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Articles about doing a PhD tend to focus on the difficulties faced by research students. Here we argue that the scientific community should also highlight the positive elements of the PhD experience., Competing Interests: CB, LL, CM, MP, EA, EB, LG, EM, AT, CA, UA, FC No competing interests declared, (© 2022, Bernery, Lusardi, Marino et al.)

Many biological quantities cannot be measured directly but rather need to be estimated from models. Estimates from models are statistical objects with variance and, when derived simultaneously, covariance. It is well known that their variance-covariance (VC) matrix must be considered in subsequent analyses. Although it is always preferable to carry out the proposed analyses on the raw data themselves, a two-step approach cannot always be avoided. This situation arises when the parameters of a multinomial must be regressed against a covariate. The Delta method is an appropriate and frequently recommended way of deriving variance approximations of transformed and correlated variables. Implementing the Delta method is not trivial, and there is a lack of a detailed information on the procedure in the literature for complex situations such as those involved in constraining the parameters of a multinomial distribution. This paper proposes a how-to guide for calculating the correct VC matrices of dependant estimates involved in multinomial distributions and how to use them for testing the effects of covariates in post hoc analyses when the integration of these analyses directly into a model is not possible. For illustrative purpose, we focus on variables calculated in capture-recapture models, but the same procedure can be applied to all analyses dealing with correlated estimates with multinomial distribution and their variances and covariances.

Understanding how individuals and populations respond to fluctuations in climatic conditions is critical to explain and anticipate changes in ecological systems. Most such studies focus on climate impacts on single populations without considering inter- and intra-population heterogeneity. However, comparing geographically dispersed populations limits the risk of faulty generalizations and helps to improve ecological and demographic models. We aimed to determine whether differences in migration tactics among and within populations would induce inter- or intra-population heterogeneity in survival in relation to winter climate fluctuations. Our study species was the Common eider (Somateria mollissima), a marine duck with a circumpolar distribution, which is strongly affected by climatic conditions during several phases of its annual cycle. Capture-mark-recapture data were collected in two arctic (northern Canada and Svalbard) and one subarctic (northern Norway) population over a period of 18, 15, and 29 years respectively. These three populations have different migration tactics and experience different winter climatic conditions. Using multi-event and mixture modelling, we assessed the association between adult female eider survival and winter conditions as measured by the North Atlantic Oscillation (NAO) index. We found that winter weather conditions affected the survival of female eiders from each of these three populations. However, different mechanisms seemed to be involved. Survival of the two migrating arctic populations was impacted directly by changes in the NAO, whereas the subarctic resident population was affected by the NAO with time lags of 2-3 years. Moreover, we found evidence for intra-population heterogeneity in the survival response to the winter NAO in the Canadian eider population, where individuals migrate to distinct wintering areas. Our results illustrate how individuals and populations of the same species can vary in their responses to climate variation. We suspect that the found variation in the survival response of birds to winter conditions is partly explained by differences in migration tactic. Detecting and accounting for inter- and intra-population heterogeneity will improve our predictions concerning the response of wildlife to global changes., (© 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.)

The energetic costs of reproduction in birds strongly depend on the climate experienced during incubation. Climate change and increasing frequency of extreme weather events may severely affect these costs, especially for species incubating in extreme environments. In this 3-year study, we used an experimental approach to investigate the effects of microclimate and nest shelter on the incubation effort of female common eiders (Somateria mollissima) in a wild Arctic population. We added artificial shelters to a random selection of nesting females, and compared incubation effort, measured as body mass loss during incubation, between females with and without shelter. Nonsheltered females had a higher incubation effort than females with artificial shelters. In nonsheltered females, higher wind speeds increased the incubation effort, while artificially sheltered females experienced no effect of wind. Although increasing ambient temperatures tended to decrease incubation effort, this effect was negligible in the absence of wind. Humidity had no marked effect on incubation effort. This study clearly displays the direct effect of a climatic variable on an important aspect of avian life-history. By showing that increasing wind speed counteracts the energetic benefits of a rising ambient temperature, we were able to demonstrate that a climatic variable other than temperature may also affect wild populations and need to be taken into account when predicting the effects of climate change.

Evidence has recently emerged that butyrophilins, which are members of the extended B7 family of co-stimulatory molecules, have diverse functions in the immune system. We found that the human and mouse genes encoding butyrophilin-2A2 (BTN2A2) are regulated by the class II trans-activator and regulatory factor X, two transcription factors dedicated to major histocompatibility complex class II expression, suggesting a role in T cell immunity. To address this, we generated Btn2a2-deficient mice. Btn2a2(-/-) mice exhibited enhanced effector CD4(+) and CD8(+) T cell responses, impaired CD4(+) regulatory T cell induction, potentiated antitumor responses, and exacerbated experimental autoimmune encephalomyelitis. Altered immune responses were attributed to Btn2a2 deficiency in antigen-presenting cells rather than T cells or nonhematopoietic cells. These results provide the first genetic evidence that BTN2A2 is a co-inhibitory molecule that modulates T cell-mediated immunity., (© 2016 Sarter et al.)

