bluuebunny/crossref_metadata_2025 huggingface dataset:
A mini-TGA protein, lacking a functional DNA-binding domain, modulates gene expression through heterogeneous association with transcription factors
Authors: Tomaž Špela , Petek Marko , Lukan Tjaša , Pogačar Karmen , Stare Katja , Prates Erica Teixeira , Jacobson Daniel A. , Zrimec Jan , Bajc Gregor , Butala Matej , Pompe Novak Maruša , Dudley Quentin , Patron Nicola , Taler-Verčič Ajda , Usenik Aleksandra , Turk Dušan , Prat Salomé , Coll Anna , Gruden Kristina
Published: March 2022

TGA transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. Here, we investigate the role of StTGA2.1, a potato TGA lacking the full bZIP, which we name a mini-TGA. Such truncated proteins have been widely assigned as loss-of-function mutants. We, however, confirm that StTGA2.1 overexpression compensates for SA-deficiency. To understand the underlying mechanisms, we show that StTGA2.1 can physically interact with StTGA2.2 and StTGA2.3, while its interaction with DNA was not detected. We investigate the changes in transcriptional regulation due to StTGA2.1 overexpression, identifying direct and indirect target genes. Using in planta transactivation assays, we confirm that StTGA2.1 interacts with StTGA2.3 to activate StPRX07, a member of class III peroxidases, which are known to play role in immune response. Finally, via structural modelling and molecular dynamics simulations, we hypothesise that the compact molecular architecture of StTGA2.1 distorts DNA conformation upon heterodimer binding to enable transcriptional activation. This study demonstrates how protein truncation can lead to novel functions and that such events should be studied carefully in other protein families.
The Evolution of Protein Folds by Creative Destruction
Authors: Alvarez-Carreño Claudia , Gupta Rohan J , Petrov Anton S. , Williams Loren Dean
Published: April 2022

Mechanisms by which new protein folds emerge and diverge pose central questions in biological sciences. Incremental mutation and step-wise adaptation explain relationships between topologically similar protein folds. However, the universe of folds is diverse and riotous, suggesting roles of more potent and creative forces. Sequence and structure similarity are observed between topologically distinct folds, indicating that proteins with distinct folds may share common ancestry.

We found evidence of common ancestry between three distinct β-barrel folds: OB, SH3 and cradle loop barrel (CLB). The data suggest a mechanism of fold evolution that interconverts SH3, OB and CLB. This mechanism, which we call creative destruction, can be generalized to explain other examples of fold evolution including circular permutation. In creative destruction, an open reading frame duplicates or otherwise merges with another to produce a fused polypeptide. A merger forces two ancestral domains into a new sequence and spatial context. The fused polypeptide can explore folding landscapes that are inaccessible to either of the independent ancestral domains. However, the folding landscapes of the fused polypeptide are not fully independent of those of the ancestral domains. Creative destruction is thus partially conservative in that a daughter fold would inherit some motifs from the ancestral folds. After a merger and refolding, adaptive processes such as mutation and loss of extraneous segments optimize the new daughter fold.

Significance

Mechanisms of emergence and early diversification of structured proteins present deep and difficult problems in evolutionary biology. Here we excavate the deepest evolutionary history, found within the translation machinery, which is an ancient molecular fossil and the birthplace of all proteins. We demonstrate common origins of some of the simplest, oldest and most common protein folds. Furthermore, the data suggest a mechanism, that we call creative destruction, that explains at molecular level how simple folds spawn more complex folds. In this mechanism, new folds emerge from old folds via gene duplication, expression, exploration of new folding landscapes and adaptation. Creative destruction explains the facile emergence of complex from simple architectures in a funneled exploration.
Dissecting Succulence: Crassulacean Acid Metabolism and Hydraulic Capacitance are Independent Adaptations in Clusia Leaves
Authors: Leverett Alistair , Hartzell Samantha , Winter Klaus , Garcia Milton , Aranda Jorge , Virgo Aurelio , Smith Abigail , Focht Paulina , Rasmussen-Arda Adam , Willats William G. T. , Cowan-Turner Daniel , Borland Anne M.
Published: April 2022

Succulence is found across the world as an adaptation to water-limited niches. The fleshy organs of succulent plants develop via enlarged photosynthetic chlorenchyma and/or achlorophyllous water storage hydrenchyma cells. The precise mechanism by which anatomical traits contribute to drought tolerance is unclear, as the effect of succulence is multifaceted. Large cells are believed to provide space for nocturnal storage of malic acid fixed by crassulacean acid metabolism (CAM), whilst also buffering water potentials by elevating hydraulic capacitance (CFT). Furthermore, the effect of CAM and elevated CFT on growth and water conservation have not been compared, despite the assumption that these adaptations often occur together.

