Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles

Background

Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes.

Results

Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences.

Conclusions

Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.     

IL-1β Production through the NLRP3 Inflammasome by Hepatic Macrophages Links Hepatitis C Virus Infection with Liver Inflammation and Disease

Chronic hepatitis C virus (HCV) infection is a leading cause of liver disease. Liver inflammation underlies infection-induced fibrosis, cirrhosis and liver cancer but the processes that promote hepatic inflammation by HCV are not defined. We provide a systems biology analysis with multiple lines of evidence to indicate that interleukin-1β (IL-1β) production by intrahepatic macrophages confers liver inflammation through HCV-induced inflammasome signaling. Chronic hepatitis C patients exhibited elevated levels of serum IL-1β compared to healthy controls. Immunohistochemical analysis of healthy control and chronic hepatitis C liver sections revealed that Kupffer cells, resident hepatic macrophages, are the primary cellular source of hepatic IL-1β during HCV infection. Accordingly, we found that both blood monocyte-derived primary human macrophages, and Kupffer cells recovered from normal donor liver, produce IL-1β after HCV exposure. Using the THP-1 macrophage cell-culture model, we found that HCV drives a rapid but transient caspase-1 activation to stimulate IL-1β secretion. HCV can enter macrophages through non-CD81 mediated phagocytic uptake that is independent of productive infection. Viral RNA triggers MyD88-mediated TLR7 signaling to induce IL-1β mRNA expression. HCV uptake concomitantly induces a potassium efflux that activates the NLRP3 inflammasome for IL-1β processing and secretion. RNA sequencing analysis comparing THP1 cells and chronic hepatitis C patient liver demonstrates that viral engagement of the NLRP3 inflammasome stimulates IL-1β production to drive proinflammatory cytokine, chemokine, and immune-regulatory gene expression networks linked with HCV disease severity. These studies identify intrahepatic IL-1β production as a central feature of liver inflammation during HCV infection. Thus, strategies to suppress NLRP3 or IL-1β activity could offer therapeutic actions to reduce hepatic inflammation and mitigate disease.     

Bi-PROF

The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 10²-10⁴ sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer.     

The Ktr potassium transport system in Staphylococcus aureus and its role in cell physiology,antimicrobial resistance and pathogenesis

Potassium (K⁺) plays a vital role in bacterial physiology, including regulation of cytoplasmic pH, turgor pressure and transmembrane electrical potential. Here, we examine the Staphylococcus aureus Ktr system uniquely comprised of two ion‐conducting proteins (KtrB and KtrD) and only one regulator (KtrA). Growth of Ktr system mutants was severely inhibited under K⁺ limitation, yet detectable after an extended lag phase, indicating the presence of a secondary K⁺ transporter. Disruption of both ktrA and the Kdp‐ATPase system, important for K⁺ uptake in other organisms, eliminated regrowth in 0.1 mM K⁺, demonstrating a compensatory role for Kdp to the Ktr system. Consistent with K⁺ transport mutations, S. aureus devoid of the Ktr system became sensitive to hyperosmotic conditions, exhibited a hyperpolarized plasma membrane, and increased susceptibility to aminoglycoside antibiotics and cationic antimicrobials. In contrast to other organisms, the S. aureus Ktr system was shown to be important for low‐K⁺ growth under alkaline conditions, but played only a minor role in neutral and acidic conditions. In a mouse competitive index model of bacteraemia, the ktrA mutant was significantly outcompeted by the parental strain. Combined, these results demonstrate a primary mechanism of K⁺ uptake in S. aureus and a role for this system in pathogenesis.     

Characterization of Vascular Disease Risk in Postmenopausal Women and Its Association with Cognitive Performance

Objectives

While global measures of cardiovascular (CV) risk are used to guide prevention and treatment decisions, these estimates fail to account for the considerable interindividual variability in pre-clinical risk status. This study investigated heterogeneity in CV risk factor profiles and its association with demographic, genetic, and cognitive variables.

