Evolutionary trajectories of primate genes involved in HIV pathogenesis.

The current availability of five complete genomes of different primate species allows the analysis of genetic divergence over the last 40 million years of evolution. We hypothesized that the interspecies differences observed in susceptibility to HIV-1 would be influenced by the long-range selective pressures on host genes associated with HIV-1 pathogenesis. We established a list of human genes (n = 140) proposed to be involved in HIV-1 biology and pathogenesis and a control set of 100 random genes. We retrieved the orthologous genes from the genome of humans and of four nonhuman primates (Pan troglodytes, Pongo pygmaeus abeli, Macaca mulatta, and Callithrix jacchus) and analyzed the nucleotide substitution patterns of this data set using codon-based maximum likelihood procedures. In addition, we evaluated whether the candidate genes have been targets of recent positive selection in humans by analyzing HapMap Phase 2 single-nucleotide polymorphisms genotyped in a region centered on each candidate gene. A total of 1,064 sequences were used for the analyses. Similar median K(A)/K(S) values were estimated for the set of genes involved in HIV-1 pathogenesis and for control genes, 0.19 and 0.15, respectively. However, genes of the innate immunity had median values of 0.37 (P value = 0.0001, compared with control genes), and genes of intrinsic cellular defense had K(A)/K(S) values around or greater than 1.0 (P value = 0.0002). Detailed assessment allowed the identification of residues under positive selection in 13 proteins: AKT1, APOBEC3G, APOBEC3H, CD4, DEFB1, GML, IL4, IL8RA, L-SIGN/CLEC4M, PTPRC/CD45, Tetherin/BST2, TLR7, and TRIM5alpha. A number of those residues are relevant for HIV-1 biology. The set of 140 genes involved in HIV-1 pathogenesis did not show a significant enrichment in signals of recent positive selection in humans (intraspecies selection). However, we identified within or near these genes 24 polymorphisms showing strong signatures of recent positive selection. Interestingly, the DEFB1 gene presented signatures of both interspecies positive selection in primates and intraspecies recent positive selection in humans. The systematic assessment of long-acting selective pressures on primate genomes is a useful tool to extend our understanding of genetic variation influencing contemporary susceptibility to HIV-1.

Cell polarity in plants: a PARspective on PINs.

Plants have acquired the ability for organized multicellular development independent from animals. Because of this, they represent an independent example in nature for the development of coordinated, complex cell polarity from the simple polarity found in unicellular eukaryotes. Plants display a striking array of polarized cell types, with different axes of polarity being defined in one cell. The most investigated and best understood aspect of plant polarity is the apical-basal polarity of the PIN family of auxin efflux facilitators, which are of crucial importance for the organization of the entire plant body. Striking differences exist between the PAR-polarity modules known in animals and the ways PINs polarize plant cells. Nonetheless, a common regulatory logic probably applies to all polarizing eukaryotic cells, which includes self-reinforcing, positive feedback loops, intricate interactions between membrane-attached proteins, lipid signatures, and the targeting of transmembrane proteins to the correct domains of the plasma membrane.

Geographical determinants of the creation of manufacturing firms: The regions of Spain

La complexitat dels mecanismes que determinen l'entrada i la sortida de signatures augmenta quan diferències geogràfiques de l'estructura de producció, la capital humana i l'atur són considerades. Variacions interregionals en la tarifa de les noves de signatures dintre de cada activitat industrial persisteixen durant els períodes llargs de temps, una circumstància que indica que hi ha determinants no-conjunturals en la capacitat de regions per a crear nous projectes industrials. Aquest estudi està preocupat amb l'establiment d'influència variables geogràfiques sobre la fundació de nous establiments de la fabricació. Les indústries (NEIX la R 25) en les regions espanyoles (el BOIG 2) han estat preses com les unitats d'anàlisis per al període 1980-1992

Walking a Fine Line: An Investigation of the Monticello Mayor and City Council, July 5, 2011

Iowa Citizen Aide - Ombudsman Office received a complaint on February 22, 2010, concerning the manner in which the mayor and several city council members for the City of Monticello (City) attempted to remove the city administrator from his position. It was alleged that the mayor and at least one council member went to the homes of other council members and sought their signatures on a letter of offer requesting the city administrator to resign or face a vote to terminate his employment. We were asked to investigate whether this action complied with Iowa’s Open Meetings Law.

