Enabling community-based metrology for wood-degrading fungi

Background: Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings. Results: We show that a widely-available and globally-regularized consumer product (Pringles™) can support the growth of wood-degrading fungi, and that growth on Pringles™-broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to ~ 75%. Conclusions: Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi

Purpose and Spirituality: Exploring the Role of Fidelity in Diverse Adolescents

Purpose is understood to reflect young people’s stable and generalized commitments to accomplish meaningful activity and contribute productively to society. Religion has been linked with purpose; however, the nature of this relationship is not well understood. Given that purpose and religion involve beliefs and devotion, the current study examined fidelity as a means of understanding this relationship in a group of religiously and culturally diverse youth from around the world. The participants were 30 adolescents aged 12-21 (M = 17.73 years) nominated for living with profound spirituality in their community. Consensual qualitative research (CQR) strategies were used. Analysis revealed that 29 of the participants reported a sense of purpose and all 30 participants described some aspect of fidelity that involved (a) beliefs, (b) values, (c) morals, and (d) resolute commitment. These findings highlight the centrality of fidelity as a link between religion and purpose among diverse youth. Future directions for research and practice are discussed

Keeping connected : identity, social connection and education for young people living with chronic illness

The ‘Keeping Connected’ project was a three year project \ud (2006-2009) co-funded by the Australian Research Council\ud and The Royal Children’s Hospital Education Institute.\ud Its focus was on young people who experience chronic illness-related \ud interruptions to their schooling. Its aims were to make visible the young\ud people, their experiences, voices, and concerns, and to explore the ways\ud in which they were being supported or hampered in various aspects\ud of their education trajectories. \ud The project brought together a large multi-disciplinary research team working\ud in collaboration with the RCH Education Institute with the aim of achieving\ud a better understanding of issues related to the support and engagement\ud of young people living and learning with ongoing health conditions.\ud Who and what do young people feel is important in creating, strengthening,\ud and maintaining educational and social connections in their lives? What do \ud parents feel are significant supports or challenges for young people (and their \ud families) experiencing interrupted schooling due to ongoing health issues?\ud What do education and health care professionals see as key areas of focus\ud in supporting young people to maintain social and educational connections?\ud This report highlights the clear and pressing need for a system of advocacy\ud on the part of young people and families within both health and education\ud systems—and between schools and hospitals. The Royal Children’s Hospital \ud Education Institute is well positioned to influence policy and practice\ud across these sectors

Enabling community-based metrology for wood-degrading fungi

Background: Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings. Results: We show that a widely-available and globally-regularized consumer product (Pringles™) can support the growth of wood-degrading fungi, and that growth on Pringles™-broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to ~ 75%. Conclusions: Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi

Perturbed mitochondria-ER contacts in live neurons that model the amyloid pathology of Alzheimer\u27s disease.

The use of fixed fibroblasts from familial and sporadic Alzheimer\u27s disease patients has previously indicated an upregulation of mitochondria-ER contacts (MERCs) as a hallmark of Alzheimer\u27s disease. Despite its potential significance, the relevance of these results is limited because they were not extended to live neurons. Here we performed a dynamic in vivo analysis of MERCs in hippocampal neurons from McGill-R-Thy1-APP transgenic rats, a model of Alzheimer\u27s disease-like amyloid pathology. Live FRET imaging of neurons from transgenic rats revealed perturbed \u27lipid-MERCs\u27 (gap width \u3c10 nm), while \u27Ca2+-MERCs\u27 (10-20 nm gap width) were unchanged. In situ TEM showed no significant differences in the lipid-MERCs:total MERCs or lipid-MERCs:mitochondria ratios; however, the average length of lipid-MERCs was significantly decreased in neurons from transgenic rats as compared to controls. In accordance with FRET results, untargeted lipidomics showed significant decreases in levels of 12 lipids and bioenergetic analysis revealed respiratory dysfunction of mitochondria from transgenic rats. Thus, our results reveal changes in MERC structures coupled with impaired mitochondrial functions in Alzheimer\u27s disease-related neurons.This article has an associated First Person interview with the first author of the paper

Media, Machines and Might: Reproducing Western Australia’s Violent State of Aboriginal Protection

