Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE results in comparison with matched FF samples, enabling us to use FFPE samples on the Infinium HumanMethylation450 Methylation array.     

Kinetics of acetylation-deacetylation of angiotensin II. Intramolecular interactions of the tyrosine and histidine side-chains

The possible existence of intramolecular interactions involving the tyrosine and histidine residues in angiotensin II has been investigated by measuring the reactivities of the functional groups in the molecule. Angiotensin II catalyzed the hydrolysis of p-nitrophenylacetate in the pH range 6.6-8.2 at higher rates than were consistent with the reactivities of the free constituent functional groups, and had 2-4% of the activity of chymotrypsin between pH 6.6 and 7.5. Treatment of angiotensin II with acetic anhydride demonstrated that the tyrosine hydroxyl and the imidazole side-chain in angiotensin II acetylated and deacetylated at markedly higher rates than for the free amino acids, indicating increased nucleophilicities and the presence of intrinsic deacetylation mechanisms for these residues in angiotensin II. These findings are consistent with the presence of tyrosine hydroxyl-histidine-carboxylate charge relay system in ANG II in aqueous environments, and suggest that ANG II may act at membrane receptors by a mechanism which is analogous to that operating in serine proteases.     

Socially isolated? How parents and neighbourhood adults influence youth behaviour in disadvantaged communities

William Julius Wilson’s model of adult joblessness, community disorganization and their effects on youth problem behaviour de-emphasizes the range in children’s outcomes across socially disorganized communities, and says little about the factors that influence this variation. It also does not address the processes by which family structure and relationships affect the well-being of African-American and poor youth. My work is part of a larger research agenda that has begun to address these issues by focusing on the differential rates of sexual activity among youth living in disadvantaged environments, and developing models to explain this variation. This work suggests that units of socially cohesive, stable adults exist among the social networks of successful children and families in poor neighbourhoods. It also points to the existence and functioning of alternative two-parent family structures and offers hypotheses for how family environment interacts with neighbourhood context to influence youth behaviour.     

A Toxoplasma type 2C serine-threonine phosphatase is involved in parasite growth in the mammalian host cell

Toxoplasma gondii is a human protozoan parasite that belongs to the phylum of Apicomplexa and causes toxoplasmosis. As the other members of this phylum, T. gondii obligatory multiplies within a host cell by a peculiar type of mitosis that leads to daughter cell assembly within a mother cell. Although parasite growth and virulence have been linked for years, few molecules controlling mitosis have been yet identified and they include a couple of kinases but not the counteracting phosphatases. Here, we report that in contrast to other animal cells, type 2C is by far the major type of serine threonine phosphatase activity both in extracellular and in intracellular dividing parasites. Using wild type and transgenic parasites, we characterized the 37 kDa TgPP2C molecule as an abundant cytoplasmic and nuclear enzyme with activity being under tight regulation. In addition, we showed that the increase in TgPP2C activity significantly affected parasite growth by impairing cytokinesis while nuclear division still occurred. This study supports for the first time that type 2C protein phosphatase is an important regulator of cell growth in T. gondii.     

Variation in the diet of the viperine snake Natvix mama in relation to prey availability

The diet of the viperine snake was compared with food availability in the Ebro Delta, a wetland largely occupied by rice fields, in 1990 and 1991. Snake selection of prey type and size was studied seasonally and by snake group: males, females and immature snakes. Overall, feeding activity (percentage of individuals with prey and number of prey per stomach) increased with food availability. Diet analysis showed that viperine snakes mainly foraged on the green frog Rana perezi (adults and tadpoles) and the carp Cyprinus earpio. Conversely, viperine snakes rejected the mosquito fish Gambusia holbroki which is the most abundant species in autumn, when Natrix maura has a low feeding activity. Statistical comparisons between viperine snake diet and prey availability showed that males selected small carp, immature snakes selected tadpoles and, in spring, females selected frogs. The selection of small carp by males may reflect a sexual divergence of trophic niche related to sexual size dimorphism, as females are larger than males. As tadpoles are presumably easier to catch than fish, tadpole selection by immature individuals may reflect variance in capture abilities. In spring, the selection of frogs by females overlapped with vitellogenesis, suggesting that females compensate for the cost of reproduction by selecting green frogs, which have a greater biomass and higher energy content than fish. Carps eaten in spring were smaller than in summer. Moreover, in summer viperine snakes selected smaller carp than the available mean size. This divergent tendency between carp size selection and carp size availability reveals how seasonal diet shifts in prey size selection may be a response to an increase in prey size.     

