Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery

Targeted sequencing is a cost-efficient way to obtain answers to biological questions in many projects, but the choice of the enrichment method to use can be difficult. In this study we compared two hybridization methods for target enrichment for massively parallel sequencing and single nucleotide polymorphism (SNP) discovery, namely Nimblegen sequence capture arrays and the SureSelect liquid-based hybrid capture system. We prepared sequencing libraries from three HapMap samples using both methods, sequenced the libraries on the Illumina Genome Analyzer, mapped the sequencing reads back to the genome, and called variants in the sequences. 74-75% of the sequence reads originated from the targeted region in the SureSelect libraries and 41-67% in the Nimblegen libraries. We could sequence up to 99.9% and 99.5% of the regions targeted by capture probes from the SureSelect libraries and from the Nimblegen libraries, respectively. The Nimblegen probes covered 0.6 Mb more of the original 3.1 Mb target region than the SureSelect probes. In each sample, we called more SNPs and detected more novel SNPs from the libraries that were prepared using the Nimblegen method. Thus the Nimblegen method gave better results when judged by the number of SNPs called, but this came at the cost of more over-sampling.     

MRI pattern recognition in multiple sclerosis normal-appearing brain areas

Objective

Here, we use pattern-classification to investigate diagnostic information for multiple sclerosis (MS; relapsing­remitting type) in lesioned areas, areas of normal­appearing grey matter (NAGM), and normal-appearing white matter (NAWM) as measured by standard MR techniques.

Methods

A lesion mapping was carried out by an experienced neurologist for Turbo Inversion Recovery Magnitude (TIRM) images of individual subjects. Combining this mapping with templates from a neuroanatomic atlas, the TIRM images were segmented into three areas of homogenous tissue types (Lesions, NAGM, and NAWM) after spatial standardization. For each area, a linear Support Vector Machine algorithm was used in multiple local classification analyses to determine the diagnostic accuracy in separating MS patients from healthy controls based on voxel tissue intensity patterns extracted from small spherical subregions of these larger areas. To control for covariates, we also excluded group-specific biases in deformation fields as a potential source of information.

Results

Among regions containing lesions a posterior parietal WM area was maximally informative about the clinical status (96% accuracy, p<10⁻¹³). Cerebellar regions were maximally informative among NAGM areas (84% accuracy, p<10⁻⁷). A posterior brain region was maximally informative among NAWM areas (91% accuracy, p<10⁻¹⁰).

Interpretation

We identified regions indicating MS in lesioned, but also NAGM, and NAWM areas. This complements the current perception that standard MR techniques mainly capture macroscopic tissue variations due to focal lesion processes. Compared to current diagnostic guidelines for MS that define areas of diagnostic information with moderate spatial specificity, we identified hotspots of MS associated tissue alterations with high specificity defined on a millimeter scale.     

Spider silk constructs enhance axonal regeneration and remyelination in long nerve defects in sheep

Background

Surgical reapposition of peripheral nerve results in some axonal regeneration and functional recovery, but the clinical outcome in long distance nerve defects is disappointing and research continues to utilize further interventional approaches to optimize functional recovery. We describe the use of nerve constructs consisting of decellularized vein grafts filled with spider silk fibers as a guiding material to bridge a 6.0 cm tibial nerve defect in adult sheep.

Methodology/Principal Findings

The nerve constructs were compared to autologous nerve grafts. Regeneration was evaluated for clinical, electrophysiological and histological outcome. Electrophysiological recordings were obtained at 6 months and 10 months post surgery in each group. Ten months later, the nerves were removed and prepared for immunostaining, electrophysiological and electron microscopy. Immunostaining for sodium channel (NaV 1.6) was used to define nodes of Ranvier on regenerated axons in combination with anti-S100 and neurofilament. Anti-S100 was used to identify Schwann cells. Axons regenerated through the constructs and were myelinated indicating migration of Schwann cells into the constructs. Nodes of Ranvier between myelin segments were observed and identified by intense sodium channel (NaV 1.6) staining on the regenerated axons. There was no significant difference in electrophysiological results between control autologous experimental and construct implantation indicating that our construct are an effective alternative to autologous nerve transplantation.