Electronic structure of few-electron concentric double quantum rings

The ground state structure of few-electron concentric double quantum rings is investigated within the local spin density approximation. Signatures of inter-ring coupling in the addition energy spectrum are identified and discussed. We show that the electronic configurations in these structures can be greatly modulated by the inter-ring distance: At short and long distances the low-lying electron states localize in the inner and outer rings, respectively, and the energy structure is essentially that of an isolated single quantum ring. However, at intermediate distances the electron states localized in the inner and the outer ring become quasidegenerate and a rather entangled, strongly-correlated system is formed.

Optical response of two-dimensional few-electron concentric double quantum rings: A local-spin-density-functional theory study

We have investigated the dipole charge- and spin-density response of few-electron two-dimensional concentric nanorings as a function of the intensity of a erpendicularly applied magnetic field. We show that the dipole response displays signatures associated with the localization of electron states in the inner and outer ring favored by the perpendicularly applied magnetic field. Electron localization produces a more fragmented spectrum due to the appearance of additional edge excitations in the inner and outer ring.

Symmetry breaking in small rotating clouds of trapped ultracold Bose atoms

We study the signatures of rotational and phase symmetry breaking in small rotating clouds of trapped ultracold Bose atoms by looking at rigorously defined condensate wave function. Rotational symmetry breaking occurs in narrow frequency windows, where energy degeneracy between the lowest energy states of different total angular momentum takes place. This leads to a complex condensate wave function that exhibits vortices clearly seen as holes in the density, as well as characteristic local phase patterns, reflecting the appearance of vorticities. Phase symmetry (or gauge symmetry) breaking, on the other hand, is clearly manifested in the interference of two independent rotating clouds.

A colorectal cancer classification system that associates cellular phenotype and responses to therapy.

Colorectal cancer (CRC) is a major cause of cancer mortality. Whereas some patients respond well to therapy, others do not, and thus more precise, individualized treatment strategies are needed. To that end, we analyzed gene expression profiles from 1,290 CRC tumors using consensus-based unsupervised clustering. The resultant clusters were then associated with therapeutic response data to the epidermal growth factor receptor-targeted drug cetuximab in 80 patients. The results of these studies define six clinically relevant CRC subtypes. Each subtype shares similarities to distinct cell types within the normal colon crypt and shows differing degrees of 'stemness' and Wnt signaling. Subtype-specific gene signatures are proposed to identify these subtypes. Three subtypes have markedly better disease-free survival (DFS) after surgical resection, suggesting these patients might be spared from the adverse effects of chemotherapy when they have localized disease. One of these three subtypes, identified by filamin A expression, does not respond to cetuximab but may respond to cMET receptor tyrosine kinase inhibitors in the metastatic setting. Two other subtypes, with poor and intermediate DFS, associate with improved response to the chemotherapy regimen FOLFIRI in adjuvant or metastatic settings. Development of clinically deployable assays for these subtypes and of subtype-specific therapies may contribute to more effective management of this challenging disease.

Milbemycins: more than efflux inhibitors for fungal pathogens.

