Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

MOTIVATION: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences. AVAILABILITY: http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html.     

T Cell-Dependence of Lassa Fever Pathogenesis

Lassa virus (LASV), the causative agent of Lassa fever (LF), is endemic in West Africa, accounting for substantial morbidity and mortality. In spite of ongoing research efforts, LF pathogenesis and mechanisms of LASV immune control remain poorly understood. While normal laboratory mice are resistant to LASV, we report that mice expressing humanized instead of murine MHC class I (MHC-I) failed to control LASV infection and develop severe LF. Infection of MHC-I knockout mice confirmed a key role for MHC-I-restricted T cell responses in controlling LASV. Intriguingly we found that T cell depletion in LASV-infected HHD mice prevented disease, irrespective of high-level viremia. Widespread activation of monocyte/macrophage lineage cells, manifest through inducible NO synthase expression, and elevated IL-12p40 serum levels indicated a systemic inflammatory condition. The absence of extensive monocyte/macrophage activation in T cell-depleted mice suggested that T cell responses contribute to deleterious innate inflammatory reactions and LF pathogenesis. Our observations in mice indicate a dual role for T cells, not only protecting from LASV, but also enhancing LF pathogenesis. The possibility of T cell-driven enhancement and immunopathogenesis should be given consideration in future LF vaccine development.     

First evidence for adoption in California sea lions

Demographic parameters such as birth and death rates determine the persistence of populations. Understanding the mechanisms that influence these rates is essential to developing effective management strategies. Alloparental behavior, or the care of non-filial young, has been documented in many species and has been shown to influence offspring survival. However, the role of alloparental behavior in maintaining population viability has not been previously studied. Here, we provide the first evidence for adoption in California sea lions and show that adoption potentially works to maintain a high survival rate of young and may ultimately contribute to population persistence. Alloparental behavior should have a positive effect on the population growth rate when the sum of the effects on fitness for the alloparent and beneficiary is positive.     

Serum protein polymorphisms in four populations of Afghanistan.

Gene frequencies of the serum proteins third component of complement (C3) transferrin (Tf), haptoglobin (Hp), group specific component (Gc), serum cholinesterase (E1), alpha1-antitrypsin (Pi), beta2-glycoprotein I (Bg), and ceruloplasmin (Cp) in the Tajiks, Pushtoons, Hazaras, and Usbeks in Afghanistan were reported. Rare variants were observed in the C3, Tf, and Pi systems.     

Persistence of high intestinal lactase activity (lactose tolerance) in Afghanistan

Summary Two hundred and seventy apparently healthy adult subjects from Afghanistan, mainly from the central and eastern parts of the country, were subjected to a lactose tolerance test. The change of blood glucose from the fasting concentration at 20 min after the administration of lactose showed a bimodal distribution. Forty-seven subjects had a rise of blood glucose concentration of more than 1.1 mmol/l and were classified as persistence of high intestinal lactase activity (PHILA), a term which lays emphasis on the fact that high lactase activity in the adult is an unusual state whose prevalence in some populations requires explanation. In the Afghan sample there were no significant differences of the frequency of PHILA in different ethnic groups.Support by Stiftung Volkswagenwerk, Hannover.     

Distribution of human adult lactase phenotypes in the population of Austria

Summary A total of 528 unrelated, apparently healthy, adult and adolescent Austrians (270 females, 258 males, mean age 22.1 years) were examined for lactose absorption capacity employing a noninvasive field test based on breath hydrogen (H₂) determination. Subjects exhibiting a change of breath hydrogen concentration of less than 15 volumes per million (vpm) after a load of 50 g lactose (n=422) were classified as lactorse absorbers, 106 probands (20.1%) showing increases of breath hydrogen concentration between 16 and 111 vpm were diagnosed as lactose malabsorbers. The distribution of the lactase phenotypes was independent of age and sex. Intolerance symptoms after lactose administration were significantly more frequent in lactose malabsorbers. Grouping of probands according to the birth-places of their grandparents revealed significant differences in the distribution of the lactase phenotypes in East and West Austria (East 25%, West 15% lactose malabsorbers). These differences are discussed in the light of the population history of these regions.     

