Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r² value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.     

Metabolic depression during aestivation does not involve remodelling of membrane fatty acids in two Australian frogs

Changes in membrane lipid composition (membrane remodelling) have been associated with metabolic depression in some aestivating snails but has not been studied in aestivating frogs. This study examined the membrane phospholipid composition of two Australian aestivating frog species Cyclorana alboguttata and Cyclorana australis. The results showed no major membrane remodelling of tissue in either frog species, or in mitochondria of C. alboguttata due to aestivation. Mitochondrial membrane remodelling was not investigated in C. australis. Where investigated in C. alboguttata, total protein and phospholipid content, and citrate synthase (CS) and cytochrome c oxidase (CCO) activities in tissues and mitochondria mostly did not change with aestivation in liver. In skeletal muscle, however, CS and CCO activities, mitochondrial and tissue phospholipids, and mitochondrial protein decreased with aestivation. These decreases in muscle indicate that skeletal muscle mitochondrial content may decrease during aestivation. Na⁺K⁺ATPase activity of both frog species showed no effect of aestivation. In C. alboguttata different fat diets had a major effect on both tissue and mitochondrial phospholipid composition indicating an ability to remodel membrane composition that is not utilised in aestivation. Therefore, changes in lipid composition associated with some aestivating snails do not occur during aestivation in these Australian frogs.     

Early Cretaceous mesofossils from Portugal and eastern North America related to the Bennettitales-Erdtmanithecales-Gnetales group

Four new genera and six new species of fossil seed (Buarcospermum tetragonium, Lignierispermum maroneae, Lobospermum glabrum, L. rugosum, L. stampanonii, Rugonella trigonospermum) are described from five Early Cretaceous mesofossil floras from Portugal and eastern North America. The four genera are distinguished by differences in size, shape, and details of seed anatomy, but all are unusual in having an outer seed envelope with a distinctive anatomical structure that surrounds the nucellus and the integument. The integument is extended apically into a long, narrow micropylar tube. The four new genera are part of a diverse, but previously unrecognized, complex of extinct plants that was widespread in Early Cretaceous vegetation and that coexisted in similar habitats with early angiosperms. The distinctive structure of these seeds, and the strong similarities to other fossil seeds (Ephedra, Ephedripites, Erdtmanispermum, Raunsgaardispermum, and some Bennettitales) already known from the Early Cretaceous, suggests that this newly recognized complex of extinct plants, together with Bennettitales, Erdtmanithecales, and Gnetales (the BEG group), is phylogenetically closely related.     

Immunological Memory Transferred with CD4 T Cells Specific for Tuberculosis Antigens Ag85B-TB10.4: Persisting Antigen Enhances Protection

Background

High levels of death and morbidity worldwide caused by tuberculosis has stimulated efforts to develop a new vaccine to replace BCG. A number of Mycobacterium tuberculosis (Mtb)-specific antigens have been synthesised as recombinant subunit vaccines for clinical evaluation. Recently a fusion protein of TB antigen Ag85B combined with a second immunodominant TB antigen TB10.4 was emulsified with a novel non-phospholipid-based liposomal adjuvant to produce a new subunit vaccine, investigated here. Currently, there is no consensus as to whether or not long-term T cell memory depends on a source of persisting antigen. To explore this and questions regarding lifespan, phenotype and cytokine patterns of CD4 memory T cells, we developed an animal model in which vaccine-induced CD4 memory T cells could transfer immunity to irradiated recipients.

Methodology/Principal Findings

The transfer of protective immunity using Ag85B-TB10.4-specific, CD45RB^low CD62L^low CD4 T cells was assessed in sub-lethally irradiated recipients following challenge with live BCG, used here as a surrogate for virulent Mtb. Donor T cells also carried an allotype marker allowing us to monitor numbers of antigen-specific, cytokine-producing CD4 T cells in recipients. The results showed that both Ag85B-TB10.4 and BCG vaccination induced immunity that could be transferred with a single injection of 3×10⁶ CD4 T cells. Ten times fewer numbers of CD4 T cells (0.3×10⁶) from donors immunised with Ag85B-TB10.4 vaccine alone, transferred equivalent protection. CD4 T cells from donors primed by BCG and boosted with the vaccine similarly transferred protective immunity. When BCG challenge was delayed for 1 or 2 months after transfer (a test of memory T cell survival) recipients remained protected. Importantly, recipients that contained persisting antigen, either live BCG or inert vaccine, showed significantly higher levels of protection (p<0.01). Overall the numbers of IFN-γ-producing CD4 T cells were poorly correlated with levels of protection.

