Decatransin, a novel natural product inhibiting protein translocation at the Sec61/SecY translocon

A new cyclic decadepsipeptide was isolated from Chaetosphaeria tulasneorum with potent bioactivity on mammalian and yeast cells. Chemogenomic profiling in S. cerevisiae indicated that the Sec61 translocon, the machinery for protein translocation and membrane insertion at the endoplasmic reticulum, is the target. The profiles were similar to those of cyclic heptadepsipeptides of a distinct chemotype (HUN-7293/cotransin) that had previously been shown to inhibit cotranslational translocation at the mammalian Sec61 translocon. Unbiased, genome-wide mutagenesis followed by full-genome sequencing in both fungal and mammalian cells identified dominant mutations in Sec61p/Sec61α1 to confer resistance. Most, but not all, of these mutations affected inhibition by both chemotypes, despite an absence of structural similarity. Biochemical analysis confirmed inhibition of protein translocation into the endoplasmic reticulum of both co- and posttranslationally translocated substrates by both chemotypes, demonstrating a mechanism independent of a translating ribosome. Most interestingly, both chemotypes were found to also inhibit SecYEG, the bacterial Sec61 homolog. We suggest "decatransin" as the name for this novel decadepsipeptide translocation inhibitor

Algebras of gaussian linear information

Gauss’sche lineare Information kommt in verschiedenen Modellen der reellen Welt vor, sowohl in den natur- wie auch in den sozialwissenschaftlichen Disziplinen. Mit der Gauss-Verteilung kann Unsicherheit oft adäquat dargestellt werden. Das Ziel dieser Dissertation ist es, verschiedene Algebren Gauss’scher Information zu beschreiben und zu vergleichen: Die einander entsprechenden Elemente und Operationen in den unterschiedlichen Algebren sollen herausgearbeitet und ihre jeweiligen rechentechnischen Vorteile hervorgehoben werden. Damit grosse Modelle computertechnisch behandelt werden können, müssen sie in unabhängige Faktoren zerlegt werden. Dies ist möglich, falls die Modelle dünn besetzt sind. Valuationsalgebren bieten ein allgemeines abstraktes Framework für lokales Rechnen mit solchen Faktorisierungen. Eine Valuationsalgebra ist eine zweisortige Struktur mit drei Operationen: Valuationen (die als Informationsstücke angesehen werden können) beziehen sich auf eine Domäne; Valuationen können auf eine Dom¨ane marginalisiert (fokussiert) und kombiniert (aggregiert) werden. Generische Algorithmen mit Nachrichtenaustausch k¨onnen angewendet werden, um ein Projektionsproblem zu lösen. Viele Anwendungsprobleme k¨onnen auf ein Projektionsproblem zurückgeführt werden: diagnostische, pr¨adiktive, Filter- und Smoothing- Probleme. Zum Beispiel bilden Gauss’sche Dichten eine Valuationsalgebra: Marginalisierung ist Integration und Kombination ist Multiplikation (plus Normalisierung). Gauss’sche Dichten können durch Gauss’sche Potentiale oder Moment- Matrizen dargestellt werden, wobei entweder die Konzentrationsmatrix oder die Varianz-Kovarianzmatrix verwendet wird. Hier sind Marginalisierung und Kombination Matrizenoperationen. Eine bedingte Gauss’sche Dichte ist die Familie von Gauss’sche Dichten über die Kopfvariabeln für einen jeweils festen Wert der Rumpfvariabeln. Eine bedingte Gauss’sche Dichte entspricht einer Gauss’schen Dichte über die Kopfvariabeln mit linearer Regression von den Rumpfvariabeln. Bedingte Gauss’sche Dichten können auf drei Arten betrachtet werden: auf geometrische, algebraische und analytische. Allgemeine Gauss’sche lineare Systeme führen zu Gauss’schen Hinweisen durch annahmen-basiertes Schliessen in Gauss’schen linearen Systemen. Die Fokalmengen Gauss’scher Hinweise sind parallele lineare Mannigfaltigkeiten derselben Dimension im Parameterraum. Gauss’sche Hinweise werden kombiniert, indem ihre Fokalmengen geschnitten werden, und marginalisiert, indem ihre Fokalmengen projiziert werden. Gauss’sche Potentiale entsprechen Gauss’schen Hinweisen mit einelementigen Fokalmengen. Gauss’sche Potentiale können zu einer Valuationsalgebra von Quotienten erweitert werden, die durch Paare von Gauss’schen Potentialen repräsentiert werden. In dieser sogenannten separativen Erweiterung können auch bedingte Gauss’sche Dichten dargestellt werden. Da eine bedingte Gauss’sche Dichte eine Quotientenfunktion zweier Gauss’scher Dichten ist, entspricht diese der Subtraktion zweier Konzentrationsmatrizen. Dies führt zu symmetrischen Gauss’schen Potentialen, deren Pseudo-Konzentrationsmatrix nur symmetrisch, aber nicht notwendigerweise positiv definit ist. Aus diesen Betrachtungen ergibt sich, dass bedingte Gauss’sche Dichten genau dann dem (bis auf ¨Aquivalenz) gleichen Gauss’schen Hinweis entsprechen, falls die bedingten Gauss’schen Dichten bis auf einen konstanten