Bioprinting Neural Systems to Model Central Nervous System Diseases

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Bistability in fatty-acid oxidation resulting from substrate inhibition

In this study we demonstrated through analytic considerations and numerical studies that the mitochondrial fatty-acid β-oxidation can exhibit bistable-hysteresis behavior. In an experimentally validated computational model we identified a specific region in the parameter space in which two distinct stable and one unstable steady state could be attained with different fluxes. The two stable states were referred to as low-flux (disease) and high-flux (healthy) state. By a modular kinetic approach we traced the origin and causes of the bistability back to the distributive kinetics and the conservation of CoA, in particular in the last rounds of the β-oxidation. We then extended the model to investigate various interventions that may confer health benefits by activating the pathway, including (i) activation of the last enzyme MCKAT via its endogenous regulator p46-SHC protein, (ii) addition of a thioesterase (an acyl-CoA hydrolysing enzyme) as a safety valve, and (iii) concomitant activation of a number of upstream and downstream enzymes by short-chain fatty-acids (SCFA), metabolites that are produced from nutritional fibers in the gut. A high concentration of SCFAs, thioesterase activity, and inhibition of the p46Shc protein led to a disappearance of the bistability, leaving only the high-flux state. A better understanding of the switch behavior of the mitochondrial fatty-acid oxidation process between a low- and a high-flux state may lead to dietary and pharmacological intervention in the treatment or prevention of obesity and or non-alcoholic fatty-liver disease

ER stress and Rho kinase activation underlie the vasculopathy of CADASIL

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) leads to premature stroke and vascular dementia. Mechanism-specific therapies for this aggressive cerebral small vessel disease are lacking. CADASIL is caused by NOTCH3 mutations that influence vascular smooth muscle cell (VSMC) function through unknown processes. We investigated molecular mechanisms underlying the vasculopathy in CADASIL focusing on endoplasmic reticulum (ER) stress and RhoA/Rho kinase (ROCK). Peripheral small arteries and VSMCs were isolated from gluteal biopsies of CADASIL patients and mesentery of TgNotch3R169C mice (CADASIL model). CADASIL vessels exhibited impaired vasorelaxation, blunted vasoconstriction, and hypertrophic remodeling. Expression of NOTCH3 and ER stress target genes was amplified and ER stress response, Rho kinase activity, superoxide production, and cytoskeleton-associated protein phosphorylation were increased in CADASIL, processes associated with Nox5 upregulation. Aberrant vascular responses and signaling in CADASIL were ameliorated by inhibitors of Notch3 (γ-secretase inhibitor), Nox5 (mellitin), ER stress (4-phenylbutyric acid), and ROCK (fasudil). Observations in human CADASIL were recapitulated in TgNotch3R169C mice. These findings indicate that vascular dysfunction in CADASIL involves ER stress/ROCK interplay driven by Notch3-induced Nox5 activation and that NOTCH3 mutation–associated vascular pathology, typical in cerebral vessels, also manifests peripherally. We define Notch3-Nox5/ER stress/ROCK signaling as a putative mechanism-specific target and suggest that peripheral artery responses may be an accessible biomarker in CADASIL

Structural Control on Megathrust Rupture and Slip Behavior: Insights From the 2016 Mw 7.8 Pedernales Ecuador Earthquake

The heterogeneous seafloor topography of the Nazca Plate as it enters the Ecuador subduction zone provides an opportunity to document the influence of seafloor roughness on slip behavior and megathrust rupture. The 2016 M$_{w}$ 7.8 Pedernales Ecuador earthquake was followed by a rich and active postseismic sequence. An internationally coordinated rapid response effort installed a temporary seismic network to densify coastal stations of the permanent Ecuadorian national seismic network. A combination of 82 onshore short and intermediate period and broadband seismic stations and six ocean bottom seismometers recorded the postseismic Pedernales sequence for over a year after the mainshock. A robust earthquake catalog combined with calibrated relocations for a subset of magnitude ≥4 earthquakes shows pronounced spatial and temporal clustering. A range of slip behavior accommodates postseismic deformation including earthquakes, slow slip events, and earthquake swarms. Models of plate coupling and the consistency of earthquake clustering and slip behavior through multiple seismic cycles reveal a segmented subduction zone primarily controlled by subducted seafloor topography, accreted terranes, and inherited structure. The 2016 Pedernales mainshock triggered moderate to strong earthquakes (5 ≤ M ≤ 7) and earthquake swarms north of the mainshock rupture close to the epicenter of the 1906M$_{w}$ 8.8 earthquake and in the segment of the subduction zone that ruptured in 1958 in a M$_{w}$ 7.7 earthquake

