bluuebunny/crossref_metadata_2025 huggingface dataset:
Vaccination and Variants: retrospective model for the evolution of Covid-19 in Italy
Authors: Fierro Annalisa , Romano Silvio , Liccardo Antonella
Published: March 2022

The last year of Covid-19 pandemic has been characterized by the continuous chase between the vaccination campaign and the appearance of new variants that put further obstacles to the possibility of eradicating the virus and returning to normality in a short period. In the present paper we consider a deterministic compartmental model to discuss the evolution of the Covid-19 in Italy as a combined effect of vaccination campaign, new variant spreading, waning immunity and mobility restrictions. We analyze the role that different mechanisms, such as behavioral changes due to variable risk perception, variation of the population mobility, seasonal variability of the virus infectivity, and spreading of new variants have had in shaping the epidemiological curve. The fundamental impact of vaccines in drastically reducing the total increase in infections and deaths is also estimated. This work further underlines the crucial importance of vaccination and adoption of adequate individual protective measures in containing the pandemic.
Effect of an Integrated Maternal and Neonatal Health Intervention on Maternal Healthcare Utilization addressing Inequity in Rural Bangladesh
Authors: Ahmed Anisuddin , Huq Nafisa Lira , Rahman Fariya , Tanwi Tania Sultana , Siddique Md. Abu Bakkar , Hossain Aniqa Tasnim , Ether Saraban Tahura , Akter Ema , Tahsina Tazeen , Arifeen Shams El , Rahman Ahmed Ehsanur
Published: March 2022

Background

Although Bangladesh has made significant improvements in maternal, neonatal, and child health, the disparity between rich and poor remains a matter for concern.

Objective

The study aimed to increase coverage of women in seeking skilled maternal healthcare services while minimizing inequity gap among different socioeconomic groups.

Methods

icddr, b implemented an integrated maternal and neonatal health (MNH) intervention between 2009 and 2012, in Shahjadpur sub-district of Shirajganj district, Bangladesh. The study was pre- and post-test in design for evaluation including baseline and endline surveys. The baseline and endline surveys were conducted among 3158 and 3540 recently delivered mothers respectively. Asset index derived from household assets using principal component analysis was categorized into five ordinal categories, i.e. Poor, Less poor, Middle, Upper middle, Rich. Inequity in maternal healthcare utilization was calculated for the baseline and endline periods using rich- to-poor ratio and the concentration index.

Result

Mean age of mothers were 23.5 and 24.3 years in baseline and endline, respectively. Reduction in rich-poor ratio was quite large in utilization of skilled 4+ antenatal care (ANC) (2.4:1 to 1.1:1), childbirth (1.7:1 to 1.0:1), and postnatal care (PNC) (2.5:1 to 1.0:1) from trained providers between these two surveys. The concentration indices (CI) in endline for skilled 4+ ANC (CI: 0.220 and 0.013), delivery (CI: 0.161 and -0.021), and PNC (CI: 0.197 and -0.004) were found to be lower than the indices in baseline period respectively.

Conclusion

The MNH intervention was successful in reducing inequity in receiving skilled 4+ ANC, delivery, and PNC in rural Bangladesh. Improvements in maternal healthcare utilizations by poor mothers would be influenced by the properly designed and integrated demand- and supply-side MNH interventions package.
A cooperative switch within the KaiC hexamer revealed by cryo-EM
Authors: Han Xu , Zhang Dongliang , Hong Lu , Yu Daqi , Wu Zhaolong , Yang Tian , Rust Michael , Tu Yuhai , Ouyang Qi
Published: March 2022

The circadian clock of cyanobacteria is based on an approximately 24h rhythm in the phosphorylation level of KaiC, a hexameric ATPase. This oscillation can be reconstituted in vitro by incubating three proteins together with ATP. Like all chemical oscillators, this system must include a nonlinear, or switch-like, feedback loop, whose nature has been unclear. Here, by using single particle cryo-EM at near-atomic resolution we identified two major conformational states of KaiC subunits, denoted as the exposed state and the buried state, which may provide a structural basis of how the KaiC hexamer changes its conformation during the (day-night) phosphorylation-dephosphorylation cycle. We classify the abundance and pattern of exposed and buried states within hexamers for more than 160,000 KaiC particles. The statistics of the spatial arrangement of the two states in hexamers can be quantitatively fit by a simple statistical physics model with an interaction energy between neighboring subunits and a local field that depends on phosphorylation state. Our study shows that phosphorylation shifts the probability of each conformation and reveals that there is substantial cooperativity between neighboring subunits, which can allow a KaiC hexamer to respond in an ultrasensitive, switch-like manner to changes in the phosphorylation level.
Mechanistic insights into the functioning of GMP synthetase: a two-subunit, allosterically regulated, ammonia tunnelling enzyme
Authors: Shivakumaraswamy Santosh , Kumar Sanjeev , Bellur Asutosh , Polisetty Satya Dev , Balaram Hemalatha
Published: March 2022

