Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles

Throughout most of the mammalian genome, genetically regulated developmental programming establishes diverse yet predictable epigenetic states across differentiated cells and tissues. At metastable epialleles (MEs), conversely, epigenotype is established stochastically in the early embryo then maintained in differentiated lineages, resulting in dramatic and systemic interindividual variation in epigenetic regulation. In the mouse, maternal nutrition affects this process, with permanent phenotypic consequences for the offspring. MEs have not previously been identified in humans. Here, using an innovative 2-tissue parallel epigenomic screen, we identified putative MEs in the human genome. In autopsy samples, we showed that DNA methylation at these loci is highly correlated across tissues representing all 3 embryonic germ layer lineages. Monozygotic twin pairs exhibited substantial discordance in DNA methylation at these loci, suggesting that their epigenetic state is established stochastically. We then tested for persistent epigenetic effects of periconceptional nutrition in rural Gambians, who experience dramatic seasonal fluctuations in nutritional status. DNA methylation at MEs was elevated in individuals conceived during the nutritionally challenged rainy season, providing the first evidence of a permanent, systemic effect of periconceptional environment on human epigenotype. At MEs, epigenetic regulation in internal organs and tissues varies among individuals and can be deduced from peripheral blood DNA. MEs should therefore facilitate an improved understanding of the role of interindividual epigenetic variation in human disease.     

Use of Fluorescent Immuno-Chemistry for the detection of Edwardsiella ictaluri in channel catfish (I. punctatus) samples

While Edwardsiella ictaluri is a major pathogen of channel catfish Ictalurus punctatus and has been discovered nearly three decades ago ^1,2, so far, to the best of these authors'' knowledge, no method has been developed to allow for the in situ visualization of the bacteria in histological sections.While bacterial localization has been determined in vivo in previous studies using plate counts ³, radiometric labeled ⁴, or bioluminescent bacteria ⁵, most of these studies have only been performed at the gross organ level, with one exception ⁶. This limitation is of particular concern because E. ictaluri has a complex infection cycle ^1,7, and it has a variety of virulence factors ^8,9. The complex interaction of E. ictaluri with its host is similar in many respects to Salmonella typhi ¹⁰, which is in the same taxonomic family.Here we describe a technique allowing for the detection of bacteria using indirect immuno-histochemistry using the monoclonal Ed9 antibody described by Ainsworth et al.¹¹.Briefly, a blocking serum is applied to paraffin embedded histological sections to prevent non-specific biding. Then, the sections are incubated with the primary antibody: E. ictaluri specific monoclonal antibody Ed9. Excess antibodies are rinsed away and the FitC labeled secondary antibodies are added. After rinsing, the sections are mounted with a fluorescent specific mounting medium.This allowed for the detection of E. ictaluri in situ in histological sections of channel catfish tissues.Download video file.^{(33M, mov)}     

Synthesis of polymerized thin films for immobilized ligand display in proteomic analysis

We describe a new material for the display of biomolecular ligands for use in proteomic analysis. We report here on the construction of the first functionalized polymerized diacetylene thin films (PDTFs) for use in displaying immobilized ligands and their application in mass spectral proteomic analysis. Functionalized polymerized thin film surfaces were constructed with diacetylene-containing biotin lipid monomers designed for the capture of proteins (streptavidin) from a complex cellular lysate and detection with mass spectrometry (MS). These materials serve as a prototype for ligand-based spotted arrays amenable to high throughput screening. Functionalized PDTFs can be easily manufactured for customized microarrays and demonstrate high protein specificity and low nonspecific protein adsorption, and the resulting microarrays constructed from these materials are compatible with several different protein analysis platforms. Our results suggest that these materials have broad potential applications for use in mass spectral-based proteomic analysis.     

Differential virulence in a multiple‐host parasite of bumble bees: resolving the paradox of parasite survival?

