A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms

Autoimmune, inflammatory, and infectious diseases present a major burden to human health and are frequently associated with loci in the human major histocompatibility complex (MHC). Here, we report a high-resolution (1.9 kb) linkage-disequilibrium (LD) map of a 4.46-Mb fragment containing the MHC in U.S. pedigrees with northern and western European ancestry collected by the Centre d'Etude du Polymorphisme Humain (CEPH) and the first generation of haplotype tag single-nucleotide polymorphisms (tagSNPs) that provide up to a fivefold increase in genotyping efficiency for all future MHC-linked disease-association studies. The data confirm previously identified recombination hotspots in the class II region and allow the prediction of numerous novel hotspots in the class I and class III regions. The region of longest LD maps outside the classic MHC to the extended class I region spanning the MHC-linked olfactory-receptor gene cluster. The extended haplotype homozygosity analysis for recent positive selection shows that all 14 outlying haplotype variants map to a single extended haplotype, which most commonly bears HLA-DRB1*1501. The SNP data, haplotype blocks, and tagSNPs analysis reported here have been entered into a multidimensional Web-based database (GLOVAR), where they can be accessed and viewed in the context of relevant genome annotation. This LD map allowed us to give coordinates for the extremely variable LD structure underlying the MHC.     

Ecosystem type drives soil eukaryotic diversity and composition in Europe

Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity and distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited in their spatial scale. Here, we analyzed an unprecedented amount of observational data of soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into the impact of a wide range of environmental conditions (climatic and edaphic) on their community composition and structure. We found that the diversity of fungi, protists, rotifers, tardigrades, nematodes, arthropods, and annelids was predominantly shaped by ecosystem type (annual and permanent croplands, managed and unmanaged grasslands, coniferous and broadleaved woodlands), and higher diversity of fungi, protists, nematodes, arthropods, and annelids was observed in croplands than in less intensively managed systems, such as coniferous and broadleaved woodlands. Also in croplands, we found more specialized eukaryotes, while the composition between croplands was more homogeneous compared to the composition of other ecosystems. The observed high proportion of overlapping taxa between ecosystems also indicates that DNA has accumulated from previous land uses, hence mimicking the land transformations occurring in Europe in the last decades. This strong ecosystem-type influence was linked to soil properties, and particularly, soil pH was driving the richness of fungi, rotifers, and annelids, while plant-available phosphorus drove the richness of protists, tardigrades, and nematodes. Furthermore, the soil organic carbon to total nitrogen ratio crucially explained the richness of fungi, protists, nematodes, and arthropods, possibly linked to decades of agricultural inputs. Our results highlighted the importance of long-term environmental variables rather than variables measured at the time of the sampling in shaping soil eukaryotic communities, which reinforces the need to include those variables in addition to ecosystem type in future monitoring programs and conservation efforts.     

Mental health problems of homeless children and families: longitudinal study

Objective: To establish the mental health needs of homeless children and families before and after rehousing. Design: Cross sectional, longitudinal study. Setting: City of Birmingham. Subjects: 58 rehoused families with 103 children aged 2-16 years and 21 comparison families of low socioeconomic status in stable housing, with 54 children. Main outcome measures: Children’s mental health problems and level of communication; mothers’ mental health problems and social support one year after rehousing. Results: Mental health problems remained significantly higher in rehoused mothers and their children than in the comparison group (mothers 26% v 5%, P=0.04; children 39% v 11%, P=0.0003). Homeless mothers continued to have significantly less social support at follow up. Mothers with a history of abuse and poor social integration were more likely to have children with persistent mental health problems. Conclusions: Homeless families have a high level of complex needs that cannot be met by conventional health services and arrangements. Local strategies for rapid rehousing into permanent accommodation, effective social support and health care for parents and children, and protection from violence and intimidation should be developed and implemented.

