bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of trimeric pre-fusion rabies virus glycoprotein in complex with two protective antibodies
Authors: Ng Weng M , Fedosyuk Sofiya , English Solomon , Augusto Gilles , Berg Adam , Thorley Luke , Segireddy Rameswara R , Bowden Thomas A , Douglas Alexander D 
Published: March 2022

SummaryRabies virus (RABV) causes lethal encephalitis and is responsible for approximately 60,000 deaths per year. As the sole virion-surface protein, the rabies virus glycoprotein (RABV-G) mediates host-cell entry. RABV-G’s pre-fusion trimeric conformation displays epitopes bound by protective neutralizing antibodies which can be induced by vaccination or passively administered for post-exposure prophylaxis. We report a 2.8-Å structure of a RABV-G trimer in the pre-fusion conformation, in complex with two neutralizing and protective monoclonal antibodies, 17C7 and 1112-1. One of these antibodies is a licensed prophylactic (17C7, Rabishield), which we show locks the protein in pre-fusion conformation. We demonstrate that targeted mutations can stabilize RABV-G in the pre-fusion conformation, a key step towards structure-guided vaccine design. These data reveal the higher-order architecture of a key therapeutic target and the structural basis of neutralization by antibodies binding two key antigenic sites, and will facilitate the development of improved vaccines and prophylactic antibodies.
An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability
Authors: Jain Kanishk , Marunde Matthew R. , Burg Jonathan M. , Gloor Susan L. , Joseph Faith M. , Poncha Karl F. , Gillespie Zachary B. , Rodriguez Keli L. , Popova Irina K. , Hall Nathan W. , Vaidya Anup , Howard Sarah A. , Taylor Hailey F. , Mukhsinova Laylo , Onuoha Ugochi C. , Patteson Emily F. , Cooke Spencer W. , Taylor Bethany C. , Weinzapfel Ellen N. , Cheek Marcus A. , Meiners Matthew J. , Fox Geoffrey C. , Namitz Kevin E. W. , Cowles Martis W. , Krajewski Krzysztof , Sun Zu-Wen , Cosgrove Michael S. , Young Nicolas L. , Keogh Michael-Christopher , Strahl Brian D. 
Published: March 2022

ABSTRACTIn nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g., K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has broader extension. Here we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on thecisH3 tail, as determined with fully-defined heterotypic nucleosomes.In vivo, H3 tail acetylation is directly and dynamically coupled withcisH3K4 methylation levels. Together, these observations reveal an acetylation ‘chromatin switch’ on the H3 tail that modulates read-write accessibility in nucleosomes and resolve the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.
Critical periods when dopamine controls behavioral responding during Pavlovian learning
Authors: Lefner Merridee J. , Stelly Claire E. , Fonzi Kaitlyn M. , Zurita Hector , Wanat Matthew J. 
Published: March 2022

AbstractRationaleLearning the association between rewards and predictive cues is critical for appetitive behavioral responding. The mesolimbic dopamine system is thought to play an integral role in establishing these cue-reward associations. The dopamine response to cues can signal differences in reward value, though this emerges only after significant training. This suggests that the dopamine system may differentially regulate behavioral responding depending on the phase of training.ObjectivesThe purpose of this study was to determine whether antagonizing dopamine receptors elicited different effects on behavior depending on the phase of training or the type of Pavlovian task.MethodsSeparate groups of male rats were trained on Pavlovian tasks in which distinct audio cues signaled either differences in reward size or differences in reward rate. The dopamine receptor antagonist flupenthixol was systemically administered prior to either the first ten sessions of training (acquisition phase) or the second ten sessions of training (expression phase) and we monitored the effect of these manipulations for an additional ten training sessions.ResultsWe identified acute effects of dopamine receptor antagonism on conditioned responding, the latency to respond, and post-reward head entries in both Pavlovian tasks. Interestingly, dopamine receptor antagonism during the expression phase produced persistent deficits in behavioral responding only in rats trained on the reward size Pavlovian task.ConclusionsTogether, our results illustrate that dopamine’s control over behavior in Pavlovian tasks depends upon one’s prior training experience and the information signaled by the cues.
Dual species transcriptomics reveals core metabolic and immunologic processes in the interaction between primary human neutrophils andNeisseria gonorrhoeaestrains
Authors: Edwards Vonetta L. , Potter Aimee D. , D’Mello Adonis , Gray Mary C. , Shetty Amol C. , Zhao Xuechu , Hill Katherine M. , Ragland Stephanie A. , Criss Alison K. , Tettelin Hervé 
Published: March 2022

