Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulent Pseudomonas aeruginosa infection converts antimicrobial amyloids into cytotoxic prions

Pseudomonas aeruginosa infection elicits the production of cytotoxic amyloids from lung endothelium, yet molecular mechanisms of host‐pathogen interaction that underlie the amyloid production are not well understood. We examined the importance of type III secretion system (T3SS) effectors in the production of cytotoxic amyloids. P aeruginosa possessing a functional T3SS and effectors induced the production and release of cytotoxic amyloids from lung endothelium, including beta amyloid, and tau. T3SS effector intoxication was sufficient to generate cytotoxic amyloid release, yet intoxication with exoenzyme Y (ExoY) alone or together with exoenzymes S and T (ExoS/T/Y) generated the most virulent amyloids. Infection with lab and clinical strains engendered cytotoxic amyloids that were capable of being propagated in endothelial cell culture and passed to naïve cells, indicative of a prion strain. Conversely, T3SS‐incompetent P aeruginosa infection produced non‐cytotoxic amyloids with antimicrobial properties. These findings provide evidence that (1) endothelial intoxication with ExoY is sufficient to elicit self‐propagating amyloid cytotoxins during infection, (2) pulmonary endothelium contributes to innate immunity by generating antimicrobial amyloids in response to bacterial infection, and (3) ExoY contributes to the virulence arsenal of P aeruginosa through the subversion of endothelial amyloid host‐defense to promote a lung endothelial‐derived cytotoxic proteinopathy.
High‐Resolution Imaging Flow Cytometry Reveals Impact of Incubation Temperature on Labeling of Extracellular Vesicles with Antibodies

Extracellular vesicles (EVs) are released from basically all cells. Over the last decade, small EVs (sEVs; 50–150 nm) have gained enormous attention in diagnostics and therapy. However, methodological limitations coupled to the lack of EV standards leave many questions in this quickly evolving field unresolved. Recently, by using enhanced green fluorescent protein (eGFP)‐labeled sEVs as biological reference material, we systematically optimized imaging flow cytometry for single sEV analysis. Furthermore, we showed that sEVs stained with different fluorescent antibodies can be analyzed in a multiparametric manner. However, many parameters potentially affecting the sEV staining procedure still require further evaluation and optimization. Here, we present a concise, systematic evaluation of the impact of the incubation temperature (4°C, room temperature and 37°C) during sEV antibody staining on the outcome of experiments involving the staining of EVs with fluorescence‐conjugated antibodies. We provide evidence that both the staining intensity and the sample recovery can vary depending on the incubation temperature applied, and that observed differences are less pronounced following prolonged incubation times. In addition, this study can serve as an application‐specific example of parameter evaluation in EV flow cytometry. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
Temperature Effects on Bud-Burst and Leaf-Fall in Subalpine Larch

Phenology was monitored in natural stands of subalpine larch (Larix lyallii Parl.) in parts of four decades. Bud-burst date varied by about six weeks from year to year, and leaf-fall date by a month, suggesting that the importance of photoperiod in these processes has been over emphasized, even in the case of leaf-fall. Most of the variation in bud-burst date is accounted for by spring temperature, while date of leaf-fall depends on both spring and summer temperatures. This rather curious observation might be explained in terms of heat-mediated leaf aging. Early bud-burst, due to warm temperatures in spring, results in early leaf-fall, and warm summers also tend to terminate the life of the leaves sooner, from which it might be inferred that longevity is governed by a heat-sum above a certain threshold temperature. In controlled environments it was shown that the threshold temperature for bud-burst is very low, less than 1.5OC, and the heat-sum requirement is less than 75 degree-days above this threshold.
Effects of transcranial direct current stimulation of prefrontal cortex on risk‐taking behavior

Recent cognitive neuroscience research shows that noninvasive brain stimulation can modify a wide range of behaviors in healthy people. Such regulation effects on human behaviors provide new insights into the neurobiology of cognitive processes and establish causal brain–behavior relations. Here, we aimed to examine the effects of transcranial electrical stimulation (TES) of the prefrontal cortex on risk‐taking.
Auxiliary α2δ1 and α2δ3 Subunits of Calcium Channels Drive Excitatory and Inhibitory Neuronal Network Development

