES

Studies identified in PubMed, Web of Science, and CancerLit.

STUDY SELECTION

The principal investigators of all studies that published data on circulating concentrations of sex steroids, IGFs, or IGFBPs and prostate cancer risk using prospectively collected blood samples were invited to collaborate.

DATA EXTRACTION

Investigators provided individual participant data on circulating concentrations of IGF-I, IGF-II, IGFBP-II, and IGFBP-III and participant characteristics to a central data set in Oxford, United Kingdom.

DATA SYNTHESIS

The study included data on 3700 men with prostate cancer and 5200 control participants. On average, case patients were 61.5 years of age at blood collection and received a diagnosis of prostate cancer 5 years after blood collection. The greater the serum IGF-I concentration, the greater the subsequent risk for prostate cancer (odds ratio [OR] in the highest vs. lowest quintile, 1.38 [95% CI, 1.19 to 1.60]; P < 0.001 for trend). Neither IGF-II nor IGFBP-II concentrations were associated with prostate cancer risk, but statistical power was limited. Insulin-like growth factor I and IGFBP-III were correlated (r = 0.58), and although IGFBP-III concentration seemed to be associated with prostate cancer risk, this was secondary to its association with IGF-I levels. Insulin-like growth factor I concentrations seemed to be more positively associated with low-grade than high-grade disease; otherwise, the association between IGFs and IGFBPs and prostate cancer risk had no statistically significant heterogeneity related to stage or grade of disease, time between blood collection and diagnosis, age and year of diagnosis, prostate-specific antigen level at recruitment, body mass index, smoking, or alcohol intake.

LIMITATIONS

Insulin-like growth factor concentrations were measured in only 1 sample for each participant, and the laboratory methods to measure IGFs differed in each study. Not all patients had disease stage or grade information, and the diagnosis of prostate cancer may differ among the studies.

CONCLUSION

High circulating IGF-I concentrations are associated with a moderately increased risk for prostate cancer.

Multiple and time-scheduled in situ DNA delivery mediated by beta-cyclodextrin embedded in a polyelectrolyte multilayer

The basic premise of gene therapy is that genes can be used to produce in situ therapeutic proteins. The controlled delivery of DNA complexes from biomaterials offers the potential to enhance gene transfer by maintaining an elevated concentration of DNA within the cellular microenvironment. Immobilization of the DNA to the substrate to which cells adhere maintains the DNA in the cell microenvironment for subsequent cellular internalization. Here, layer-by-layer (LBL) films made from poly(L-glutamic acid) (PLGA) and poly(L-lysine) (PLL) containing DNA were built in the presence of charged cyclodextrins. The biological activities of these polyelectrolyte films were tested by means of induced production of a specific protein in the nucleus or in the cytoplasm by cells in contact with the films. This type of coating offers the possibility for either simultaneous or sequential interfacial delivery of different DNA molecules aimed at cell transfection. These results open the route to numerous potential applications in patch vaccination, for example.

Unusual splice sites revealed by mutagenic inactivation of an authentic splice site of the rabbit beta-globin gene

Only one of six point mutations of the sequence around one end of the larger of the introns of the rabbit beta-globin gene seriously affects the normal removal of the intron and splicing of the gene. That mutation converts a GT sequence, invariably found at the 5' end of introns, into an AT, which is no longer recognized as a signal for intron removal. Instead, three normally unused (cryptic) sites are used, leading to aberrant gene transcripts. One of the cryptic sites is an exception to the invariable GT sequence.

Rose: generating sequence families

MOTIVATION

We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs.

RESULTS

The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes.

AVAILABILITY

Rose is available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available upon request.

CONTACT

folker@TechFak.Uni-Bielefeld.DE

Randomized trial of antioxidant vitamins to prevent acute adverse effects of radiation therapy in head and neck cancer patients

PURPOSE

Many cancer patients take antioxidant vitamin supplements with the hope of improving the outcome of conventional therapies and of reducing the adverse effects of these treatments. A randomized trial was conducted to determine whether supplementation with antioxidant vitamins could reduce the occurrence and severity of acute adverse effects of radiation therapy and improve quality of life without compromising treatment efficacy.

PATIENTS AND METHODS

We conducted a randomized, double-blind, placebo-controlled trial among 540 head and neck cancer patients treated with radiation therapy. Patients were randomly assigned into two arms. The supplementation with alpha-tocopherol (400 IU/d) and beta-carotene (30 mg/d) or placebos was administered during radiation therapy and for 3 years thereafter. During the course of the trial, supplementation with beta-carotene was discontinued because of ethical concerns.

