Degradation of endocytosed epidermal growth factor and virally ubiquitinated major histocompatibility complex class I is independent of mammalian ESCRTII

Models for protein sorting at multivesicular bodies in the endocytic pathway of mammalian cells have relied largely on data obtained from yeast. These data suggest the essential role of four ESCRT complexes in multivesicular body protein sorting. However, the putative mammalian ESCRTII complex (hVps25p, hVps22p, and hVps36p) has no proven functional role in endosomal transport. We have characterized the human ESCRTII complex and investigated its function in endosomal trafficking. The human ESCRTII proteins interact with one another, with hVps20p (a component of ESCRTIII), and with their yeast homologues. Our interaction data from yeast two-hybrid studies along with experiments with purified proteins suggest an essential role for the N-terminal domain of hVps22p in the formation of a heterotetrameric ESCRTII complex. Although human ESCRTII is found in the cytoplasm and in the nucleus, it can be recruited to endosomes upon overexpression of dominant-negative hVps4Bp. Interestingly, we find that small interference RNA depletion of mammalian ESCRTII does not affect degradation of epidermal growth factor, a known cargo of the multivesicular body protein sorting pathway. We also show that depletion of the deubiquitinating enzymes AMSH (associated molecule with the SH3 domain of STAM (signal transducing adaptor molecule)) and UBPY (ubiquitin isopeptidase Y) have opposite effects on epidermal growth factor degradation, with UBPY depletion causing dramatic swelling of endosomes. Down-regulation of another cargo, the major histocompatibility complex class I in cells expressing the Kaposi sarcoma-associated herpesvirus protein K3, is unaffected in ESCRTII-depleted cells. Our data suggest that mammalian ESCRTII may be redundant, cargo-specific, or not required for protein sorting at the multivesicular body.     

Root Growth Effects on Soluble C and P in Manured and Non-manured Soils

There is limited research on relationships between root characteristics and soil chemical properties and processes. Because previous studies have shown specific C compounds may release previously sorbed P and make P more plant-available, crops which contribute to high soil C levels could play an important role in soil P cycling. The objectives of this study were to determine (1) whether rotation crops had different amounts of root growth, (2) whether different amounts of root growth among the crop species could be related to different levels of soluble soil C and (3) whether there were differences in P concentration among the soils under different crops that could be related to soluble C soil concentration. Roots and soil from potato (Solanum tuberosum L.), barley (Hordeum vulgare L.), soybean (Glycine max (L.) Merr.), and a forage consisting of alfalfa (Medicago sativa L.) and timothy (Phleum pretense L.) were sampled from the Aroostook Research Farm in Presque Isle, Maine, during the summers of 2003 and 2004 to determine root length density (RLD) and soluble C and P concentrations. Half of the sampled plots were amended with beef manure and half were not amended. Barley and forage consistently had higher RLD than potato or soybean crops. Barley and forage typically had higher concentrations of soluble soil C than potato or soybean, but the differences were significant at only three of the five sampling dates. RLD was significantly correlated to soluble C (r=0.56) only for amended soils on the August 2003 sampling date. For other dates r values were non-significant and ranged from 0.32 to 0.49. As with soil C, soluble soil P levels were typically higher in barley and forage than in potato or soybean crops. Significant differences were detected at four of the five sampling dates. Correlations between soluble C and soluble P were significant at two of the five sampling dates (r = 0.58 and 0.62) in amended soils and one of five sampling dates (r = 0.80) in unamended soils. Although the correlations between RLD and soluble C were not significant at every sampling date, the August 2003 data do suggest a possible effect of roots on soluble C. In addition, significant correlations between soluble C and soluble P at several sampling dates suggest a relationship between these parameters. Therefore cropping systems that include crops with higher amounts of root growth may promote increased soluble soil C levels and enhance P bioavailability.     

Fetal-specific CD8+ cytotoxic T cell responses develop during normal human pregnancy and exhibit broad functional capacity

Tolerance of the semiallogeneic fetus presents a significant challenge to the maternal immune system during human pregnancy. T cells with specificity for fetal epitopes have been detected in women with a history of previous pregnancy, but it has been thought that such fetal-specific cells were generally deleted during pregnancy as a mechanism to maintain maternal tolerance of the fetus. We used MHC-peptide dextramer multimers containing an immunodominant peptide derived from HY to identify fetal-specific T cells in women who were pregnant with a male fetus. Fetal-specific CD8(+) T lymphocytes were observed in half of all pregnancies and often became detectable from the first trimester. The fetal-specific immune response increased during pregnancy and persisted in the postnatal period. Fetal-specific cells demonstrated an effector memory phenotype and were broadly functional. They retained their ability to proliferate, secrete IFN-γ, and lyse target cells following recognition of naturally processed peptide on male cells. These data show that the development of a fetal-specific adaptive cellular immune response is a normal consequence of human pregnancy and that unlike reports from some murine models, fetal-specific T cells are not deleted during human pregnancy. This has broad implications for study of the natural physiology of pregnancy and for the understanding of pregnancy-related complications.     