Guanosine 5’-monophosphate (GMP) synthetases, enzymes that catalyze the conversion of xanthosine 5’-monophosphate (XMP) to GMP are comprised of two different catalytic units, which are either two domains of a polypeptide chain or two subunits that associate to form a complex. The glutamine amidotransferase (GATase) unit hydrolyzes glutamine generating ammonia and the ATP pyrophosphatase (ATPPase) unit catalyzes the formation of AMP-XMP intermediate. The substrate-bound ATPPase allosterically activates GATase and the ammonia thus generated is tunnelled to the ATPPase active site where it reacts with AMP-XMP generating GMP. In ammonia tunnelling enzymes reported thus far, a tight complex of the two subunits is observed, while the interaction of the two subunits of Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is transient with the underlying mechanism of allostery and substrate channelling largely unclear. Here, we present a mechanistic model encompassing the various steps in the catalytic cycle of MjGMPS based on biochemical experiments, crystal structure and cross-linking mass spectrometry guided integrative modelling. pH dependence of enzyme kinetics establish that ammonia is tunnelled across the subunits with the lifetime of the complex being ≤ 0.5 s. The crystal structure of XMP-bound ATPPase subunit reported herein highlights the role of conformationally dynamic loops in enabling catalysis. The structure of MjGMPS derived using restraints obtained from cross-linking mass spectrometry has enabled the visualization of subunit interactions that enable allostery under catalytic conditions. We integrate the results and propose a functional mechanism for MjGMPS detailing the various steps involved in catalysis.

Graphical Abstract
A high-performance genetically encoded fluorescent indicator for in vivo cAMP imaging
Authors: Wang Liang , Wu Chunling , Peng Wanling , Zhou Ziliang , Zeng Jianzhi , Li Xuelin , Yang Yini , Yu Shuguang , Zou Ye , Huang Mian , Liu Chang , Chen Yefei , Li Yi , Ti Panpan , Liu Wenfeng , Gao Yufeng , Zheng Wei , Gao Shangbang , Lu Zhonghua , Ren Pei-Gen , Ng Ho Leung , He Jie , Chen Shoudeng , Xu Min , Li Yulong , Chu Jun
Published: March 2022

cAMP is a key second messenger that regulates diverse cellular functions including neural plasticity. However, the spatiotemporal dynamics of intracellular cAMP in intact organisms are largely unknown due to low sensitivity and/or brightness of current genetically encoded fluorescent cAMP indicators. Here, we report the development of the new circularly permuted GFP (cpGFP)-based cAMP indicator G-Flamp1, which exhibits a large fluorescence increase (a maximum ΔF/F0 of 1100% in HEK293T cells), relatively high brightness, appropriate affinity (a Kd of 2.17 µM) and fast response kinetics (an association and dissociation half-time of 0.20 s and 0.087 s, respectively). Furthermore, the crystal structure of the cAMP-bound G-Flamp1 reveals one linker connecting the cAMP-binding domain to cpGFP adopts a distorted β-strand conformation that may serve as a fluorescence modulation switch. We demonstrate that G-Flamp1 enables sensitive monitoring of endogenous cAMP signals in brain regions that are implicated in learning and motor control in living organisms such as fruit flies and mice.
Influence of age and cognitive performance on resting-state functional connectivity of dopaminergic and noradrenergic centres
Authors: Zareba Michal Rafal , Furman Wiktoria , Binder Marek
Published: March 2022

