bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syntaxin 3-SPI 2 dependent cross-talk facilitates the division of Salmonella containing vacuole (SCV)
Authors: Chatterjee Ritika , Mehta Nishi , Gangi Setty Subba Rao , Chakravortty Dipshikha 
Published: August 2022

AbstractIntracellular membrane fusion is mediated by membrane-bridging complexes of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs). SNARE proteins are one of the key players in the vesicular transport. Several reports shed light on intracellular bacteria modulating host SNARE machinery to establish infection successfully. The critical SNAREs in macrophages responsible for phagosome maturation are Syntaxin 3 (STX3) and Syntaxin 4 (STX4). Salmonella actively modulates its vacuole membrane composition to escape lysosomal fusion. A report showed that Salmonella containing vacuole (SCV) harbors recycling endosomal SNARE Syntaxin 12 (STX12). However, the role of host SNAREs in SCV biogenesis and pathogenesis is unclear. Upon knockdown of STX3, we have observed a reduction in bacterial proliferation and is restored upon the overexpression of STX3. Post infected live-cell imaging of cells showed STX3 localises to the SCV membranes and thus might help in fusion of SCV with intracellular vesicles to acquire membrane for its division. We also found this interaction abrogated when we infected with SPI-2 encoded T3SS apparatus mutant (STM ΔssaV) but not with SPI-1 encoded T3SS (STM ΔinvC). These observations were also consistent in mice model of Salmonella infection. Together, these results shed a light on the effector molecules secreted through SPI-2 encoded by T3SS possibly involved in interaction with host SNARE STX3, which is essential to maintain the division of Salmonella in SCV and maintenance the principle single bacterium per vacuole.SynopsisSalmonella Typhimurium infection in murine macrophage leads to upregulation of host Syntaxin 3 both at transcript and protein levels at late stage of infection. Syntaxin 3 cross-talk with Salmonella containing vacuoles (SCVs) is essential for establishment of replicative niche in host macrophages. The cross-talk between STX3 and SCVs is Salmonella pathogenicity island 2 (SPI-2) dependent and is consistent in mice model of Salmonella Typhimurium infection.
Hormone-sleep interactions predict cerebellar connectivity and behavior in aging females
Authors: Ballard Hannah K. , Jackson T. Bryan , Hicks Tracey H. , Cox Sydney J. , Miller Abigail C. , Maldonado Ted , Bernard Jessica A. 
Published: August 2022

AbstractSex hormones fluctuate over the course of the female lifespan and are associated with brain health and cognition. Thus, hormonal changes throughout female adulthood, and with menopause in particular, may contribute to sex differences in brain function and behavior. Further, sex hormones have been correlated with sleep patterns, which also exhibit sex-specific impacts on the brain and behavior. As such, the interplay between hormones and sleep may contribute to late-life brain and behavioral outcomes in females. Here, in a sample of healthy middle-aged and older females (n = 79, ages 35-86), we evaluated the effect of hormone-sleep interactions on cognitive and motor performance as well as cerebellar-frontal network connectivity. Salivary samples were used to measure 17β-estradiol, progesterone, and testosterone levels while overnight actigraphy was used to quantify sleep patterns. Cognitive behavior was quantified using the composite average of standardized scores on memory, processing speed, and attentional tasks, and motor behavior was indexed with sequence learning, balance, and dexterity tasks. We analyzed resting-state connectivity correlations for two specific cerebellar-frontal networks: a Crus I to dorsolateral prefrontal cortex network and a Lobule V to primary motor cortex network. In sum, results indicate that sex hormones and sleep patterns interact to predict cerebellar-frontal connectivity and behavior in aging females. Together, the current findings further highlight the potential consequences of endocrine aging in females and suggest that the link between sex hormones and sleep patterns may contribute, in part, to divergent outcomes between sexes in advanced age.HighlightsHormone-sleep interactions influence resting-state cerebellar-frontal connectivityCognitive and motor behavior are impacted by hormone-sleep relationshipsSex hormones and sleep patterns may contribute to aging outcomes in females
Molecular mechanism underlying desensitization of the proton-activated chloride channel PAC
Authors: Osei-Owusu James , Ruan Zheng , Matasic Daniel S. , Lü Wei , Qiu Zhaozhu 
Published: August 2022

