Coronavirus Antibody Responses before COVID-19 Pandemic,Africa and Thailand

Prior immune responses to coronaviruses might affect human SARS-CoV-2 response. We screened 2,565 serum and plasma samples collected from 2013 through early 2020, before the COVID-19 pandemic began, from 2,250 persons in 4 countries in Africa (Kenya, Nigeria, Tanzania, and Uganda) and in Thailand, including persons living with HIV-1. We detected IgG responses to SARS-CoV-2 spike (S) subunit 2 protein in 1.8% of participants. Profiling against 23 coronavirus antigens revealed that responses to S, subunit 2, or subunit 1 proteins were significantly more frequent than responses to the receptor-binding domain, S-Trimer, or nucleocapsid proteins (p<0.0001). We observed similar responses in persons with or without HIV-1. Among all coronavirus antigens tested, SARS-CoV-2, SARS-CoV-1, and Middle East respiratory syndrome coronavirus antibody responses were much higher in participants from Africa than in participants from Thailand (p<0.01). We noted less pronounced differences for endemic coronaviruses. Serosurveys could affect vaccine and monoclonal antibody distribution across global populations.     

ALS- and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy

TANK-binding kinase 1 (TBK1) is a multifunctional kinase with an essential role in mitophagy, the selective clearance of damaged mitochondria. More than 90 distinct mutations in TBK1 are linked to amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia, including missense mutations that disrupt the abilities of TBK1 to dimerize, associate with the mitophagy receptor optineurin (OPTN), autoactivate, or catalyze phosphorylation. We investigated how ALS-associated mutations in TBK1 affect Parkin-dependent mitophagy using imaging to dissect the molecular mechanisms involved in clearing damaged mitochondria. Some mutations cause severe dysregulation of the pathway, while others induce limited disruption. Mutations that abolish either TBK1 dimerization or kinase activity were insufficient to fully inhibit mitophagy, while mutations that reduced both dimerization and kinase activity were more disruptive. Ultimately, both TBK1 recruitment and OPTN phosphorylation at S177 are necessary for engulfment of damaged mitochondra by autophagosomal membranes. Surprisingly, we find that ULK1 activity contributes to the phosphorylation of OPTN in the presence of either wild-type or kinase-inactive TBK1. In primary neurons, TBK1 mutants induce mitochondrial stress under basal conditions; network stress is exacerbated with further mitochondrial insult. Our study further refines the model for TBK1 function in mitophagy, demonstrating that some ALS-linked mutations likely contribute to disease pathogenesis by inducing mitochondrial stress or inhibiting mitophagic flux. Other TBK1 mutations exhibited much less impact on mitophagy in our assays, suggesting that cell-type–specific effects, cumulative damage, or alternative TBK1-dependent pathways such as innate immunity and inflammation also factor into the development of ALS in affected individuals.

