bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired spatial learning and suppression of sharp wave ripples by cholinergic activation at the goal location
Authors: Jarzebowski Przemyslaw , Tang Clara S. , Paulsen Ole , Hay Y. Audrey
Published: May 2020

The hippocampus plays a central role in long-term memory formation, and different hippocampal network states are thought to have different functions in this process. These network states are controlled by neuromodulatory inputs, including the cholinergic input from the medial septum. Here, we used optogenetic stimulation of septal cholinergic neurons to understand how cholinergic activity affects different stages of spatial memory formation in a reward-based navigation task in mice. We found that optogenetic stimulation of septal cholinergic neurons (1) impaired memory formation when activated at goal location but not during navigation; (2) reduced sharp wave-ripple (SWR) incidence at goal location; and (3) reduced SWR incidence and enhanced the-ta-gamma oscillations during sleep. These results underscore the importance of appropriate timing of cholinergic input in long-term memory formation, which might help explain the limited success of cholinesterase inhibitor drugs in treating memory impairment in Alzheimer’s disease.
Soil microbial diversity and litter decomposition increase along a forest recovery gradient in tropical montane forests of Malaysian Borneo
Authors: Sniegocki Renee , Moon Jessica B. , Rutrough Abigail L. , Gireneus Jude , Seelan Jaya Seelan S. , Weindorf David C. , Farmer Michael C. , Naithani Kusum
Published: May 2020

Logging and forest conversion are occurring at alarming rates in the tropical forests. These disturbances alter soil chemistry and microbial diversity, and disrupt carbon cycling through shifts in litter decomposition. Direct links between microbial diversity and soil properties such as pH are well established; however, the indirect impacts of logging and forest conversion on microbial diversity and litter decomposition are poorly understood. We investigated how soil properties and soil functions change across a forest recovery gradient in the tropical montane forests of Malaysian Borneo. We used surface (top 5 cm) soil to assess soil physicochemical properties, next-generation DNA sequencing to assess soil microbial diversity, and standardized litterbags to assess litter decomposition and stabilization. Our results show that soils of the older forests harbored significantly greater microbial diversity, decomposed litter faster, and stabilized greater amounts of litter than soils of the younger forests and converted sites. These results suggest that logging and forest conversion significantly affect soil microbial diversity and can have lasting effects on carbon cycling in tropical montane forests.
Neuronal and glial 3D chromatin architecture illustrates cellular etiology of brain disorders
Authors: Hu Benxia , Won Hyejung , Mah Won , Park Royce , Kassim Bibi , Spiess Keeley , Kozlenkov Alexey , Crowley Cheynna A , Pochareddy Sirisha ,   PsychENCODE consortium, Li Yun , Dracheva Stella , Sestan Nenad , Akbarian Schahram , Geschwind Daniel H.
Published: May 2020

Cellular heterogeneity in the human brain obscures the identification of robust cellular regulatory networks. Here we integrated genome-wide chromosome conformation in purified neurons and glia with transcriptomic and enhancer profiles to build the gene regulatory landscape of two major cell classes in the human brain. Within glutamatergic and GABAergic neurons, we were able to link enhancers to their cognate genes via neuronal chromatin interaction profiles. These cell-type-specific regulatory landscapes were then leveraged to gain insight into the cellular etiology of several brain disorders. We found that Alzheimer’s disease (AD)-associated epigenetic dysregulation was linked to neurons and oligodendrocytes, whereas genetic risk factors for AD highlighted microglia as a central cell type, suggesting that different cell types may confer risk to the disease via different genetic mechanisms. Moreover, neuronal subtype-specific annotation of genetic risk factors for schizophrenia and bipolar disorder identified shared (parvalbumin-expressing interneurons) and distinct cellular etiology (upper layer neurons for bipolar and deeper layer projection neurons for schizophrenia) between these two closely related psychiatric illnesses. Collectively, these findings shed new light on cell-type-specific gene regulatory networks in brain disorders.
How are adversities during COVID-19 affecting mental health? Differential associations for worries and experiences and implications for policy
Authors: Wright Liam , Steptoe Andrew , Fancourt Daisy
Published: May 2020

Importance

Multiple data sources suggest that COVID-19 is having adverse effects on mental health. But it is vital to understand what is causing this: worries over potential adversities due to the pandemic, or the toll of experiencing adverse events.

Objective

To explore the time-varying longitudinal relationship between (i) worries about adversity, and (ii) experience of adversity, and both anxiety and depression and test the moderating role of socio-economic position.

Design

Longitudinal cohort study

Setting

Community study

Participants

A well-stratified sample of UK adults recruited into the UCL COVID -19 Social Study (a panel study collecting data weekly during the Covid-19 pandemic) via a combination of convenience and targeted recruitment. The sample was weighted to population proportions of gender, age, ethnicity, education and geographical location.