Methods

A latent profile analysis was applied to data from 727 recently postmenopausal women enrolled in the Kronos Early Estrogen Prevention Study (KEEPS). Women were cognitively healthy, within three years of their last menstrual period, and free of current or past CV disease. Education level, apolipoprotein E ε4 allele (APOE4), ethnicity, and age were modeled as predictors of latent class membership. The association between class membership, characterizing CV risk profiles, and performance on five cognitive factors was examined. A supervised random forest algorithm with a 10-fold cross-validation estimator was used to test accuracy of CV risk classification.

Results

The best-fitting model generated two distinct phenotypic classes of CV risk 62% of women were “low-risk” and 38% “high-risk”. Women classified as low-risk outperformed high-risk women on language and mental flexibility tasks (p = 0.008) and a global measure of cognition (p = 0.029). Women with a college degree or above were more likely to be in the low-risk class (OR = 1.595, p = 0.044). Older age and a Hispanic ethnicity increased the probability of being at high-risk (OR = 1.140, p = 0.002; OR = 2.622, p = 0.012; respectively). The prevalence rate of APOE-ε4 was higher in the high-risk class compared with rates in the low-risk class.

Conclusion

Among recently menopausal women, significant heterogeneity in CV risk is associated with education level, age, ethnicity, and genetic indicators. The model-based latent classes were also associated with cognitive function. These differences may point to phenotypes for CV disease risk. Evaluating the evolution of phenotypes could in turn clarify preclinical disease, and screening and preventive strategies.ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00154180","term_id":"NCT00154180"}}NCT00154180     

Does the Earth's Magnetic Field Serve as a Reference for Alignment of the Honeybee Waggle Dance?

The honeybee (Apis mellifera) waggle dance, which is performed inside the hive by forager bees, informs hive mates about a potent food source, and recruits them to its location. It consists of a repeated figure-8 pattern: two oppositely directed turns interspersed by a short straight segment, the “waggle run”. The waggle run consists of a single stride emphasized by lateral waggling motions of the abdomen. Directional information pointing to a food source relative to the sun''s azimuth is encoded in the angle between the waggle run line and a reference line, which is generally thought to be established by gravity. Yet, there is tantalizing evidence that the local (ambient) geomagnetic field (LGMF) could play a role. We tested the effect of the LGMF on the recruitment success of forager bees by placing observation hives inside large Helmholtz coils, and then either reducing the LGMF to 2% or shifting its apparent declination. Neither of these treatments reduced the number of nest mates that waggle dancing forager bees recruited to a feeding station located 200 m north of the hive. These results indicate that the LGMF does not act as the reference for the alignment of waggle-dancing bees.     

Communication ecology of webbing clothes moth: attractiveness and characterization of male-produced sonic aggregation signals

Abstract:  We tested the hypothesis that the webbing clothes moth, Tineola bisselliella (Hum.) (Lep., Tineidae), uses sonic signals in addition to pheromonal signals for communication. To record sound from individual or groups of moths of either or both sexes, we used a digital recording system, microphones sensitive to sonic and/or ultrasonic frequencies, and speakers capable of emitting sonic and ultrasonic sound. In a soundproof environment, male T. bisselliella produced sounds of 27 decibels (dB, sound pressure level; 0 dB corresponds to 20  μ Pa), with a base frequency of 40–50 Hz and a harmonic frequency of 80–100 Hz. Sound intensity and frequency increased to 55 dB and 65–75 Hz (with ≥3 harmonic frequencies), respectively, when calling males were near (<2 cm) conspecifics of either sex. There was no evidence that females produce sound and no evidence for ultrasonic sound production by either sex. In Y-tube bioassay experiments, virgin male and female T. bisselliella preferred played-back sonic signals from males to silent control stimuli, whereas mated females showed no preference for either stimulus. In arena bioassay experiments, males as well as virgin and mated females preferred played-back sonic signals from males over a white noise control. Use of pheromonal and sonic signals by T. bisselliella would be adaptive, because the capacity for sonic communication persists even if sensory adaptation or habituation to pheromonal signals occurred. This hypothesis is consistent with the fact that other inhabitants of enclosed microhabitats, such as the greater wax moth, Galleria mellonella L., and Indian meal moth, Plodia interpunctella (Hb.), have also evolved analogous multimodal communication systems.     