Plasmacytoid dendritic cells (pDCs) are not only potent inflammatory cytokine producers but also function as antigen-presenting cells (APCs). We have shown that vaccination using CpG-B activated tumor antigen (Ag) presenting pDCs induce Th17 cells that promote intratumoral immune cell recruitment, including antitumor cytotoxic T lymphocytes CTLs. Therefore, strategies targeting both innate and adaptive pDC functions may improve antitumor T-cell immunity.

Th17 cells represent a particular subset of T helper lymphocytes characterized by high production of IL-17 and other inflammatory cytokines. Th17 cells participate in antimicrobial immunity at mucosal and epithelial barriers and particularly fight against extracellular bacteria and fungi. While a role for Th17 cells in promoting inflammation and autoimmune disorders has been extensively and elegantly demonstrated, it is still controversial whether and how Th17 cells influence tumor immunity. Although Th17 cells specifically accumulate in many different types of tumors compared to healthy tissues, the outcome might however differ from a tumor type to another. Th17 cells were consequently associated with both good and bad prognoses. The high plasticity of those cells toward cells exhibiting either anti-inflammatory or in contrast pathogenic functions might contribute to Th17 versatile functions in the tumor context. On one hand, Th17 cells promote tumor growth by inducing angiogenesis (via IL-17) and by exerting themselves immunosuppressive functions. On the other hand, Th17 cells drive antitumor immune responses by recruiting immune cells into tumors, activating effector CD8(+) T cells, or even directly by converting toward Th1 phenotype and producing IFN-γ. In this review, we are discussing the impact of the tumor microenvironment on Th17 cell plasticity and function and its implications in cancer immunity.

Plasmacytoid dendritic cells (pDC) rapidly and massively produce type I IFN and other inflammatory cytokines in response to foreign nucleic acids, thereby indirectly influencing T-cell responses. Moreover, antigen (Ag)-presenting pDCs directly regulate T-cell differentiation. Depending on the immune environment, pDCs exhibit either tolerogenic or immunogenic properties. Here, we show that CpG-activated pDCs promote efficient Th17 differentiation. Indeed, Th17 responses are defective in mice selectively lacking MHCII on pDCs upon antigenic challenge. Importantly, in those mice, the frequency of Th17 cells infiltrating solid tumors is impaired. As a result, the recruitment of infiltrating leukocytes in tumors, including tumor-specific cytotoxic T lymphocytes (CTL), is altered and results in increased tumor growth. Importantly, following immunization with tumor Ag and CpG-B, MHCII-restricted Ag presentation by pDCs promotes the differentiation of antitumor Th17 cells that induce intratumor CTL recruitment and subsequent regression of established tumors. Our results highlight a new role for Ag presenting activated pDCs in promoting the development of Th17 cells and impacting on antitumor immunity., (©2014 American Association for Cancer Research.)

The apoptotic machinery plays a key role in hematopoietic cell homeostasis. Terminally differentiated cells are eliminated, at least in part, by apoptosis, whereas part of the apoptotic machinery, including one or several caspases, is required to go through very specific steps of the differentiation pathways. A number of hematological diseases involve a deregulation of this machinery, which in most cases is a decrease in cell sensitivity to pro-apoptotic signals through over-expression of anti-apoptotic molecules. In some situations however, e.g. in the erythroid lineage of low grade myelodysplastic syndromes, cell sensitivity to apoptosis is increased in a death receptor-dependent manner and cell death pathways are inhibited only when these diseases progress into high grade and acute leukemia. Therapeutic strategies targeting the apoptotic machinery specifically block cell death inhibitors that are over-expressed in transformed cells, mainly Bcl-2-related proteins and Inhibitor of Apoptosis Proteins (IAPs). Another strategy is the activation of the extrinsic pathway to apoptosis, mainly through the death receptor agonist Tumor necrosis factor-Related Apoptosis Inducing Ligand (TRAIL) or agonistic antibodies targeting TRAIL receptors. The use of inhibitors of death receptors could make sense when these receptors are involved in excessive cell death or activation of survival pathways. Most of the drugs targeting apoptotic pathways introduced in clinics have demonstrated their tolerability. Their efficacy, either alone or in combination with other drugs such as demethylating agents and histone deacetylase inhibitors, is currently tested in both myeloid and lymphoid hematological diseases., (Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.)

Plasmacytoid dendritic cells (pDCs) are a particular subset of DCs that link innate and adaptive immunity. They are responsible for the substantial production of type 1 interferon (IFN-I) in response to viral RNA or DNA through activation of TLR7 and 9. Furthermore, pDCs present antigens (Ag) and induce naïve T cell differentiation. It has been demonstrated that pDCs can induce immunogenic T cell responses through differentiation of cytotoxic CD8(+) T cells and effector CD4(+) T cells. Conversely, pDCs exhibit strong tolerogenic functions by inducing CD8(+) T cell deletion, CD4(+) T cell anergy, and Treg differentiation. However, since IFN-I produced by pDCs efficiently activates and recruits conventional DCs, B cells, T cells, and NK cells, pDCs also indirectly affect the nature and the amplitude of adaptive immune responses. As a consequence, the precise role of Ag-presenting functions of pDCs in adaptive immunity has been difficult to dissect in vivo. Additionally, different experimental procedures led to conflicting results regarding the outcome of T cell responses induced by pDCs. During the development of autoimmunity, pDCs have been shown to play both immunogenic and tolerogenic functions depending on disease, disease progression, and the experimental conditions. In this review, we will discuss the relative contribution of innate and adaptive pDC functions in modulating T cell responses, particularly during the development of autoimmunity.

