bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and phenotypic characterization of experimentally selected resistantLeishmania donovanireveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound
Authors: Hefnawy Aya , Negreira Gabriel , Jara Marlene , Cotton James A. , Maes Ilse , D’ Haenens Erika , Imamura Hideo , Cuypers Bart , Monsieurs Pieter , Mouchtoglou Christina , De Winter Hans , Berriman Matt , Sanders Mandy , Martin Julio , de Muylder Geraldine , Dujardin Jean-Claude , Sterckx Yann G.-J. , Domagalska Malgorzata Anna 
Published: January 2021

AbstractThe implementation of prospective drug resistance (DR) studies in the R&D pipelines is a common practice for many infectious diseases, but not for Neglected Tropical Diseases. Here, we explored and demonstrated the importance of this approach, using as paradigmsLeishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK ‘Leishbox’ to treat VL. We experimentally selected resistance to TCMDC-143345 in vitro and characterized resistant parasites at genomic and phenotypic levels. We found that it took more time to develop resistance to TCMDC-143345 than to other drugs in clinical use and that there was no cross resistance to these drugs, suggesting a new and unique mechanism. By whole genome sequencing, we found two mutations in the gene encoding theL. donovanidynamin-1-like protein (LdoDLP1) that were fixed at highest drug pressure. Through phylogenetic analysis, we identified LdoDLP1 as a family member of the dynamin-related proteins, a group of proteins that impacts the shapes of biological membranes by mediating fusion and fission events, with a putative role in mitochondrial fission. We found thatL. donovanilines genetically engineered to harbor the two identified LdoDLP1 mutations were resistant to TCMDC-143345 and displayed altered mitochondrial properties. By homology modeling, we showed how the two LdoDLP1 mutations may influence protein structure and function. Taken together, our data reveal a clear involvement of LdoDLP1 in the adaptation/resistance ofL. donovanito TCMDC-143345.ImportanceHumans and their pathogens are continuously locked in a molecular arms race during which the eventual emergence of pathogen drug resistance (DR) seems inevitable. For neglected tropical diseases (NTDs), DR is generally studied retrospectively, once it has already been established in clinical settings. We previously recommended to keep one step ahead in the host-pathogen arms race and implement prospective DR studies in the R&D pipeline, a common practice for many infectious diseases, but not for NTDs. Here, usingLeishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK ‘Leishbox’ to treat VL, as paradigms, we experimentally selected resistance to the compound and proceeded to genomic and phenotypic characterization of DR parasites. The results gathered in the present study suggest a new DR mechanism involving theL. donovanidynamin-1 like protein (LdoDLP1) and demonstrate the practical relevance of prospective DR studies.
Dynamics of antibodies to SARS-CoV-2 in convalescent plasma donors
Authors: Steenhuis Maurice , van Mierlo Gerard , Derksen Ninotska I.L. , Ooijevaar-de Heer Pleuni , Kruithof Simone , Loeff Floris L. , Berkhout Lea C. , Linty Federica , Reusken Chantal , Reimerink Johan , Hogema Boris , Zaaijer Hans , van de Watering Leo , Swaneveld Francis , van Gils Marit J. , Bosch Berend Jan , van Ham Marieke , Brinke Anja ten , Vidarsson Gestur , van der Schoot Ellen C. , Rispens Theo 
Published: January 2021

AbstractThe novel SARS-CoV-2 virus emerged in late 2019 and has caused a global health and economic crisis. The characterization of the human antibody response to SARS-CoV-2 infection is vital for serosurveillance purposes as well for treatment options such as transfusion with convalescent plasma or immunoglobin products derived from convalescent plasma. In this study, we measured antibody responses in 844 longitudinal samples from 151 RT-PCR positive SARS-CoV-2 convalescent adults during the first 34 weeks after onset of symptoms. All donors were seropositive at the first sampling moment and only one donor seroreverted during follow-up analysis. Anti-RBD IgG and anti-nucleocapsid IgG levels slowly declined with median half-life’s of 62 and 59 days during 2-5 months after symptom onset, respectively. The rate of decline of antibody levels diminished during extended follow-up. In addition, the magnitude of the IgG response correlated with neutralization capacity measured in a classic plaque reduction assay as well in our in-house developed competition assay. The result of this study gives valuable insight into the longitudinal response of antibodies to SARS-CoV-2.
No association between the SARS-CoV-2 variants and mortality rates in the Eastern Mediterranean Region
Authors: Omais Saad , Kharroubi Samer , Zaraket Hassan 
Published: January 2021

