bluuebunny/crossref_metadata_2025 huggingface dataset:
Polyelectrolyte brush bilayer under shear at linear and nonlinear response regimes: A combination of the density functional theory framework and the scaling theory
Authors: Edwards Mike J.
Published: May 2021

The density functional theory framework and the scaling theory are employed to approach the problem of the Polyelectrolyte brush bilayer under shear. It turns out that, the system at shear rates larger than a critical shear rate undergo a global restructuring during which chains stretch in the shear direction. In the absence of the electrostatic interactions as well as the hydrodynamic interactions, this global restructuring causes a sublinear scaling of the shear stress with the shear rate which makes the shear thinning effect. Nevertheless, in the presence of the hydrodynamic interactions, not only there is no sublinear regime but also a weak superlinear regime which makes a weak shear thickening effect. In the presence of the electrostatic interactions, the stress tensor components change by their second Virial coefficients, however, their shear rate power law are untouched. Nonetheless, the kinetic friction coefficient is independent of the electrostatic interactions. This suggests that the lubrication is not very much different than the neutral bilayers and the electrostatic interactions do not change that. The results of this study offers that maybe nature uses another mechanism to reduce friction coefficient in synovial joint and other biological systems.

SIGNIFICANCE

The significance of this study is that it strongly criticizes the theoretical approach to the same system which is already published (T. Kreer,Soft Matter,12, 3479 (2016)). Moreover, the results of this study may help our understanding from Biological systems and optimization of artificial synovial joint which is the core of this study.
The cellular architecture of microvessels, pericytes and neuronal cell types in organizing regional brain energy homeostasis in mice
Authors: Wu Yuan-ting , Bennett Hannah C. , Chon Uree , Vanselow Daniel J. , Zhang Qingguang , Muñoz-Castañeda Rodrigo , Cheng Keith C. , Osten Pavel , Drew Patrick J. , Kim Yongsoo
Published: May 2021

Cerebrovasculature and its mural cells must meet dynamic energy demands of different neuronal cell types across the brain, but their spatial relationship is largely unknown. Here, we apply brain-wide mapping methods to create a comprehensive cellular-resolution resource comprising the distribution of and quantitative relationship between cerebrovasculature, pericytes, and glutamatergic and GABAergic neurons, including neuronal nitric oxide synthase-positive (nNOS+) neurons and their subtypes, as well as simulation-ready vascular tracing data in mice. We discover strikingly high densities of vasculature and pericytes with high blood perfusion in primary motor-sensory cortices compared to association cortices that show significant positive and negative correlation with parvalbumin+ and nNOS+ neurons, respectively. Thalamo-striatal areas linked to primary motor-sensory cortices also contain high densities of vasculature and pericytes compared to association areas. Collectively, our results unveil a finely tuned spatial relationship between cerebrovascular network and neuronal cell composition in meeting regional energy needs of the brain.
Network-based integration of epigenetic landscapes unveils molecular programs underlying human T follicular helper cell differentiation
Authors: Mahajan Vinay S , Rahman Syed A , Viswanadham Vinayak V , Yuen Grace J , Sun Na , Mattoo Hamid , Pillai Shiv S , Das Jishnu
Published: May 2021

T follicular helper (Tfh) cells play a critical role in T-dependent humoral immune responses. While genetic programs controlling Tfh cell differentiation have been extensively studied using murine models, studies in humans have been hampered by the lack of a robust in vitro differentiation system for Tfh cells. We characterized epigenomic landscapes across stages of Tfh cell differentiation in a healthy human tonsil using ATAC-Seq and CUT&RUN for selected histone modifications. We combined these epigenomic datasets and integrated them with the reference human protein interactome using a novel network propagation approach. Our approach uncovered subnetworks integral to Tfh cell differentiation. These subnetworks captured known Tfh cell drivers to a greater extent than conventional gene-centric analyses would, and also revealed novel modules that may be required for Tfh cell differentiation. We find that human Tfh cell subnetworks are functionally associated with specific immune signaling cascades including cytokine receptor driven pathways. Analyses of transcriptomic data revealed that in addition to these immune pathways being significantly dysregulated in severe COVID-19, the corresponding Tfh cell subnetworks are also transcriptionally perturbed to a similar extent. This provides a molecular mechanistic basis for the previously observed impaired Tfh cell differentiation and loss of germinal centers in severe COVID-19.
Predicting Moisture Content During Maize Nixtamalization Using Machine Learning with NIR Spectroscopy
Authors: Burns Michael J. , Renk Jonathan S. , Eickholt David P. , Gilbert Amanda M. , Hattery Travis J. , Holmes Mark , Anderson Nickolas , Waters Amanda J. , Kalambur Sathya , Flint-Garcia Sherry A. , Yandeau-Nelson Marna D. , Annor George A. , Hirsch Candice N.
Published: May 2021