We assessed the relationship between succulent anatomical adaptations, CAM and CFT, across the genus Clusia. In addition, we simulated the effects of CAM and CFT on growth and water conservation during drought using the Photo3 model.

Within Clusia leaves, CAM and CFT are independent traits: CAM requires large palisade chlorenchyma cells, whereas hydrenchyma tissue governs interspecific differences in CFT. In addition, our model suggests that CAM supersedes CFT as a means to maximise CO2 assimilation and minimise transpiration during drought.

Our study challenges the assumption that CAM and CFT are mutually dependent traits within succulent leaves.
Retinal ganglion cell endowment is correlated with optic tract fiber cross section, not density
Authors: Taskin Huseyin O , Qiao Yuchuan , Sydnor Valerie J , Cieslak Matthew , Haggerty Edda B , Satterthwaite Theodore D , Morgan Jessica IW , Shi Yonggang , Aguirre Geoffrey K
Published: April 2022

There is substantial variation between healthy individuals in the number of retinal ganglion cells (RGC) in the eye, with commensurate variation in the number of axons in the optic tracts. Fixel-based analysis of diffusion MR produces estimates of fiber density (FD) and cross section (FC). Using these fixel measurements along with retinal imaging, we asked if individual differences in RGC tissue volume are correlated with individual differences in FD and FC measurements obtained from the optic tracts, and subsequent structures along the cortical visual pathway. We find that RGC endowment is correlated with optic tract FC, but not with FD. RGC volume had a decreasing relationship with measurements from subsequent regions of the visual system (LGN volume, optic radiation FC/FD, and V1 surface area). However, we also found that the variations in each visual area were correlated with the variations in its immediately adjacent visual structure. We only observed these serial correlations when FC is used as the measure of interest for the optic tract and radiations, but no significant relationship was found when FD represented these white matter structures. From these results, we conclude that the variations in RGC endowment, LGN volume, and V1 surface area are better predicted by the overall cross section of the optic tract and optic radiations as compare to the intra-axonal restricted signal component of these white matter pathways. Additionally, the presence of significant correlations between adjacent, but not distant, anatomical structures suggests that there are multiple, local sources of anatomical variation along the visual pathway.
Bacteriophages antagonize cGAS-like immunity in bacteria
Authors: Huiting Erin , Athukoralage Januka , Guan Jingwen , Silas Sukrit , Carion Héloïse , Bondy-Denomy Joseph
Published: March 2022

The recently discovered cyclic-oligonucleotide-based anti-phage signaling system (CBASS) is related to eukaryotic cGAS-STING anti-viral immunity and is present in diverse prokaryotes. However, our understanding of how CBASS detects, inhibits, and co-evolves with phages is limited because CBASS function has only been studied in reconstituted heterologous systems. Here, we identify a phage-encoded CBASS antagonist (acbIIA1,anti-cbass type II-A gene 1) necessary for phage replication in the presence of endogenous CBASS immunity in Pseudomonas aeruginosa. acbIIA1 homologs are encoded by numerous lytic and temperate phages infecting Gram-negative bacteria. Deletion of acbIIA1 renders multiple phages susceptible to CBASS, but phages can then escape immune function via mutations in the major capsid gene. These mutants suggest that CBASS is activated by, or targets, the late-expressed phage capsid. Together, we establish a native model system to study CBASS and identify a common phage-encoded CBASS antagonist, demonstrating that CBASS is a bona fide anti-phage immune system in nature.

Graphical Abstract
Structural insights into crista junction formation by the Mic60-Mic19 complex
Authors: Bock-Bierbaum Tobias , Funck Kathrin , Wollweber Florian , Lisicki Elisa , Laborenz Janina , Noel Jeffrey K. , Hessenberger Manuel , von der Malsburg Alexander , von der Malsburg Karina , Bernert Carola , Kunz Séverine , Riedel Dietmar , Lilie Hauke , Jakobs Stefan , van der Laan Martin , Daumke Oliver
Published: March 2022

Mitochondrial cristae membranes are the oxidative phosphorylation sites in cells. Crista junctions (CJs) form the highly curved neck regions of cristae and are thought to function as selective entry gates into the cristae space. Little is known about how CJs are generated and maintained. We show that the central coiled-coil domain of the mitochondrial contact and cristae organizing system (MICOS) subunit Mic60 forms an elongated, bow tie-shaped tetrameric assembly. Mic19 promotes Mic60 tetramerization via a conserved interface between the Mic60 mitofilin and Mic19 CHCH domains. Dimerization of mitofilin domains exposes a crescent-shaped membrane-binding site with convex curvature tailored to interact with curved CJ necks. Our study suggests that the Mic60-Mic19 subcomplex transverses CJs as a molecular strut, thereby controlling CJ architecture and function.
Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population
Authors: Shen Yiran , Khatri Bhuwan , Rananaware Santosh , Li Danmeng , Ostrov David A. , Jain Piyush K , Lessard Christopher J. , Nguyen Cuong Q.
Published: March 2022

COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. The widespread clinical symptoms encompass a large group of asymptomatic COVID-19 patients, raising a crucial question regarding genetic susceptibility, e.g., whether individual differences in immunity play a role in patient symptomatology and how much human leukocyte antigen (HLA) contributes to this. To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. We identified two loci on chromosomes 5q32 and 11p12, which reach the significance threshold of suggestive association (p<1×10-5 threshold adjusted for multiple trait testing) and are associated with the COVID-19 susceptibility in the European ancestry (index rs17448496: odds ratio [OR] = 0.173; 95% confidence interval [CI], 0.08–0.36 for G allele; p=5.15× 10-5 and index rs768632395: OR = 0.166; 95% CI, 0.07–0.35 for A allele; p= 4.25×10-6, respectively), which were associated with two genes, PPP2R2B at 5q32, and LRRC4C at 11p12, respectively. To explore the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases. Using In-silico binding predictions to map the binding of risk/protective HLA to the viral structural proteins, we found the differential presentation of viral peptides in both ancestries. Lastly, extrapolation of the identified HLA from the cohort to the worldwide population revealed notable correlations. The study uncovers possible differences in susceptibility to COVID-19 in different ancestral origins in the genetic background, which may provide new insights into the pathogenesis and clinical treatment of the disease.
Computational rewiring of allosteric pathways reprograms GPCR selective responses to ligands
Authors: Keri D. , Hijazi M. , Oggier A. , Barth P.
Published: April 2022

G-protein-coupled receptors (GPCRs) are the largest class of cell surface receptors and drug targets, and respond to a wide variety of chemical stimuli to activate diverse cellular functions. Understanding and predicting how ligand binding triggers a specific signaling response is critical for drug discovery and design but remains a major challenge. Here, computational design of GPCR allosteric functions is used to uncover the mechanistic relationships between agonist ligand chemistry, receptor sequence, structure, dynamics and allosteric signaling in the dopamine D2 receptor. Designed gain of function D2 variants for dopamine displayed very divergent G-protein signaling responses to other ligand agonists that strongly correlated with ligand structural similarity. Consistent with these observations, computational analysis revealed distinct topologies of allosteric signal transduction pathways for each ligand-bound D2 pair that were perturbed differently by the designs. We leveraged these findings by rewiring ligand-specific pathways and designed receptors with highly selective ligand responses. Overall, our study suggests that distinct ligand agonists can activate a given signaling effector through specific “allosteric activator” moieties that engage partially independent signal transmission networks in GPCRs. The results provide a mechanistic framework for understanding and predicting the impact of sequence polymorphism on receptor pharmacology, informing selective drug design and rationally designing receptors with highly selective ligand responses for basic and therapeutic applications.
Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it
Authors: Tejedor Andres R. , Sanchez-Burgos Ignacio , Estevez-Espinosa Maria , Garaizar Adiran , Collepardo-Guevara Rosana , Ramirez Jorge , Espinosa Jorge R.
Published: April 2022

Biomolecular condensates, some of which are liquid-like during health, can age over time becoming gel-like pathological systems. One potential source of loss of liquid-like properties during ageing of RNA-binding protein condensates is the progressive formation of inter-protein β-sheets. To bridge microscopic understanding between accumulation of inter-protein β-sheets over time and the modulation of FUS and hnRNPA1 condensate viscoelasticity, we develop a multiscale simulation approach. Our method integrates atomistic simulations with sequence-dependent coarse-grained modelling of condensates that exhibit accumulation of inter-protein β-sheets over time. We reveal that inter-protein β-sheets notably increase condensate viscosity but does not transform the phase diagrams. Strikingly, the network of molecular connections within condensates is drastically altered, culminating in gelation when the network of strong β-sheets fully percolates. However, high concentrations of RNA decelerate the emergence of inter-protein β-sheets. Our study uncovers molecular and kinetic factors explaining how the accumulation of inter-protein β-sheets can trigger liquid-to-solid transitions in condensates, and suggests a potential mechanism to slow such transitions down.
Prediction of infectivity of SARS-CoV2: Mathematical model with analysis of docking simulation for spike proteins and angiotensin-converting enzyme 2
Authors: Takaoka Yutaka , Sugano Aki , Morinaga Yoshitomo , Ohta Mika , Miura Kenji , Kataguchi Haruyuki , Kumaoka Minoru , Kimura Shigemi , Maniwa Yoshimasa
Published: April 2022