RESULTS

Patients randomly assigned in the supplement arm tended to have less severe acute adverse effects during radiation therapy (odds ratio [OR], 0.72; 95% CI, 0.52 to 1.02). The reduction was statistically significant when the supplementation combined alpha-tocopherol and beta-carotene for adverse effects to the larynx (OR, 0.38; 95% CI, 0.21 to 0.71) and overall at any site (OR, 0.38; 95% CI, 0.20 to 0.74). Quality of life was not improved by the supplementation. The rate of local recurrence of the head and neck tumor tended to be higher in the supplement arm of the trial (hazard ratio, 1.37; 95% CI, 0.93 to 2.02).

CONCLUSION

Supplementation with high doses of alpha-tocopherol and beta-carotene during radiation therapy could reduce the severity of treatment adverse effects. However, this trial suggests that use of high doses of antioxidants as adjuvant therapy might compromise radiation treatment efficacy.

Cleansing without compromise: the impact of cleansers on the skin barrier and the technology of mild cleansing

Cleanser technology has come a long way from merely cleansing to providing mildness and moisturizing benefits as well. It is known that harsh surfactants in cleansers can cause damage to skin proteins and lipids, leading to after-wash tightness, dryness, barrier damage, irritation, and even itch. In order for cleansers to provide skin-care benefits, they first must minimize surfactant damage to skin proteins and lipids. Secondly, they must deposit and deliver beneficial agents such as occlusives, skin lipids, and humectants under wash conditions to improve skin hydration, as well as mechanical and visual properties. While all surfactants tend to interact to some degree with lipids, their interaction with proteins can vary significantly, depending upon the nature of their functional head group. In vitro, ex vivo, and in vivo studies have shown that surfactants that cause significant skin irritation interact strongly with skin proteins. Based on this understanding, several surfactants and surfactant mixtures have been identified as "less irritating" mild surfactants because of their diminished interactions with skin proteins. Surfactants that interact minimally with both skin lipids and proteins are especially mild. Another factor that can aggravate surfactant-induced dryness and irritation is the pH of the cleanser. The present authors' recent studies demonstrate that high pH (pH 10) solutions, even in the absence of surfactants, can increase stratum corneum (SC) swelling and alter lipid rigidity, thereby suggesting that cleansers with neutral or acidic pH, close to SC-normal pH 5.5, may be potentially less damaging to the skin. Mildness enhancers and moisturizing agents such as lipids, occlusives, and humectants minimize damaging interactions between surfactants, and skin proteins and lipids, and thereby, reduce skin damage. In addition, these agents play an ameliorative role, replenishing the skin lipids lost during the wash period. The present review discusses the benefits of such agents and their respective roles in improving the overall health of the skin barrier.

A Randomized Trial of Antioxidant Vitamins to Prevent Second Primary Cancers in Head and Neck Cancer Patients

BACKGROUND

Although low dietary intakes of antioxidant vitamins and minerals have been associated with higher risks of cancer, results of trials testing antioxidant supplementation for cancer chemoprevention have been equivocal. We assessed whether supplementation with antioxidant vitamins could reduce the incidence of second primary cancers among patients with head and neck cancer.

METHODS

We conducted a multicenter, double-blind, placebo-controlled, randomized chemoprevention trial among 540 patients with stage I or II head and neck cancer treated by radiation therapy between October 1, 1994, and June 6, 2000. Supplementation with alpha-tocopherol (400 IU/day) and beta-carotene (30 mg/day) or placebo began on the first day of radiation therapy and continued for 3 years after the end of radiation therapy. In the course of the trial, beta-carotene supplementation was discontinued after 156 patients had enrolled because of ethical concerns. The remaining patients received alpha-tocopherol or placebo only. Survival was evaluated by Kaplan-Meier analysis. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). All statistical tests were two-sided.

RESULTS

After a median follow-up of 52 months, second primary cancers and recurrences of the first tumor were diagnosed in 113 and 119 participants, respectively. The effect of supplementation on the incidence of second primary cancers varied over time. Compared with patients receiving placebo, patients receiving alpha-tocopherol supplements had a higher rate of second primary cancers during the supplementation period (HR = 2.88, 95% CI = 1.56 to 5.31) but a lower rate after supplementation was discontinued (HR = 0.41, 95% CI = 0.16 to 1.03). Similarly, the rate of having a recurrence or second primary cancer was higher during (HR = 1.86, 95% CI = 1.27 to 2.72) but lower after (HR = 0.71, 95% CI = 0.33 to 1.53) supplementation with alpha-tocopherol. The proportion of participants free of second primary cancer overall after 8 years of follow-up was similar in both arms.