ABSTRACTNeisseria gonorrhoeae(the gonococcus, Gc) is the causative agent of the sexually transmitted infection gonorrhea. Gc is a prominent threat to human health by causing severe and lifelong clinical sequelae, including infertility and chronic pelvic pain, which is amplified by the emergence of “superbug” strains that are resistant to all current antibiotics. Gc is highly adapted to colonize human mucosal surfaces, where it survives despite initiating a robust inflammatory response and influx of polymorphonuclear leukocytes (PMNs or neutrophils) that typically clear bacteria. Here, dual-species RNA-sequencing (RNA-seq) was used to define Gc and PMN transcriptional profiles alone and after infection. Three strains of Gc and three human donors’ transcriptional responses were assessed to characterize core host and bacterial responses. Comparative analysis of Gc transcripts revealed major overlap between the Gc response to PMNs, iron, and hydrogen peroxide; specifically, the TonB system and TonB dependent transporters (TDT) were upregulated in response to PMNs. We experimentally confirmed that induction of the iron-dependent TDT TbpB is responsive to the presence of PMNs and thattonBis required for Gc survival from PMNs. Pathway analysis of PMN transcripts induced by Gc infection revealed differential expression of genes driving pathways involved in cell adhesion and migration, inflammatory responses, and inflammation resolution. Production of pro-inflammatory cytokines, including IL1B and IL8, the adhesion factor ICAM1, and the anti-inflammatory prostaglandin PGE2 was confirmed to be induced in PMNs in response to Gc. Together, this study represents a comprehensive and experimentally validated dual-species transcriptomic analysis of three isolates of Gc and primary human PMNs that gives insight into how this bacterium survives innate immune onslaught to cause disease in humans.
Transposon Mutagenesis Reveals RBMS3 as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis
Authors: Vaishnavi Aria , Juan Joseph , Scherzer Michael T. , VanVeen J. Edward , Stehn Christopher , Hackett Christopher S. , Dupuy Adam , Chmura Steven A. , van der Weyden Louise , Newberg Justin Y. , Mann Karen M. , Liu Annie , Rust Alistair G. , Weiss William A. , Adams David J. , Grossmann Allie , Mann Michael B. , McMahon Martin 
Published: March 2022

