Difference in number of loci of swine leukocyte antigen classical class I genes among haplotypes

The structure of the entire genomic region of swine leukocyte antigen (SLA)-the porcine major histocompatibility complex--was recently elucidated in a particular haplotype named Hp-1.0 (H01). However, it has been suggested that there are differences in the number of loci of SLA genes, particularly classical class I genes, among haplotypes. To clarify the between-haplotype copy number variance in genes of the SLA region, we sequenced the genomic region carrying SLA classical class I genes on two different haplotypes, revealing increments of up to six in the number of classical class I genes in a single haplotype. All of the SLA-1(-like) (SLA-1 and newly designated SLA-12) and SLA-3 genes detected in the haplotypes thus analyzed were transcribed in the individual. The process by which duplication of SLA classical class I genes was likely to have occurred was interpreted from an analysis of repetitive sequences adjacent to the duplicated class I genes.     

Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants

The plant circadian clock plays an important role in enhancing performance and increasing vegetative yield. Much of our current understanding of the mechanism and function of the plant clock has come from the development of Arabidopsis thaliana as a model circadian organism. Key to this rapid progress has been the development of robust circadian markers, specifically circadian-regulated luciferase reporter genes. Studies of the clock in crop species and non-model organisms are currently hindered by the absence of a simple high-throughput universal assay for clock function, accuracy and robustness. Delayed fluorescence (DF) is a fundamental process occurring in all photosynthetic organisms. It is luminescence-produced post-illumination due to charge recombination in photosystem II (PSII) leading to excitation of P680 and the subsequent emission of a photon. Here we report that the amount of DF oscillates with an approximately 24-h period and is under the control of the circadian clock in a diverse selection of plants. Thus, DF provides a simple clock output that may allow the clock to be assayed in vivo in any photosynthetic organism. Furthermore, our data provide direct evidence that the nucleus-encoded, three-loop circadian oscillator underlies rhythms of PSII activity in the chloroplast. This simple, high-throughput and non-transgenic assay could be integrated into crop breeding programmes, the assay allows the selection of plants that have robust and accurate clocks, and possibly enhanced performance and vegetative yield. This assay could also be used to characterize rapidly the role and function of any novel Arabidopsis circadian mutant.     

Control of Cell Proliferation,Organ Growth,and DNA Damage Response Operate Independently of Dephosphorylation of the Arabidopsis Cdk1 Homolog CDKA;1

Entry into mitosis is universally controlled by cyclin-dependent kinases (CDKs). A key regulatory event in metazoans and fission yeast is CDK activation by the removal of inhibitory phosphate groups in the ATP binding pocket catalyzed by Cdc25 phosphatases. In contrast with other multicellular organisms, we show here that in the flowering plant Arabidopsis thaliana, cell cycle control does not depend on sudden changes in the phosphorylation pattern of the PSTAIRE-containing Cdk1 homolog CDKA;1. Consistently, we found that neither mutants in a previously identified CDC25 candidate gene nor plants in which it is overexpressed display cell cycle defects. Inhibitory phosphorylation of CDKs is also the key event in metazoans to arrest cell cycle progression upon DNA damage. However, we show here that the DNA damage checkpoint in Arabidopsis can also operate independently of the phosphorylation of CDKA;1. These observations reveal a surprising degree of divergence in the circuitry of highly conserved core cell cycle regulators in multicellular organisms. Based on biomathematical simulations, we propose a plant-specific model of how progression through the cell cycle could be wired in Arabidopsis.     

Land use history of Village Bay,Hirta, St Kilda World Heritage Site: A palynological investigation of plaggen soils

This paper presents findings based on a palynological investigation of artificially accreting (plaggen) soils from the settlement of Village Bay, Hirta, in the St Kilda archipelago, which was perhaps the most distant and inhospitable outpost of sustained human habitation in the British Isles. The soils were developed principally through the addition of turf ash and seabird waste, although some ash may have been derived from upland peats. It is assumed that the woodland pollen signal (much lower in the soils than in an upland peat site nearby) represents off-island sources. Corylus avellana-type pollen (frequent in upland sites), along with Potentilla-type, may provide markers in the Village Bay profiles for the addition of ashed hillside turf, and possibly peat, to the plaggen soils. Cereal-type pollen is well represented through the profiles and is often strongly associated with the record for Chrysanthemum segetum (corn marigold), a frequent indicator of arable land. The Brassicaceae signal may partly reflect the cultivation of cabbages; Chelidonium majus (greater celandine) may have been grown for medicinal use. Soil mixing has rendered radiocarbon dating meaningless at this site, but the establishment of a change in cultivation regime before AD 1830 may have been identified from the patterns of pollen concentration and preservation in the profiles.     

Identification of natural killer cell receptor clusters in the platypus genome reveals an expansion of C-type lectin genes

Natural killer (NK) cell receptors belong to two unrelated, but functionally analogous gene families: the immunoglobulin superfamily, situated in the leukocyte receptor complex (LRC) and the C-type lectin superfamily, located in the natural killer complex (NKC). Here, we describe the largest NK receptor gene expansion seen to date. We identified 213 putative C-type lectin NK receptor homologs in the genome of the platypus. Many have arisen as the result of a lineage-specific expansion. Orthologs of OLR1, CD69, KLRE, CLEC12B, and CLEC16p genes were also identified. The NKC is split into at least two regions of the genome: 34 genes map to chromosome 7, two map to a small autosome, and the remainder are unanchored in the current genome assembly. No NK receptor genes from the LRC were identified. The massive C-type lectin expansion and lack of Ig-domain-containing NK receptors represents the most extreme polarization of NK receptors found to date. We have used this new data from platypus to trace the possible evolutionary history of the NK receptor clusters. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mhc haplotype H6 is associated with sustained control of SIVmac251 infection in Mauritian cynomolgus macaques

