In utero arsenic exposure and epigenome-wide associations in placenta,umbilical artery,and human umbilical vein endothelial cells

Exposure to arsenic early in life has been associated with increased risk of several chronic diseases and is believed to alter epigenetic programming in utero. In the present study, we evaluate the epigenome-wide association of arsenic exposure in utero and DNA methylation in placenta (n = 37), umbilical artery (n = 45) and human umbilical vein endothelial cells (HUVEC) (n = 52) in a birth cohort using the Infinium HumanMethylation450 BeadChip array. Unadjusted and cell mixture adjusted associations for each tissue were examined along with enrichment analyses relative to CpG island location and omnibus permutation tests of association among biological pathways. One CpG in artery (cg26587014) and 4 CpGs in placenta (cg12825509; cg20554753; cg23439277; cg21055948) reached a Bonferroni adjusted level of significance. Several CpGs were differentially methylated in artery and placenta when controlling the false discovery rate (q-value<0.05), but none in HUVEC. Enrichment of hypomethylated CpG islands was observed for artery while hypermethylation of open sea regions were present in placenta relative to prenatal arsenic exposure. The melanogenesis pathway was differentially methylated in artery (Max F P < 0.001), placenta (Max F P < 0.001), and HUVEC (Max F P = 0.02). Similarly, the insulin-signaling pathway was differentially methylated in artery (Max F P = 0.02), placenta (Max F P = 0.02), and HUVEC (Max F P = 0.02). Our results show that prenatal arsenic exposure can alter DNA methylation in artery and placenta but not in HUVEC. Further studies are needed to determine if these alterations in DNA methylation mediate the effect of prenatal arsenic exposure and health outcomes later in life.     

Identification of diamino chromone-2-carboxamides as MCHr1 antagonists with minimal hERG channel activity

A series of potent 2-carboxychromone-based melanin-concentrating hormone receptor 1 (MCHr1) antagonists were synthesized and evaluated for hERG (human Ether-a-go-go Related Gene) channel affinity and functional blockade. Basic dialkylamine-terminated analogs were found to weakly bind the hERG channel and provided marked improvement in a functional patch-clamp assay versus previously reported antagonists of the series.     

Atmospheric water vapor as driver of litter decomposition in Mediterranean shrubland and grassland during rainless seasons

Litter production in many drought‐affected ecosystems coincides with the beginning of an extended season of no or limited rainfall. Because of lack of moisture litter decomposition during such periods has been largely ignored so far, despite potential importance for the overall decay process in such ecosystems. To determine drivers and extent of litter decay in rainless periods, a litterbag study was conducted in Mediterranean shrublands, dwarf shrublands and grasslands. Heterogeneous local and common straw litter was left to decompose in open and shaded patches of various field sites in two study regions. Fresh local litter lost 4–18% of its initial mass over about 4 months without rainfall, which amounted to 15–50% of total annual decomposition. Lab incubations and changes in chemical composition suggested that litter was degraded by microbial activity, enabled by absorption of water vapor from the atmosphere. High mean relative humidity of 85% was measured during 8–9 h of most nights, but the possibility of fog deposition or dew formation at the soil surface was excluded. Over 95% of the variation in mass loss and changes in litter nitrogen were explained by characteristics of water‐vapor uptake by litter. Photodegradation induced by the intense solar radiation was an additional mechanism of litter decomposition as indicated by lignin dynamics. Lignin loss from litter increased with exposure to ultraviolet radiation and with initial lignin concentration, together explaining 90%–97% of the variation in lignin mass change. Our results indicate that water vapor, solar radiation and litter quality controlled decomposition and changes in litter chemistry during rainless seasons. Many regions worldwide experience transient periods without rainfall, and more land area is expected to undergo reductions in rainfall as a consequence of climate change. Therefore, absorption of water vapor might play a role in decomposition and nutrient cycling in an increasing number of ecosystems.     

Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted

Background

Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Little work has been done that simultaneously examines the spectrum of both types of changes in human tumors on a genome-wide scale and results so far have been limited and mixed. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC.

Methodology/Principal Findings

We have extended a prior analysis of 1,413 cancer-associated loci for epigenetic changes in HNSCC by integrating DNA copy number alterations, measured at 500,000 polymorphic loci, in a case series of 19 primary HNSCC tumors. We have previously demonstrated that local copy number does not bias methylation measurements in this array platform. Importantly, we found that the global pattern of copy number alterations in these tumors was significantly associated with tumor methylation profiles (p<0.002). However at the local level, gene promoter regions did not exhibit a correlation between copy number and methylation (lowest q = 0.3), and the spectrum of genes affected by each type of alteration was unique.

Conclusion/Significance

This work, using a novel and robust statistical approach demonstrates that, although a “second hit” mechanism is not likely the predominant mode of action for epigenetic dysregulation in cancer, the patterns of methylation events are associated with the patterns of allele loss. Our work further highlights the utility of integrative genomics approaches in exploring the driving somatic alterations in solid tumors.     

