Membrane Binding and Homodimerization of Atg16 Via Two Distinct Protein Regions is Essential for Autophagy in Yeast

Macroautophagy is a bulk degradation mechanism in eukaryotic cells. Efficiency of an essential step of this process in yeast, Atg8 lipidation, relies on the presence of Atg16, a subunit of the Atg12–Atg5-Atg16 complex acting as the E3-like enzyme in the ubiquitination-like reaction. A current view on the functional structure of Atg16 in the yeast S. cerevisiae comes from the two crystal structures that reveal the Atg5-interacting α-helix linked via a flexible linker to another α-helix of Atg16, which then assembles into a homodimer. This view does not explain the results of previous in vitro studies revealing Atg16-dependent deformations of membranes and liposome-binding of the Atg12–Atg5 conjugate upon addition of Atg16. Here we show that Atg16 acts as both a homodimerizing and peripheral membrane-binding polypeptide. These two characteristics are imposed by the two distinct regions that are disordered in the nascent protein. Atg16 binds to membranes in vivo via the amphipathic α-helix (amino acid residues 113–131) that has a coiled-coil-like propensity and a strong hydrophobic face for insertion into the membrane. The other protein region (residues 64–99) possesses a coiled-coil propensity, but not amphipathicity, and is dispensable for membrane anchoring of Atg16. This region acts as a Leu-zipper essential for formation of the Atg16 homodimer. Mutagenic disruption in either of these two distinct domains renders Atg16 proteins that, in contrast to wild type, completely fail to rescue the autophagy-defective phenotype of atg16Δ cells. Together, the results of this study yield a model for the molecular mechanism of Atg16 function in macroautophagy.     

Evolutionary assembly of cooperating cell types in an animal chemical defense system

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Prophylactic and curative effects of Bacopa monniera in gastric ulcer models.

Bacopa monniera Wettst. (BM, syn. Herpestis monniera L; Scrophulariaceae), is an Ayurvedic drug used as a rasayana. Its fresh juice was earlier reported to have significant antiulcerogenic activity. In continuation, methanolic extract of BM (BME) standardized to bacoside-A content (percentage-38.0 ± 0.9), when given in the dose of 10–50 mg/kg, twice daily for 5 days, showed dose-dependent anti-ulcerogenic on various gastric ulcer models induced by ethanol, aspirin, 2 h cold restraint stress and 4 h pylorus ligation. BME in the dose of 20 mg/kg, given for 10 days, twice daily showed healing effects against 50% acetic acid-induced gastric ulcers. Further work was done to investigate the possible mechanisms of its action by studying its effect on various mucosal offensive acid-pepsin secretion and defensive factors like mucin secretion, mucosal cell shedding, cell proliferation and antioxidant activity in rats. BME 20 mg/kg showed no effect on acid-pepsin secretion, increased mucin secretion, while it decreased cell shedding with no effect on cell proliferation. BME showed significant antioxidant effect per se and in stressed animals. Thus, the gastric prophylactic and curative effects of BME may be due to its predominant effect on mucosal defensive factors.     

Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Concerns over the reductionist nature of the domestication of forest-tree species focus on the possibility of potential genetic erosion during this process. To address these concerns, genetic diversity assessments in a breeding zone the Province of British Columbia “interior” spruce (Picea glauca×engelmanni) program was conducted using allozyme markers. Genetic-variation comparisons were made between natural and production (seed orchard) populations as well as seed and seedling crops produced from the same breeding zone’s seed orchard. The natural population sample consisted of a total of 360 trees representing three stands within each of three watersheds present in the Shuswap-Adams low-elevation zone of interior British Columbia. Small amounts of genetic differentiation were observed among the nine natural populations (4%) and this was attributable to extensive gene flow Consequently, the sum of these nine populations was considered as a baseline for the genetic variation present in the breeding zone. The comparisons between the seed orchard and the breeding zone produced a similar percentage of polymorphic loci while the expected hetrozygosity (0.207 vs 0.210) and the average number of alleles per locus (2.7 vs 2.4) were slightly lower in the seed orchard. A total of seven natural populations’ rare alleles were not present in the orchard population, while one allele was unique to the orchard. The %P increased to 70.6% in the seedlot, but dropped to the natural populations level (64.7%) in the plantation. The observed increase in %P was a result of pollen contamination in the orchard. It is suspected that the reduction in the plantation was caused by an unintentional selection in the nursery. Simulated roguing in the orchard did not drastically reduce even if up to 50% of the orchard’s clones were rogued. However, roguing was associated with a reduction in the average number of alleles per locus (i.e., sampling effect). Received: 2 January 1996 / Accepted: 24 May 1996     

Gradients in maize roots: local elongation and pH

The elongation rate, the gradient of the local elongation rate and the surface pH of maize roots were measured over 12 h. A data bank was constituted by storing these values. By sorting these results on the basis of different elongation rates, different classes of root were obtained. Two classes were chosen: the low-growth roots and the high-growth roots. The mean growth of these two root classes was stable with time and differed significantly from one another. The surface pH of the elongation zone was the same for the roots of these two classes, but the roots selected for their higher growth rate had a larger acid efflux in this zone.     

