Combinatorial peptide library-based identification of peptide ligands for tumor-reactive cytolytic T lymphocytes of unknown specificity.

A novel approach for the identification of tumor antigen-derived sequences recognized by CD8(+) cytolytic T lymphocytes (CTL) consists in using synthetic combinatorial peptide libraries. Here we have screened a library composed of 3.1 x 10(11) nonapeptides arranged in a positional scanning format, in a cytotoxicity assay, to search the antigen recognized by melanoma-reactive CTL of unknown specificity. The results of this analysis enabled the identification of several optimal peptide ligands, as most of the individual nonapeptides deduced from the primary screening were efficiently recognized by the CTL. The results of the library screening were also analyzed with a mathematical approach based on a model of independent and additive contribution of individual amino acids to antigen recognition. This biometrical data analysis enabled the retrieval, in public databases, of the native antigenic peptide SSX-2(41-49), whose sequence is highly homologous to the ones deduced from the library screening, among the ones with the highest stimulatory score. These results underline the high predictive value of positional scanning synthetic combinatorial peptide library analysis and encourage its use for the identification of CTL ligands.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PURPOSE: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. METHODS: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. RESULTS: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease. CONCLUSIONS: The MDH1 gene is not the cause of RP28-linked arRP. Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration.

Flow targeted 3D steady-state free-precession coronary MR angiography: comparison of three different imaging approaches.

PURPOSE: To compare 3 different flow targeted magnetization preparation strategies for coronary MR angiography (cMRA), which allow selective visualization of the vessel lumen. MATERIAL AND METHODS: The right coronary artery of 10 healthy subjects was investigated on a 1.5 Tesla MR system (Gyroscan ACS-NT, Philips Healthcare, Best, NL). A navigator-gated and ECG-triggered 3D radial steady-state free-precession (SSFP) cMRA sequence with 3 different magnetization preparation schemes was performed referred to as projection SSFP (selective labeling of the aorta, subtraction of 2 data sets), LoReIn SSFP (double-inversion preparation, selective labeling of the aorta, 1 data set), and inflow SSFP (inversion preparation, selective labeling of the coronary artery, 1 data set). Signal-to-noise ratio (SNR) of the coronary artery and aorta, contrast-to-noise ratio (CNR) between the coronary artery and epicardial fat, vessel length and vessel sharpness were analyzed. RESULTS: All cMRA sequences were successfully obtained in all subjects. Both projection SSFP and LoReIn SSFP allowed for selective visualization of the coronary arteries with excellent background suppression. Scan time was doubled in projection SSFP because of the need for subtraction of 2 data sets. In inflow SSFP, background suppression was limited to the tissue included in the inversion volume. Projection SSFP (SNR(coro): 25.6 +/- 12.1; SNR(ao): 26.1 +/- 16.8; CNR(coro-fat): 22.0 +/- 11.7) and inflow SSFP (SNR(coro): 27.9 +/- 5.4; SNR(ao): 37.4 +/- 9.2; CNR(coro-fat): 24.9 +/- 4.8) yielded significantly increased SNR and CNR compared with LoReIn SSFP (SNR(coro): 12.3 +/- 5.4; SNR(ao): 11.8 +/- 5.8; CNR(coro-fat): 9.8 +/- 5.5; P < 0.05 for both). Longest visible vessel length was found with projection SSFP (79.5 mm +/- 18.9; P < 0.05 vs. LoReIn) whereas vessel sharpness was best in inflow SSFP (68.2% +/- 4.5%; P < 0.05 vs. LoReIn). Consistently good image quality was achieved using inflow SSFP likely because of the simple planning procedure and short scanning time. CONCLUSION: Three flow targeted cMRA approaches are presented, which provide selective visualization of the coronary vessel lumen and in addition blood flow information without the need of contrast agent administration. Inflow SSFP yielded highest SNR, CNR and vessel sharpness and may prove useful as a fast and efficient approach for assessing proximal and mid vessel coronary blood flow, whereas requiring less planning skills than projection SSFP or LoReIn SSFP.

Medical residents' feedback on needs and acquired skills following a short course on cross-cultural competence

Objectives The purpose of this study is to assess short and long term changes in knowledge, attitudes, and skills among medical residents following a short course on cultural competency and to explore their perspectives on the experience. Methods Eighteen medical residents went through a short training programme comprised of two seminars lasting 30' and 60' respectively over two days. Three months later, we conducted three focus groups, with 17 residents to explore their thoughts, perspectives and feedback about the course. To measure changes over time, we carried out a quantitative sequential survey before the seminars, three days after, and three months later using the Multicultural Assessment Questionnaire. Results Residents expressed a wide variety of perspectives on the main themes related to the content of the training - culture, trialogue, stereotypes, status, epidemiology, history and geopolitics - and related to its organization - relevance, volume, timing, target audience, training tools, and working material. Using the MAQ, we observed a higher global performance score (n=16) at three days (median=38) compared to results before the training (median=33) revealing a median difference of 5.5 points (z=2.4, p=0.015). This difference was still present at three months (∆=4.5, z=2.4, p=0.018), mainly due to knowledge acquisition (∆=3) rather than attitudes (∆=0) or skills (∆=1). Conclusions Cross-cultural competence training not only brings awareness of multicultural issues but also helps participants understand their own cultures, perception of others and preconceived ideas. Physicians' education should however also focus on improving implementation of acquired knowledge in cross-cultural competence.