Variants of a coronavirus (SARS-CoV-2) have been spreading in a global pandemic. Improved understanding of the infectivity of future new variants is important so that effective countermeasures against them can be quickly undertaken. In our research reported here, we aimed to predict the infectivity of SARS-CoV-2 by using a mathematical model with molecular simulation analysis, and we used phylogenetic analysis to determine the evolutionary distance of the spike protein gene (S gene) of SARS-CoV-2. We subjected the six variants and the wild type of spike protein and human angiotensin-converting enzyme 2 (ACE2) to molecular docking simulation analyses to understand the binding affinity of spike protein and ACE2. We then utilized regression analysis of the correlation coefficient of the mathematical model and the infectivity of SARS-CoV-2 to predict infectivity. The evolutionary distance of the S gene correlated with the infectivity of SARS-CoV-2 variants. The coefficient of the mathematical model obtained with results of molecular docking simulation also correlated with the infectivity of SARS-CoV-2 variants. These results suggest that the data from the docking simulation for the receptor binding domain of variant spike proteins and human ACE2 were valuable for prediction of SARS-CoV-2 infectivity. In addition, we developed a mathematical model for prediction of SARS-CoV-2 variant infectivity by using binding affinity obtained via molecular docking and the evolutionary distance of the S gene.
In vitro reconstitution of calcium-dependent recruitment of the human ESCRT machinery in lysosomal membrane repair
Authors: Shukla Sankalp , Larsen Kevin P. , Ou Chenxi , Rose Kevin , Hurley James H.
Published: March 2022

The endosomal sorting complex required for transport (ESCRT) machinery has been shown to be centrally involved in repair of damage to both the plasma and lysosome membranes. ESCRT recruitment to sites of damage occurs on a fast time scale, and Ca2+ has been proposed to play a key signaling role in the process. Here, we show that the Ca2+-binding regulatory protein ALG-2 binds directly to negatively charged membranes in a Ca2+-dependent manner. Next, by monitoring the colocalization of ALIX with ALG-2 on negatively charged membranes, we show that ALG-2 recruits ALIX to the membrane. Furthermore, we show that ALIX recruitment to membrane orchestrates the downstream assembly of late-acting CHMP4B, CHMP3, CHMP2A subunits along with the AAA+ ATPase VPS4B. Finally, we show that ALG-2 can also recruit the ESCRT-III machinery to the membrane via the canonical ESCRT-I/II pathway. Our reconstitution experiments delineate the minimal sets of components needed to assemble the entire membrane repair machinery and open a new avenue for mechanistic understanding of endolysosomal membrane repair.

Significance statement

One of the ways by which protein aggregates can propagate and lead to progression of a neurodegenerative disease is by damaging the membrane that is destined to degrade the misfolded, aggregated protein. ESCRT machinery has been implicated in sealing these damaged membranes, and the nature of the membrane recruitment trigger signal for this machinery is a major open question. Here, we show in vitro that ALG-2 can bring ESCRT machinery to membranes in a Ca2+-dependent manner.
Multi-environment genome-wide association mapping of culm morphology traits in barley
Authors: Bretani G. , Shaaf S. , Tondelli A. , Cattivelli L. , Delbono S. , Waugh R. , Thomas W. , Russell J. , Bull H. , Igartua E. , Casas A. , Gracia P. , Rossi R. , Schulman A. , Rossini L.
Published: April 2022

In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image-analysis based protocol to accurately phenotype culm diameter and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in 7 different environments revealed genetic control as supported by high heritability values, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. In addition, culm traits showed strong negative correlations with lodging but weak correlations with plant height across row-types, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 QTLs for the studied traits, including subpopulation-specific QTLs and several main effect loci for culm traits showing negative effects on lodging without impacting plant height. Providing first insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments.

One-sentence summary

Genetic analysis of a diverse collection of European barleys reveals genomic regions underpinning stem morphological features associated with lodging resistance.
Selective IL13Rα2-Targeted Functionality of IL13-Ligand CARs is Enhanced by Inclusion of 4-1BB Co-Stimulation
Authors: Starr Renate , Yang Xin , Aguilar Brenda , Gumber Diana , Huard Stephanie , Wang Dongrui , Chang Wen-Chung , Brito Alfonso , Chiu Vivian , Ostberg Julie R. , Badie Benham , Forman Stephen J. , Alizadeh Darya , Wang Leo D. , Brown Christine E.
Published: March 2022