Estimating species relative abundances from museum records

Funding: C.F., U.B. and D.J.R. acknowledge COST Action ‘European Soil-Biology Data Warehouse for Soil Protection’ (EUdaphobase), CA18237, supported by COST (European Cooperation in Science and Technology). AEM thanks the Leverhulme Trust (RPG-2019-401). D.B.B. was supported by an NSF Postdoc Research Fellowship in Biology (NSF 000733206), S.M.R. was supported by an NSERC Discovery Grant Author Contributions, A.V.S. was supported by NSF 1755336, C.S.M was supported by NSF 1398620 and N.J.G was supported by NSF 2019470.1. Dated, geo-referenced museum specimens are a rich data source for reconstructing species' distribution and abundance patterns. However, museum records are potentially biased towards over-representation of rare species, and it is unclear whether museum records can be used to estimate relative abundance in the field. 2. We assembled 17 coupled field and museum datasets to quantitatively compare relative abundance estimates with the Dirichlet distribution. Collectively, these datasets comprise 73,039 museum records and 1,405,316 field observations of 2,240 species. 3. Although museum records of rare species overestimated relative abundance by 1-fold to over 100-fold (median study = 9.0), the relative abundance of species estimated from museum occurrence records was strongly correlated with relative abundance estimated from standardized field surveys (r2 range of 0.10-0.91, median study = 0.43). 4. These analyses provide a justification for estimating species relative abundance with carefully curated museum occurrence records, which may allow for the detection of temporal or spatial shifts in the rank ordering of common and rare species.Publisher PDFPeer reviewe

A solution scan of societal options to reduce transmission and spread of respiratory viruses: SARS-CoV-2 as a case study.

Societal biosecurity - measures built into everyday society to minimize risks from pests and diseases - is an important aspect of managing epidemics and pandemics. We aimed to identify societal options for reducing the transmission and spread of respiratory viruses. We used SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as a case study to meet the immediate need to manage the COVID-19 pandemic and eventually transition to more normal societal conditions, and to catalog options for managing similar pandemics in the future. We used a 'solution scanning' approach. We read the literature; consulted psychology, public health, medical, and solution scanning experts; crowd-sourced options using social media; and collated comments on a preprint. Here, we present a list of 519 possible measures to reduce SARS-CoV-2 transmission and spread. We provide a long list of options for policymakers and businesses to consider when designing biosecurity plans to combat SARS-CoV-2 and similar pathogens in the future. We also developed an online application to help with this process. We encourage testing of actions, documentation of outcomes, revisions to the current list, and the addition of further options

A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers

HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism

Recommendations on data sharing in HIV drug resistance research

• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens.  • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens.  • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines.  • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing.  • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions.  • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV

Central nervous system rather than immune cell-derived BDNF mediates axonal protective effects early in autoimmune demyelination

Brain-derived neurotrophic factor (BDNF) is involved in neuronal and glial development and survival. While neurons and astrocytes are its main cellular source in the central nervous system (CNS), bioactive BDNF is also expressed in immune cells and in lesions of multiple sclerosis and its animal model experimental autoimmune encephalomyelitis (EAE). Previous data revealed that BDNF exerts neuroprotective effects in myelin oligodendrocyte glycoprotein-induced EAE. Using a conditional knock-out model with inducible deletion of BDNF, we here show that clinical symptoms and structural damage are increased when BDNF is absent during the initiation phase of clinical EAE. In contrast, deletion of BDNF later in the disease course of EAE did not result in significant changes, either in the disease course or in axonal integrity. Bone marrow chimeras revealed that the deletion of BDNF in the CNS alone, with no deletion of BDNF in the infiltrating immune cells, was sufficient for the observed effects. Finally, the therapeutic effect of glatiramer acetate, a well-characterized disease-modifying drug with the potential to modulate BDNF expression, was partially reversed in mice in which BDNF was deleted shortly before the onset of disease. In summary, our data argue for an early window of therapeutic opportunity where modulation of BDNF may exert neuroprotective effects in experimental autoimmune demyelination