Thoughts on Aneuploidy

Aneuploidy refers to karyotypic abnormalities characterized by gain or loss of individual chromosomes. This condition is associated with disease and death in all organisms in which it has been studied. We have characterized the effects of aneuploidy on yeast and primary mouse cells and found it to be detrimental at the cellular level. Furthermore, we find that aneuploid cells exhibit phenotypes consistent with increased energy need and proteotoxic stress. These observations, together with the finding that the additional chromosomes found in aneuploid cells are active, lead us to propose that aneuploidy causes an increased burden on protein synthesis and protein quality-control pathways and so induces an aneuploidy stress response.National Institutes of Health (U.S.) (Grant GM56800)Charles A. King Trust (Postdoctoral Fellowship)Human Frontiers Science Program (Postdoctoral Fellowship

Mind your Ps: A probabilistic model to aid the interpretation of molecular epidemiology data

Background: Assessing relatedness of pathogen sequences in clinical samples is a core goal in molecular epidemiology. Tools for Bayesian analysis of phylogeny, such as the BEAST software package, have been typically used in the analysis of sequence/time data in public health. However, they are computationally-, time-, and knowledge-intensive, demanding resources that many laboratories do not have available or cannot allocate frequently. Methods: To evaluate a faster and simpler alternative method to support the routine interpretation of sequence data for epidemiology, we obtained sequences for two regions in the measles virus genome, N-450 and MF-NCR, from patient samples of genotypes B3, D4 and D8 taken between 2011 and 2017 in the UK and Romania. A mathematical model incorporating time, possible shared ancestry and the Poisson distribution describing the number of expected substitutions at a given time point was developed to exclude epidemiological relatedness between pairs of sequences. The model was validated against the commonly used Bayesian phylogenetic method using an independent dataset collected in 2017–19. Findings: We demonstrate that our model, using time and sequence information to predict whether two samples may be related within a given time frame, minimises the risk of erroneous exclusion of relatedness. An easy-to-use implementation in the form of a guide and spreadsheet is provided for convenient application. Interpretation: The proposed model only requires a previously calculated substitution rate for the locus and pathogen of interest. It allows for an informed but quick decision on the likelihood of relatedness between two samples within a time frame, without the need for phylogenetic reconstruction, thus facilitating rapid epidemiological interpretation of sequence data.This work was funded by the United Kingdom Health Security Agency (UKHSA). The World Health Orga- nization European Regional Office funded Aurora Fernández-García and Mihaela Lazar training visits to UKHSAS

Molecular recognition of lipopolysaccaride by the lantibiotic nisin

Nisin is a lanthionine antimicrobial effective against diverse Gram-positive bacteria and is used as a food preservative worldwide. Its action is mediated by pyrophosphate recognition of the bacterial cell wall receptors lipid II and undecaprenyl pyrophosphate. Nisin/receptor complexes disrupt cytoplasmic membranes, inhibit cell wall synthesis and dysregulate bacterial cell division. Gram-negative bacteria are much more tolerant to antimicrobials including nisin. In contrast to Gram-positives, Gram-negative bacteria possess an outer membrane, the major constituent of which is lipopolysaccharide (LPS). This contains surface exposed phosphate and pyrophosphate groups and hence can be targeted by nisin. Here we describe the impact of LPS on membrane stability in response to nisin and the molecular interactions occurring between nisin and membrane-embedded LPS from different Gram-negative bacteria. Dye release from liposomes shows enhanced susceptibility to nisin in the presence of LPS, particularly rough LPS chemotypes that lack an O-antigen whereas LPS from microorganisms sharing similar ecological niches with antimicrobial producers provides only modest enhancement. Increased susceptibility was observed with LPS from pathogenic Klebsiella pneumoniae compared to LPS from enteropathogenic Salmonella enterica and gut commensal Escherichia coli. LPS from Brucella melitensis, an intra-cellular pathogen which is adapted to invade professional and non-professional phagocytes, appears to be refractory to nisin. Molecular complex formation between nisin and LPS was studied by solid state MAS NMR and revealed complex formation between nisin and LPS from most organisms investigated except B. melitensis. LPS/nisin complex formation was confirmed in outer membrane extracts from E. coli

Joint Effect of Genetic and Lifestyle Risk Factors on Type 2 Diabetes Risk among Chinese Men and Women