Discovery and optimization of a series of liver X receptor antagonists

The present report describes our efforts to convert an existing LXR agonist into an LXR antagonist using a structure-based approach. A series of benzenesulfonamides was synthesized based on structural modification of a known LXR agonist and was determined to be potent dual liver X receptor (LXR α/β) ligands. Herein we report the identification of compound 54 as the first reported LXR antagonist that is suitable for pharmacological in vivo evaluation in rodents.     

DOA1/UFD3 plays a role in sorting ubiquitinated membrane proteins into multivesicular bodies

Ubiquitin (Ub) is a sorting signal that targets integral membrane proteins to the interior of the vacuole/lysosome by directing them into lumenal vesicles of multivesicular bodies (MVBs). The Vps27-Hse1 complex, which is homologous to the Hrs-STAM complex in mammalian cells, serves as a Ub-sorting receptor at the surface of early endosomes. We have found that Hse1 interacts with Doa1/Ufd3. Doa1 is known to interact with Cdc48/p97 and Ub and is required for maintaining Ub levels. We find that the Hse1 Src homology 3 domain binds directly to the central PFU domain of Doa1. Mutations in Doa1 that block Hse1 binding but not Ub binding do not alter Ub levels but do result in the missorting of the MVB cargo GFP-Cps1. Loss of Doa1 also causes a synthetic growth defect when combined with loss of Vps27. Unlike the loss of Doa1 alone, the doa1Delta vps27Delta double mutant phenotype is not suppressed by Ub overexpression, demonstrating that the effect is not due to indirect consequence of lowered Ub levels. Loss of Doa1 results in a defect in the accumulation of GFP-Ub within yeast vacuoles, implying that there is a reduction in the flux of ubiquitinated membrane proteins through the MVB pathway. This defect was also reflected by an inability to properly sort Vph1-GFP-Ub, a modified subunit of the multiprotein vacuolar ATPase complex, which carries an in-frame fusion of Ub as an MVB sorting signal. These results reveal novel roles for Doa1 in helping to process ubiquitinated membrane proteins for sorting into MVBs.     

Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs

Thermodynamic parameters are reported for duplex formation of 40 self-complementary RNA duplexes containing wobble terminal base pairs with all possible 3′ single and double-nucleotide overhangs, mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest neighbor analysis, the addition of a single 3′ dangling nucleotide increases the stability of duplex formation up to 1 kcal/mol in a sequence-dependent manner. The addition of a second dangling nucleotide increases the stability of duplexes closed with wobble base pairs in an idiosyncratic manner. The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3′ single or double-nucleotide overhangs. Phylogenetic analysis of naturally occurring miRNAs was performed. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for the 5′ single terminal overhangs adjacent to wobble closing base pairs are also presented.     

A particular case and a general pattern: hyperaggressive behaviour by one species may mediate avifaunal decreases in fragmented Australian forests

We quantitatively assessed edge effects associated with elevated abundance of a hyper aggressive bird species, the noisy miner Manorina melanocephala, in fragmented eucalypt forest adjoining developed land. Long‐term data from Toohey Forest, subtropical Australia, show that noisy miner colonies intensively occupy a zone of 20 m from the forest edge, with frequent use occurring up to 100 m from the edge, but little beyond 200 m. Within noisy miner colonies, the abundance and species richness of other birds were both about half those recorded at nearby transects which were outside the colonies' main activity area. Bird species smaller than noisy miners, which are also those with similar diets, were collectively 20–25 times more abundant, and their species richness tenfold greater, outside miner colonies than within them, whereas larger species, which have less dietary overlap, did not differ. Exclusion of small insectivorous birds has been hypothesised to cause elevated insect herbivore density, but we found no difference between tree crown defoliation or dieback rates within versus outside miner colonies. Aggression by noisy miners can be viewed as a mechanism of interspecific competition, since miners have a relatively large body size for their diet and are hence able to exclude virtually all potential competitors at relatively little cost. We examine evidence indicating that reduced bird diversity in eucalypt forest fragments of eastern Australia is often simply the effect of noisy miner occupancy of edges, acting directly on the densities of other species through their aggressive behaviour. With an edge effect 200 m deep, a remnant 10 ha in size is likely to become entirely occupied by noisy miners, and this is a size threshold that has been commonly reported in association with area‐standardised avian diversity reductions. Convergent patterns of species loss from small forest fragments in different continents are the result of different underlying ecological processes.