HP1 reshapes nucleosome core to promote phase separation of heterochromatin

Heterochromatin affects genome function at many levels. It enables heritable gene repression, maintains chromosome integrity and provides mechanical rigidity to the nucleus1,2. These diverse functions are proposed to arise in part from compaction of the underlying chromatin2. A major type of heterochromatin contains at its core the complex formed between HP1 proteins and chromatin that is methylated on histone H3, lysine 9 (H3K9me). HP1 is proposed to use oligomerization to compact chromatin into phase-separated condensates3-6. Yet, how HP1-mediated phase separation relates to chromatin compaction remains unclear. Here we show that chromatin compaction by the Schizosaccharomyces pombe HP1 protein Swi6 results in phase-separated liquid condensates. Unexpectedly, we find that Swi6 substantially increases the accessibility and dynamics of buried histone residues within a nucleosome. Restraining these dynamics impairs compaction of chromatin into liquid droplets by Swi6. Our results indicate that Swi6 couples its oligomerization to the phase separation of chromatin by a counterintuitive mechanism, namely the dynamic exposure of buried nucleosomal regions. We propose that such reshaping of the octamer core by Swi6 increases opportunities for multivalent interactions between nucleosomes, thereby promoting phase separation. This mechanism may more generally drive chromatin organization beyond heterochromatin

Ten years of Genome Medicine.

This year marks the 10th anniversary of Genome Medicine. The journal was launched to meet the need in the community for a platform to publish impactful and open science that advances basic and clinical research—using genetic, genomic, omic, and systems approaches—that has the potential to revolutionize the practice of medicine. We have seen the journal evolve along with the changing landscape of health and disease, including the increasing use of genome-scale approaches in medical research and clinical practice, the generation and analysis of patient- and population-level data, and the clinical implementation of these approaches in precision medicine and public health. Genome Medicine, guided by our renowned Section Editors, continues to serve an ever-growing community of interdisciplinary researchers. Here, our Section Editors discuss the major advances in the field and their applications in genomic medicine during the past decade

The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

<p>Abstract</p> <p>Background</p> <p>The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues.</p> <p>Results</p> <p>We have developed an integrated software system for the automated analysis and representation of H/D exchange data that has been titled "The Deuterator". Novel approaches have been implemented that enable high throughput analysis, automated determination of deuterium incorporation, and deconvolution of overlapping peptides. This has been achieved by using methods involving iterative theoretical envelope fitting, and consideration of peak data within expected <it>m/z </it>ranges. Existing common file formats have been leveraged to allow compatibility with the output from the myriad of MS instrument platforms and peptide sequence database search engines.</p> <p>A web-based interface is used to integrate the components of The Deuterator that are able to analyze and present mass spectral data from instruments with varying resolving powers. The results, if necessary, can then be confirmed, adjusted, re-calculated and saved. Additional tools synchronize the curated calculation parameters with replicate time points, increasing throughput. Saved results can then be used to plot deuterium buildup curves and 3D structural overlays. The system has been used successfully in a production environment for over one year and is freely available as a web tool at the project home page <url>http://deuterator.florida.scripps.edu</url>.</p> <p>Conclusion</p> <p>The automated calculation and presentation of H/D exchange data in a user interface enables scientists to organize and analyze data efficiently. Integration of the different components of The Deuterator coupled with the flexibility of common data file formats allow this system to be accessible to the broadening H/D exchange community.</p

Effect on health-related quality of life of the X-Bolt dynamic plating system versus the sliding hip screw for the fixation of trochanteric fractures of the hip in adults: the WHiTE Four randomized clinical trial

