1,25-dihydroxyvitamin D3 impairs NF-κB activation in human naïve B cells

1α,25-dihydroxyvitamin D₃ (calcitriol), the bioactive metabolite of vitamin D, modulates the activation and inhibits IgE production of anti-CD40 and IL-4 stimulated human peripheral B cells. Engagement of CD40 results in NF-κB p50 activation, which is essential for the class switch to IgE. Herein, we investigated by which mechanism calcitriol modulates NF-κB mediated activation of human naïve B cells. Naïve B cells were predominantly targeted by calcitriol in comparison with memory B cells as shown by pronounced induction of the VDR target gene cyp24a1. Vitamin D receptor activation resulted in a strongly reduced p105/p50 protein and mRNA expression in human naïve B cells. This effect is mediated by impaired nuclear translocation of p65 and consequently reduced binding of p65 to its binding site in the p105 promoter. Our data indicate that the vitamin D receptor reduces NF-κB activation by interference with NF-κB p65 and p105. Thus, the vitamin D receptor inhibits costimulatory signal transduction in naïve B cells, namely by reducing CD40 signaling.     

Immunity promotes virulence evolution in a malaria model

Evolutionary models predict that host immunity will shape the evolution of parasite virulence. While some assumptions of these models have been tested, the actual evolutionary outcome of immune selection on virulence has not. Using the mouse malaria model, Plasmodium chabaudi, we experimentally tested whether immune pressure promotes the evolution of more virulent pathogens by evolving parasite lines in immunized and nonimmunized (“naïve”) mice using serial passage. We found that parasite lines evolved in immunized mice became more virulent to both naïve and immune mice than lines evolved in naïve mice. When these evolved lines were transmitted through mosquitoes, there was a general reduction in virulence across all lines. However, the immune-selected lines remained more virulent to naïve mice than the naïve-selected lines, though not to immunized mice. Thus, immune selection accelerated the rate of virulence evolution, rendering parasites more dangerous to naïve hosts. These results argue for further consideration of the evolutionary consequences for pathogen virulence of vaccination.     

BMP antagonists and FGF signaling contribute to different domains of the neural plate in Xenopus

In ectodermal explants from Xenopus embryos, inhibition of BMP signaling is sufficient for neural induction, leading to the idea that neural fate is the default state in the ectoderm. Many of these experiments assayed the action of BMP antagonists on animal caps, which are relatively naïve explants of prospective ectoderm, and different results have led to debate regarding both the mechanism of neural induction and the appropriateness of animal caps as an assay system. Here we address whether BMP antagonists are only able to induce neural fates in pre-patterned explants, and the extent to which neural induction requires FGF signaling. We suggest that some discrepancies in conclusion depend on the interpretations of sox gene expression, which we show not only marks definitive neural tissue, but also tissue that is not yet committed to neural fates. Part of the early sox2 domain requires FGF signaling, but in the absence of organizer signaling, this domain reverts to epidermal fates. We also reinforce the evidence that ectodermal explants are naïve, and that explants that lack any dorsal prepattern are readily neuralized by BMP antagonists, even when FGF signaling is inhibited.     

Analyzing the homeostasis of signaling proteins by a combination of Western blot and fluorescence correlation spectroscopy

The determination of intracellular protein concentrations is a prerequisite for understanding protein interaction networks in systems biology. Today, protein quantification is based either on mass spectrometry, which requires large cell numbers and sophisticated measurement protocols, or on quantitative Western blotting, which requires the expression and purification of a recombinant protein as a reference. Here, we present a method that uses a transiently expressed fluorescent fusion protein of the protein-of-interest as an easily accessible reference in small volumes of crude cell lysates. The concentration of the fusion protein is determined by fluorescence correlation spectroscopy, and this concentration is used to calibrate the intensity of bands on a Western blot. We applied this method to address cellular protein homeostasis by determining the concentrations of the plasma membrane-located transmembrane scaffolding protein LAT and soluble signaling proteins in naïve T cells and transformed T-cell lymphoma (Jurkat) cells (with the latter having nine times the volume of the former). Strikingly, the protein numbers of soluble proteins scaled with the cell volume, whereas that of the transmembrane protein LAT scaled with the membrane surface. This leads to significantly different stoichiometries of signaling proteins in transformed and naïve cells in concentration ranges that may translate directly into differences in complex formation.     