Lack of high throughput phenotyping systems for determining moisture content during the maize nixtamalization cooking process has led to difficulty in breeding for this trait. This study provides a high throughput, quantitative measure of kernel moisture content during nixtamalization based on NIR scanning of uncooked maize kernels. Machine learning was utilized to develop models based on the combination of NIR spectra and moisture content determined from a scaled-down benchtop cook method. A linear support vector machine (SVM) model with a Spearman’s rank correlation coefficient of 0.852 between wet lab and predicted values was developed from 100 diverse temperate genotypes grown in replicate across two environments. This model was applied to NIR data from 501 diverse temperate genotypes grown in replicate in five environments. Analysis of variance revealed environment explained the highest percent of the variation (51.5%), followed by genotype (15.6%) and genotype-by-environment interaction (11.2%). A genome-wide association study identified 26 significant loci across five environments that explained between 5.04% and 16.01% (average = 10.41%). However, genome-wide markers explained 10.54% to 45.99% (average = 31.68%) of the variation, indicating the genetic architecture of this trait is likely complex and controlled by many loci of small effect. This study provides a high-throughput method to evaluate moisture content during nixtamalization that is feasible at the scale of a breeding program and provides important information about the factors contributing to variation of this trait for breeders and food companies to make future strategies to improve this important processing trait.

Key Message

Moisture content during nixtamalization can be accurately predicted from NIR spectroscopy when coupled with a support vector machine (SVM) model, is strongly modulated by the environment, and has a complex genetic architecture.
In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
Authors: Jin Minjun , Tavella Franco , Wang Shiyuan , Yang Qiong
Published: May 2021

Cells control the properties of the cytoplasm to ensure the proper functioning of biochemical processes. Recent studies showed that the density of the cytoplasm varies in both physiological and pathological states of cells undergoing growth, division, differentiation, apoptosis, senescence, and metabolic starvation. Little is known about how cellular processes cope with these cytoplasmic variations. Here we study how a cell cycle oscillator comprising cyclin -dependent kinase (CDK1) responds to cytoplasmic density changes by systematically diluting or concentrating a cycling Xenopus egg cytoplasm in cell-like microfluidic droplets. We found that the cell cycle maintains robust oscillations over a wide range of deviations from the endogenous density by as low as 0.2x to more than 1.22x. A further dilution or concentration from these values will arrest the system in a low or high steady-state of CDK1 activity, respectively. Interestingly, diluting a concentrated arrested cytoplasm recovers its oscillatory behavior but requires a significantly lower concentration than 1.22x. Thus, the cell cycle switches reversibly between oscillatory and stable steady states at distinct thresholds depending on the direction of density tuning, forming a hysteresis loop. We recapitulated these observations by a mathematical model. The model predicted that Wee1 and Cdc25 positive feedback do not contribute to the observed robustness, confirmed by experiments. Nevertheless, modulating these feedback strengths and cytoplasmic density changes the total number of cycles, revealing a new role of Wee1 and Cdc25 in controlling the cycle number of early embryonic extracts. Our system can be applied to study how cytoplasmic density affects other cellular processes.
Cross-species identification of cancer-resistance associated genes uncovers their relevance to human cancer risk
Authors: Nair Nishanth Ulhas , Cheng Kuoyuan , Naddaf Lamis , Sharon Elad , Pal Lipika R. , Rajagopal Padma S. , Unterman Irene , Aldape Kenneth , Hannenhalli Sridhar , Day Chi-Ping , Tabach Yuval , Ruppin Eytan
Published: May 2021

Cancer is an evolutionarily conserved disease that occurs in a wide variety of species. We applied a comparative genomics approach to systematically characterize the genes whose conservation levels significantly correlates positively (PC) or negatively (NC) with a broad spectrum of cancer-resistance estimates, computed across almost 200 vertebrate species. PC genes are enriched in pathways relevant to tumor suppression including cell cycle, DNA repair, and immune response, while NC genes are enriched with a host of metabolic pathways. The conservation levels of the PC and NC genes in a species serve to build the first genomics-based predictor of its cancer resistance score. We find that PC genes are less tolerant to loss of function (LoF) mutations, are enriched in cancer driver genes and are associated with germline mutations that increase human cancer risk. Furthermore, their expression levels are associated with lifetime cancer risk across human tissues. Finally, their knockout in mice results in increased cancer incidence. In sum, we find that many genes associated with cancer resistance across species are implicated in human cancers, pointing to several additional candidate genes that may have a functional role in human cancer.
Efficacy Estimates for Various COVID-19 Vaccines: What we Know from the Literature and Reports
Authors: Shapiro Julia , Dean Natalie E. , Madewell Zachary J. , Yang Yang , Halloran M.Elizabeth , Longini Ira
Published: May 2021

In this report, we provide summary estimates, from publications and reports, of vaccine efficacy (VE) for the COVID-19 vaccines that are being rolled out on a global scale. We find that, on average, the efficacy against any disease with infection is 85% (95% CI: 71 - 93%) after a fully course of vaccination. The VE against severe disease, hospitalization or death averages close to 100%. The average VE against infection, regardless of symptoms, is 84% (95% CI: 70 - 91%). We also find that the average VE against transmission to others for infected vaccinated people is 48% (95% CI: 45 - 52%). Finally, we prove summary estimates of the VE against any disease with infection for some of the variants of concern (VOC). The average VE for the VOCγ(P1) is 61% (95% CI: 43 - 73%). The average VE for the VOCα(B.1.1.7),β(B.1.351), andδ(B.1.617.2) after dose 1 are 48% (95% CI: 44 - 51%), 35% (95% CI: -11 - 62%), and 33% (95% CI: 21 - 43%), respectively. The average VE for the VOCα(B.1.1.7),β(B.1.351), andδ(B.1.617.2) after dose 2 are 85% (95% CI: 25 - 97%), 57% (95% CI: 14 - 78%), and 78% (95% CI: 28 - 93%), respectively.
Early Detection of COVID-19 Outbreaks Using Human Mobility Data
Authors: Guan Grace , Dery Yotam , Yechezkel Matan , Ben-Gal Irad , Yamin Dan , Brandeau Margaret L.
Published: May 2021

