RNA exosome mutations in pontocerebellar hypoplasia alter ribosome biogenesis and p53 levels.

The RNA exosome is a ubiquitously expressed complex of nine core proteins (EXOSC1-9) and associated nucleases responsible for RNA processing and degradation. Mutations in EXOSC3, EXOSC8, EXOSC9, and the exosome cofactor RBM7 cause pontocerebellar hypoplasia and motor neuronopathy. We investigated the consequences of exosome mutations on RNA metabolism and cellular survival in zebrafish and human cell models. We observed that levels of mRNAs encoding p53 and ribosome biogenesis factors are increased in zebrafish lines with homozygous mutations of exosc8 or exosc9, respectively. Consistent with higher p53 levels, mutant zebrafish have a reduced head size, smaller brain, and cerebellum caused by an increased number of apoptotic cells during development. Down-regulation of EXOSC8 and EXOSC9 in human cells leads to p53 protein stabilisation and G2/M cell cycle arrest. Increased p53 transcript levels were also observed in muscle samples from patients with EXOSC9 mutations. Our work provides explanation for the pathogenesis of exosome-related disorders and highlights the link between exosome function, ribosome biogenesis, and p53-dependent signalling. We suggest that exosome-related disorders could be classified as ribosomopathies

Levels of nitrate, nitrite and nitrosamines in model sausages during heat treatment and in vitro digestion – The impact of adding nitrite and spinach (Spinacia oleracea L.)

publishedVersio

Towards fairer conservation: Perspectives and ideas from early‐career researchers

The Black Lives Matter Movement, which gained unprecedented global momentum in mid-2020, triggered critical reflection on systemic discrimination of disadvantaged groups across many domains of society. It prompted us, as early-career researchers (ECRs) in conservation science, to examine our own awareness of ongoing injustices within our field, the role we play in perpetuating or countering these injustices, and how to move forward. Colonialist ideologies and power dynamics throughout the history of conservation practice and research have left a long-lasting legacy of inequality and systemic racism. While improvements have been made, these legacies continue to influence teaching and practice today. In this perspective piece, we reflect on the impacts of conservation’s colonial past and how the sector has developed. We then explore how current traditional routes into conservation, and the dominance of these approaches, can leave ECRs underprepared to address modern-day conservation issues due to a limited understanding of conservation’s history and key theories from other fields. We end by offering a set of suggestions encouraging others to learn and practise fairer and more inclusive conservation practices

New Results for the Correlation Functions of the Ising Model and the Transverse Ising Chain

In this paper we show how an infinite system of coupled Toda-type nonlinear differential equations derived by one of us can be used efficiently to calculate the time-dependent pair-correlations in the Ising chain in a transverse field. The results are seen to match extremely well long large-time asymptotic expansions newly derived here. For our initial conditions we use new long asymptotic expansions for the equal-time pair correlation functions of the transverse Ising chain, extending an old result of T.T. Wu for the 2d Ising model. Using this one can also study the equal-time wavevector-dependent correlation function of the quantum chain, a.k.a. the q-dependent diagonal susceptibility in the 2d Ising model, in great detail with very little computational effort.Comment: LaTeX 2e, 31 pages, 8 figures (16 eps files). vs2: Two references added and minor changes of style. vs3: Corrections made and reference adde

Multicriteria plan optimization in the hands of physicians: a pilot study in prostate cancer and brain tumors

