Linkage disequilibrium patterns and tagSNP transferability among European populations

The pattern of linkage disequilibrium (LD) is critical for association studies, in which disease-causing variants are identified by allelic association with adjacent markers. The aim of this study is to compare the LD patterns in several distinct European populations. We analyzed four genomic regions (in total, 749 kb) containing candidate genes for complex traits. Individuals were genotyped for markers that are evenly distributed at an average spacing of approximately 2-4 kb in eight population-based samples from ongoing epidemiological studies across Europe. The Centre d'Etude du Polymorphisme Humain (CEPH) trios of the HapMap project were included and were used as a reference population. In general, we observed a conservation of the LD patterns across European samples. Nevertheless, shifts in the positions of the boundaries of high-LD regions can be demonstrated between populations, when assessed by a novel procedure based on bootstrapping. Transferability of LD information among populations was also tested. In two of the analyzed gene regions, sets of tagging single-nucleotide polymorphisms (tagSNPs) selected from the HapMap CEPH trios performed surprisingly well in all local European samples. However, significant variation in the other two gene regions predicts a restricted applicability of CEPH-derived tagging markers. Simulations based on our data set show the extent to which further gain in tagSNP efficiency and transferability can be achieved by increased SNP density.     

Ligand depletion negatively controls the mitogenic activity of epidermal growth factor

EGF activates the ErbB1 receptor, but there appears only a limited correlation between its receptor binding affinity and mitogenic activity. This is indicated by our present observation that in cells with high ErbB1 expression, including SUM102 breast tumor cells, low affinity EGF/Notch chimeras have similarly high mitogenic activity as EGF, in spite of the fact that EGF is superior in inducing receptor tyrosine phosphorylation and p42/p44 MAP-kinase activity. However, as a result of receptor-mediated internalisation high-affinity ligands such as EGF are depleted much more rapidly from the extracellular medium than low-affinity EGF/Notch chimeras. As a consequence, the mitogenic activity of EGF on ErbB1 overexpressing cells is limited by substantial degradation of internalised ligand in the period before cells enter S-phase, a phenomenon that is not observed for low affinity mutant ligands. The mitogenic activity of EGF on ErbB1 overexpressing cells does therefore not only depend on the applied concentration but also on the total amount of ligand added, and is strongly underestimated when tested in a limited assay volume. No such dependence on the incubation volume was observed for EGF activity on cells with low ErbB1 expression levels and on cells for which EGF is growth inhibitory.     

Preventing Acute Malnutrition among Young Children in Crises: A Prospective Intervention Study in Niger

Background

Finding the most appropriate strategy for the prevention of moderate acute malnutrition (MAM) and severe acute malnutrition (SAM) in young children is essential in countries like Niger with annual “hunger gaps.” Options for large-scale prevention include distribution of supplementary foods, such as fortified-blended foods or lipid-based nutrient supplements (LNSs) with or without household support (cash or food transfer). To date, there has been no direct controlled comparison between these strategies leading to debate concerning their effectiveness. We compared the effectiveness of seven preventive strategies—including distribution of nutritious supplementary foods, with or without additional household support (family food ration or cash transfer), and cash transfer only—on the incidence of SAM and MAM among children aged 6–23 months over a 5-month period, partly overlapping the hunger gap, in Maradi region, Niger. We hypothesized that distributions of supplementary foods would more effectively reduce the incidence of acute malnutrition than distributions of household support by cash transfer.

