KLF6 and STAT3 Co-Occupy Regulatory DNA and Functionally Synergize to Promote Axon Growth in CNS Neurons

The failure of axon regeneration in the CNS limits recovery from damage and disease. Members of the KLF family of transcription factors can exert both positive and negative effects on axon regeneration, but the underlying mechanisms are unclear. Here we show that forced expression of KLF6 promotes axon regeneration by corticospinal tract neurons in the injured spinal cord. RNA sequencing identified 454 genes whose expression changed upon forced KLF6 expression in vitro, including sub-networks that were highly enriched for functions relevant to axon extension including cytoskeleton remodeling, lipid synthesis, and bioenergetics. In addition, promoter analysis predicted a functional interaction between KLF6 and a second transcription factor, STAT3, and genome-wide footprinting using ATAC-Seq data confirmed frequent co-occupancy. Co-expression of the two factors yielded a synergistic elevation of neurite growth in vitro. These data clarify the transcriptional control of axon growth and point the way toward novel interventions to promote CNS regeneration

Testate amoebae as palaeohydrological proxies in Sürmene Aǧaçbaşi Yaylasi Peatland (Northeast Turkey)

Testate amoebae as palaeohydrological proxies in sürmene ağaçbaşi yaylasi peatland (northeast Turkey) Testate amoebae are unicellular micro-organisms whose hydrological sensitivity and good preservation in peats make them valuable proxies for past peatland surface wetness, and therefore climate. Previous testate amoebae transfer functions have been spatially restricted with no studies from Asia. To derive a transfer function, a sequence of samples was extracted from an ombrotrophic peatland in Turkey and amoebae counted. The internal structure of the data was explored using principal components analysis and relationships with the environmental data tested by redundancy analyses. Transfer function models were developed using a variety of techniques. As in other regions, depth to water table is the most important control on amoebae community composition. Transfer function performance was initially poor, primarily due to the inclusion of samples from areas of the site that had been heavily affected by peat cutting and had distinctly different amoebae communities. Model performance is improved by selective sample exclusion, reducing jack-knifed root mean square error of prediction to 7.1 cm. The model was tested using an initial palaeoecological data-set. Overlap with the training set was limited, although a hydrological reconstruction using this model produces similar results to a transfer function derived from northern European peatlands. This study provides the first testate amoebae transfer function from Asia and demonstrates that hydrological preferences of many of the key taxa are consistent across a large area of the Northern Hemisphere. The transfer function will allow detailed palaeoclimate reconstruction from this peatland, adding to our knowledge of Holocene climatic change in southwest Asia

Long-term Follow up of Van Nes Rotationplasty for Congenital Proximal Focal Femoral Deficiency

Van Nes rotationplasty may be used for patients with congenital proximal focal femoral deficiency (PFFD). The lower limb is rotated to use the ankle and foot as a functional knee joint within a prosthesis. A small series of cases was investigated to determine the long-term outcome. At a mean of 21.5 years (11 to 45) after their rotationplasty, a total of 12 prosthetic patients completed the Short-Form (SF)-36, Faces Pain Scale-Revised, Harris hip score, Oswestry back pain score and Prosthetic Evaluation Questionnaires, as did 12 age- and gender-matched normal control participants. A physical examination and gait analysis, computerised dynamic posturography (CDP), and timed ‘Up & Go’ testing was also completed. Wilcoxon Signed rank test was used to compare each PFFD patient with a matched control participant with false discovery rate of 5%. There were no differences between the groups in overall health and well-being on the SF-36. Significant differences were seen in gait parameters in the PFFD group. Using CDP, the PFFD group had reduced symmetry in stance, and reduced end point and maximum excursions. Patients who had undergone Van Nes rotationplasty had a high level of function and quality of life at long-term follow-up, but presented with significant differences in gait and posture compared with the control group

Emergent properties arising from spatial heterogeneity influence fungal community dynamics

Community dynamics are mediated by species interactions, and within communities spatial heterogeneity and intransitive relationships promote coexistence. However, few experimental studies have assessed effects of heterogeneity on the interactions of competing individuals. Wood decay basidiomycete fungi are ideal for studying community structure and dynamics because they are easy to manipulate in laboratory microcosms, and communities resolve themselves rapidly. Most studies have only used simplistic pair-wise interactions in a 2-D plane, but here we investigate a three-species community in an environmentally realistic novel 3-dimensional system. We show how spatial heterogeneity and patch size dynamics are important for coexistence, and how competitive interactions change over different spatial dimensions. Emergent properties arose with increased spatial heterogeneity: the weakest competitor co-occurred with the community when its territory was less fragmented, and interactions became intransitive

Implications of Arm Restraint on Lower Extremity Kinetics During Gait

Background Literature indicates the importance of the upper extremities in providing stability and propulsion for the body during ambulation. However, the kinetic implications of upper extremity restraint during gait are not as well documented. Aim The objective of this study was to examine the effect of arm restraint (unilateral and bilateral) on lower extremity joint kinetics during walking. Methods Twenty-three healthy young participants were instrumented for three dimensional motion analysis, and tested in four randomly ordered upper extremity restraint conditions (unrestrained, bilateral restraint, right side restraint, and left side restraint). Temporal spatial parameters and gait/phase-specific lower extremity kinetics and kinematics were measured. For each restraint condition, pointwise differences from the unrestrained condition were compared using a two-way ANOVA model of restraint condition (“Condition”) and gait cycle phase (“Timing”). Results Decreases in walking speed and stride length were observed for all restraint conditions. Differences in kinetic demands were also noted, primarily at the hip and knee. Conclusion Upper extremity restraint in healthy young adults leads to significant changes in temporal-spatial parameters and proximal joint kinetics, most prominently during periods of load accommodation and balance

