Time‐dependent classification accuracy curve under marker‐dependent sampling

Evaluating the classification accuracy of a candidate biomarker signaling the onset of disease or disease status is essential for medical decision making. A good biomarker would accurately identify the patients who are likely to progress or die at a particular time in the future or who are in urgent need for active treatments. To assess the performance of a candidate biomarker, the receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC) are commonly used. In many cases, the standard simple random sampling (SRS) design used for biomarker validation studies is costly and inefficient. In order to improve the efficiency and reduce the cost of biomarker validation, marker‐dependent sampling (MDS) may be used. In a MDS design, the selection of patients to assess true survival time is dependent on the result of a biomarker assay. In this article, we introduce a nonparametric estimator for time‐dependent AUC under a MDS design. The consistency and the asymptotic normality of the proposed estimator is established. Simulation shows the unbiasedness of the proposed estimator and a significant efficiency gain of the MDS design over the SRS design.     

Hsp90‐dependent regulatory circuitry controlling temperature‐dependent fungal development and virulence

The pathogenic fungi Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans are an increasing cause of human mortality, especially in immunocompromised populations. During colonization and adaptation to various host environments, these fungi undergo morphogenetic alterations that allow for survival within the host. One key environmental cue driving morphological changes is external temperature. The Hsp90 chaperone protein provides one mechanism to link temperature with the signalling cascades that regulate morphogenesis, fungal development and virulence. Candida albicans is a model system for understanding the connections between morphogenesis and Hsp90. Due to the high degree of conservation in Hsp90, many of the connections in C. albicans may be extrapolated to other fungal pathogens or parasites. Examining the role of Hsp90 during development and morphogenesis in these three major fungal pathogens may provide insight into key aspects of adaptation to the host, leading to additional avenues for therapy.     

Branching patterns in phylogenies cannot distinguish diversity‐dependent diversification from time‐dependent diversification

One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.     

Flavin oxidation in flavin‐dependent N‐monooxygenases

Siderophore A (SidA) from Aspergillus fumigatus is a flavin‐containing monooxygenase that hydroxylates ornithine (Orn) at the amino group of the side chain. Lysine (Lys) also binds to the active site of SidA; however, hydroxylation is not efficient and H₂O₂ is the main product. The effect of pH on steady‐state kinetic parameters was measured and the results were consistent with Orn binding with the side chain amino group in the neutral form. From the pH dependence on flavin oxidation in the absence of Orn, a pK_a value >9 was determined and assigned to the FAD‐N5 atom. In the presence of Orn, the pH dependence displayed a pK_a value of 6.7 ±0.1 and of 7.70 ±0.10 in the presence of Lys. Q102 interacts with NADPH and, upon mutation to alanine, leads to destabilization of the C4a‐hydroperoxyflavin (FAD_OOH). Flavin oxidation with Q102A showed a pK_a value of ~8.0. The data are consistent with the pK_a of the FAD N5‐atom being modulated to a value >9 in the absence of Orn, which aids in the stabilization of FAD_OOH. Changes in the FAD‐N5 environment lead to a decrease in the pK_a value, which facilitates elimination of H₂O₂ or H₂O. These findings are supported by solvent kinetic isotope effect experiments, which show that proton transfer from the FAD N5‐atom is rate limiting in the absence of a substrate, however, is significantly less rate limiting in the presence of Orn and or Lys.     

Frequency‐dependent and density‐dependent larval competition between life‐history strains of a fly,Lucilia cuprina

1. Competition was created between the larvae of two life‐history strains of the blowfly Lucilia cuprina (Wiedemann) that have different requirements for larval resource acquisition. Adult females of one strain had the ability to mature eggs in the absence of adult feeding (autogeny) whereas the other strain lacked this ability. Autogeny shifts the burden of resource acquisition from adults to larvae, potentially leading to greater competition at this earlier life history stage. 2. A replacement series was used to determine the per‐capita competitive effect between strains relative to the intra‐strain effect, and density‐ and frequency‐dependent variation in this per‐capita effect was then evaluated. Evidence was found of competitive superiority of autogenous larvae when they occurred at a low frequency and low density, but their competitive ability was lost or reversed at higher frequencies and densities. 3. A dynamic competitive environment created by frequency and density dependence can account for the maintenance of genetic diversity for major life‐history traits. Such competition may explain why autogeny is rare in field populations of L. cuprina even although underlying genetic variation for the trait seems to be present.     