Conclusions/Significance

The Ag85B-TB10.4 vaccine, with or without BCG-priming, generated TB-specific CD4 T cells that transferred protective immunity in mice challenged with BCG. The level of protection was enhanced in recipients containing a residual source of specific antigen that could be either viable or inert.     

Vertical flux of particulate matter in an Arctic fjord: the case of lack of the sea-ice cover in Adventfjorden 2006–2007

Seasonal dynamics of suspended minerals, organic matter, particulate, and dissolved organic carbon (DOC), chlorophyll, and their vertical fluxes were studied in a small Arctic fjord (Adventfjorden, Spitsbergen) from November 2006 to October 2007. The fjord was usually covered with fast ice in winter, but remained open throughout the year since 2005. The open-water winter period caused increased wave action and resuspension of organic and mineral particles. The lack of sea-ice in spring accelerated the onset of the productive season. The earlier light signal also caused an earlier appearance of mesozooplanktonic organisms, accompanied by a significant increase of the DOC pool in the water. In the cold period (winter and spring) 47% of the annual organic matter settled on the sampling site, a lot coming from the spring diatom bloom in April. Summer melt (July, August) resulted in turbid and brackish fjord surface water with stratification and increase of both suspended particles and sedimentation, causing 60% of the annual minerals and 53% of the annual organic matter to settle at the sampling site. Increased dissolved organic carbon (DOC) through sloppy feeding on the mixo- and heterotrophic protista by the abundant mesozooplankton indicated intensive secondary production, resulting in a maximum fecal pellets flux of >5 mg C m⁻² day⁻¹. A warmer climate with reduced sea-ice cover in fjords will advance the onset of the spring bloom and will also result in a larger input of turbid melt water in summer, restricting the light availability and enhancing flocculation and thereby sedimentation.     

A Novel CCR5 Mutation Common in Sooty Mangabeys Reveals SIVsmm Infection of CCR5-Null Natural Hosts and Efficient Alternative Coreceptor Use In Vivo

In contrast to HIV infection in humans and SIV in macaques, SIV infection of natural hosts including sooty mangabeys (SM) is non-pathogenic despite robust virus replication. We identified a novel SM CCR5 allele containing a two base pair deletion (Δ2) encoding a truncated molecule that is not expressed on the cell surface and does not support SIV entry in vitro. The allele was present at a 26% frequency in a large SM colony, along with 3% for a CCR5Δ24 deletion allele that also abrogates surface expression. Overall, 8% of animals were homozygous for defective CCR5 alleles and 41% were heterozygous. The mutant allele was also present in wild SM in West Africa. CD8+ and CD4+ T cells displayed a gradient of CCR5 expression across genotype groups, which was highly significant for CD8+ cells. Remarkably, the prevalence of natural SIVsmm infection was not significantly different in animals lacking functional CCR5 compared to heterozygous and homozygous wild-type animals. Furthermore, animals lacking functional CCR5 had robust plasma viral loads, which were only modestly lower than wild-type animals. SIVsmm primary isolates infected both homozygous mutant and wild-type PBMC in a CCR5-independent manner in vitro, and Envs from both CCR5-null and wild-type infected animals used CXCR6, GPR15 and GPR1 in addition to CCR5 in transfected cells. These data clearly indicate that SIVsmm relies on CCR5-independent entry pathways in SM that are homozygous for defective CCR5 alleles and, while the extent of alternative coreceptor use in SM with CCR5 wild type alleles is uncertain, strongly suggest that SIVsmm tropism and host cell targeting in vivo is defined by the distribution and use of alternative entry pathways in addition to CCR5. SIVsmm entry through alternative pathways in vivo raises the possibility of novel CCR5-negative target cells that may be more expendable than CCR5+ cells and enable the virus to replicate efficiently without causing disease in the face of extremely restricted CCR5 expression seen in SM and several other natural host species.     