The process of ageing is associated with structural and functional changes in the brain, with a decline in cognitive functions observed as its inevitable symptom, even in the absence of neurodegenerative changes. A body of literature suggests dopamine and noradrenaline as prominent candidate molecules to mediate these effects, however, the knowledge regarding the underlying mechanisms is scarce. To fill this gap, we compared local and distant resting-state functional connectivity patterns of ventral tegmental area, substantia nigra pars compacta and locus coeruleus in healthy young (20-35 years; N = 37) and older adults (55-80 years; N = 27). Additionally, we sought long-range functional connectivity patterns of these structures associated with performance in tasks probing executive, attentional and reward functioning, as well as compared the functional coupling of the left and right substantia nigra. The results showed that each substantia nigra had stronger coupling with ipsilateral cortical and subcortical areas along with contralateral cerebellum, and that strength of functional connections of this structure with angular gyrus and lateral orbitofrontal cortex predicted the visuomotor search abilities. In turn, ageing was associated with increased local synchronisation in the ventral tegmental area, and differences in functional connectivity of the dopaminergic midbrain with numerous cortical and subcortical structures. Locus coeruleus functional coupling showed no differences between the groups and was not associated with any of the behavioural functions. To the best of our knowledge, this work is the first one to report the age-related effects on midbrain local synchronisation and its connectivity with key recipients of dopaminergic innervation, such as striatum, anterior cingulate and insula.
Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic
Authors: Nasimiyu Carolyne , Matoke-Muhia Damaris , Rono Gilbert K. , Osoro Eric , Obado Daniel O. , Mwangi J. Milkah , Mwikwabe Nicholas , Thiong’o Kelvin , Dawa Jeanette , Ngere Isaac , Gachohi John , Kariuki Samuel , Amukoye Evans , Mureithi Marianne , Ngere Philip , Amoth Patrick , Were Ian , Makayotto Lyndah , Nene Vishvanath , Abworo Edward O. , Njenga M. Kariuki , Seifert Stephanie N. , Oyola Samuel O.
Published: March 2022

Background

Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression.

Methods

SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens.

Results

Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, ofAlpha(74.9% genomes),Delta(98.7%), andOmicron(87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country.

Conclusions

The emergence ofAlpha, Delta, andOmicronvariants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.
Discriminatory ability of gas chromatography-ion mobility spectrometry to identify patients hospitalised with COVID-19 and predict prognosis
Authors: Nazareth Joshua , Pan Daniel , Kim Jee Whang , Leach Jack , Brosnan James G , Ahmed Adam , Brodrick Emma , Wicaksono Alfian , Daulton Emma , Williams Caroline , Haldar Pranabashis , Covington James A. , Pareek Manish , Sahota Amandip
Published: March 2022

Background

Tests that can diagnose COVID-19 rapidly and predict prognosis would be significantly beneficial. We studied the ability of breath analysis using gas chromatography-ion mobility spectrometry (GC-IMS) for diagnosis of COVID-19 and as a predictor for subsequent requirement for Continuous Positive Airway Pressure (CPAP).

Methods

We undertook a single centre prospective observational study in patients with COVID-19, other respiratory tract infections and healthy controls. Participants provided one breath sample for GC-IMS analysis. We used cross validation analysis to create models that were then tested against the original cohort data. Further multivariable analysis was undertaken to adjust for differences between the comparator groups.

Results

Between 01/02/2021 and 24/05/2021 we recruited 113 participants, of whom 72 (64%) had COVID-19, 20 (18%) had another respiratory tract infection and 21 (19%) were healthy controls. Differentiation between patients with COVID-19 and healthy controls, and patients with COVID-19 and those with other respiratory tract infections, was achieved with high accuracy. Identification of patients with subsequent requirement for CPAP was completed with moderate accuracy and was not independently associated on multivariable analysis.

Conclusions

We have shown that GC-IMS has a high capability to distinguish between acute COVID-19 infection and other disease states. Breath analysis shows promise as a predictor of subsequent requirement for CPAP in hospitalised patients with COVID-19. This platform has considerable benefits due to the test being rapid, non-invasive and not requiring specialist laboratory processing.
Influence of landscape patterns on the exposure of LASV across diverse regions within the Republic of Guinea
Authors: Longet Stephanie , Leggio Cristina , Bore Joseph Akoi , Tipton Tom , Hall Yper , Koundouno Fara Raymond , Key Stephanie , Bower Hilary , Bhattacharyya Tapan , Magassouba N’Faly , Günther Stephan , Henao-Restrapo Ana-Maria , Rossman Jeremy S. , Konde Mandy Kader , Fornace Kimberly , Carroll Miles W.
Published: March 2022