Metal‐dependent assembly of a protein nano‐cage

Short, alpha‐helical coiled coils provide a simple, modular method to direct the assembly of proteins into higher order structures. We previously demonstrated that by genetically fusing de novo–designed coiled coils of the appropriate oligomerization state to a natural trimeric protein, we could direct the assembly of this protein into various geometrical cages. Here, we have extended this approach by appending a coiled coil designed to trimerize in response to binding divalent transition metal ions and thereby achieve metal ion‐dependent assembly of a tetrahedral protein cage. Ni²⁺, Co²⁺, Cu²⁺, and Zn²⁺ ions were evaluated, with Ni²⁺ proving the most effective at mediating protein assembly. Characterization of the assembled protein indicated that the metal ion–protein complex formed discrete globular structures of the diameter expected for a complex containing 12 copies of the protein monomer. Protein assembly could be reversed by removing metal ions with ethylenediaminetetraacetic acid or under mildly acidic conditions.     

Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support

Diversification rates vary over time, yet the factors driving these variations remain unclear. Temporal declines in speciation rates have often been interpreted as the effect of ecological limits, competition, and diversity dependence, emphasising the role of biotic factors. Abiotic factors, such as climate change, are also supposed to have affected diversification rates over geological time scales, yet direct tests of these presumed effects have mainly been limited to few clades well represented in the fossil record. If warmer climatic periods have sustained faster speciation, this could explain slowdowns in speciation during the Cenozoic climate cooling. Here, we apply state‐of‐the art diversity‐dependent and temperature‐dependent phylogenetic models of diversification to 218 tetrapod families, along with constant rate and time‐dependent models. We confirm the prevalence of diversification slowdowns, and find as much support for temperature‐dependent than diversity‐dependent models. These results call for a better integration of these two processes in studies of diversification dynamics.     

Context‐dependent conservation of the cavity‐nesting European Roller

To maximize the effectiveness of conservation interventions, it is crucial to have an understanding of how intraspecific variation determines the relative importance of potential limiting factors. For bird populations, limiting factors include nest‐site availability and foraging resources, with the former often addressed through the provision of artificial nestboxes. However, the effectiveness of artificial nestboxes depends on the relative importance of nest‐site vs. foraging resource limitations. Here, we investigate factors driving variation in breeding density, nestbox occupation and productivity in two contrasting study populations of the European Roller Coracias garrulus, an obligate cavity‐nesting insectivorous bird. Breeding density was more than four times higher at the French study site than at the Latvian site, and there was a positive correlation between breeding density (at the 1‐km² scale) and nest‐site availability in France, whereas there was a positive correlation between breeding density and foraging resource availability in Latvia. Similarly, the probability of a nestbox being occupied increased with predicted foraging resource availability in Latvia but not in France. We detected no positive effect of foraging resource availability on productivity at either site, with most variation in breeding success driven by temporal effects: a seasonal decline in France and strong interannual fluctuations in Latvia. Our results indicate that the factors limiting local breeding density can vary across a species' range, resulting in different conservation priorities. Nestbox provisioning is a sufficient short‐term conservation solution at our French study site, where foraging resources are typically abundant, but in Latvia the restoration of foraging habitat may be more important.     

Activity‐dependent secretion of alpha‐synuclein by enteric neurons

There is growing evidence supporting a role of extracellular alpha‐synuclein in the spreading of Parkinson's disease (PD) pathology. Recent pathological studies have raised the possibility that the enteric nervous system (ENS) is one of the initial sites of alpha‐synuclein pathology in PD. We therefore undertook this survey to determine whether alpha‐synuclein can be secreted by enteric neurons. Alpha‐synuclein secretion was assessed by immunoblot analysis of the culture medium from primary culture of ENS. We show that alpha‐synuclein is physiologically secreted by enteric neurons via a conventional, endoplasmic reticulum/Golgi‐dependent exocytosis, in a neuronal activity‐regulated manner. Our study is the first to evidence that enteric neurons are capable of secreting alpha‐synuclein, thereby providing new insights into the role of the ENS in the pathophysiology of PD.     

