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A prodromal phase of Parkinson’s disease (PD) may precede motor manifestations by decades. PD patients’ siblings are at higher risk for PD, but the prevalence and distribution of prodromal symptoms are unknown. The study objectives were (1) to assess motor and non-motor features estimating prodromal PD probability in PD siblings recruited within the European PROPAG-AGEING project; (2) to compare motor and non-motor symptoms to the well-established DeNoPa cohort. 340 PD siblings from three sites (Bologna, Seville, Kassel/Goettingen) underwent clinical and neurological evaluations of PD markers. The German part of the cohort was compared with German de novo PD patients (dnPDs) and healthy controls (CTRs) from DeNoPa. Fifteen (4.4%) siblings presented with subtle signs of motor impairment, with MDS-UPDRS-III scores not clinically different from CTRs. Symptoms of orthostatic hypotension were present in 47 siblings (13.8%), no different to CTRs (p = 0.072). No differences were found for olfaction and overall cognition; German-siblings performed worse than CTRs in visuospatial-executive and language tasks. 3/147 siblings had video-polysomnography-confirmed REM sleep behavior disorder (RBD), none was positive on the RBD Screening Questionnaire. 173/300 siblings had

PROPAG-AGEING consortium., A prodromal phase of Parkinson’s disease (PD) may precede motor manifestations by decades. PD patients’ siblings are at higher risk for PD, but the prevalence and distribution of prodromal symptoms are unknown. The study objectives were (1) to assess motor and non-motor features estimating prodromal PD probability in PD siblings recruited within the European PROPAG-AGEING project; (2) to compare motor and non-motor symptoms to the well-established DeNoPa cohort. 340 PD siblings from three sites (Bologna, Seville, Kassel/Goettingen) underwent clinical and neurological evaluations of PD markers. The German part of the cohort was compared with German de novo PD patients (dnPDs) and healthy controls (CTRs) from DeNoPa. Fifteen (4.4%) siblings presented with subtle signs of motor impairment, with MDS-UPDRS-III scores not clinically different from CTRs. Symptoms of orthostatic hypotension were present in 47 siblings (13.8%), no different to CTRs (p = 0.072). No differences were found for olfaction and overall cognition; German-siblings performed worse than CTRs in visuospatial-executive and language tasks. 3/147 siblings had video-polysomnography-confirmed REM sleep behavior disorder (RBD), none was positive on the RBD Screening Questionnaire. 173/300 siblings had, This project has received funding from the European Union’s Horizon 2020 research and innovation program Propag‐Ageing under grant agreement no. 634821.

Additional file 2: Figure 1. Representation of all executions (6, 12 and 24 processors) on all 3 samples based on processors usage along time for both NPS and strategies (Fig. 3 as well).

Additional file 1: Tables 1–4. Average execution time for pipeline's tasks, for all processors configuration and for each strategy.

Additional file 3. Figure 2. Representation of all executions (6, 12 and 24 processors) on all 3 samples based on memory usage along time for both NPS and strategies (Fig. 4 as well).

Additional file 4. Figure 3. Representation of all executions (4, 8 and 16 processors) on 2 samples based on processors usage along time for both NPS and strategies (all possible 2-samples combinations are reported).

Supplemental Material, sj-pdf-1-vet-10.1177_03009858211066862 for Canine smooth muscle tumors: A clinicopathological study by Giancarlo Avallone, Valeria Pellegrino, Luisa Vera Muscatello, Paola Roccabianca, Gastone Castellani, Claudia Sala, Marco Tecilla, Paola Valenti and Giuseppe Sarli in Veterinary Pathology

Additional file 5. Figure 4. Representation of all executions (4, 8 and 16 processors) on 2 samples based on memory usage along time for both NPS and strategies (all possible 2-samples combinations are reported).

Additional file 2 Dataset statistics.

Understanding the factors that control the dynamics of interacting species is a fundamental problem in ecology. The nature of the interactions among different species is usually not completely understood, but it is assumed that the species interaction plays an important role in the ecosystem properties as predicted by the niches models for an ecosystem. However, recent studies point out as the neutral hypothesis proposed by Hubbell of non-interacting species with an external source from the surrounding environment, allows to explain the relative species abundance distribution when the ecosystem has reached a stationary situation. In this paper we use the concept of fitness landscape to introduce a random dynamical model that describes the evolution of different communities near a stationary situation. The average dynamics can be associated to a system of Lotka-Volterra equations with mutualistic interactions. Then we derive a Master equation that satisfies the detailed balance condition of thermodynamical equilibria and allows to analytically compute the relative species abundance distribution near the stationary state as a multinomial negative distribution. These results suggest a possible approach to a synthetic theory that joins the niche theories and the Hubbell's neutral theory for RSA distribution.