The restricted diversity of the major histocompatibility complex (MHC) of Mauritian cynomolgus macaques provides powerful opportunities for insight into host-viral interactions and cellular immune responses that restrict lentiviral infections. However, little is known about the effects of Mhc haplotypes on control of SIV in this species. Using microsatellite-based genotyping and allele-specific PCR, Mhc haplotypes were deduced for 35 macaques infected with the same stock of SIVmac251. Class I haplotype H6 was associated with a reduction in chronic phase viraemia (p = 0.0145) while a similar association was observed for H6 class II (p = 0.0063). An increase in chronic phase viraemia, albeit an insignificant trend, was observed in haplotype H5-positive animals. These results further emphasise the value of genetically defined populations of non-human primates in AIDS research and provide a foundation for detailed characterisation of MHC restricted cellular immune responses and the effects of host genetics on SIV replication in cynomolgus macaques. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Glycoprofiling Bifidobacterial Consumption of Galacto-Oligosaccharides by Mass Spectrometry Reveals Strain-Specific,Preferential Consumption of Glycans

Galacto-oligosaccharides (GOS) are versatile food ingredients that possess prebiotic properties. However, at present there is a lack of precise analytical methods to demonstrate specific GOS consumption by bifidobacteria. To better understand the role of GOS as prebiotics, purified GOS (pGOS) without disaccharides and monosaccharides was prepared and used in bacterial fermentation experiments. Growth curves showed that all bifidobacteria assayed utilized and grew on pGOS preparations. We used a novel mass spectrometry approach involving matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance (MALDI-FTICR) to determine the composition of oligosaccharides in GOS syrup preparations. MALDI-FTICR analysis of spent fermentation media demonstrated that there was preferential consumption of selected pGOS species by different bifidobacteria. The approach described here demonstrates that MALDI-FTICR is a rapid-throughput tool for comprehensive profiling of oligosaccharides in GOS mixtures. In addition, the selective consumption of certain GOS species by different bifidobacteria suggests a means for targeting prebiotics to enrich select bifidobacterial species.Galacto-oligosaccharides (GOS) are nondigestible carbohydrates and versatile food ingredients that possess prebiotic properties (1). In addition, other health benefits have been reported to result from consumption of these oligosaccharides, such as stimulation of intestinal mobility and mineral absorption, elimination of ammonium, and colon cancer prevention, as well as protection against certain pathogenic bacterial infections (6, 11, 19).The physicochemical characteristics of GOS have enabled them to be incorporated in food as prebiotic ingredients. GOS have been of interest in acidic beverages and fermented milk formulations since they exhibit increased thermal stability in acidic environments compared to fructo-oligosaccharides (16, 21). Thus, in the past decade, the applications of GOS in human food products have included dairy products, sugar replacements, diet supplements, and infant formula (11).Commercial GOS preparations are produced by enzymatic treatment of lactose with β-galactosidases from different sources, such as fungi, yeast, or bacteria, which results in a mixture of oligomers with various chain lengths (1). Thus, the basic structure of GOS includes a lactose core at the reducing end, which is typically elongated with up to six galactose residues. Structural diversity in GOS preparations is dependent on the enzyme used in the transgalactosylation reaction and the experimental conditions used, such as pH and temperature (5).Considerable effort has been made to understand the effects of GOS in vivo, and most studies have described the impact of GOS on intestinal bacterial population shifts and production of short-chain fatty acids attributed to bacterial fermentation. While there have a been a variety of in vitro studies characterizing the growth of different gut microbes on GOS, the majority of these studies used commercially available preparations of GOS. These commercial preparations contain high concentrations of monosaccharides (i.e., galactose and glucose) and the disaccharide lactose, both of which remain in the product after the transgalactosylation reaction. However, monosaccharides are the preferred substrates for most microorganisms when they are available in a mixed-carbon source (2). Thus, to evaluate growth on GOS, removal of monosaccharides and lactose is helpful (15).An analytical method currently used to measure GOS in food and feed products is high-pH anion-exchange chromatography (HPAEC) coupled to analysis with a pulse amperometric detector (PAD) (4). Van Laere and coworkers have used this method to monitor GOS fermentation in Bifidobacterium adolescentis cultures (20). However, HPAEC-PAD analysis is time-consuming and thus a low-throughput method. More importantly, due to the detector, in HPAEC-PAD analysis there is a differential response to oligosaccharides with higher degrees of polymerization (DP). Thus, new analytical approaches are needed to specifically characterize the consumption of GOS and other prebiotics by probiotic bacteria.We have previously developed analytical methods employing high-mass-accuracy and high-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) to characterize bacterial consumption of human milk oligosaccharides and fructo-oligosaccharides (9, 10, 14, 17). The matrix-assisted laser desorption ionization (MALDI)-FTICR method is a sensitive and robust analytical method with high-performance capability, and it allows rapid and unambiguous assignment of oligosaccharide signals.The aims of the present study were to investigate the oligosaccharide composition of GOS syrup preparations using MALDI-FTICR MS, to test lactose-free purified GOS (pGOS) as a sole carbon source in bifidobacterial fermentation experiments, and to determine the pGOS consumption profile by MALDI-FTICR MS. Four major bifidobacterial phylotypes, B. adolescentis, Bifidobacterium breve, Bifidobacterium longum subsp. infantis, and Bifidobacterium longum subsp. longum, were used, and our results demonstrate that there is differential consumption of individual GOS species by various bifidobacteria, which provides a conceptual basis for targeted enrichment of specific bifidobacterial strains using specific GOS fractions.