VGCCs are multisubunit complexes that play a crucial role in neuronal signaling. Auxiliary α2δ subunits of VGCCs modulate trafficking and biophysical properties of the pore-forming α1 subunit and trigger excitatory synaptogenesis. Alterations in the expression level of α2δ subunits were implicated in several syndromes and diseases, including chronic neuropathic pain, autism, and epilepsy. However, the contribution of distinct α2δ subunits to excitatory/inhibitory imbalance and aberrant network connectivity characteristic for these pathologic conditions remains unclear. Here, we show that α2δ1 overexpression enhances spontaneous neuronal network activity in developing and mature cultures of hippocampal neurons. In contrast, overexpression, but not downregulation, of α2δ3 enhances neuronal firing in immature cultures, whereas later in development it suppresses neuronal activity. We found that α2δ1 overexpression increases excitatory synaptic density and selectively enhances presynaptic glutamate release, which is impaired on α2δ1 knockdown. Overexpression of α2δ3 increases the excitatory synaptic density as well but also facilitates spontaneous GABA release and triggers an increase in the density of inhibitory synapses, which is accompanied by enhanced axonaloutgrowth in immature interneurons. Together, our findings demonstrate that α2δ1 and α2δ3 subunits play distinct but complementary roles in driving formation of structural and functional network connectivity during early development. An alteration in α2δ surface expression during critical developmental windows can therefore play a causal role and have a profound impact on the excitatory-to-inhibitory balance and network connectivity. SIGNIFICANCE STATEMENT The computational capacity of neuronal networks is determined by their connectivity. Chemical synapses are the main interface for transfer of information between individual neurons. The initial formation of network connectivity requires spontaneous electrical activity and the calcium channel-mediated signaling. We found that, in early development, auxiliary α2δ3 subunits of calcium channels foster presynaptic release of GABA, trigger formation of inhibitory synapses, and promote axonal outgrowth in inhibitory interneurons. In contrast, later in development, α2δ1 subunits promote the glutamatergic neurotransmission and synaptogenesis, as well as strongly enhance neuronal network activity. We propose that formation of connectivity in neuronal networks is associated with a concerted interplay of α2δ1 and α2δ3 subunits of calcium channels.
Lower body negative pressure protects brain perfusion in aviation gravitational stress induced by push–pull manoeuvre

Rapid alterations of gravitational stress during high‐performance aircraft push–pull manoeuvres induce dramatic shifts in volume and pressure within the circulation system, which may result in loss of consciousness due to the rapid and significant reduction in cerebral perfusion. There are still no specific and effective countermeasures so far. We found that lower body negative pressure (LBNP), applied prior to and during −Gz and released at the subsequent transition to +Gz, could effectively counteract gravitational haemodynamic stress induced by a simulated push–pull manoeuvre and improve cerebral diastolic perfusion in human subjects. We developed a LBNP strategy that effectively protects cerebral perfusion at rapid −Gz to +Gz transitions via improving cerebral blood flow and blood pressure during push–pull manoeuvres and highlight the importance of the timing of the intervention. Our findings provide a systemic link of integrated responses between the peripheral and cerebral haemodynamic changes during push–pull manoeuvres.
Acute chloroquine poisoning: A comprehensive experimental toxicology assessment of the role of diazepam

Resurgence in the use of chloroquine as a potential treatment for COVID‐19 has seen recent cases of fatal toxicity due to unintentional overdoses. Protocols for the management of poisoning recommend diazepam, although there are uncertainties in its pharmacology and efficacy in this context. The aim was to assess the effects of diazepam in experimental models of chloroquine cardiotoxicity.
Long-term Increases in Oxygen Depletion in the Bottom Waters of Boulder Basin, Lake Mead, Nevada-Arizona, USA