ABSTRACT

Chimeric antigen receptor (CAR) T cell immunotherapy is emerging as a powerful strategy for cancer therapy; however, an important safety consideration is the potential for off-tumor recognition of normal tissue. This is particularly important as ligand-based CARs are optimized for clinical translation. Our group has developed and clinically translated an IL13(E12Y) ligand- based CAR targeting the cancer antigen IL13Rα2 for treatment of glioblastoma (GBM). There remains limited understanding of how IL13-ligand CAR design impacts the activity and selectivity for the intended tumor-associated target IL13Rα2 versus the more ubiquitous unintended target IL13Rα1. In this study, we functionally compared IL13(E12Y)-CARs incorporating different intracellular signaling domains, including first-generation CD3ζ- containing CARs (IL13ζ), second-generation 4-1BB- (CD137) or CD28-containing CARs (IL13- BBζ or IL13-28ζ), and third-generation CARs containing both 4-1BB and CD28 (IL13-28BBζ). In vitro co-culture assays at high tumor burden establish that 2nd generation IL13-BBζ or IL13- 28ζ outperform first-generation IL13ζ and 3rd generation IL13-28BBζ CAR designs, with IL13- BBζ providing superior CAR proliferation and in vivo anti-tumor potency in human xenograft mouse models. IL13-28ζ displayed a lower threshold for antigen recognition, resulting in higher off-target IL13Rα1 reactivity both in vitro and in vivo. Syngeneic mouse models of GBM also demonstrate safety and anti-tumor potency of murine IL13-BBζ CAR T cells delivered systemically after lymphodepletion. These findings support the use of IL13-BBζ CARs for greater selective recognition of IL13Rα2 over IL13Rα1, higher proliferative potential, and superior anti-tumor responsiveness. This study exemplifies the potential of modulating factors outside the antigen targeting domain of a CAR to improve selective tumor recognition..
An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences
Authors: Gurun Burcu , Horton Wesley , Murugan Dhaarini , Zhu Biqing , Leyshock Patrick , Kumar Sushil , Byrne Katelyn T. , Vonderheide Robert H. , Margolin Adam A. , Mori Motomi , Spellman Paul T. , Coussens Lisa M. , Speed Terence P.
Published: April 2022

T cell receptor (TCR) repertoires can be profiled using next generation sequencing (NGS) to monitor dynamical changes in response to disease and other perturbations. Several strategies for profiling TCRs have been recently developed with different benefits and drawbacks. Genomic DNA-based bulk sequencing, however, remains the most cost-effective method to profile TCRs. The major disadvantage of this method is the need for multiplex target amplification with a large set of primer pairs with potentially very different amplification efficiencies. One approach addressing this problem is by iteratively adjusting the concentrations of the primers based on their efficiencies, and then computationally correcting any remaining bias. Yet there are no standard, publicly available protocols to process and analyze raw sequencing data generated by this method. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both approaches, we show that the concordance between bulk clonality metrics obtained from using the commercial kits and that developed herein is high. Therefore, we suggest the method presented here as an inexpensive and non-commercial alternative for measuring and monitoring adaptive dynamics in TCR clonotype repertoire.
Endothelial Caspase-9 Promotes Glial Changes, Inflammation, and Contrast Sensitivity Decline in Retinal Vascular Injury
Authors: Ortiz Crystal Colón , Neal Albertine M. , Avrutsky Maria I. , Choi Monica , Smart Jade , Lawson Jacqueline , Troy Carol M.
Published: March 2022

Retinal glial cells— microglia, astrocytes, and Müller glia—provide homeostatic support, regulate vascular blood flow, and react to injury by releasing inflammatory cytokines. Glial reactivity has been shown to be relevant for retinal vascular pathology and neuronal death. Non-apoptotic expression of endothelial caspase-9 (EC Casp9) was recently identified as a key mediator of retinal edema, hypoxic-ischemic injury, and neurodegeneration in retinal vein occlusion (RVO). In the current study we aimed to determine the glial responses that are modulated by EC Casp9 as a means to identify relevant neuro-immune mechanisms for the development of retinal edema and neurodegeneration. To this end we used a mouse model of RVO and a tamoxifen inducible EC Casp9 KO mouse line. We show that EC Casp9 leads to an increase in reactive microglia and to macrogliosis in a time-dependent manner. RVO induced an EC Casp9 dependent astroglial caspase-6 and cleavage of GFAP. Cytokine array analysis revealed that RVO increases expression of inflammatory cytokines out of which CX3CL1, IGF-1, IL-4, LIX, IL-1α, M-CSF, TNF-α, IL-1β, IL-10, and VEGF-A, were regulated by EC Casp9. Moreover, we found that EC Casp9 deletion resulted in protection from contrast sensitivity decline one day post-RVO. These results demonstrate that caspase-9 in hypoxic endothelial cells regulates retinal inflammatory signaling in microglia, astrocytes and Müller cells and changes in visual function.
OTTERS: A powerful TWAS framework leveraging summary-level reference data
Authors: Dai Qile , Zhou Geyu , Zhao Hongyu , Võsa Urmo , Franke Lude , Battle Alexis , Teumer Alexander , Lehtimäki Terho , Raitakari Olli , Esko Tõnu ,   eQTLGen Consortium, Epstein Michael P. , Yang Jingjing
Published: April 2022

Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.
HTL/KAI2 signalling substitutes for light to control plant germination
Authors: Bunsick Michael , Xu Zhenhua , Pescetto Gianni , Ly George , Hountalas Jenna , Boyer François-Didier , McErlean Christopher S. P. , Scholes Julie D. , Lumba Shelley
Published: March 2022