IGF‐I regulates the age‐dependent signaling peptide humanin

Aging is influenced by endocrine pathways including the growth hormone/insulin‐like growth factor‐1 (GH/IGF) axis. Mitochondrial function has also been linked to the aging process, but the relevant mitochondrial signals mediating the effects of mitochondria are poorly understood. Humanin is a novel signaling peptide that acts as a potent regulator of cellular stress responses and protects from a variety of in vitro and in vivo toxic and metabolic insults. The circulating levels of humanin decline with age in mice and humans. Here, we demonstrate a negative correlation between the activity of the GH‐IGF axis and the levels of humanin, as well as a positive correlation between humanin and lifespan in mouse models with altered GH/IGF‐I axis. Long‐lived, GH‐deficient Ames mice displayed elevated humanin levels, while short‐lived GH‐transgenic mice have reduced humanin levels. Furthermore, treatment with GH or IGF‐I reduced circulating humanin levels in both mice and human subjects. Our results indicate that GH and IGF are potent regulators of humanin levels and that humanin levels correlate with lifespan in mice. This suggests that humanin represents a circulating mitochondrial signal that participates in modulating the aging process, adding a coordinated mitochondrial element to the endocrine regulation of aging.     

State‐dependent attacks in a mosquito

Mosquito biting frequency and meal size are considered to be important parameters in the epidemiology of insect‐vectored diseases such as malaria. Because both parameters are likely to depend on the size and energetic state of adult mosquitoes, the present study investigates the effects of body size and energy state on attack behaviours in the malaria mosquito, Anopheles gambiae. Attack rates are measured as well as total time spent before giving up for individual females when provided with an unobtainable human hand (i.e. mosquitoes are dislodged every time that they land). The factorial design considers two body sizes, small and large, as well as three sugar deprivation states, 0, 1 and 2 days. The results reveal a positive effect of size on attack rate and a nonlinear effect of energy state, where mosquitoes of intermediate energy state show lower attack rates than either 2‐day food‐deprived or nondeprived mosquitoes. Moreover, attack rate is negatively associated with persistence time in nondeprived and 2‐day food‐deprived Anopheles but is unrelated to persistence time in 1‐day food‐deprived mosquitoes, Interestingly, although persistence times are generally inversely related to attack rates, they are not significantly influenced by either energetic or size states.     

The biodiversity‐dependent ecosystem service debt

Habitat destruction is driving biodiversity loss in remaining ecosystems, and ecosystem functioning and services often directly depend on biodiversity. Thus, biodiversity loss is likely creating an ecosystem service debt: a gradual loss of biodiversity‐dependent benefits that people obtain from remaining fragments of natural ecosystems. Here, we develop an approach for quantifying ecosystem service debts, and illustrate its use to estimate how one anthropogenic driver, habitat destruction, could indirectly diminish one ecosystem service, carbon storage, by creating an extinction debt. We estimate that c. 2–21 Pg C could be gradually emitted globally in remaining ecosystem fragments because of plant species loss caused by nearby habitat destruction. The wide range for this estimate reflects substantial uncertainties in how many plant species will be lost, how much species loss will impact ecosystem functioning and whether plant species loss will decrease soil carbon. Our exploratory analysis suggests that biodiversity‐dependent ecosystem service debts can be globally substantial, even when locally small, if they occur diffusely across vast areas of remaining ecosystems. There is substantial value in conserving not only the quantity (area), but also the quality (biodiversity) of natural ecosystems for the sustainable provision of ecosystem services.     