Exposures

Worries or experiences of adversities during the COVID-19 pandemic

Outcomes

Anxiety (GAD-7) and depression (PHQ-9)

Results

Data were analysed from 41,909 UK adults (weighted data: 51% female, aged 18-99) followed up across 6 weeks (178,430 observations). Using fixed effects regression was used to explore within-person variation over time, cumulative number of worries and experience of adversities were both related to higher levels of anxiety and depression. Number of worries were associated more with anxiety than depression, but number of experiences were equally related to anxiety and depression. Individuals of lower socio-economic position were more negatively affected psychologically by adverse experiences.

Conclusions & relevance

Measures over the first few weeks of lockdown in the UK appear to have been insufficient at reassuring people given we are still seeing clear associations with poor mental health both for cumulative worries and also for a range of specific worries relating to finance, access to essentials, personal safety and COVID-19. Interventions are required that both seek to prevent adverse events (e.g. redundancies) and that reassure individuals and support adaptive coping strategies.

Key points

Question

How do worries over potential adversities due to the COVID-19 pandemic, or the toll of experiencing adverse events affect mental health?

Findings

Cumulative number of worries and experience of adversities were both related to higher levels of anxiety and depression during COVID-19, especially amongst individuals of lower socio-economic position.

Meaning

During a pandemic, interventions are required that both seek to prevent adverse events (e.g. redundancies) and that reassure individuals and support adaptive coping strategies.
Semantic and geographical analysis of Covid-19 trials reveals a fragmented clinical research landscape likely to impair informativeness
Authors: Tini Giulia , Duso Bruno Achutti , Bellerba Federica , Corso Federica , Gandini Sara , Minucci Saverio , Pelicci Piergiuseppe , Mazzarella Luca
Published: May 2020

Background

The unprecedented impact of the Covid-19 pandemics on modern society has ignited a “gold rush” for effective treatment and diagnostic strategies, with a significant diversion of economical, scientific and human resources towards dedicated clinical research. We aimed to describe trends in this rapidly changing landscape to inform adequate resource allocation.

Methods

We developed informatic tools (Covid Trial Monitor) to analyze in real time growth rate, geographical distribution and characteristics of Covid-19 related trials. We defined structured semantic ontologies with controlled vocabularies to categorize trial interventions, study endpoints and study designs. Data and analyses are publicly available at https://bioinfo.ieo.it/shiny/app/CovidCT

Results

We observe a clear prevalence of monocentric trials with highly heterogeneous endpoints and a significant disconnect between geographic distribution and disease prevalence, implying that most countries would need to recruit unrealistic percentages of their total prevalent cases to fulfill enrolment.

Conclusions

This geographically and methodologically incoherent growth sheds doubts on the actual feasibility of locally reaching target sample sizes and the probability of most of these trials providing reliable and transferable result. We call for the harmonization of clinical trial design criteria for Covid19 and the increased use of larger master protocols incorporating elements of adaptive designs. Covid Trial Monitor identifies critical issues in current Covid19-related clinical research and represents a useful resource for researchers and policymakers to improve the quality and efficiency of related trials
Testing, tracing and isolation in compartmental models
Authors: Sturniolo Simone , Waites William , Colbourn Tim , Manheim David , Panovska-Griffiths Jasmina
Published: May 2020

Existing compartmental mathematical modelling methods for epidemics, such as SEIR models, cannot accurately represent effects of contact tracing. This makes them inappropriate for evaluating testing and contact tracing strategies to contain an outbreak. An alternative used in practice is the application of agent- or individual-based models (ABM). However ABMs are complex, less well-understood and much more computationally expensive. This paper presents a new method for accurately including the effects of Testing, contact-Tracing and Isolation (TTI) strategies in standard compartmental models. We derive our method using a careful probabilistic argument to show how contact tracing at the individual level is reflected in aggregate on the population level. We show that the resultant SEIR-TTI model accurately approximates the behaviour of a mechanistic agent-based model at far less computational cost. The computational efficiency is such that it can be easily and cheaply used for exploratory modelling to quantify the required levels of testing and tracing, alone and with other interventions, to assist adaptive planning for managing disease outbreaks.

Author Summary

The importance of modeling to inform and support decision making is widely acknowledged. Understanding how to enhance contact tracing as part of the Testing-Tracing-Isolation (TTI) strategy for mitigation of COVID is a key public policy questions. Our work develops the SEIR-TTI model as an extension of the classic Susceptible, Exposed, Infected and Recovered (SEIR) model to include tracing of contacts of people exposed to and infectious with COVID-19. We use probabilistic argument to derive contact tracing rates within a compartmental model as aggregates of contact tracing at an individual level. Our adaptation is applicable across compartmental models for infectious diseases spread. We show that our novel SEIR-TTI model can accurately approximate the behaviour of mechanistic agent-based models at far less computational cost. The SEIR-TTI model represents an important addition to the theoretical methodology of modelling infectious disease spread and we anticipate that it will be immediately applicable to the management of the COVID-19 pandemic.
Changing travel patterns in China during the early stages of the COVID-19 pandemic
Authors: Gibbs Hamish , Liu Yang , Pearson Carl AB , Jarvis Christopher I , Grundy Chris , Quilty Billy J , Diamond Charlie ,   LSHTM CMMID COVID-19 working group, Eggo Rosalind M
Published: May 2020

Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.

