bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic killing of drug-induced bacteriostatic cells
Authors: Gil-Gil Teresa , Berryhill Brandon A. 
Published: September 2024

SynopsisBackgroundThere is a long-standing belief that bacteriostatic drugs are inherently antagonistic to the action of bactericidal antibiotics. This belief is primarily due to the fact that the action of most bactericidal antibiotics requires the target bacteria to be growing. Since bacteriostatic drugs stop the growth of treated bacteria, these drugs would necessarily work against one another. We have recently shown that bacteria treated with high concentrations of bacteriostatic drugs retain some metabolic activity, dividing on average once per day.ObjectivesWe seek to determine if this low level of growth is sufficient to allow for bactericidal antibiotics of different classes to still kill after bacteria are treated with bacteriostatic drugs.MethodsWe first treatedEscherichia coliandStaphylococcus aureuswith two different bacteriostatic drugs, followed by one of three bactericidal drugs of three different classes. The density of these bacteria was tracked over six days to determine the amount of killing that occurred.ResultsOur results question this long-standing belief by demonstrating conditions where sequential treatment with a bacteriostatic then bactericidal antibiotic is as or more effective than treatment with a bactericidal drug alone.ConclusionsThese results raise the need to investigate the pharmacodynamics of the joint action of bacteriostatic and bactericidal antibioticsin vitroandin vivo.
Allosteric modulation of the Lon protease by effector binding and local charges
Authors: Ogdahl Justyne L , Chien Peter 
Published: September 2024

AbstractThe ATPase Associated with diverse cellular Activities (AAA+) family of proteases play crucial roles in cellular proteolysis and stress responses. Like other AAA+ proteases, the Lon protease is known to be allosterically regulated by nucleotide and substrate binding. Although it was originally classified as a DNA binding protein, the impact of DNA binding on Lon activity is unclear. In this study, we characterize the regulation of Lon by single-stranded DNA (ssDNA) binding and serendipitously identify general activation strategies for Lon. Upon binding to ssDNA, Lon’s ATP hydrolysis rate increases due to improved nucleotide binding, leading to enhanced degradation of protein substrates, including physiologically important targets. We demonstrate that mutations in basic residues that are crucial for Lon’s DNA binding not only reduces ssDNA binding but result in charge-specific consequences on Lon activity. Introducing negative charge at these sites induces activation akin to that induced by ssDNA binding, whereas neutralizing the charge reduces Lon’s activity. Based on single molecule measurements we find that this change in activity is correlated with changes in Lon oligomerization. Our study provides insights into the complex regulation of the Lon protease driven by electrostatic contributions from either DNA binding or mutations.HighlightsssDNA binding allosterically activates Lon ATP hydrolysisNegative charge at DNA binding site is sufficient for Lon activationNeutralization of charge at DNA binding site inhibits Lon ATP hydrolysisLon activity is linked to formation of stable Lon hexamersSignificanceThe energy-dependent protease Lon is integral in both eukaryotic and prokaryotic physiology, contributing to protein quality control, stress management, developmental regulation, and pathogenicity. The ability to precisely regulate protein levels through targeted degradation underscores a need for tunability. We find that single-stranded DNA (ssDNA) acts as an allosteric regulator of Lon, leading to enhanced enzymatic activity. Mutations in basic residues crucial for DNA binding were found to affect Lon activity in a charge-specific manner highlighting the importance of electrostatic interactions regulating Lon’s function. Changes in Lon activity due to ssDNA binding or mutations were correlated with its oligomerization state. Our findings provide insights into the activation strategies of Lon, emphasizing the role of electrostatic contribution that modulate nucleotide affinity, oligomerization and proteolysis to advance our understanding of the complex regulatory mechanisms of the Lon protease.
In vivodetection of protein-protein interactions with single molecule resolution
Authors: Davi Marilyne , Ladant Daniel 
Published: September 2024