Lassa fever virus (LASV) is the causative agent of Lassa fever, a disease endemic in West Africa. Exploring the relationships between environmental factors and LASV transmission across ecologically diverse regions can provide crucial information for the design of appropriate interventions and disease monitoring. We measured LASV-specific IgG seropositivity in 1286 sera collected in Coastal and Forested Guinea. Our results showed that exposure to LASV was heterogenous between the sites. The LASV IgG seropositivity was 11.9% (95% CI 9.7-14.5) in Coastal site, while it was 59.6% (95% CI 55.5-63.5) in Forested region. Interestingly, exposure was significantly associated with age, with seropositivity increasing with age in the Coastal site. Finally, we also found significant associations between exposure risk to LASV and landscape fragmentation in Coastal and Forested regions. This study may help to define the regions with an increased exposure risk to LASV where a close surveillance of LASV circulation is needed.
Dendrites use mechanosensitive channels to proofread ligand-mediated guidance during morphogenesis
Authors: Tao Li , Coakley Sean , Shi Rebecca , Shen Kang
Published: March 2022

Ligand-receptor interactions guide axon navigation and dendrite arborization. Mechanical forces also influence guidance choices. However, the nature of such mechanical stimulations, the mechanosensors identity and how they interact with guidance receptors are unknown. Here, we demonstrate that mechanosensitive DEG/ENaC channels are required for dendritic arbor morphogenesis in Caenorhabditis elegans. Inhibition of DEG/ENaC channels causes reduced dendritic outgrowth and branching in vivo, a phenotype that is alleviated by overexpression of the mechanosensitive channels PEZO-1/Piezo or YVC1/TrpY1. DEG/ENaCs trigger local Ca2+ transients in growing dendritic filopodia via activation of L-type voltage-gated Ca2+ channels. Anchoring of filopodia by guidance ligand/receptor is required for the mechanical activation of DEG/ENaC channels. Therefore, mechanosensitive channels serve as a checkpoint for appropriate chemoaffinity by activating Ca2+ transients required for neurite growth.
Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation
Authors: Millrine David , Cummings Thomas , Matthews Stephen P. , Peter Joshua J. , Magnussen Helge , Macartney Thomas , Lamoliatte Frederic , Knebel Axel , Kulathu Yogesh
Published: March 2022

An essential first step in the posttranslational modification of proteins with UFM1, UFMylation, is the proteolytic cleavage of pro-UFM1 to expose a C-terminal glycine. Of the two UFM1-specific proteases (UFSPs) identified in humans, only UFSP2 is reported to be active since the annotated sequence of UFSP1 lacks critical catalytic residues. Nonetheless, efficient UFM1 maturation occurs in cells lacking UFSP2 suggesting the presence of another active protease. We hereby identify a long isoform of UFSP1 to be this protease. Cells lacking both UFSPs show complete loss of UFMylation resulting from an absence of mature UFM1. While UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26, UFSP1 acts earlier in the pathway to mature UFM1 and cleave a potential auto-inhibitory modification on UFC1, thereby controlling activation of UFMylation. In summary, our studies reveal important distinctions in substrate specificity and localization-dependent functions for the two proteases in regulating UFMylation.
First report of kdr L1014F and ace-1 G119S insecticide resistance in Belgian Culex (Diptera: Culicidae) mosquitoes
Authors: Wang Lanjiao , Soto Alina , Remue Laure , Rosas Ana Lucia Rosales , De Coninck Lander , Verwimp Sam , Bouckaert Johanna , Vanwinkel Mathias , Matthijnssens Jelle , Delang Leen
Published: March 2022

The emergence of West Nile virus and Usutu virus in Europe poses a significant risk to public health. In the absence of efficient antiviral therapy or vaccine candidates, the only strategy to control these arboviruses is to target the Culex (Diptera: Culicidae) mosquito vector. However, the selection pressure caused by exposure to insecticides for vector control or agricultural pest control can lead to insecticide resistance, thereby reducing the efficacy of insecticide-based vector control interventions. In Culex mosquitoes, two of the most common amino acid substitutions associated with insecticide resistance are the kdr L1014F in voltage gated sodium channels and G119S in acetylcholinesterase.

In this study, Culex pipiens biotype pipiens, Culex torrentium, and Culex modestus were sampled from 2019 to 2021 in three distinct environmental habitats (urban, peri-urban, and agricultural) in and around the city of Leuven, Belgium. Individual mosquitoes were screened for two mutations resulting in L1014F and G119S amino acid substitutions. Both mutations were observed in Culex pipiens and Culex modestus but not in Culex torrentium mosquitoes across the four collection sites. Furthermore, multi-resistance or cross-resistance in Culex pipiens could be a threat in these areas, as both mutations were observed at low frequencies.

