GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Background

Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.

Results

GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.

Conclusions

GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.     

Elucidation of excogallochaols A-D, four unusual diterpenoids from the Chinese mangrove Excoecaria agallocha

Diterpenoids, excoagallochaols A-D (1-4), with an unprecedented skeleton, were isolated from the ethyl acetate extract of the stems and leaves of the mangrove Excoecaria agallocha L. The structures of these metabolites were elucidated on the basis of detailed analysis of their spectroscopic data and by comparison with those of related compounds reported in literature.     

Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood

Profiling amino acids and acylcarnitines in whole blood spots is a powerful tool in the laboratory diagnosis of several inborn errors of metabolism. Emerging data suggests that altered blood levels of amino acids and acylcarnitines are also associated with common metabolic diseases in adults. Thus, the identification of common genetic determinants for blood metabolites might shed light on pathways contributing to human physiology and common diseases. We applied a targeted mass-spectrometry-based method to analyze whole blood concentrations of 96 amino acids, acylcarnitines and pathway associated metabolite ratios in a Central European cohort of 2,107 adults and performed genome-wide association (GWA) to identify genetic modifiers of metabolite concentrations. We discovered and replicated six novel loci associated with blood levels of total acylcarnitine, arginine (both on chromosome 6; rs12210538, rs17657775), propionylcarnitine (chromosome 10; rs12779637), 2-hydroxyisovalerylcarnitine (chromosome 21; rs1571700), stearoylcarnitine (chromosome 1; rs3811444), and aspartic acid traits (chromosome 8; rs750472). Based on an integrative analysis of expression quantitative trait loci in blood mononuclear cells and correlations between gene expressions and metabolite levels, we provide evidence for putative causative genes: SLC22A16 for total acylcarnitines, ARG1 for arginine, HLCS for 2-hydroxyisovalerylcarnitine, JAM3 for stearoylcarnitine via a trans-effect at chromosome 1, and PPP1R16A for aspartic acid traits. Further, we report replication and provide additional functional evidence for ten loci that have previously been published for metabolites measured in plasma, serum or urine.In conclusion, our integrative analysis of SNP, gene-expression and metabolite data points to novel genetic factors that may be involved in the regulation of human metabolism. At several loci, we provide evidence for metabolite regulation via gene-expression and observed overlaps with GWAS loci for common diseases. These results form a strong rationale for subsequent functional and disease-related studies.     

Microsphaerol and Seimatorone: Two New Compounds Isolated from the Endophytic Fungi,Microsphaeropsis sp. and Seimatosporium sp.

A new polychlorinated triphenyl diether named microsphaerol ( 1 ), has been isolated from the endophtic fungus Microsphaeropsis sp. An intensive phytochemical investigation of the endophytic fungus Seimatosporium sp., led to the isolation of a new naphthalene derivative named seimatorone ( 2 ) and eight known compounds, i.e., 1‐(2,6‐dihydroxyphenyl)‐3‐hydroxybutan‐1‐one ( 3 ), 1‐(2,6‐dihydroxyphenyl)butan‐1‐one ( 4 ), 1‐(2‐hydroxy‐6‐methoxyphenyl)butan‐1‐one ( 5 ), 5‐hydroxy‐2‐methyl‐4H‐chromen‐4‐one ( 6 ), 2,3‐dihydro‐5‐hydroxy‐2‐methyl‐4H‐chromen‐4‐one ( 7 ), 8‐methoxynaphthalen‐1‐ol ( 8 ), nodulisporins A and B ( 9 and 10 , resp.), and daldinol ( 11 ). The structures of 1 and 2 were elucidated by detailed spectroscopic analysis including ¹H‐ and ¹³C‐NMR, COSY, HMQC, HMBC, and HR‐EI‐MS, while the structures of the known compounds were deduced from comparison of their spectral data with those in the literature. Preliminary studies revealed that microsphaerol ( 1 ) showed good antibacterial activities against B. Megaterium and E. coli, and good antilagal and antifungal activities against C. fusca, M. violaceum, respectively. On the other hand, seimatorone ( 2 ) exhibited moderate antibacterial, antialgal, and antifungal activities.     

Relationship between avian range limits and plant transition zones in Maine

Aim To determine if vegetation complexity associated with transition zones may be a contributing factor affecting bird species distributions in Maine, USA, and in increased numbers of bird species at about 45° north latitude in northeastern North America. Location Maine, USA; North America north of Mexico. Methods We delineated the ranges within Maine (86,156 km²) of 186 bird species and 240 woody plants using literature and expert review. Maps showing species richness and numbers of range limits, at 324 km² resolution, were developed for woody plants and groups of breeding birds: forest specialists, forest generalists, and those that used barren and urban habitats, early successional areas, and wetlands or open water. Two plant transition zones for Maine were identified previously, with the north–south transition zone mapped across eastern North America. Patterns in bird distribution maps were compared to woody plant maps and to transition zones. Results When the distributions of forest specialists were compared to the north–south vegetation transition zone in Maine, they were spatially coincident, but were not for other groups. Forest specialists had more species with range limits in the state (61%) than generalists (13%) or any other group. At a continental‐scale, the vegetation transition zone within eastern North America agreed fairly well with the areas of highest bird richness. Main conclusions A bird transition zone occurs in Maine and across eastern North America, akin to and overlapping the vegetation transition zone. Seasonality is likely the primary source of the inverse gradient in bird richness in the eastern USA, as reported by others. However, vegetation structure and habitat selection at very broad spatial scales appear to contribute to the reversed gradient. North of the vegetation transition zone, forest structure is simpler and coniferous forests more dominant, and this may contribute to reduced bird species richness. However, the northern (> 49°) typical gradient in bird species richness has been related to many hypotheses, and several are likely involved in the genesis of the gradient.     

Muscarinic cholinergic receptor binding in rat hindlimb somatosensory cortex following partial deafferentation by sciatic nerve transection.

Peripheral nerve injury or amputation leads to extensive changes within the central representations of the mammalian body surface. The mechanisms responsible for post-traumatic reorganization of these maps in adults may also, at least partly, underlie a more general feature of the somatosensory system--the capacity for stimulus-dependent plasticity. Acetylcholine has been implicated in both of these processes. We studied the binding of the ligands [3H]QNB and [3H]pirenzepine in rat hindlimb somatosensory cortex from 1 to 14 days following sciatic nerve transection. Although the [3H]QNB binding was not different from normal levels in tissue homogenates of the affected somatosensory cortex, differences were demonstrated when binding was measured on a layer-by-layer basis. [3H]QNB binding was changed only in certain layers, at certain times. The predominant effects appeared to be a decrease in binding in the middle layers from 4 to 14 days after the transection. Combining the [3H]QNB data with data obtained from the more M1-selective ligand [3H]pirenzepine suggested that complex changes occur among several muscarinic receptors, including receptors with non-M1 subtype characteristics. Moreover, unilateral nerve transection affects the hindlimb somatosensory regions in both hemispheres.     

Refinements of and commentary on the silver staining techniques of Fernández-Galiano

The original ammoniacal silver carbonate staining technique and subsequent modification developed by Fernández-Galiano are useful for investigating ciliate protozoan systematics and/or ciliate cortical structure and morphogenesis. The technique is complicated, however, by both uncertainties arising from the need to count drops of reagents and subjective control of the staining intensity. I have resolved these complications by defining volumes of reagents rather than using drops and by defining a range of staining times. I also comment on various steps of the techniques. My techniques are simplified and refined to produce consistent, high quality staining results.