SUMMARYProtein-protein interactions are central in all biological processes. Methods capable of detecting interactions within living, intact cells have been particularly useful to identify and characterize protein interaction networks. We describe here an exquisitely sensitive regulatory circuit that can detect in bacteria, protein-protein interaction with single molecule sensitivity. This approach involves the interaction-mediated reconstitution of a cyclic AMP signaling cascade inEscherichia colitaking advantage of the high catalytic activity of the adenylate cyclase (AC) fromBordetella pertussisupon activation by its natural activator, calmodulin (CaM). We show that a single complex of interacting hybrid proteins per cell is enough to confer a selectable trait to the host. Thisexquisitelysensitiveadenylatecyclasehybrid (ESACH) system allows for directin vivoselection of ligands exhibiting high affinity for given targets or for studying interactions involving toxic proteins. The extreme sensitivity of the AC/CaM/cAMP signaling cascade may thus be harnessed to interrogate biological processes with single molecule resolution in live bacteria and could be exploited to design novel synthetic regulatory networks operating at, or even below, the theoretical threshold limit of one molecule per cell.
Electrophysiological responses reveal a dedicated learning mechanism to process salient consonant sounds in human newborns
Authors: Barbieri Paolo , Sarasso Pietro , Rossi-Sebastiano Alice , Frascaroli Jacopo , Poles Karol , Peila Chiara , Coscia Alessandra , Garbarini Francesca , Ronga Irene 
Published: September 2024

ABSTRACTIsolating relevant sounds in the auditory stream is a crucial feature accomplished by human infants and a pivotal ability for language acquisition. Therefore, it is reasonable to postulate the existence of early mechanisms reorienting attention toward salient acoustic stimuli. Previous studies suggest that infants consider consonant sounds as more salient than dissonant ones, because the former resemble human vocalizations. However, systematic evidence investigating the neural processes underlying consonance tuning in newborns is still scarce. Here, we investigate newborns’ ability to recognize and learn salient auditory stimuli by collecting Mismatch Responses (MMRs) to consonant and dissonant sounds and by computing the trial-by-trial correlation of the neural signal with Bayesian Surprise (a theoretical measure of learning). We present 22 healthy newborns (40.4 ± 15.8 hours) with a pseudo-random sequence of deviant and standard auditory events, while we record their electroencephalogram. Our results show that newborns exhibit a neural encoding of auditory regularities for all sound types (consonant and dissonant), as demonstrated by the presence of MMRs and significant correlation of the neural signal with Bayesian Surprise. Furthermore, consonant and dissonant sounds elicited MMRs and correlations with Bayesian Surprise of opposite polarities, with consonant auditory stimulation evoking negative responses, reminiscent of an adult-like MMR. Overall, our findings suggest that newborns display a dedicated perceptual learning mechanism for salient consonant sounds. We speculate that this mechanism might represent an evolutionary-achieved neural tuning to detect and learn salient auditory stimuli with acoustic features resembling human vocalizations.SIGNIFICANCE STATEMENTDiscriminating salient sounds in noisy sensory streams is a fundamental ability displayed by human infants, pivotal for acquiring crucial skills including language. Our study shed light on this ability by: (1) investigating perceptual learning mechanisms in newborns’ with a neurocomputational approach; (2) exploring the role of salient consonant sounds in modulating such mechanisms. Since human vocalizations are often consonant, the presence of a mechanism dedicated to enhance the processing of consonant sounds in newborns would confer evolutionary advantages. Our findings, indicating that newborns possess a dedicated and more refined perceptual learning mechanism to process consonance, corroborates this hypothesis. We speculate that this neural mechanism might facilitate the identification of salient acoustic input and support language acquisition in early infancy.
Single-cell transcriptome analysis reveals CD34 as a novel marker of human sinoatrial node pacemaker cardiomyocytes
Authors: Lim Amos A. , Pouyabahar Delaram , Ashraf Mishal , Huang Kate , Lohbihler Michelle , Chang Matthew L. , Murareanu Brandon M. , Tran Thinh , Mazine Amine , Bader Gary , Laksman Zachary , Protze Stephanie 
Published: September 2024