ABSTRACTMutationally-activated BRAFV600E is detected in ~2% of all human non-small cell lung cancers (NSCLC), and serves as a predictive biomarker for treatment of patients with FDA-approved pathway-targeted therapies that inhibit signaling by the BRAFV600E oncoprotein kinase. In genetically engineered mouse (GEM) models, expression of BRAFV600E in alveolar type 2 (AT2) pneumocytes initiates the development of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinomas. To identify genes that might cooperate with BRAFV600E for malignant lung cancer progression we employed Sleeping Beauty (SB)-mediated transposon mutagenesis, which dramatically accelerated the onset of lethal lung adenocarcinomas. Amongst the diverse group of genes identified by this in vivo screen was Rbms3 (RNA binding motif single-stranded interacting protein 3), an RNA-binding protein implicated as a possible tumor suppressor. Using CRISPR/CAS9 gene editing we confirmed that RBMS3 silencing cooperated with BRAFV600E to promote progression of malignant lung cancer with a distinct micropapillary architecture. Moreover, RBMS3 silencing also cooperated with BRAFV600E to promote the growth of lung organoids in vitro. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of b-catenin (CTNNB1), suggesting that RBMS3 silencing may result in elevated signaling through the WNT>CTNNB1>c-MYC pathway. Finally, analyses of patient samples in The Cancer Genome Atlas (TCGA) revealed that the region of chromosome 3 encompassing RBMS3 is frequently lost in NSCLC and correlates with poor patient prognosis. Collectively, SB-mediated transposon mutagenesis has revealed the ability of a novel tumor suppressor, RBMS3, to cooperate with BRAFV600E to promote lung carcinogenesis, and suggests that RBMS3 silencing may contribute to malignant progression of numerous human lung cancers.SIGNIFICANCEThe BRAFV600E oncoprotein kinase is a potent initiator of benign lung tumorigenesis, but is insufficient to elicit malignant lung adenocarcinoma without additional cooperating alterations. Sleeping Beauty-mediated transposon mutagenesis has revealed a number of genes that cooperate with BRAFV600E to promote lung cancer progression, in particular Rbms3, which encodes an RNA binding protein. Hence, this genetic screen provides a deeper understanding of the molecular mechanisms underlying BRAFV600E-driven lung carcinogenesis, and is an important step improving our ability to successfully target this disease.
Pleiotropic effects onE. coliphysiology of the AraC-like regulator from prophage origin, AppY
Authors: Derdouri Naoual , Ginet Nicolas , Denis Yann , Ansaldi Mireille , Battesti Aurélia 
Published: March 2022

ABSTRACTBacterial genome diversity is largely due to prophages, which are viral genomes integrated into the genomes of bacteria. Most prophage genes are silent, but those that are expressed can provide unexpected properties to their host. Using as a modelE. coliK-12, that carries 9 defective prophages in its genome, we aimed at highlighting the impact of viral genes on host physiology. We focused our work on AppY, a transcriptional regulator encoded on the DLP12 prophage. By performing RNA-Seq experiments, we showed that AppY production modulates the expression of more than 200 genes; among them, 13 were identified by ChIP-Seq as direct AppY targets. AppY directly and positively regulates several genes involved in the acid stress response including the master regulator genegadE, but alsonhaRandgadY, two genes involved in biofilm formation. Moreover, AppY indirectly and negatively impacts bacterial motility by favouring the degradation of FlhDC, the master regulator of the flagella biosynthesis. As a consequence of these regulatory effects, AppY increased acid stress resistance and biofilm formation while also causing a strong defect in motility. We therefore demonstrate here that AppY is a central regulator from phage origin that controls the expression of bacterial master regulators to provide benefits toE. coliunder stress conditions. Our research shed light on the importance to consider the genetic dialogue occurring between prophages and bacteria to fully understand bacterial physiology.
Mycobacterial Serine/Threonine phosphatase PstP is phospho-regulated and localized to mediate control of cell wall metabolism
Authors: Shamma Farah , Rego E. Hesper , Boutte Cara C. 
Published: March 2022

ABSTRACTThe mycobacterial cell wall is profoundly regulated in response to environmental stresses, and this regulation contributes to antibiotic tolerance. The reversible phosphorylation of different cell wall regulatory proteins is a major mechanism of cell wall regulation. Eleven Serine/Threonine protein kinases (STPKs) phosphorylate many critical cell wall-related proteins in mycobacteria. PstP is the sole serine/ threonine phosphatase, but few proteins have been verified as PstP substrates. PstP is itself phosphorylated but the role of its phosphorylation in regulating its activity has been unclear. In this study we aim to discover novel substrates of PstP in Mycobacterium tuberculosis (Mtb). We show in vitro that PstP dephosphorylates two regulators of peptidoglycan in Mtb, FhaA and Wag31. We also show that a phospho-mimetic mutation of T137 on PstP negatively regulates its catalytic activity against the cell wall regulators FhaA, Wag31, CwlM, PknB and PknA, and that the corresponding mutation in Mycobacterium smegmatis (Msmeg) causes mis-regulation of peptidoglycan in vivo. We show that PstP is localized to the septum, which likely restricts its access to certain substrates. These findings on the regulation of PstP provide insight into the control of cell wall metabolism in mycobacteria.
Balancing activation and costimulation of CAR tunes signaling dynamics and enhances therapeutic potency
Authors: Duan Yanting , Chen Jiangqing , Meng Xianhui , Liu Longwei , Shang Kai , Wu Xiaoyan , Wang Yajie , Huang Zihan , Liu Houyu , Huang Yanjie , Zhou Chun , Gao Xiaofei , Wang Yingxiao , Sadelain Michel , Sun Jie 
Published: March 2022