Response of Reticulitermes flavipes (Isoptera: Rhinotermitidae) to disturbance in laboratory arenas at different temperatures and soldier proportions

This study examined the evacuation response of groups of Reticulitermes flavipes (Kollar) workers after disturbance in laboratory arenas across a range of temperatures (16, 21, and 27 degrees C) and soldier proportions (1, 3, and 5%). Groups of workers and soldiers were disturbed in a central chamber and then monitored during a 5-d period to examine the percentage that initially evacuated, percentage of evacuees that returned, time to evacuate, time to return, and rates (percentage per hour) of evacuation and return between different temperatures and between soldier levels. Disturbance response patterns were observed that generally consisted of partial evacuation followed by movement back into disturbed areas. General alarm responses were observed and initiated specific alarm responses that resulted in more termites eventually returning to disturbed areas than originally evacuated. The typical evacuation response was not observed in groups with 5% soldiers. Instead, clustering in disturbed areas replaced evacuation. Regression revealed significant correlations between temperature and evacuation time, return time, evacuation rate, and return rate, indicating that R. flavipes alarm behaviors are influenced by temperature. There was a significant correlation between soldier proportions and the percentage of evacuees returning to disturbed areas. Analysis of variance (ANOVA) revealed significant differences between temperatures in the time to evacuate, evacuation rate, time to return, and return rate. ANOVA also showed significant differences between soldier proportions in the mean percentage of evacuees from and the rate of return to disturbed areas. Our results demonstrate that temperature influences the rate, but not the magnitude, of alarm response, whereas the influence of soldiers may not be as important in the context of general alarm as specific alarm.     

Feature-specific penalized latent class analysis for genomic data

Genomic data are often characterized by a moderate to large number of categorical variables observed for relatively few subjects. Some of the variables may be missing or noninformative. An example of such data is loss of heterozygosity (LOH), a dichotomous variable, observed on a moderate number of genetic markers. We first consider a latent class model where, conditional on unobserved membership in one of k classes, the variables are independent with probabilities determined by a regression model of low dimension q. Using a family of penalties including the ridge and LASSO, we extend this model to address higher-dimensional problems. Finally, we present an orthogonal map that transforms marker space to a space of "features" for which the constrained model has better predictive power. We demonstrate these methods on LOH data collected at 19 markers from 93 brain tumor patients. For this data set, the existing unpenalized latent class methodology does not produce estimates. Additionally, we show that posterior classes obtained from this method are associated with survival for these patients.     

Parental care trade‐offs in the inter‐brood phase in Barn Swallows Hirundo rustica

In seasonal environments with limited time and energy resources, double‐brooded birds face trade‐offs in the timing of their two reproductive attempts and in the effort allocated to the first and the second broods. In the Barn Swallow Hirundo rustica a long care period for the first brood enhances the survival of first‐brood chicks, but also delays the start of the second brood, which in turn reduces the survival prospects of second‐brood chicks. Probably as a response to this trade‐off, double‐brooded Barn Swallows reduce the period of post‐fledging care for first‐brood fledglings. By radiotracking whole families, we investigated the determinants of this behaviour and its consequences for the survival of the first‐brood fledglings. The end of the females’ investment in post‐fledging care of the first brood was related to the beginning of egg synthesis for the second clutch. With the start of egg synthesis, females significantly reduced provisioning rates to the first‐brood fledglings to less than one‐fifth of the previous rates, while the proportion of time they spent foraging remained high. Assuming that the females’ foraging success was constant, we conclude that their energy income was allocated to egg production rather than fledgling provision. Males did not compensate for the females’ reduced feeding rates. Thus the start of egg production for the second clutch had a marked effect on the quantity of food received by first‐brood fledglings. In parallel with the changes in parental behaviour and provisioning rates, we observed a marked drop in the daily survival rate of first‐brood chicks. These results support the hypothesis that females face a strong trade‐off in the allocation of energy to subsequent broods. Energy allocation to a second clutch involves a cost in terms of reduced provisioning, and as a result the survival of first‐brood chicks is compromised. This is probably outweighed by the improved success of an early second brood.     

Dynamics of the Microbiota in Response to Host Infection

Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. We developed a computational framework to discover time-varying signatures for individual taxa, and to automatically group signatures to identify microbial sub-communities within the larger gut ecosystem that demonstrate common behaviors. Application of this model to the 16S rDNA dataset revealed dynamic alterations in the microbiota at multiple levels of resolution, from effects on systems-level metrics to changes across anatomic sites for individual taxa and species. These analyses revealed unique, time-dependent microbial signatures associated with host responses at different stages of colitis. Signatures included a Mucispirillum OTU associated with early disruption of the colonic surface mucus layer, prior to the onset of symptomatic colitis, and members of the Clostridiales and Lactobacillales that increased with successful resolution of inflammation, after clearance of the pathogen. Quantitative culture data validated findings for predominant species, further refining and strengthening model predictions. These findings provide new insights into the complex behaviors found within host ecosystems, and define several time-dependent microbial signatures that may be leveraged in studies of other infectious or inflammatory conditions.     

History of Parvovirus B19 infection is associated with a DNA methylation signature in childhood acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) likely has a multistep etiology, with initial genetic aberrations occurring early in life. An abnormal immune response to common infections has emerged as a plausible candidate for triggering the proliferation of pre-leukemic clones and the fixation of secondary genetic mutations and epigenetic alterations. We investigated whether evidence of infection with a specific common myelotropic childhood virus, parvovirus B19 (PVB19), relates to patterns of gene promoter DNA methylation in ALL patients. We serologically tested bone marrow samples at diagnosis of B-cell ALL for PVB19 infection and DNA methylation using a high-throughput bead array and found that 4.2% and 36.7% of samples were seroreactive to PVB19 IgM and IgG, respectively. Leukemia samples were grouped by DNA methylation pattern. Controlling for age and immunophenotype, unsupervised modeling confirmed that the DNA methylation pattern was associated with history of PVB19 (assessed by IgG, p = 0.02), but not recent infection (assessed by IgM). Replication assays on single genes were consistent with the association. The data indicate that a common viral illness may drive specific DNA methylation patterns in susceptible B-precursor cells, contributing to the leukemogenic potential of such cells. Infections may impact childhood leukemia by altering DNA methylation patterns and specific key genes in susceptible cells; these changes may be retained even after the clearance of infection.