Folding Pathways of Prion and Doppel

The relevance of various residue positions for the stability and the folding characteristics of the prion protein are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. Highly significant correlations are found between the most relevant sites in our analysis and the single point mutations known to be associated with the arousal of the genetic forms of prion disease (caused by the conformational change from the cellular to the scrapie isoform). Considerable insight into the conformational change is provided by comparing the folding process of prion and doppel (a newly discovered protein) sharing very similar native state topology: the folding pathways of the former can be grouped in two main classes according to which tertiary structure contacts are formed first enroute to the native state. For the latter a single class of pathways leads to the native state. Our results are consistent and supportive of the recent experimental findings that doppel lacks the scrapie isoform and that such remarkably different behavior results from differences in the region containing the two $\beta-$strands and the intervening helix.Comment: 16 pages, 2 tables, 5 figure

Modelled land use and land cover change emissions – a spatio-temporal comparison of different approaches

This is the final version. Available on open access from Copernicus Publications via the DOI in this recordCode and data availability: Scripts and data are available upon request from the corresponding author.Quantifying the net carbon flux from land use and land cover changes (fLULCC) is critical for understanding the global carbon cycle and, hence, to support climate change mitigation. However, large-scale fLULCC is not directly measurable and has to be inferred from models instead, such as semi-empirical bookkeeping models and process-based dynamic global vegetation models (DGVMs). By definition, fLULCC estimates are not directly comparable between these two different model types. As an important example, DGVM-based fLULCC in the annual global carbon budgets is estimated under transient environmental forcing and includes the socalled loss of additional sink capacity (LASC). The LASC results from the impact of environmental changes on land carbon storage potential of managed land compared to potential vegetation and accumulates over time, which is not captured in bookkeeping models. The fLULCC from transient DGVM simulations, thus, strongly depends on the timing of land use and land cover changes mainly because LASC accumulation is cut off at the end of the simulated period. To estimate the LASC, the fLULCC from pre-industrial DGVM simulations, which is independent of changing environmental conditions, can be used. Additionally, DGVMs using constant present-day environmental forcing enable an approximation of bookkeeping estimates. Here, we analyse these three DGVM-derived fLULCC estimations (under transient, pre-industrial, and present-day forcing) for 12 models within 18 regions and quantify their differences as well as climate-and CO2-induced components and compare them to bookkeeping estimates. Averaged across the models, we find a global fLULCC (under transient conditions) of 2:00:6 PgC yr1 for 2009-2018, of which 40% are attributable to the LASC (0:80:3 PgC yr1). From 1850 onward, the fLULCC accumulated to 18956 PgC with 4015 PgC from the LASC. Around 1960, the accumulating nature of the LASC causes global transient fLULCC estimates to exceed estimates under presentday conditions, despite generally increased carbon stocks in the latter. Regional hotspots of high cumulative and annual LASC values are found in the USA, China, Brazil, equatorial Africa, and Southeast Asia, mainly due to deforestation for cropland. Distinct negative LASC estimates in Europe (early reforestation) and from 2000 onward in the Ukraine (recultivation of post-Soviet abandoned agricultural land), indicate that fLULCC estimates in these regions are lower in transient DGVM compared to bookkeeping approaches. Our study unravels the strong dependence of fLULCC estimates on the time a certain land use and land cover change event happened to occur and on the chosen time period for the forcing of environmental conditions in the underlying simulations. We argue for an approach that provides an accounting of the fLULCC that is more robust against these choices, for example by estimating a mean DGVM ensemble fLULCC and LASC for a defined reference period and homogeneous environmental changes (CO2 only)

Altered miRNA expression network in locus coeruleus of depressed suicide subjects