AbstractBackgroundPrimary human T cells engineered with chimeric antigen receptors (CARs) ex vivo can be adoptively transferred to treat cancer. CD19-targeting CAR with CD28 costimulatory domain and CD3ζ activation domain have been approved by the US FDA for treating B cell malignancies.MethodsHere we generated mutation of immunorecpetor tyrosine-based activation motifs (ITAMs) in CD3ζ, namely 1XX CAR, which altered the balance of activation and costimulation. Next we investigated whether 1XX design could enhance therapeutic potency against solid tumors. We constructed both CD19- and AXL-specific 1XX CARs and compared theirin vitroandin vivofunctions with their WT counterparts.ResultsEven though 1XX CARs decreased cytotoxicity against tumor cellsin vitro, they showed better anti-tumor efficacy in both pancreatic and melanoma mouse models. Detailed analysis revealed that 1XX CAR-T cells proliferated more in response to antigen stimulationin vitro, persisted longerin vivoand had higher percentage of central memory cells. As 1XX modification directly calibrates CAR activation potential, we utilized fluorescence resonance energy transfer (FRET)-based biosensor to monitor signaling dynamics downstream of CARs. Decreased ITAM numbers in 1XX resulted in similar ZAP70 activation, while 1XX induced higher Ca2+elevation and faster Erk activation than WT CAR, which may contribute to the better therapeutic potency of 1XX.ConclusionsOur results established the surpiosity of 1XX against two targets in different solid tumor models and shed light on the underlying molecular mechanism of CAR signaling, paving the way for the clinical application of 1XX CARs against solid tumors.
Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer
Authors: Luong Thong T. , Li Zheqi , Priedigkeit Nolan , Parker Phoebe S. , Böhm Stefanie , Rapchak Kyle , Lee Adrian V. , Bernstein Kara A. 
Published: March 2022

AbstractHuman RECQL4 is a member of the RecQ family of DNA helicases and functions during DNA replication and repair.RECQL4mutations are associated with developmental defects and cancer. AlthoughRECQL4mutations lead to disease,RECQL4overexpression is also observed in cancer, including breast and prostate. Thus, tight regulation of RECQL4 protein levels is crucial for genome stability. Because mammalianRECQL4is essential, how cells regulate RECQL4 protein levels is largely unknown. Utilizing budding yeast, we investigated theRECQL4homolog,HRQ1, during DNA crosslink repair. We find that Hrq1 functions in the error-free template switching pathway to mediate DNA intrastrand crosslink repair. Although Hrq1 repairs cisplatin-induced lesions, it is paradoxically degraded by the proteasome following cisplatin treatment. By identifying the targeted lysine residues, we show that preventing Hrq1 degradation results in increased recombination and mutagenesis. Like yeast, human RECQL4 is similarly degraded upon exposure to crosslinking agents. Furthermore, over-expression ofRECQL4results in increased RAD51 foci, which is dependent on its helicase activity. Using bioinformatic analysis, we observe thatRECQL4overexpression correlates with increased recombination and mutations. Overall, our study uncovers a role for Hrq1/RECQL4 in DNA intrastrand crosslink repair and provides further insight how misregulation of RECQL4 can promote genomic instability, a cancer hallmark.
On the regulation of photosynthesis in pea leaves exposed to oscillating light
Authors: Lazár Dušan , Niu Yuxi , Nedbal Ladislav 
Published: March 2022

