The C terminus of the mycobacterium ESX-1 secretion system substrate ESAT-6 is required for phagosomal membrane damage and virulence

Mycobacterium tuberculosis and its close relative Mycobacterium marinum infect macrophages and induce the formation of granulomas, organized macrophage-rich immune aggregates. These mycobacterial pathogens can accelerate and co-opt granuloma formation for their benefit, using the specialized secretion system ESX-1, a key virulence determinant. ESX-1-mediated virulence is attributed to the damage it causes to the membranes of macrophage phagosomal compartments, within which the bacteria reside. This phagosomal damage, in turn, has been attributed to the membranolytic activity of ESAT-6, the major secreted substrate of ESX-1. However, mutations that perturb ESAT-6 membranolytic activity often result in global impairment of ESX-1 secretion. This has precluded an understanding of the causal and mechanistic relationships between ESAT-6 membranolysis and ESX-1-mediated virulence. Here, we identify two conserved residues in the unstructured C-terminal tail of ESAT-6 required for phagosomal damage, granuloma formation and virulence. Importantly, these ESAT-6 mutants have near-normal levels of secretion, far higher than the minimal threshold we establish is needed for ESX-1-mediated virulence early in infection. Unexpectedly, these loss-of-function ESAT-6 mutants retain the ability to lyse acidified liposomes. Thus, ESAT-6 virulence functions in vivo can be uncoupled from this in vitro surrogate assay. These uncoupling mutants highlight an enigmatic functional domain of ESAT-6 and provide key tools to investigate the mechanism of phagosomal damage and virulence.

Apathy, Executive Function, and Emotion Recognition Are the Main Drivers of Functional Impairment in Behavioral Variant of Frontotemporal Dementia

Background: The cognitive and neuropsychiatric deficits present in patients with behavioral variant frontotemporal dementia (bvFTD) are associated with loss of functionality in the activities of daily living (ADLs). The main purpose of this study was to examine and explore the association between the cognitive and neuropsychiatric features that might prompt functional impairment of basic, instrumental, and advanced ADL domains in patients with bvFTD.Methods: A retrospective cross-sectional study was conducted with 27 patients with bvFTD in its early stage (<2 years of evolution) and 32 healthy control subjects. A neuropsychological assessment was carried out wherein measures of cognitive function and neuropsychiatric symptoms were obtained. The informant-report Technology–Activities of Daily Living Questionnaire was used to assess the percentage of functional impairment in the different ADL domains. To identify the best determinants, three separate multiple regression analyses were performed, considering each functional impairment as the dependent variable and executive function, emotion recognition, disinhibition, and apathy as independent variables.Results: For the basic ADLs, a model that explains 28.2% of the variability was found, in which the presence of apathy (β = 0.33, p = 0.02) and disinhibition (β = 0.29, p = 0.04) were significant factors. Concerning instrumental ADLs, the model produced accounted for 63.7% of the functional variability, with the presence of apathy (β = 0.71, p < 0.001), deficits in executive function (β = −0.36, p = 0.002), and lack of emotion recognition (β = 0.28, p = 0.017) as the main contributors. Finally, in terms of advanced ADLs, the model found explained 52.6% of the variance, wherein only the presence of apathy acted as a significant factor (β = 0.59, p < 0.001).Conclusions: The results of this study show the prominent and transverse effect of apathy in the loss of functionality throughout all the ADL domains. Apart from that, this is the first study that shows that the factors associated with loss of functionality differ according to the functional domain in patients with bvFTD in its early stage. Finally, no other study has analyzed the impact of the lack of emotion recognition in the functionality of ADLs. These results could guide the planning of tailored interventions that might enhance everyday activities and the improvement of quality of life.

