Proteome analysis of protein partners to nucleosomes containing canonical H2A or the variant histones H2A.Z or H2A.X

Although the existence of histone variants has been known for quite some time, only recently are we grasping the breadth and diversity of the cellular processes in which they are involved. Of particular interest are the two variants of histone H2A, H2A.Z and H2A.X because of their roles in regulation of gene expression and in DNA double-strand break repair, respectively. We hypothesize that nucleosomes containing these variants may perform their distinct functions by interacting with different sets of proteins. Here, we present our proteome analysis aimed at identifying protein partners that interact with nucleosomes containing H2A.Z, H2A.X or their canonical H2A counterpart. Our development of a nucleosome-pull down assay and analysis of the recovered nucleosome-interacting proteins by mass spectrometry allowed us to directly compare nuclear partners of these variant-containing nucleosomes to those containing canonical H2A. To our knowledge, our data represent the first systematic analysis of the H2A.Z and H2A.X interactome in the context of nucleosome structure.     

MHC class I A region diversity and polymorphism in macaque species

The HLA-A locus represents a single copy gene that displays abundant allelic polymorphism in the human population, whereas, in contrast, a nonhuman primate species such as the rhesus macaque (Macaca mulatta) possesses multiple HLA-A-like (Mamu-A) genes, which parade varying degrees of polymorphism. The number and combination of transcribed Mamu-A genes present per chromosome display diversity in a population of Indian animals. At present, it is not clearly understood whether these different A region configurations are evolutionarily stable entities. To shed light on this issue, rhesus macaques from a Chinese population and a panel of cynomolgus monkeys (Macaca fascicularis) were screened for various A region-linked variations. Comparisons demonstrated that most A region configurations are old entities predating macaque speciation, whereas most allelic variation (>95%) is of more recent origin. The latter situation contrasts the observations of the major histocompatibility complex class II genes in rhesus and cynomolgus macaques, which share a high number of identical alleles (>30%) as defined by exon 2 sequencing.     

The subtilisin-like protease AprV2 is required for virulence and uses a novel disulphide-tethered exosite to bind substrates

Many bacterial pathogens produce extracellular proteases that degrade the extracellular matrix of the host and therefore are involved in disease pathogenesis. Dichelobacter nodosus is the causative agent of ovine footrot, a highly contagious disease that is characterized by the separation of the hoof from the underlying tissue. D. nodosus secretes three subtilisin-like proteases whose analysis forms the basis of diagnostic tests that differentiate between virulent and benign strains and have been postulated to play a role in virulence. We have constructed protease mutants of D. nodosus; their analysis in a sheep virulence model revealed that one of these enzymes, AprV2, was required for virulence. These studies challenge the previous hypothesis that the elastase activity of AprV2 is important for disease progression, since aprV2 mutants were virulent when complemented with aprB2, which encodes a variant that has impaired elastase activity. We have determined the crystal structures of both AprV2 and AprB2 and characterized the biological activity of these enzymes. These data reveal that an unusual extended disulphide-tethered loop functions as an exosite, mediating effective enzyme-substrate interactions. The disulphide bond and Tyr92, which was located at the exposed end of the loop, were functionally important. Bioinformatic analyses suggested that other pathogenic bacteria may have proteases that utilize a similar mechanism. In conclusion, we have used an integrated multidisciplinary combination of bacterial genetics, whole animal virulence trials in the original host, biochemical studies, and comprehensive analysis of crystal structures to provide the first definitive evidence that the extracellular secreted proteases produced by D. nodosus are required for virulence and to elucidate the molecular mechanism by which these proteases bind to their natural substrates. We postulate that this exosite mechanism may be used by proteases produced by other bacterial pathogens of both humans and animals.     

Soil reconstruction after mining fails to restore soil function in an Australian arid woodland