Stratigraphy of the Cenomanian-Turonian Oceanic Anoxic Event OAE2 in shallow shelf sequences of NE Egypt

Two shallow water late Cenomanian to early Turonian sequences of NE Egypt have been investigated to evaluate the response to OAE2. Age control based on calcareous nannoplankton, planktic foraminifera and ammonite biostratigraphies integrated with delta(13)C stratigraphy is relatively good despite low diversity and sporadic occurrences. Planktic and benthic foraminiferal faunas are characterized by dysoxic, brackish and mesotrophic conditions, as indicated by low species diversity, low oxygen and low salinity tolerant planktic and benthic species, along with oyster-rich limestone layers. In these subtidal to inner neritic environments the OAE2 delta(13)C excursion appears comparable and coeval to that of open marine environments. However, in contrast to open marine environments where anoxic conditions begin after the first delta(13)C peak and end at or near the Cenomanian-Turonian boundary, in shallow coastal environments anoxic conditions do not appear until the early Turonian. This delay in anoxia appears to be related to the sea-level transgression that reached its maximum in the early Turonian, as observed in shallow water sections from Egypt to Morocco. (C) 2011 Elsevier Ltd. All rights reserved.

Three short perioperative infusions of n-3 PUFAs reduce systemic inflammation induced by cardiopulmonary bypass surgery: a randomized controlled trial.

BACKGROUND: Fish oil (FO) has antiinflammatory effects, which might reduce systemic inflammation induced by a cardiopulmonary bypass (CPB). OBJECTIVE: We tested whether perioperative infusions of FO modify the cell membrane composition, inflammatory responses, and clinical course of patients undergoing elective coronary artery bypass surgery. DESIGN: A prospective randomized controlled trial was conducted in cardiac surgery patients who received 3 infusions of 0.2 g/kg FO emulsion or saline (control) 12 and 2 h before and immediately after surgery. Blood samples (7 time points) and an atrial biopsy (during surgery) were obtained to assess the membrane incorporation of PUFAs. Hemodynamic data, catecholamine requirements, and core temperatures were recorded at 10-min intervals; blood triglycerides, nonesterified fatty acids, glucose, lactate, inflammatory cytokines, and carboxyhemoglobin concentrations were measured at selected time points. RESULTS: Twenty-eight patients, with a mean ± SD age of 65.5 ± 9.9 y, were enrolled with no baseline differences between groups. Significant increases in platelet EPA (+0.86%; P = 0.0001) and DHA (+0.87%; P = 0.019) were observed after FO consumption compared with at baseline. Atrial tissue EPA concentrations were higher after FO than after control treatments (+0.5%; P < 0.0001). FO did not significantly alter core temperature but decreased the postoperative rise in IL-6 (P = 0.018). Plasma triglycerides increased transiently after each FO infusion. Plasma concentrations of glucose, lactate, and blood carboxyhemoglobin were lower in the FO than in the control group on the day after surgery. Arrhythmia incidence was low with no significant difference between groups. No adverse effect of FO was detected. CONCLUSIONS: Perioperative FO infusions significantly increased PUFA concentrations in platelet and atrial tissue membranes within 12 h of the first FO administration and decreased biological and clinical signs of inflammation. These results suggest that perioperative FO may be beneficial in elective cardiac surgery with CPB. This trial was registered at clinicaltrials.gov as NCT00516178.

trome, trEST and trGEN: databases of predicted protein sequences.

We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these two databases plus a new database (trome), which uses alignments of EST data to HTG or full genomes to generate virtual transcripts and coding sequences. This new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases.

Short term behavioural consequences of denied access to environmental facilities in milk

Selostus: Eräiden ympäristövirikkeiden saatavuuden estämisen välittömät vaikutukset tarhaminkin käyttäytymiseen

Three-stranded DNA structure; is this the secret of DNA homologous recognition?

A novel type of triple-stranded DNA structure was proposed by several groups to play a crucial role in homologous recognition between single- and double-stranded DNA molecules. In this still putative structure a duplex DNA was proposed to co-ordinate a homologous single strand in its major groove side. In contrast to the well-characterized pyrimidine-purine-pyrimidine triplexes in which the two like strands are antiparallel and which are restricted to poly-pyrimidine-containing stretches, the homology-specific triplexes would have like strands in parallel orientation and would not be restricted to any particular sequence provided that there is a homology between interacting DNA molecules. For many years the stereo-chemical possibility of forming homology-dependent three- or four-stranded DNA structures during the pairing stage of recombination reactions was seriously considered in published papers. However, only recently has there been a marked increase in the number of papers that have directly tested the formation of triple-stranded DNA structures during the actual pairing stage of the recombination reaction. Unfortunately the results of these tests are not totally clear cut; while some laboratories presented experimental evidence consistent with the formation of triplexes, others studying the same or very similar systems offered alternative explanations. The aim of this review is to present the current state of the central question in the mechanism of homologous recombination, namely, what kind of DNA structure is responsible for DNA homologous recognition. Is it a novel triplex structure or just a classical duplex?