Existing antifungal agents are still confronted to activities limited to specific fungal species and to the development of resistance. Several improvements are possible either by tackling and overcoming resistance or exacerbating the activity of existing antifungal agents. In Candida glabrata, azole resistance is almost exclusively mediated by ABC transporters (including C. glabrata CDR1 [CgCDR1] and CgCDR2) via gain-of-function mutations in the transcriptional activator CgPDR1 or by mitochondrial dysfunctions. We also observed that azole resistance was correlating with increasing virulence and fitness of C. glabrata in animal models of infection. This observation motivated the re-exploitation of ABC transporter inhibitors as a possible therapeutic intervention to decrease not only the development of azole resistance but also to interfere with the virulence of C. glabrata. Milbemycins are known ABC transporter inhibitors, and here we used commercially available milbemycin A3/A4 oxim derivatives to verify this effect. As expected, the derivatives were inhibiting C. glabrata efflux with the highest activity for A3 oxim below 1 μg/ml. More surprising was that oxim derivatives had intrinsic fungicidal activity above 3.2 μg/ml, thus highlighting effects additional to the efflux inhibition. Similar values were obtained with C. albicans. Our data show that the fungicidal activity could be related to reactive oxygen species formation in these species. Transcriptional analysis performed both in C. glabrata and C. albicans exposed to A3 oxim highlighted a core of commonly regulated genes involved in stress responses, including genes involved in oxidoreductive processes, protein ubiquitination, and vesicle trafficking, as well as mitogen-activated protein kinases. However, the transcript profiles contained also species-specific signatures. Following these observations, experimental treatments of invasive infections were performed in mice treated with the commercial A3/A4 oxim preparation alone or in combination with fluconazole. Tissue burden analysis revealed that oxims on their own were able to decrease fungal burdens in both Candida species. In azole-resistant isolates, oxims acted synergistically in vivo with fluconazole to reduce fungal burden to levels of azole-susceptible isolates. In conclusion, we show here the potential of milbemycins not only as drug efflux inhibitors but also as effective fungal growth inhibitors in C. glabrata and C. albicans.

Simultaneous coexpression of memory-related and effector-related genes by individual human CD8 T cells depends on antigen specificity and differentiation.

Phenotypic and functional cell properties are usually analyzed at the level of defined cell populations but not single cells. Yet, large differences between individual cells may have important functional consequences. It is likely that T-cell-mediated immunity depends on the polyfunctionality of individual T cells, rather than the sum of functions of responding T-cell subpopulations. We performed highly sensitive single-cell gene expression profiling, allowing the direct ex vivo characterization of individual virus-specific and tumor-specific T cells from healthy donors and melanoma patients. We have previously shown that vaccination with the natural tumor peptide Melan-A-induced T cells with superior effector functions as compared with vaccination with the analog peptide optimized for enhanced HLA-A*0201 binding. Here we found that natural peptide vaccination induced tumor-reactive CD8 T cells with frequent coexpression of both memory/homing-associated genes (CD27, IL7R, EOMES, CXCR3, and CCR5) and effector-related genes (IFNG, KLRD1, PRF1, and GZMB), comparable with protective Epstein-Barr virus-specific and cytomegalovirus-specific T cells. In contrast, memory/homing-associated and effector-associated genes were less frequently coexpressed after vaccination with the analog peptide. Remarkably, these findings reveal a previously unknown level of gene expression diversity among vaccine-specific and virus-specific T cells with the simultaneous coexpression of multiple memory/homing-related and effector-related genes by the same cell. Such broad functional gene expression signatures within antigen-specific T cells may be critical for mounting efficient responses to pathogens or tumors. In summary, direct ex vivo high-resolution molecular characterization of individual T cells provides key insights into the processes shaping the functional properties of tumor-specific and virus-specific T cells.

Role of HIV-1-specific CD4 T cells.

PURPOSE OF REVIEW: Most of the studies investigating antiviral immunity have predominantly focused on CD8 T cells. However, numerous recent studies have highlighted the importance of HIV-1-specific CD4 T cells in the antiviral immune response, and have also revealed the high level of complexity and heterogeneity of the virus-specific CD4 T-cell responses. An understanding of the role of these key players in the antiviral immune response is of fundamental importance.RECENT FINDINGS: A comprehensive investigation of several features of virus-specific CD4 T-cell responses, including the magnitude, breadth, function and phenotype, has recently been performed. In particular, HIV-1-specific CD4 T-cell responses have been studied in different stages of HIV-1 infection, i.e. acute and chronic phase, under conditions of spontaneous (long-term non-progressors) or antiviral therapy-mediated control of virus replication or uncontrolled virus replication. Different phenotypical and functional patterns of HIV-1-specific CD4 T-cell responses were associated with different conditions of controlled versus uncontrolled virus replication, thus allowing the identification of signatures of protective immune responses. Robust and diverse virus-specific CD4 T-cell responses have been observed. These responses, however, were not predictive of nonprogressive versus progressive HIV-1-associated disease.SUMMARY: There is an urgent need to delineate the immune correlates of protective T-cell responses in order to develop novel immunological markers to evaluate the degree of immune restoration of antiviral therapy as well as the potential effectiveness of HIV vaccine-induced T-cell immune responses.