AbstractDesensitization is a common property of membrane receptors, including ion channels. The newly identified proton-activated chloride (PAC) channel plays an important role in regulating the pH and size of organelles in the endocytic pathway, and is also involved in acid-induced cell death. However, how the PAC channel desensitizes is largely unknown. Here, we show by patch-clamp electrophysiological studies that PAC undergoes pH-dependent desensitization upon prolonged acid exposure. Through structure-guided and comprehensive mutagenesis, we identified several residues critical for PAC desensitization, including histidine (H) 98, glutamic acid (E) 94, and aspartic acid (D) 91 at the extracellular extension of the transmembrane helix 1 (TM1), as well as E107, D109, and E250 at the extracellular domain (ECD)–transmembrane domain (TMD) interface. Structural analysis and molecular dynamic simulations revealed extensive interactions between residues at the TM1 extension and those at the ECD–TMD interface. These interactions likely facilitate PAC desensitization by stabilizing the desensitized conformation of TM1, which undergoes a characteristic rotational movement from the resting and activated states to the desensitized state. Our studies establish a new paradigm of channel desensitization in this ubiquitously expressed ion channel and pave the way for future investigation of its relevance in cellular physiology and disease.
Evidence for coordinated evolution at amino acid sites of SARS-CoV-2 spike
Authors: Neverov A.D. , Fedonin G.G. , Popova A.V. , Bykova D.I. , Bazykin G.A. 
Published: August 2022

AbstractIt is currently unclear why SARS-Cov-2 has adapted in a stepwise manner, with multiple beneficial mutations accumulating in a rapid succession at the origins of VOCs. Here, we searched for coordinated evolution of amino acid sites in the spike protein of SARS-Cov-2. We searched for concordantly evolving site pairs (CSP) for which changes at one site were rapidly followed by changes at the other site in the same lineage. We detected 46 sites which formed 45 CSP. Sites in CSP were closer to each other in the protein structure than random pairs, indicating that concordant evolution has a functional basis. Notably, site pairs carrying lineage defining mutations of the four VOCs that circulated before May 2021 are enriched in CSP, indicating that the origin of these VOCs could have been facilitated by positive epistasis. Additionally, we detected four discordantly evolving pairs of sites where mutations at one site unexpectedly rarely occurred on the background of a specific allele at another site, namely on the wild-type D at site 614 (for two pairs) or at derived Y in the site 501 (for two other pairs). Our findings hint that positive epistasis between accumulating mutations could have delayed the assembly of advantageous combinations of mutations comprising at least some of the VOCs.
Signature of random connectivity in the distribution of neuronal tuning curves
Authors: Orhan Pierre , Duszkiewicz Adrian , Peyrache Adrien 
Published: August 2022

ABSTRACTUnderstanding the relationship between circuit properties and the organization of neuronal population activity is a fundamental question in neuroscience. The fine tuning of neuronal activity to specific values of environmental or internal features are canonical examples of how information is encoded in the brain, possibly resulting from precisely organized inputs. Yet, in the cortex, finely tuned neurons are often recorded together with neurons whose tuning is much less specific, for example those of inhibitory neurons, and the connectivity statistics accounting for the overall distribution of tuning curves is unclear. Here, using recordings in the mouse head-direction system, we first show both in simulation and analytically that random linear combinations of ideal finely tuned inputs reproduce the distribution of fast-spiking neuron tuning curves, a class of neurons believed to operate in the linear regime. This transformation preserves, on the population level, the singular spectrum of the input tuning curves but the relative power of each singular component is independently distributed in each output cell, leading to a distribution ranging from uni-modal to symmetrically tuned cells. We then generalize the model to a non-linear transformation of the inputs, combined with background inhibition. Using recordings from input neurons in the thalamus, where tuning curves are near-ideal, the model reproduces for various levels of inhibition the entire range of observed neuronal responses in the cortex, from precisely and narrowly tuned neurons to multipeak excitatory cells, as well as symmetrical tuning curves of inhibitory neurons. We replicate these findings in a dataset of hippocampal recordings. In conclusion, the full distribution of tuning curves is a signature of input connectivity statistics, which, for fast-spiking neurons and thalamocortical circuits, is likely to be random rather than specifically organized.
Direct measurement of appressorium turgor using a molecular mechanosensor in the rice blast fungus Magnaporthe oryzae
Authors: Ryder Lauren S. , Lopez Sergio G. , Michels Lucile , Eseola Alice B. , Sprakel Joris , Ma Weibin , Talbot Nicholas J. 
Published: August 2022

