Assignment strategies for large proteins by magic-angle spinning NMR: the 21-kDa disulfide-bond-forming enzyme DsbA.

We present strategies for chemical shift assignments of large proteins by magic-angle spinning solid-state NMR, using the 21-kDa disulfide-bond-forming enzyme DsbA as prototype. Previous studies have demonstrated that complete de novo assignments are possible for proteins up to approximately 17 kDa, and partial assignments have been performed for several larger proteins. Here we show that combinations of isotopic labeling strategies, high field correlation spectroscopy, and three-dimensional (3D) and four-dimensional (4D) backbone correlation experiments yield highly confident assignments for more than 90% of backbone resonances in DsbA. Samples were prepared as nanocrystalline precipitates by a dialysis procedure, resulting in heterogeneous linewidths below 0.2 ppm. Thus, high magnetic fields, selective decoupling pulse sequences, and sparse isotopic labeling all improved spectral resolution. Assignments by amino acid type were facilitated by particular combinations of pulse sequences and isotopic labeling; for example, transferred echo double resonance experiments enhanced sensitivity for Pro and Gly residues; [2-(13)C]glycerol labeling clarified Val, Ile, and Leu assignments; in-phase anti-phase correlation spectra enabled interpretation of otherwise crowded Glx/Asx side-chain regions; and 3D NCACX experiments on [2-(13)C]glycerol samples provided unique sets of aromatic (Phe, Tyr, and Trp) correlations. Together with high-sensitivity CANCOCA 4D experiments and CANCOCX 3D experiments, unambiguous backbone walks could be performed throughout the majority of the sequence. At 189 residues, DsbA represents the largest monomeric unit for which essentially complete solid-state NMR assignments have so far been achieved. These results will facilitate studies of nanocrystalline DsbA structure and dynamics and will enable analysis of its 41-kDa covalent complex with the membrane protein DsbB, for which we demonstrate a high-resolution two-dimensional (13)C-(13)C spectrum.

Neoadjuvant and adjuvant strategies in renal cell carcinoma: more questions than answers.

The current standard treatment for early stage (I-III) renal cell cancer (RCC) is surgery. While the prognosis of stage I tumors is excellent, stage II and particularly stage III have a high risk of relapse. The adjuvant treatment of patients with RCC remains an area of investigation, with patient selection being a key aspect. There are currently two prognostic nomograms to establish the risk of relapse in patients with resected RCC. The results of earlier studies of adjuvant therapy, including the use chemotherapy and/or immunotherapy after nephrectomy have failed to show any benefit in the outcome of patients at risk of developing local recurrence or distant metastases. Two recent phase III trials with vaccines (autologous tumor cell vaccine and autologous tumor-derived heat shock protein peptide complex-96) have shown promising, albeit still preliminary, results. In the metastatic RCC setting, recent advances in the molecular understanding of oncogenic pathways have led to the development of new therapeutic strategies with the use of targeted therapies in the adjuvant setting. Neoadjuvant treatment is another treatment modality currently being evaluated for patients with early disease and in patients with metastatic RCC with inoperable primary tumors. The questions that remain unanswered include activity of these agents in early stages of the disease, patient selection, optimal start time of the adjuvant treatment, and finally, the optimal length of treatment.

Melanin-based colouration predicts natal dispersal in the barn owl, Tyto alba

Searching for a suitable breeding site is an important decision in the life of most animals. The decisions where to settle and how far to travel before doing so depend on many factors. Individual differences in dispersal distance could result from different strategies (e.g. specialists versus generalists), which might result in similar reproductive success in different habitats, or different competitive abilities to acquire a territory close to the natal site. The barn owl is polymorphic in melanic coloration, which is associated with many physiological and behavioural traits such as habitat choice, stress response and docility, raising the possibility that the coloration is also related to dispersal. We studied natal dispersal (from rearing site to site of first breeding attempt) and breeding dispersal (from one breeding site to the next) in barn owls using a long-term data set. Darker reddish individuals moved further than paler individuals during natal dispersal, but not during breeding dispersal. A cross-fostering experiment showed that the colour of the biological and foster parents had no influence on dispersal distance. The distance dispersed by parents and same-sex offspring was correlated, whereas natal and breeding dispersal were not repeatable within individuals, indicating that they are two different processes. Given that the distance travelled in natal dispersal appears to be heritable, the underlying genes might be coupled to those related to coloration. We discuss hypotheses to explain the potential adaptive function of the link between coloration and natal dispersal.

Effect of Emotion and Personality on Deviation from Purely Rational Decision-Making

Human decision-making has consistently demonstrated deviation from "pure" rationality. Emotions are a primary driver of human actions and the current study investigates how perceived emotions and personality traits may affect decision-making during the Ultimatum Game (UG). We manipulated emotions by showing images with emotional connotation while participants decided how to split money with a second player. Event-related potentials (ERPs) from scalp electrodes were recorded during the whole decision-making process. We observed significant differences in the activity of central and frontal areas when participants offered money with respect to when they accepted or rejected an offer. We found that participants were more likely to offer a higher amount of money when making their decision in association with negative emotions. Furthermore, participants were more likely to accept offers when making their decision in association with positive emotions. Honest, conscientious, and introverted participants were more likely to accept offers. Our results suggest that factors others than a rational strategy may predict economic decision-making in the UG.

Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.

Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.

Signalling, mating success and paternal investment in sticklebacks (Gasterosteus aculeatus): A theoretical model

I present an optimisation model that links paternal investment, male display and female choice. Although deviced for sticklebacks, it readily applies to other fish with male guarding behaviour. It relies on a few basic assumptions on the ways hatching success depends on paternal investment and clutch size, and male survival on paternal investment and signaling. Paternal investment is here a state-dependent decision, and signal a condition-dependent handicap by which males inform females of how much they are willing to invest. Series of predictions are derived on female and male breeding strategies, including optimal levels of signaling and paternal investment as functions of clutch size, own condition, and residual reproductive value, as well as alternative strategies such as egg kleptoparasitism. Some predictions already have empirical support, for which the present model provides new interpretations. Other might readily be tested, e.g. by simple clutch-size manipulations.

Development and validation of a clinical decision rule for the diagnosis of influenza.

INTRODUCTION: A clinical decision rule to improve the accuracy of a diagnosis of influenza could help clinicians avoid unnecessary use of diagnostic tests and treatments. Our objective was to develop and validate a simple clinical decision rule for diagnosis of influenza. METHODS: We combined data from 2 studies of influenza diagnosis in adult outpatients with suspected influenza: one set in California and one in Switzerland. Patients in both studies underwent a structured history and physical examination and had a reference standard test for influenza (polymerase chain reaction or culture). We randomly divided the dataset into derivation and validation groups and then evaluated simple heuristics and decision rules from previous studies and 3 rules based on our own multivariate analysis. Cutpoints for stratification of risk groups in each model were determined using the derivation group before evaluating them in the validation group. For each decision rule, the positive predictive value and likelihood ratio for influenza in low-, moderate-, and high-risk groups, and the percentage of patients allocated to each risk group, were reported. RESULTS: The simple heuristics (fever and cough; fever, cough, and acute onset) were helpful when positive but not when negative. The most useful and accurate clinical rule assigned 2 points for fever plus cough, 2 points for myalgias, and 1 point each for duration <48 hours and chills or sweats. The risk of influenza was 8% for 0 to 2 points, 30% for 3 points, and 59% for 4 to 6 points; the rule performed similarly in derivation and validation groups. Approximately two-thirds of patients fell into the low- or high-risk group and would not require further diagnostic testing. CONCLUSION: A simple, valid clinical rule can be used to guide point-of-care testing and empiric therapy for patients with suspected influenza.

Historical contingency affects signaling strategies and competitive abilities in evolving populations of simulated robots.

One of the key innovations during the evolution of life on earth has been the emergence of efficient communication systems, yet little is known about the causes and consequences of the great diversity within and between species. By conducting experimental evolution in 20 independently evolving populations of cooperatively foraging simulated robots, we found that historical contingency in the occurrence order of novel phenotypic traits resulted in the emergence of two distinct communication strategies. The more complex foraging strategy was less efficient than the simpler strategy. However, when the 20 populations were placed in competition with each other, the populations with the more complex strategy outperformed the populations with the less complex strategy. These results demonstrate a tradeoff between communication efficiency and robustness and suggest that stochastic events have important effects on signal evolution and the outcome of competition between distinct populations.

Individual and dyadic coping strategies in the aftermath of a traumatic experience

This study was designed to explore individual and dyadic coping strategies in the aftermath of a traumatic event. Eighteen persons having experienced a physical assault or a road accident within six to twelve months before the study, and eighteen matched control persons were recruited together with their partners. Each participant and his/her partner filled in several questionnaires on individual and dyadic coping strategies, level of stress and PTSD-symptomatology. Results indicate that participants having experienced a trauma, compared to controls, report a general lack of dyadic coping and, when facing daily hassles, specific decreases in individual coping strategies. These differences are discussed in the context of marital coping processes.

Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii.

ABSTRACT: BACKGROUND: Sphingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. Thus far, however, little is known about the adaptive strategies used by Sphingomonas bacteria to respond to changes in water potential. To improve our understanding, strain RW1 was perturbed with either the cell-permeating solute sodium chloride or the non-permeating solute polyethylene glycol with a molecular weight of 8000 (PEG8000). These solutes are assumed to simulate the solute and matric components of the total water potential, respectively. The responses to these perturbations were then assessed and compared using a combination of growth assays, transcriptome profiling, and membrane fatty acid analyses. RESULTS: Under conditions producing a similar decrease in water potential but without effect on growth rate, there was only a limited shared response to perturbation with sodium chloride or PEG8000. This shared response included the increased expression of genes involved with trehalose and exopolysaccharide biosynthesis and the reduced expression of genes involved with flagella biosynthesis. Mostly, the responses to perturbation with sodium chloride or PEG8000 were very different. Only sodium chloride triggered the increased expression of two ECF-type RNA polymerase sigma factors and the differential expression of many genes involved with outer membrane and amino acid metabolism. In contrast, only PEG8000 triggered the increased expression of a heat shock-type RNA polymerase sigma factor along with many genes involved with protein turnover and repair. Membrane fatty acid analyses further corroborated these differences. The degree of saturation of membrane fatty acids increased after perturbation with sodium chloride but had the opposite effect and decreased after perturbation with PEG8000. CONCLUSIONS: A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.