Deciphering signalling pathways is essential to understanding how organisms respond to environmental cues but elucidating how these signalling pathways evolve in new environments is less clear.1,2 Most plants, for example, monitor multiple environmental cues to optimize the time and place to germinate. Some root parasitic plants, however, germinate in response to small molecules like strigolactones (SLs) emanating from host roots3,4 whilst a number of ephemeral weeds germinate in response to chemicals called karrikins (KARs) released after a forest fire.5,6 Although these species represent distinct clades, they use the same HYPOSENSITIVE TO LIGHT/KARRIKIN INSENSITIVE 2 (HTL/KAI2) signalling pathway to perceive strigolactones or karrikins, which suggests convergent evolution.3,5 Because specialist lifestyles are derived traits, it is not clear if HTL/KAI2 signalling in these species evolved from a specific germination-signalling pathway or whether this pathway had other functions that were co-opted for specialist germination circumstances. Here, we show HTL/KAI2 signalling in Arabidopsis bypasses the light requirement for germination. In part, this is because the HTL/KAI2 downstream component, SMAX1 impinges on PHYTOCHROME INTERACTING FACTOR 1/PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIF1/PIL5)-regulated hormone response pathways conducive to germination. We identified Arabidopsis accessions that can germinate in the dark, which had altered expression of HTL/KAI2 signalling components, suggesting that divergence in this signalling pathway occurs in nature. Moreover, Arabidopsis HTL/KAI2-regulated gene signatures were observed in germinating Striga seed. The ability of HTL/KAI2 signalling to substitute for light advances an explanation for how some specialist plants evolved their underground germination behaviour in response to specific environments.
Glucocorticoids Mediate Transcriptome-wide Alternative Polyadenylation: Mechanisms and Functional Implications
Authors: Le Nguyen Thanh Thanh , Liu Duan , Gao Huanyao , Ye Zhenqing , Lee Jeong-Heon , Wei Lixuan , Yu Jia , Zhang Lingxin , Wang Liewei , Ordog Tamas , Weinshilboum Richard M.
Published: March 2022

Alternative polyadenylation (APA) is a common genetic regulatory mechanism that generates distinct 3′ ends for RNA transcripts. Changes in APA have been associated with multiple biological processes and disease phenotypes. However, the role of hormones and their drug analogs in APA remains largely unknown. In this study, we investigated transcriptome-wide the impact of glucocorticoids on APA in 30 human B-lymphoblastoid cell lines. We found that glucocorticoids could regulate APA of a subset of genes, possibly by changing the expression of 142 RNA-binding proteins, some with known APA-regulating properties. Interestingly, genes with glucocorticoid-mediated APA were enriched in viral translation-related pathways, while genes with glucocorticoid-mediated expression were enriched in interferon and interleukin pathways, suggesting that glucocorticoid-mediated APA might result in functional consequences distinct from gene expression. Glucocorticoid-mediated APA was also cell-type-specific, suggesting an action of glucocorticoids that may be unique to immune regulation. We also observed evidence for genotype-dependent glucocorticoid-mediated APA, providing potential functional mechanisms for a series of common genetic variants that had previously been associated with immune disorders, but without a clear mechanism. In summary, this study reports a series of novel observations regarding the impact of glucocorticoids on APA, suggesting novel avenues for mechanistic studies of hormonal biology.
A fluctuation-based approach to infer kinetics and topology of cell-state switching
Authors: Saint-Antoine Michael , Grima Ramon , Singh Abhyudai
Published: April 2022

In the noisy cellular environment, RNAs and proteins are subject to considerable stochastic fluctuations in copy numbers over time. As a consequence, single cells within the same isoclonal population can differ in their expression profile and reside in different phenotypic states. The dynamic nature of this intercellular variation, where individual cells can transition between different states over time makes it a particularly hard phenomenon to characterize. Here we propose a novel fluctuation-test approach to infer the kinetics of transitions between cell states. More specifically, single cells are randomly drawn from the population and grown into cell colonies. After growth for a fixed number of generations, the number of cells residing in different states is assayed for each colony. In a simple system with reversible switching between two cell states, our analysis shows that the extent of colony-to-colony fluctuations in the fraction of cells in a given state is monotonically related to the switching kinetics. Several closed-form formulas for inferring the switching rates from experimentally quantified fluctuations are presented. We further extend this approach to multiple cell states where harnessing fluctuation signatures can reveal both the topology and the rates of cell-state switching. In summary, our analysis provides a powerful approach for dissecting cell-state transitions based on asingletime point measurement. This is especially important for scenarios where a measurement involves killing the cell (for example, performing single-cell RNA-seq or assaying whether a microbial/cancer cell is in a drug-sensitive or drug-tolerant state), and hence the state of the same cell cannot be measured at different time points.
Brequinar and Dipyridamole in Combination Exhibits Synergistic Antiviral Activity Against SARS-CoV-2 in vitro: Rationale for a host-acting antiviral treatment strategy for COVID-19
Authors: Demarest James F. , Kienle Maryline , Boytz RuthMabel , Ayres Mary , Kim Eun Jung , Chung Donghoon , Gandhi Varsha , Davey Robert , Sykes David B. , Shohdy Nadim , Pottage John C. , Kumar Vikram S.
Published: April 2022