Abstract Long-term changes in the hypolimnetic volumetric oxygen demand (HVOD) of Boulder Basin, Lake Mead were determined from dissolved oxygen profiles collected from 1991 to 2007. HVOD is the rate at which oxygen in a deep layer in contact with the sediments is depleted during the period of thermal and/or chemical stratification. Generally, the rate at which oxygen is depleted is correlated to the amount of organic debris in the hypolimnion and sediments. The sediment oxygen demand reflects historical organic loading, while HVOD is a measure of productivity because of the organic particles settling from above. The lower hypolimnion in Boulder Basin remains relatively stable during the stratification period, enabling the calculation of HVOD in the near-bottom water layer. Small increases and/or decreases that occur in temperature and dissolved oxygen concentrations are detectable. Boulder Basin fully destratifies every other year on average, but mixes only partially in the spring (before May) of the remaining years. The HVOD rates after partial and complete destratification have been assessed separately for 1995–2005. The annual HVOD rate is generally lower the year after partial destratification than after complete destratification due to greater downward transport of oxygen into the hypolimnion. The HVOD of Boulder Basin is variable depending on loading of nutrients and water into the Basin. The rate dropped significantly following commencement of advanced wastewater treatment practices in 1994. The rates then increased 1996–2006 at a rate of approximately 0.75 mg DO/m3/day per year, or about 7% annually. During those years the inputs of nutrients steadily increased. Rates have been dropping from 2005 to present (2007) following further reduction of phosphorus input. A multiple regression analysis revealed that HVOD is significantly positive related to the total phosphorus concentration in Las Vegas Bay, but significantly negative to inflows of Colorado River water. That means HVOD was highest when reservoir water was nutrient-rich and flow rates were low. HVOD should be considered a major tool for monitoring trophic state changes in Boulder Basin.
Mitochondrial Dysfunction: A Common Hallmark Underlying Comorbidity between sIBM and Other Degenerative and Age-Related Diseases

Sporadic inclusion body myositis (sIBM) is an inflammatory myopathy associated, among others, with mitochondrial dysfunction. Similar molecular features are found in Alzheimer’s disease (AD) and Type 2 Diabetes Mellitus (T2DM), underlying potential comorbidity. This study aims to evaluate common clinical and molecular hallmarks among sIBM, AD, and T2DM. Comorbidity with AD was assessed in n = 14 sIBM patients by performing neuropsychological and cognitive tests, cranial magnetic resonance imaging, AD cerebrospinal fluid biomarkers (levels of amyloid beta, total tau, and phosphorylated tau at threonine-181), and genetic apolipoprotein E genotyping. In the same sIBM cohort, comorbidity with T2DM was assessed by collecting anthropometric measures and performing an oral glucose tolerance test and insulin determinations. Results were compared to the standard population and other myositis (n = 7 dermatomyositis and n = 7 polymyositis). Mitochondrial contribution into disease was tested by measurement of oxidative/anaerobic and oxidant/antioxidant balances, respiration fluxes, and enzymatic activities in sIBM fibroblasts subjected to different glucose levels. Comorbidity of sIBM with AD was not detected. Clinically, sIBM patients showed signs of misbalanced glucose homeostasis, similar to other myositis. Such misbalance was further confirmed at the molecular level by the metabolic inability of sIBM fibroblasts to adapt to different glucose conditions. Under the standard condition, sIBM fibroblasts showed decreased respiration (0.71 ± 0.08 vs. 1.06 ± 0.04 nmols O2/min; p = 0.024) and increased anaerobic metabolism (5.76 ± 0.52 vs. 3.79 ± 0.35 mM lactate; p = 0.052). Moreover, when glucose conditions were changed, sIBM fibroblasts presented decreased fold change in mitochondrial enzymatic activities (−12.13 ± 21.86 vs. 199.22 ± 62.52 cytochrome c oxidase/citrate synthase ratio; p = 0.017) and increased oxidative stress per mitochondrial activity (203.76 ± 82.77 vs. −69.55 ± 21.00; p = 0.047), underlying scarce metabolic plasticity. These findings do not demonstrate higher prevalence of AD in sIBM patients, but evidences of prediabetogenic conditions were found. Glucose deregulation in myositis suggests the contribution of lifestyle conditions, such as restricted mobility. Additionally, molecular evidences from sIBM fibroblasts confirm that mitochondrial dysfunction may play a role. Monitoring T2DM development and mitochondrial contribution to disease in myositis patients could set a path for novel therapeutic options.
Dissemination of Pseudomonas savastanoi pv. savastanoi populations and subsequent appearance of olive knot disease.