AbstractAs the novel coronavirus SARS-CoV-2 continues to spread in all countries, there is a growing interest in monitoring and understanding the impact of emerging strains on virus transmission and disease severity. Here, we analyzed SARS-CoV-2 genomic sequences reported in the Eastern Mediterranean Region (EMR) countries, as of 1 January 2021. The majority (∼75%) of these sequences originated from three out of 22 EMR countries, and 65.8% of all sequences belonged to GISAID clades GR, GH, G and GV. A delay ranging between 30-150 days from sample collection to sequence submission was observed across all countries, limiting the utility of such data in informing public health policies. We identified ten common non-synonymous mutations represented among SARS-CoV-2 in the EMR and several country-specific ones. Two substitutions, spike_D614G and NSP12_P323L, were predominantly concurrent in most countries. While the single incidence of NSP12_P323L was positively correlated with higher case fatality rates in EMR, no such association was established for the double (spike_D614G and NSP12_P323L) concurrent variant across the region. Our study identified critical data gaps in EMR highlighting the importance of enhancing surveillance and sequencing capacities in the region.
Neurophysiological and brain structural markers of cognitive frailty differs from Alzheimer’s disease
Authors: Kocagoncu Ece , Nesbitt David , Emery Tina , Hughes Laura , Henson Richard N. ,   Cam-CAN, Rowe James B. 
Published: January 2021

AbstractWith increasing life span, there is growing importance of understanding the mechanisms of successful cognitive ageing. In contrast, cognitive frailty has been proposed to be a precursor to Alzheimer’s disease. Here we test the hypothesis that cognitively frail adults represent a branch of healthy ageing, distinct from latent dementia. We used electro-magnetoencephalography and magnetic resonance imaging to investigate the structural and neurophysiological features of cognitive frailty in relation to healthy aging, and clinical presentations of mild cognitive impairment and Alzheimer’s disease. Cognitive performance of the cognitively frail group was similar to those with mild cognitive impairment. We used a novel cross-modal oddball task to induce mismatch responses to unexpected stimuli. Both controls and cognitively frail showed stronger mismatch responses and larger temporal grey matter volume, compared to people with mild cognitive impairment and Alzheimer’s disease. Our results suggest that cognitively frail represents a spectrum of normal ageing rather than incipient or undiagnosed Alzheimer’s disease. Lower cognitive reserve, hearing impairment and medical comorbidity might contribute to the aetiology of cognitive impairment.
Hierarchical Regulation of Autophagy During Adipocyte Differentiation
Authors: Ahmed Mahmoud , Lai Trang Huyen , Pham Trang Minh , Zada Sahib , Elashkar Omar , Hwang Jin Seok , Kim Deok Ryong 
Published: January 2021

AbstractWe previously showed that some adipogenic transcription factors such as CEBPB and PPARG directly and indirectly regulate autophagy gene expression in adipogenesis. The order and the effect of these events are undetermined. In this study, we modeled the gene expression, DNA-binding of transcriptional regulators, and histone modifications during adipocyte differentiation and evaluated the effect of the regulators on gene expression in terms of direction and magnitude. Then, we identified the overlap of the transcription factors and co-factors binding sites and targets. Finally, we built a chromatin states model based on the histone marks and studied their relation with the factors’ binding. Adipogenic factors differentially regulated autophagy genes as part of the differentiation program. Co-regulators associated with specific transcription factors and preceded them to the regulatory regions. Transcription factors differed in the binding time and location, and their effect on expression was either localized or long-lasting. Adipogenic factors disproportionately targeted genes coding for autophagy-specific transcription factors. To sum, a hierarchical arrangement between adipogenic transcription factors and co-factors drives the regulation of autophagy during adipocyte differentiation.
Estimating the rate of plasmid transfer with an adapted Luria–Delbrück fluctuation analysis
Authors: Kosterlitz Olivia , Tirado Adamaris Muñiz , Wate Claire , Elg Clint , Bozic Ivana , Top Eva M. , Kerr Benjamin 
Published: January 2021