Sexual reward in male rats: effects of sexual experience on conditioned place preferences associated with ejaculation and intromissions

Various behavioral models and studies have provided evidence suggesting that male rat sexual behavior has rewarding and reinforcing properties. However, there is little information regarding the rewarding values of the different components of sexual behavior. Therefore, this study used a conditioned place preference (CPP) paradigm to address whether ejaculation and intromissions differ in their rewarding incentive values. We also addressed whether the differential rewarding values were dependent on prior sexual experience. Sexually naïve and experienced males received one pairing of either intromissions or ejaculation with one of the chambers in the CPP box. The amount of time spent in each chamber of the CPP apparatus after conditioning was then measured. Both sexually naïve and sexually experienced males formed a CPP for ejaculation, while only sexually naïve, and not sexually experienced, males formed a CPP for intromissions. Moreover, in sexually naïve males, multiple pairings of ejaculation with the designated chamber resulted in a CPP relative to the control chamber paired with display of intromissions. These data support the hypothesis that there is a hierarchy of rewarding sexual behavior, with ejaculation being the most rewarding component, and that the rewarding incentive value of other components of sexual behavior is dependent upon prior sexual experience.     

B Cell Receptor Signaling-Based Index as a Biomarker for the Loss of Peripheral Immune Tolerance in Autoreactive B Cells in Rheumatoid Arthritis

This study examines the loss of peripherally induced B cell immune tolerance in Rheumatoid arthritis (RA) and establishes a novel signaling-based measure of activation in a subset of autoreactive B cells - the Induced tolerance status index (ITSI). Naturally occurring naïve autoreactive B cells can escape the “classical” tolerogenic mechanisms of clonal deletion and receptor editing, but remain peripherally tolerized through B cell receptor (BCR) signaling inhibition (postdevelopmental “receptor tuning” or anergy). ITSI is a statistical index that numerically determines the level of homology between activation patterns of BCR signaling intermediaries in B cells that are either tolerized or activated by auto antigen exposure, and thus quantifies the level of peripheral immune tolerance. The index is based on the logistic regression analysis of phosphorylation levels in a panel of BCR signaling proteins. Our results demonstrate a new approach to identifying autoreactive B cells based on their BCR signaling features.     

Predicting potential cancer genes by integrating network properties, sequence features and functional annotations

The discovery of novel cancer genes is one of the main goals in cancer research. Bioinformatics methods can be used to accelerate cancer gene discovery, which may help in the understanding of cancer and the development of drug targets. In this paper, we describe a classifier to predict potential cancer genes that we have developed by integrating multiple biological evidence, including protein-protein interaction network properties, and sequence and functional features. We detected 55 features that were significantly different between cancer genes and non-cancer genes. Fourteen cancer-associated features were chosen to train the classifier. Four machine learning methods, logistic regression, support vector machines (SVMs), BayesNet and decision tree, were explored in the classifier models to distinguish cancer genes from non-cancer genes. The prediction power of the different models was evaluated by 5-fold cross-validation. The area under the receiver operating characteristic curve for logistic regression, SVM, Baysnet and J48 tree models was 0.834, 0.740, 0.800 and 0.782, respectively. Finally, the logistic regression classifier with multiple biological features was applied to the genes in the Entrez database, and 1976 cancer gene candidates were identified. We found that the integrated prediction model performed much better than the models based on the individual biological evidence, and the network and functional features had stronger powers than the sequence features in predicting cancer genes.     

Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Na?ve Bayes

Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader) were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that the proposed DBPPred can be an alternative perspective predictor for large-scale determination of DNA-binding proteins.     