Background: The purpose of this study was to demonstrate the feasibility of physician driven planning in intensity modulated radiotherapy (IMRT) with a multicriteria optimization (MCO) treatment planning system and template based plan optimization. Exploiting the full planning potential of MCO navigation, this alternative planning approach intends to improve planning efficiency and individual plan quality. Methods: Planning was retrospectively performed on 12 brain tumor and 10 post-prostatectomy prostate patients previously treated with MCO-IMRT. For each patient, physicians were provided with a template-based generated Pareto surface of optimal plans to navigate, using the beam angles from the original clinical plans. We compared physician generated plans to clinically delivered plans (created by dosimetrists) in terms of dosimetric differences, physician preferences and planning times. Results: Plan qualities were similar, however physician generated and clinical plans differed in the prioritization of clinical goals. Physician derived prostate plans showed significantly better sparing of the high dose rectum and bladder regions (p(D1) < 0.05; D1: dose received by 1% of the corresponding structure). Physicians’ brain tumor plans indicated higher doses for targets and brainstem (p(D1) < 0.05). Within blinded plan comparisons physicians preferred the clinical plans more often (brain: 6:3 out of 12, prostate: 2:6 out of 10) (not statistically significant). While times of physician involvement were comparable for prostate planning, the new workflow reduced the average involved time for brain cases by 30%. Planner times were reduced for all cases. Subjective benefits, such as a better understanding of planning situations, were observed by clinicians through the insight into plan optimization and experiencing dosimetric trade-offs. Conclusions: We introduce physician driven planning with MCO for brain and prostate tumors as a feasible planning workflow. The proposed approach standardizes the planning process by utilizing site specific templates and integrates physicians more tightly into treatment planning. Physicians’ navigated plan qualities were comparable to the clinical plans. Given the reduction of planning time of the planner and the equal or lower planning time of physicians, this approach has the potential to improve departmental efficiencies

Phenotypic convergence of Menkes and Wilson disease.

Menkes disease is an X-linked multisystem disorder with epilepsy, kinky hair, and neurodegeneration caused by mutations in the copper transporter ATP7A. Other ATP7A mutations have been linked to juvenile occipital horn syndrome and adult-onset hereditary motor neuropathy.1,2 About 5%-10% of the patients present with "atypical Menkes disease" characterized by longer survival, cerebellar ataxia, and developmental delay.2 The intracellular copper transport is regulated by 2 P type ATPase copper transporters ATP7A and ATP7B. These proteins are expressed in the trans-Golgi network that guides copper to intracellular compartments, and in copper excess, it relocates copper to the plasma membrane to pump it out from the cells.3ATP7B mutations cause Wilson disease with dystonia, ataxia, tremor, and abnormal copper accumulation in the brain, liver, and other organs.4

Multifocal demyelinating motor neuropathy and hamartoma syndrome associated with a de novo PTEN mutation.

OBJECTIVE: To describe a patient with a multifocal demyelinating motor neuropathy with onset in childhood and a mutation in phosphatase and tensin homolog (PTEN), a tumor suppressor gene associated with inherited tumor susceptibility conditions, macrocephaly, autism, ataxia, tremor, and epilepsy. Functional implications of this protein have been investigated in Parkinson and Alzheimer diseases. METHODS: We performed whole-exome sequencing in the patient's genomic DNA validated by Sanger sequencing. Immunoblotting, in vitro enzymatic assay, and label-free shotgun proteomic profiling were performed in the patient's fibroblasts. RESULTS: The predominant clinical presentation of the patient was a childhood onset, asymmetric progressive multifocal motor neuropathy. In addition, he presented with macrocephaly, autism spectrum disorder, and skin hamartomas, considered as clinical criteria for PTEN-related hamartoma tumor syndrome. Extensive tumor screening did not detect any malignancies. We detected a novel de novo heterozygous c.269T>C, p.(Phe90Ser) PTEN variant, which was absent in both parents. The pathogenicity of the variant is supported by altered expression of several PTEN-associated proteins involved in tumorigenesis. Moreover, fibroblasts showed a defect in catalytic activity of PTEN against the secondary substrate, phosphatidylinositol 3,4-trisphosphate. In support of our findings, focal hypermyelination leading to peripheral neuropathy has been reported in PTEN-deficient mice. CONCLUSION: We describe a novel phenotype, PTEN-associated multifocal demyelinating motor neuropathy with a skin hamartoma syndrome. A similar mechanism may potentially underlie other forms of Charcot-Marie-Tooth disease with involvement of the phosphatidylinositol pathway

Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration

Human genetic factors predispose to tuberculosis (TB). We studied 7.6 million genetic variants in 5,530 people with pulmonary TB and in 5,607 healthy controls. In the combined analysis of these subjects and the follow-up cohort (15,087 TB patients and controls altogether), we found an association between TB and variants located in introns of the ASAP1 gene on chromosome 8q24 (P = 2.6 × 10−11 for rs4733781; P = 1.0 × 10−10 for rs10956514). Dendritic cells (DCs) showed high ASAP1 expression that was reduced after Mycobacterium tuberculosis infection, and rs10956514 was associated with the level of reduction of ASAP1 expression. The ASAP1 protein is involved in actin and membrane remodeling and has been associated with podosomes. The ASAP1-depleted DCs showed impaired matrix degradation and migration. Therefore, genetically determined excessive reduction of ASAP1 expression in M. tuberculosis–infected DCs may lead to their impaired migration, suggesting a potential mechanism of predisposition to TB

Comparison of an in-house real-time duplex PCR assay with commercial HOLOGIC® APTIMA assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in urine and extra-genital specimens

Abstract Background Extra-genital Neisseria gonorrhoeae and Chlamydia trachomatis infections are mostly asymptomatic, and important reservoir sites of infection as they often go undetected and may be more difficult to eradicate with recommended therapeutic regimens. Commercial nucleic acid amplification tests (NAATs) have not received regulatory approval for the detection of N. gonorrhoeae and C. trachomatis in extra-genital specimens. The HOLOGIC® APTIMA Combo2 assay for N. gonorrhoeae and C. trachomatis has performed well in evaluations using extra-genital specimens. Methods We assessed the performance of an in-house real-time duplex PCR assay for the detection of N. gonorrhoeae and C. trachomatis in urine and extra-genital specimens using the HOLOGIC® APTIMA assays as gold standard comparators. Urine, oropharyngeal and ano-rectal specimens were collected from each of 200 men-who-have-sex-with-men (MSM) between December 2011 and July 2012. Results For N. gonorrhoeae detection, the in-house PCR assay showed 98.5–100% correlation agreement with the APTIMA assays, depending on specimen type. Sensitivity for N. gonorrhoeae detection was 82.4% for ano-rectal specimens, 83.3% for oropharyngeal specimens, and 85.7% for urine; and specificity was 100% with all specimen types. The positive predictive value (PPV) for N. gonorrhoeae detection was 100% and the negative predictive value (NPV) varied with sample type, ranging from 98.5–99.5%. For C. trachomatis detection, correlation between the assays was 100% for all specimen types. The sensitivity, specificity, PPV and NPV of the in-house PCR assay was 100% for C. trachomatis detection, irrespective of specimen type. Conclusion The in-house duplex real-time PCR assay showed acceptable performance characteristics in comparison with the APTIMA® assays for the detection of extra-genital N. gonorrhoeae and C. trachomatis

Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke

Genetic factors have been implicated in stroke risk but few replicated associations have been reported. We conducted a genome-wide association study (GWAS) in ischemic stroke and its subtypes in 3,548 cases and 5,972 controls, all of European ancestry. Replication of potential signals was performed in 5,859 cases and 6,281 controls. We replicated reported associations between variants close to PITX2 and ZFHX3 with cardioembolic stroke, and a 9p21 locus with large vessel stroke. We identified a novel association for a SNP within the histone deacetylase 9(HDAC9) gene on chromosome 7p21.1 which was associated with large vessel stroke including additional replication in a further 735 cases and 28583 controls (rs11984041, combined P = 1.87×10−11, OR=1.42 (95% CI) 1.28-1.57). All four loci exhibit evidence for heterogeneity of effect across the stroke subtypes, with some, and possibly all, affecting risk for only one subtype. This suggests differing genetic architectures for different stroke subtypes