AbstractTo increase our basic understanding of the ecology and evolution of conjugative plasmids, we need a reliable estimate of their rate of transfer between bacterial cells. However, accurate estimates of plasmid transfer have remained elusive due to biological and experimental complexity. Current methods to measure transfer rate can be confounded by many factors. A notable example involves plasmid transfer between different strains or species where the rate that one type of cell donates the plasmid is not equal to the rate at which the other cell type donates. Asymmetry in these rates has the potential to bias or constrain current transfer estimates, thereby limiting our capabilities for estimating transfer in microbial communities. Inspired by the classic fluctuation analysis of Luria and Delbrück, we develop a novel approach, the Luria-Delbrück method (‘LDM’), for estimating plasmid transfer rate. Our new approach embraces the stochasticity of conjugation departing from the current deterministic population dynamic methods. In addition, the LDM overcomes obstacles of traditional methods by not being affected by different growth and transfer rates for each population within the assay. Using stochastic simulations and experiments, we show that the LDM has high accuracy and precision for estimation of transfer rates compared to the most widely used methods, which can produce estimates that differ from the LDM estimate by orders of magnitude.Significance StatementConjugative plasmids play significant roles in the ecology and evolution of microbial communities. Notably, antibiotic resistance genes are often encoded on conjugative plasmids. Thus, conjugation—the transfer of a plasmid copy from one cell to another—is a common way for antibiotic resistance to spread between important clinical pathogens. For both public health modeling and a basic understanding of microbial population biology, accurate estimates of this fundamental rate are of great consequence. We show that widely used methods can lead to biased estimates, deviating from true values by several orders of magnitude. Therefore, we developed a new approach, inspired by the classic fluctuation analysis of Luria and Delbrück, for accurately assessing the rate of plasmid conjugation under a variety of conditions.
Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging
Authors: Seim Ian , Roden Christine A. , Gladfelter Amy S. 
Published: January 2021

AbstractViruses must efficiently and specifically package their genomes while excluding cellular nucleic acids and viral sub-genomic fragments. Some viruses use specific packaging signals, which are conserved sequence/structure motifs present only in the full-length genome. Recent work has shown that viral proteins important for packaging can undergo liquid-liquid phase separation (LLPS), where one or two viral nucleic acid binding proteins condense with the genome. The compositional simplicity of viral components lends itself well to theoretical modeling compared to more complex cellular organelles. Viral LLPS can be limited to one or two viral proteins and a single genome that is enriched in LLPS-promoting features. In our previous study, we observed that LLPS-promoting sequences of SARS-CoV-2 are located at the 5ʹ and 3ʹ ends of the genome, whereas the middle of the genome is predicted to consist mostly of solubilizing elements. Is this arrangement sufficient to drive single genome packaging, genome compaction, and genome cyclization? We addressed these questions using a coarse-grained polymer model, LASSI, to study the LLPS of nucleocapsid protein with RNA sequences that either promote LLPS or solubilization. With respect to genome cyclization, we find the most optimal arrangement restricts LLPS-promoting elements to the 5ʹ and 3ʹ ends of the genome, consistent with the native spatial patterning. Genome compaction is enhanced by clustered LLPS-promoting binding sites, while single genome packaging is most efficient when binding sites are distributed throughout the genome. These results suggest that many and variably positioned LLPS-promoting signals can support packaging in the absence of a singular packaging signal which argues against necessity of such a feature. We hypothesize that this model should be generalizable to multiple viruses as well as cellular organelles like paraspeckles, which enrich specific, long RNA sequences in a defined arrangement.Statement of significanceThe COVID-19 pandemic has motivated research of the basic mechanisms of coronavirus replication. A major challenge faced by viruses such as SARS-CoV-2 is the selective packaging of a large genome in a relatively small capsid while excluding host and sub-genomic nucleic acids. Genomic RNA of SARS-CoV-2 can condense with the Nucleocapsid (N-protein), a structural protein component critical for packaging of many viruses. Notably, certain regions of the genomic RNA drive condensation of N-protein while other regions solubilize it. Here, we explore how the spatial patterning of these opposing elements promotes single genome compaction, packaging, and cyclization. This model informs futurein silicoexperiments addressing spatial patterning of genomic features that are experimentally intractable because of the length of the genome.
Resolving the molecular fingerprint of the distal carboxy tail in modulating CaV1 calcium dependent inactivation
Authors: Sang Lingjie , Vieira Daiana C. O. , Yue David T. , Ben-Johny Manu , Dick Ivy E. 
Published: January 2021