Background

Contact mixing plays a key role in the spread of COVID-19. Thus, mobility restrictions of varying degrees up to and including nationwide lockdowns have been implemented in over 200 countries. To appropriately target the timing, location, and severity of measures intended to encourage social distancing at a country level, it is essential to predict when and where outbreaks will occur, and how widespread they will be.

Methods

We analyze aggregated, anonymized health data and cell phone mobility data from Israel. We develop predictive models for daily new cases and the test positivity rate over the next 7 days for different geographic regions in Israel. We evaluate model goodness of fit using root mean squared error (RMSE). We use these predictions in a five-tier categorization scheme to predict the severity of COVID-19 in each region over the next week. We measure magnitude accuracy (MA), the extent to which the correct severity tier is predicted.

Results

Models using mobility data outperformed models that did not use mobility data, reducing RMSE by 17.3% when predicting new cases and by 10.2% when predicting the test positivity rate. The best set of predictors for new cases consisted of 1-day lag of past 7-day average new cases, along with a measure of internal movement within a region. The best set of predictors for the test positivity rate consisted of 3-days lag of past 7-day average test positivity rate, along with the same measure of internal movement. Using these predictors, RMSE was 4.812 cases per 100,000 people when predicting new cases and 0.79% when predicting the test positivity rate. MA in predicting new cases was 0.775, and accuracy of prediction to within one tier was 1.0. MA in predicting the test positivity rate was 0.820, and accuracy to within one tier was 0.998.

Conclusions

Using anonymized, macro-level data human mobility data along with health data aids predictions of when and where COVID-19 outbreaks are likely to occur. Our method provides a useful tool for government decision makers, particularly in the post-vaccination era, when focused interventions are needed to contain COVID-19 outbreaks while mitigating the collateral damage of more global restrictions.
Co-designing an online COmmunity suPporting familiEs after Sudden Cardiac Death (COPE-SCD) in the young
Authors: Yeates Laura , Gardner Karen , Do Judy , van den Heuvel Lieke , Fleming Gabrielle , Semsarian Christopher , McEwen Alison , Adlard Leesa , Ingles Jodie
Published: May 2021

Objective

To co-design an online support intervention for families after sudden cardiac death (SCD) in the young (<35 years).

Design

Co-design of a SCD family intervention by stakeholder focus groups.

Setting

Families and healthcare professionals with experience in SCD in the young.

Participants

Semi-structured online focus groups were held with key stakeholders, i.e. family members who had experienced young SCD, healthcare professionals and researchers. Guided discussions were used to develop an online support intervention. Thematic analysis of discussions and iterative feedback on draft materials guided content development.

Results

Four focus groups were held (10-12 participants per group). Stakeholder involvement facilitated development of high-level ideas and priority issues. Creative content and materials were developed based on user preference for stories, narratives and information reflecting everyday experience of families navigating the legal and medical processes surrounding SCD, normalising and supporting grief responses in the context of family relationships, and fostering hope. Emphasis on accessibility led to the overarching need for digital information and online engagement. These insights allowed development of an online intervention - COPE-SCD: A COmmunity suPporting familiEs after Sudden Cardiac Death - which includes a website and online support program.

Conclusion

Using co-design with stakeholders we have developed a support intervention that directly addresses the needs of SCD families and fills a large gap in existing health care. We will evaluate COPE-SCD to determine whether this is an effective intervention for support of families following a young SCD.

Strengths and limitations of this study

Healthcare providers and consumer representatives participated as stakeholders in support intervention design.

Co-design allowed development of a support intervention incorporating innovative ideas to meet user needs.

Focus groups were limited in size and may not fully represent the needs of the wider community affected by sudden cardiac death in the young.
Whole human genome 5’-mC methylation analysis using long read nanopore sequencing
Authors: Silva Catarina , Machado Miguel , Ferrão José , Rodrigues Sebastião , Vieira Luís
Published: May 2021