AbstractThe sinoatrial node (SAN) regulates the heart rate throughout life. Failure of this primary pacemaker results in life-threatening, slow heart rhythm. Despite its important function, the cellular and molecular composition of the human SAN is not completely resolved. Particularly, no cell surface marker to identify and isolate SAN pacemaker cells has been reported to date. Here we used single-nuclei/cell RNA sequencing of fetal and human pluripotent stem cell (hPSC)- derived SAN cells and show that the SAN consists of three subtypes of pacemaker cells, including Core SAN, SAN, and Transitional Cells. Our study identified a host of novel Core SAN markers including MYH11, BMP4, and the cell surface antigen CD34. We demonstrate that sorting for CD34+cells from cardiac hPSC differentiations enriches for SAN cells with a functional pacemaker phenotype. This novel SAN pacemaker cell surface marker is highly valuable for future hPSC- based disease modelling, drug discovery, cell replacement therapies, as well as the delivery of therapeutics to SAN cellsin vivousing antibody-drug conjugates.
A hippocampal astrocytic sequence emerges during learning and memory
Authors: Senne Ryan A. , Suthard Rebecca L. , Cao Rui , Monasterio Amy H. , Reusch Evan A. , Buzharsky Michelle D. , Howard Marc W. , Ramirez Steve 
Published: September 2024

AbstractThe dorsal hippocampus is a heterogeneous structure with numerous cell types involved in generating and maintaining detailed representations of space and time. Prior work has established that pyramidal cells contribute to these crucial aspects of episodic memory. For example, hippocampal “time cells” encode temporal information through sequential activity. However, the role of non-neuronal cell types are less often explored. In this study, we investigated dorsal hippocampal CA1 astrocytes using one-photon calcium imaging in freely moving animals during a contextual fear conditioning paradigm. To our knowledge, this is the first time a study has successfully performed longitudinal registration of astrocytic cell population using 1p calcium imaging, thus permitting the tracking of a stable population of these cells in freely-moving mice. In response to foot shock, astrocytes generated robust calcium-event sequences with a time-compressed structure akin to canonical hippocampal time cells. Upon re-exposure to the conditioned context, these astrocytic sequences persisted in the absence of shock, maintaining their time-compressed structure. Moreover, astrocytes active on the previous day retained a preserved sequential structure, indicating memory-specific properties. This phenomenon was not observed in a context different from the initial fear conditioning chamber. Taken together, these results present a potentially paradigm-shifting notion that astrocytes play a significant role in the representation of temporal information processing across learning and memory.
Fast and slow synaptic plasticity enables concurrent control and learning
Authors: Bicknell Brendan A. , Latham Peter E. 
Published: September 2024

AbstractDuring many tasks the brain receives real-time feedback about performance. What should it do with that information, at the synaptic level, so that tasks can be performed as well as possible? The conventional answer is that it should learn by incrementally adjusting synaptic strengths. We show, however, that learning on its own is severely suboptimal. To maximize performance, synaptic plasticity should also operate on a much faster timescale – essentially, the synaptic weights should act as a control signal. We propose a normative plasticity rule that embodies this principle. In this, fast synaptic weight changes greedily suppress downstream errors, while slow synaptic weight changes implement statistically optimal learning. This enables near-perfect task performance immediately, efficient task execution on longer timescales, and confers robustness to noise and other perturbations. Applied in a cerebellar microcircuit model, the theory explains longstanding experimental observations and makes novel testable predictions.
Full-length structure and heme binding in the transcriptional regulator HcpR
Authors: Belvin B. Ross , Musayev Faik N. , Escalante Carlos , Lewis Janina P. 
Published: September 2024