The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised the efficacy of currently available vaccines and monoclonal antibody (mAb)-based treatment options for COVID-19. The limited number of authorized small-molecule direct-acting antivirals present challenges with pill burden, the necessity for intravenous administration or potential drug interactions. There remains an unmet medical need for effective and convenient treatment options for SARS-CoV-2 infection. SARS-CoV-2 is an RNA virus that depends on host intracellular ribonucleotide pools for its replication. Dihydroorotate dehydrogenase (DHODH) is a ubiquitous host enzyme that is required for de novo pyrimidine synthesis. The inhibition of DHODH leads to a depletion of intracellular pyrimidines, thereby impacting viral replication in vitro. Brequinar (BRQ) is an orally available, selective, and potent low nanomolar inhibitor of human DHODH that has been shown to exhibit broad spectrum inhibition of RNA virus replication. However, host cell nucleotide salvage pathways can maintain intracellular pyrimidine levels and compensate for BRQ-mediated DHODH inhibition. In this report, we show that the combination of BRQ and the salvage pathway inhibitor dipyridamole (DPY) exhibits strong synergistic antiviral activity in vitro against SARS-CoV-2 by enhanced depletion of the cellular pyrimidine nucleotide pool. The combination of BRQ and DPY showed antiviral activity against the prototype SARS-CoV-2 as well as the Beta (B.1.351) and Delta (B.1.617.2) variants. These data support the continued evaluation of the combination of BRQ and DPY as a broad-spectrum, host-acting antiviral strategy to treat SARS-CoV-2 and potentially other RNA virus infections.
Reducing societal impacts of SARS-CoV-2 interventions through subnational implementation
Authors: Dekker Mark M. , Coffeng Luc E. , Pijpers Frank P. , Panja Debabrata , de Vlas Sake J.
Published: April 2022

To curb the initial spread of SARS-CoV-2, many countries relied on nation-wide implementation of non-pharmaceutical intervention measures, resulting in substantial socio-economic impacts. Potentially, subnational implementations might have had less of a societal impact, but comparable epidemiological impact. Here, using the first COVID-19 wave in the Netherlands as a case in point, we address this issue by developing a high-resolution analysis framework that uses a demographically-stratified population and a spatially-explicit, dynamic, individual contact-pattern based epidemiology, calibrated to hospital admissions data and mobility trends extracted from mobile phone signals and Google. We demonstrate how a subnational approach could achieve similar level of epidemiological control in terms of hospital admissions, while some parts of the country could stay open for a longer period. Our framework is exportable to other countries and settings, and may be used to develop policies on subnational approach as a better strategic choice for controlling future epidemics.
Mesenchymal Stem Cells Sense the Toughness of Nanomaterials and Interfaces
Authors: Peng Lihui , Matellan Carlos , del Rio Hernandez Armando , Gautrot Julien E.
Published: April 2022

Stem cells are known to sense and respond to a broad range of physical stimuli arising from their extra-cellular environment. In particular, the role of the mechanical properties (Youngs or shear modulus, viscoelasticity) of biomaterials has extensively been shown to have a significant impact on the adhesion, spreading, expansion and differentiation of stem cells. In turn, cells exert forces on their environment that can lead to striking changes in shape, size and contraction of associated tissues, and may result in mechanical disruption and functional failure. However, no study has so far correlated stem cell phenotype and biomaterials toughness. Indeed, disentangling toughness-mediated cell response from other mechanosensing processes has remained elusive as it is particularly challenging to uncouple Youngs’ or shear moduli from toughness, within a range relevant to cell-generated forces. In this report, we show how the design of macromolecular architecture of polymer nanosheets regulates interfacial toughness, independently to interfacial shear storage modulus, and how this, in turn, controls the expansion of mesenchymal stem cells at liquid interfaces.
Affective enhancement of episodic memory is associated with widespread patterns of intrinsic functional connectivity across the adult lifespan
Authors: Katsumi Yuta , Moore Matthew
Published: April 2022