IntApop: A web service for predicting apoptotic protein interactions in humans

Apoptosis, a type of cell death, is necessary for maintaining tissue homeostasis and removing malignant cells. Interrupted apoptosis process contributes to carcinogenesis, developmental defects, autoimmune diseases and neurological disorders. Due to the complexity of the process, the molecular dynamics and relative interactions of individual proteins responsible for the activation or inhibition of apoptosis should be researched systematically. In this study, we integrate known protein interactions from databases DIP, IntAct, MINT, HPRD and BioGRID by Naïve Bayes classifier. The receiver operation characteristic (ROC) curve with the area under the ROC curve (AUC) of 0.797 indicates it has a good performance in prediction. Then, we predict the global human apoptotic protein interactions network. Within it, we not only identify the already known interactions of caspases (caspase-8/-10, caspase-9, caspase-3/-6/-7) and Bcl-2 family, but also reveal that Bid can interact with casein kinases (CSK21/22/2B, KC1A, KC1E); both of B2LA1 and B2CL2 can interact with Bid, Bax and Bak; caspase-8 interacts with autophagic proteins (MLP3B, MLP3A and LRRk2). Consequently, we make an initial step to develop the web service IntApop that provides an appropriate platform for apoptosis researchers, systems biologists and translational clinician scientists to predict apoptotic protein interactions in human. In addition, the interaction network can be visualized online, making it a widely applicable systems biology tool for apoptosis and cancer researchers.     

Choice of resident costimulatory molecule can influence cell fate in human naïve CD4+ T cell differentiation

With antigen stimulation, naïve CD4+ T cells differentiate to several effector or memory cell populations, and cytokines contribute to differentiation outcome. Several proteins on these cells receive costimulatory signals, but a systematic comparison of their differential effects on naïve T cell differentiation has not been conducted. Two costimulatory proteins, CD28 and ICAM-1, resident on human naïve CD4+ T cells were compared for participation in differentiation. Under controlled conditions, and with no added cytokines, costimulation through either CD3+CD28 or CD3+CAM-1 induced differentiation to T effector and T memory cells. In contrast, costimulation through CD3+ICAM-1 induced differentiation to Treg cells whereas costimulation through CD3+CD28 did not.     

Integrated prediction of the helical membrane protein interactome in yeast

At least a quarter of all genes in most genomes contain putative transmembrane (TM) helices, and helical membrane protein interactions are a major component of the overall cellular interactome. However, current experimental techniques for large-scale detection of protein-protein interactions are biased against membrane proteins. Here, we define protein-protein interaction broadly as co-complexation, and develop a weighted-voting procedure to predict interactions among yeast helical membrane proteins by optimally combining evidence based on diverse genome-wide information such as sequence, function, localization, abundance, regulation, and phenotype. We use logistic regression to simultaneously optimize the weights of all evidence sources for best discrimination based on a set of known helical membrane protein interactions. The resulting integrated classifier not only significantly outperforms classifiers based on any single genomic feature, but also does better than a benchmark Na?ve Bayes classifier (using a simplifying assumption of conditional independence among features). Finally, we apply the optimized classifier genome-wide, and construct a comprehensive map of predicted helical membrane protein interactome in yeast. This can serve as a guide for prioritizing further experimental validation efforts.     

NKG2D splice variants: a reexamination of adaptor molecule associations

NKG2D is a homodimeric C-type lectin-related receptor expressed on natural killer (NK) cells and T cells. In mice, alternative deoxyribonucleic acid (DNA) splicing generates two isoforms of NKG2D that differ in the length of their cytoplasmic domains. Their ability to induce cellular activation is mediated via association with two membrane-bound, signaling adaptor molecules, DAP10 and DAP12. It has been reported that the long form of NKG2D associates exclusively with DAP10, whereas the short variant can interact with either adaptor. The short isoform was reported to be almost undetectable in naïve NK cells. Using two distinct cell types, we demonstrate that like the short isoform, the long variant of NKG2D also associates not only with DAP10 but also with DAP12. Using reporter cells (70Z/3), we demonstrate that DAP12 can compete equally with DAP10 for association with both variants of NKG2D when DAP10 and DAP12 are coexpressed. Cross-linking either isoform of NKG2D induces a calcium flux when associated exclusively with DAP10 or DAP12. Moreover, using quantitative polymerase chain reaction (PCR), we also show that the short isoform of NKG2D is expressed in naïve NK cells. Our data suggest that signaling via mouse NKG2D isoforms is more complex than originally presented.     

