The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution

Genes in pieces and spliceosomal introns are a landmark of eukaryotes, with intron invasion usually assumed to have happened early on in evolution. Here, we analyse the intron landscape of Micromonas, a unicellular green alga in the Mamiellophyceae lineage, demonstrating the co-existence of several classes of introns and the occurrence of recent massive intron invasion. This study focuses on two strains, CCMP1545 and RCC299, and their related individuals from ocean samplings, showing that they not only harbour different classes of introns depending on their location in the genome, as for other Mamiellophyceae, but uniquely carry several classes of repeat introns. These introns, dubbed introner elements (IEs), are found at novel positions in genes and have conserved sequences, contrary to canonical introns. This IE invasion has a huge impact on the genome, doubling the number of introns in the CCMP1545 strain. We hypothesize that each IE class originated from a single ancestral IE that has been colonizing the genome after strain divergence by inserting copies of itself into genes by intron transposition, likely involving reverse splicing. Along with similar cases recently observed in other organisms, our observations in Micromonas strains shed a new light on the evolution of introns, suggesting that intron gain is more widespread than previously thought

The quantitative surface analysis of an antioxidant additive in a lubricant oil matrix by desorption electrospray ionization mass spectrometry

Rationale Chemical additives are incorporated into commercial lubricant oils to modify the physical and chemical properties of the lubricant. The quantitative analysis of additives in oil-based lubricants deposited on a surface without extraction of the sample from the surface presents a challenge. The potential of desorption electrospray ionization mass spectrometry (DESI-MS) for the quantitative surface analysis of an oil additive in a complex oil lubricant matrix without sample extraction has been evaluated. Methods The quantitative surface analysis of the antioxidant additive octyl (4-hydroxy-3,5-di-tert-butylphenyl)propionate in an oil lubricant matrix was carried out by DESI-MS in the presence of 2-(pentyloxy)ethyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate as an internal standard. A quadrupole/time-of-flight mass spectrometer fitted with an in-house modified ion source enabling non-proximal DESI-MS was used for the analyses. RESULTS An eight-point calibration curve ranging from 1 to 80 μg/spot of octyl (4-hydroxy-3,5-di-tert-butylphenyl)propionate in an oil lubricant matrix and in the presence of the internal standard was used to determine the quantitative response of the DESI-MS method. The sensitivity and repeatability of the technique were assessed by conducting replicate analyses at each concentration. The limit of detection was determined to be 11 ng/mm additive on spot with relative standard deviations in the range 3-14%. CONCLUSIONS The application of DESI-MS to the direct, quantitative surface analysis of a commercial lubricant additive in a native oil lubricant matrix is demonstrated

A Stochastic Approach to Shortcut Bridging in Programmable Matter

In a self-organizing particle system, an abstraction of programmable matter, simple computational elements called particles with limited memory and communication self-organize to solve system-wide problems of movement, coordination, and configuration. In this paper, we consider a stochastic, distributed, local, asynchronous algorithm for "shortcut bridging", in which particles self-assemble bridges over gaps that simultaneously balance minimizing the length and cost of the bridge. Army ants of the genus Eciton have been observed exhibiting a similar behavior in their foraging trails, dynamically adjusting their bridges to satisfy an efficiency trade-off using local interactions. Using techniques from Markov chain analysis, we rigorously analyze our algorithm, show it achieves a near-optimal balance between the competing factors of path length and bridge cost, and prove that it exhibits a dependence on the angle of the gap being "shortcut" similar to that of the ant bridges. We also present simulation results that qualitatively compare our algorithm with the army ant bridging behavior. Our work gives a plausible explanation of how convergence to globally optimal configurations can be achieved via local interactions by simple organisms (e.g., ants) with some limited computational power and access to random bits. The proposed algorithm also demonstrates the robustness of the stochastic approach to algorithms for programmable matter, as it is a surprisingly simple extension of our previous stochastic algorithm for compression.Comment: Published in Proc. of DNA23: DNA Computing and Molecular Programming - 23rd International Conference, 2017. An updated journal version will appear in the DNA23 Special Issue of Natural Computin

Direct analysis of oil additives by high-field asymmetric waveform ion mobility spectrometry-mass spectrometry combined with electrospray ionization and desorption electrospray ionization

© 2016 American Chemical Society. The analysis of corrosion inhibitors in the presence and absence of an oil matrix is reported using electrospray ionization (ESI) and desorption electrospray ionization (DESI), hyphenated with miniaturized high-field asymmetric waveform ion mobility spectrometry (FAIMS) and mass spectrometry (MS). The target analytes were successfully ionized in solution by ESI and directly from steel surfaces using DESI ambient ionization at levels ≥0.0004% w/w (4 ppm) in oil. Differences in the mass spectral profiles observed for the additive/oil mixture are attributed to differences between the ESI and DESI ionization processes. The use of FAIMS improved selectivity for ESI generated analyte ions through reduction in the chemical noise resulting from the oil matrix. DESI enabled the direct, rapid, native state interrogation of oil samples on steel surfaces without sample pretreatment, and the hyphenation of DESI with the miniaturized FAIMS enhanced the relative analyte responses of the surface-active corrosion inhibitors