DNA methylation is a type of epigenetic modification that affects gene expression regulation and is associated with several human diseases. Microarray and short read sequencing technologies are often used to study 5’-methylcytosine (5’-mC) modification of CpG dinucleotides in the human genome. Although both technologies produce trustable results, the evaluation of the methylation status of CpG sites suffers from the potential side effects of DNA modification by bisulfite and the ambiguity of mapping short reads in repetitive and highly homologous genomic regions, respectively. Nanopore sequencing is an attractive alternative for the study of 5’-mC since the long reads produced by this technology allow to resolve those genomic regions more easily. Moreover, it allows direct sequencing of native DNA molecules using a fast library preparation procedure. In this work we show that 10X coverage depth nanopore sequencing, using DNA from a human cell line, produces 5’-mC methylation frequencies consistent with those obtained by methylation microarray and digital restriction enzyme analysis of methylation. In particular, the correlation of methylation values ranged from 0.73 to 0.90 using an average genome sequencing coverage depth <2X or a minimum read support of 17X for each CpG site, respectively. We also showed that a minimum of 5 reads per CpG yields strong correlations (>0.89) between sequencing runs and an almost uniform variation in methylation frequencies of CpGs across the entire value range. Furthermore, nanopore sequencing was able to correctly display methylation frequency patterns according to genomic annotations, including a majority of unmethylated and methylated sites in the CpG islands and inter-CpG island regions, respectively. These results demonstrate that low coverage depth nanopore sequencing is a fast, reliable and unbiased approach to the study of 5’-mC in the human genome.
Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics
Authors: Záhonová Kristína , Treitli Sebastian Cristian , Le Tien , Škodová-Sveráková Ingrid , Hanousková Pavla , Čepička Ivan , Tachezy Jan , Hampl Vladimír
Published: May 2021

Pelomyxa schiedti is a free-living amoeba belonging to the group Archamoebae, which encompasses anaerobes bearing mitochondrion-related organelles (MROs) – hydrogenosomes in free-living Mastigamoeba balamuthi and mitosomes in the human pathogen Entamoeba histolytica. Anaerobic peroxisomes, another adaptation to anaerobic lifestyle, were identified only recently in M. balamuthi. We found evidence for both these organelles in the single-cell-derived genome and transcriptome of P. schiedti, and corresponding vesicles were tentatively revealed in electron micrographs. In silico reconstructed MRO metabolism seems similar to that of M. balamuthi harboring respiratory complex II, electron-transferring flavoprotein, partial TCA cycle running presumably in reductive direction, pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenases, glycine cleavage system, and sulfate activation pathway. The cell disposes with an expanded set of NIF enzymes for iron sulfur cluster assembly, but their localization remains unclear. Quite contrary, out of 67 predicted peroxisomal enzymes, only four were reported also in M. balamuthi, namely peroxisomal processing peptidase, nudix hydrolase, inositol 2-dehydrogenase, and D-lactate dehydrogenase. Other putative functions of peroxisomes could be pyridoxal 5I⍰-phosphate biosynthesis, amino acid and carbohydrate metabolism, and hydrolase activities. Future experimental evidence is necessary to define functions of this surprisingly enzyme-rich anaerobic peroxisome.

Author summary

A major part of the microbial diversity cannot be cultured in isolation, and so it escapes from traditional ways of investigation. In this paper, we demonstrate the successful approach for generating good-quality genome and transcriptome drafts from a peculiar amoeba Pelomyxa schiedti using single-cell methods. P. schiedti is a member of Archamoebae clade harboring microaerobic protists including a free-living Mastigamoeba balamuthi and a human parasite Entamoeba histolytica. Mitochondria and peroxisomes represent two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform to anaerobic mitochondria, hydrogenosomes, mitosomes, and various transition stages in between, all of which encompass different enzymatic capacity. Anaerobic peroxisomes have been first noticed in M. balamuthi, but their function remained unclear for now. Data obtained in this study were used for revealing the presence and for the detailed functional annotations of anaerobic derivates of mitochondria and peroxisomes in P. schiedti, which were corroborated by transmission electron microscopy.
Sylites: Multipurpose markers for the visualization of inhibitory synapses
Authors: Khayenko Vladimir , Schulte Clemens , Reis Sara L. , Avraham Orly , Schietroma Cataldo , Worschech Rafael , Nordblom Noah F. , Kachler Sonja , Villmann Carmen , Heinze Katrin G. , Schlosser Andreas , Schueler-Furman Ora , Tovote Philip , Specht Christian G. , Maric Hans Michael
Published: May 2021

We introduce Sylites – small and versatile fluorogenic affinity probes for high-contrast visualization of inhibitory synapses. Having stoichiometric labeling and exceptional selectivity for neuronal gephyrin, a hallmark protein of the inhibitory post-synapse, Sylites enable superior synapse staining compared with antibodies. Combined with super-resolution microscopy, Sylites allow precise nanoscopic measurements of the synapse. In brain tissue, Sylites reveal the three-dimensional distribution of inhibitory synapses within just an hour.
A Dynamic Affective Core to bind the Contents, Context, and Value of Conscious Experience
Authors: Kishida Kenneth T. , Sands L. Paul
Published: May 2021