Round robin investigation of methods for recovering human enteric viruses from sludge

To select a tentative standard method for detection of viruses in sludge the American Society for Testing and Materials D19:24:04:04 Subcommittee Task Group initiated round robin comparative testing of two procedures that, after initial screening of several methodologies, were found to meet the basic criteria considered essential by the task group. Eight task group member laboratories agreed to perform round robin testing of the two candidate methods, namely, The Environmental Protection Agency or low pH-AlCl3 method and the Glass or sonication-extraction method. Five different types of sludge were tested. For each particular type of sludge, a single laboratory was designated to collect the sludge in a single sampling, make samples, and ship it to the participating laboratories. In most cases, participating laboratories completed all the tests within 48 h of sample arrival. To establish the reproducibility of the methods, each laboratory tested each sludge sample in triplicate for the two candidate virus methods. Each processed sludge sample was quantitatively assayed for viruses by the procedures of each individual round robin laboratory. To attain a more uniform standard of comparison, a sample of each processed sample from all laboratories was reassayed with one cell line and passage number by a single laboratory (Environmental Protection Agency Environmental Monitoring and Support Laboratory, Cincinnati, Ohio). When the data were statistically analyzed, the Environmental Protection Agency method was found to yield slightly higher virus recoveries for all sludge types, except the dewatered sludge. The precisions of both methods were not significantly different.(ABSTRACT TRUNCATED AT 250 WORDS)     

Local grassland restoration affects insect communities

1. It is hypothesised that ecological restoration in grasslands can induce an alternative stable state shift in vegetation. The change in vegetation influences insect community assemblages and allows for greater functional redundancy in pollination and refuge for native insect species. 2. Insect community assemblages at eight coastal California grassland sites were evaluated. Half of these sites had undergone restoration through active revegetation of native grassland flora and half were non‐restored. Insects were collected from Lupinus bicolor (Fabaceae) within 2 × 2‐m² plots in spring 2017. Lupinus bicolor is a common native species that is used in California restoration projects, and home and state landscaping projects. 3. Ordination demonstrated that insect community assemblages were different between restored and non‐restored sites. These differences were seen in insect functional groups as well as taxa‐specific differences and were found to be driven by environmental characteristics such as non‐native forb cover. 4. Functional redundancy of herbivores decreased at restored sites, while pollinators became more redundant compared with non‐restored sites. The assemblages of the common species found at restoration sites contained more native insects than those found at non‐restored sites, including species such as Bombus vosnesenskii. 5. Local grassland restoration has the potential to induce an alternative stable state change and affect insect community assemblages. Additionally, it was found that grassland restoration can be a potential conservation tool to provide refugia for bumblebees (Bombus), but additional studies are required to fully understand its broader applicability.     

A subclass of proteins and sulfated macromolecules secreted by AtT-20 (mouse pituitary tumor) cells is sorted with adrenocorticotropin into dense secretory granules

The AtT-20 cell, a mouse pituitary tumor line that secretes adrenocorticotropin and beta-endorphin, sorts the proteins it externalizes into two exocytotic pathways. Cells that are labeled with [35S]methionine or [35S]sulfate can be shown to transport three acidic polypeptides (65,000, 60,000, and 37,000 mol wt) and at least two sulfated macromolecules into storage secretory granules. When the cells are stimulated by the secretagogue 8-bromo-cAMP, these polypeptides are coordinately secreted with mature adrenocorticotropin into the culture medium. In contrast, a completely different set of secreted polypeptides and sulfated macromolecules does not enter a storage form and is transported to the cell surface more rapidly. Their secretion from the cells is constitutive and does not require the presence of secretagogues. These molecules, like a viral membrane glycoprotein described previously (Gumbiner, B., and R. B. Kelly, 1982, Cell, 28:51-59) are not found in isolated secretory granules and therefore must reach the cell surface in a different exocytotic vesicle. The segregation of a subclass of secretory macromolecules into the secretory granules, despite the existence of another potential secretory pathway, suggests that these molecules have specific functions related to regulated hormone secretion or storage. Presumably all of the proteins secreted by the regulated secretory granule pathway share some common property that targets them to the secretory granule.