Treballs Finals del Màster d'Economia, Facultat d'Economia i Empresa, Universitat de Barcelona, Curs: 2016-2018, Tutor : Pilar Sorribas Navarro, Although existing research reveals interesting relations explaining redistribution demand, little is known about the impact of the contract type and the macroeconomic context in shaping redistribution preferences of individuals. We analyze the Spanish dual labor market to provide causal evidence of the effect of temporal contracts in determining preferences for redistribution. To do so, exact matching is applied to Spanish data from the European Social Survey for the period 2002-2014. Furthermore, we analyze the heterogeneous effect of the contract type by studying the impact of the economic crisis starting in 2008. Our results give causal support to the insurance theory by showing that the fact of holding a temporal contract increases preferences for redistribution. Nevertheless, this effect disappears when the effect of the adverse macroeconomic context is considered. The riskier economic context makes risk perception of individuals holding permanent contracts increase, which results in stronger demand for redistribution. This macroeconomic effect determining preferences for redistribution appears to be stronger than the individual determinant of holding a specific contract type.

Figure S1. Plots of Copy Number Analysis and phylogenetic tree using WES data. A 18 Mb region on chromosome 6 (q21-22.33) is indicated (red box), where CNV analysis identified a copy gain in PT (A) and M1 (B), as reported in Additional file 1: Table S2. (C) In the second chest metastasis (M2) a focal amplification was detected in the 6q22.33 region, spanning RNF146 and ECHDC1 genes (black arrowhead). (D) SNPhylo analysis results, showing the genetic distance between the three tumor samples. Numbers indicate the branch length from central node. The distance between two tumors is equal to the sum of their branch length. Analysis was performed according to [6]. (PDF 137 kb)

Supplementary methods and metarials. (DOCX 79 kb)

The cell envelope of Mycobacterium tuberculosis contains glycans and lipids of peculiar structure that play prominent roles in the biology and pathogenesis of tuberculosis. Consequently, the chemical structure and biosynthesis of the cell wall have been intensively investigated in order to identify novel drug targets. Here, we validate that the function of phosphatidyl- myo -inositol mannosyltransferase PimA is vital for M. tuberculosis in vitro and in vivo . PimA initiates the biosynthesis of phosphatidyl- myo -inositol mannosides by transferring a mannosyl residue from GDP-Man to phosphatidyl- myo -inositol on the cytoplasmic side of the plasma membrane. To prove the essential nature of pimA in M. tuberculosis , we constructed a pimA conditional mutant by using the TetR-Pip off system and showed that downregulation of PimA expression causes bactericidality in batch cultures. Consistent with the biochemical reaction catalyzed by PimA, this phenotype was associated with markedly reduced levels of phosphatidyl- myo -inositol dimannosides, essential structural components of the mycobacterial cell envelope. In addition, the requirement of PimA for viability was clearly demonstrated during macrophage infection and in two different mouse models of infection, where a dramatic decrease in viable counts was observed upon silencing of the gene. Notably, depletion of PimA resulted in complete clearance of the mouse lungs during both the acute and chronic phases of infection. Altogether, the experimental data highlight the importance of the phosphatidyl- myo -inositol mannoside biosynthetic pathway for M. tuberculosis and confirm that PimA is a novel target for future drug discovery programs.

The function of EspI, a 70 kDa protein in Mycobacterium tuberculosis, has remained unclear. Although EspI is encoded by a gene within the esx-1 locus, in this study we clarify previous conflicting results and show that EspI is not essential for ESX-1-mediated secretion or virulence in M. tuberculosis. We also provide evidence that reduction of cellular ATP levels in wild-type M. tuberculosis using the drug bedaquiline completely blocks ESX-1-mediated secretion. Remarkably, M. tuberculosis lacking EspI fails to exhibit this phenotype. Furthermore, mutagenesis of a highly conserved ATP-binding motif in EspI renders M. tuberculosis incapable of shutting down ESX-1-mediated secretion during ATP depletion. Collectively these results show that M. tuberculosis EspI negatively regulates the ESX-1 secretion system in response to low cellular ATP levels and this function requires the ATP-binding motif. In light of our results the potential significance of EspI in ESX-1 function during latent tuberculosis infection and reactivation is also discussed.