One sentence summary:

Understanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.
CoV-AbDab: the Coronavirus Antibody Database
Authors: Raybould Matthew I. J. , Kovaltsuk Aleksandr , Marks Claire , Deane Charlotte M.
Published: May 2020

The emergence of a novel strain of betacoronavirus, SARS-CoV-2, has led to a pandemic that has been associated with hundreds of thousands of deaths. Research is ongoing around the world to create vaccines and therapies to minimise rates of disease spread and mortality. Crucial to these efforts are molecular characterisations of neutralising antibodies to SARS-CoV-2. Such antibodies would be valuable for measuring vaccine efficacy, diagnosing exposure, and developing effective biotherapeutics. Here, we describe our new database, CoV-AbDab, which already contains data on over 380 published/patented antibodies and nanobodies known to bind to at least one betacoronavirus. This database is the first consolidation of antibodies known to bind SARS-CoV-2 and other betacoronaviruses such as SARS-CoV-1 and MERS-CoV. We supply relevant metadata such as evidence of cross-neutralisation, antibody/nanobody origin, full variable domain sequence (where available) and germline assignments, epitope region, links to relevant PDB entries, homology models, and source literature. Our preliminary analysis exemplifies a spectrum of potential applications for the database, including identifying characteristic germline usage biases in receptor-binding domain antibodies and contextualising the diagnostic value of the SARS-CoV binding CDRH3s through comparison to over 500 million antibody sequences from SARS-CoV serologically naive individuals. Community submissions are invited to ensure CoV-AbDab is efficiently updated with the growing body of data analysing SARS-CoV-2. CoV-AbDab is freely available and downloadable on our website athttp://opig.stats.ox.ac.uk/webapps/coronavirus.
Viral manipulation of mechanoresponsive signaling disassembles processing bodies
Authors: Castle Elizabeth L. , Robinson Carolyn-Ann , Douglas Pauline , Rinker Kristina D. , Corcoran Jennifer A.
Published: May 2020

Processing bodies (PBs) are ribonucleoprotein granules that suppress cytokine mRNA translation that are targeted for disassembly by many viruses. Kaposi’s sarcoma-associated herpesvirus is the etiological agent of the inflammatory endothelial cancer, Kaposi’s sarcoma, and a PB-regulating virus. The virus encodes Kaposin B (KapB), which induces actin stress fibres (SFs) and cell spindling as well as PB disassembly. We now show that KapB-mediated PB disassembly requires actin rearrangements, RhoA effectors and the mechanoresponsive transcription activator, YAP. Moreover, ectopic expression of active YAP or exposure of ECs to mechanical forces caused PB disassembly in the absence of KapB and mechanoresponsive PB disassembly also required YAP. Using the viral protein KapB, we identified a new consequence of the exposure of cells to mechanical forces that alter actin dynamics and activate YAP, namely the disassembly of PBs.

Importance

For the first time, we demonstrate that processing bodies (PBs), cytoplasmic sites of RNA decay, are regulated by mechanical signaling events that alter actin dynamics and that this requires the mechanoresponsive transcription factor, YAP. Using the overexpression of a viral protein called KapB, known previously to mediate PB disassembly, we show that actin stress fibers (SFs) and the mechanoresponsive transcription factor, YAP, are required for PB loss. We also show that other established mechanical signals (shear stress or stiff extracellular matrix) that lead to the formation of SFs and activate YAP also cause PB disassembly. This is important because it means that KapB activates, from the inside out, a pathway that links cell shape to post-transcriptional gene regulation via cytoplasmic PBs.
Characterisation of ovine bone marrow-derived stromal cells (oBMSC) and evaluation of chondrogenically inducedmicro-pellets for cartilage tissue repairin vivo
Authors: Futrega K. , Music E. , Robey P.G. , Gronthos S. , Crawford R.W. , Saifzadeh S. , Klein T.J. , Doran M.R.
Published: May 2020

Background

Bone marrow stromal cells (BMSC) show promise in cartilage repair, and sheep are the most common large animal pre-clinical model. The objective of this study was to characterize ovine BMSC (oBMSC)in vitro, and to evaluate the capacity of chondrogenicmicro-pellets manufactured from oBMSC or ovine articular chondrocytes (oACh) to repair osteochondral defects in sheep.