Diabétologie [Diabetes].

The new recommendations on the pharmacological treatment of type 2 diabetes have introduced two important changes. The first is to have common strategies between European and American diabetes societies. The second, which is certainly the most significant, is to develop a patient centred approach suggesting therapies that take into account the patient's preferences and use of decision support tools. The individual approach integrates six factors: the capacity and motivation of the patient to manage his illness and its treatment, the risks of hypoglycemia, the life expectancy, the presence of co-morbidities and vascular complications, as well as the financial resources of the patient and the healthcare system. Treatment guidelines for cardiovascular risk reduction in diabetic remains the last point to develop.

Cancer du sein : la pathologie, pierre angulaire de la décision therapeutique [Breast cancer: pathology, the cornerstone of therapeutic decision]

Tailoring adjuvant therapy in breast cancer patients relies on prognostic and predictive factors, most of which are currently established by histopathological analysis of tumors. The quality of the assessment of the former (i.e.: tumor size, lymph node status, tumor grade, HER2 status, and lymphovascular invasion) and the latter (estrogen and progesteron receptors expression, HER2 overexpression or amplification) is an essential prerequisite for an optimal therapeutic decision. If the prognostic and predictive values of multigenes signatures are confirmed by on-going clinical studies, this approach could enter the clinical practice in the coming years and result in improved accuracy of adjuvant therapies in breast cancer patients. This approach might especially allow avoiding overtreatment in patients at low risk of recurrence.

Male beach workers and western female tourists : livelihood strategies in Kenya's south coast region

Recent years have seen an emerging knowledge base and increasing public interest and awareness of sexual-economic relationships between local men and Western women, in different touristic regions around the world. However, to date, Western perspectives on the phenomenon make up the bulk of the existent literature. Questioning the dominant discourse of 'romance tourism' and representations of male participants as 'victims-opportunists', this dissertation explores male beach workers' experiences with, and perspectives on sexual-economic relationships between Kenyan men and visiting Western women in Kenya's South Coast region. The men were not considered in isolation; their experiences and perspectives are situated in relation to their family ties, social networks and the political economy of beach tourism. The study shows that locally these relationships are clearly understood as livelihood strategies for the visited. Men seek to establish long-term intimate relationships with female tourists as a means to accessing life's basic necessities for themselves and for their families and overall to improve their standards of living. It is argued that these relationships are a response to the poverty and inequalities generated by socio-economic changes over time. They are also a response to local gender role prescriptions that hinge male social value on men's capacity to marry, procreate and provide intergenerational social and economic support. The men's parallel quest for non-sexual economically motivated friendships with visiting foreign tourists termed "family friends" is a salient finding, that serves to reinforce the finding that the sexual- economic relationships are above all livelihood strategies. Résumé Ces dernières années ont vu l'émergence d'une base de connaissance, ainsi que d'un intérêt et d'une prise de conscience accrue du public, à l'égard des relations économico-sexuelles entre hommes locaux et femmes occidentales, dans différentes régions touristiques du monde. Cependant, à ce jour, des perspectives occidentales sur ce phénomène constituent l'essentiel de la littérature existante. En remettant en question le discours dominant du «romance tourism» (tourisme sentimental) et les représentations qui conçoivent les hommes participants comme étant 'victimes-opportunistes', cette thèse explore les expériences, et les visions qu'ont les travailleurs de plage sur les relations économico-sexuelles entre hommes Kenyans et femmes Occidentales dans la région de la côte sud du Kenya. Les hommes n'ont pas été considérés de manière isolée; leurs expériences et leurs perspectives sont situées par rapport à leur liens familiaux, leur réseaux sociaux et aussi par rapport à l'économie politique du tourisme balnéaire. L'étude montre que sur place ces relations sont clairement conçues comme des stratégies de survie pour les participants hôtes. Les hommes cherchent à établir des relations de long durée avec des femmes touristes comme moyen d'accéder à des biens et des services qui constituent des nécessités de bases, pour eux et pour leur familles et globalement pour relever leur niveau de vie! L'étude fait valoir que ces relations sont une réponse à la pauvreté et aux inégalités sociales crées par des dynamiques socio-économiques au fil du temps. Elles sont aussi une réponse au prescriptions sociales locales par lesquelles la valeur sociale masculine est définie à travers la capacité des hommes à se marier, à procréer et d'assurer un soutien intergénérationnel social et économique. La quête, en parallèle, de relations d'amitiés non-sexuelles à motivation économique, dénommé « family friends », par des hommes, est un résultat saillant de cette étude qui vient renforcer l'observation que les relations économico-sexuelles relèvent avant tout des stratégies de survie.