These results provide the first report of kdr L1014F and ace-1 G119S resistance in Culex pipiens and Culex modestus mosquitoes from Belgium, highlighting the importance of mosquito surveillance to design effective arbovirus outbreak control strategies.
Synthetic oxepanoprolinamide iboxamycin is highly active against human pathogen Listeria monocytogenes
Authors: Brodiazhenko Tetiana , Turnbull Kathryn Jane , Wu Kelvin J.Y. , Takada Hiraku , Tresco Ben I.C. , Tenson Tanel , Myers Andrew G. , Hauryliuk Vasili
Published: March 2022

Listeriosis is a dangerous food-borne bacterial disease caused by the Gram-positive Bacillota (Firmicute) bacterium Listeria monocytogenes. In this report, we show that the synthetic lincosamide iboxamycin is highly active against L. monocytogenes and can overcome the intrinsic lincosamide resistance mediated by VgaL/Lmo0919, a member of ABCF ATPase resistance determinants that act by directly removing the antibiotic from the ribosome. While iboxamycin is not bactericidal against L. monocytogenes, it displays a pronounced postantibiotic effect, which is a valuable pharmacokinetic feature. Experiments in L. monocytogenes infection models are necessary to further assess the potential of iboxamycin as a novel drug for treatment of listeriosis. We demonstrate that VmlR ARE ABCF of Bacillota bacterium Bacillus subtilis grants significant (33-fold increase in MIC) protection from iboxamycin, while LsaA ABCF of Enterococcus faecalis grants an 8-fold protective effect. Furthermore, the VmlR-mediated iboxamycin resistance is cooperative with that mediated by the Cfr 23S rRNA methyltransferase resistance determinant, resulting in up to a 512-fold increase in MIC. Therefore, emergence and spread of ABCF ARE variants capable of defeating next-generation lincosamides in the clinic is possible and should be closely monitored.
Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas
Authors: Lamanna Francesco , Hervas-Sotomayor Francisca , Oel A. Phillip , Jandzik David , Sobrido-Cameán Daniel , Martik Megan L. , Green Stephen A. , Brüning Thoomke , Mößinger Katharina , Schmidt Julia , Schneider Celine , Sepp Mari , Murat Florent , Smith Jeramiah J. , Bronner Marianne E. , Rodicio María Celina , Barreiro-Iglesias Antón , Medeiros Daniel M. , Arendt Detlev , Kaessmann Henrik
Published: March 2022

The vertebrate brain emerged more than ∼500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey – a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits – based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of the core cell type composition, tissue structures, and gene expression programs of the ancestral brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral vertebrate brain was likely devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors on the jawed vertebrate lineage. Our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.
Label-free three-photon imaging of intact human cerebral organoids: tracking early events in brain development and deficits in Rett Syndrome
Authors: Yildirim Murat , Delepine Chloe , Feldman Danielle , Pham Vincent , Chou Stephanie , Kan Ip Jacque Pak , Nott Alexi , Tsai Li-Huei , Ming Guo-li , So Peter T. C. , Sur Mriganka
Published: March 2022

Human cerebral organoids are unique in their development of progenitor-rich zones akin to ventricular zones from which neuronal progenitors differentiate and migrate radially. Analyses of cerebral organoids thus far have been performed in sectioned tissue or in superficial layers due to their high scattering properties. Here, we demonstrate label-free three-photon imaging of whole, uncleared intact organoids (∼2 mm depth) to assess early events of early human brain development. Optimizing a custom-made three-photon microscope to image intact cerebral organoids generated from Rett Syndrome patients, we show defects in the ventricular zone volumetric structure of mutant organoids compared to isogenic control organoids. Long-term imaging live organoids reveals that shorter migration distances and slower migration speeds of mutant radially migrating neurons are associated with more tortuous trajectories. Our label-free imaging system constitutes a particularly useful platform for tracking normal and abnormal development in individual organoids, as well as for screening therapeutic molecules via intact organoid imaging.
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

Rabies 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

In 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

Rationale

Learning 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.

Objectives

The 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.

Methods

Separate 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.

Results

We 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.

Conclusions

Together, 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

Neisseria 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

Mutationally-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.

SIGNIFICANCE

The 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

Bacterial 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

The 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

Background

Primary 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.

Methods

Here 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.

Results

Even 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.

Conclusions

Our 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

Human 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

Plants 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.

Highlight

Measurement 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

Climate 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

Cooperative 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.