CONCLUSIONS

alpha-Tocopherol supplementation produced unexpected adverse effects on the occurrence of second primary cancers and on cancer-free survival.

Impact of anastomotic leakage on oncological outcome after rectal cancer resection

BACKGROUND

: Anastomotic leakage has a major impact on morbidity and mortality in rectal cancer surgery. Its relevance to oncological outcome is controversial. This observational study investigated the influence of anastomotic leakage on oncological outcome.

METHODS

: Data for 1741 patients undergoing curative resection of rectal cancer (located less than 12 cm from the anal verge) with normal healing were compared with those for 303 patients who experienced anastomotic leakage. Morbidity, mortality and long-term oncological outcomes were analysed.

RESULTS

: Median follow-up was 40 months. Patients with anastomotic leakage had a higher postoperative mortality rate than those with no leakage (4.3 versus 1.2 per cent; P < 0.001). Patients with leakage necessitating surgical treatment had a higher 5-year local recurrence rate (17.5 versus 10.1 per cent; P = 0.006) and a lower 5-year disease-free survival rate (70.9 versus 75.4 per cent; P = 0.020) than those without leakage. Patients with anastomotic leakage not requiring surgical intervention did not have a worse oncological outcome.

CONCLUSION

: A negative prognostic impact of anastomotic leakage on local recurrence and disease-free survival was found only for patients with leakage needing surgical revision.

Different pathways mediate virus inducibility of the human IFN-alpha 1 and IFN-beta genes

Multimerization of GAAANN generates sequences frequent in virus-inducible promoters. We distinguished different types of (GAAANN)4 sequences mediating virus inducibility. Type I (NN = GT, GC, CT, or CC) responds to IFNs and to IRF-1 and causes silencing. Type II (NN = TG) and type III (NN = CG) neither silence nor respond to IRF-1 or IFN. Type III mediates constitutive transcription and binds the constitutive IEFga factor, whereas type II binds the novel "TG protein". IFN-beta and IFN-alpha 1 promoters contain different response elements: The former has a type I-like sequence (PRDI) and an NF-kappa B-binding sequence (PRDII); the latter has a type II-like "TG sequence" and possibly additional elements but does not bind NF-kappa B. Type I, type II, and NF-kappa B elements represent three distinct terminal pathways mediating virus induction.

Treatment of biliary obstruction in selected patients by endoscopic ultrasonography (EUS)-guided transluminal biliary drainage

BACKGROUND AND STUDY AIMS

Endoscopic retrograde cholangiopancreatography (ERCP)-guided implantation of a biliary endoprosthesis or stent is the gold standard treatment for biliary obstructions. When the papilla cannot be traversed because there is pyloric or duodenal stenosis, or the catheter cannot be introduced, or because of previous gastrointestinal surgery (Billroth II gastric resection, Whipple procedure, gastrectomy with Roux-en-Y reconstruction), the alternative treatment is considered to be percutaneous transhepatic cholangiography and drainage (PTCD). The aim of the study was to investigate the further alternative of endoscopic ultrasound (EUS)-guided transgastric or transjejunal biliary drainage where PTCD failed or was declined, and particularly, the feasibility and outcome of this option.

PATIENTS AND METHODS

Over 3 years all appropriate consecutive patients (as defined above) were enrolled in this prospective, observational, single-center, case series study, and patient and intervention data were recorded. Feasibility was characterized by success rate (regression of cholestasis), and outcomes by complication rate, mortality, and follow-up findings.

RESULTS

Between November 2002 and December 2005, eight patients (in 10 interventions) underwent this new biliary drainage procedure. The routes were transesophageal (n = 1), transgastric (n = 4), and transjejunal (n = 3, including a rendezvous technique with ERCP [n = 1]). The indications were cholestasis, arising from recurrent tumor growth (n = 5, 62.5%), that included gastric carcinoma after previous gastrectomy (n = 4) and a periampullary carcinoma after previous Whipple procedure (n = 1); arising from Klatskin tumor (n = 2, 25%); and from benign stenosis of a hepaticojejunostomy (n = 1, 12.5%). Five patients (62.5%) received a metal stent, and three (37.5%) had a plastic prosthesis (8.5-Fr double-pigtail). The technical success rate was 90% (9/10) and the clinical success rate was 88.9% (8/9). There was only one case of cholangitis (12.5%) and slight postinterventional pain, but no severe complications such as bleeding or perforation, and no mortality. During follow-up (range 4 weeks to 3 years) re-interventions were needed in two patients (20%) because of increasing cholestasis; these resulted in technical success and clinical improvement.