Parasite virulence determines both the impact that parasites have on their hosts and parasite fitness. While most studies of virulence have involved single-species host–parasite interactions, the majority of parasites are likely to use multiple concurrent host species. Our understanding of how this impacts on parasite epidemiology and virulence is limited. Using the bumble bee Bombus lucorum , which exists in sympatry with B. terrestris in multi-species assemblages, and their generalist micosporidian parasite Nosema bombi , we tested whether the apparent paradox of parasite maintenance due to parasite virulence in a single host, B. terrestris , could be resolved through understanding the parasite's virulence in this sympatric host species. Nosema bombi significantly impacted colony growth, individual longevity, and individual development in B. lucorum . However, these effects were different both qualitatively and quantitatively to the parasite's impact in B. terrestris . Infected colonies of B. lucorum successfully produced both male and female reproductives, and infected female reproductives were capable of successful mating. Variation in life-history across host species may explain differences in the virulence, or impact of the parasite in B. terrestris and B. lucorum , with species with shorter life-cycles being more likely to transfer the parasite from one annual generation to the next. These results suggest that to understand the virulence and epidemiology of multi-host parasites we need to examine their ecological interactions across their various host species.     

Mapping the depth dependence of shear properties in articular cartilage

Determining the depth dependence of the shear properties of articular cartilage is essential for understanding the structure-function relation in this tissue. Here, we measured spatial variations in the shear modulus G of bovine articular cartilage using a novel technique that combines shear testing, confocal imaging and force measurement. We found that G varied by up to two orders of magnitude across a single sample, exhibited a global minimum 50-250 microm below the articular surface in a region just below the superficial zone and was roughly constant at depths > 1000 microm (the "plateau region"). For plateau strains gamma(plateau) approximately 0.75% and overall compressive strains epsilon approximately 5%, G(min) and G(plateau) were approximately 70 and approximately 650 kPa, respectively. In addition, we found that the shear modulus profile depended strongly on the applied shear and axial strains. The greatest change in G occurred at the global minimum where the tissue was highly nonlinear, stiffening under increased shear strain, and weakening under increased compressive strain. Our results can be explained through a simple thought model describing the observed nonlinear behavior in terms of localized buckling of collagen fibers and suggest that compression may decrease the vulnerability of articular cartilage to shear-induced damage by lowering the effective strain on individual collagen fibrils.     

The Retinoblastoma Protein Is Linked to the Activation of Ras

The inner membrane-bound protein Ras integrates various extracellular signals that are subsequently communicated from the cytoplasm to the nucleus via the Raf/MEK/MAPK cascade. Here we show that the retinoblastoma protein pRb, previously reported to be a nuclear target of this pathway, can in turn influence the activation state of Ras. Rb-deficient fibroblasts display elevated levels (up to 30-fold) of activated Ras during G(1). Expression of wild-type pRb or a number of pRb mutants defective in E2F regulation reverses this effect. We provide evidence that the mid-G(1) activation of Ras in Rb-deficient cells, which occurs at the level of guanine nucleotide binding, differs from that of epidermal growth factor-induced stimulation of Ras, being dependent on protein synthesis. The aberrant levels of Ras activity associated with loss of pRb may be responsible for the differentiation defects in Rb-deficient cells, because suppression of Ras activity in Rb(-/-) fibroblasts restores the transactivation function of MyoD and the expression of a late marker of skeletal muscle differentiation. These data suggest that nuclear-cytoplasmic communication between pRb and Ras is bidirectional.     