Methods and Findings

We conducted a prospective intervention study in 48 rural villages located within 15 km of a health center supported by Forum Santé Niger (FORSANI)/Médecins Sans Frontières in Madarounfa. Seven groups of villages (five to 11 villages) were allocated to different strategies of monthly distributions targeting households including at least one child measuring 60 cm–80 cm (at any time during the study period whatever their nutritional status): three groups received high-quantity LNS (HQ-LNS) or medium-quantity LNS (MQ-LNS) or Super Cereal Plus (SC+) with cash (€38/month [US$52/month]); one group received SC+ and family food ration; two groups received HQ-LNS or SC+ only; one group received cash only (€43/month [US$59/month]). Children 60 cm–80 cm of participating households were assessed at each monthly distribution from August to December 2011. Primary endpoints were SAM (weight-for-length Z-score [WLZ]<−3 and/or mid-upper arm circumference [MUAC]<11.5 cm and/or bipedal edema) and MAM (−3≤WLZ<−2 and/or 11.5≤MUAC<12.5 cm). A total of 5,395 children were included in the analysis (615 to 1,054 per group). Incidence of MAM was twice lower in the strategies receiving a food supplement combined with cash compared with the cash-only strategy (cash versus HQ-LNS/cash adjusted hazard ratio [HR] = 2.30, 95% CI 1.60–3.29; cash versus SC+/cash HR = 2.42, 95% CI 1.39–4.21; cash versus MQ-LNS/cash HR = 2.07, 95% CI 1.52–2.83) or with the supplementary food only groups (HQ-LNS versus HQ-LNS/cash HR = 1.84, 95% CI 1.35–2.51; SC+ versus SC+/cash HR = 2.53, 95% CI 1.47–4.35). In addition, the incidence of SAM was three times lower in the SC+/cash group compared with the SC+ only group (SC+ only versus SC+/cash HR = 3.13, 95% CI 1.65–5.94). However, non-quantified differences between groups, may limit the interpretation of the impact of the strategies.

Conclusions

Preventive distributions combining a supplementary food and cash transfer had a better preventive effect on MAM and SAM than strategies relying on cash transfer or supplementary food alone. As a result, distribution of nutritious supplementary foods to young children in conjunction with household support should remain a pillar of emergency nutritional interventions. Additional rigorous research is vital to evaluate the effectiveness of these and other nutritional interventions in diverse settings.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01828814","term_id":"NCT01828814"}}NCT01828814 Please see later in the article for the Editors'' Summary     

Hair regeneration in a solfugid chemotactile sensillum during moulting (Arachnida: Solifugae)

Summary The hair regeneration of a chemotactile sensillum was studied in the sunspiderGluvia during moulting. The sensilla in the old cuticle remain connected to the epidermis by dendrites which extend outwards during apolysis. The trichogen cells forming the new hairshaft in the exuvial space grow along the chemoreceptive dendrites, while the mechanoreceptive dendrites run separately. Morphogenetic aspects are discussed in comparison to results from other arthropods.     

Comparative annotation of viral genomes with non-conserved gene structure

MOTIVATION: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading frames. Since one amino acid is encoded by a triplet of nucleic acids, up to three genes may be coded for simultaneously in one direction. Conventional hidden Markov model (HMM)-based gene-finding algorithms may typically find it difficult to identify multiple coding regions, since in general their topologies do not allow for the presence of overlapping or nested genes. Comparative methods have therefore been restricted to likelihood ratio tests on potential regions as to being double or single coding, using the fact that the constrictions forced upon multiple-coding nucleotides will result in atypical sequence evolution. Exploiting these same constraints, we present an HMM based gene-finding program, which allows for coding in unidirectional nested and overlapping reading frames, to annotate two homologous aligned viral genomes. Our method does not insist on conserved gene structure between the two sequences, thus making it applicable for the pairwise comparison of more distantly related sequences. RESULTS: We apply our method to 15 pairwise alignments of six different HIV2 genomes. Given sufficient evolutionary distance between the two sequences, we achieve sensitivity of approximately 84-89% and specificity of approximately 97-99.9%. We additionally annotate three pairwise alignments of the more distantly related HIV1 and HIV2, as well as of two different hepatitis viruses, attaining results of approximately 87% sensitivity and approximately 98.5% specificity. We subsequently incorporate prior knowledge by 'knowing' the gene structure of one sequence and annotating the other conditional on it. Boosting accuracy close to perfect we demonstrate that conservation of gene structure on top of nucleotide sequence is a valuable source of information, especially in distantly related genomes. AVAILABILITY: The Java code is available from the authors.     

The KdpC subunit of the Escherichia coli K+-transporting KdpB P-type ATPase acts as a catalytic chaperone

