bluuebunny/crossref_metadata_2025 huggingface dataset:
Methods for detecting and monitoring Salmonella infection and chronic carriage in living mice using bioluminescent in vivo imaging
Authors: Bennett Aliyah Nicole , Laipply Baileigh , Gunn John Spencer
Published: September 2024

Salmonella enterica serovar Typhi primarily persists in chronic carriers by forming biofilms on gallstones in the gallbladder. We have developed a gallstone mouse model to study chronic carriage. To better understand the infection timeline and differentiate between mice that have maintained long-term gallbladder carriage from those that have cleared infection, we utilized bioluminescent S. Typhimurium and in vivo imaging to detect and track the organ-specific presence of bacteria in living mice. The mice infected with our bioluminescent S. Typhimurium showed luminescence in the abdomen as early as three days by comparison to the mice infected with non-luminescent wild type S. Typhimurium. With our methods, we achieve image resolution such that we can confidently identify the presence of S. Typhimurium in the gallbladder at >60 days post-infection. Using these methods we have determined that the minimum number of bacteria necessary to detect luminescence in the mice is 103 colony forming units (CFUs), and that 1 out of 6 initially infected mice will remain persistently infected for greater than 60 days, with gallbladder bacterial loads reaching upwards of 103 per mg of tissue. Given that our limit of detection of luminescence is 103 CFUs, our sensitivity is robust enough to identify the bacterial loads present in the average chronically infected mouse. Quantification of individual organs’ bacterial CFUs and comparison of luminescence between WT and luminescent S. Typhimurium validates that our technique is specific and sensitive enough to detect organ specific infection in our model of typhoidal chronic carriage.
The Cardioprotective Role of Neutrophil-Specific STING in Myocardial Ischemia/Reperfusion Injury
Authors: Brockman Maegan L. , Scruggs Triniti A. , Wang Lanfang , Kabboul Gabriella , Calvert John W. , Levit Rebecca D.
Published: September 2024

Background

Neutrophils are the most rapid and abundant immune cells to infiltrate the myocardium following myocardial ischemia/reperfusion injury (MI/R). Neutrophil heterogeneity has not been well characterized in MI/R, and studies have shown conflicting results regarding the impact of neutrophil depletion on cardiac injury. We thus aim to study the impact of neutrophils with enriched type I interferon signature and the role of STING (stimulator of interferon genes) signaling in neutrophils on cardiac reperfusion injury.

Methods

We utilized single-cell RNA sequencing to study neutrophil heterogeneity in response to MI/R. We generated a neutrophil-specific STING knockout mouse to assess the role of neutrophil STING in a model of MI/R. We examined cardiac function following injury via echocardiography and assessed the immune cell trajectory following injury utilizing flow cytometry.

Results

We identified a population of neutrophils with enriched type I interferon signaling and response to type I interferon following MI/R. We found that genetic deletion of neutrophil-specific STING led to worsened cardiac function following MI/R. Further investigation of the immune response by flow cytometry revealed decreased neutrophil infiltration into the myocardium and a shift in macrophage polarization.

Conclusions

Our findings suggest that neutrophil-specific STING is cardioprotective in MI/R, partly due to its effects on downstream immune cells. These results demonstrate that early alterations or therapeutic interventions can influence key events in the resolution of inflammation following MI/R.
Massive Compression for High Data Rate Macromolecular Crystallography (HDRMX): Impact on Diffraction Data and Subsequent Structural Analysis
Authors: Bernstein Herbert J. , Soares Alexei S. , Horvat Kimberly , Jakoncic Jean
Published: September 2024

New higher-count-rate, integrating, large area X-ray detectors with framing rates as high as 17,400 images per second are beginning to be available. These will soon be used for specialized MX experiments but will require optimal lossy compression algorithms to enable systems to keep up with data throughput. Some information may be lost. Can we minimize this loss with acceptable impact on structural information? To explore this question, we have considered several approaches: summing short sequences of images, binning to create the effect of larger pixels, use of JPEG-2000 lossy wavelet-based compression, and use of Hcompress, which is a Haar-wavelet-based lossy compression borrowed from astronomy. We also explore the effect of the combination of summing, binning, and Hcompress or JPEG-2000. In each of these last two methods one can specify approximately how much one wants the result to be compressed from the starting file size. These provide particularly effective lossy compressions that retain essential information for structure solution from Bragg reflections.