Pseudomonas savastanoi pv. savastanoi (Psv) is the causal agent of olive knot disease. The bacterium survives epiphytically and gains ingress through new wounds where infections and colonization result in knot formation. The natural spread of the bacterium and the subsequent appearance of the disease in olive orchards is poorly understood. The aim of this study was to monitor Psv epiphytic populations in inoculated plants with knots versus non-inoculated healthy trees within the same orchard over four years. Additionally, disease severity was measured in both inoculated and non-inoculated control trees. Epiphytic Psv populations moved from inoculated to non-inoculated trees, although average Psv populations were higher in inoculated trees. Olive knot severity increased over the course of the study in all treatments and cultivars, with all plants reaching a high level of disease by the end of the study. However, the delay in the onset of disease was longer in non-inoculated than in inoculated trees. Molecular typing of Psv isolates recovered from non-inoculated control trees confirmed that they were similar to the inoculated strain. These data demonstrate that Psv can move over short distances in olive orchards through dissemination of epiphytic bacteria and suggest a relationship between the presence of epiphytic Psv and the number of knots on trees.
Brentuximab vedotin in combination with rituximab, cyclophosphamide, doxorubicin, and prednisone as frontline treatment for patients with CD30-positive B-cell lymphomas

We conducted a phase I/II multicenter trial using six cycles of brentuximab vedotin (BV) in combination with rituximab, cyclophosphamide, doxorubicin, and prednisone (R-CHP) for treatment of patients with CD30-positive B-cell lymphomas. Thirty-one patients were evaluable for toxicity and 29 for efficacy including 22 with primary mediastinal B-cell lymphoma, five with diffuse large B-cell lymphoma, and two with gray zone lymphoma. There were no treatmentrelated deaths; 32% of patients had non-hematologic grade 3/4 toxicities. The overall response rate was 100% (95% confidence interval [95% CI]: 88-100) with 86% (95% CI: 68-96) of patients achieving complete response at the end of systemic treatment. Consolidative radiation following end-of-treatment response assessment was permissible and used in 52% of all patients including 59% of the patients with primary mediastinal B-cell lymphoma. With a median follow-up of 30 months, the 2- year progression-free survival and overall survival rates were 85% (95% CI: 66-94) and 100%, respectively. In the cohort with primary mediastinal B-cell lymphoma, the 2-year progression-free survival rate was 86% (95% CI: 62-95). In summary, BV-R-CHP with or without consolidative radiation is a feasible and active frontline regimen for CD30-positive Bcell lymphomas (ClinicalTrials.gov identifier: NCT01994850).
Low Vitamin D Levels Predict Mortality in Ankylosing Spondylitis Patients: A Nationwide Population-Based Cohort Study

In this study, we aimed to examine the effect of vitamin D deficiency on all-cause mortality in ankylosing spondylitis (AS) patients and in the general population. This is a retrospective-cohort study based on the electronic database of the largest health-maintenance organization in Israel. AS patients who were first diagnosed between 2002–2007 were included. Controls were matched by age, gender and enrollment-time. Follow-up continued until death or end of study follow-up on 1 July 2019. Laboratory measures of serum 25-hydroxyvitamin-D levels during the entire follow-up period were obtained. A total of 919 AS patients and 4519 controls with a mean time of follow-up of 14.3 years were included. The mean age at the time of enrollment was 52 years, and 22% of them were females. AS was associated with a higher proportion of vitamin D deficiency (odds ratio 1.27 [95% confidence-interval (CI) 1.03–1.58]). In AS patients, insufficient levels of vitamin D (<30 ng/mL) were significantly associated with increased incidence of all-cause mortality (hazard ratio (HR) 1.59 [95% CI 1.02–2.50]). This association was more prominent with the decrease in vitamin D levels (< 20 ng/mL, HR 1.63 [95% CI 1.03–2.60]; <10 ng/mL, HR 1.79 [95% CI 1.01–3.20]) and among male patients (<30 ng/mL, HR 2.11 [95% CI 1.20–3.72]; <20 ng/mL, HR 2.12 [95% CI 1.19–3.80]; <10 ng/mL, HR 2.23 [95% CI 1.12–4.43]). However, inadequate levels of vitamin D among controls were not associated with an increased all-cause mortality. Our study has shown that vitamin D deficiency is more common in AS patients than controls and is linked to an increased risk for all-cause mortality. These results emphasize the need for randomized-controlled trials to evaluate the benefits of vitamin D supplementation as a secondary prevention of mortality in patients with chronic inflammatory rheumatic disease.
Intermittent hypercapnic hypoxia induces respiratory hypersensitivity to fentanyl accompanied by tonic respiratory depression by endogenous opioids