Non-replicating or dormant cells of Mycobacterium tuberculosis constitute a challenge to tuberculosis (TB) therapy because of their tolerance or phenotypic resistance to most drugs. Here, we propose a simple model for testing drugs against non-growing cells that exploits the 18b strain of M. tuberculosis, a streptomycin (STR)-dependent mutant. Optimal conditions were established that allow 18b cells to replicate in the presence of STR and to survive, but not multiply, following its withdrawal. In the presence of the antibiotic, M. tuberculosis 18b was susceptible to the currently approved TB drugs, isoniazid (INH) and rifampin (RIF), and to the experimental drugs, TMC207, PA-824, meropenem (MER), benzothiazinone (BTZ) and moxifloxacin (MOXI). After STR depletion, the strain displayed greatly reduced susceptibility to the cell wall inhibitors, INH and BTZ, but showed increased susceptibility to RIF and PA-824 while MOXI and MER appeared equipotent under both conditions. The same potency ranking was found against non-replicating M. tuberculosis 18b after treatment of chronically infected mice with five of these drugs. Despite the growth arrest, strain 18b retains significant metabolic activity in vitro remaining positive in the resazurin reduction assay. On adaption to 96-well format, this assay was shown to be suitable for high-throughput screening with strain 18b to find new inhibitors of dormant M. tuberculosis.

Hierarchical clustering of differentially expressed genes in SS18b and the results from previous works with 2-fold differences displayed as shrunk and expanded images. (PDF 748 kb)

Genes from H37Rv that are deleted in the genome of 18b. (DOCX 19 kb)

InDels larger than 100 bp between the 18b and the H37Rv genomes. (DOCX 32 kb)

In Mycobacterium tuberculosis the decaprenyl-phospho-d-arabinofuranose (DPA) pathway is a validated target for the drugs ethambutol and benzothiazinones. To identify other potential drug targets in the pathway, we generated conditional knock-down mutants of each gene involved using the TET-PIP OFF system. dprE1, dprE2, ubiA, prsA, rv2361c, tkt and rpiB were confirmed to be essential under non-permissive conditions, whereas rv3807c was not required for survival. In the most vulnerable group, DprE1-depleted cells died faster in vitro and intracellularly than those lacking UbiA and PrsA. Downregulation of DprE1 and UbiA resulted in similar phenotypes, namely swelling of the bacteria, cell wall damage and lysis as observed at the single cell level, by real time microscopy and electron microscopy. By contrast, depletion of PrsA led to cell elongation and implosion, which was suggestive of a more pleiotropic effect. Drug sensitivity assays with known DPA-inhibitors supported the use of conditional knock-down strains for target-based whole-cell screens. Together, our work provides strong evidence for the vulnerability of all but one of the enzymes in the DPA pathway and generates valuable tools for the identification of lead compounds targeting the different biosynthetic steps. PrsA, phosphoribosyl-pyrophosphate synthetase, appears to be a particularly attractive new target for drug discovery.

Genes from H37Rv that are deleted in the genome of 18b. (DOCX 19 kb)

Genes from 18b that are deleted in the genome of H37Rv. (DOCX 16 kb)

Benzothiazinones (BTZs) are a class of compounds found to be extremely potent against both drug-susceptible and drug-resistant Mycobacterium tuberculosis strains. The potency of BTZs is explained by their specificity for their target decaprenylphosphoryl-D-ribose oxidase (DprE1), in particular by covalent binding of the activated form of the compound to the critical cysteine 387 residue of the enzyme. To probe the role of C387, we used promiscuous site-directed mutagenesis to introduce other codons at this position into dprE1 of M. tuberculosis. The resultant viable BTZ-resistant mutants were characterized in vitro, ex vivo, and biochemically to gain insight into the effects of these mutations on DprE1 function and on M. tuberculosis. Five different mutations (C387G, C387A, C387S, C387N, and C387T) conferred various levels of resistance to BTZ and exhibited different phenotypes. The C387G and C387N mutations resulted in a lower growth rate of the mycobacterium on solid medium, which could be attributed to the significant decrease in the catalytic efficiency of the DprE1 enzyme. All five mutations rendered the mycobacterium less cytotoxic to macrophages. Finally, differences in the potencies of covalent and noncovalent DprE1 inhibitors in the presence of C387 mutations were revealed by enzymatic assays. As expected from the mechanism of action, the covalent inhibitor PBTZ169 only partially inhibited the mutant DprE1 enzymes compared to the near-complete inhibition with a noncovalent DprE1 inhibitor, Ty38c. This study emphasizes the importance of the C387 residue for DprE1 activity and for the killing action of covalent inhibitors such as BTZs and other recently identified nitroaromatic inhibitors.