Regulation of monocyte apoptosis by the protein kinase Cdelta-dependent phosphorylation of caspase-3

Monocytes are central components of the innate immune response and normally circulate for a short period of time before undergoing spontaneous apoptosis. During inflammation, differentiation, or oncogenic transformation, the life span of monocytes is prolonged by preventing the activation of the apoptotic program. Here we showed that caspase-3, a cysteine protease required for monocyte apoptosis, is a phosphoprotein. We identified protein kinase Cdelta (PKCdelta) as a member of the protein kinase C family that associates with and phosphorylates caspase-3. The PKCdelta-dependent phosphorylation of caspase-3 resulted in an increase in the activity of caspase-3. This effect of PKCdelta is specific to caspase-3, as evidenced by the absence of similar effects on caspase-9. The activity of PKCdelta precedes the activation of caspase-3 during spontaneous monocyte apoptosis and in monocyte-induced apoptosis. We found that the overexpression of PKCdelta resulted in an increase of apoptosis, whereas its inhibition blocked caspase-3 activity and decreased apoptosis. Our results provided evidence that the PKCdelta-dependent phosphorylation of caspase-3 provided a novel pro-apoptotic mechanism involved in the regulation of monocyte life span.     

The EF-Hand Ca2+ Binding Protein MICU Choreographs Mitochondrial Ca2+ Dynamics in Arabidopsis

Plant organelle function must constantly adjust to environmental conditions, which requires dynamic coordination. Ca²⁺ signaling may play a central role in this process. Free Ca²⁺ dynamics are tightly regulated and differ markedly between the cytosol, plastid stroma, and mitochondrial matrix. The mechanistic basis of compartment-specific Ca²⁺ dynamics is poorly understood. Here, we studied the function of At-MICU, an EF-hand protein of Arabidopsis thaliana with homology to constituents of the mitochondrial Ca²⁺ uniporter machinery in mammals. MICU binds Ca²⁺ and localizes to the mitochondria in Arabidopsis. In vivo imaging of roots expressing a genetically encoded Ca²⁺ sensor in the mitochondrial matrix revealed that lack of MICU increased resting concentrations of free Ca²⁺ in the matrix. Furthermore, Ca²⁺ elevations triggered by auxin and extracellular ATP occurred more rapidly and reached higher maximal concentrations in the mitochondria of micu mutants, whereas cytosolic Ca²⁺ signatures remained unchanged. These findings support the idea that a conserved uniporter system, with composition and regulation distinct from the mammalian machinery, mediates mitochondrial Ca²⁺ uptake in plants under in vivo conditions. They further suggest that MICU acts as a throttle that controls Ca²⁺ uptake by moderating influx, thereby shaping Ca²⁺ signatures in the matrix and preserving mitochondrial homeostasis. Our results open the door to genetic dissection of mitochondrial Ca²⁺ signaling in plants.     

Impacts of dust on plant health,survivorship and plant communities in semi‐arid environments

There is a general perception that dust accumulation on plant surfaces causes negative impacts to plants. Consequently, it is common for environmental regulatory agencies to apply vegetation monitoring requirements to oil, gas and mining developments. We use two independent, medium‐term monitoring studies in semi‐arid Australia to examine this relationship at two scales: plant health and survivorship of a threatened subspecies (Tetratheca paynterae paynterae: Elaeocarpaceae) at Windarling Range between 2003 and 2014; and changes in plant health and floristic composition on Barrow Island between 2009 and 2014. Accumulation of dust decreased rapidly with distance from source. At Windarling Range, even at the site with the highest dust load, there was no significant impact on Tetratheca paynterae paynterae compared with the less dusty sites for 10 years. Similarly, there was no significant effect between distance from the source of dust and floristic composition on Barrow Island for 5 years. The probability of plants transitioning to a lower health condition between one year and the next did not appear to be related to dust load. This is further supported by comparing the same site before and after paving the road (removal of dust source), which showed no clear trends. Trends in plant health are likely to be driven more by the variability of cumulative rainfall in the preceding 5 months than dust load. The observed temporal variation in the mean dust load may also be related to variation in rainfall. In conclusion, in these case studies from semi‐arid Australia, we find no evidence to support the perception that, under the observed climatic condition and dust deposition rates up to 20 or 77 g m^?2 per month at Windarling Range and Barrow Island, respectively, dust accumulation on plants causes negative impacts.