More than 40 genetic susceptibility loci have been reported for type 2 diabetes (T2D). Recently, the combined effect of genetic variants has been investigated by calculating a genetic risk score. We evaluated 36 genome-wide association study (GWAS) identified SNPs in 2,679 T2D cases and 3322 controls in middle-age Han Chinese. Fourteen SNPs were significantly associated with T2D in analysis adjusted for age, sex and BMI. We calculated two genetic risk scores (GRS) (GRS1 with all the 36 SNPs and GRS2 with the 14 SNPs significantly associated with T2D). The odds ratio for T2D with each GRS point (per risk allele) was 1.08 (95% CI: 1.06–1.09) for GRS1 and 1.15 (95% CI: 1.13–1.18) for GRS2. The OR for quintiles were 1.00, 1.26, 1.69, 1.95 and 2.18 (P\u3c0.0001) for GRS1 and 1.00, 1.33, 1.60, 2.03 and 2.80 (P\u3c0.001) for GRS2. Participants in the higher tertile of GRS1 and the higher BMI category had a higher risk of T2D compared to those on the lower tertiles of the GRS1 and of BMI (OR = 11.08; 95% CI: 7.39–16.62). We found similar results when we investigated joint effects between GRS1 and WHR terciles and exercise participation. We finally investigated the joint effect between tertiles of GRSs and a composite high risk score (no exercise participation and high BMI and WHR) on T2D risk. We found that compared to participants with low GRS1 and no high risk factors for T2D, those with high GRS1 and three high risk factors had a higher risk of T2D (OR = 13.06; 95% CI: 8.65–19.72) but the interaction factor was of marginal significance. The association was accentuated when we repeated analysis with the GRS2. In conclusion we found an association between GRS and lifestyle factors, alone and in combination, contributed to the risk of and T2D among middle age Chinese

Can the pyruvate: ferredoxin oxidoreductase (PFOR) gene be used as an additional marker to discriminate among Blastocystis strains or subtypes?

Background Blastocystis spp. are the most prevalent intestinal eukaryotes identified in humans, with at least 17 genetic subtypes (ST) based on genes coding for the small-subunit ribosomal RNA (18S). It has been argued that the 18S gene should not be the marker of choice to discriminate between STs of these strains because this marker exhibits high intra-genomic polymorphism. By contrast, pyruvate:ferredoxin oxidoreductase (PFOR) is a relevant enzyme involved in the core energy metabolism of many anaerobic microorganisms such as Blastocystis, which, in other protozoa, shows more polymorphisms than the 18S gene and thus may offer finer discrimination when trying to identify Blastocystis ST. Therefore, the objective of the present study was to assess the suitability of the PFOR gene as an additional marker to discriminate among Blastocystis strains or subtypes from symptomatic carrier children. Methods Faecal samples from 192 children with gastrointestinal symptoms from the State of Mexico were submitted for coprological study. Twenty-one of these samples were positive only for Blastocystis spp.; these samples were analysed by PCR sequencing of regions of the 18S and PFOR genes. The amplicons were purified and sequenced; afterwards, both markers were assessed for genetic diversity. Results The 18S analysis showed the following frequencies of Blastocystis subtypes: ST3 = 43%; ST1 = 38%; ST2 = 14%; and ST7 = 5%. Additionally, using subtype-specific primer sets, two samples showed mixed Blastocystis ST1 and ST2 infection. For PFOR, Bayesian inference revealed the presence of three clades (I-III); two of them grouped different ST samples, and one grouped six samples of ST3 (III). Nucleotide diversity (π) and haplotype polymorphism (θ) for the 18S analysis were similar for ST1 and ST2 (π = ~0.025 and θ = ~0.036); remarkably, ST3 showed almost 10-fold lower values. For PFOR, a similar trend was found: clade I and II had π = ~0.05 and θ = ~0.05, whereas for clade III, the values were almost 6-fold lower. Conclusions Although the fragment of the PFOR gene analysed in the present study did not allow discrimination between Blastocystis STs, this marker grouped the samples in three clades with strengthened support, suggesting that PFOR may be under different selective pressures and evolutionary histories than the 18S gene. Interestingly, the ST3 sequences showed lower variability with probable purifying selection in both markers, meaning that evolutionary forces drive differential processes among Blastocystis STs

Measurements of Differential Reflectivity in Snowstorms and Warm Season Stratiform Systems