Aims Surgical treatment of hip fracture is challenging; the bone is porotic and fixation failure can be catastrophic. Novel implants are available which may yield superior clinical outcomes. This study compared the clinical effectiveness of the novel X-Bolt Hip System (XHS) with the sliding hip screw (SHS) for the treatment of fragility hip fractures. Methods We conducted a multicentre, superiority, randomized controlled trial. Patients aged 60 years and older with a trochanteric hip fracture were recruited in ten acute UK NHS hospitals. Participants were randomly allocated to fixation of their fracture with XHS or SHS. A total of 1,128 participants were randomized with 564 participants allocated to each group. Participants and outcome assessors were blind to treatment allocation. The primary outcome was the EuroQol five-dimension five-level health status (EQ-5D-5L) utility at four months. The minimum clinically important difference in utility was pre-specified at 0.075. Secondary outcomes were EQ-5D-5L utility at 12 months, mortality, residential status, mobility, revision surgery, and radiological measures. Results Overall, 437 and 443 participants were analyzed in the primary intention-to-treat analysis in XHS and SHS treatment groups respectively. There was a mean difference of 0.029 in adjusted utility index in favour of XHS with no evidence of a difference between treatment groups (95% confidence interval -0.013 to 0.070; p = 0.175). There was no evidence of any differences between treatment groups in any of the secondary outcomes. The pattern and overall risk of adverse events associated with both treatments was similar. Conclusion Any difference in four-month health-related quality of life between the XHS and SHS is small and not clinically important. There was no evidence of a difference in the safety profile of the two treatments; both were associated with lower risks of revision surgery than previously reported

Fiber-optic chemical sensors for competitive binding fluoroimmunoassay

This paper describes the development of a fiber-optic chemical sensor based on the principle of competitive-binding fluorescence immunoassay. Rabbit immunoglobln G (IgG) is covalently Immobilized on the distal sensing tip of a quartz optical fiber. The sensor is exposed to fluorescein Isothiocyanate (FITC) labeled and unlabeled anti-rabbit IgG. The 488-nm line of an argon-ion laser provides excitation of sensor-bound analyte. This results in fluorescence emission at the optical fiber‧s sensing tip. Sensor response is inversely proportional to the amount of unlabeled anti-IgG In the sample. Limits of detection (LOD) vary with Incubation time, sample size, and measurement conditions. For 10-μL samples, typical LOD are 25 fmol of unlabeled antibody In a 20-min Incubation period. These results Indicate that each fiber-optic fluoroimmunosensor can be constructed to perform a single sensitive, rapid, low-volume immunoassay, in in situ or benchtop applications. © 1987, American Chemical Society. All rights reserved

Transglutaminase 2 limits the extravasation and the resultant myocardial fibrosis associated with factor XIII-A deficiency

Background and aims Transglutaminase (TG) 2 and Factor (F) XIII-A have both been implicated in cardiovascular protection and repair. This study was designed to differentiate between two competing hypotheses: that TG2 and FXIII-A mediate these functions in mice by fulfilling separate roles, or that they act redundantly in this respect. Methods Atherosclerosis was assessed in brachiocephalic artery plaques of fat-fed mixed strain apolipoprotein (Apo)e deficient mice that lacked either or both transglutaminases. Cardiac fibrosis was assessed both in the mixed strain mice and also in C57BL/6J Apoe expressing mice lacking either or both transglutaminases. Results No difference was found in the density of buried fibrous caps within brachiocephalic plaques from mice expressing or lacking these transglutaminases. Cardiac fibrosis developed in both Apoe/F13a1 double knockout and F13a1 single knockout mice, but not in Tgm2 knockout mice. However, concomitant Tgm2 knockout markedly increased fibrosis, as apparent in both Apoe/Tgm2/F13a1 knockout and Tgm2/F13a1 knockout mice. Amongst F13a1 knockout and Tgm2/F13a1 knockout mice, the extent of fibrosis correlated with hemosiderin deposition, suggesting that TG2 limits the extravasation of blood in the myocardium, which in turn reduces the pro-fibrotic stimulus. The resulting fibrosis was interstitial in nature and caused only minor changes in cardiac function. Conclusions These studies confirm that FXIII-A and TG2 fulfil different roles in the mouse myocardium. FXIII-A protects against vascular leakage while TG2 contributes to the stability or repair of the vasculature. The protective function of TG2 must be considered when designing clinical anti-fibrotic therapies based upon FXIII-A or TG2 inhibition

Frequency of rare recessive mutations in unexplained late onset cerebellar ataxia.

Sporadic late onset cerebellar ataxia is a well-described clinical presentation with a broad differential diagnosis that adult neurologists should be familiar with. However, despite extensive clinical investigations, an acquired cause is identified in only a minority of cases. Thereafter, an underlying genetic basis is often considered, even in those without a family history. Here we apply whole exome sequencing to a cohort of 12 patients with late onset cerebellar ataxia. We show that 33% of 'idiopathic' cases harbor compound heterozygous mutations in known ataxia genes, including genes not included on multi-gene panels, or primarily associated with an ataxic presentation