Conclusions/Significance

This study demonstrates that spider silk enhances Schwann cell migration, axonal regrowth and remyelination including electrophysiological recovery in a long-distance peripheral nerve gap model resulting in functional recovery. This improvement in nerve regeneration could have significant clinical implications for reconstructive nerve surgery.     

Airborne birch and oak pollen grains and birch pollen allergens at a common sampling station in Stockholm

In the present study, the airborne concentrations of birch and oak pollen grains and birch pollen allergens have been recorded in samples from a common sampling station in Stockholm. The sampling period was between April 22^nd and May 31^st 2003. The objectives were to evaluate if analysis of allergen particles in parallel with pollen grains would be relevant to aid subjects suffering from pollinosis. Days with low birch pollen counts had relatively high nominal allergen concentrations in the beginning of the sampling period. The birch pollen grain concentration peaks, during the dry pollination culmination interval in the middle of the period, were associated with correspondingly lower nominal concentrations of allergens than grains. At the end of the sampling period very high nominal amounts of allergen appeared, as reflected by high concentrations of oak pollen grains. The high allergen concentrations were obtained as a result of inherent cross‐reactivity of anti‐ Bet v 1 antibodies with Que a antigens, which are immunologically analogous with Bet v 1. Allergen concentrations increased and decreased after light and heavy rain, respectively. Results obtained indicate that adding a pollen count forecast with allergen concentration data should aid pollen allergic subjects to avoid particulate allergens which might be expected to penetrate more easily than pollen grains into indoor environments.     

Characterization of Cholesterol Homeostasis in Telomerase-immortalized Tangier Disease Fibroblasts Reveals Marked Phenotype Variability

We compared the consequences of an ABCA1 mutation that produced an apparent lack of atherosclerosis (Tangier family 1, N935S) with an ABCA1 mutation with functional ABCA1 knockout that was associated with severe atherosclerosis (Tangier family 2, Leu⁵⁴⁸:Leu⁵⁷⁵-End), using primary and telomerase-immortalized fibroblasts. Telomerase-immortalized Tangier fibroblasts of family 1 (TT1) showed 30% residual cholesterol efflux capacity in response to apolipoprotein A-I, whereas telomerase-immortalized Tangier fibroblasts of family 2 (TT2) showed only 20%. However, there were a number of secondary differences that were often stronger and may help to explain the more rapid development of atherosclerosis in family 2. First, the total cellular cholesterol content increase was 2–3-fold and 3–5-fold in TT1 and TT2 cells, respectively. The corresponding increase in esterified cholesterol concentration was 10- and 40-fold, respectively. Second, 24-, 25-, and 27-hydroxycholesterol concentrations were moderately increased in TT1 cells, but were increased as much as 200-fold in TT2 cells. Third, cholesterol biosynthesis was moderately decreased in TT1 cells, but was markedly decreased in TT2 cells. Fourth, potentially atheroprotective LXR-dependent SREBP1c signaling was normal in TT1, but was rather suppressed in TT2 cells. Cultivated primary Tangier fibroblasts were characterized by premature aging in culture and were associated with less obvious biochemical differences. In summary, these results may help to understand the differential atherosclerotic susceptibility in Tangier disease and further demonstrate the usefulness of telomerase-immortalized cells in studying this cellular phenotype. The data support the contention that side chain-oxidized oxysterols are strong suppressors of cholesterol biosynthesis under specific pathological conditions in humans.     

Effects of waterlogging on the solubility and redox state of Sb in a shooting range soil and its uptake by grasses: a tank experiment

Aims

The effects of waterlogging on redox state and solubility of antimony (Sb) in a calcareous shooting range soil and its uptake by forage grass Lolium perenne L. and pasture weed Holcus lanatus L. were investigated.

Methods

Grasses were grown on semi-waterlogged or waterlogged shooting range soil in a laboratory tank. The soil solution was sampled at various depths over time and analyzed for the concentrations of Sb(III), Sb(V) and total Sb, as well as other trace elements.