AbstractHcpR is a CRP-family transcriptional regulator found in many Gram-negative anaerobic bacteria. In the perio-pathogenPorphyromonas gingivalis,HcpR is crucial for the response to reactive nitrogen species such as nitric oxide (NO). Binding of NO to the heme group of HcpR leads to transcription of the redox enzyme Hcp. However, the molecular mechanisms of heme binding to HcpR remain unknown. In this study we present the 2.3Å structure of theP. gingivalisHcpR. Interdomain interactions present in the structure help to form a hydrophobic pocket in the N-terminal sensing domain. A comparison analysis with other CRP-family members reveals that the molecular mechanisms of HcpR-mediated regulation may be distinct from other family members. Using docking studies, we identify a putative heme binding site in the sensing domain.In vitrocomplementation and mutagenesis studies verify Met68 as an important residue in activation of HcpR. Finally, heme binding studies with purified forms of recombinant HcpR support Met68 and His149 residues as important for proper heme coordination in HcpR.
Ultrastructure expansion microscopy of axonemal dynein in islet primary cilia
Authors: Dong Xinhang , Jo Jeong Hun , Hughes Jing 
Published: September 2024

ABSTRACTPrimary cilia are vital sensory organelles whose structures are challenging to study due to their solitary nature and intricate cytoskeleton. Current imaging modalities are limited in their ability to visualize structural details that are important for understanding primary cilia function. Ultrastructure expansion microscopy (U-ExM) is a recent superresolution imaging technique that physically expands biological specimens using a swellable hydrogel, allowing structural interrogation of small cellular components such as cilia. In this study, we apply U-ExM to mouse and human pancreatic islets to visualize the axonemal cytoskeleton and associated proteins in primary cilia. Our study reveals the expression of axonemal dynein in islet primary cilia and centrioles, with DNAI1 being a principal subunit which we validate using targeted shRNA knockdown. We conclude that U-ExM is suitable for localizing protein expression in pancreatic islet cilia which contain axonemal dynein.
Appraising the HIV Prevention Cascade methodology to improve HIV prevention targets: Lessons learned from a general population pilot study in east Zimbabwe
Authors: Moorhouse Louisa R. , Imai-Eaton Jeffrey W , Maswera Rufuworkuda , Tsenesa Blessing , Magoge-Mandizvidza Phyllis , Moyo Brian , Mugurungi Owen , Nyamukapa Constance , Hallett Timothy B , Gregson Simon 
Published: September 2024

AbstractIntroductionMultiple HIV Prevention Cascades (HPC) formulations have been proposed to assist advocacy, monitoring of progress of HIV prevention implementation and research to identify ways to increase use of HIV prevention methods. Schaefer and colleagues proposed a unifying formulation suitable for widespread use across different populations which could be used for routine monitoring or advocacy. Robust methods for defining and interpreting this HPC formulation using real world data is required.MethodsData collected as part of the Manicaland Pilot HIV Prevention Cascades Study, east Zimbabwe, in 2018-19, was used to validate the HPC framework for PrEP, VMMC, male condom and combination prevention method use. Validation measures included feasibility of populating the HPC, contrasting simple vs complex measures of the HPC (using 2-sample proportion test), and testing ability of main bars to predict prevention use and testing whether sub-bars explained why people were lost from the HPC using logistic regression.ResultsIt was possible to populate the HPC for both individual and combined prevention methods using pilot survey data. Most steps were associated with prevention method usage outcomes, except for VMMC. There were significant overlaps between individuals reporting positive responses for the main bar and those citing barriers to motivation. To refine the HPC’s access bar definition, it is suggested to also consider individuals who report access barriers. While the HPC framework identifies barriers to individual prevention methods, challenges arise in identifying those for combined prevention.DiscussionOur study successfully utilised questionnaires from the Manicaland HPC pilot survey to measure the HPC for individual and combined prevention methods. This demonstrates the feasibility of populating this framework using general population survey data and designated questionnaire modules. We propose a final formulation of the HPC, questionnaire modules and methods to create it. With proper evaluation and promotion, the HPC can enhance prevention services, aiding in the crucial reduction of HIV incidence.
Digitalization capability and digital product and service innovation performance: empirical evidence from China
Authors: Yang Chen , Zhang Lu , Ling Xuehang , Qin Xin , Li Mingyue 
Published: September 2024