Faktor gleich sind. In anderen Worten tragen Gauss’sche Likelihood-Funktionen dieselbe Information wie Gauss’sche Hinweise. Dies erklärt, wieso annahmen-basiertes Schliessen aus (über-)bestimmten Gauss’schen linearen Systemen zu denselben Schätzern führt wie die Maximum- Likelihood-Methode. Variabeln können lineare Kombinationen anderer Variabeln sein. Dies erlegt lineare Einschränkungen auf den Parameterraum. Durch annahmen-basiertes Schliessen werden Algorithmen für Inferenz, Kombination und Marginalisierung für symmetrische Gauss’sche Potentiale mit linearen Gleichungen hergeleitet. Schliesslich wird gezeigt, wie Gauss’sche lineare Systeme in der Sprache Abel ausgedrückt werden können. Anfragen über komplexe Gauss’sche lineare Systeme können durch Abel beantwortet werden. Symmetrische Gauss’sche Potentiale werden anhand mehrerer Beispiele illustriert.Gaussian linear information arises in many real-world models of the natural and social sciences. The Gaussian distribution has turned out to appropriately represent uncertainty in many linear models. The main goal of this thesis is to describe and to compare different algebras of Gaussian linear information: Corresponding elements and operations in the various algebras are revealed and the respective computational advantages are highlighted. In order to make large models computationally tractable, they have to be decomposed into independent factors by exploiting sparsity. For such factorisations, valuation algebras provide a general, abstract framework for local computations. A valuation algebra is a two-sorted algebra with three operations: valuations (which may be seen as pieces of information) refer to a domain of interest; valuations can be marginalised (focussed) to a domain of interest, and they may be combined (aggregated). Generic message-passing schemes can be used to answer projection problems. Many problems in applications can be reduced to a projection problem: diagnostic estimation, prediction, filtering, smoothing. For instance, Gaussian densities form a valuation algebra: marginalisation is integration, and combination is multiplication (plus renormalisation). Gaussian densities may be represented by Gaussian potentials or moment matrices, using either the concentration or the variance-covariance matrix, respectively. Here, marginalisation and combination are matrix operations. A conditional Gaussian density is the family of Gaussian densities obtained on the head variables by fixing a value for the tail variables. A conditional Gaussian density corresponds to a Gaussian density on the head variables plus a linear regression on the tail variables. Conditional Gaussian densities can be analysed in three ways: geometric, algebraic and analytic. General Gaussian linear systems lead to Gaussian hints by assumption-based inference. Gaussian hints have focal sets which are parallel linear manifolds of the same dimension in the parameter space. Combination corresponds to intersection of focal sets and marginalisation to projection of focal sets. Gaussian potentials correspond to Gaussian hints whose focal sets are all singletons. Gaussian potentials can be extended to a valuation algebra of quotients which are represented by pairs of Gaussian potentials. Conditional Gaussian densities can be represented in the so-called separative extension of Gaussian potentials. Since a conditional Gaussian density is a quotient function of two Gaussian densities, the concentration matrix in the exponent of the denominator can be subtracted from the concentration matrix in the exponent of the numerator. This leads to a new representation of symmetric Gaussian potentials whose pseudo-concentration matrix is only symmetric but not necessarily positive definite. The main result of these considerations is that different conditional Gaussian densities turn out to be linked to the same Gaussian hints (up to equivalence) if and only if the conditional Gaussian densities are equal up to a constant factor. In other words, Gaussian likelihood functions bear the full information contained in Gaussian hints. This explains why assumption-based reasoning on (over-)determined Gaussian linear systems reproduces the estimation results based on the maximum-likelihood principle. Variables may be linear combinations of other variables. This imposes linear restrictions on the parameter space. In the spirit of assumption-based reasoning, algorithms for inference, the combination and marginalisation are derived for symmetric Gaussian potentials with deterministic equations. Finally, it is shown how Gaussian linear systems can be expressed in the language Abel. Queries on a complex Gaussian linear system can be answered in the Abel system. Several examples illustrate the new approach of symmetric Gaussian potentials