Weighted Venn diagrams representing overlap of the differential gene expression results from this work with those from stationary phase induction and response to macrophage infection. (PDF 163 kb)

Pathogenicity of Mycobacterium tuberculosis (M. tb) is mediated by the ESX-1 secretion system, which exports EsxA and EsxB, the major virulence factors that are co-secreted with EspA and EspC. Functional information about ESX-1 components is scarce. Here, it was shown that EspC associates with EspA in the cytoplasm and membrane, then polymerizes during secretion from M. tb. EspC was localized by immuno-gold electron microscopy in whole cells or cryosections as a surface-exposed filamentous structure that seems to span the cell envelope. Consistent with these findings, purified EspC homodimerizes via disulphide bond formation, multimerizes and self-assembles into long filaments in vitro. The C-terminal domain is required for multimerization as truncation and selected point mutations therein impact EspC filament formation, thus reducing secretion of EsxA and causing attenuation of M. tb. The data are consistent with EspC serving either as a modulator of ESX-1 function or as a component of the secretion apparatus.

Hierarchical clustering of differentially expressed genes in SS18b and the results from previous works with 2-fold differences displayed as shrunk and expanded images. (PDF 748 kb)

Genes from 18b that are deleted in the genome of H37Rv. (DOCX 16 kb)

SNPs unique to M. tuberculosis 18b from a comparison with 1793 M. tuberculosis genomes. (DOCX 25 kb)

Protein coding genes that are annotated as functional in H37Rv and as pseudogenes in 18b. (DOCX 21 kb)

Hierarchical clustering of differentially expressed genes in SS18b and from previous works showing >2-fold differences. (PDF 332 kb)

Hierarchical clustering of differentially expressed genes in SS18b and from previous works showing >2-fold differences. (PDF 332 kb)

Improved genetic tools are required to identify new drug targets in Mycobacterium tuberculosis. To this aim, genetic approaches, targeting either transcription and/or protein degradation, have been developed to appraise gene essentiality and to test the impact of gene silencing on bacterial survival. Here, we successfully combined the Tet-Pip OFF system, which downregulates transcription through the TetR and Pip repressors, with SspB-mediated protein degradation to study depletion of the transketolase encoded by the tkt (rv1449c) gene. We show that depletion of Tkt using the RNA silencing and protein degradation (RSPD) system arrested growth of M.tuberculosis in vitro faster than the Tet-Pip OFF system alone. In addition, we extended the new combined approach to an ex vivo model of M.tuberculosis infection in THP-1 cells. Tkt-depleted bacteria displayed reduced virulence as compared to wild type bacilli, thus confirming the essentiality of the enzyme for intracellular growth.

Positions of IS6110 in the genome sequences of M. tuberculosis 18b and H37Rv. (DOCX 27 kb)

SNPs unique to M. tuberculosis 18b from a comparison with 1793 M. tuberculosis genomes. (DOCX 25 kb)

Genes in the genome of 18b that span two genes in H37Rv. (DOCX 24 kb)

Background: In Mycobacterium tuberculosis and in Mycobacterium smegmatis the furA-katG loci, encoding the FurA regulatory protein and the KatG catalase-peroxidase, are highly conserved. In M. tuberculosis furA-katG constitute a single operon, whereas in M. smegmatis a single mRNA covering both genes could not be found. In both species, specific 5' ends have been identified: the first one, located upstream of the furA gene, corresponds to transcription initiation from the furA promoter; the second one is the katG mRNA 5' end, located in the terminal part of furA.