AbstractPlants grow in nature often in fluctuating irradiance. In the laboratory, the dynamics of photosynthesis is usually explored by instantaneously exposing dark-adapted plants to constant light and detecting the dark-to-light transient, which is only a poor approximation of natural phenomena. Aiming at a better approximation, we exposed pea leaves to oscillating light and measured, during oscillations, changes in function of photosystem I and II and of the proton-motive force at the thylakoid membrane. The dynamics depends on the oscillation period, leaving information about the regulatory networks. As demonstrated for selected period of the oscillation of 60 s, the regulations try to keep reactions centres of photosystems I and II open. A possible evaluation of obtained data is presented and involvement of particular processes in regulation of photosynthesis is discussed. The forced oscillations provide information-rich fingerprint of complex regulatory networks. Further progress in understanding the networks is expected from experiments involving chemical interventions, plant mutants, and by using mathematical modelling and the system identification and system control tools, as already applied in other parts of science.HighlightMeasurement of photosynthetic signals during illumination of plants by light, whose intensity oscillates as sinus function provides information about regulation of photosynthesis in fluctuating light.
Spatio-temporal model and machine learning method reveal process of phenological shift under climate change of North Pacific spiny dogfish
Authors: Kanamori Yuki , Yano Toshikazu , Okamura Hiroshi , Yagi Yuta 
Published: March 2022

AbstractClimate change has disrupted natural phenological patterns, including migration. Despite extensive studies of phenological shifts in migration by climate change and driving factors of migration, a few issues remain unresolved. In particular, little is known about the complex effects of driving factors on migration with interactions and nonlinearity, and partitioning of the effects of factors into spatial, temporal, and spatio-temporal effects. The Pacific spiny dogfish Squalus suckleyi (hereafter “spiny dogfish”) is a coastal elasmobranchii that migrates southward for parturition and northward for feeding in the western North Pacific. Here, to elucidate the migration patterns as well as the driving factors under climate change, we first examined long-term changes in the timing and geographic location of migration by applying a spatio-temporal model to ca. 5-decade time series data for the presence/absence of spiny dogfish in the western North Pacific. We then evaluated the spatial, temporal, and spatio-temporal effects of driving factors (sea surface temperature [SST], depth, productivity, and magnetic fields) on seasonal occurrence patterns using a machine learning model. We found that the migration area did not change over ca. 5 decades, whereas the migration timing advanced by a month after 2000. The spatial effects of magnetic fields and depth were consistently large and the spatial and spatio-temporal effects of SST increased in the migration season, even though temporal effect of SST was always weak. These results suggest that the migration area of spiny dogfish was stable over time because their spatial distribution was determined by geographic features, whereas the migration timing advanced by tracking a suitable SST location which increased steeply after 2000. Therefore, temperature as well as other factors influence migration simultaneously under climate change and underline the importance of paying attention biotic/abiotic factors including temperature and process-based understanding to predict future impacts of climate change on phenological shifts.
Experimental evidence that animal societies vary in size due to sex differences in cooperation
Authors: Melgar Julian , Schou Mads F. , Bonato Maud , Brand Zanell , Engelbrecht Anel , Cloete Schalk W. P. , Cornwallis Charlie K. 
Published: March 2022

AbstractCooperative breeding societies allow the costs of reproduction to be shared. However, as groups become larger, such benefits often decrease and competition increases. This is predicted to select for an optimal group size, yet variation in groups is a ubiquitous feature of cooperative breeding animals. Here we experimentally established groups (ngroups=96) of cooperative breeding ostriches,Struthio camelus, with different numbers of males and females and manipulated the potential for cooperation over incubation. There was a clear optimal group size for males. Their reproductive success was maximized in groups with four or more females and no other males, irrespective of cooperation over incubation. Conversely, female reproductive success was strongly dependent on the benefits of cooperating over incubation, being maximized in groups with either many males or many females. In intermediate sized groups, both male and female reproductive success was reduced by sexual conflict over the timing of mating and incubation. Our experiments show that sex differences in the opposing forces of cooperation and competition can explain why variation in cooperative groups is widespread.