PurposeDigital product and service innovations (DPSI) has attracted widespread attention from both management scholars and practitioners. Previous studies have documented that information technology (IT) capability and digital orientation positively influence DPSI performance. However, the question of whether and how digitalization capability can facilitate DPSI performance remains unresolved. This paper fills these gaps by investigating the mediating role of improvisation capability and the moderating role of technological turbulence.Design/methodology/approachThis study used two-wave data from 240 matched digital transformation department leaders and senior managers from Chinese firms and examined the hypotheses deploying hierarchical regression and bootstrapping.FindingsOur analyses reveal positive, significant links between digitalization capability and improvisation capability and between improvisation capability and DPSI performance. The findings further show that the effect of digitalization capability on DPSI performance is partially mediated by improvisation capability and that technological turbulence strengthens the indirect relationship between digitalization capability and DPSI performance through improvisation capability.Originality/valueIntegrating resource-based view, this research provides evidence that the extent to which improvisation capability mediates the relationship between digitalization capability and DPSI performance depends on technological turbulence. It provides a new direction for digitalization capability and DPSI performance.
Optimal supply chain green innovation and subsidy strategy: producer subsidy versus consumer subsidy
Authors: Lai Zhixuan , Lou Gaoxiang , Guo Yuhan , Tu Xuechen , Zhao Yushan 
Published: September 2024

PurposeConsidering two types of subsidies for producers (supplier and manufacturer) and one for consumers based on product greenness and sales quantity, this study aims to formulate optimal supply chain green innovation and subsidy strategies, and to achieve this goal with the support of information systems.Design/methodology/approachThis study introduces a composite green-product supply chain where suppliers focus on green innovation for component greenness and manufacturers focus on green innovation for manufacturing process greenness. Game theory modeling is applied to investigate the differences of product greenness, supply chain members’ profit and social welfare under different government subsidy strategies.FindingsIncreasing the unit greenness subsidy coefficient can boost product greenness and supply chain members’ profits, but does not always raise social welfare. When the government exclusively offers subsidies to producers, subsidies should be allocated to suppliers when there is a significant disparity in supply chain green innovation costs. Conversely, it is more beneficial to subsidize manufacturers. Consumer subsidies have the potential to enhance both environmental and economic performance in the supply chain compared with producer-exclusive subsidies, but may not always maximize social welfare when supply chain members have low unit costs associated with green innovation.Originality/valueThis study examines the optimal decisions for green supply chain innovation and government subsidy strategies. Supply chain members and the government can use the information system to collect and evaluate the cost of upstream and downstream green innovation, and then develop reasonable collaborative green innovation and subsidy strategies.
Trade dependence and cultural distance: An analysis of economic interactions and humanistic exchanges between China and ASEAN countries
Authors: Li Hanhui , Pamintuan Cavin , Nisar Asad , Rafique Rabia 
Published: September 2024

AbstractThis study examines the influence of trade dependence, encompassing both export and import dependence, and economic dependence on cultural distance within the context of China and ASEAN countries from 1995 to 2020. Employing random‐effects models and, we investigate the impact of these dependencies on cultural distance and explore the moderating effects of humanistic exchange. Our findings reveal that trade dependence, export dependence, import dependence, and economic dependence exert negative effects on cultural distance between China and ASEAN countries. These findings are supported by the robustness test. We further analyze the moderating effects of humanistic exchange on the relationship between trade dependence, economic dependence, and cultural distance, confirming significant moderating effects specifically for trade dependence. Additionally, we observe that regional trade agreements and cultural exchange programs have heterogeneous effects on the relationship between trade and economic dependence and cultural distance, particularly among China and ASEAN countries with established agreements and programs.