A workplace intervention to promote stair climbing: greater effects in the overweight

Objective: Stair climbing is a lifestyle physical activity that uses more calories per minute than jogging. This study tested an intervention designed to promote stair climbing in a workplace. Because previous studies provide only equivocal evidence of the effects of increased stair climbing in worksites, a formal comparison of the effects of the intervention on stair ascent and descent was made. Research Methods and Procedures: In a five‐story public sector building, a 2‐week baseline was followed by 6 weeks of an intervention involving a 23½‐ × 16½‐inch poster in the lobby, the same poster and six messages affixed to the stair risers between floors, and an 11¾‐ × 8¼‐inch point‐of‐choice prompt at the elevators. Stair and elevator choices (n = 26,806) were videotaped throughout and subsequently coded for direction of travel, traveler's sex, and traveler's load. Weight status was coded using silhouettes beside the computer monitor. Results: A significant effect of the intervention on stair climbing was greater in those coded as overweight (+5.4%; odds ratio = 1.33) than in individuals of normal weight (+2.5%; odds ratio = 1.12). Although stair descent was more common than ascent, the intervention had similar effects for both directions of travel. Discussion: Stair climbing at work has few barriers and seems to be a type of physical activity that is acceptable to overweight individuals. The relatively weak effect of workplace interventions compared with results for public access staircases may reflect uncontrolled effects such as the immediate availability of the elevator for the traveler.     

Absence of seasonal variation in great tit offspring sex ratios

When the timing of breeding affects the reproductive value of sons and daughters differently, parents are expected to increase their fitness by changing the offspring sex ratio during the course of the breeding season. Previous studies have shown that in great tits Parus major hatching date has a stronger effect on the fitness of juvenile males than on that of juvenile females. We tested whether this difference was reflected in a seasonal decline in the proportion of sons per breeding attempt. Although offspring sex ratio was more variable than would be expected from a binomial distribution, there was no significant relationship between the proportion of sons and the laying date of the clutch. Moreover, individual females did not adjust the sex ratio of their offspring following an experimental delay of breeding. This study therefore fails to demonstrate adaptive seasonal variation in great tit offspring sex ratios.     

Sex pheromone of Nearctic Agriotes mancus and its similarity to that of three Palearctic Agriotes invasive in North America

1. The wheat wireworm, Agriotes mancus (Coleoptera: Elateridae), is a predominant elaterid pest species in the Nearctic region, with a life history and morphology similar to those of Agriotes obscurus, Agriotes lineatus and Agriotes sputator, three Palearctic pest elaterids invasive in North America. Here, we report the identification and field testing of the sex pheromone of A. mancus.
2. We collected headspace volatiles from female beetles on Porapak Q, and analysed aliquots of Porapak extract by gas chromatography with electroantennographic detection (GC-EAD) and by GC-mass spectrometry. In GC-EAD recordings, two esters—geranyl butanoate and geranyl hexanoate—elicited antennal responses from A. mancus males. In field experiments, trap lures containing both geranyl butanoate and geranyl hexanoate afforded large captures of A. mancus males, which were—on average—approximately 30-fold higher than captures in traps baited with a single ester.
3. Traps baited with geranyl butanoate as a single-component lure captured a significant number of Palearctic A. sputator, indicating the establishment of A. sputator in its invaded Nearctic range.
4. With the A. mancus sex pheromone now known, it can be included in the development of pheromone-based programmes to monitor and manage native and invasive Agriotes pests in North America.