COLOX: a new blood-based test for colorectal cancer (CRC)screening

BACKGROUND: The objective is to develop a cost-effective, reliable and non invasive screening test able to detect early CRCs and adenomas. This is done on a nucleic acids multigene assay performed on peripheral blood mononuclear cells (PBMCs). METHODS: A colonoscopy-controlled study was conducted on 179 subjects. 92 subjects (21 CRC, 30 adenoma >1 cm and 41 controls) were used as training set to generate a signature. Other 48 subjects kept blinded (controls, CRC and polyps) were used as a test set. To determine organ and disease specificity 38 subjects were used: 24 with inflammatory bowel disease (IBD),14 with other cancers (OC). Blood samples were taken and PBMCs were purified. After the RNA extraction, multiplex RT-qPCR was applied on 92 different candidate biomarkers. After different univariate and multivariate analysis 60 biomarkers with significant p-values (<0.01) were selected. 2 distinct biomarker signatures are used to separate patients without lesion from those with CRC or with adenoma, named COLOX CRC and COLOX POL. COLOX performances were validated using random resampling method, bootstrap. RESULTS: COLOX CRC and POL tests successfully separate patients without lesions from those with CRC (Se 67%, Sp 93%, AUC 0.87), and from those with adenoma > 1cm (Se 63%, Sp 83%, AUC 0.77). 6/24 patients in the IBD group and 1/14 patients in the OC group have a positive COLOX CRC. CONCLUSION: The two COLOX tests demonstrated a high Se and Sp to detect the presence of CRCs and adenomas > 1 cm. A prospective, multicenter, pivotal study is underway in order to confirm these promising results in a larger cohort.

Geographical determinants of the creation of manufacturing firms: The regions of Spain

La complexitat dels mecanismes que determinen l'entrada i la sortida de signatures augmenta quan diferències geogràfiques de l'estructura de producció, la capital humana i l'atur són considerades. Variacions interregionals en la tarifa de les noves de signatures dintre de cada activitat industrial persisteixen durant els períodes llargs de temps, una circumstància que indica que hi ha determinants no-conjunturals en la capacitat de regions per a crear nous projectes industrials. Aquest estudi està preocupat amb l'establiment d'influència variables geogràfiques sobre la fundació de nous establiments de la fabricació. Les indústries (NEIX la R 25) en les regions espanyoles (el BOIG 2) han estat preses com les unitats d'anàlisis per al període 1980-1992

Modelling plant species distribution in alpine grasslands using airborne imaging spectroscopy.

Remote sensing using airborne imaging spectroscopy (AIS) is known to retrieve fundamental optical properties of ecosystems. However, the value of these properties for predicting plant species distribution remains unclear. Here, we assess whether such data can add value to topographic variables for predicting plant distributions in French and Swiss alpine grasslands. We fitted statistical models with high spectral and spatial resolution reflectance data and tested four optical indices sensitive to leaf chlorophyll content, leaf water content and leaf area index. We found moderate added-value of AIS data for predicting alpine plant species distribution. Contrary to expectations, differences between species distribution models (SDMs) were not linked to their local abundance or phylogenetic/functional similarity. Moreover, spectral signatures of species were found to be partly site-specific. We discuss current limits of AIS-based SDMs, highlighting issues of scale and informational content of AIS data.