Methods

oBMSC were characterised for surface marker expression using flow cytometry and evaluated for tri-lineage differentiation. oBMSCmicro-pellets were manufactured in a microwell platform, and chondrogenesis was compared at 2%, 5%, and 20% O2. The capacity of cartilagemicro-pellets manufactured from oBMSC or oACh to repair osteochondral defects in adult sheep was evaluated in an 8-week pilot study. Expanded oBMSC were positive for CD44 and CD146 and negative for CD45.

Results

The common adipogenic induction medium ingredient, 3-Isobutyl-1-methylxanthine (IBMX) was toxic to oBMSC, but adipogenesis could be restored by excluding IBMX from the medium. BMSC chondrogenesis was optimal in a 2% O2atmosphere.Micro-pellets formed from oBMSC or oACh appeared morphologically similar, but hypertrophic genes were elevated in oBMSCmicro-pellets. While oAChmicro-pellets formed cartilage-like repair tissue in sheep, oBMSCmicro-pellets did not.

Conclusion

The sensitivity of oBMSC to IBMX highlights species-species differences between oBMSC and hBMSC.Micro-pellets manufactured from oBMSC were not effective in repairing osteochondral defects, while oAChmicro-pellets enabled modest repair. While oBMSC can be driven to form cartilage-like tissue in vitro, their effective use in cartilage repair will require mitigation of hypertrophy.
Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey
Authors: Adebalı Ogün , Bırcan Aylin , Çırcı Defne , İşlek Burak , Kilinç Zeynep , Selçuk Berkay , Turhan Berk
Published: May 2020

COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find two of the seventeen sub-clusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.
Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation
Authors: Martin Erik W. , Thomasen F. Emil , Milkovic Nicole M. , Cuneo Matthew J. , Grace Christy R. , Nourse Amanda , Lindorff-Larsen Kresten , Mittag Tanja
Published: May 2020

Liquid-liquid phase separation underlies the membrane-less compartmentalization of cells. Intrinsically disordered low-complexity domains (LCDs) often mediate phase separation, but how their phase behavior is modulated by folded domains is incompletely understood. Here, we interrogate the interplay between folded and disordered domains of the RNA-binding protein hnRNPA1. The LCD of hnRNPA1 is sufficient for mediating phase separationin vitro. However, we show that the folded RRM domains and a folded solubility-tag modify the phase behavior, even in the absence of RNA. Notably, the presence of the folded domains reverses the salt dependence of the driving force for phase separation relative to the LCD alone. Small-angle X-ray scattering experiments and coarse-grained MD simulations show that the LCD interacts transiently with the RRMs and/or the solubility-tag in a salt-sensitive manner, providing a mechanistic explanation for the observed salt-dependent phase separation. These data point to two effects from the folded domains: (1) electrostatically mediated interactions that compact hnRNPA1 and contribute to phase separation, and (2) increased solubility at higher ionic strengths mediated by the folded domains. The interplay between disordered and folded domains can modify the dependence of phase behavior on solution conditions and can obscure signatures of physicochemical interactions underlying phase separation.

Graphical abstract

hnRNPA1 phase separation is highly salt sensitive.

Phase separation of the low-complexity domain (LCD) of hnRNPA1 increases with NaCl. In contrast, phase separation of full-length hnRNPA1 is saltsensitive. At low NaCl concentrations, electrostatic RRM-LCD interactions occur and can contribute positively to phase separation, but they are screened at high NaCl concentrations. The folded domains solubilize hnRNPA1 under these conditions and prevent phase separation.
TOR signaling modulates Cdk8-dependentGALgene expression inSaccharomyces cerevisiae
Authors: Hawe Nicole , Mestnikov Konstantin , Horvath Riley , Eji-Lasisi Mariam , Lam Cindy , Rohde John , Sadowski Ivan
Published: May 2020

Cdk8 of the RNA Polymerase II mediator complex regulates genes by phosphorylating sequence specific transcription factors. Despite conserved importance for eukaryotic transcriptional regulation, the signals regulating Cdk8 are unknown. Full induction of the yeastGALgenes requires phosphorylation of Gal4 by Cdk8, and we exploited this requirement for growth ofgal3yeast on galactose to identify mutants affecting Cdk8 activity. Several mutants from the screen produced defects in TOR signaling. A mutant designatedgalfour throttle (gft) 1,gft1, was identified as an allele ofhom3, encoding aspartokinase. Defects ingft1/hom3caused hypersensitivity to rapamycin, and constitutive nuclear localization of Gat1. Furthermore, mutations oftor1ortco89, encoding TORC1 components, also preventedGALexpression ingal3yeast, andtco89was determined to be allelic togft7. Disruption ofcdc55, encoding a subunit of PP2A regulated by TOR signaling, suppressed the effect ofgft1/hom3, gft7/tco89, andtor1mutations onGALexpression ingal3yeast, but not ofcdk8/srb10disruptions or Gal4 S699A mutation. Mutations ofgft1/hom3andtor1did not affect kinase activity of Cdk8in vitro, but caused loss of Gal4 phosphorylationin vivo. These observations demonstrate that TOR signaling regulatesGALinduction through the activity of PP2A/ Cdc55, and are consistent with the contention that Cdk8-dependent phosphorylation of Gal4 S699 is opposed by PP2A/ Cdc55 dephosphorylation. These results provide insight into how induction of transcription by a specific inducer can be modulated by global nutritional signals through regulation of Cdk8-dependent phosphorylation.
Direct and indirect effects of maternal, paternal, and offspring genotypes: Trio-GCTA
Authors: Eilertsen Espen Moen , Jami Eshim Shahid , McAdams Tom A. , Hannigan Laurie J. , Havdahl Alexandra S. , Magnus Per Minor , Evans David M. , Ystrom Eivind
Published: May 2020