The channel activities of the full-length prion and truncated proteins

Prion disease is a fatal neurodegenerative disorder, in which the cellular prion protein PrPC is converted to a misfolded prion which in turn is hypothesized to permeabilize cellular membranes. The pathways leading to toxicity in prion disease are not yet completely elucidated and whether it also includes formation of membrane pores remains to be answered. Prion protein consists of two domains: a globular domain (GD) and a flexible N-terminus (FT) domain. Although a proximal nine polybasic amino acid (FT(23-31)) sequence of FT is a prerequisite for cellular membrane permeabilization, other functional domain regions may influence FT(23-31) and its permeabilization. By using single-channel electrical recordings, we reveal that FT(23-50) dominates the membrane permeabilization within the full-length mouse PrP (mPrP(23-230)). The other domain of FT(51-110) or C-terminal domain down-regulates the channel activity of FT(23-50) and the full-length mouse PrP (mPrP(23-230)). The addition of prion mimetic antibody, POM1 significantly enhances mPrP(23-230) membrane permeabilization, whereas POM1-Y104A, a POM1 mutant that binds to PrP but cannot elicit toxicity has negligible effect on membrane permeabilization. Additionally, anti-N-terminal antibody POM2 or Cu2+ stabilizes FT domain, thus provoking FT(23-110) channel activity. Furthermore, our setup provides a more direct method without an external fused protein to study the channel activity of truncated PrP in the lipid membranes. We therefore hypothesize that the primary N-terminal residues are essential for membranes permeabilization and other functional segments play a vital role to modulate the pathological effects of PrP-medicated neurotoxicity. This may yield essential insights into molecular mechanisms of prion neurotoxicity to cellular membranes in prion disease.

Structure of putative tumor suppressor ALDH1L1

Putative tumor suppressor ALDH1L1, the product of natural fusion of three unrelated genes, regulates folate metabolism by catalyzing NADP+-dependent conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Cryo-EM structures of tetrameric rat ALDH1L1 revealed the architecture and functional domain interactions of this complex enzyme. Highly mobile N-terminal domains, which remove formyl from 10-formyltetrahydrofolate, undergo multiple transient inter-domain interactions. The C-terminal aldehyde dehydrogenase domains, which convert formyl to CO2, form unusually large interfaces with the intermediate domains, homologs of acyl/peptidyl carrier proteins (A/PCPs), which transfer the formyl group between the catalytic domains. The 4′-phosphopantetheine arm of the intermediate domain is fully extended and reaches deep into the catalytic pocket of the C-terminal domain. Remarkably, the tetrameric state of ALDH1L1 is indispensable for catalysis because the intermediate domain transfers formyl between the catalytic domains of different protomers. These findings emphasize the versatility of A/PCPs in complex, highly dynamic enzymatic systems.

Anterior cingulate metabolite levels, memory, and inhibitory control in abstinent men and women with Alcohol Use Disorder

Aims: Alcohol use disorder (AUD), has been shown to have harmful cognitive and physiological effects, including altered brain chemistry. Further, although men and women may differ in vulnerability to the neurobiological effects of AUD, results of existing studies have been conflicting. Brain metabolite levels and cognitive functions were examined in a cross section of men with AUD (AUDm) and women with AUD (AUDw) to determine degree of abnormalities after extended periods of abstinence (mean, six years), and to evaluate gender differences in cognitive and metabolite measures. Methods: Participants were 40 abstinent individuals with AUD (22 AUDw, 18 AUDm) and 50 age-equivalent non-AUD comparison participants (26 NCw, 24 NCm). Proton magnetic resonance spectroscopy (MRS) was employed at 3 Tesla to acquire metabolite spectra from the dorsal anterior cingulate cortex (dACC). Brain metabolites N-acetylaspartate (NAA), choline (Cho), myo-Inositol (mI), and glutamate & glutamine (Glx) were examined relative to measures of memory and inhibitory control. Results: Metabolite levels in the AUD group showed no significant differences from the NC group. Memory and inhibitory-control impairments were observed in the AUD group. There also were significant group-specific associations between metabolite ratios and measures of inhibitory control. There were no Group-by-Gender interactions for the four metabolite ratios. Conclusions: These findings demonstrate that brain metabolite levels in men and women with AUD, following long-term abstinence, do not differ from individuals without AUD. The data also provide evidence of associations between metabolite levels and measures of inhibitory control, a functional domain important for curtailing harmful drinking.