Hysteresis in muscle

This paper presents examples of hysteresis from a broad range of scientific disciplines and demonstrates a variety of forms including clockwise, counterclockwise, butterfly, pinched and kiss-and-go, respectively. These examples include mechanical systems made up of springs and dampers which have been the main components of muscle models for nearly one hundred years. For the first time, as far as the authors are aware, hysteresis is demonstrated in single fibre muscle when subjected to both lengthening and shortening periodic contractions. The hysteresis observed in the experiments is of two forms. Without any relaxation at the end of lengthening or shortening, the hysteresis loop is a convex clockwise loop, whereas a concave clockwise hysteresis loop (labeled as "kiss-and-go") is formed when the muscle is relaxed at the end of lengthening and shortening. This paper also presents a mathematical model which reproduces the hysteresis curves in the same form as the experimental data

Disease Progression Modelling in Chronic Obstructive Pulmonary Disease (COPD)

RATIONALE: The decades-long progression of Chronic Obstructive Pulmonary Disease (COPD) renders identifying different trajectories of disease progression challenging. OBJECTIVES: To identify subtypes of COPD patients with distinct longitudinal progression patterns using a novel machine-learning tool called "Subtype and Stage Inference (SuStaIn)", and to evaluate the utility of SuStaIn for patient stratification in COPD. METHODS: We applied SuStaIn to cross-sectional CT imaging markers in 3698 GOLD1-4 patients and 3479 controls from the COPDGene study to identify COPD patient subtypes. We confirmed the identified subtypes and progression patterns using ECLIPSE data. We assessed the utility of SuStaIn for patient stratification by comparing SuStaIn subtypes and stages at baseline with longitudinal follow-up data. MEASUREMENTS AND MAIN RESULTS: We identified two trajectories of disease progression in COPD: a "Tissue→Airway" subtype (n=2354, 70.4%) in which small airway dysfunction and emphysema precede large-airway wall abnormalities, and an "Airway→Tissue" subtype (n=988, 29.6%) in which large-airway wall abnormalities precede emphysema and small airway dysfunction. Subtypes were reproducible in ECLIPSE. Baseline stage in both subtypes correlated with future FEV1/FVC decline (r=-0.16 (p<0.001) in the Tissue→Airway group; r=-0.14 (p=0.011) in the Airway→Tissue group). SuStaIn placed 30% of smokers with normal lung function at non-baseline stages suggesting imaging changes consistent with early COPD. Individuals with early changes were 2.5 times more likely to meet COPD diagnostic criteria at follow-up. CONCLUSIONS: We demonstrate two distinct patterns of disease progression in COPD using SuStaIn, likely representing different endotypes. One-third of healthy smokers have detectable imaging changes, suggesting a new biomarker of 'early COPD'

The role of childhood social position in adult type 2 diabetes: Evidence from the English Longitudinal Study of Ageing

Copyright @ 2014 Pikhartova et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: Socioeconomic circumstances in childhood and early adulthood may influence the later onset of chronic disease, although such research is limited for type 2 diabetes and its risk factors at the different stages of life. The main aim of the present study is to examine the role of childhood social position and later inflammatory markers and health behaviours in developing type 2 diabetes at older ages using a pathway analytic approach. Methods. Data on childhood and adult life circumstances of 2,994 men and 4,021 women from English Longitudinal Study of Ageing (ELSA) were used to evaluate their association with diabetes at age 50 years and more. The cases of diabetes were based on having increased blood levels of glycated haemoglobin and/or self-reported medication for diabetes and/or being diagnosed with type 2 diabetes. Father's job when ELSA participants were aged 14 years was used as the measure of childhood social position. Current social characteristics, health behaviours and inflammatory biomarkers were used as potential mediators in the statistical analysis to assess direct and indirect effects of childhood circumstances on diabetes in later life. Results: 12.6 per cent of participants were classified as having diabetes. A disadvantaged social position in childhood, as measured by father's manual occupation, was associated at conventional levels of statistical significance with an increased risk of type 2 diabetes in adulthood, both directly and indirectly through inflammation, adulthood social position and a risk score constructed from adult health behaviours including tobacco smoking and limited physical activity. The direct effect of childhood social position was reduced by mediation analysis (standardised coefficient decreased from 0.089 to 0.043) but remained statistically significant (p = 0.035). All three indirect pathways made a statistically significantly contribution to the overall effect of childhood social position on adulthood type 2 diabetes. Conclusions: Childhood social position influences adult diabetes directly and indirectly through inflammatory markers, adulthood social position and adult health behaviours. © 2014Pikhartova et al.; licensee BioMed Central Ltd.Economic and Social Research Council-funded International Centre for Life Course Studies in Society and Health (RES-596-28-0001)

Negative phenotypic and genetic associations between copulation duration and longevity in male seed beetles

Reproduction can be costly and is predicted to trade-off against other characters. However, while these trade-offs are well documented for females, there has been less focus on aspects of male reproduction. Furthermore, those studies that have looked at males typically only investigate phenotypic associations, with the underlying genetics often ignored. Here, we report on phenotypic and genetic trade-offs in male reproductive effort in the seed beetle, Callosobruchus maculatus. We find that the duration of a male's first copulation is negatively associated with subsequent male survival, phenotypically and genetically. Our results are consistent with life-history theory and suggest that like females, males trade-off reproductive effort against longevity