The biogeochemical properties of soils drive ecosystem function and vegetation dynamics, and hence soil restoration after mining should aim to reinstate the soil properties and hydrological dynamics of remnant ecosystems. The aim of this study is to assess soil structure in two vegetation types in an arid ecosystem, and to understand how these soil properties compare to a reconstructed soil profile after mining. In an arid ecosystem in southeast Australia, soil samples were collected at five depths (to 105 cm) from remnant woodland and shrubland sites, and sites either disturbed or totally reconstructed after mining. We assessed soil physico‐chemical properties and microbial activity. Soils in the remnant arid ecosystem had coarse‐textured topsoils that overlay clay horizons, which allows water to infiltrate and avoid evaporation, but also slows drainage to deeper horizons. Conversely, reconstructed soils had high sand content at subsoil horizons and high bulk density and compaction at surface layers (0–20 cm). Reconstructed soils had topsoils with higher pH and electrical conductivity. The reconstructed soils did not show increased microbial activity with time since restoration. Overall, the reconstructed soil horizons were not organized in a way that allowed rainfall infiltration and water storage, as is imperative to arid‐zone ecosystem function. Future restoration efforts in arid ecosystems should focus on increasing sand content of soils near the surface, to reduce evaporative water loss and improve soil quality and plant health.     

Environmental enrichment for nonhuman primates: theory and application

Investigators have an obligation to promote the psychological well-being of nonhuman primates used in research. Considerable emphasis has been placed on providing nonhuman primates with enriched environments as a means to achieve this objective. A framework is provided that consists of a set of hypotheses about well-being, and the extent to which exposure to various enrichment devices and procedures actually promotes well-being is evaluated. Two hypotheses are concerned with fostering species-typical behavior: use (versus nonuse) of the enrichment, and whether use of enrichment helps normalize other aspects of the behavioral repertoire. Two additional hypotheses are concerned with abnormal behavior: whether currently existing enrichment lowers levels of abnormal behavior, and whether it prevents the behavior. This framework is applied to various enrichment strategies ranging from toys and foraging devices to social interaction. Most devices are used by nonhuman primates and thus constitute an important way to enrich the captive environment. However, enrichment devices vary as to their effectiveness in normalizing the behavioral repertoire and eliminating abnormal behavior. Only social contact satisfies the goal of promoting a wide variety of species-typical activities while at the same time reducing or preventing the development of abnormal behavior.     

Stereotypic and self-injurious behavior in rhesus macaques: a survey and retrospective analysis of environment and early experience

Abnormal behavior in captive rhesus monkeys can range from active whole-body and self-directed stereotypies to self-injurious behavior (SIB). Although abnormal behaviors are common in singly-housed rhesus monkeys, the type and frequency of these behaviors are highly variable across individual animals, and the factors influencing them are equally varied. The purpose of this investigation was to survey abnormal behavior in a large population of rhesus macaques, to characterize the relationship between stereotypies and self-injury, and to identify potential risk factors for these aberrant behaviors. Behavioral assessments of 362 individually housed rhesus monkeys were collected at the New England Regional Primate Research Center (NERPRC) and combined with colony records. Of the 362 animals surveyed, 321 exhibited at least one abnormal behavior (mean: 2.3, range: 1-8). The most common behavior was pacing. Sex differences were apparent, with males showing more abnormal behavior than females. SIB was also associated with stereotypies. Animals with a veterinary record of self-injury exhibited a greater number of self-directed stereotypies than those that did not self-injure. Housing and protocol conditions, such as individual housing at an early age, longer time housed individually, greater number of blood draws, and nursery rearing, were shown to be risk factors for abnormal behavior. Thus, many factors may influence the development and maintenance of abnormal behavior in captive primates. Some of these factors are intrinsic to the individual (e.g., sex effects), whereas others are related to colony management practices, rearing conditions, and research protocols.     

Sequence requirements for RNA binding by HuR and AUF1

The stability of RNAs bearing AU-rich elements in their 3'-UTRs, and thus the level of expression of their protein products, is regulated by interactions with cytoplasmic RNA-binding proteins. Binding by HuR generally leads to mRNA stabilization and increased protein production, whereas binding by AUF1 isoforms generally lead to rapid degradation of the mRNA and reduced protein production. The exact nature of the interplay between these and other RNA-binding proteins remains unclear, although recent studies have shown close interactions between them and even suggested competition between the two for binding to their cognate recognition sequences. Other recent reports have suggested that the sequences recognized by the two proteins are different. We therefore performed a detailed in vitro analysis of the binding site(s) for HuR and AUF1 present in androgen receptor mRNA to define their exact target sequences, and show that the same sequence is contacted by both proteins. Furthermore, we analysed a proposed HuR target within the 3'-UTR of MTA1 mRNA, and show that the contacted bases lie outside of the postulated motif and are a better match to a classical ARE than the postulated motif. The defining features of these HuR binding sites are their U-richness and single strandedness.