AbstractCa2+/calmodulin-dependent inactivation (CDI) of CaVchannels is a critical regulatory process required for tuning the kinetics of Ca2+entry for different cell types and physiologic responses. Calmodulin (CaM) resides on the IQ domain of the CaVcarboxy-tail, such that Ca2+binding initiates a reduction in channel open probability, manifesting as CDI. This regulatory process exerts a significant impact on Ca2+entry and is tailored by alternative splicing. CaV1.3 and CaV1.4 feature a long-carboxy-tail splice variant that modulates CDI through a competitive mechanism. In these channels, the distal-carboxy-tail (DCT) harbors an inhibitor of CDI (ICDI) module that competitively displaces CaM from the IQ domain, thereby diminishing CDI. While this overall mechanism is now well-described, the detailed interaction loci for ICDI binding to the IQ domain is yet to be elucidated. Here, we perform alanine-scanning mutagenesis of the IQ and ICDI domains and evaluate the contribution of neighboring regions. We identify multiple critical residues within the IQ domain, ICDI and the nearby A region of the channel, which are required for high affinity IQ/ICDI binding. Importantly, disruption of this interaction commensurately diminishes ICDI function, as seen by the re-emergence of CDI in mutant channels. Furthermore, analysis of the homologous ICDI region of CaV1.2 reveals a selective effect of this channel region on CaV1.3 channels, implicating a cross-channel modulatory scheme in cells expressing both channel subtypes. In all, these findings provide new insights into a molecular rheostat that fine tunes Ca2+entry and supports normal neuronal and cardiac function.
Self-organized stem cell-derived human lung buds with proximo-distal patterning and novel targets of SARS-CoV-2
Authors: Rosado-Olivieri E.A. , Razooky B. , Hoffmann H.-H. , De Santis R. , Rice C.M. , Brivanlou A.H 
Published: January 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the global COVID-19 pandemic and the lack of therapeutics hinders pandemic control1–2. Although lung disease is the primary clinical outcome in COVID-19 patients1–3, how SARS-CoV-2 induces tissue pathology in the lung remains elusive. Here we describe a high-throughput platform to generate tens of thousands of self-organizing, nearly identical, and genetically matched human lung buds derived from human pluripotent stem cells (hPSCs) cultured on micropatterned substrates. Strikingly,in vitro-derived human lung buds resemble fetal human lung tissue and displayin vivo-like proximo-distal coordination of alveolar and airway tissue differentiation whose 3D epithelial self-organization is directed by the levels of KGF. Single-cell transcriptomics unveiled the cellular identities of airway and alveolar tissue and the differentiation of WNThicycling alveolar stem cells, a human-specific lung cell type4. These synthetic human lung buds are susceptible to infection by SARS-CoV-2 and endemic coronaviruses and can be used to track cell type-dependent susceptibilities to infection, intercellular transmission and cytopathology in airway and alveolar tissue in individual lung buds. Interestingly, we detected an increased susceptibility to infection in alveolar cells and identified cycling alveolar stem cells as targets of SARS-CoV-2. We used this platform to test neutralizing antibodies isolated from convalescent plasma that efficiently blocked SARS-CoV-2 infection and intercellular transmission. Our platform offers unlimited, rapid and scalable access to disease-relevant lung tissue that recapitulate key hallmarks of human lung development and can be used to track SARS-CoV-2 infection and identify candidate therapeutics for COVID-19.
Activation of GSDME compensates for GSDMD deficiency in a mouse model of NLRP3 inflammasomopathy
Authors: Wang Chun , Yang Tong , Xiao Jianqiu , Xu Canxin , Alippe Yael , Sun Kai , Kanneganti Thirumala-Devi , Monahan Joseph B. , Abu-Amer Yousef , Lieberman Judy , Mbalaviele Gabriel 
Published: January 2021