AbstractMany plant pathogenic fungi forcibly enter their hosts to cause disease. The rice blast fungus Magnaporthe oryzae, for example, infects plants using a specialised infection cell called an appressorium, which generates enormous turgor to drive a rigid penetration peg through the rice leaf cuticle. While these vast internal pressures are a critical weapon in fungal host penetration, they have remained very challenging to probe directly during host invasion, leaving our understanding of these extreme cellular mechanics incomplete. Here, we combine Fluorescence Lifetime Imaging (FLIM) with a membrane-targeting molecular mechanoprobe to quantify changes in membrane tension as a direct proxy for appressorial turgor in M. oryzae. We report that mature melanin-pigmented M. oryzae appressoria display a heterogeneous low fluorescence lifetime and high membrane tension, consistent with enormous turgor. These extreme pressures lead to large-scale spatial heterogeneities in membrane mechanics, much greater than observed in any other cell type previously, highlighting the extreme mechanics of turgor-driven appressorium-mediated plant infection. By contrast, appressoria of non-pathogenic melanin-deficient mutants, alb1 and buf1, or immature non-melanised appressoria, exhibit high fluorescence lifetime, consistent with low membrane tension and turgor, that remain spatially homogeneous. To evaluate the method, we investigated turgor dynamics in a range of mutants impaired in appressorium function. We show that the turgor sensor kinase mutant Δsln1, recently proposed to generate excess appressorium turgor, displayed a significantly higher membrane tension compared to an isogenic wild type M. oryzae strain. This non-invasive, live cell imaging technique allows direct quantification and visualization of the enormous turgor pressures deployed during pathogen infection.
Alveolar epithelial progenitor cells drive lung regeneration via dynamic changes in chromatin topology modulated by lineage-specific Nkx2-1 activity
Authors: Toth Andrea , Kannan Paranthaman , Snowball John , Kofron J. Matthew , Wayman Joseph A. , Bridges James P. , Miraldi Emily R. , Swarr Daniel , Zacharias William J. 
Published: August 2022

AbstractLung epithelial regeneration after acute injury requires coordination of extensive cellular and molecular processes controlling proliferation and differentiation of specialized alveolar cells to pattern the morphologically complex alveolar gas exchange surface. During regeneration, specialized Wnt-responsive alveolar epithelial progenitor (AEP) cells, a subset of alveolar type 2 (AT2) cells, proliferate and transition to alveolar type 1 (AT1) cells, though the precise molecular and epigenetic determinants of these processes remain unclear. Here, we report a refined primary murine alveolar organoid assay which recapitulates critical aspects of in vivo regeneration, providing a tractable model to dissect these regenerative processes. Clonal expansion of single AEPs generate complex alveolar organoids with extensive structural maturation and organization. These organoids contain properly patterned AT1 and AT2 cells surrounding numerous alveolar-like cavities with minimal structural contribution from mesenchymal cells, implying extensive cell autonomous regenerative function encoded in adult AEPs. Leveraging a time series of paired scRNAseq and scATACseq, we identified the AEP state at single cell resolution and described two distinct AEP to AT1 intermediate states: a widely reported Krt8+ transitional state defined by cell stress markers and a second state defined by differential activation of signaling pathways mediating AT1 cell differentiation. Transcriptional regulatory network (TRN) analysis demonstrated that these AT1 transition states were driven by distinct regulatory networks controlled in part by differential activity of Nkx2-1. Genetic ablation of Nkx2-1 in AEP-derived organoids was sufficient to cause transition to a proliferative stressed Krt8+ state characterized by disorganized, uncontrolled growth. Finally, AEP-specific deletion of Nkx2-1 in adult mice led to rapid loss of AEP state, clonal expansion, and disorganization of alveolar structure, implying a continuous requirement for Nkx2-1 in maintenance and function of adult lung progenitors. Together, these data provide new insight into cellular hierarchies in lung regeneration and implicate dynamic epigenetic maintenance via lineage transcription factors as central to control of facultative progenitor activity in AEPs.
Negative allosteric modulation of the glucagon receptor by RAMP2
Authors: Kumar Kaavya Krishna , O’Brien Evan S. , Habrian Chris H. , Latorraca Naomi R. , Wang Haoqing , Tuneew Inga , Montabana Elizabeth , Marqusee Susan , Hilger Daniel , Isacoff Ehud Y. , Mathiesen Jesper Mosolff , Kobilka Brian K. 
Published: August 2022