The organized behavior of differential radar reflectivity (ZDR) is documented in the cold regions of a wide variety of stratiform precipitation types occurring in both winter and summer. The radar targets and attendant cloud microphysical conditions are interpreted within the context of measurements of ice crystal types in laboratory diffusion chambers in which humidity and temperature are both stringently controlled. The overriding operational interest here is in the identification of regions prone to icing hazards with long horizontal paths. Two predominant regimes are identified: category A, which is typified by moderate reflectivity (from 10 to 30 dBZ) and modest +ZDR values (from 0 to +3 dB) in which both supercooled water and dendritic ice crystals (and oriented aggregates of ice crystals) are present at a mean temperature of −13°C, and category B, which is typified by small reflectivity (from −10 to +10 dBZ) and the largest +ZDR values (from +3 to +7 dB), in which supercooled water is dilute or absent and both flat-plate and dendritic crystals are likely. The predominant positive values for ZDR in many case studies suggest that the role of an electric field on ice particle orientation is small in comparison with gravity. The absence of robust +ZDR signatures in the trailing stratiform regions of vigorous summer squall lines may be due both to the infusion of noncrystalline ice particles (i.e., graupel and rimed aggregates) from the leading deep convection and to the effects of the stronger electric fields expected in these situations. These polarimetric measurements and their interpretations underscore the need for the accurate calibration of ZDR.United States. Federal Aviation Administration (Air Force Contract FA8721-05-C-0002

Response timing in the lunge and target change in elite versus medium-level fencers.

The aim of the present work is to examine the differences between two groups of fencers with different levels of competition, elite and medium level. The timing parameters of the response reaction have been compared together with the kinetic variables which determine the sequence of segmented participation used during the lunge with a change in target during movement. A total of 30 male sword fencers participated, 13 elite and 17 medium level. Two force platforms recorded the horizontal component of the force and the start of the movement. One system filmed the movement in 3D, recording the spatial positions of 11 markers, while another system projected a mobile target over a screen. For synchronisation, an electronic signal enabled all the systems to be started simultaneously. Among the timing parameters of the reaction response, the choice reaction time (CRT) to the target change during the lunge was measured. The results revealed differences between the groups regarding the flight time, horizontal velocity at the end of the acceleration phase, and the length of the lunge, these being higher for the elite group, as well as other variables related to the temporal sequence of movement. No significant differences have been found in the simple reaction time or in CRT. According to the literature, the CRT appears to improve with sports practice, although this factor did not differentiate the elite from medium-level fencers. The coordination of fencing movements, that is, the right technique, constitutes a factor that differentiates elite fencers from medium-level ones

Genome-wide Analysis of Motor Progression in Parkinson Disease

BACKGROUND AND OBJECTIVES: The genetic basis of Parkinson disease (PD) motor progression is largely unknown. Previous studies of the genetics of PD progression have included small cohorts and shown a limited overlap with genetic PD risk factors from case-control studies. Here, we have studied genomic variation associated with PD motor severity and early-stage progression in large longitudinal cohorts to help to define the biology of PD progression and potential new drug targets. METHODS: We performed a GWAS meta-analysis of early PD motor severity and progression up to 3 years from study entry. We used linear mixed-effect models with additive effects, corrected for age at diagnosis, sex, and the first 5 genetic principal components to assess variability in axial, limb, and total Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) III scores. RESULTS: We included 3,572 unrelated European ancestry patients with PD from 5 observational cohorts and 1 drug trial. The average AAO was 62.6 years (SD = 9.83), and 63% of participants were male. We found an average increase in the total MDS-UPDRS III score of 2.3 points/year. We identified an association between PD axial motor progression and variation at the GJA5 locus at 1q12 (β = -0.25, SE = 0.04, p = 3.4e-10). Exploration of the regulation of gene expression in the region (cis-expression quantitative trait loci [eQTL] analysis) showed that the lead variant was associated with expression of ACP6, a lysophosphatidic acid phosphatase that regulates mitochondrial lipid biosynthesis (cis-eQTL p-values in blood and brain RNA expression data sets: <10-14 in eQTLGen and 10-7 in PsychEncode). DISCUSSION: Our study highlights the potential role of mitochondrial lipid homeostasis in the progression of PD, which may be important in establishing new drug targets that might modify disease progression