Afferent inhibition and cortical silent periods in shoulder primary motor cortex and effect of a suprascapular nerve block in people experiencing chronic shoulder pain

© 2015 International Federation of Clinical Neurophysiology. Objective: To characterise short afferent inhibition (SAI) and the cortical silent period (CSP) in the primary motor cortex representations of the infraspinatus muscle in healthy adults and people experiencing chronic shoulder pain, to determine the impact of a suprascapular nerve block (SSNB). Methods: Neurophysiological measures were obtained in 18 controls and 8 patients with chronic shoulder pain, pre and post SSNB and 1 week later. Pain intensity was assessed by a visual analogue scale. Results: SAI was apparent in controls (all P < 0.03) and a CSP was observed which reduced in the presence of SAI (all P < 0.0001). Compared to controls, shoulder pain patients demonstrated higher active motor threshold (P = 0.046), less SAI (P = 0.044), a longer CSP (P = 0.048) and less modulation of the CSP by SAI (P = 0.045). Higher motor thresholds were related to higher pain scores (P = 0.009). The SSNB immediately restored SAI (P = 0.013), with a positive relationship between increased SAI and reduced pain (P = 0.031). The SSNB further reduced modulation of CSP by SAI at 1 week post injection (P = 0.006). Conclusions: SAI and the CSP were present and demonstrated robust interaction in controls, which was aberrant in patients. The SSNB transiently restored SAI but had no effect on the CSP; however CSP modulation by SAI was further attenuated 1 week post injection. Significance: The current findings improve understanding of the neurophysiology of the shoulder motor cortex and its modulation by chronic pain. The effect of SSNB in shoulder pain patients should be interpreted with caution until proven in a larger population. Interventions that target intracortical inhibition might increase efficacy in people with chronic shoulder pain

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

Introns in a wide range of organisms including plants, animals and fungi are able to increase the expression of the gene that they are contained in. This process of intron-mediated enhancement (IME) is most thoroughly studied in Arabidopsis thaliana, where it has been shown that enhancing introns are typically located near the promoter and are compositionally distinct from downstream introns. In this study, we perform a comprehensive comparative analysis of several sequenced plant genomes. We find that enhancing sequences are conserved in the multi-cellular plants but are either absent or unrecognizable in algae. IME signals are preferentially located towards the 5′-end of first introns but also appear to be enriched in 5′-UTRs and coding regions near the transcription start site. Enhancing introns are found most prominently in genes that are highly expressed in a wide range of tissues. Through site-directed mutagenesis in A. thaliana, we show that IME signals can be inserted or removed from introns to increase or decrease gene expression. Although we do not yet know the specific mechanism of IME, the predicted signals appear to be both functional and highly conserved

Effects of neutron irradiation on the brittle to ductile transition in single crystal tungsten

Only limited data exist on the effect of neutron irradiation on the brittle to ductile transition (BDT) in tungsten. This work investigates the increase in brittle to ductile transition temperature (BDTT) following neutron irradiation to 1.67 displacements per atom, using four-point bend tests over a range of temperatures (623-1173 K) and strain rates (3.5 x 10$^{-7}$- 2.5 x 10$^{-5}$ s$^{-1}$). The BDTT was found to increase by 500 K after irradiation. The activation energy for the BDT was determined using Arrhenius analysis of the four-point bend tests. Nanoindentation strain-rate jump tests were used to characterise the activation volume for dislocation motion. These were quantified as 1.05 eV and 4.6 b³ respectively, very close to values found for unirradiated tungsten. This suggests that kink-pair formation is the controlling mechanism for the BDT before and after irradiation. This work also carries out a unique verification of inventory-code-modelling (via FISPACT-II) of transmutation of tungsten to rhenium and osmium under neutron irradiation using two independent techniques (X-ray and gamma-ray spectroscopy). These results show that modelling can correctly predict this transmutation, provided that an accurate neutron spectrum is used. This is a critical result given the widespread use of inventory codes such as FISPACT-II, and the associated nuclear data libraries, for modelling transmutation of tungsten

Effects of neutron irradiation on the brittle to ductile transition in single crystal tungsten

Only limited data exist on the effect of neutron irradiation on the brittle to ductile transition (BDT) in tungsten. This work investigates the increase in brittle to ductile transition temperature (BDTT) following neutron irradiation to 1.67 displacements per atom, using four-point bend tests over a range of temperatures (623–1173 K) and strain rates (3.5 × 10−7 - 2.5 × 10−5 s−1). The BDTT was found to increase by 500 K after irradiation. The activation energy for the BDT was determined using Arrhenius analysis of the four-point bend tests. Nanoindentation strain-rate jump tests were used to characterise the activation volume for dislocation motion. These were quantified as 1.05 eV and 18 b3 respectively, very close to values found for unirradiated tungsten. This suggests that kink-pair formation is the controlling mechanism for the BDT before and after irradiation. This work also carries out a unique verification of inventory-code-modelling (via FISPACT-II) of transmutation of tungsten to rhenium and osmium under neutron irradiation using two independent techniques (X-ray and gamma-ray spectroscopy). These results show that modelling can correctly predict this transmutation, provided that an accurate neutron spectrum is used. This is a critical result given the widespread use of inventory codes such as FISPACT-II, and the associated nuclear data libraries, for modelling transmutation of tungsten

Mutational Biases and Selective Forces Shaping the Structure of Arabidopsis Genes

Recently features of gene expression profiles have been associated with structural parameters of gene sequences in organisms representing a diverse set of taxa. The emerging picture indicates that natural selection, mediated by gene expression profiles, has a significant role in determining genic structures. However the current situation is less clear in plants as the available data indicates that the effect of natural selection mediated by gene expression is very weak. Moreover, the direction of the patterns in plants appears to contradict those observed in animal genomes. In the present work we analized expression data for >18000 Arabidopsis genes retrieved from public datasets obtained with different technologies (MPSS and high density chip arrays) and compared them with gene parameters. Our results show that the impact of natural selection mediated by expression on genes sequences is significant and distinguishable from the effects of regional mutational biases. In addition, we provide evidence that the level and the breadth of gene expression are related in opposite ways to many structural parameters of gene sequences. Higher levels of expression abundance are associated with smaller transcripts, consistent with the need to reduce costs of both transcription and translation. Expression breadth, however, shows a contrasting pattern, i.e. longer genes have higher breadth of expression, possibly to ensure those structural features associated with gene plasticity. Based on these results, we propose that the specific balance between these two selective forces play a significant role in shaping the structure of Arabidopsis genes

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Background: Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. Results: The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. Conclusions: The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration

Longer First Introns Are a General Property of Eukaryotic Gene Structure

While many properties of eukaryotic gene structure are well characterized, differences in the form and function of introns that occur at different positions within a transcript are less well understood. In particular, the dynamics of intron length variation with respect to intron position has received relatively little attention. This study analyzes all available data on intron lengths in GenBank and finds a significant trend of increased length in first introns throughout a wide range of species. This trend was found to be even stronger when using high-confidence gene annotation data for three model organisms (Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster) which show that the first intron in the 5′ UTR is - on average - significantly longer than all downstream introns within a gene. A partial explanation for increased first intron length in A. thaliana is suggested by the increased frequency of certain motifs that are present in first introns. The phenomenon of longer first introns can potentially be used to improve gene prediction software and also to detect errors in existing gene annotations

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene

Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Citation: Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., . . . Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1). doi:10.1186/s13059-015-0582-8Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. © 2015 Chapman et al. licensee BioMed Central.Additional Authors: Muehlbauer, G. J.;Stein, N.;Rokhsar, D. S