AbstractReceptor activity-modifying proteins (RAMPs) modulate the activity of many Family B heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs). The glucagon receptor (GCGR), a Family B GPCR responsible for maintenance of proper blood sugar levels, interacts with RAMP2, though the purpose and consequence of this interaction is poorly understood. Using a series of biochemical and cell-based assays, we show that RAMP2 interacts with and broadly inhibits GCGR-induced downstream signaling. Hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS) demonstrates that RAMP2 enhances local flexibility in select locations in and near the receptor extracellular domain (ECD) as well as at a key region in the 6th transmembrane helix, while single-molecule fluorescence resonance energy transfer (smFRET) experiments show that this RAMP2-induced ECD disorder results in inhibition of active and intermediate states of the intracellular face of the receptor. Using cryo-electron microscopy (cryoEM), we determined the structure of the GCGR-Gs complex at 2.9 Å resolution in the presence of RAMP2. RAMP2 apparently does not interact with GCGR in an ordered manner, yet the ECD of GCGR is indeed largely disordered in the presence of RAMP2. This disorder is accompanied by rearrangements of several key areas of the receptor, resulting in the formation of a likely unproductive complex. Together, our studies suggest that RAMP2 acts as a negative allosteric modulator of GCGR by enhancing conformational sampling of the ECD.
Effects of the manager's goal orientation on frontline service employees' service–sales ambidexterity conversion
Authors: Yen HsiuJu Rebecca , Hu Paul Jen-Hwa , Liao Yi-Chun , Wu Jiun-Yu 
Published: August 2022

PurposeAmbidextrous frontline service employees (FSEs), capable of delivering quality services and carrying out sales responsibilities too, are crucial to service firms. This study seeks to extend ambidexterity research by examining how a manager's goal orientation could influence FSEs' ambidextrous conversion. The authors draw on achievement goal theory and conceptualize a link between a manager's achievement goal orientation and employees' service–sales ambidexterity (SSA). The authors then apply conservation of resources theory to complement this high-level conceptualization, hypothesize mediating roles of important resources that can facilitate employees' SSA, and the authors test them empirically.Design/methodology/approachThis study adopts a questionnaire survey design. The empirical test relies on multilevel path analyses of dyadic data from 341 FSEs and 39 managers of a major logistics service company in Taiwan.FindingsManagers with a prominent learning goal orientation can facilitate and foster FSEs' SSA through developmental inducements and change-related self-efficacy, two important resources for their ambidextrous conversion. Managers with a strong performance-avoid goal orientation instead might hinder employees' SSA conversion, due to a negative impact on developmental inducements. Furthermore, SSA enhances FSEs' service delivery value and sales performance.Originality/valueBy analyzing and empirically testing the influence pathways of essential resources perceived by FSEs, which channel the effects of a manager's goal orientation to employees' SSA conversion, this study offers insights about how managers can support and foster FSEs' service–sales ambidextrous conversion.
Rates and physicochemical drivers of microbial anabolic activity in deep‐sea sediments and implications for deep time
Authors: Meyer Nicolette R. , Parada Alma E. , Kapili Bennett J. , Fortney Julian L. , Dekas Anne E. 
Published: August 2022