In Bacteria and Archaea, high-affinity potassium uptake is mediated by the ATP-driven KdpFABC complex. On the basis of the biochemical properties of the ATP-hydrolyzing subunit KdpB, the transport complex is classified as type IA P-type ATPase. However, the KdpA subunit, which promotes K(+) transport, clearly resembles a potassium channel, such that the KdpFABC complex represents a chimera of ion pumps and ion channels. In the present study, we demonstrate that the blending of these two groups of transporters in KdpFABC also entails a nucleotide-binding mechanism in which the KdpC subunit acts as a catalytic chaperone. This mechanism is found neither in P-type ATPases nor in ion channels, although parallels are found in ABC transporters. In the latter, the ATP nucleotide is coordinated by the LSGGQ signature motif via double hydrogen bonds at a conserved glutamine residue, which is also present in KdpC. High-affinity nucleotide binding to the KdpFABC complex was dependent on the presence of this conserved glutamine residue in KdpC. In addition, both ATP binding to KdpC and ATP hydrolysis activity of KdpFABC were sensitive to the accessibility, presence or absence of the hydroxyl groups at the ribose moiety of the nucleotide. Furthermore, the KdpC subunit was shown to interact with the nucleotide-binding loop of KdpB in an ATP-dependent manner around the ATP-binding pocket, thereby increasing the ATP-binding affinity by the formation of a transient KdpB/KdpC/ATP ternary complex.     

The Staphylococcus aureus Protein Sbi Acts as a Complement Inhibitor and Forms a Tripartite Complex with Host Complement Factor H and C3b

The Gram-positive bacterium Staphylococcus aureus, similar to other pathogens, binds human complement regulators Factor H and Factor H related protein 1 (FHR-1) from human serum. Here we identify the secreted protein Sbi (Staphylococcus aureus binder of IgG) as a ligand that interacts with Factor H by a—to our knowledge—new type of interaction. Factor H binds to Sbi in combination with C3b or C3d, and forms tripartite Sbi∶C3∶Factor H complexes. Apparently, the type of C3 influences the stability of the complex; surface plasmon resonance studies revealed a higher stability of C3d complexed to Sbi, as compared to C3b or C3. As part of this tripartite complex, Factor H is functionally active and displays complement regulatory activity. Sbi, by recruiting Factor H and C3b, acts as a potent complement inhibitor, and inhibits alternative pathway-mediated lyses of rabbit erythrocytes by human serum and sera of other species. Thus, Sbi is a multifunctional bacterial protein, which binds host complement components Factor H and C3 as well as IgG and β₂-glycoprotein I and interferes with innate immune recognition.     

Generation of EST and microarray resources for functional genomic studies on chicken intestinal health

Expressed sequenced tags (ESTs) and microarray resources have a great impact on the ability to study host response in mice and humans. Unfortunately, these resources are not yet available for domestic farm animals. The aim of this study was to provide genomic resources to study chicken intestinal health, in particular malabsorption syndrome (MAS), which affects mainly the intestine. Therefore a normalized and subtracted cDNA library containing more than 7000 clones was prepared. Randomly chosen clones were sequenced for control purposes. New ESTs were found and multiple ESTs not identified in the chicken intestine before were observed. The number of non-specific ESTs in this cDNA library was low. Based on this normalized and subtracted library a cDNA microarray was made. In a preliminary hybridization experiment with the microarray, genes were identified to be up- or downregulated in MAS infected chickens. This indicates that the generated resources are valuable tools to investigate chicken intestinal health by whole genome expression analysis approaches.     

Impact of Varicella-Zoster Virus on Dendritic Cell Subsets in Human Skin during Natural Infection