The private and dynamic nature of conscious subjective experience poses an empirical challenge that has led neuroscience-based theories about consciousness to note the importance of ‘the hard problem’ of explaining how subjective phenomenal experience can arise from neural activity but set it aside and focus on the ‘easier’ problems associated with information representation and behavior. This approach leaves a major gap in our understanding of the neural mechanisms underlying conscious subjective experience and its dynamic nature. However, computational methods integrated with a variety of tools for measuring human brain activity are beginning to link dynamic changes in subjective affect with reproducible neurobehavioral signals in humans. In particular, research applying computational reinforcement learning theory has shown tremendous utility in investigating human choice behavior and the role the dopaminergic system plays in dynamic behavioral control. This research is beginning to reveal an explicit connection between the dynamics of dopaminergic signals and dynamic changes in subjective affect. However, it should be obvious that the dopaminergic system alone is not sufficient to explain all of the complexities of affective dynamics. We review foundational work, highlight current problems and open questions, and propose a Dynamic Affective Core Hypothesis that integrates advances in our understanding of the representation of the content and context of conscious experiences with our nascent understanding about how these representations acquire and retain affective subjective value.
Crosstalk between Fat Mass and Obesity-related (FTO) and multiple WNT signaling pathways
Authors: Kim Hyunjoon , Jang Soohyun , Lee Young-suk
Published: May 2021

Fat Mass and Obesity-related (FTO) gene is associated with a diverse set of human diseases. Yet, the functional landscape of FTO remains largely unknown, most likely owing to its wide range of mechanistic roles and cell-type-specific targets. Here, we discover the intricate role of FTO in multiple WNT signaling pathways. Re-analyses of public data identified the bifurcation of canonical and noncanonical WNT pathways as the major role of FTO. In FTO-depleted cells, we find that the canonical WNT/β-Catenin signaling is inhibited in a non-cell autonomous manner via the upregulation of DKK1. Simultaneously, this upregulation of DKK1 promotes cell migration via activating the noncanonical WNT/PCP pathway. Unexpectedly, we also find that the canonical WNT/STOP signaling induces the accumulation of cytoplasmic FTO proteins. This subsequently leads to the stabilization of mRNAs via RNA demethylation, revealing a previously uncharacterized mode of WNT action in RNA regulation. Altogether, this study places the functional context of FTO at the branching point of multiple WNT signaling pathways which may explain the wide spectrum of FTO functions.
Multiomic Characterization of Stage I Lung Adenocarcinoma Reveals Distinct Genetic and Immunologic Features of Recurrent Disease
Authors: Kratz Johannes R. , Li Jack Z. , Tsui Jessica , Lee Jen C. , Ding Vivianne W. , Rao Arjun A. , Mann Michael J. , Chan Vincent , Combes Alexis J. , Krummel Matthew F. , Jablons David M.
Published: May 2021

Background

Recurrence after surgery for early-stage lung cancer is common, occurring between 30-50% of the time. Despite the popularization of prognostic gene signatures in early-stage lung cancer that allow us to better predict which patients may recur, why patients recur after surgery remains unclear.

Methods

Using a large cohort of lung adenocarcinoma patients with complete genetic, genomic, epigenetic and clinical profiling, a recurrence classifier was developed which identifies patients at highest risk of recurrence. The genetic, genomic, and epigenetic profiles of stage I patients with low-vs. high-risk of recurrence were compared. To characterize the tumor immune microenvironment of recurrent stage I tumors, single cell RNA-seq was performed on fresh tissue samples undergoing lung adenocarcinoma resection at UCSF to identify unique immune population markers and applied to the large stage I lung adenocarcinoma cohort using digital cytometry.

Results

Recurrence high-risk stage I lung adenocarcinomas demonstrated a higher mutation burden than low-risk tumors, however, none of the known canonical lung cancer driver mutations were more prevalent in high-risk tumors. Transcriptomic analysis revealed widespread activation of known cancer and cell cycle pathways with simultaneous downregulation of immune response pathways including antigen presentation and Th1/Th2 activation. Tumors at high-risk of recurrence displayed depleted adaptive immune populations, and depletion of adaptive immune populations was independently prognostic of recurrence in stage I lung adenocarcinomas.

Conclusion

Recurrent stage I lung adenocarcinomas display distinct features of genomic and genetic instability including increased tumor mutation burden, neoantigen load, activation of numerous mitotic and cell cycle genes, and decreased genome-wide methylation burden. Relative depletion of infiltrating adaptive immune populations may allow these tumors to escape immunosurveillance and recur after surgery.
GPI anchor remodeling by the plant PGAP1 ortholog HLD1 is essential for Papaver self-incompatibility
Authors: Lin Zongcheng , Xie Fei , Triviño Marina , Zhao Tao , Coppens Frederik , Sterck Lieven , Bosch Maurice , Franklin-Tong Vernonica E. , Nowack Moritz K.
Published: May 2021

In eukaryotes, glycosylphosphatidylinositol anchored proteins (GPI-APs) are tethered to the outer leaflet of the plasma membrane where they function as key regulators of a plethora of biological processes. Self-incompatibility (SI) plays a pivotal role regulating fertilization in higher plants through recognition and rejection of ‘self’ pollen. Here we used Arabidopsis thaliana lines engineered to be self-incompatible by expression of Papaver SI determinants for an SI suppressor screen. We identify HLD1, an ortholog of human GPI-inositol deacylase PGAP1, whose mutation completely abolishes the SI response. We show that HLD1 functions as a GPI-inositol deacylase and that this GPI-remodeling activity is essential for SI. Using GFP-SKU5 as a representative GPI-AP, we show that HLD1 mutation does not affect GPI-AP production and targeting, but alters the configuration of mature GPI-APs. This prevents GPI-AP release from the plasma membrane, suggesting that this process plays a critical role in the regulation of SI. Our data not only identify GPI anchoring as a new pathway of SI providing new directions to investigate SI mechanisms, but identifies for the first time a function for GPI-AP remodeling by inositol deacylation in plants.