Sleep apnoea increases susceptibility to opioid‐induced respiratory depression (OIRD). Endogenous opioids are implicated as a contributing factor in sleep apnoea. Rats exposed to sleep‐phase chronic intermittent hypercapnic hypoxia (CIHH) for 7 days exhibited exaggerated OIRD to systemic fentanyl both while anaesthetized and artificially ventilated and while conscious and breathing spontaneously, implicating heightened CNS inhibitory efficacy of fentanyl. CIHH also induced tonic endogenous opioid suppression of neural inspiration. Sleep‐related episodes of hypercapnic hypoxia, as in sleep apnoea, promote hypersensitivity to OIRD, with tonic respiratory depression by endogenous opioids implicated as a potential underlying cause.
Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane

Significance The KRAS oncogene is frequently mutated in human cancers, and cancer-associated mutations are constitutively activated, which stimulates RAF kinase activity at the plasma membrane. Membrane-anchored KRAS engages the RAS-binding domain (RBD) of RAF, and the adjacent cysteine-rich domain (CRD) interacts with the plasma membrane via a poorly defined mechanism. Studying this multidomain, membrane-dependent interaction has been a major challenge; hence, assembly of the full KRAS–RAF complex on the membrane is not well-understood. We determined NMR-based structures of a KRAS:RBD–CRD complex on a lipid bilayer, revealing how multivalent, dynamic protein–protein and protein–lipid interactions stabilize the complex in two states and how perturbation of this equilibrium by a cancer-associated CRAF mutation promotes CRAF activation, potentially via KRAS dimerization. Membrane anchoring of farnesylated KRAS is critical for activation of RAF kinases, yet our understanding of how these proteins interact on the membrane is limited to isolated domains. The RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF engage KRAS and the plasma membrane, unleashing the kinase domain from autoinhibition. Due to experimental challenges, structural insight into this tripartite KRAS:RBD–CRD:membrane complex has relied on molecular dynamics simulations. Here, we report NMR studies of the KRAS:CRAF RBD–CRD complex. We found that the nucleotide-dependent KRAS–RBD interaction results in transient electrostatic interactions between KRAS and CRD, and we mapped the membrane interfaces of the CRD, RBD–CRD, and the KRAS:RBD–CRD complex. RBD–CRD exhibits dynamic interactions with the membrane through the canonical CRD lipid-binding site (CRD β7–8), as well as an alternative interface comprising β6 and the C terminus of CRD and β2 of RBD. Upon complex formation with KRAS, two distinct states were observed by NMR: State A was stabilized by membrane association of CRD β7–8 and KRAS α4–α5 while state B involved the C terminus of CRD, β3–5 of RBD, and part of KRAS α5. Notably, α4–α5, which has been proposed to mediate KRAS dimerization, is accessible only in state B. A cancer-associated mutation on the state B membrane interface of CRAF RBD (E125K) stabilized state B and enhanced kinase activity and cellular MAPK signaling. These studies revealed a dynamic picture of the assembly of the KRAS–CRAF complex via multivalent and dynamic interactions between KRAS, CRAF RBD–CRD, and the membrane.
Dietary Betaine Addition Promotes Hepatic Cholesterol Synthesis, Bile Acid Conversion, and Export in Rats

It is widely reported how betaine addition regulates lipid metabolism but how betaine affects cholesterol metabolism is still unknown. This study aimed to investigate the role of betaine in hepatic cholesterol metabolism of Sprague-Dawley rats. Rats were randomly allocated to four groups and fed with a basal diet or a high-fat diet with or without 1% betaine. The experiment lasted 28 days. The results showed that dietary betaine supplementation reduced the feed intake of rats with final weight unchanged. Serum low-density-lipoprotein cholesterol was increased with the high-fat diet. The high-fat diet promoted cholesterol synthesis and excretion by enhancing the HMG-CoA reductase and ABCG5/G8, respectively, which lead to a balance of hepatic cholesterol. Rats in betaine groups showed a higher level of hepatic total cholesterol. Dietary betaine addition enhanced cholesterol synthesis as well as conversion of bile acid from cholesterol by increasing the levels of HMGCR and CYP7A1. The high-fat diet decreased the level of bile salt export pump, while dietary betaine addition inhibited this decrease and promoted bile acid efflux and increased total bile acid levels in the intestine. In summary, dietary betaine addition promoted hepatic cholesterol metabolism, including cholesterol synthesis, conversion of bile acids, and bile acid export.