The Importance of extraction protocol on the analysis of novel waste sources of lignocellulosic biomass

peer-reviewedAs the utilization and consumption of lignocellulosic biomass increases, so too will the need for an adequate supply of feedstock. To meet these needs, novel waste feedstock materials will need to be utilized. Exploitation of these novel feedstocks will require information both on the effects of solvent extraction on the succeeding analysis of potential novel feedstocks and how accurate current methodologies are in determining the composition of novel lignocellulosic feedstocks, particularly the carbohydrate and lignin fractions. In this study, the effects of solvent extraction on novel feedstocks, including tree foliage, tree bark and spent mushroom compost, with 95% ethanol, water and both sequentially were examined. Chemical analyses were carried out to determine the moisture content, ash, extractives, post-hydrolysis sugars, Klason lignin (KL) and acid-soluble lignin (ASL) within the selected feedstocks. The result of extraction could be seen most strongly for Klason lignin, with a strong association between higher levels of Klason lignin levels and greater amounts of non-removed extractives (tree foliage and bark). Higher Klason lignin levels are reported to be due the condensation of non-removed extractives during hydrolysis, hence the lower Klason lignin determinations following extraction are more exact. In addition, total sugar determinations were lower following extractions. This is because of the solubility of non-cell-wall carbohydrates; thus, the determinations following extraction are more accurate representations of structural cell-wall polysaccharides such as cellulose. Such determinations will assist in determining the best way to utilize novel feedstocks such as those analyzed in this work

Psychopolitics: Peter Sedgwick’s legacy for mental health movements

This paper re-considers the relevance of Peter Sedgwick's Psychopolitics (1982) for a politics of mental health. Psychopolitics offered an indictment of ‘anti-psychiatry’ the failure of which, Sedgwick argued, lay in its deconstruction of the category of ‘mental illness’, a gesture that resulted in a politics of nihilism. ‘The radical who is only a radical nihilist’, Sedgwick observed, ‘is for all practical purposes the most adamant of conservatives’. Sedgwick argued, rather, that the concept of ‘mental illness’ could be a truly critical concept if it was deployed ‘to make demands upon the health service facilities of the society in which we live’. The paper contextualizes Psychopolitics within the ‘crisis tendencies’ of its time, surveying the shifting welfare landscape of the subsequent 25 years alongside Sedgwick's continuing relevance. It considers the dilemma that the discourse of ‘mental illness’ – Sedgwick's critical concept – has fallen out of favour with radical mental health movements yet remains paradigmatic within psychiatry itself. Finally, the paper endorses a contemporary perspective that, while necessarily updating Psychopolitics, remains nonetheless ‘Sedgwickian’

Exploring predictive performance: A reanalysis of the geospace model transition challenge

The Pulkkinen et al. (2013) study evaluated the ability of five different geospace models to predict surface dB/dt as a function of upstream solar drivers. This was an important step in the assessment of research models for predicting and ultimately preventing the damaging effects of geomagnetically induced currents. Many questions remain concerning the capabilities of these models. This study presents a reanalysis of the Pulkkinen et al. (2013) results in an attempt to better understand the models’ performance. The range of validity of the models is determined by examining the conditions corresponding to the empirical input data. It is found that the empirical conductance models on which global magnetohydrodynamic models rely are frequently used outside the limits of their input data. The prediction error for the models is sorted as a function of solar driving and geomagnetic activity. It is found that all models show a bias toward underprediction, especially during active times. These results have implications for future research aimed at improving operational forecast models.Key PointsGeospace models of dB/dt frequently underpredict dB/dtOf five models tested, the SWMF is least likely to underpredict dB/dtEmpirical conductance models used by global MHD are frequently used outside their range of validityPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136305/1/swe20406.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136305/2/swe20406_am.pd

Comparison of predictive estimates of high‐latitude electrodynamics with observations of global‐scale Birkeland currents

Two of the geomagnetic storms for the Space Weather Prediction Center Geospace Environment Modeling challenge occurred after data were first acquired by the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE). We compare Birkeland currents from AMPERE with predictions from four models for the 4–5 April 2010 and 5–6 August 2011 storms. The four models are the Weimer (2005b) field‐aligned current statistical model, the Lyon‐Fedder‐Mobarry magnetohydrodynamic (MHD) simulation, the Open Global Geospace Circulation Model MHD simulation, and the Space Weather Modeling Framework MHD simulation. The MHD simulations were run as described in Pulkkinen et al. (2013) and the results obtained from the Community Coordinated Modeling Center. The total radial Birkeland current, ITotal, and the distribution of radial current density, Jr, for all models are compared with AMPERE results. While the total currents are well correlated, the quantitative agreement varies considerably. The Jr distributions reveal discrepancies between the models and observations related to the latitude distribution, morphologies, and lack of nightside current systems in the models. The results motivate enhancing the simulations first by increasing the simulation resolution and then by examining the relative merits of implementing more sophisticated ionospheric conductance models, including ionospheric outflows or other omitted physical processes. Some aspects of the system, including substorm timing and location, may remain challenging to simulate, implying a continuing need for real‐time specification.Key PointsPresents the first comparison between observed field‐aligned currents and models previously evaluated for space weather operational useThe model and observed integrated currents are well correlated, but the ratio between them ranges from 1/3 to 3The 2‐D current densities are weakly correlated with observations implying significant areas for improvements in the modelsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136469/1/swe20415_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136469/2/swe20415.pd