CONCLUSION

EUS-guided transgastric or transjejunal biliary drainage is a reasonable, feasible and encouraging treatment option in selected patients as indicated, with a low peri-interventional risk. It broadens the therapeutic spectrum but still needs further evaluation and follow-up investigation.

Immunomodulation by perioperative administration of n-3 fatty acids

It has been increasingly reported that administration of n-3 fatty acids is beneficial in patients with inflammatory processes. This effect is most likely caused by different biological characteristics, including an immunomodulating effect of the products derived from n-3 fatty acids through eicosanoid metabolism. The aim of this study was to investigate the effect of perioperative administration of n-3 fatty acids on inflammatory and immune responses as well as on the postoperative course of patients with extended surgical interventions of the abdomen. In particular, the effect of n-3 fatty acids on interleukin-6 release and on granulocyte/monocyte function (HLA-DR expression) was studied. There was a downregulation of the inflammatory response, and, simultaneously, a smaller postoperative immune suppression in the n-3 fatty acid group. In addition, we observed shorter postoperative periods in the intensive care unit and on the regular medical wards as well as lower rates of severe infections. The results suggest that perioperative administration of n-3 fatty acids may have a favourable effect on outcome in patients with severe surgical interventions by lowering the magnitude of inflammatory response and by modulating the immune response.

Antihypertensive drug use and the risk of prostate cancer (Canada)

PURPOSE

To verify if exposure to antihypertensive drugs was associated to prostate cancer (PC) risk.

METHODS

We conducted a matched case-control study using record linkage between two population-based databases. We defined exposure as a binary variable and in terms of timing and cumulative duration of use. We controlled for detection bias and Aspirin use.

RESULTS

Among the 2221 cases and 11,105 controls, use of any antihypertensive agent was associated with an adjusted relative risk of PC of 0.98 (CI, 0.88-1.08). Of the different classes of antihypertensives, only beta-blockers (BBs) were associated with a reduction in PC risk (OR = 0.86, CI = 0.77-0.96). In those who cumulated < 1, 1-4, and > or = 4 years of BB use, the risk was 0.89 (0.75-1.05), 0.91 (0.75-1.09), and 0.82 (0.69-0.96), respectively. Also, subjects with > or = 4 years of alpha-blocker (ABs) use had a non-significant 25% reduction in PC risk.

CONCLUSIONS

Our results suggest that BBs and long-term use of ABs may prevent PC whereas calcium channel blockers or angiotensin-converting enzyme inhibitors do not influence PC risk.

Antioxidant vitamins supplementation and mortality: a randomized trial in head and neck cancer patients

There has been concern that long-term supplementation with high-dose antioxidant vitamins, especially vitamin E (alpha-tocopherol), may increase all-cause mortality. We conducted a randomized controlled trial with alpha-tocopherol (400 IU/day) and beta-carotene (30 mg/day) supplements among 540 head and neck cancer patients treated by radiation therapy. Supplementation with beta-carotene was discontinued during the trial. The supplements were given during radiation therapy and for 3 additional years. During the follow-up (median 6.5 years), 179 deaths were recorded. All death certificates were obtained. All-cause and cause-specific mortality rates were compared between the 2 arms of the trial by Cox regression. All-cause mortality was significantly increased in the supplement arm: hazard ratio: 1.38, 95% confidence interval 1.03-1.85. Cause-specific mortality rates tended to be higher in the supplement arm than in the placebo arm. Our results concur with previous reports to suggest that high-dose vitamin E could be harmful.

Combination chemotherapy with docetaxel and cisplatin for locally advanced and metastatic gastric cancer

BACKGROUND

Poor treatment results obtained with palliative chemotherapy for advanced gastric cancer indicate the need for new effective and well-tolerated regimens.

PATIENTS AND METHODS

Forty-three patients with locally advanced or metastatic gastric cancer were enrolled in a phase II study to evaluate the efficacy and safety of combination chemotherapy with doxetacel 75 mg/m2 and cisplatin 75 mg/m2 given every three weeks.