Learning-based dynamic capabilities in closed-loop supply chains: an expert study

Purpose Product returns information gives firms an opportunity for continuous strategic adaptation by allowing them to understand the reasons for product returns, learning from them and improving their products and processes accordingly. By applying the Dynamic Capabilities (DCs) view in the context of closed-loop supply chains (CLSC), this study explores how firms can continuously learn from product returns information.Design/methodology/approach This study adopts a qualitative Delphi study-inspired approach. Experts from industry and academia are interviewed in two interview rounds. First round of interviews are based on extant research, while the second round allows the experts to elaborate and correct the results.Findings This study culminates into a conceptual model for incremental learning from product returns information. The results indicate incremental learning from product returns can potentially lead to a competitive advantage. Additionally, the authors identify the sources of information, capabilities along with their microfoundations and the manifestations of product return information. Three propositions are formulated embedding the findings in DC theory.Research limitations/implications This study supports extant literature in confirming the value of product returns information and opens concrete avenues for research by providing several propositions.Practical implications This research elucidates the practices, processes and resources required for firms to utilize product returns information for continuous strategic adaptation. Practitioners can use these results while implementing continuous learning practices in their organizations.Originality/value This study presents the first systematic framework for incremental learning from product returns information. The authors apply the DC framework to a new functional domain, namely CLSC management and product returns management. Furthermore, the authors offer a concrete example of how organizational learning and DC intersect, thus advancing DC theoretical knowledge.

Effect of chocolate on older patients with cancer in palliative care: a randomised controlled study

Background Older advanced stage cancer patients, with changes in nutritional status, represent an important demand for palliative care. The aim was to determine the effects of 4 weeks of chocolate consumption on the nutritional status of older cancer patients in palliative care. Methods Older cancer patients in palliative care with ambulatory (n = 46) monitoring were randomized to control (CG, n = 15), intervention with 55% cocoa chocolate (IG1, n = 16) and intervention with white chocolate (IG2, n = 15) groups and evaluated before and after 4 weeks for nutritional status (primary outcome), evaluated by the Mini Nutritional Assessment tool (MNA). Food consumption, anthropometry, body composition, laboratory parameters and quality of life (QL) with the European Organization for the Research and Treatment of Cancer instrument were also evaluated. Results IG1 progressed with increased screening (estimated difference [95% CI]: − 1.3 [− 2.2;-0.4], p < 0.01), and nutritional (estimated difference [95% CI]: − 1.3 [− 2.5;-0.1], p = 0.04) scores on the MNA, with no change in anthropometry and body composition. Regarding antioxidant capacity, reduced glutathione levels increased (estimated difference [95% CI]: − 0.8 [− 1.6;-0.02], p = 0.04) and malondealdehyde levels decreased in IG2 (estimated difference [95% CI]:+ 4.9 [+ 0.7;+ 9.1], p = 0.02). Regarding QL, functionality improved in IG1, with higher score in the functional domain (estimated difference [95% CI]:-7.0 [− 13.3;-0.7], p = 0.03). Conclusions The consumption of chocolate with a greater cocoa content may contribute to the improvement of the nutritional status and functionality among older cancer patients in palliative care. The consumption of white chocolate was associated with improved oxidative stress. Trial registration A randomized clinical trial (ClinicalTrials.gov NCT04367493).

Mirror Therapy Rehabilitation in Stroke: A Scoping Review of Upper Limb Recovery and Brain Activities

Background. Mirror therapy (MT) has been used as a treatment for various neurological disorders. Recent application of electroencephalogram (EEG) to the MT study allows researchers to gain insight into the changes in brain activity during the therapy. Objective. This scoping review is aimed at mapping existing evidence and identifying knowledge gaps about the effects of MT on upper limb recovery and its application for individuals with chronic stroke. Methods and Materials. A scoping review through a systematic literature search was conducted using PubMed, CINAHL, PsycINFO, and Scopus databases. Twenty articles published between 2010 and 2020 met the inclusion criteria. The efficacy of MT on upper limb recovery and brain activity during MT were discussed according to the International Classification of Functioning, Disability and Health (ICF). Results. A majority of the studies indicated positive effects of MT on upper limb recovery from the body structure/functional domain. All studies used EEG to indicate brain activation during MT. Conclusion. MT is a promising intervention for improving upper limb function for individuals with chronic stroke. This review also highlights the need to incorporate EEG into the MT study to capture brain activity and understand the mechanism underlying the therapy.

Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes

SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. However, autonomous genome annotation of SARS-CoV-2 genes, proteins, and domains is not readily accomplished by existing methods and results in missing or incorrect sequences. To overcome this limitation, we developed a novel semi-supervised pipeline for automated gene, protein, and functional domain annotation of SARS-CoV-2 genomes that differentiates itself by not relying on the use of a single reference genome and by overcoming atypical genomic traits that challenge traditional bioinformatic methods. We analyzed an initial corpus of 66,000 SARS-CoV-2 genome sequences collected from labs across the world using our method and identified the comprehensive set of known proteins with 98.5% set membership accuracy and 99.1% accuracy in length prediction, compared to proteome references, including Replicase polyprotein 1ab (with its transcriptional slippage site). Compared to other published tools, such as Prokka (base) and VAPiD, we yielded a 6.4- and 1.8-fold increase in protein annotations. Our method generated 13,000,000 gene, protein, and domain sequences—some conserved across time and geography and others representing emerging variants. We observed 3362 non-redundant sequences per protein on average within this corpus and described key D614G and N501Y variants spatiotemporally in the initial genome corpus. For spike glycoprotein domains, we achieved greater than 97.9% sequence identity to references and characterized receptor binding domain variants. We further demonstrated the robustness and extensibility of our method on an additional 4000 variant diverse genomes containing all named variants of concern and interest as of August 2021. In this cohort, we successfully identified all keystone spike glycoprotein mutations in our predicted protein sequences with greater than 99% accuracy as well as demonstrating high accuracy of the protein and domain annotations. This work comprehensively presents the molecular targets to refine biomedical interventions for SARS-CoV-2 with a scalable, high-accuracy method to analyze newly sequenced infections as they arise.

The Role of Flagellin B in Vibrio anguillarum-Induced Intestinal Immunity and Functional Domain Identification

Vibrio anguillarum, an opportunistic pathogen of aquatic animals, moves using a filament comprised of polymerised flagellin proteins. Flagellins are essential virulence factors for V. anguillarum infection. Herein, we investigated the effects of flagellins (flaA, flaB, flaC, flaD and flaE) on cell apoptosis, TLR5 expression, and production of IL-8 and TNF-α. FlaB exhibited the strongest immunostimulation effects. To explore the functions of flaB in infection, we constructed a flaB deletion mutant using a two-step recombination method, and in vitro experiments showed a significant decrease in the expression of TLR5 and inflammatory cytokines compared with wild-type cells. However in the in vivo study, expression of inflammatory cytokines and intestinal mucosal structure showed no significant differences between groups. Additionally, flaB induced a significant increase in TLR5 expression based on microscopy analysis of fluorescently labelled TLR5, indicating interactions between the two proteins, which was confirmed by native PAGE and yeast two-hybrid assay. Molecular simulation of interactions between flaB and TLR5 was performed to identify the residues involved in binding, revealing two binding sites. Then, based on molecular dynamics simulations, we carried out thirteen site-directed mutations occurring at the amino acid sites of Q57, N83, N87, R91, D94, E122, D152, N312, R313, N320, L97, H316, I324 in binding regions of flaB protein by TLR5, respectively. Surface plasmon resonance (SPR) was employed to compare the affinities of flaB mutants for TLR5, and D152, D94, I324, N87, R313, N320 and H316 were found to mediate interactions between flaB and TLR5. Our comprehensive and systematic analysis of V. anguillarum flagellins establishes the groundwork for future design of flagellin-based vaccines.