Varicella-zoster virus (VZV) causes varicella and herpes zoster, diseases characterized by distinct cutaneous rashes. Dendritic cells (DC) are essential for inducing antiviral immune responses; however, the contribution of DC subsets to immune control during natural cutaneous VZV infection has not been investigated. Immunostaining showed that compared to normal skin, the proportion of cells expressing DC-SIGN (a dermal DC marker) or DC-LAMP and CD83 (mature DC markers) were not significantly altered in infected skin. In contrast, the frequency of Langerhans cells was significantly decreased in VZV-infected skin, whereas there was an influx of plasmacytoid DC, a potent secretor of type I interferon (IFN). Langerhans cells and plasmacytoid DC in infected skin were closely associated with VZV antigen-positive cells, and some Langerhans cells and plasmacytoid DC were VZV antigen positive. To extend these in vivo observations, both plasmacytoid DC (PDC) isolated from human blood and Langerhans cells derived from MUTZ-3 cells were shown to be permissive to VZV infection. In VZV-infected PDC cultures, significant induction of alpha IFN (IFN-α) did not occur, indicating the VZV inhibits the capacity of PDC to induce expression of this host defense cytokine. This study defines changes in the response of DC which occur during cutaneous VZV infection and implicates infection of DC subtypes in VZV pathogenesis.Varicella-zoster virus (VZV) is a highly species-specific human herpesvirus that causes the diseases varicella (chicken pox) and herpes zoster (shingles). Varicella results from the primary phase of infection and is characterized by a diffuse rash of vesiculopustular lesions that appear in crops and usually resolve within 1 to 2 weeks (7, 26). Primary infection is initiated by inoculation of mucosal sites, such as the upper respiratory tract and the conjunctiva, with infectious virus, usually contained within respiratory droplets (3, 23). Following inoculation, there is a 10- to 21-day incubation period during which VZV is transported to the regional lymph nodes; however, it remains unclear which cell types are responsible for transport of VZV during natural infection (3). It has been hypothesized that dendritic cells (DC) of the respiratory mucosa may be among the first cells to encounter VZV during primary infection and are capable of virus transport to the draining lymph nodes (1, 45). It is postulated that within lymph nodes, VZV undergoes a period of replication, resulting in a primary cell-associated viremia, during which time virus is transported to the reticuloendothelial organs, where it undergoes another period of replication that results in a secondary cell-associated viremia and virus transport to the skin (3, 23). However, VZV has recently been shown to have tropism for human tonsillar CD4⁺ T lymphocytes (37), and it has been demonstrated that these T lymphocytes express skin homing markers that may allow them to transport VZV directly from the lymph node to the skin during primary viremia (38). Once the virus reaches the skin, it infects cutaneous epithelial cells, resulting in distinctive vesiculopustular lesions.During the course of primary infection, VZV establishes a lifelong latent infection within the sensory ganglia, from which virus may reactivate years later to cause herpes zoster (22, 42, 53). VZV reactivation results in the production of new infectious virus and a characteristic vesiculopustular rash, which differs from that of varicella insofar as the distribution of the lesions is typically unilateral and covers only 1 to 2 dermatomes (8). In both primary and reactivated VZV infection of human skin, VZV antigens are detectable in the epidermis and dermis (2, 30, 46, 47, 49, 52), and although some studies have examined the immune infiltrate present in these lesions, most have focused on T lymphocytes, macrophages, and NK cells (40, 48, 50, 51, 58). The role of DC subsets in VZV infection in human skin has not been previously explored in vivo.Our laboratory provided the first evidence that VZV could productively infect human immature and mature monocyte-derived dendritic cells (MDDC) in vitro (1, 45), and Hu and Cohen (2005) showed that VZV ORF47 was critical for replication of virus in human immature DC but not mature DC (29). However, whether DC become directly infected during natural VZV skin infection and the impact VZV infection may have on DC subsets has yet to be elucidated. The two subsets of DC that are normally present in the skin and which may be involved in the pathogenesis of VZV infection are the Langerhans cells (LC) of the epidermis and dermal DC (DDC) (60). LC are present in an immature state in uninfected skin and in upper respiratory tract epithelium. Upon capture of foreign antigens, LC have the capacity to migrate from the periphery to the lymph nodes, where they seek interaction with T lymphocytes (60). Although the location of cutaneous DC suggests that they are a DC subset likely to be involved in the pathogenesis of VZV infection, other subsets of DC, such as the blood-derived myeloid DC (MDC) and plasmacytoid DC (PDC), are also potentially important in the pathogenesis of VZV infection. Of particular interest are PDC, since these cells are important in innate antiviral immune responses due to their ability to recruit to sites of inflammation and secrete high levels of alpha interferon (IFN-α) (6, 18, 56). PDC also participate in adaptive immune responses through their secretion of cytokines and chemokines that promote activation of effector cells, including NK cells, NKT cells, B lymphocytes, and T lymphocytes, and also through their capacity to present antigen to T lymphocytes (9, 63). Whether PDC and LC can be infected with VZV and their roles during infection have not been previously studied.In this study, we sought to identify and compare the subsets of DC present in human skin lesions following natural VZV infection and to assess DC permissiveness to VZV infection. We utilized immunohistochemical (IHC) and immunofluorescent (IFA) staining to characterize DC subsets within the skin of multiple patients with either varicella or herpes zoster, and identified profound changes in the frequency of LC and PDC as a consequence of cutaneous VZV infection. In addition, some LC and PDC costained with a range of VZV antigens indicative of productive infection. PDC isolated from human blood and LC derived from the MUTZ-3 cells were shown to be permissive to productive VZV infection in vitro. This study defines changes in the type and distribution of DC during natural cutaneous VZV infection and implicates infection of specific DC subsets in VZV pathogenesis.