Etiology of Carpal Tunnel Syndrome in a Large Cohort of Children

(1) Background: Carpal tunnel syndrome (CTS), a compressive mononeuropathy of the median nerve at the wrist, is rare in childhood and occurs most frequently due to secondary causes. (2) Methods: Medical history, electrodiagnostic findings, and imaging data of patients with CTS from two pediatric neuromuscular centers were analyzed retrospectively. The etiology of CTS was investigated and compared with the literature. (3) Results: We report on a cohort of 38 CTS patients (n = 22 females, n = 29 bilateral, mean age at diagnosis 9.8 years). Electrodiagnostic studies of all patients revealed slowing of the antidromic sensory or orthodromic mixed nerve conduction velocities across the carpal tunnel or lack of the sensory nerve action potential and/or prolonged distal motor latencies. Median nerve ultrasound was diagnostic for CTS and confirmed tumorous and vascular malformations. Etiology was secondary in most patients (n = 29; 76%), and mucopolysaccharidosis was the most frequent underlying condition (n = 14; 37%). Idiopathic CTS was rare in this pediatric cohort (n = 9; 24%). (4) Conclusion: Since CTS in childhood is predominantly caused by an underlying disorder, a thorough evaluation and search for a causative condition is recommended in this age group

Can molecular markers stratify the diagnostic value of high-grade prostatic intraepithelial neoplasia?

The diagnostic performance of isolated high-grade prostatic intraepithelial neoplasia in prostatic biopsies has recently been questioned, and molecular analysis of high-grade prostatic intraepithelial neoplasia has been proposed for improved prediction of prostate cancer. Here, we retrospectively studied the value of isolated high-grade prostatic intraepithelial neoplasia and the immunohistochemical markers ?-methylacyl coenzyme A racemase, Bcl-2, annexin II, and Ki-67 for better risk stratification of high-grade prostatic intraepithelial neoplasia in our local Swiss population. From an initial 165 diagnoses of isolated high-grade prostatic intraepithelial neoplasia, we refuted 61 (37%) after consensus expert review. We used 30 reviewed high-grade prostatic intraepithelial neoplasia cases with simultaneous biopsy prostate cancer as positive controls. Rebiopsies were performed in 66 patients with isolated high-grade prostatic intraepithelial neoplasia, and the median time interval between initial and repeat biopsy was 3 months. Twenty (30%) of the rebiopsies were positive for prostate cancer, and 10 (15%) showed persistent isolated high-grade prostatic intraepithelial neoplasia. Another 2 (3%) of the 66 patients were diagnosed with prostate cancer in a second rebiopsy. Mean prostate-specific antigen serum levels did not significantly differ between the 22 patients with prostate cancer and the 44 without prostate cancer in rebiopsies, and the 30 positive control patients, respectively (median values, 8.1, 7.7, and 8.8 ng/mL). None of the immunohistochemical markers, including ?-methylacyl coenzyme A racemase, Bcl-2, annexin II, and Ki-67, revealed a statistically significant association with the risk of prostate cancer in repeat biopsies. Taken together, the 33% risk of being diagnosed with prostate cancer after a diagnosis of high-grade prostatic intraepithelial neoplasia justifies rebiopsy, at least in our not systematically prostate-specific antigen-screened population. There is not enough evidence that immunohistochemical markers can reproducibly stratify the risk of prostate cancer after a diagnosis of isolated high-grade prostatic intraepithelial neoplasia

Etiology of Carpal Tunnel Syndrome in a Large Cohort of Children

(1) Background: Carpal tunnel syndrome (CTS), a compressive mononeuropathy of the median nerve at the wrist, is rare in childhood and occurs most frequently due to secondary causes. (2) Methods: Medical history, electrodiagnostic findings, and imaging data of patients with CTS from two pediatric neuromuscular centers were analyzed retrospectively. The etiology of CTS was investigated and compared with the literature. (3) Results: We report on a cohort of 38 CTS patients (n = 22 females, n = 29 bilateral, mean age at diagnosis 9.8 years). Electrodiagnostic studies of all patients revealed slowing of the antidromic sensory or orthodromic mixed nerve conduction velocities across the carpal tunnel or lack of the sensory nerve action potential and/or prolonged distal motor latencies. Median nerve ultrasound was diagnostic for CTS and confirmed tumorous and vascular malformations. Etiology was secondary in most patients (n = 29; 76%), and mucopolysaccharidosis was the most frequent underlying condition (n = 14; 37%). Idiopathic CTS was rare in this pediatric cohort (n = 9; 24%). (4) Conclusion: Since CTS in childhood is predominantly caused by an underlying disorder, a thorough evaluation and search for a causative condition is recommended in this age group