Values,Errors, and Precautions

In the environmental health literature, errors in interpreting studies or data are not infrequent. Many are of the Type II variety. Common solecisms of this type are: treating the criterion of p < 0.05 as a sacrament; demanding complete confounder control; arguing for the existence of phantom confounders; arguing that the effect size is trivial; building nonveridical models; arguing for no effect from inadequate sample size; demanding causal proof; arguing that causality is reversed; conducting a ballot of published studies. These are examined in this paper.     

An association between a lymphocyte antigen in sheep and the response to vaccination against the parasite Trichostrongylus colubriformis

Lymphocyte antigens were tested in sheep which had been selected for responsiveness to vaccination against the intestinal nematode Trichostrongylus colubriformis. These sheep had been bred in an assortative mating programme which produced offspring designated as either “high responders” or “low responders”, with highly heritable resistance or susceptibility.Ovine lymphocyte antigen (OLA) typing antisera were obtained from parous ewes in the course of matings which produced the high and low responder flocks. A particular antigen (SY1) was found to be present in high frequency on the lymphocytes of high responder (72·2%) and in lower frequency (21·9%) on the lymphocytes of low responder rams. In ewes, the frequency for high responders was 65·7% and for low responders it was 33·5%. A similar association between the SY1 antigen and low faecal egg count was found in random-bred sheep which had been vaccinated with irradiated larvae and challenged with normal larvae. The conclusion was drawn that this lymphocyte antigen was likely to be part of the sheep major histocompatibility complex which influenced the immune response of sheep to vaccination against the parasite.     

Les Pseudholaster (Echinoidea,Holasteroida) du Crétacé de France

In the order of Holasteroida, the fossil record highlights a contradiction between the genus Pseudholaster that appears in the Aptian, whose plastron is prostostern close to the Jurassic ancestors and the genus Holaster, which appears in the Valanginian, whose meridostern plastron appears more derived. This inconsistency can be explained by the ignorance of the plastronal architecture on the part of the early authors. A review of the species of Pseudholaster from the Cretaceous period of France was therefore carried out. The objective was to statistically determine the discriminating morphological characters, and to study the modifications of the architecture of the interambulacrum 5 of the French species belonging to this genus, as well as to the species included in the genus Holaster incorrectly by earlier authors. This review of the species of the genus Pseudholaster begins with a study of the ontogeny of the species Holaster intermedius Münster in Goldfuss, 1826–1833, first representative of the genus Pseudholaster, which appears in the Hauterivian in the Parisian and Rhodano-vocontian basins. The modifications during growth concern the overall shape, but also the plastron architecture: the number of plastron plates increases while the number of plates located between the peristome and the periproct remains fixed. The plastron of this species is protosternal and not meridosternal as Lambert pointed out. The labrum is cupuliform in contact with the second sternal 5a2 by a narrow digitation. However, this arrangement differs from that observed on a protosternal breastplate. This apomorphism of the plastron plate pattern, called “labrotaxienne”, is found in all the Pseudholaster studied, and the study of the architecture of the interambulacrum 5 also reveals a gradual decrease in the number of preanal plates between the oldest (Hauterivian) and the younger (Cenomanian-Lower Turonian) species studied. Most of the French species have been revised, with some synonyms. A new species, P. neraudeaui, is the last known Pseudholaster dated from the upper Cenomanian and lower Turonian of southwestern France. Our study illustrates the evolution of the genus Pseudholaster between the Hauterivian and the early Turonian in France. The interest of the study is to show that the appearance of the genus Pseudholaster is older than that of the genus Holaster. Pseuholaster intermedius, of Hauterivian age, possesses a derived protostern plastron called here “labrotaxien” and not meridostern as defined historically by Lambert, and to reveal that the number of preanals decreases over geological time. This data is essential for future phylogenetic studies. On a palaeobiogeographical level, the study reveals the expansion of the genus Pseudholaster during early Cretaceous in western Europe, with diversification during the Albian, its disappearance during late Cenomanian in the Paris basin while it still persists in the Aquitain basin, its predilection for circalitoral environments.