Indirect genetic effects from relatives may result in misleading quantifications of heritability, but can also be of interest in their own right. In this paper we propose Trio-GCTA, a model for separating direct and indirect genetic effects when genome-wide single nucleotide polymorphism data have been collected from parent-offspring trios. The model is applicable to phenotypes obtained from any of the family members. We discuss appropriate parameter interpretations and apply the method to four exemplar phenotypes; offspring birth weight, offspring temperament, maternal relationship satisfaction, and paternal body-mass index, using real data from the Norwegian Mother, Father and Child Cohort Study (MoBa).
The Receptor Kinase BRI1 promotes cell proliferation in Arabidopsis by phosphorylation- mediated inhibition of the growth repressing peptidase DA1
Authors: Dong Hui , Smith Caroline , Prior Rachel , Carter Ross , Dumenil Jack , Saalbach Gerhard , McKenzie Neil , Bevan Michael
Published: May 2020

Brassinosteroids (BR) have centrally important functions in plant growth by promoting cell proliferation and cell expansion through phosphorylation-mediated regulatory cascades that are initiated by perception of BR by receptor-like kinases of the BRI1 family. These BR-mediated growth responses have been explained by transcriptional controls mediated by phosphorylation of BES1/BZR1 transcription factors. Here we link BRI1-mediated phosphorylation to another growth regulatory network that directly mediates protein stability. BRI1 and its co-receptor BAK1 phosphorylate and inhibit the activities of the growth repressor DA1 by promoting the formation of high molecular weight complexes. Phospho-mimic forms of DA1 are less active while phospho-dead mutants have increased growth-repressive activity, while their regulatory monoubiquitylation is unaffected. BR inhibition of DA1 activity maintains higher levels of DA1 substrates such as UBP15 that sustain the potential for cell proliferation during leaf growth. Reduced BR levels lead to activation of DA1 peptidase activity and a transition from cell proliferation to cell growth and differentiation. This dual monoubiquitylation-phosphorylation regulation supports the key role of BR levels in maintaining the proliferative potential of cells during organ growth.
Dengue and Zika virus infection are impaired by small molecule ER proteostasis regulator 147 in an ATF6-independent manner
Authors: Almasy Katherine M. , Davies Jonathan P. , Lisy Samantha M. , Tirgar Reyhaneh , Tran Sirena C. , Plate Lars
Published: May 2020

Flaviviruses, including Dengue and Zika, are widespread human pathogens, however, no broadly active therapeutics exist to fight infection. Here, we establish the recently discovered pharmacologic modulator of ER proteostasis147as an effective host-centered antiviral strategy. Compound147reduces infection by attenuating viral replication without causing toxicity in host cells.147is a preferential activator of the ATF6 pathway of the unfolded protein response, which requires targeting of cysteine residues primarily on protein disulfide isomerases (PDIs). We find that the antiviral activity of147is independent of ATF6 induction but does require modification of reactive thiols on protein targets. Targeting PDIs using RNAi and other PDI small molecule inhibitors was unable to recapitulate the antiviral effects, suggesting additional identified protein targets of147may mediate the activity. Importantly,147can impair infection of multiple strains of Dengue and Zika virus, indicating that it is suitable as a broad-spectrum antiviral agent.
Shifting carbon flux from non-transient starch to lipid allows oil accumulation in transgenic tobacco leaves
Authors: Chu Kevin L. , Jenkins Lauren M. , Bailey Sally R. , Kambhampati Shrikaar , Koley Somnath , Foley Kevin , Arp Jennifer J. , Czymmek Kirk J. , Bates Philip D. , Allen Doug K.
Published: May 2020