Influence of Illuminance and Forager Experience on Use of Orientation Cues in Social Wasps (Vespinae)

We tested the influence of illuminance and level of forager experience on nest orientation behavior of the social wasps Vespula vulgaris, Vespa crabro, and Dolichovespula saxonica in an artificial laboratory tunnel system. The number of wasps which oriented themselves chemically via a terrestrial trail or used visual orientation were determined at different illuminance levels for foragers which were naïve or experienced with the tunnel system. In V. vulgaris and D. saxonica, mainly the young and naïve foragers used the chemical trail for orientation in brightness. Experienced foragers used visual cues for nest orientation. In V. crabro, naïve and experienced foragers followed the chemical trail in a similar intensity. In darkness, when visual orientation was limited, the relative importance of the chemical trail increased dramatically in all species and all experience classes.     

Naïve Encounters with Chimpanzees in the Goualougo Triangle, Republic of Congo

We describe the behavior of an unhabituated population of chimpanzees in the Goualougo Triangle, Republic of Congo. We encountered chimpanzee parties on 218 occasions during two field seasons (February 1999–December 1999, June 2000–June 2001). Overall contact rate was 0.63 contacts per day in the field (n = 347). During the first 5 min of observation, we recorded individual responses as curious, ignore, hide, or depart. In contrast to other unhabituated chimpanzees, curiosity was the most common response (84%) of individuals in the Goualougo Triangle. However, the responses were deeply integrated in the group's reaction to our arrival and behavior throughout an encounter. Based on the behavior of the majority of individuals in a group, we categorized entire contact events as naïve, ignore, nervous, or depart. Naïve contacts accounted for 69% of all encounters. Other contacts types occurred much less frequently: nervous (12%), depart (11%), ignore (8%). Naïve contacts were characterized by chimpanzees that continued to exhibit curiosity throughout the encounter, the arrival of other individuals at the contact location, and relatively prolonged contact with observers (average duration: 136 min). It is likely that the high frequency of curious responses and naïve contacts are due to the remote location of the Goualougo Triangle and the chimpanzees's lack of experience with humans. Documentation of this naïve phenomenon has been successfully used to lobby for the protection of the chimpanzees and their habitat.     

Dual Gating Mechanism and Function of P2X7 Receptor Channels

The ATP-gated P2X7 receptor channel (P2X7R) operates as a cytolytic and apoptotic receptor but also controls sustained cellular responses, including cell growth and proliferation. However, it has not been clarified how the same receptor mediates such opposing effects. To address this question, we have combined electrophysiological, imaging, and mathematical studies using wild-type and mutant rat P2X7Rs. Activation of naïve (not previously stimulated) receptors by low agonist concentrations caused monophasic slow desensitizing currents and internalization of receptors without other changes in the cellular morphology, much like other P2XRs. In contrast, saturating agonist concentrations induced high-amplitude biphasic currents, reflecting pore dilation and causing rapid cell swelling and lysis. The existence of these two signaling patterns was accounted for using a revised Markov-state model that included, in addition to naïve and sensitized states, desensitized states. Occupancy of one or two ATP-binding sites of naïve receptors favored a slow transition to desensitized states, whereas occupancy of the third binding site favored a transition to sensitized/dilated states. Consistent with model predictions, nondilating P2X7R mutants always generated desensitizing currents. These results suggest that the level of saturation of the ligand binding sites determines the nature of the P2X7R gating and cellular actions.     

Diterpene, 16-phyllocladanol enhances Th1 polarization induced by LPS-primed DC, but not TNF-alpha-primed DC

16-Phyllocladanol is diterpene isolated form the heartwood of Cryptomeria japonica. We demonstrate that the effect of 16-phyllocladanol on the phenotypic and functional maturation of human monocytes-derived DC in vitro. Human monocytes were exposed to 16-phyllocladanol alone, or in combination with LPS and thereafter co-cultured with naïve T cells. The expression levels of CD83 and HLA-DR on LPS-primed DC were enhanced by 16-phyllocladanol. 16-Phyllocladanol dose-dependently augmented the T cell stimulatory capacity in an allo MLR to LPS-primed DC and the production of IL-12p70 by LPS-primed DC. The cytokine production by 16-phyllocladanol-primed DC was not inhibited by anti-TLR2 and 4 mAbs. IFN-γ secretion from naïve T cells co-cultured with DC differentiated with LPS was also augmented by 16-phyllocladanol. These results suggest that the enhancement of Th1 cells polarization to LPS-primed DC induced by 16-phyllocladanol via the activation of IL-12p70 and independent on TLR2 or TLR4.     