Beja And Nilotes: Nomadic pastoralist groups in the Sudan with opposite distributions of the adult lactase phenotypes

Lactose tolerance tests with breath hydrogen determination were performed on 585 apparently healthy adolescents and adults in the Democratic Republic of the Sudan. Out of the total, 303 probands belong to the tribal group Beja, traditional nomadic pastoralists in the desert zone between the Nile and the Red Sea. The 282 Nilotes (mainly Dinka) are members of seminomadic cattle breeding tribes in the south of the Sudan. In both populations milk consumption is substantial but only in the Beja true milk dependence, sufficient to result in selective pressures in favour of the lactase persistence allele, is likely to exist. The proportion of lactose malabsorbers was 16.8% in the Beja and 74.5% in the Nilotes. The high prevalence of lactose malabsorption among the Nilotes fits into a converging gradient of lactase gene frequencies along the Nile Valley. The Beja are the first nomadic desert population in North Africa in whom a high prevalence of lactase persistence has been demonstrated on a numerically sufficient sample.     

A new family of interspersed repetitive DNA sequences in the mouse genome

Repetitive DNA sequences near immunoglobulin genes in the mouse genome (Steinmetz et al., 1980a,b) were characterized by restriction mapping and hybridization. Six sequences were determined that turned out to belong to a new family of dispersed repetitive DNA. From the sequences, which are called R1 to R6, a 475 base-pair consensus sequence was derived. The R family is clearly distinct from the mouse B1 family (Krayev et al., 1980). According to saturation hybridization experiments, there are about 100,000 R sequences per haploid genome, and they are probably distributed throughout the genome. The individual R sequences have an average divergence from the consensus sequence of 12.5%, which is largely due to point mutations and, among those, to transitions. Some R sequences are severly truncated. The R sequences extend into A-rich sequences and are flanked by short direct repeats. Also, two large insertions in the R2 sequence are flanked by direct repeats. In the neighbourhood of and within R sequences, stretches of DNA have been identified that are homologous to parts of small nuclear RNA sequences. Mouse satellite DNA-like sequences and members of the B1 family were also found in close proximity to the R sequences. The dispersion of R sequences within the mouse genome may be a consequence of transposition events. The possible role of the R sequences in recombination and/or gene conversion processes is discussed.     

Electron crystallography reveals the structure of metarhodopsin I

Rhodopsin is the prototypical G protein-coupled receptor, responsible for detection of dim light in vision. Upon absorption of a photon, rhodopsin undergoes structural changes, characterised by distinct photointermediates. Currently, only the ground-state structure has been described. We have determined a density map of a photostationary state highly enriched in metarhodopsin I, to a resolution of 5.5 A in the membrane plane, by electron crystallography. The map shows density for helix 8, the cytoplasmic loops, the extracellular plug, all tryptophan residues, an ordered cholesterol molecule and the beta-ionone ring. Comparison of this map with X-ray structures of the ground state reveals that metarhodopsin I formation does not involve large rigid-body movements of helices, but there is a rearrangement close to the bend of helix 6, at the level of the retinal chromophore. There is no gradual build-up of the large conformational change known to accompany metarhodopsin II formation. The protein remains in a conformation similar to that of the ground state until late in the photobleaching process.     

Structure of bovine rhodopsin in a trigonal crystal form

We have determined the structure of bovine rhodopsin at 2.65 A resolution using untwinned native crystals in the space group P3(1), by molecular replacement from the 2.8 A model (1F88) solved in space group P4(1). The new structure reveals mechanistically important details unresolved previously, which are considered in the membrane context by docking the structure into a cryo-electron microscopy map of 2D crystals. Kinks in the transmembrane helices facilitate inter-helical polar interactions. Ordered water molecules extend the hydrogen bonding networks, linking Trp265 in the retinal binding pocket to the NPxxY motif near the cytoplasmic boundary, and the Glu113 counterion for the protonated Schiff base to the extracellular surface. Glu113 forms a complex with a water molecule hydrogen bonded between its main chain and side-chain oxygen atoms. This can be expected to stabilise the salt-bridge with the protonated Schiff base linking the 11-cis-retinal to Lys296. The cytoplasmic ends of helices H5 and H6 have been extended by one turn. The G-protein interaction sites mapped to the cytoplasmic ends of H5 and H6 and a spiral extension of H5 are elevated above the bilayer. There is a surface cavity next to the conserved Glu134-Arg135 ion pair. The cytoplasmic loops have the highest temperature factors in the structure, indicative of their flexibility when not interacting with G protein or regulatory proteins. An ordered detergent molecule is seen wrapped around the kink in H6, stabilising the structure around the potential hinge in H6. These findings provide further explanation for the stability of the dark state structure. They support a mechanism for the activation, initiated by photo-isomerisation of the chromophore to its all-trans form, that involves pivoting movements of kinked helices, which, while maintaining hydrophobic contacts in the membrane interior, can be coupled to amplified translation of the helix ends near the membrane surfaces.