Key messages

• Homeless children and their mothers have a high level of mental health problems
• Homeless families experience many risk factors, such as domestic violence, abuse, and family and social disruption
• In two fifths of children and a quarter of mothers, mental health problems persisted after rehousing
• In contrast with a comparison group of families of low socioeconomic status, a substantial proportion of homeless families remained residentially and socially unstable

     

Comparative Electrophoretic and Amino Acid Analyses of Isolated Membranes from Streptococcus pyogenes and Stabilized L-Form

Major quantitative, but not qualitative, differences in the various species of proteins in purified membranes from Streptococcus pyogenes and its stabilized L-form have been demonstrated by acidic and alkaline disc gel electrophoresis with and without urea. The fact that no significant differences in the amino acid content or composition between these two membranes could be demonstrated emphasizes that these results are probably due to changes in the relative amounts of the various species of proteins in this subcellular component. The possibility of these protein changes in the L-form membrane being related to its inability to synthesize a rigid cell wall is discussed. Finally, phage-associated lysin, routinely used for removal of the group A streptococcal cell wall, does not appear to affect the protein profile or amino acid composition of the membrane either metabolically or nonmetabolically.     

Synapsis and DNA cleavage in phiC31 integrase-mediated site-specific recombination

The Streptomyces phage C31 encodes an integrase belonging to the serine recombinase family of site-specific recombinases. The well studied serine recombinases, the resolvase/invertases, bring two recombination sites together in a synapse, and then catalyse a concerted four-strand staggered break in the DNA substrates whilst forming transient covalent attachments with the recessed 5′ ends. Rotation of one pair of half sites by 180° relative to the other pair occurs, to form the recombinant configuration followed by ligation of the DNA backbone. Here we address the nature of the recombination intermediates formed by C31 integrase when acting on its substrates attP and attB. We have identified intermediates containing integrase covalently attached to cleaved DNA substrates, attB or attP, by analysis of complexes in gels and after treatment of these complexes with proteinases. Using a catalytically inactive integrase mutant, S12A, the synaptic complexes containing integrase, attP and attB were identified. Furthermore, we have shown that attB mutants containing insertions or deletions are blocked in recombination at the stage of strand cleavage. Thus, there is a strict spacing requirement within attB, possibly for correct positioning of the catalytic serine relative to the scissile phosphate in the active site. Finally, using integrase S12A we confirmed the inability of attL and attR or other combinations of sites to form a stable synapse, indicating that the directionality of integrative recombination is determined at synapsis.     

The effect of terpenoid extracts from 15 pine species on the feeding behavioural sequence of the late instars of the pine processionary caterpillar Thaumetopoea pityocampa

The feeding behaviour of the pine processionary (PPC) caterpillar Thaumetopoea pityocampa Den. and Schiff. (Lepidoptera, Thaumetopoeidae) in L3-L4 stages was explored by means of laboratory arena feeding trials and natural substrates. In the bioassays, volatile extracts of 15 pine species, 8 of which are naturally growing in Greece, were incorporated. An analytical model was developed based on the principle of multinomial logit regression with five outcomes on the basis of the behavioural feeding sequence of the caterpillars. The outcomes were the five steps in which the feeding behavioural sequence was decomposed. The model's suitability (MacFadden's rho(2)=0.229, P<10(-4)) was examined when including 10 terpenes that were judged significant through a stepwise canonical discriminant analysis. The proposed model was superior to a random one and the two models resulting from the addition and subtraction of 4 terpenes to the already 10 existing compounds. The most informative model was built on the terpenes caryophyllene oxide, terpinolene, myrcene, germacrene D, eudesmol, limonene, beta-pinene, beta-caryophyllene, alpha-pinene and manoyl oxide. The background terpenes were present in the model and of particular importance. No special behavioural role, either as promoter or inhibitor could be assigned to the individual volatile metabolites, since no constant pattern among behavioural steps was observed. For instance, beta-caryophyllene while acts as promoter of attraction and trial bite it is a suppressor of partial feeding and strongly inhibits complete needle consumption. The monoterpene limonene, on the other hand, seems to be a suppressor of partial and complete feeding. The overall methodological scheme and the analytical modelling tool could be proved a suitable research protocol in unfolding the ecological role of a complex mixture of secondary metabolites. Those who develop safe practical systems can use this.