TNF receptor–associated family member–associated NF-κB activator (TANK)-binding kinase 1 (TBK1) plays a critical role in several cellular pathways implicated in the neurodegenerative disease amyotrophic lateral sclerosis (ALS), including selective clearance of mitochondria and regulation of inflammation. More than 90 mutations in TBK1 have been linked to ALS, including several mutations identified in patients with the co-occurring degenerative disease, fronto-temporal dementia (ALS-FTD) (1, 2). Some TBK1 mutations are classified as loss of function variants while others are missense mutations with unclear contributions to disease pathogenesis (1, 3–6). The latter category includes mutations shown to disrupt the ability of TBK1 to dimerize, associate with the mitophagy receptor optineurin (OPTN), autoactivate, or catalyze phosphorylation (7–9). Given the importance of TBK1 in mitophagy (10), and the necessity of mitochondrial quality control to the maintenance of neuronal homeostasis (11, 12), functional analysis of ALS-associated missense mutations in TBK1 is necessary to determine the impact of mutant TBK1 in the neurodegeneration characteristic of ALS.TBK1 has three primary domains, 1) a kinase domain, 2) a ubiquitin-like domain, and 3) a scaffold dimerization domain, which are followed by a flexible C terminus domain (CTD) (Fig. 1A) (13–15). Two TBK1 monomers dimerize along their scaffold dimerization domains, while kinase activity is activated via autophosphorylation of the critical serine residue 172 (S172) within the activation loop of the kinase domain (14). Due to the conformation of the TBK1 dimer, it is unlikely that the monomers within a dimer can self-activate, so multimer formation is thought to be required for trans-autophosphorylation and kinase activation (13, 14). TBK1 multimerization may be promoted by association of TBK1 via its CTD with adaptor proteins including OPTN, TANK, Sintbad, and NAK-associated protein 1 (NAP1) (7, 16, 17). ALS-linked missense mutations are distributed throughout the protein, with some mutations disrupting dimerization, kinase activity, or both and others disrupting the association of TBK1 with adaptors, potentially inhibiting TBK1 multimerization and activation (Fig. 1B) (3, 6–8).Open in a separate windowFig. 1.ALS-linked TBK1 mutations are found throughout the molecule and induce biochemical, biophysical, and cellular deficits. (A) Protein databank structure for TANK-binding kinase 1 (TBK1) (PDB 4IWO) (13). Domains are designated by color coding: kinase domain residues 1 to 308 (blue), ubiquitin-like domain residues 309 to 387 (yellow), and scaffolding dimerization domain residues 388 to 657 (red). ALS-linked mutations are indicated by arrows and labels of their respective colors. Some mutations likely disrupt the structure of TBK1, a phenomenon not represented by this model. (B) Table summarizing biochemical results for the ALS-linked mutants published by Ye et al. (8) and the engineered kinase-inactive D135N-TBK1 (gray). (C) Confocal section of a HeLa cell (outlined in white) expressing a mitochondria-localized fluorophore (blue), Parkin (green), and WT-TBK1 (magenta), fixed after treatment with CCCP for 90 min. The Inset (white box) and zoom images (Right) exhibit rounded mitochondria that have recruited Parkin and TBK1. A volume rendering is also shown (Right, bottom row). (Scale bars: zoom out, 10 μm; zoom in, 2 μm.) (D) Relative signal intensities for mitochondria, Parkin, and TBK1 are quantified across the diameter of a damaged mitochondria (white dashed line in C, zoom). (E and F) HeLa cells depleted of endogenous TBK1 expressing Parkin, OPTN, and WT- (E) or E696K- (F) TBK1, fixed after treatment with CCCP for 90 min. Inset (white box) and zoom images (Left) demonstrate multiple rings with colocalized mitophagy components. (Scale bars: zoom out, 10 μm; zoom in, 4 μm.) (G) Quantification of E and F as rings/μm² for each cell. n = 22 to 25 cells from three independent experiments. Dashed line, median; dotted lines, 25th and 75th quartiles. ****P < 0.0001 by Student’s unpaired t test. Images E and F shown here are insets; for representative images of whole fields, reference SI Appendix, Fig. S2B.TBK1 is an essential regulator of mitophagy, a stepwise pathway for clearance of damaged mitochondria (10, 18). Mitophagy is triggered by loss of mitochondrial membrane potential, leading to the stabilization of PTEN-induced putative kinase 1 (PINK1) on the outer mitochondrial membrane (OMM) (19) where it phosphorylates ubiquitin (20). Phosphorylated ubiquitin recruits the E3 ubiquitin ligase, Parkin (20, 21), which is activated by PINK1 phosphorylation and then ubiquitinates OMM proteins (20, 22–25). These modifications promote proteasomal degradation of mitofusins, preventing the damaged organelle from re-fusing with the healthy mitochondrial network and resulting in a small, rounded mitochondrion (26). Ubiquitination of OMM proteins also promotes recruitment of the mitophagy receptors OPTN, nuclear dot 52 kDa protein (NDP52), Tax1-binding protein 1 (TAX1BP1), next to BRCA gene 1 protein (NBR1), and p62/sequestosome1 (10, 27–30), though OPTN and NDP52 are sufficient and redundant in carrying out mitochondrial clearance in HeLa cells (29). Phosphorylation of OPTN at S177 by TBK1 at the OMM enhances the binding of OPTN to ubiquitin chains (18). OPTN then drives recruitment of the core autophagy machinery, including the unc-51-like autophagy activating kinase (ULK1) complex, to initiate formation of the double membraned phagophore that engulfs the damaged organelle (31–33). In this process, microtubule-associated protein 1A/1B-light chain 3 (LC3) is lipidated and subsequently incorporated into the elongating phagophore (10, 27, 34). The LC3-interacting region of OPTN facilitates efficient engulfment by the autophagosome (10), while TBK1-mediated phosphorylation of OPTN enhances the binding of the receptor to LC3 (35). A feed-forward mechanism in which initial LC3-positive membranes recruit more OPTN and NDP52 leads to accelerated mitochondrial engulfment (36). The newly formed compartment fuses with lysosomes to complete degradation of the organelle (30, 37, 38).We undertook a functional analysis of ALS-associated TBK1 missense mutations that have been characterized by biochemical and biophysical assays but confer unknown effects on the cellular pathways that involve TBK1. We determined the extent of recruitment of TBK1 mutants to depolarized, Parkin-positive mitochondria, the effect of mutant TBK1 expression on OPTN recruitment and phosphorylation, and the resulting downstream engulfment of fragmented mitochondria by LC3-positive autophagosomes. Expression of some ALS-linked mutations profoundly disrupted TBK1 recruitment and activity during mitochondrial clearance, while others only marginally affected the pathway. Neurons expressing TBK1 mutations demonstrated higher baseline levels of mitochondrial stress and an inability to manage induced oxidative damage, both of which may contribute to neurodegeneration. Our data suggest a nuanced model of TBK1 function, wherein TBK1 phosphorylates OPTN directly, while TBK1 recruitment also facilitates OPTN phosphorylation via an ULK1-dependent pathway. Furthermore, we demonstrate that ALS and ALS-FTD–associated missense mutations in TBK1 can lead to disordered or delayed mitochondrial clearance and a cellular deficiency in mitochondrial homeostasis.     