Social and temporal organization in an ant colony

Ant colonies are known for their complex and efficient social organization that com-pletely lacks hierarchical structure. However, due to methodological difficulties in follow¬ing all ants of a colony, it was until now impossible to investigate the social and temporal organization of colonies. We developed a tracking system that allows tracking the posi¬tions and orientations of several hundred individually labeled ants continuously, providing for the first time quantitative long term data on all individuals of a colony. These data permit reconstructing trajectories, activity patterns and social networks of all ants in a colony and enable us to investigate ant behavior quantitatively in previously unpreceded ways. By analyzing the spatial positions and social interactions of all ants in six colonies for 41 days we show that ant colonies are organized in groups of nurses, nest patrollers and foragers. Workers of each group were highly interconnected and occupied similar spa¬tial locations in the nest. Groups strongly segregated spatially, and were characterized by unique behavioral signatures. Nurses spent most of their time on the brood. Nest patrollers frequently visited the rubbish pile, and foragers frequently visited the forag¬ing arena. In addition nurses were on average younger than nest patrollers who were, in turn, younger than foragers. We further show that workers had a preferred behav¬ioral trajectory and moved from nursing to nest patrolling, and from nest patrolling to foraging. By analyzing the activity patterns of all ants we show that only a third of all workers in a colony exhibit circadian rhythms and that these rhythms shortened by on av¬erage 42 minutes in constant darkness, thereby demonstrating the presence of a functional endogenous clock. Most rhythmic workers were foragers suggesting that rhythmicity is tightly associated with task. Nurses and nest patrollers were arrhythmic which most likely reflects plasticity of the circadian clock, as isolated workers in many species exhibit circadian rhythmicity. Altogether our results emphasize that ant colonies, despite their chaotic appearance, repose on a strong underlying social and temporal organization. - Les colonies de fourmis sont connues pour leur organisation sociale complexe et effi-cace, charactérisée par un manque absolu de structure hiérarchique. Cependant, puisqu'il est techniquement très difficile de suivre toutes les fourmis d'une colonie, il a été jusqu'à maintenant impossible d'étudier l'organisation sociale et temporelle des colonies de four-mis. Nous avons développé un système qui permet d'extraire en temps réel à partir d'images vidéo les positions et orientations de plusieurs centaines de fourmis marquées individuellement. Nous avons pu ainsi générer pour la première fois des données quanti-tatives et longitudinales relatives à des fourmis appartenant à une colonie. Ces données nous ont permis de reconstruire la trajectoire et l'activité de chaque fourmi ainsi que ses réseaux sociaux. Ceci nous a permis d'étudier de manière exhaustive et objective le com-portement de tous les individus d'une colonie. En analysant les données spatiales et les interactions sociales de toutes les fourmis de six colonies qui ont été filmées pendant 41 jours, nous montrons que les fourmis d'une même colonie se répartissent en trois groupes: nourrices, patrouilleuses et approvisionneuses. Les fourmis d'un même groupe interagis-sent fréquemment et occupent le même espace à l'intérieur du nid. L'espace propre à un groupe se recoupe très peu avec celui des autres. Chaque groupe est caractérisé par un comportement typique. Les nourrices s'affairent surtout autour du couvain. Les pa-trouilleuses font de fréquents déplacements vers le tas d'ordures, et les approvisionneuses sortent souvent du nid. Les nourrices sont en moyenne plus jeunes que les patrouilleuses qui, à leur tour, sont plus jeunes que les approvisionneuses. De plus, nous montrons que les ouvrières changent de tâche au cours de leur vie, passant de nourrice à patrouilleuse puis à approvisionneuse. En analysant l'activité de chaque fourmi, nous montrons que seulement un tiers des ouvrières d'une colonie présente des rythmes circadiens et que ces rythmes diminuent en moyenne de 42 minutes lorsqu'il y a obscurité constante, ce qui démontre ainsi la présence d'une horloge endogène. De plus, la plupart des approvi¬sionneuses ont une activité rythmique alors que les nourrices et patrouilleuses présentent une activité arythmique, ce qui suggère que la rythmicité est étroitement associée à la tâche. L'arythmie des nourrices et patrouilleuses repose probablement sur une plasticité de l'horloge endogène car des ouvrières de nombreuses espèces font preuve d'une ryth¬micité circadienne lorsqu'elles sont isolées de la colonie. Dans l'ensemble nos résultats révèlent qu'une colonie de fourmis se fonde sur une solide organisation sociale et tem¬porelle malgré son apparence chaotique.