Bronchial epithelial cells produce IL-5: Implications for local immune responses in the airways

IL-5 is a pleiotropic cytokine that promotes eosinophil differentiation and survival. While naïve bronchial epithelial cells (BEC) produce low levels of IL-5, the role of BEC-derived IL-5 in allergic airway inflammation is unknown. We now show that BEC, isolated from mice with OVA-induced allergic airway disease (AAD), produced elevated levels of IL-5 mRNA and protein as compared to BEC from naïve mice. To determine the contribution of BEC-derived IL-5 to effector responses in the airways, IL-5 deficient bone marrow chimeric mice were generated in which IL-5 expression was restricted to stromal (e.g. BEC) or hematopoietic cells. When subjected to AAD, IL-5 produced by BECs contributed to mucous metaplasia, airway eosinophilia, and OVA-specific IgA levels. Thus, IL-5 production by BEC can impact the microenvironment of the lung, modifying pathologic and protective immune responses in the airways.     

Requirement of B-Raf,C-Raf,and A-Raf for the growth and survival of mouse embryonic stem cells

Extracellular signal-regulated kinases (ERKs) have been implicated to be dispensable for self-renewal of mouse embryonic stem (ES) cells, and simultaneous inhibition of both ERK signaling and glycogen synthase kinase 3 (GSK3) not only allows mouse ES cells to self-renew independent of extracellular stimuli but also enables more efficient derivation of naïve ES cells from mouse and rat strains. Interestingly, some ERKs stay active in mouse ES cells which are maintained in regular medium containing leukemia inhibitory factor (LIF) and bone morphogenetic protein (BMP). Yet, the upstream signaling for ERK activation and their roles in mouse ES cells, other than promoting or priming differentiation, have not been determined. Here we found that mouse ES cells express three forms of Raf kinases, A-Raf, B-Raf, and C-Raf. Knocking-down each single Raf member failed to affect the sustained ERK activity, neither did A-Raf and B-Raf double knockdown or B-Raf and C-Raf double knockdown change it in ES cells. Interestingly, B-Raf and C-Raf double knockdown, not A-Raf and B-Raf knockdown, inhibited the maximal ERK activation induced by LIF, concomitant with the slower growth of ES cells. On the other hand, A-Raf, B-Raf, and C-Raf triple knockdown markedly inhibited both the maximal and sustained ERK activity in ES cells. Moreover, Raf triple knockdown, similar to the treatment of U-0126, an MEK inhibitor, significantly inhibited the survival and proliferation of ES cells, thereby compromising the colony propagation of mouse ES cells. In summary, our data demonstrate that all three Raf members are required for ERK activation in mouse ES cells and are involved in growth and survival of mouse ES cells.     

Moving together: Incidental leaders and naïve followers

Elucidating whether common general mechanisms govern collective movements in a wide range of species is a central issue in the study of social behaviour. In this paper, we describe a new experimental paradigm for studying the dynamic of collective movements. Some sheep (Ovis aries) were first trained to move towards a coloured panel, in response to a sound cue. We present data comparing the behaviour of test groups composed of one of the trained sheep and 3 naïve sheep, and control groups composed of 4 naïve sheep. In the tests, for both test and control groups, sheep were observed for 20 min before the sound cue was delivered and the panel made visible. Before the sound, trained and naïve sheep were similar in terms of activity budgets, spatial distribution, social behaviour and spontaneous movement initiation. After the sound, trained sheep moved toward the panel and systematically triggered a collective movement in all test groups. The results suggest that any individual moving away from the group can elicit a collective movement. Our experimental protocol provides an opportunity to quantify mechanisms involved in group movements, and to investigate differences between species and the effect of social context on collective decision-making.     

Peripheral survival of naïve CD8<Superscript>+</Superscript> T cells

Maintenance of a sufficient population of naïve CD8⁺ T cells in the peripheral lymphoid compartment is critical for immunocompetence. Peripheral T cell number is a function of T cell generation, survival, and death. Homeostasis, a critical balance between survival and death, must exist to prevent either lymphopenia or lymphocytosis. In the current review, we discuss known requirements for the survival of naïve peripheral CD8⁺ T cells as well as mechanisms of death when survival signals are lost. We also discuss associations between survival and homeostasis-driven proliferation, and highlight the gaps in our knowledge of these critical processes.