SUV39h‐ and A‐type lamin‐dependent telomere nuclear rearrangement

Telomeres are specialized chromatin structures that are situated at the end of linear chromosomes and play an important role in cell senescence and immortalization. Here, we investigated whether changes in histone signature influence the nuclear arrangement and positioning of telomeres. Analysis of mouse embryonic fibroblasts revealed that telomeres were organized into specific clusters that partially associated with centromeric clusters. This nuclear arrangement was influenced by deficiency of the histone methyltransferase SUV39h, LMNA deficiency, and the histone deacetylase inhibitor Trichostatin A (TSA). Similarly, nuclear radial distributions of telomeric clusters were preferentially influenced by TSA, which caused relocation of telomeres closer to the nuclear center. Telomeres also co‐localized with promyelocytic leukemia bodies (PML). This association was increased by SUV39h deficiency and decreased by LMNA deficiency. These differences could be explained by differing levels of the telomerase subunit, TERT, in SUV39h‐ and LMNA‐deficient fibroblasts. Taken together, our data show that SUV39h and A‐type lamins likely play a key role in telomere maintenance and telomere nuclear architecture. J. Cell. Biochem. 109: 915–926, 2010. © 2010 Wiley‐Liss, Inc.     

Review and comparison of ROC curve estimators for a time‐dependent outcome with marker‐dependent censoring

To quantify the ability of a marker to predict the onset of a clinical outcome in the future, time‐dependent estimators of sensitivity, specificity, and ROC curve have been proposed accounting for censoring of the outcome. In this paper, we review these estimators, recall their assumptions about the censoring mechanism and highlight their relationships and properties. A simulation study shows that marker‐dependent censoring can lead to important biases for the ROC estimators not adapted to this case. A slight modification of the inverse probability of censoring weighting estimators proposed by Uno et al. (2007) and Hung and Chiang (2010a) performs as well as the nearest neighbor estimator of Heagerty et al. (2000) in the simulation study and has interesting practical properties. Finally, the estimators were used to evaluate abilities of a marker combining age and a cognitive test to predict dementia in the elderly. Data were obtained from the French PAQUID cohort. The censoring appears clearly marker‐dependent leading to appreciable differences between ROC curves estimated with the different methods.     

Bromodomain‐dependent stage‐specific male genome programming by Brdt

Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post‐meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis‐specific gene expression program. In meiotic and post‐meiotic cells, Brdt initiates a genuine histone acetylation‐guided programming of the genome by activating essential genes and repressing a ‘progenitor cells’ gene expression program. At post‐meiotic stages, a global chromatin hyperacetylation gives the signal for Brdt's first bromodomain to direct the genome‐wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.     

A post‐translational,c‐di‐GMP‐dependent mechanism regulating flagellar motility

Elevated levels of the second messenger cyclic dimeric GMP, c‐di‐GMP, promote transition of bacteria from single motile cells to surface‐attached multicellular communities. Here we describe a post‐translational mechanism by which c‐di‐GMP initiates this transition in enteric bacteria. High levels of c‐di‐GMP induce the counterclockwise bias in Escherichia coli flagellar rotation, which results in smooth swimming. Based on co‐immunoprecipitation, two‐hybrid and mutational analyses, the E. coli c‐di‐GMP receptor YcgR binds to the FliG subunit of the flagellum switch complex, and the YcgR–FliG interaction is strengthened by c‐di‐GMP. The central fragment of FliG binds to YcgR as well as to FliM, suggesting that YcgR–c‐di‐GMP biases flagellum rotation by altering FliG‐FliM interactions. The c‐di‐GMP‐induced smooth swimming promotes trapping of motile bacteria in semi‐solid media and attachment of liquid‐grown bacteria to solid surfaces, whereas c‐di‐GMP‐dependent mechanisms not involving YcgR further facilitate surface attachment. The YcgR–FliG interaction is conserved in the enteric bacteria, and the N‐terminal YcgR/PilZN domain of YcgR is required for this interaction. YcgR joins a growing list of proteins that regulate motility via the FliG subunit of the flagellum switch complex, which suggests that FliG is a common regulatory entryway that operates in parallel with the chemotaxis that utilizes the FliM‐entryway.