Norepinephrine (NE) is produced primarily by neurons in the locus coeruleus (LC). Retrograde and ultrastructural examinations reveal that the core of the LC and its surrounding region receives afferent projections from several brain areas which provide multiple neurochemical inputs to the LC with changes in LC neuronal firing, making it a highly coordinated event. Although NE and mediated signaling systems have been studied in relation to suicide and psychiatric disorders that increase the risk of suicide including depression, less is known about the corresponding changes in molecular network within LC. In this study, we examined miRNA networks in the LC of depressed suicide completers and healthy controls. Expression array revealed differential regulation of 13 miRNAs. Interaction between altered miRNAs and target genes showed dense interconnected molecular network. Functional clustering of predicated target genes yielded stress induced disorders that collectively showed the complex nature of suicidal behavior. In addition, 25 miRNAs were pairwise correlated specifically in the depressed suicide group, but not in the control group. Altogether, our study revealed for the first time the involvement of LC based dysregulated miRNA network in disrupting cellular pathways associated with suicidal behavior

MicroRNA Expression Is Down-Regulated and Reorganized in Prefrontal Cortex of Depressed Suicide Subjects

<div><h3>Background</h3><p>Recent studies suggest that alterations in expression of genes, including those which regulate neural and structural plasticity, may be crucial in the pathogenesis of depression. MicroRNAs (miRNAs) are newly discovered regulators of gene expression that have recently been implicated in a variety of human diseases, including neuropsychiatric diseases.</p> <h3>Methodology/Principal Findings</h3><p>The present study was undertaken to examine whether the miRNA network is altered in the brain of depressed suicide subjects. Expression of miRNAs was measured in prefrontal cortex (Brodmann Area 9) of antidepressant-free depressed suicide (n = 18) and well-matched non-psychiatric control subjects (n = 17) using multiplex RT-PCR plates. We found that overall miRNA expression was significantly and globally down-regulated in prefrontal cortex of depressed suicide subjects. Using individual tests of statistical significance, 21 miRNAs were significantly decreased at p = 0.05 or better. Many of the down-regulated miRNAs were encoded at nearby chromosomal loci, shared motifs within the 5′-seeds, and shared putative mRNA targets, several of which have been implicated in depression. In addition, a set of 29 miRNAs, whose expression was not pairwise correlated in the normal controls, showed a high degree of co-regulation across individuals in the depressed suicide group.</p> <h3>Conclusions/Significance</h3><p>The findings show widespread changes in miRNA expression that are likely to participate in pathogenesis of major depression and/or suicide. Further studies are needed to identify whether the miRNA changes lead to altered expression of prefrontal cortex mRNAs, either directly (by acting as miRNA targets) or indirectly (e.g., by affecting transcription factors).</p> </div

Genomic and Epigenomic Responses to Chronic Stress Involve miRNA-Mediated Programming

Stress represents a critical influence on motor system function and has been shown to impair movement performance. We hypothesized that stress-induced motor impairments are due to brain-specific changes in miRNA and protein-encoding gene expression. Here we show a causal link between stress-induced motor impairment and associated genetic and epigenetic responses in relevant central motor areas in a rat model. Exposure to two weeks of mild restraint stress altered the expression of 39 genes and nine miRNAs in the cerebellum. In line with persistent behavioural impairments, some changes in gene and miRNA expression were resistant to recovery from stress. Interestingly, stress up-regulated the expression of Adipoq and prolactin receptor mRNAs in the cerebellum. Stress also altered the expression of Prlr, miR-186, and miR-709 in hippocampus and prefrontal cortex. In addition, our findings demonstrate that miR-186 targets the gene Eps15. Furthermore, we found an age-dependent increase in EphrinB3 and GabaA4 receptors. These data show that even mild stress results in substantial genomic and epigenomic changes involving miRNA expression and associated gene targets in the motor system. These findings suggest a central role of miRNA-regulated gene expression in the stress response and in associated neurological function

Allopregnanolone-induced rise in intracellular calcium in embryonic hippocampal neurons parallels their proliferative potential