Results

Although the reduction of Sb(V) to Sb(III) under increased waterlogging time decreased Sb solubility, it increased Sb uptake by L. perenne from 1.1 to 1.7 mg?kg^?1 (and to a lesser extent H. lanatus), implying preferential uptake of Sb(III) by this grass. The tank showed considerable variation in redox conditions with depth and plant treatment. The soil root zone (30 cm for L. perenne and 15 cm for H. lanatus) instead of the water saturated bottom, showed the highest manganese (Mn) and iron (Fe) concentrations in solution, accompanied by a higher proportion of Sb(III) in solution than the bottom zone of the tank.

Conclusions

Waterlogging can increase the risk of Sb entering the food chain from shooting range soil.     

Fish diversity in European lakes: geographical factors dominate over anthropogenic pressures

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Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces

Key message

In two Spanish barley landraces with outstanding resistance to scald, the Rrs1 _Rh4 locus was fine mapped including all known markers used in previous studies and closely linked markers were developed.

Abstract

Scald, caused by Rhynchosporium commune, is one of the most prevalent barley diseases worldwide. A search for new resistance sources revealed that Spanish landrace-derived lines SBCC145 and SBCC154 showed outstanding resistance to scald. They were crossed to susceptible cultivar Beatrix to create large DH-mapping populations of 522 and 416 DH lines that were scored for disease resistance in the greenhouse using two R. commune isolates. To ascertain the pattern of resistance, parents and reference barley lines with known scald resistance were phenotyped with a panel of differential R. commune isolates. Subpopulations were genotyped with the Illumina GoldenGate 1,536 SNP Assay and a large QTL in the centromeric region of chromosome 3H, known to harbour several scald resistance genes and/or alleles, was found in both populations. Five SNP markers closest to the QTL were converted into CAPS markers. These CAPS markers, together with informative SSR markers used in other scald studies, confirmed the presence of the Rrs1 locus. The panel of differential scald isolates indicated that the allele carried by both donors was Rrs1 _Rh4 . The genetic distance between Rrs1 and its flanking markers was 1.2 cM (11_0010) proximally and 0.9 cM (11_0823) distally, which corresponds to a distance of just below 9 Mbp. The number and nature of scald resistance genes on chromosome 3H are discussed. The effective Rrs1 allele found and the closely linked markers developed are already useful tools for molecular breeding programs and provide a good step towards the identification of candidate genes.     

The role of Müller glia and microglia in glaucoma

Cells of Müller glia and microglia react to neuronal injury in glaucoma. The change to a reactive phenotype initiates signaling cascades that may serve a neuroprotective role, but may also proceed to promote damaging effects on retinal neurons. Both effects appear to occur most likely in parallel in glaucoma, but the underlying mechanisms and signaling pathways that specifically promote protective versus destructive roles of reactive glial cells are mostly unclear. More research is needed to understand the homeostatic signaling network in which retinal glia cells are embedded to maintain or restore neuronal function after injury.     

Distribution of microglia in the postnatal murine nigrostriatal system

Parkinson’s disease (PD) is characterized by the degeneration of dopaminergic neurons in the substantia nigra (SN) and the subsequent loss of striatal target innervation. Neuroinflammatory responses have been described for virtually all PD cases analysed. Microglia are the resident immune cells of the central nervous system and, thus, are the mediators of neuroinflammation. Approximately 12% of all central nervous system cells are microglia but the distribution and density of microglia differ within distinct brain regions. Interestingly, the SN has been shown to contain more microglia than adjacent structures. We have analysed changes in microglia numbers and in microglial morphology in the postnatal murine nigrostriatal system at various stages ranging from postnatal day 0 (P0) up to 24 months of age. We clearly show that the microglia numbers in the SN and in the striatum dramatically increase from P0 to P15 and significantly decrease in both areas in 18-month-old and 24-month-old animals. Moreover, microglia in the nigrostriatal system of aged mice show signs of dystrophy and degeneration, such as cytoplasmic inclusions, deramification of their processes and membrane blebbing. Our results support the hypothesis of microglial dystrophy during aging in the murine nigrostriatal system, accompanied by subsequent impairment of normal microglial functions. Microglial dysfunction during aging might be a potential risk factor for the development and/or progression of PD.