One sentence summary

The Papaver self-incompatibility response requires GPI-anchor modification by HLD1, an ortholog of the mammalian PGAP1.
Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes
Authors: Billaud Maud , Lamy-Besnier Quentin , Lossouarn Julien , Moncaut Elisabeth , Dion Moira B. , Moineau Sylvain , Traoré Fatoumata , Le Chatelier Emmanuelle , Denis Catherine , Estelle Jordi , Achard Caroline , Zemb Olivier , Petit Marie-Agnès
Published: May 2021

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.
High vitamin B2 production by the Lactiplantibacillus plantarum B2 strain carrying a mutation in the aptamer P1 helix of the FMN-riboswitch that regulates expression of the bacterial rib operon
Authors: Ripa Inés , Ruiz-Masó José Ángel , De Simone Nicola , Russo Pasquale , Spano Giuseppe , del Solar Gloria
Published: May 2021

Manufacturing of probiotics and functional foods using lactic acid bacteria that overproduce vitamin B2 has gained growing interest due to ariboflavinosis problems affecting populations of both developing and affluent countries. Two isogenic Lactiplantibacillus plantarum strains, namely a riboflavin-producing parental strain (UFG9) and a roseoflavin-resistant strain (B2) that carries a mutation in the FMN-aptamer of the potential rib operon riboswitch, were analyzed for production and intra- and extracellular accumulation of flavins, as well as for regulation of the rib operon expression. Strain B2 accumulated in the medium one of the highest levels of riboflavin+FMN ever reported for lactic acid bacteria, exceeding by ~25 times those accumulated by UFG9. Inside the cells, concentration of FAD was similar in both strains, while that of riboflavin+FMN was ~6-fold higher in B2. Mutation B2 could decrease the stability of the aptamer’s regulatory P1 helix even in the presence of the effector, thus promoting the antiterminator structure of the riboswitch ON state. Although the B2-mutant riboswitch showed an impaired regulatory activity, it retained partial functionality being still sensitive to the effector. The extraordinary capacity of strain B2 to produce riboflavine, together with its metabolic versatility and probiotic properties, can be exploited for manufacturing multifunctional foods.
Structural basis of PETISCO complex assembly during piRNA biogenesis inC. elegans
Authors: Perez-Borrajero Cecilia , Podvalnaya Nadezda , Holleis Kay , Lichtenberger Raffael , Karaulanov Emil , Simon Bernd , Basquin Jérôme , Hennig Janosch , Ketting René F. , Falk Sebastian
Published: May 2021

Piwi-interacting RNAs (piRNAs) constitute a class of small RNAs that bind PIWI proteins and are essential to repress transposable elements in the animal germline, thereby promoting genome stability and maintaining fertility.C. eleganspiRNAs (21U RNAs) are transcribed individually from minigenes as precursors that require 5’ and 3’ processing. This process depends on the PETISCO complex, consisting of four proteins: IFE-3, TOFU-6, PID-3, and ERH-2. We employ biochemical and structural biology approaches to characterize the PETISCO architecture and its interaction with RNA, together with its effector proteins TOST-1 and PID-1. These two proteins define different PETISCO functions: PID-1 governs 21U processing whereas TOST-1 links PETISCO to an unknown process essential for early embryogenesis.

Here, we show that PETISCO forms an octameric assembly with each subunit present in two copies. Determination of structures of the TOFU-6/PID-3 and PID-3/ERH-2 subcomplexes, supported byin vivostudies of subunit interaction mutants, allows us to propose a model for the formation of the TOFU-6/PID-3/ERH-2 core complex, and its functionality in germ cells and early embryos. Using NMR spectroscopy, we demonstrate that TOST-1 and PID-1 bind to a common surface on ERH-2, located opposite its PID-3 binding site, explaining how PETISCO can mediate different cellular roles.
Biphasic effects of IL-27 during Staphylococcus aureus implant-associated osteomyelitis in mice
Authors: Morita Yugo , Franchini Anthony M. , Owen John R. , Martinez John C. , Daiss John L. , de Mesy Bentley Karen L. , Kates Stephen L. , Schwarz Edward M. , Muthukrishnan Gowrishankar
Published: May 2021