Several cysteine proteases of the caspase family play a central role in many forms of cell death by apoptosis. Other enzymes of the family are involved in cytokine maturation along inflammatory response. In recent years, several caspases involved in cell death were shown to play a role in other cellular processes such as proliferation and differentiation. In the present review, we summarize the current knowledge of the role of caspases in the differentiation of erythroid cells and macrophages. Based on these two examples, we show that the nature of involved enzymes, the pathways leading to their activation in response to specific growth factors, and the specificity of the target proteins that are cleaved by the activated enzymes strongly differ from one cell type to another. Deregulation of these pathways is thought to play a role in the pathophysiology of low-grade myelodysplastic syndromes, characterized by excessive activation of caspases and erythroid precursor apoptosis, and that of chronic myelomonocytic leukemia, characterized by a defective activation of caspases in monocytes exposed to M-CSF, which blocks their differentiation.

Acute liver failure (ALF) of infectious origin results from massive Fas-mediated hepatocyte apoptosis. To cure Fas-induced ALF in mice, we have designed a noninvasive procedure for intrahepatic transfer of a plasmid that encodes a molecule inhibiting Fas-Fas ligand interaction. For that purpose, naked pDNA encoding green fluorescent protein (GFP) or the Fas-Fc chimeric protein was transferred into mice by the biliary route. Ten percent of hepatocytes expressed GFP. After pFas-Fc transfer, about 40 ng of Fas-Fc protein per milliliter could be detected in sera from day 4 to day 28. Serum recombinant Fas-Fc could neutralize Fas-induced cell death in vitro. Furthermore, pFas-Fc biliary transfer efficiently protected mice against Fas-mediated ALF, because survival rates (p < 0.01), serum transaminase activities (p < 0.05), and histological data (p < 0.02) were improved versus control pTNFR-Fc-transfected mice. In conclusion, naked pDNA encoding Fas-Fc is efficiently expressed by hepatocytes after biliary gene transfer in mice. This method, devoid of virus-related risks, could be considered for the treatment of Fas-mediated ALF in humans.

IL-1 is a key cytokine involved in the inflammatory response. The type II receptor of IL-1 (IL-1RII) acts as a decoy receptor, binding and inhibiting the effect of IL-1. This study was undertaken to establish whether IL-1RII can ameliorate collagen-induced arthritis, a model of inflammatory arthritis in mice. We used human keratinocytes transfected with the human (h)IL-1 RII gene as a source of hIL-1 RII protein. We showed that these cells expressed both the membrane and soluble form of receptor. In vitro, IL-1-stimulated murine macrophage cells showed a decreased expression of TNF-alpha in the presence of hIL-1 RII. We engrafted the hIL-1RII-transfected cells in the back of mice developing collagen-induced arthritis. We found that clinical and histological parameters of arthritis were significantly decreased in mice treated with cells producing hIL-1RII. In addition, hIL-1RII administration was able to reduce the expression of mRNA for IL-6 and myeloperoxidase in the joints of treated animals. These data show that hIL-1 RII anti-inflammatory properties in the model of collagen-induced arthritis in mice and could have a regulatory role in rheumatoid arthritis.

The present study was aimed at investigating whether the expression of Fas ligand (FasL) by CHO cells transfected with IL-4 (CHO/IL-4) or IL-10 (CHO/IL-10) genes would improve the effect of the cytokine. DBA/ 1 mice immunized with type II collagen were treated with suboptimal doses of transfected CHO cells (a single s. c. injection of 2 x 10(5) cells) around onset of arthritis. Severe collagen-induced arthritis (CIA) developed in the control groups injected with PBS, CHO /beta-galactosidase/FasL, CHO/IL-4 or CHO/IL-10 cells. In contrast, administration of CHO/IL-4/FasL, but not CHO/IL-10/FasL, cells significantly reduced the clinical severity and resulted in rapid and sustained suppressive effect. Amelioration of CIA was not due to a prolonged in vivo secretion of IL-4 since expression of FasL by CHO cells shortened the in vivo survival of the xenogeneic cells. In fact, administration of FasL(+) cells was associated with a decreased proportion of Mac1(+) neutrophils in the blood and an increased expression of myeloperoxidase at the site of engineered cell engraftment. These findings suggest that the mechanism underlying the beneficial effect of IL-4 delivered by cells expressing FasL involves the combination of the anti-inflammatory properties of IL-4 and the apoptosis of Fas(+) Mac1(+) granulocytes participating in the pathogenic process.