AbstractThe D301N NLRP3 mutation in mice (D303N in humans) causes severe multi-organ damage and early death driven by the constitutively activated NLRP3 (NLRP3ca) inflammasome. Triggered inflammasomes activate caspase-1 to process IL-1 family cytokines and gasdermin D (GSDMD), generating N-terminal fragments, which oligomerize within the plasma membrane to form pores, which cause inflammatory cell death (pyroptosis) and through which IL-1β and IL-18 are secreted. GSDMD activation is central to disease symptoms since spontaneous inflammation inNlrp3ca;Gsdmd-/-mice is negligible. Unexpectedly, whenNlrp3ca;Gsdmd-/-mice were challenged with LPS or TNF-α, they secreted high amounts of IL-1β and IL-18, suggesting an alternative GSDMD-independent inflammatory pathway. Here we show that GSDMD deficient macrophages subjected to inflammatory stimuli activate caspase-8, -3 and GSDME-dependent cytokine release and pyroptosis. Caspase-8, -3 and GSDME also activated pyroptosis when NLRP3 was stimulated in caspase-1 deficient macrophages. Thus, a salvage caspase-8, -3-GSDME inflammatory pathway is activated following NLRP3 activation when the canonical NLRP3-caspase-1-GSDMD is blocked. Surprisingly, the active metabolite of the GSDMD-inhibitor disulfiram, inhibited not only GSDMD but also GSDME-mediated inflammationin vitroand suppressed severe inflammatory disease symptoms inNlrp3camice, a model for severe neonatal multisystem inflammatory disease. Although disulfiram did not directly inhibit GSDME, it suppressed inflammasome activation in GSDMD-deficient cells. Thus, the combination of inflammatory signals and NLRP3caoverwhelmed the protection provided by GSDMD deficiency, rewiring signaling cascades through caspase-8, -3 and GSDME to propagate inflammation. This functional redundancy suggests that concomitant inhibition of GSDMD and GSDME may be necessary to suppress disease in inflammasomopathy patients.
Geographic search, potential absorptive capacity and radical innovation performance: the moderating role of collaborative network
Authors: Zhang Feng , Zhu Lei , Lyu Chongchong 
Published: January 2021

PurposeA firm's geographic boundaries represent an important demarcation line when searching for new knowledge. Prior research on geographic search has generated conflicting results concerning its influence on firm innovation outcomes. The purpose of this study is to fill the gap by examining how and under which conditions geographic search affects firm radical innovation performance.Design/methodology/approachThis study hypothesizes a positive association between a firm's geographic search and radical innovation performance, which is mediated by potential absorptive capacity (PAC). It further proposes that the influence of geographic search on PAC will be moderated by a firm's collaborative network. Drawing on a random sample of 286 Chinese manufacturing firms, the theoretical model is tested.FindingsThe study's results show a positive relationship between geographic search and radical innovation performance, which is partially mediated by PAC. Moreover, attributes of collaborative networks (i.e. diverse location of and strong relational ties with partners) are observed to enhance the positive effect of geographic search on PAC.Originality/valueThis paper advances the understanding of how and when firms can better capture the benefits of geographic search in the development of radical innovation.