Interleukin-27 is a pleiotropic cytokine whose reported functions during bacterial infections are debated as an area of active research. To address this, we investigated the role of IL-27 signaling during Staphylococcus aureus osteomyelitis. Clinically, we observed elevated serum IL-27 levels (20-fold higher, p<0.05) in patients with S. aureus osteomyelitis compared to uninfected patients undergoing elective total joint replacement. Remarkably, IL-27 serum levels immediately following septic death were 60-fold higher vs. uninfected patients (p<0.05), suggesting that IL-27 may be a biomarker of end-stage infection and/or cytokine storm. To test this, we hypothesized that IL-27 mediates bacterial clearance during the acute phase of S. aureus osteomyelitis, and subsequently suppresses inflammation to prevent cytokine storm and osteolysis during chronic infection. In mice, we observed that systemic IL-27 delivery by a recombinant adeno-associated viral vector (rAAV-IL-27) ameliorates surgical site soft tissue infection and peri-implant bone loss during the establishment of implant-associated S. aureus osteomyelitis. This effect was not observed in IL-27 receptor α knock-out mice, suggesting a direct role of IL-27/IL-27R signaling on immune and bone cell functions. Examination of IL-27-mediated immune responses via transcriptome analyses of infected tibiae demonstrated that IL-27 is a biphasic cytokine with IL-27/IL-27R activating immunostimulatory responses including Th17, IL-2, TLR, and iNOS signaling early, and subsequently suppressing these pathways during chronic infection. Ex vivo confirmation using murine macrophages revealed that IL-27 co-stimulates TLR signaling to increase the production of nitric oxide, and immunomodulatory cytokines such as IL-10, IL-21, IL-31, and TNF-β, but is not a chemokine.

Author Summary

Staphylococcus aureus is the most common pathogen in orthopaedic infections, and hard-to-treat (MRSA) strains cause >50% of these infections. Thus, there is an urgent need to develop immunotherapies to treat these life-threatening S. aureus infections. Currently, the role of multifunctional IL-27 on S. aureus osteomyelitis is unknown. In a clinical study, we observed that IL-27 is an important biomarker for identifying S. aureus osteomyelitis patients, and that elevated serum IL-27 levels correlated with adverse clinical outcomes, such as septic death. In our efforts to uncover the underlying mechanisms, we reveal that IL-27 is a biphasic cytokine, activating proinflammatory immune pathways, including Th17 responses, early during acute S. aureus osteomyelitis, and subsequently repressing them during the chronic phase to prevent cytokine storm and bone damage. These results indicate that immune modulation of IL-27/IL-27R signaling could be a viable therapeutic strategy in mitigating S. aureus osteomyelitis.
Topic: Hyper immune Bovine Colostrum as a Low-Cost, Large-Scale Source of Antibodies against COVID-19
Authors: Nili Hassan , Bouzari Majid , Attaran Hamid Reza , Golab Nader Ghaleh , Rabani Mohammad
Published: May 2021

Many different strategies have been used to fight against COVID-19 pandemic as a therapeutics or prophylaxis approaches. However, none of them so far have used, passive immune transfer using products from immunized farm animals. Hyper immune bovine colostrums (HBC) have been used against many different respiratory and gastrointestinal tracts infections during past decades.

Six mixed Holstein X Semental dairy cattle’s in their 6-7 months of gestation period years were chosen for hyper immunization with COVID-19 vaccine. An isolated and very well protected site was selected and equipped according to animal husbandry code of practice, used for animal experimentation. Specific IgG level against SARS-CoV-2 virus was measured before and after vaccination in the sera, and in the colostrum following parturition. Very high specific IgG level was detected one week following second vaccination in the sera and in first colostrums after parturition. Safety of the product was approved following phase 1 of clinical trials in 40 healthy volunteers. Phase 2 of the clinical trials is underway. Early results show effectiveness of the product in reducing sore throat and cough in early stages of SARS-CoV-2 infection.
Highly diverse flavobacterial phages as mortality factor during North Sea spring blooms
Authors: Bartlau Nina , Wichels Antje , Krohne Georg , Adriaenssens Evelien M. , Heins Anneke , Fuchs Bernhard M. , Amann Rudolf , Moraru Cristina
Published: May 2021

It is generally recognized that phages have a modulating role in the marine environment. Therefore, we hypothesized that phages can be a mortality factor for the dense heterotrophic bacterial population succeeding in phytoplankton blooms. For the marine carbon cycle, spring phytoplankton blooms are important recurring events. In this study, we focused onFlavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms –DuplodnaviriaandMonodnaviria. Taxonomic analysis allowed us to delineate ten new phage genera and seven new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating indicated that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years indicated that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
Mapping the functional connectivity of ecosystem services supply across a regional landscape
Authors: Field Rachel D. , Parrott Lael
Published: May 2021

Sustainably managing multifunctional landscapes for production of multiple ecosystem services (ES) requires thorough understanding of the interactions between ES and the ecological processes that drive them. We build upon landscape connectivity theory to present a spatial approach for assessing functional connections between multiple ES at the landscape scale. We demonstrate application of the approach using existing ES supply mapping data for plant agriculture, waterflow regulation, and landscape aesthetics. The connections we observed between these three ES revealed high-value multifunctional linkages on the landscape that were not necessarily predictable from supply area mapping, nor from land use or land cover data. By providing spatial information on ES connectivity, our approach enables local and regional environmental planning and management that takes full consideration of the complex, multi-scale interactions between ecological processes, land use and land cover, and ecosystem service supply on a landscape.
Targeted deletion of the RNA-binding protein Caprin1 leads to progressive hearing loss and impairs recovery from noise exposure in mice
Authors: Nolan Lisa S. , Chen Jing , Cláudia Gonçalves Ana , Bullen Anwen , Steel Karen P. , Dawson Sally J. , Gale Jonathan E.
Published: May 2021