Physician anaesthesia providers in Switzerland today and tomorrow: results of the National Anaesthesia Workforce Study (NAWOS)

The Swiss healthcare system is highly ranked, given its unrestricted access to specialised care and short waiting lists for surgery. However, the need for anaesthetic and surgical care is escalating owing to the increasing size and ageing of the Swiss population. In addition, to address the persistent and recurrent SARS-CoV-2 pandemic crisis, the speciality of anaesthesia is under tremendous pressure to maintain an effective workforce in order to address population needs. The current number, characteristics and future evolution of the physician anaesthesia workforce in Switzerland are currently unknown. The purpose of this study was to assess the size and professional and sociodemographic characteristics of the current anaesthesia workforce in Switzerland and to forecast its development up to 2034

Decatransin, a novel natural product inhibiting protein translocation at the Sec61/SecY translocon

A new cyclic decadepsipeptide was isolated from Chaetosphaeria tulasneorum with potent bioactivity on mammalian and yeast cells. Chemogenomic profiling in S. cerevisiae indicated that the Sec61 translocon, the machinery for protein translocation and membrane insertion at the endoplasmic reticulum, is the target. The profiles were similar to those of cyclic heptadepsipeptides of a distinct chemotype (HUN-7293/cotransin) that had previously been shown to inhibit cotranslational translocation at the mammalian Sec61 translocon. Unbiased, genome-wide mutagenesis followed by full-genome sequencing in both fungal and mammalian cells identified dominant mutations in Sec61p/Sec61α1 to confer resistance. Most, but not all, of these mutations affected inhibition by both chemotypes, despite an absence of structural similarity. Biochemical analysis confirmed inhibition of protein translocation into the endoplasmic reticulum of both co- and posttranslationally translocated substrates by both chemotypes, demonstrating a mechanism independent of a translating ribosome. Most interestingly, both chemotypes were found to also inhibit SecYEG, the bacterial Sec61 homolog. We suggest "decatransin" as the name for this novel decadepsipeptide translocation inhibitor

Data from: Identification and evaluation of novel acetolactate synthase inhibitors as antifungal agents

High-throughput phenotypic screening against yeast Saccharomyces cerevisiae revealed a series of triazolo-pyrimidine-sulfonamide compounds with broad-spectrum antifungal activity, no significant cytotoxicity, and low protein binding. To elucidate the target of this series we have applied a chemogenomic profiling approach using the S. cerevisiae deletion collection. All compounds of the series yielded highly similar profiles that suggested acetolactate synthase (Ilv2p, catalyzes the first common step in branched chain amino acid biosynthesis) as a possible target. High correlation to profiles of known Ilv2p inhibitors like chlorimuron-ethyl provided further evidence for a similar mechanism of action. Genome-wide mutagenesis in S. cerevisiae identified 13 resistant clones with 3 different mutations in the catalytic subunit of acetolactate synthase that also conferred cross-resistance to established Ilv2p inhibitors. Mapping the mutations into the published Ilv2p crystal structure outlined the chlorimuron-ethyl binding cavity and it was possible to dock the triazolo-pyrimidine-sulfonamide compound into this pocket in silico. However, fungal growth inhibition could be bypassed through supplementation with exogenous branched chain amino acids, or by the addition of serum to the medium in all of the fungal organisms tested except for Aspergillus fumigatus. Thus, these data support the identification of triazolo-pyrimidine-sulfonamide as inhibitors of acetolactate synthase but suggest that targeting may be compromised due to the possibility of nutrient bypass in vivo

Supplemental_Data.zip

The compressed Supplemental_Data.zip archive contains two files: 1. Supplemental Data_S3, the complete HIP HOP profiles are provided as tab delimited .txt files. The sensitivity and z-scores for all HIP strains present in the pool across all tested compounds are listed in the HIP-exp-scores-annotation.txt file, scores for all HOP strains present in the pool are listed in the HOP-exp-scores-annotation.txt file. To reproduce the plots depicted in the article the sensitivity can be plotted on the y-axis, the z-score on the x-axis. Each gene is annotated with systematic name, common name, description, GO category etc. 2. The Supplemental_Data_S4.zip file containing the in silico docking solution. It is provided as a standard Protein Data Bank file named 1N0H_compound1_docked.pdb. UNK1 refers to the docked compound 1, all other structures are labeled as in the original 1N0H.pdb file downloaded from RCSB protein databank www.pdb.org