<p>Abstract</p> <p>Background</p> <p>Factors that regulate intracellular calcium concentration are known to play a critical role in brain function and neural development, including neural plasticity and neurogenesis. We previously demonstrated that the neurosteroid allopregnanolone (APα; 5α-pregnan-3α-ol-20-one) promotes neural progenitor proliferation <it>in vitro </it>in cultures of rodent hippocampal and human cortical neural progenitors, and <it>in vivo </it>in triple transgenic Alzheimer's disease mice dentate gyrus. We also found that APα-induced proliferation of neural progenitors is abolished by a calcium channel blocker, nifedipine, indicating a calcium dependent mechanism for the proliferation.</p> <p>Methods</p> <p>In the present study, we investigated the effect of APα on the regulation of intracellular calcium concentration in E18 rat hippocampal neurons using ratiometric Fura2-AM imaging.</p> <p>Results</p> <p>Results indicate that APα rapidly increased intracellular calcium concentration in a dose-dependent and developmentally regulated manner, with an EC₅₀of 110 ± 15 nM and a maximal response occurring at three days <it>in vitro</it>. The stereoisomers 3β-hydroxy-5α-hydroxy-pregnan-20-one, and 3β-hydroxy-5β-hydroxy-pregnan-20-one, as well as progesterone, were without significant effect. APα-induced intracellular calcium concentration increase was not observed in calcium depleted medium and was blocked in the presence of the broad spectrum calcium channel blocker La³⁺, or the L-type calcium channel blocker nifedipine. Furthermore, the GABA_Areceptor blockers bicuculline and picrotoxin abolished APα-induced intracellular calcium concentration rise.</p> <p>Conclusion</p> <p>Collectively, these data indicate that APα promotes a rapid, dose-dependent, stereo-specific, and developmentally regulated increase of intracellular calcium concentration in rat embryonic hippocampal neurons via a mechanism that requires both the GABA_Areceptor and L-type calcium channel. These data suggest that APα-induced intracellular calcium concentration increase serves as the initiation mechanism whereby APα promotes neurogenesis.</p

DNA methylation, the early-life social environment and behavioral disorders

One of the outstanding questions in behavioral disorders is untangling the complex relationship between nurture and nature. Although epidemiological data provide evidence that there is an interaction between genetics (nature) and the social and physical environments (nurture) in a spectrum of behavioral disorders, the main open question remains the mechanism. Emerging data support the hypothesis that DNA methylation, a covalent modification of the DNA molecule that is a component of its chemical structure, serves as an interface between the dynamic environment and the fixed genome. We propose that modulation of DNA methylation in response to environmental cues early in life serves as a mechanism of life-long genome adaptation. Under certain contexts, this adaptation can turn maladaptive resulting in behavioral disorders. This hypothesis has important implications on understanding, predicting, preventing, and treating behavioral disorders including autism that will be discussed

A new stress sensor and risk factor for suicide: The T allele of the functional genetic variant in the GABRA6 gene

© 2017 The Author(s). Low GABA transmission has been reported in suicide, and GABRA6 rs3219151 T allele has been associated with greater physiological and endocrine stress response in previous studies. Although environmental stress also plays a role in suicide, the possible role of this allele has not been investigated in this respect. In our present study effect of rs3219151 of GABRA6 gene in interaction with recent negative life events on lifetime and current depression, current anxiety, as well as lifetime suicide were investigated using regression models in a white European general sample of 2283 subjects. Post hoc measures for phenotypes related to suicide risk were also tested for association with rs3219151 in interaction with environmental stress. No main effect of the GABRA6 rs3219151 was detected, but in those exposed to recent negative life events GABRA6 T allele increased current anxiety and depression as well as specific elements of suicide risk including suicidal and death-related thoughts, hopelessness, restlessness and agitation, insomnia and impulsiveness as measured by the STOP task. Our data indicate that stress-associated suicide risk is elevated in carriers of the GABRA6 rs3219151 T allele with several independent markers and predictors of suicidal behaviours converging to this increased risk