Volatile organic compounds of Metarhizium brunneum influence the efficacy of entomopathogenic nematodes in insect control

The entomopathogenic fungus (EPF) Metarhizium brunneum occupies the same ecological niche as entomopathogenic nematodes (EPN), with both competing for insects as a food source in the rhizosphere. Interactions between these biocontrol agents can be antagonistic or synergistic. To better understand these interactions, this study focussed on investigating the effect of M. brunneum volatile organic compounds (VOCs), 1-octen-3-ol and 3-octanone, on EPN survival and behaviour. These VOCs proved to be highly toxic to the infective juveniles (IJs) of the EPN Steinernema carpocapsae, Steinernema feltiae and Heterorhabditis bacteriophora with mortality being dose dependent. Chemotaxis studies of H. bacteriophora IJs in Pluronic F127 gel revealed significant preference for the VOCs compared with controls for all tested concentrations. The VOCs also impacted on the test insects in a dose-dependent manner with 3-octanone being more toxic to Galleria mellonella, Cydia splendana and Curculio elephas larvae than 1-octen-3-ol. Mortality of C. splendana and G. mellonella larvae was significantly higher when exposed to relatively high doses (>25%) of 3-octanone. Lower doses of 3-octanone and 1-octen-3-ol immobilised test insects, which recovered after exposure to fresh air for 2 hrs. In depth studies on H. bacteriophora showed that exposure of IJs to > 10% concentration of 3-octanone or 1-octen-3-ol negatively affected infectivity whereas exposure to lower doses (0.1%, 0.01%) had no effect. The VOCs affected IJs, reducing penetration efficacy and the number of generations inside G. mellonella but they failed to inhibit the bacterial symbiont, Photorhabdus kayaii. The ecological significance of VOCs and how they could influence EPF-EPN insect interactions is discussed

Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature

Decomposition of lignin-rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress-selected constituent of the same communities, in response to constant and diurnally cycling temperature. We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely, E. glandulosa showed little differential response to the experimental treatments. Synthesis. By demonstrating temperature-dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community-mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well-annotated genomes

Interdependence of primary metabolism and xenobiotic mitigation characterizes the proteome of 'Bjerkandera adusta' during wood decomposition

The aim of the current work was to identify key features of the fungal proteome involved in the active decay of beechwood blocks by the white rot fungus Bjerkandera adusta at 20°C and 24°C. A combination of protein and domain analyses ensured a high level of annotation, which revealed that while the variation in the proteins identified was high between replicates, there was a considerable degree of functional conservation between the two temperatures. Further analysis revealed differences in the pathways and processes employed by the fungus at the different temperatures, particularly in relation to nutrient acquisition and xenobiotic mitigation. Key features showing temperature-dependent variation in mechanisms for both lignocellulose decomposition and sugar utilization were found, alongside differences in the enzymes involved in mitigation against damage caused by toxic phenolic compounds and oxidative stress.IMPORTANCE This work was conducted using the wood decay fungus B. adusta, grown on solid wood blocks to closely mimic the natural environment, and gives greater insight into the proteome of an important environmental fungus during active decay. We show that a change in incubation temperature from 20°C to 24°C altered the protein profile. Proteomic studies in the field of white-rotting basidiomycetes have thus far been hampered by poor annotation of protein databases, with a large proportion of proteins simply with unknown function. This study was enhanced by extensive protein domain analysis, enabling a higher level of functional assignment and greater understanding of the proteome composition. This work revealed a strong interdependence of the primary process of nutrient acquisition and specialized metabolic processes for the detoxification of plant extractives and the phenolic breakdown products of lignocellulose

The whiff of decay: Linking volatile production and extracellular enzymes to outcomes of fungal interactions at different temperatures

The terrestrial carbon cycle is largely driven by photosynthetic plants and decomposer organisms that process biomass to CO2. In forest ecosystems, the decomposers are predominantly wood decay fungi, and the response of community structure and activity to increasing global temperatures is likely critical to forest biogeochemical processes. Metabolic products can drive community structure and substrate utilisation, and the role of volatile organic compounds (VOCs), as well as extracellular enzymes, are of particular interest. Pair-wise interactions of a community of basidiomycetes were made under 3 different microclimate conditions that mimic fluctuations in local climate conditions, and the outcome of interactions was assessed in terms of: (1) which fungus won the confrontation or whether it was a draw (deadlock); (2) the production of volatile organic compounds (VOCs) and enzyme activities; and (3) the rate of decomposition. While substrate utilisation and exploitation in terms of decomposition was not affected, community response to changing temperature was underpinned by altered outcomes of interactions and changes to territory occupation, which were reflected by changes in VOC production and extracellular enzyme activity. This study underlines the importance of understanding the impact of community structure on carbon cycling in forest ecosystems under a changing climate