Self-love and sociability: the ‘rudiments of commerce’ in the state of nature

Istvan Hont’s classic work on the theoretical links between the seventeenth-century natural jurists Hugo Grotius and Samuel Pufendorf and the eighteenth-century Scottish political economists remains a popular trope among intellectual and economic historians of various stamps. Despite this, a common criticism levelled at Hont remains his relative lack of engagement with the relationship between religion and economics in the early modern period. This paper challenges this aspect of Hont’s narrative by drawing attention to an alternative, albeit complementary, assessment of the natural jurisprudential heritage of eighteenth-century British political economy. Specifically, the article attempts to map on to Hont’s thesis the Christian Stoic interpretation of Grotius and Pufendorf which has gained greater currency in recent years. In doing so, the paper argues that Grotius and Pufendorf’s contributions to the ‘unsocial sociability’ debate do not necessarily lead directly to the Scottish school of political economists, as is commonly assumed. Instead, it contends that a reconsideration of Grotius and Pufendorf as neo-Stoic theorists, particularly via scrutiny of their respective adaptations of the traditional Stoic theory of oikeiosis, steers us towards the heart of the early English ‘clerical’ Enlightenment

Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

Integrating and conjugative elements (ICEs) are one of the three principal types of self-transmissible mobile genetic elements in bacteria. ICEs, like plasmids, transfer via conjugation; but unlike plasmids and similar to many phages, these elements integrate into and replicate along with the host chromosome. Members of the SXT/R391 family of ICEs have been isolated from several species of gram-negative bacteria, including Vibrio cholerae, the cause of cholera, where they have been important vectors for disseminating genes conferring resistance to antibiotics. Here we developed a plasmid-based system to capture and isolate SXT/R391 ICEs for sequencing. Comparative analyses of the genomes of 13 SXT/R391 ICEs derived from diverse hosts and locations revealed that they contain 52 perfectly syntenic and nearly identical core genes that serve as a scaffold capable of mobilizing an array of variable DNA. Furthermore, selection pressure to maintain ICE mobility appears to have restricted insertions of variable DNA into intergenic sites that do not interrupt core functions. The variable genes confer diverse element-specific phenotypes, such as resistance to antibiotics. Functional analysis of a set of deletion mutants revealed that less than half of the conserved core genes are required for ICE mobility; the functions of most of the dispensable core genes are unknown. Several lines of evidence suggest that there has been extensive recombination between SXT/R391 ICEs, resulting in re-assortment of their respective variable gene content. Furthermore, our analyses suggest that there may be a network of phylogenetic relationships among sequences found in all types of mobile genetic elements

Are Reports of Psychological Stress Higher in Occupational Studies? A Systematic Review across Occupational and Population Based Studies

This study was funded by the UK Ministry of Defence (MoD)

Replication and active partition of integrative and conjugative elements (ICEs) of the SXT/R391 family : the line between ICEs and conjugative plasmids is getting thinner

Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a family of ICEs

Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs). While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS), in Actinobacteria a single DNA FtsK/SpoIIIE-like translocation protein is required. To date, the role and diversity of ICEs in Actinobacteria have received little attention. Putative ICEs were searched for in 275 genomes of Actinobacteria using HMM-profiles of proteins involved in ICE maintenance and transfer. These exhaustive analyses revealed 144 putative FtsK/SpoIIIE-type ICEs and 17 putative T4SS-type ICEs. Grouping of the ICEs based on the phylogenetic analyses of maintenance and transfer proteins revealed extensive exchanges between different sub-families of ICEs. 17 ICEs were found in Actinobacteria from the genus Frankia, globally important nitrogen-fixing microorganisms that establish root nodule symbioses with actinorhizal plants. Structural analysis of ICEs from Frankia revealed their unexpected diversity and a vast array of predicted adaptive functions. Frankia ICEs were found to excise by site-specific recombination from their host's chromosome in vitro and in planta suggesting that they are functional mobile elements whether Frankiae live as soil saprophytes or plant endosymbionts. Phylogenetic analyses of proteins involved in ICEs maintenance and transfer suggests that active exchange between ICEs cargo-borne and chromosomal genes took place within the Actinomycetales order. Functionality of Frankia ICEs in vitro as well as in planta lets us anticipate that conjugation and ICEs could allow the development of genetic manipulation tools for this challenging microorganism and for many other Actinobacteria