Plant leaf biomass is composed predominantly of carbohydrate and protein with less than 5% dry weight allocated to lipid and less than 1% of total lipid in the form of triacylglycerols (TAGs). The combined overexpression of multiple genes involved in different aspects of TAG synthesis and stabilization can result in TAG accumulation to over 30% dry weight in tobacco leaves, presumably requiring many metabolic adjustments within plant cells. The metabolic consequences to the combined source and sink capacities of high oil accumulating transgenic tobacco leaves compared to wild-type were inspected across development and photoperiod by utilizing foliar biomass components and13CO2flux through central carbon intermediates. Lipid biosynthesis was investigated through assessment of acyl-acyl carrier protein (ACP) pools using a recently derived quantification method that was extended to accommodate isotopic labeling. Lipids accumulated stepwise over plant development in the high-oil leaves, with13CO2-labeling studies confirming increased carbon flux to lipids. The large increase in lipid content was concurrent with a decrease in foliar starch, with limited contribution from non-sucrose soluble sugars, indicating a redirection of carbon from starch to lipids. Starch accumulated non-transiently with plant age in wild-type leaves, suggesting an inherent capacity for a developmentally-regulated carbon sink in tobacco leaves that may have enabled the programmed altered carbon partitioning to lipids in transgenics. These studies provide insight into the metabolic plasticity of dual source-sink leaves over development and may in part explain recent successful leaf lipid engineering efforts in tobacco.

One sentence summary

Engineering high oil accumulation in tobacco leaves is enabled by inherent source-sink plasticity associated with non-transient foliar starch accumulation over development.
Chitosan inhibits septin-mediated plant infection by the rice blast fungusMagnaporthe oryzaein a Protein Kinase C and Nox1 NADPH oxidase-dependent manner
Authors: Lopez-Moya Federico , Martin-Urdiroz Magdalena , Oses-Ruiz Miriam , Fricker Mark D. , Littlejohn George R. , Lopez-Llorca Luis V. , Talbot Nicholas J.
Published: May 2020

Chitosan is a partially deacetylated linear polysaccharide composed of β-1,4-linked units of D-glucosamine and N-acetyl glucosamine. As well as acting as a structural component of fungal cell walls, chitosan can be applied as a potent antifungal agent. However, the mode-of-action of chitosan in fungal pathogens is poorly understood.

Here, we report that chitosan is effective for control of rice blast disease. Chitosan application impairs growth of the blast fungusMagnaporthe oryzaeand has a pronounced effect on appressorium-mediated plant infection. Chitosan inhibits septin-mediated F-actin re-modelling at the appressorium pore, thereby preventing re-polarisation of the infection cell and rice leaf cuticle penetration.

We found that chitosan causes plasma membrane permeabilization ofM. oryzaeand affects NADPH oxidase-dependent synthesis of reactive oxygen species, essential for septin ring formation and fungal pathogenicity. Our data further show that the toxicity of chitosan toM. oryzaerequires the protein kinase C-dependent cell wall integrity pathway and the Nox1 NADPH oxidase. A conditionally lethal, analogue (PP1)-sensitive mutant of Pkc1 is partially remediated for growth in the presence of chitosan and PP1, while Δnox1mutants increase their glucan/chitin cell wall ratio, rendering them resistant to chitosan.

Taken together, our data show that chitosan is a potent fungicide for control of the rice blast fungus which involves the cell wall integrity pathway, disrupts plasma membrane and inhibits septin-mediated plant infection.
Structure and Dynamic Basis of Molecular Recognition Between Acyltransferase and Carrier Protein inE. coliFatty Acid Synthesis
Authors: Misson Laetitia E. , Mindrebo Jeffrey T. , Davis Tony D. , Patel Ashay , McCammon J. Andrew , Noel Joseph P. , Burkart Michael D.
Published: May 2020

Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units inde novofatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use theEscherichia coliFAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the first x-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.

Significance Statement

The essential role of acyltransferases (ATs) in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways, namely the selection and loading of starter and extender units onto acyl carrier proteins (ACPs), relies on catalytically productive ACP-AT interactions. Here, we describe and interrogate the first structure of a type II FAS malonyl-CoA:ACP-transacylase (MAT) in covalent complex with its cognate ACP. We combine structural, mutational, crosslinking and kinetic data with molecular dynamics simulations to describe a highly flexible and robust protein-protein interface, substrate-induced active site reorganization, and key subdomain motions that likely govern FAS function. These findings strengthen a mechanistic understanding of molecular recognitions between ACPs and partner enzymes and provide new insights for engineering AT-dependent biosynthetic pathways.
Predictors of COVID-19 incidence, mortality, and epidemic growth rate at the country level
Authors: Leung Nicole Y. , Bulterys Michelle A. , Bulterys Philip L.
Published: May 2020

Background. The burden of the coronavirus disease 2019 (COVID-19) pandemic has been geographically disproportionate. Certain weather factors and population characteristics are thought to drive transmission, but studies examining these factors are limited. We aimed to identify weather, sociodemographic, and geographic drivers of COVID-19 at the global scale using a comprehensive collection of country/territory-level data, and to use discovered associations to estimate the timing of community transmission.

Methods. We examined COVID-19 cases and deaths reported up to May 2, 2020 across 205 countries and territories in relation to weather data collected from capital cities for the eight weeks prior to and four weeks after the date of the first reported case, as well as country/territory-level population, geographic, and planetary data. We performed univariable and multivariable regression modeling and odds ratio analyses to investigate associations with COVID-19 cases, deaths, and epidemic growth rate. We also conducted maximum likelihood analysis to estimate the timing of initial community spread.

