Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Am. muticum introgression lines

Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is limited by poor genomic resolution and limited understanding of the genomic impact of introgression breeding. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that introgressed genes tend to be downregulated, shifting the expression balance of triads towards suppression of the introgressed region, with no discernible compensation in the expression of the homoeologous copies. This analysis explores the genomic impact of introgression breeding and provides an affordable way for breeders to better characterise introgression lines and more effectively deploy wild relative variation.

White trauma: tracing trauma informed recovery and white supremacy in social work practice

This qualitative research study examines how five prominent recovery oriented community based organizations talk out loud about themselves, their service population and recovery. Using a critical discourse analysis, pervasive discursive patterns were revealed through thematic analysis. This study details the way in which trauma-informed care quietly manifests alongside the same guiding principles as the recovery model, creating a compounded site of power whereby one lives both inside and outside the bounds of the other. The purpose of this study is to call attention to the illusive nature of these widely-celebrated models, disrupting the unchecked, institutionalized supremacy of the whiteness that prevails within. Applying the concept of creaming to social service provision in Toronto, this study makes the claim that white trauma is centred within recovery oriented service construction and provision given it causes the least structural disruption. This process ultimately sustains the feel-good culture that envelops recovery based and trauma-informed social work.

White trauma: tracing trauma informed recovery and white supremacy in social work practice

This qualitative research study examines how five prominent recovery oriented community based organizations talk out loud about themselves, their service population and recovery. Using a critical discourse analysis, pervasive discursive patterns were revealed through thematic analysis. This study details the way in which trauma-informed care quietly manifests alongside the same guiding principles as the recovery model, creating a compounded site of power whereby one lives both inside and outside the bounds of the other. The purpose of this study is to call attention to the illusive nature of these widely-celebrated models, disrupting the unchecked, institutionalized supremacy of the whiteness that prevails within. Applying the concept of creaming to social service provision in Toronto, this study makes the claim that white trauma is centred within recovery oriented service construction and provision given it causes the least structural disruption. This process ultimately sustains the feel-good culture that envelops recovery based and trauma-informed social work.

A Momentary Impact Injury of Vertebral Endplates, even without Structural Disruption, Initiates Disc Degeneration In Vitro.

Background ： It has been acknowledged that the intervertebral disc degeneration(IDD) is associated with an aberrant cell-medicated response to structural failures, such as vertebral burst fracture, radial fissures, and endplate fracture. However, whether a momentary impact injury of the endplates without structural disruption, is sufficiently to initiate disc degeneration remains elusive. This study was to further evolve an in vitro momentary impact injury model of IDD and to investigate if a momentary impact load of the endplates without structural disruption could initiate IDD. Methods. Rat spinal segments (from L1/2 to L5/6, n=54) were harvested and randomly assigned into three groups: Control (n=18), Low Impact (12 J/cm 3 , n=18) and High Impact (25 J/cm 3 , n=18). Samples in both of the impact groups were subjected to axial momentary impact load using a custom-made apparatus, and cultured for 14 days. The degenerative process was investigated by using histomorphology and real-time PCR. Results: The discs in both of the impact groups showed significant degenerative changes at 14 days, both of which showed much higher histological scores and up-regulation of the catabolic (MMP-9, MMP-13) genes transcription than that of the control group ( P ＜0.05). The discs with endplate fracture compared to that with intact endplate also showed strongly up-regulated catabolic (MMP-9, MMP-13) genes transcription, and more significant degenerative changes based on the histological scoring ( P ＜0.05). Conclusion: This study demonstrated that a momentary impact load (12 J/cm 3 ) on the spinal segments of the rats could initiate IDD at 14 days after injury and not only endplate fracture but also a momentary impact injury without structural disruption could also promote IDD.

Structural disruption of exonic stem–loops immediately upstream of the intron regulates mammalian splicing

Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem–loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.

A Momentary Impact Injury of Vertebral Endplates, even without Structural Disruption, Initiates Disc Degeneration In Vitro.

Background ： It has been acknowledged that the intervertebral disc degeneration(IDD) is associated with an aberrant cell-medicated response to structural failures, such as vertebral burst fracture, radial fissures, and endplate fracture. However, whether a momentary impact injury of the endplates without structural disruption is sufficiently to initiate disc degeneration remains elusive. This study was to further evolve an in vitro momentary impact injury model of IDD and to investigate if a momentary impact load of the endplates without structural disruption could initiate IDD. Methods. Rats spinal segments (from L1/2 to L5/6, n=54) were harvested and randomly assigned into three groups: Control (n=18), Low Impact (12 J/cm 3 , n=18) and High Impact (25 J/cm 3 , n=18). Samples in both of the impact groups were subjected axial momentary impact load using a custom-made apparatus, and cultured for 14 days. The degenerative process was investigated by using histomorphology and real-time PCR. Results: The discs in both of the impact groups showed significant degenerative changes at 14 days, both of which showed much higher histological scores and up-regulation of the catabolic (MMP-9, MMP-13) genes transcription than that of the control group ( P ＜0.05). The discs with endplate fracture compared to that with intact endplate also showed strongly up-regulated catabolic (MMP-9, MMP-13) genes transcription, and more significant degenerative changes based on the histological scoring ( P ＜0.05). Conclusion: This study demonstrated that a momentary impact load (12 J/cm 3 ) on the spinal segments of the rats could initiate IDD at 14 days after injury and not only endplate fracture but also a momentary impact injury without structural disruption could also promote IDD.