Glucocorticoids and progestins signal the initiation and enhance the rate of myelin formation

Dexamethasone and progesterone have been found to accelerate the time of initiation and enhance the rate of myelin synthesis in Schwann cell/neuronal cocultures. The expression of mRNA for cytochrome P450scc (converts cholesterol to pregnenolone), 3β-hydroxysteroid dehydrogenase (converts pregnenolone to progesterone), and the progesterone receptor were detected and markedly induced during peak myelin formation in the cocultures. The mRNA for the glucocorticoid receptor was detected, but was found to be constituitively expressed. In addition, the specific activity of 3β-hydroxysteroid dehydrogenase was measured and found to increase by 10-fold. The mRNA for cytochrome P450scc and 3β-hydroxysteroid dehydrogenase also were found to be induced during the differentiation of O-2A precursor cells to oligodendrocytes. Fibroblast growth factor and platelet-derived growth factor were found to have proliferative effects on Schwann cells, but they had no effect on the initiation or the rate of myelin formation. These results demonstrate that myelin-forming cells have inducible enzymes responsible for steroid biosynthesis and suggest a critical role for endogenous steroid hormones in signaling the initiation and enhancing the rate of myelin formation.     

Reductions in emissions from deforestation from Indonesia’s moratorium on new oil palm,timber, and logging concessions