Findings. Lower temperature (p<0.0001), lower humidity (p=0.006), higher altitude (p=0.0080), higher percentage of urban population (p<0.0001), increased air travelers (p=0.00019), and higher prevalence of obesity (p<0.0001) were strong independent predictors of national COVID-19 incidence, mortality, and epidemic growth rate. Temperature at 5-7 weeks before the first reported case best predicted epidemic growth, suggesting that significant community transmission was occurring on average 1-2 months prior to detection.

Interpretation. The results of this ecologic analysis demonstrate that global COVID-19 burden and timing of country-level epidemic growth can be predicted by weather and population factors. In particular, we find that cool, dry, and higher altitude environments, as well as more urban and obese populations, may be conducive to more rapid epidemic spread.

Funding sources: None.
Effects of Different Strategies for Exploiting Genomic Selection in Perennial Ryegrass Breeding Programs
Authors: Esfandyari Hadi , Fè Dario , Tessema Biructawit Bekele , Janss Lucas L. , Jensen Just
Published: May 2020

Genomic selection (GS) is a potential pathway to accelerate genetic gain for perennial ryegrass(Lolium perenneL.). The main objectives of the present study were to investigate the level of genetic gain and accuracy by applying GS in commercial perennial ryegrass breeding programs. Different scenarios were compared to a conventional breeding program. Simulated scenarios differed in the method of selection and structure of the breeding program. Two scenarios (Phen-Y12 and Phen) for phenotypic selection and three scenarios (GS-Y12, GS and GS-SP) were considered for genomic breeding schemes. All breeding schemes were simulated for 25 cycles. The amount of genetic gain achieved was different across scenarios. Compared to phenotypic scenarios, GS scenarios resulted in a significantly larger genetic gain for the simulated traits. This was mainly due to more efficient selection of plots and single plants based on GEBV. Also, GS allows for reduction in cycle time, which led to at least a doubling or a trebling of genetic gain compared to the traditional program. Reduction in additive genetic variance levels were higher with GS scenarios than with phenotypic selection. The results demonstrated that implementation of GS in ryegrass breeding is possible and presents an opportunity to make very significant improvements in genetic gains.
The role of incoherent feedforward circuits in regulating precision of event timing
Authors: Dey Supravat , Kannoly Sherin , Bokes Pavol , Dennehy John J , Singh Abhyudai
Published: May 2020

Triggering of cellular events often relies on the level of a key gene product crossing a critical threshold. Achieving precision in event timing in spite of noisy gene expression facilitates high-fidelity functioning of diverse processes from biomolecular clocks, apoptosis and cellular differentiation. Here we investigate the role of an incoherent feedforward circuit in regulating the time taken by a bacterial virus (bacteriophage lambda) to lyse an infectedEscherichia colicell. Lysis timing is the result of expression and accumulation of a single lambda protein (holin) in theE. colicell membrane up to a critical threshold level, which triggers the formation of membrane lesions. This easily visualized process provides a simple model system for characterizing event-timing stochasticity in single cells. Intriguingly, lambda’s lytic pathway synthesizes two functionally opposite proteins: holin and antiholin from the same mRNA in a 2:1 ratio. Antiholin sequesters holin and inhibits the formation of lethal membrane lesions, thus creating an incoherent feedforward circuit. We develop and analyze a stochastic model for this feedforward circuit that considers correlated bursty expression of holin/antiholin, and their concentrations are diluted from cellular growth. Interestingly, our analysis shows the noise in timing is minimized when both proteins are expressed at an optimal ratio, hence revealing an important regulatory role for antiholin. These results are in agreement with single cell data, where removal of antiholin results in enhanced stochasticity in lysis timing.
Ramifications of the diverse mRNA patterns inAcanthamoeba royreba
Authors: Tyndall Richard , Ali Ibne , Newsome Anthony
Published: May 2020

Free-living amoebae are distributed worldwide and can be found in a variety of environments. While most Acanthamoebae have been isolated from soil and water,A. royrebaandA. culbertsoniwere isolated from mammalian cell cultures.A. royreba’sisolation from placental and tumoral tissue, its unusual ability to grow in mammalian cell culture media at 35°C, and the presence of a primitive centriole, prompted us to investigate the potential for mammalian information inA. royreba.While some soil amoeba contain small amounts of fungal and bacterial information, presumably from the microbes they phagocytosed, the informational content ofA. royreba,in some instances, was very different with > 70% of the mRNA being non-amoebic. Here we show that the proteins and mRNA content associated withA. royrebaare extremely diverse and represent multiple Kingdoms, Orders, Phyla, and Genera from around the globe. The information inA. royreba,such as placental proteins from numerous mammals, the preponderance of non-amoebic mRNA, and its ability to tolerate harsh environments including Megarad irradiation, leads to a discussion regarding the possible role of this amoebae as an immunological gatekeeper protecting fetal or malignant tissue from destruction and its potential as a vehicle for panspermia.
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection
Authors: Minervina Anastasia A. , Komech Ekaterina A. , Titov Aleksei , Koraichi Meriem Bensouda , Rosati Elisa , Mamedov Ilgar Z. , Franke Andre , Efimov Grigory A. , Chudakov Dmitriy M. , Mora Thierry , Walczak Aleksandra M. , Lebedev Yuri B. , Pogorelyy Mikhail V.
Published: May 2020