Phylogenetic relationships and divergence times among dormice (Rodentia, Gliridae) based on three nuclear genes

We examined phylogenetic relationships among six species representing three subfamilies, Glirinae, Graphiurinae and Leithiinae with sequences from three nuclear protein-coding genes (apolipoprotein B, APOB; interphotoreceptor retinoid-binding protein, IRBP; recombination-activating gene 1, RAG1). Phylogenetic trees reconstructed from maximum-parsimony (MP), maximum-likelihood (ML) and Bayesian-inference (BI) analyses showed the monophyly of Glirinae (Glis and Glirulus) and Leithiinae (Dryomys, Eliomys and Muscardinus) with strong support, although the branch length maintaining this relationship was very short, implying rapid diversification among the three subfamilies. Divergence time estimates were calculated from ML (local clock model) and Bayesian-dating method using a calibration point of 25 Myr (million years) ago for the divergence between Glis and Glirulus, and 55 Myr ago for the split between lineages of Gliridae and Sciuridae on the basis of fossil records. The results showed that each lineage of Graphiuros, Glis, Glirulus and Muscardinus dates from the Late Oligocene to the Early Miocene period, which is mostly in agreement with fossil records. Taking into account that warm climate harbouring a glirid-favoured forest dominated from Europe to Asia during this period, it is considered that this warm environment triggered the prosperity of the glirid species through the rapid diversification. Glirulus japonicas is suggested to be a relict of this ancient diversification during the warm period.

Hyponatremia and short-term outcomes in patients with acute pulmonary embolism

BACKGROUND: Hyponatremia, a marker of neurohormonal activation, is associated with poor outcomes in acute cardiorespiratory diseases such as myocardial infarction, right and left ventricular heart failure, and pneumonia. The prognostic value of hyponatremia in patients with acute pulmonary embolism (PE) is unknown. We sought to assess whether hyponatremia at presentation was associated with mortality and hospital readmission in patients hospitalized with PE. METHODS: We studied patient discharges with a primary diagnosis of PE from 185 acute care hospitals in Pennsylvania (1/2000-11/2002). We defined hyponatremia as a serum sodium level ≤135 mmol/l, measured at the time of patient presentation. The study outcomes were 30-day all-cause mortality and hospital readmission. We used random-intercept logistic regression to examine the association between hyponatremia and mortality. We adjusted for baseline patient (race, insurance, severity of illness using the Pulmonary Embolism Severity Index) and hospital characteristics (region, hospital size and teaching status). We used the same approach to examine the association between hyponatremia and readmission among patients who were discharged alive. RESULTS: Among 13,728 patient discharges with PE, 2907 (21.1%) had hyponatremia at the time of presentation. Patients with hyponatremia were older (P<0.001) and more likely to have a history of cancer (P<0.001), heart failure (P<0.001), or chronic lung disease (P=0.002) than patients without hyponatremia. Patients with hyponatremia had a higher unadjusted cumulative 30-day mortality (15.2% vs 8.0%;P<0.001) and readmission rate (15.9% vs 11.8%; P< 0.001) than patients without hyponatremia (Figure). After adjustment for race, insurance, severity of illness, and hospital factors, hyponatremia was associated with a significantly greater odds of death (OR 1.71, 95% CI: 1.50-1.95) and hospital readmission (OR 1.29, 95% CI: 1.14-1.46). CONCLUSIONS: In this large, statewide sample of unselected patients with acute PE, hyponatremia was relatively common and was an independent predictor of short-term mortality and hospital readmission. Given that sodium is a low-cost, easily available laboratory parameter, it may be potentially useful in risk-stratifying patients with PE.

In vivo measurement of glycine with short echo-time 1H MRS in human brain at 7 T.

OBJECT: To determine whether glycine can be measured at 7 T in human brain with (1)H magnetic resonance spectroscopy (MRS). MATERIALS AND METHODS: The glycine singlet is overlapped by the larger signal of myo-inositol. Density matrix simulations were performed to determine the TE at which the myo-inositol signal was reduced the most, following a single spin-echo excitation. (1)H MRS was performed on an actively shielded 7 T scanner, in five healthy volunteers. RESULTS: At the TE of 30 ms, the myo-inositol signal intensity was substantially reduced. Quantification using LCModel yielded a glycine-to-creatine ratio of 0.14 +/- 0.01, with a Cramer-Rao lower bound (CRLB) of 7 +/- 1%. Furthermore, quantification of metabolites other than glycine was possible as well, with a CRLB mostly below 10%. CONCLUSION: It is possible to detect glycine at 7 T in human brain, at the short TE of 30 ms with a single spin-echo excitation scheme.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.