To reduce greenhouse gas emissions from deforestation, Indonesia instituted a nationwide moratorium on new license areas (“concessions”) for oil palm plantations, timber plantations, and logging activity on primary forests and peat lands after May 2011. Here we indirectly evaluate the effectiveness of this policy using annual nationwide data on deforestation, concession licenses, and potential agricultural revenue from the decade preceding the moratorium. We estimate that on average granting a concession for oil palm, timber, or logging in Indonesia increased site-level deforestation rates by 17–127%, 44–129%, or 3.1–11.1%, respectively, above what would have occurred otherwise. We further estimate that if Indonesia’s moratorium had been in place from 2000 to 2010, then nationwide emissions from deforestation over that decade would have been 241–615 MtCO₂e (2.8–7.2%) lower without leakage, or 213–545 MtCO₂e (2.5–6.4%) lower with leakage. As a benchmark, an equivalent reduction in emissions could have been achieved using a carbon price-based instrument at a carbon price of $3.30–7.50/tCO₂e (mandatory) or $12.95–19.45/tCO₂e (voluntary). For Indonesia to have achieved its target of reducing emissions by 26%, the geographic scope of the moratorium would have had to expand beyond new concessions (15.0% of emissions from deforestation and peat degradation) to also include existing concessions (21.1% of emissions) and address deforestation outside of concessions and protected areas (58.7% of emissions). Place-based policies, such as moratoria, may be best thought of as bridge strategies that can be implemented rapidly while the institutions necessary to enable carbon price-based instruments are developed.Reducing deforestation in Indonesia can contribute to climate-change mitigation at a globally significant scale. Estimates of annual greenhouse gas emissions from deforestation in Indonesia and the associated degradation of peat soils ranged from 0.32 to 1.91 GtCO₂e during 2000–2010 (1–6) (SI Appendix, Fig. S1) relative to a global total of 40–49 GtCO₂e from 2000 to 2010 (7). Deforestation in Indonesia is largely driven by the expansion of profitable and legally sanctioned oil palm and timber plantations and logging operations (5, 8–13). National and provincial governments zone areas of forest land to be logged or converted to plantation agriculture, and then district governments issue licenses to individual companies for these purposes (“concessions”) (14, 15). Substantial deforestation occurs outside of legally sanctioned concession areas as well.In May 2010, the national government of Indonesia announced a moratorium prohibiting district governments from granting new concession licenses (16, 17). The moratorium covered licenses for three types of activities: (i) conversion of primary forests and peat lands to oil palm plantations (oil palm concessions); (ii) conversion of primary forests and peat lands to fast-growing tree plantations for pulp and paper (timber concessions); and (iii) logging of commercially valuable tree species within forests (logging concessions). The moratorium was enacted in the context of a national strategy for reducing emissions from deforestation (REDD+) (18), a national target of reducing greenhouse gas emissions projected to 2020 by 26–41% while increasing gross domestic product by 7% per year (19), and a $1 billion bilateral cooperative agreement with Norway on reducing emissions from deforestation (20). The moratorium came into force in May 2011 (21) and was extended in May 2013 for an additional 2 y (22).The moratorium was conceived as both a stepping-stone to reforming Indonesia’s complex forest tenure system and a mechanism for reducing deforestation in its own right (23). The moratorium has been criticized for not covering secondary (i.e., logged) forests, for providing potential loopholes for food and energy security, for periodic downward revisions to the total moratorium area, for leaving a grace period between the announcement and the implementation of the moratorium during which licenses could still be obtained, and for not curtailing deforestation within existing concessions (24–27). Furthermore it has been noted that Indonesia’s deforestation rate has continued an upward trend from 2000 through 2012, even after the implementation of the moratorium in 2011 (28, 29). However, the effectiveness of the moratorium in reducing emissions from deforestation has yet to be quantified. Deforestation in recent years might have been even higher in the absence of a moratorium.Here we have evaluated the effectiveness of the moratorium policy by analyzing annual nationwide data on deforestation, the boundaries and license dates of concessions, and potential agricultural revenue from 2000 to 2010, the decade preceding the moratorium. The decade preceding the moratorium is ideal for scenario analysis because we can’t know where concessions would have been designated post-2011 without a moratorium, but we do know where pre-2010 concessions would not have been with a moratorium. Thus, we are able to construct a counterfactual scenario in which the moratorium policy in its current form was applied over the previous decade, and compare emissions under this simulated scenario to the emissions that actually occurred.We first answered the question: How much did the designation of a concession increase local (grid cell-level) deforestation above what would have occurred there without a concession? We used panel econometric techniques to control for potentially confounding geographic and time-variant factors and to construct upper and lower bounds around the magnitude of the treatment effect. Next, we answered the question: How much lower would Indonesia’s emissions from deforestation have been from 2000 to 2010 if no new concessions had been granted on primary forests and peat lands during that period? We aggregated estimates of local (grid cell-level) land-use change to the national level, accounted for geographic displacement of deforestation caused by market feedbacks (“leakage”), and applied grid cell-specific carbon emission factors for deforestation and peat degradation. Finally, we answered the question: At what carbon price would a price-based instrument have achieved an equivalent reduction in emissions over the same time period? We compared the estimated emission reductions from the place-based moratorium policy with the estimated emission reductions from a hypothetical carbon price-based instrument, adapting the Open Source Impacts of REDD+ Incentives Spreadsheet (OSIRIS) Indonesia model (4). We examined both a mandatory carbon price-based instrument (e.g., a cap-and-trade or symmetric tax-and-subsidy program) and a voluntary carbon price-based instrument (e.g., a project-level REDD+ program with business-as-usual reference levels).With this paper we contribute to several literatures. First, we expand the literature on quasi-experimental evaluation of the causal impact of conservation measures (30), such as protected areas (31–33), payment-for-ecosystem-services programs (33, 34), logging concessions (35), and clearing bans (36), to include agricultural concessions. Even though agricultural concessions are used to legally sanction deforestation on at least 150 million hectares of forest in at least 12 countries (37), and curtailing the expansion of such concessions represents a potentially promising policy for reducing emissions from deforestation, the effects of agricultural concessions on deforestation have only been estimated obliquely in econometric studies exploring other topics (4, 38, 39). Additionally, to our knowledge our paper is the first to transform area-based treatment effects to emissions-based treatment effects. Second, our paper is rare in that it uses panel data and techniques. Nearly all previous spatially explicit econometric studies of land-use change have necessarily relied upon cross-sectional analyses because of data availability constraints. In a meta-analysis of 117 such studies (40), only three have previously used panel methods (39, 41, 42). This paper is at the forefront of what is likely to be a proliferation of panel econometric analyses enabled by the recent availability of reliable, annual, globally consistent data on patterns of forest loss (28). Third, our paper is rare in that it calibrates the effect of land-use designations empirically. Nearly all previous land-use change scenario analyses have assumed idealized perfect effectiveness of conservation measures or complete conversion without such measures. A recent review of this literature found that only 1 of 71 peer-reviewed studies explicitly incorporated the difference in probable threat between reserved and nonreserved scenarios (43). Finally, our paper is to our knowledge the first to compare the effectiveness of place-based policies with alternative carbon price-based instruments for climate change mitigation within a landscape.     