COVID-19 is a global pandemic caused by the SARS-CoV-2 coronavirus. T cells play a key role in the adaptive antiviral immune response by killing infected cells and facilitating the selection of virus-specific antibodies. However neither the dynamics and cross-reactivity of the SARS-CoV-2-specific T cell response nor the diversity of resulting immune memory are well understood. In this study we use longitudinal high-throughput T cell receptor (TCR) sequencing to track changes in the T cell repertoire following two mild cases of COVID-19. In both donors we identified CD4+ and CD8+ T cell clones with transient clonal expansion after infection. The antigen specificity of CD8+ TCR sequences to SARS-CoV-2 epitopes was confirmed by both MHC tetramer binding and presence in large database of SARS-CoV-2 epitope-specific TCRs. We describe characteristic motifs in TCR sequences of COVID-19-reactive clones and show preferential occurence of these motifs in publicly available large dataset of repertoires from COVID-19 patients. We show that in both donors the majority of infection-reactive clonotypes acquire memory phenotypes. Certain T cell clones were detected in the memory fraction at the pre-infection timepoint, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2.
Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells
Authors: Ulianov Sergey V. , Velichko Artem K. , Magnitov Mikhail D. , Luzhin Artem V. , Golov Arkadiy K. , Ovsyannikova Natalia , Kireev Igor I. , Tyakht Alexander V. , Gavrilov Alexey A. , Kantidze Omar L. , Razin Sergey V.
Published: May 2020

Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome nanodomains and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, but increased further mixing of the chromatin compartments and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.
Repurposing of Miglustat to inhibit the coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2
Authors: Rajasekharan Sreejith , Bonotto Rafaela Milan , Kazungu Yvette , Alves Lais Nascimento , Poggianella Monica , Orellana Pamela Martinez , Skoko Natasa , Polez Sulena , Marcello Alessandro
Published: May 2020

Repurposing clinically available drugs to treat the new coronavirus disease COVID-19 is an urgent need in these early stages of the SARS-CoV-2 pandemic, when very few treatment options are available. The iminosugar Miglustat is a well-characterized drug for the treatment of rare genetic lysosome storage diseases such as Gaucher and Niemann-Pick type C, and has also been described to be active against a variety of enveloped viruses. The activity of Miglustat is here demonstrated for SARS-CoV-2 at concentrations achievable in the plasma by current clinical regimens without cytotoxicity. The drug acts at the post-entry level and leads to a marked decrease of viral proteins and release of infectious virus. The mechanism resides in the inhibitory activity towards α-glucosidases that are involved in early stages of glycoprotein N-linked oligosaccharide processing in the endoplasmic reticulum, leading to a marked decrease of the viral Spike protein. The wealth of available data on the clinical use of Miglustat for the treatment of lysosomal storage disorders and the antiviral properties against SARS-CoV-2 make it an ideal candidate for drug repurposing.
Age-related changes in the motor planning strategy slow down motor initiation in elderly adults
Authors: Frolov Nikita S. , Pitsik Elena N. , Maksimenko Vladimir A. , Grubov Vadim V. , Kiselev Anton R. , Wang Zhen , Hramov Alexander E.
Published: May 2020

Age-related changes in the human brain functioning crucially affect the motor system, causing increased reaction time, low ability to control and execute movements, difficulties in learning new motor skills. The lifestyle and lowered daily activity of elderly adults, along with the deficit of motor and cognitive brain functions, might lead to the developed ambidexterity, i.e. the loss of dominant limb advances. Despite the broad knowledge about the changes in cortical activity directly related to the motor execution, less is known about age-related differences in the motor initiation phase. We hypothesize that the latter strongly influences the behavioral characteristics, such as reaction time, the accuracy of motor performance, etc. Here, we compare the neuronal processes underlying the motor planning of fine motor tasks between elderly and young subjects. We demonstrate that aging significantly reduces the speed of motor initiation in the dominant hand task due to the different motor planning strategies employed by elderly and young adults. Based on the results of the whole-scalp electroencephalography (EEG) analysis, we suggest that young adults tend to use the efficient and fast mechanism of motor working memory. In contrast, elderly adults involve a more demanding sensorimotor integration process similar to the non-dominant hand task.