Genes in the genome of 18b that span two genes in H37Rv. (DOCX 24 kb)

Positions of IS6110 in the genome sequences of M. tuberculosis 18b and H37Rv. (DOCX 27 kb)

Weighted Venn diagrams representing overlap of the differential gene expression results from this work with those from stationary phase induction and response to macrophage infection. (PDF 163 kb)

Novel gene predictions in the genome of 18b. (DOCX 17 kb)

Protein coding genes that are annotated as functional in H37Rv and as pseudogenes in 18b. (DOCX 21 kb)

Hierarchical clustering of differentially expressed genes in SS18b and previous works. Expanded version of Fig. 4 including gene names. (PDF 239 kb)

Hierarchical clustering of differentially expressed genes in SS18b and previous works. Expanded version of Fig. 4 including gene names. (PDF 239 kb)

Novel gene predictions in the genome of 18b. (DOCX 17 kb)

Creutzfeldt-Jakob disease (CJD) is characterized by a broad phenotypic spectrum regarding symptoms, progression, and molecular features. Current sporadic CJD (sCJD) classification recognizes six main clinical-pathological phenotypes. This work investigates the molecular basis of the phenotypic heterogeneity of prion diseases through a multi-omics analysis of the two most common sCJD subtypes: MM1 and VV2. We performed DNA target sequencing on 118 genes on a cohort of 48 CJD patients and full exome RNA sequencing on post-mortem frontal cortex tissue on a subset of this cohort. DNA target sequencing identified multiple potential genetic contributors to the disease onset and phenotype, both in terms of coding, damaging-predicted variants, and enriched groups of SNPs in the whole cohort and the two subtypes. The results highlight a different functional impairment, with VV2 associated with higher impairment of the pathways related to dopamine secretion, regulation of calcium release and GABA signaling, showing some similarities with Parkinson’s disease both on a genomic and a transcriptomic level. MM1 showed a gene expression profile with several traits shared with different neurodegenerative, without an apparent distinctive characteristic or similarities with a specific disease. In addition, integrating genomic and transcriptomic data led to the discovery of several sites of ADAR-mediated RNA editing events, confirming and expanding previous findings in animal models. On the transcriptomic level, this work represents the first application of RNA sequencing on CJD human brain samples. Here, a good clusterization of the transcriptomic profiles of the two subtypes was achieved, together with the finding of several differently impaired pathways between the two subtypes. The results add to the understanding of the molecular features associated with sporadic CJD and its most common subtypes, revealing strain-specific genetic signatures and functional similarities between VV2 and Parkinson’s disease and providing preliminary evidence of RNA editing modifications in human sCJD.

PURPOSE Recurrently mutated genes and chromosomal abnormalities have been identified in myelodysplastic syndromes (MDS). We aim to integrate these genomic features into disease classification and prognostication. METHODS We retrospectively enrolled 2,043 patients. Using Bayesian networks and Dirichlet processes, we combined mutations in 47 genes with cytogenetic abnormalities to identify genetic associations and subgroups. Random-effects Cox proportional hazards multistate modeling was used for developing prognostic models. An independent validation on 318 cases was performed. RESULTS We identify eight MDS groups (clusters) according to specific genomic features. In five groups, dominant genomic features include splicing gene mutations ( SF3B1, SRSF2, and U2AF1) that occur early in disease history, determine specific phenotypes, and drive disease evolution. These groups display different prognosis (groups with SF3B1 mutations being associated with better survival). Specific co-mutation patterns account for clinical heterogeneity within SF3B1- and SRSF2-related MDS. MDS with complex karyotype and/or TP53 gene abnormalities and MDS with acute leukemia–like mutations show poorest prognosis. MDS with 5q deletion are clustered into two distinct groups according to the number of mutated genes and/or presence of TP53 mutations. By integrating 63 clinical and genomic variables, we define a novel prognostic model that generates personally tailored predictions of survival. The predicted and observed outcomes correlate well in internal cross-validation and in an independent external cohort. This model substantially improves predictive accuracy of currently available prognostic tools. We have created a Web portal that allows outcome predictions to be generated for user-defined constellations of genomic and clinical features. CONCLUSION Genomic landscape in MDS reveals distinct subgroups associated with specific clinical features and discrete patterns of evolution, providing a proof of concept for next-generation disease classification and prognosis.

In this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.