RESULTS

Thirty-nine patients were evaluable for response. Four achieved a complete response and twelve a partial response, for an overall response rate of 37.2% (16 of 43 patients; 95% confidence interval (CI): 22.98-53.72). Median time to progression was 6.1 months and median overall survival 10.4 months. Forty-two percent of all patients were still alive at one year and twelve percent at two years. The major toxicity was leukopenia which reached grade 3-4 in 18.6% (n = 8) of the patients. However, no febrile neutropenia occurred. Non-haematological toxicities were usually mild to moderate. Grade 3 toxicities included diarrhea (9% of the patients), nausea and vomiting (7%), and alopecia (7%). Severe ototoxicity with or without peripheral neuropathy developed after completion of chemotherapy in two patients.

CONCLUSIONS

These results suggest that the combination of docetaxel and cisplatin has moderate toxicity and is an effective regimen for the treatment of advanced gastric cancer, both with regard to response rate and survival.

Diet, mammographic features of breast tissue, and breast cancer risk

This case-control study was designed to reevaluate the association of the morphology of breast tissue seen on mammograms with breast cancer risk and to assess the relation of diet, especially intake of fat and vitamin A, to the high-risk mammographic images. The cases included 290 patients with newly diagnosed breast cancer who were first treated in Quebec in 1982-1984. The controls included 645 women who participated in the Canadian National Breast Screening Study. Risk of breast cancer was higher among women with the P2 or DY parenchymal pattern (relative risk (RR) = 3.7, 95% confidence interval (Cl) 2.0-7.0) than it was among those with the N1 pattern. Moreover, risk increased regularly with the extent of nodular and homogeneous densities on the mammogram. Relative risk was 5.5 (95% Cl 2.3-13.2) for women in whom 60% or more of the volume of the breast showed either nodular or homogeneous densities compared with women without such densities. Among controls, increase in energy-adjusted saturated fat intake was associated with an increase in extent of high-risk mammographic features. Energy-adjusted polyunsaturated fat or cholesterol intake did not, however, appear to influence the morphology of breast tissue seen on the mammogram. Increasing carotenoid and fiber intakes were associated with a reduction of the extent of densities on the mammogram, but retinol intake seemed to have little or no effect on mammographic features. These data suggest that elevation in saturated fat intake and reduction in carotenoid and fiber intakes may be related to an increase in breast cancer risk through effects of these nutrients on breast tissue morphology.

Antioxidant vitamin and mineral supplementation and prostate cancer prevention in the SU.VI.MAX trial

Randomized trials have shown, unexpectedly, that supplementation with selenium or vitamin E is associated with a reduction of prostate cancer risk. We assess whether a supplementation with low doses of antioxidant vitamins and minerals could reduce the occurrence of prostate cancer and influence biochemical markers. The SU.VI.MAX trial comprised 5,141 men randomized to take either a placebo or a supplementation with nutritional doses of vitamin C, vitamin E, beta-carotene, selenium and zinc daily for 8 years. Biochemical markers of prostate cancer risk such as prostate-specific antigen (PSA) and insulin-like growth factors (IGFs) were measured on plasma samples collected at enrollment and at the end of follow-up from 3,616 men. Cox regression models were used to estimate the hazard ratio and related 95% confidence interval of prostate cancer associated with the supplementation and to examine whether the effect differed among predetermined susceptible subgroups. During the follow-up, 103 cases of prostate cancer were diagnosed. Overall, there was a moderate nonsignificant reduction in prostate cancer rate associated with the supplementation (hazard ratio = 0.88; 95% CI = 0.60-1.29). However, the effect differed significantly between men with normal baseline PSA (< 3 microg/L) and those with elevated PSA (p = 0.009). Among men with normal PSA, there was a marked statistically significant reduction in the rate of prostate cancer for men receiving the supplements (hazard ratio = 0.52; 95% CI = 0.29-0.92). In men with elevated PSA at baseline, the supplementation was associated with an increased incidence of prostate cancer of borderline statistical significance (hazard ratio = 1.54; 95% CI = 0.87-2.72). The supplementation had no effect on PSA or IGF levels. Our findings support the hypothesis that chemoprevention of prostate cancer can be achieved with nutritional doses of antioxidant vitamins and minerals.

UGA is translated as cysteine in pheromone 3 of Euplotes octocarinatus

Pheromone 3 mRNA of the ciliate Euplotes octocarinatus contains three in-frame UGA codons that are translated as cysteines. This was revealed from cDNA sequencing and from plasma desorption mass spectrometry of cleaved pheromone 3 in connection with pyridylethylation of the fragments. N-terminal sequence analysis of carboxymethylated protein confirmed this conclusion for the first of the three UGA codons. Besides UGA the common cysteine codons UGU and UGC are also used to encode cysteine. UAA functions as a termination codon. No UAG codon was found. In connection with results reported for other ciliates, this suggests that the role of the classic termination codons had not yet been established when the ciliates started to diverge from other eukaryotes.