Cell cycle associated protein 1 (Caprin1) is an RNA-binding protein that can regulate the cellular post-transcriptional response to stress. It is a component of both stress granules and neuronal RNA granules and is implicated in neurodegenerative disease, synaptic plasticity and long-term memory formation. Our previous work suggested that Caprin1 also plays a role in the response of the cochlea to stress. Here, targeted inner ear-deletion of Caprin1 in mice leads to an early onset, progressive hearing loss. Auditory brainstem responses from Caprin1-deficient mice show reduced thresholds, with a significant reduction in wave-I amplitudes compared to wildtype. Whilst hair cell structure and numbers were normal, the inner hair cell-spiral ganglion neuron (IHC-SGN) synapse revealed abnormally large post-synaptic GluA2 receptor puncta, a defect consistent with the observed wave-I reduction. Unlike wildtype mice, mild-noise-induced hearing threshold shifts in Caprin1-deficient mice did not recover. Oxidative stress triggered TIA-1/HuR-positive stress granule formation in ex-vivo cochlear explants from Caprin1-deficient mice, showing that stress granules could still be induced. Taken together, these findings suggest that Caprin1 plays a key role in maintenance of auditory function, where it regulates the normal status of the IHC-SGN synapse.
DnaA and SspA Regulation of the iraD gene of E. coli: an alternative DNA damage response independent of LexA/RecA
Authors: Sass Thalia H. , Ferrazzoli Alexander E. , Lovett Susan T.
Published: May 2021

The transcription factor RpoS (σS) of Escherichia coli controls a large number of genes important for tolerance of a variety of stress conditions. IraD promotes the post-translation stability of RpoS by inhibition of RssB, an adaptor protein for ClpXP degradation. We have previously documented DNA damage induction of iraD expression, independent of the SOS response. Both iraD and rpoS are required for tolerance to DNA damaging treatments such as H2O2 and the replication inhibitor azidothymidine in the log phase of growth. Using luciferase gene fusions to the 672 bp iraD upstream region, we show here that both promoters of iraD are induced by AZT. Genetic analysis suggests that both promoters are repressed by DnaA-ATP, partially dependent on a putative DnaA box at −81 bp, and regulated by RIDA (regulatory inactivation of DnaA), dependent on the DnaN processivity clamp. By electrophoretic mobility shift assays we show that purified DnaA protein binds to the iraD upstream region, so DnaA regulation of IraD is likely to be direct. DNA damage induction of iraD during log phase growth is abolished in the dnaA-T174P mutant, suggesting that DNA damage, in some way, relieves DnaA repression, possibly through the accumulation of replication clamps and enhanced RIDA. We demonstrate that the RNA-polymerase associated factor, SspA (stringent starvation protein A), induced by the accumulation of ppGpp, also affects IraD expression, with a positive effect on constitutive expression and a negative effect on AZT-induced expression, in a fashion independent of DnaA.

SIGNIFICANCE

DNA damage can lead to cell death or genomic instability. Cells have evolved transcriptional responses that sense DNA damage and up-regulate tolerance and repair factors; the LexA/RecA-regulated SOS response in E. coli was the first example of such a system. This work describes an alternative DNA damage response, controlled by DnaA and the IraD post-translational regulator of RpoS. The cellular signals for this response, we propose, are empty replication processivity (β) clamps that accumulate at replication blocks. IraD expression is also regulated by stringent starvation protein, SspA, induced by nutrient deprivation. This SOS-independent DNA damage response integrates a signal of incomplete replication with starvation to modulate expression of genes that promote the completion of replication.
Establishment of pan-Influenza A (H1-H18) and pan-Influenza B (pre-split, Vic/Yam) Pseudotype Libraries for efficient vaccine antigen selection
Authors: Del Rosario Joanne Marie M. , da Costa Kelly A.S. , Asbach Benedikt , Ferrara Francesca , Ferrari Matteo , Wells David A. , Mann Gurdip Singh , Ameh Veronica O. , Sabeta Claude T. , Banyard Ashley C. , Kinsley Rebecca , Scott Simon D. , Wagner Ralf , Heeney Jonathan L. , Carnell George W. , Temperton Nigel J.
Published: May 2021

We have developed an influenza hemagglutinin (HA) pseudotype library encompassing Influenza A subtypes HA1-18, and Influenza B subtypes (both lineages) to be employed in influenza pseudotype microneutralization (pMN) assays. The pMN is highly sensitive and specific for detecting virus-specific neutralizing antibodies against influenza viruses and can be used to assess antibody functionality in vitro. Here we show the production of these viral HA pseudotypes and their employment as substitutes for wildtype viruses in influenza serological and neutralization assays. We demonstrate its utility in detecting serum response to vaccination with the ability to evaluate cross-subtype neutralizing responses elicited by specific vaccinating antigens. Our findings may inform further pre-clinical studies involving immunization dosing regimens in mice and may help in the creation and selection of better antigens for vaccine design. These HA pseudotypes can be harnessed to meet strategic objectives that contribute to the strengthening of global influenza surveillance, expansion of seasonal influenza prevention and control policies, and strengthening pandemic preparedness and response.