This paper addresses the prevalence of state violence directed at Aboriginal people. It examines how violence has been reproduced in recent years in the space of Western Australia through mutually-reinforcing relations of financial interest, and how the function of private capital accumulation – in state violence against sovereign Aboriginal people – has remained hidden in white sight. This paper argues that state violence is legitimised through a discourse of Aboriginal protection. After outlining how this discourse and violence have operated in Western Australia, the paper provides a substantive narrative challenging the routine reproduction of state violence against Aboriginal bodies through a close reading of public and media texts. These texts relate to state violence against a blockade preventing land-clearing machines from entering Aboriginal country in mid 2011; state violence against the Nyoongar Tent Embassy in early 2012; and, the government's announcement in May 2011 that it would amend the Aboriginal Heritage Act. Through this analysis, lines are drawn between media, machines and might for the purpose of enabling white sight to see private capital accumulation functioning within the reproduction of state violence against Aboriginal people

Marijuana use and DNA methylation-based biological age in young adults

BACKGROUND: Marijuana is the third most commonly used drug in the USA and efforts to legalize it for medical and recreational use are growing. Despite the increase in use, marijuana\u27s effect on aging remains understudied and understanding the effects of marijuana on molecular aging may provide novel insights into the role of marijuana in the aging process. We therefore sought to investigate the association between cumulative and recent use of marijuana with epigenetic age acceleration (EAA) as estimated from blood DNA methylation. RESULTS: A random subset of participants from The Coronary Artery Risk Development in Young Adults (CARDIA) Study with available whole blood at examination years (Y) 15 and Y20 underwent epigenomic profiling. Four EAA estimates (intrinsic epigenetic age acceleration, extrinsic epigenetic age acceleration, PhenoAge acceleration, and GrimAge acceleration) were calculated from DNA methylation levels measured at Y15 and Y20. Ever use and cumulative marijuana-years were calculated from the baseline visit to Y15 and Y20, and recent marijuana use (both any and number of days of use in the last 30 days) were calculated at Y15 and Y20. Ever use of marijuana and each additional marijuana-year were associated with a 6-month (P \u3c 0.001) and a 2.5-month (P \u3c 0.001) higher average in GrimAge acceleration (GAA) using generalized estimating equations, respectively. Recent use and each additional day of recent use were associated with a 20-month (P \u3c 0.001) and a 1-month (P \u3c 0.001) higher GAA, respectively. A statistical interaction between marijuana-years and alcohol consumption on GAA was observed (P = 0.011), with nondrinkers exhibiting a higher GAA (β = 0.21 [95% CI 0.05, 0.36], P = 0.008) compared to heavy drinkers (β = 0.05 [95% CI - 0.09, 0.18], P = 0.500) per each additional marijuana-year. No associations were observed for the remaining EAA estimates. CONCLUSIONS: These findings suggest cumulative and recent marijuana use are associated with age-related epigenetic changes that are related to lifespan. These observed associations may be modified by alcohol consumption. Given the increase in use and legalization, these findings provide novel insight on the effect of marijuana use on the aging process as captured through blood DNA methylation

Another look at the root of the angiosperms reveals a familiar tale

Since the advent of molecular phylogenetics more than 25 years ago, a major goal of plant systematists has been to discern the root of the angiosperms. While most studies indicate that Amborella trichopoda is sister to all remaining extant flowering plants, support for this position has varied with respect to both the sequence data sets and analyses employed. Recently, Goremykin et al. (2013) questioned the “Amborella-sister hypothesis” using a “noise-reduction” approach and reported a topology with Amborella + Nymphaeales (water lilies) sister to all remaining angiosperms. Through a series of analyses of both plastid genomes and mitochondrial genes, we continue to find mostly strong support for the Amborella-sister hypothesis and offer a rebuttal of Goremykin et al. (2013). The major tenet of Goremykin et al. is that the Amborella-sister position is determined by noisy data – i.e. characters with high rates of change and lacking true phylogenetic signal. To investigate the signal in these noisy data further, we analyzed the discarded characters from their noise-reduced alignments. We recovered a tree identical to that of the currently accepted angiosperm framework, including the position of Amborella as sister to all other angiosperms, as well as all other major clades. Thus, the signal in the “noisy” data is consistent with that of our complete data sets – arguing against the use of their noise-reduction approach. We also determined that one of the alignments presented by Goremykin et al. yields results at odds with their central claim – their data set actually supports Amborella as sister to all other angiosperms, as do larger plastid data sets we present here that possess more complete taxon sampling both within the monocots and for angiosperms in general. Previous unpartitioned, multi-locus analyses of mtDNA data have provided the strongest support for Amborella + Nymphaeales as sister to other angiosperms. However, our analysis of third codon positions from mtDNA sequence data also supports the Amborella-sister hypothesis. Finally, we challenge the conclusion of Goremykin et al. that the first flowering plants were aquatic and herbaceous, reasserting that even if Amborella + water lilies, or water lilies alone, are sister to the rest of the angiosperms, the earliest angiosperms were not necessarily aquatic and/or herbaceous