A comparative assessment of the performance of a state-of-the art small footprint dedicated cardiovascular CT scanner

IntroductionWith increasing adoption of CT coronary angiography (CTA) there is increasing demand for cost-effective, small footprint, dedicated cardiac scanners. We compared a state-of-the-art, small footprint dedicated cardiac scanner (DCCT) to a standard multidetector scanner (MDCT).MethodsThe study was a retrospective unblinded single centre study. A total of 800 patients were included, with 400 undergoing a DCCT and MDCT coronary CTA scanning, respectively. Image quality was assessed using a 4-point grading score. Image noise and artifact, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), and acceptance rate for CT-derived fractional flow reserve (FFRct) were recorded.ResultsOverall image quality was higher in the DCCT group (3.8 ± 0.55 vs 3.6 ± 0.69; p = 0.042). There was no difference in overall image noise (p = 0.131) or artifact (p = 0.295). SNR was superior in the DCCT group (14.2 ± 6.85 vs 11.4 ± 3.32; p < 0.005) as was CNR (12.7 ± 6.77 vs 11.9 ± 3.29; p < 0.005). The heart rate was lower in the DCCT group (56 ± 9.1 vs 59 ± 8.1; p < 0.005). No difference in the dose length product (DLP median 244.53 (IQR 105.6) vs 237.63 (IQR 160.1); p = 0.313) or FFR_CT acceptance rate (100 vs 97.7%; p > 0.05) was noted. Independent predictors of excellent quality regardless of scanner type were age (p = 0.011), heart rate <65 bpm (p < 0.005), and body mass index < 35 (p < 0.005).ConclusionA DCCT scanner is capable of image quality similar to modern current generation general purpose CT technology. Such technology appears to be a viable option to serve the increasing demand for CTCA imaging.     

Hypothermic responses to 8-OH-DPAT in the Ts65Dn mouse model of Down syndrome

Recently, we have demonstrated that potassium channels containing G-protein-activated potassium channel 2 (GIRK2) subunits play a significant role in hypothermia induced by several neurotransmitter receptor agonists, including the serotonin (5-HT)1A/5-HT7 receptor agonist 8-OH-DPAT [R-(+)-8-hydroxy-2-(di-n-propylamino) tetralin]. The GIRK2 gene is located in human chromosome 21 (its mouse ortholog, Girk2, is in mouse chromosome 16). Down syndrome is produced by the trisomy of chromosome 21. Here, we used quantitative radiotelemetry to investigatehypothermic responses to 8-OH-DPAT in the Down syndrome mouse model Ts65Dn (which carries an extra chromosomal 16 segment containing Girk2). Our results indicate that, in relation to euploid controls, Ts65Dn mice display significantly increased hypothermic responses to 8-OH-DPAT. This finding may be relevant to the understanding of previously reported differences in serotoninergic neurotransmission in persons with Down syndrome.     

Can you have dementia with an MMSE score of 30?

OBJECTIVE: To investigate the possibility that a patient with a diagnosis oF probable Alzheimer's disease (AD) can still obtain a score oF 30/30 on the Mini-Mental State Exam (MMSE). DESIGN: Chart review. Setting. The McGill University/Jewish General Hospital Memory Clinic. PARTICIPANTS: Participants were selected From the Memory Clinic's patient database. All underwent comprehensive evaluations, including relevant blood work and a computed tomographic scan or a magnetic resonance imaging scan oF the brain to rule out other causes oF dementia. MEASUREMENTS: All patients had one or more neuropsychological evaluation. Data oF all psychometric testing, including the MMSE, were gathered From these visits. Results. Eight patients were Found to meet the criteria oF AD although achieving a score oF 30/30 on the MMSE. Four oF 8 patients achieved this score although they were taking cholinesterase inhibitors. CONCLUSION: Although rare, it is possible to achieve a score oF 30/30 on the MMSE even iF a subject is suFFering From a dementing illness.