Iterative image transformations for an automatic screening of cervical smears

The new generation of image analysis systems permits the use of iterative image transformations. It is now possible to construct algorithms where the elementary steps are not arithmetic operations but image transformations. This will be illustrated by two examples. In the first, the absorption image of Feulgen Stained nuclei is processed by contrast algorithms in order to detect suspect cells. In the second, free lying cells are separated from overlapping cells and other artefacts by the use of skeletonization procedures.

Double-blind, randomized, controlled trial of fish oil supplements in prevention of recurrence of stenosis after coronary angioplasty

BACKGROUND

Previous studies suggest that recurrence of coronary stenosis after percutaneous transluminal coronary angioplasty (PTCA) might be prevented with dietary supplements rich in omega-3 fatty acids. The purpose of the present study was to evaluate this hypothesis. In addition, the relation between usual dietary consumption of omega-3 fatty acids and restenosis was assessed.

METHODS AND RESULTS

A double-blind, randomized, controlled trial was conducted in which 205 patients undergoing a first PTCA received 15 capsules per day containing 1 g of either fish oil (2.7 g/day of eicosapentaenoic acid, 1.8 g/day of docosahexaenoic acid) or olive oil. The treatment was started 3 weeks before PTCA and continued for 6 months thereafter. Dietary intake was assessed by food frequency questionnaire. At 6 months after PTCA, patients underwent a control angiography. All angiographic lesions were measured by quantitative computer analysis. Four criteria were used to define restenosis. Restenosis occurred less often in the fish oil group (22.0-35.6% depending on the definition) than in the control group (40.0-53.3%). After controlling for other risk factors of restenosis, the association of fish oil supplementation with a lower frequency of restenosis was statistically significant (p = 0.03) for three of four definitions. After adjustment, a dietary intake of omega-3 fatty acids of more than 0.15 g/day was also associated with a lower frequency of restenosis (p less than or equal to 0.03).

CONCLUSIONS

This trial documented the protective effect of fish oil supplements on the recurrence of coronary stenosis 6 months after PTCA. The study results suggest that a dietary intervention could be useful in preventing restenosis.

Trifluoromethyl nitrogen heterocycles: synthetic aspects and potential biological targets

The synthetic methodologies and the potential biological targets of α-trifluoromethylated nitrogen heterocycles are presented.

Alcohol and nutrients in relation to colon cancer in middle-aged adults

A population-based case-control study was conducted from 1985 to 1989 in western Washington State to assess the relation between nutrients and the incidence of colon cancer in men and women aged 30-62. A food frequency questionnaire was used to document the usual diet 7 years before diagnosis for 424 cases and at a similar time for 414 controls. Alcohol consumption was strongly related to the risk of colon cancer in both men and women, with age-adjusted odds ratios (ORs) of colon cancer = 1.0, 1.9, 1.7, and 2.6 for 0, < 10, 10-29, and > or = 30 g/day intake for men and adjusted odds ratios = 1.0, 1.3, 1.8, and 2.5 for the same categories for women. The trend odds ratio associated with a one-category increment in the four-level alcohol consumption variable was 1.3 (95% confidence interval (CI) 1.0-1.5) in men and 1.4 (95% CI 1.0-1.7) in women. For both sexes, higher dietary fiber intakes were associated with lower relative risks for colon cancer, with age-, energy-, and alcohol-adjusted odds ratios = 1.0, 0.9, 0.8, and 0.6 across quartiles of consumption for men (trend OR for a one-quartile increment = 0.8, 95% CI 0.7-1.1) and adjusted odds ratios = 1.0, 0.9, 0.5, and 0.5 for women (trend OR = 0.8, 95% CI 0.6-1.0). In men, this was mostly attributable to intake of cereal fiber (trend OR = 0.8, 95% CI 0.6-1.0) while, in women, this association mostly reflected the effect of fruit fiber (trend OR = 0.8, 95% CI 0.6-0.9) and vegetable fiber (trend OR = 0.8, 95% CI 0.7-1.0). Calcium was associated with a decreased risk of colon cancer among women only (adjusted OR across quartiles = 1.0, 0.5, 0.6, 0.3; trend OR = 0.7, 95% CI 0.6-1.0). There was no indication of an association between colon cancer and fat or protein consumption or dietary vitamins.