AbstractSediment microorganisms influence global climate and redox by altering rates of organic carbon burial. However, the activity and ecology of benthic microorganisms are poorly characterized, especially in the deep sea. Here, we conducted nearly 300 stable isotope tracer experiments in sediments from the Pacific and Atlantic oceans (100–4500 m water depth) to determine the rates, spatial distribution, and physicochemical controls on microbial total anabolic activity, nitrogen fixation, and inorganic/organic carbon uptake. Using correlative and manipulative approaches, we find that total activity is limited primarily by organic carbon and/or energy. Activity correlates significantly with distance from shore, sediment depth, C:N ratios, and overlying chlorophyll concentrations and is stimulated by carbon but not nitrogen additions. Consistent with this, nitrogen fixation was undetected despite relatively low concentrations of porewater ammonium and the previous detection of nifH genes. Inorganic carbon uptake accounted for 7%–55% of carbon assimilation per sample (median 21%), suggesting chemoautotrophy is an important and unappreciated source of labile carbon in deep‐sea sediments. Community 16S rRNA was dominated by Bacteria (<2% Archaea), primarily Desulfobacterales of the Deltaproteobacteria. Leveraging our findings, we modelled global benthic microbial activity through geologic time and find the potential for significant shifts in total activity with supercontinental cycles.
Border carbon adjustments: rationale, design and impact
Authors: Keen Michael , Parry Ian , Roaf James 
Published: August 2022

AbstractThis paper assesses the rationale, design and impact of border carbon adjustments (BCAs). Large disparities in carbon pricing between countries raise concerns about competitiveness and emissions leakage. BCAs are potentially the most effective domestic instrument for addressing these challenges – but design details are critical. For example, limiting coverage of the BCA to energy‐intensive, trade‐exposed industries facilitates administration, and initially benchmarking BCAs on domestic emissions intensities would ease the transition for trading partners with emission‐intensive production. It is also important to consider how to apply BCAs across countries with different approaches to the mitigation of emissions, and the treatment of exports. BCAs alone do not solve the free‐rider problem in carbon pricing, but might ease it, and be a step towards an effective international carbon price floor.
Simple method for evaluating achievement degree of lung dose optimization in individual patients with locally advanced non‐small cell lung cancer treated with intensity modulated radiotherapy
Authors: Abe Takanori , Iino Misaki , Saito Satoshi , Aoshika Tomomi , Ryuno Yasuhiro , Ohta Tomohiro , Igari Mitsunobu , Hirai Ryuta , Kumazaki Yu , Miura Yu , Kaira Kyoichi , Kagamu Hiroshi , Noda Shinei , Kato Shingo 
Published: August 2022

AbstractBackgroundIn this study, we developed a simple method for evaluating achievement degree of lung dose optimization in individual patients with locally advanced non‐small cell lung cancer (NSCLC) treated with intensity modulated radiotherapy (IMRT).MethodsData of 28 patients with stage IIB to IIIC NSCLC were retrospectively analyzed. All patients were treated with IMRT and a simulated three‐dimensional conformal radiotherapy (3D‐CRT) plan created for them. Dose‐volume parameters of lung were analyzed for their correlation with radiation pneumonitis (RP).ResultsOver a median follow‐up of 14 months, grade 1 pneumonitis was diagnosed in 14 patients (50%), grade 2 pneumonitis in 11 (39%), and grade 3 pneumonitis in one (4%). Two patients did not develop pneumonitis. None of the patients developed grade 4 or 5 pneumonitis. Regarding dose‐volume parameter ratios between IMRT and simulated 3D‐CRT, receiver operating characteristic analysis showed that mean lung dose (MLD)IMRT/MLD3D‐CRT had the largest area under curve (0.750). Cumulative 6‐month incidences of grade 2 or greater RP were 78.4% versus 19.5% (MLDIMRT/MLD3D‐CRT, ≥1.0 or less); this difference was significant (p < 0.05).ConclusionsWe found that cutoff values for dose volume parameter ratios significantly predict grade 2 or greater RP. We believe that these parameter ratios could be useful in assisting evaluation of achievement degree of lung dose optimization in IMRT for LA‐NSCLC.