Subjectively arousing experiences tend to be better remembered than neutral ones. While numerous task-related neuroimaging studies have revealed the neural mechanisms associated with this phenomenon, it remains unclear how variability in the extent to which individuals show superior memory for subjectively arousing stimuli is associated with theintrinsicfunctional organization of their brains. Here, we addressed this issue using functional magnetic resonance imaging data collected at rest from a sample drawn from the Cambridge Centre for Ageing Neuroscience cohort (N= 269, 18-86 years). Specifically, we performed multi-voxel pattern analysis of intrinsic functional connectivity, an unbiased, data-driven approach to examine whole-brain voxel-wise connectivity patterns. This technique allowed us to reveal the most important features from the high-dimensional, whole-brain connectivity structure without a priori hypotheses about the topography and direction of functional connectivity differences. Behaviorally, both item and associative memory accuracy were enhanced for trials with affectively arousing (positive or negative) stimuli than those with neutral ones. Whole-brain multi-voxel pattern analysis of functional connectivity revealed that the affective enhancement of memory was associated with intrinsic connectivity patterns of spatially distributed brain regions belonging to several functional networks in the cerebral cortex. Post hoc seed-based brain-behavior regression analysis and principal component analysis of the resulting correlation maps showed that these connectivity patterns were in turn primarily characterized by the involvement of heteromodal association (dorsal attention, salience, and default mode) networks as well as select subcortical structures (striatum, thalamus, and cerebellum). Collectively, these findings suggest that the affective enhancement of episodic memory may be characterized as a whole-brain phenomenon, possibly supported by intrinsic functional interactions across several networks and structures in the brain.
Characterization of EDS1-independent plant defense responses against bacterial pathogens using Duckweed/Pseudomonaspathosystems
Authors: Baggs E.L , Tiersma M.B , Abramson B.W , Michael T.P , Krasileva K.V
Published: April 2022

ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) mediates the induction of defense responses against pathogens in most land plants. However, it has recently been shown that a few species have lost EDS1. It is unknown how defense against disease unfolds and evolves in the absence of EDS1. Here we utilize duckweeds; a collection of aquatic species that lack EDS1, to investigate this question. We successfully established duckweed-Pseudomonaspathosystems and were able to characterize pathogen-induced responses in an immune system that lacks the EDS1 signaling pathway. We show that the copy number of infection-associated genes and the infection-induced transcriptional responses of duckweeds differ from that of other model species. Moreover, we show that the conservation of canonical Microbe Triggered Immunity and Effector Triggered Immunity pathways varies between duckweed species. This work shows that pathogen defense has evolved along different trajectories and uncovers alternative genomic and transcriptional reprogramming. Specifically, the miAMP1 domain containing proteins, which are absent in Arabidopsis, show pathogen responsive upregulation in duckweeds. Despite such divergence between Arabidopsis and duckweed species, we find evidence for the conservation of upregulation of certain genes and the role of hormones in response to disease. Our work highlights the importance of expanding the pool of model species to study defense responses that have evolved in the plant kingdom, including those independent of EDS1.
Temporal and Spatial Resolution of a Protein Quake that Activates Hydrogen Tunneling in Soybean Lipoxygenase
Authors: Zaragoza Jan Paulo T. , Offenbacher Adam R. , Hu Shenshen , Gee Christine L. , Firestein Zachary M. , Minnetian Natalie , Deng Zhenyu , Fan Flora , Iavarone Anthony T. , Klinman Judith P.
Published: April 2022

The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen deuterium exchange experiments to detect a radiating cone of aliphatic side chains that extends from the iron active site of SLO to the protein-solvent interface. Employing eight variants of SLO, nanosecond fluorescence Stokes shifts have been measured using a probe appended to the identified surface loop. We report a remarkable identity of the enthalpies of activation for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within the identified thermal network. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, these new data implicate a thermally initiated, cooperative protein quake as the source of the activation of SLO. These findings indicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis.
Active Anemosensing Hypothesis: How Flying Insects Could Estimate Ambient Wind Direction Through Sensory Integration & Active Movement
Authors: van Breugel Floris , Jewell Renan , Houle Jaleesa
Published: April 2022

Estimating the direction of ambient fluid flow is a crucial step during chemical plume tracking for flying and swimming animals. How animals accomplish this remains an open area of investigation. Recent calcium imaging with tethered flying Drosophila has shown that flies encode the angular direction of multiple sensory modalities in their central complex: orientation, apparent wind (or airspeed) direction, and direction of motion. Here we describe a general framework for how these three sensory modalities can be integrated over time to provide a continuous estimate of ambient wind direction. After validating our framework using a flying drone, we use simulations to show that ambient wind direction can be most accurately estimated with trajectories characterized by frequent, large magnitude turns. Furthermore, sensory measurements and estimates of their derivatives must be integrated over a period of time that incorporates at least one of these turns. Finally, we discuss approaches that insects might use to simplify the required computations, and present a list of testable predictions. Together, our results suggest that ambient flow estimation may be an important driver underlying the zigzagging maneuvers characteristic of plume tracking animals’ trajectories.