Cytokine response profiles predict species-specific infection patterns in human GI nematodes

This study investigated associations between pre-treatment cytokine expression and infection patterns, before and after de-worming, in humans exposed to two gastrointestinal nematode species. Quantitative measures of Ascaris lumbricoides and Trichuris trichiura infection (based on faecal egg counts) were estimated immediately before and 8-9 months after treatment in a Cameroonian population. Whole blood cytokine responses to parasite-derived antigens were assayed immediately pre-treatment. An overall measure of the tendency towards species-specific infection (increasing with A. lumbricoides faecal egg counts and decreasing with T. trichiura faecal egg counts) was significantly positively related to IL-10 levels in older (14-57 year) hosts. There was a significant negative influence of IL-5 on reinfection probability in T. trichiura but not A. lumbricoides. This effect coincided with reduced reinfection success in T. trichiura compared to A. lumbricoides. T(H)2 cytokine expression by younger hosts (4-13 year) was negatively associated with contemporary A. lumbricoides faecal egg counts before treatment. Following treatment, the pre-treatment T(H)2 cytokine expression data for younger hosts (now reflecting responsiveness 8-9 months in the past) were negatively associated with T. trichiura faecal egg counts. Taken together, these observations suggest a successional interaction between T(H)2-driven immune responses and species infection over time. However, any differential effects of the measured immune responses on species-specific recruitment, maturation and mortality were superimposed upon (and outweighed by) the effects of other factors favouring coinfection.     

Modulation of KCNQ4 channel activity by changes in cell volume

KCNQ4 channels expressed in HEK 293 cells are sensitive to cell volume changes, being activated by swelling and inhibited by shrinkage, respectively. The KCNQ4 channels contribute significantly to the regulatory volume decrease (RVD) process following cell swelling. Under isoosmotic conditions, the KCNQ4 channel activity is modulated by protein kinases A and C, G protein activation, and a reduction in the intracellular Ca2+ concentration, but these signalling pathways are not responsible for the increased channel activity during cell swelling.     

Ionic and pH signalling from roots to shoots of flooded tomato plants in relation to stomatal closure

Soil flooding damages shoot systems by inhibiting root functioning. An example is the inhibition of water uptake brought about by decreased root hydraulic conductance. The extent of any resulting foliar dehydration this causes is limited by partial stomatal closure that begins within 4 h and is maintained for several days. Root to shoot signals that promote closure in flooded tomato plants have remained elusive but may include changes in solute delivery to the shoot by transpiration. Accordingly, we examined total osmolites and selected mineral ions in samples of xylem sap flowing at rates approximating whole plant transpiration. After 2.5 h flooding,delivery of total osmolites and of PO₄ ^3-SO₄ ^2-Ca²⁺K⁺NO₃ ^– and H⁺strongly decreased while Na⁺ remained excluded. Several hours later, deliveries of osmolites, PO₄ ^3-, SO₄ ^2-, Ca²⁺, and Na⁺ rose above control values, suggesting that, after approximately 10 h, root integrity became degraded and solute uptake de-regulated. Deliveries of NO₃ ^– remained below control values. Reducing or eliminating the supply of K⁺ to detached leaves to test the potential of decreased K⁺ delivery to close stomata proved negative. Decrease in H⁺ delivery was associated with sap alkalisation. However, raising the pH of buffer from 6.0 or 6.5 to 7.0 did not close stomata when tested in the presence of abscisic acid (ABA) at a concentration (10 mol m^–3) typical of the transpiration stream of flooded plants. It is concluded that despite their rapidity and scale, negative messages in the form of increased pH and decreased solute delivery from roots to shoots are, themselves, unlikely initiators of stomatal closure in flooded tomato plants.