Synopsis

New higher-count-rate, integrating, large area X-ray detectors with framing rates as high as 17,400 images per second are beginning to be available. These will soon be used for specialized MX experiments but will require optimal lossy compression algorithms to enable systems to keep up with data throughput. Some information may be lost. Can we minimize this loss with acceptable impact on structural information?
Hippocampal ERK2 dimerization is critical for memory reconsolidation and synaptic plasticity
Authors: Ramos Santiago Ojea , Medina Candela , Krawczyk María del Carmen , Millan Julieta , Acutain María Florencia , Romano Arturo Gabriel , Baez María Verónica , Urbano Francisco José , Boccia Mariano Martín , Feld Mariana
Published: September 2024

Extensive research has focused on extracellular-signal regulated kinase (ERK) 1/2 phosphorylation across various memory and plasticity models. However, the precise mechanism linking ERK activity to memory stabilization and restabilization are still poorly understood, and the role of ERK1/2 dimerization remains unexplored. ERK dimerization is essential for the binding and activation of cytoplasmic targets, many of which have been strongly implicated in memory and plasticity. In this work, we studied the role of ERK2 dimerization in memory and synaptic plasticity through several experimental approaches. We found that reactivation of a weak inhibitory avoidance (wIA) memory led to a significant reduction in hippocampal ERK2 dimerization. Furthermore, intrahippocampal infusion of DEL-22379 (DEL), an ERK dimerization inhibitor, following memory reactivation had a bidirectional effect: it blocked the reconsolidation of a strong inhibitory avoidance (sIA) memory, but enhanced the reconsolidation of a wIA memory. Moreover, DEL administration blocked hippocampal ERK2 dimerization in vivo and impaired high-frequency stimulation-induced long-term potentiation (LTP) in hippocampal slices. These findings demonstrate for the first time that ERK2 dimerization occurs in the intact rodent nervous system and plays a pivotal role in plasticity and memory. While further research is needed, this study highlights the relevance of ERK dimerization in these processes.
Exploring yield stability and the fitness landscape of maize landrace root phenotypesin silico
Authors: Lopez-Valdivia Ivan , Rangarajan Harini , Vallebueno-Estrada Miguel , Lynch Jonathan P.
Published: September 2024

Integrated root phenotypes contribute to environmental adaptation and yield stability. We used the functional-structural plant/soil modelOpenSimRoot_v2to reconstruct the root phenotypes and environments of eight maize landraces to understand the phenotypic and environmental factors associated with broad adaptation. We found that accessions from low phosphorus regions have root phenotypes with shallow growth angles and greater nodal root numbers, allowing them to adapt to their native environments by improved topsoil foraging. We used machine learning algorithms to detect the most important phenotypes responsible for adaptation to multiple environments. The most important phene states responsible for stability across environments are large cortical cell size and reduced diameter of roots in nodes 5 and 6. When we dissected the components of root diameter, we observed that large cortical cell size improved growth by 28%, 23 % and 114%, while reduced cortical cell file number alone improved shoot growth by 137%, 66% and 216%, under drought, nitrogen and phosphorus stress, respectively. Functional-structural analysis of 96 maize landraces from the Americas, previously phenotyped in mesocosms in the greenhouse, suggested that parsimonious anatomical phenotypes, which reduce the metabolic cost of soil exploration, are the main phenotypes associated with adaptation to multiple environments, while root architectural traits were related to adaptation to specific environments. Our results indicate that integrated phenotypes with root anatomical phenes that reduce the metabolic cost of soil exploration will increase tolerance to stress across multiple environments and therefore improve yield stability, regardless of their root architecture.
CORELSA - Remote stethoscope system for fast and standardized auscultations of large numbers of patients with respiratory syndromes
Authors: Ides Kris , Aerts Arne , Baeyens Rens , Balemans Niels , Bosschaerts Tom , Cazaerck Jonathan , Ceulemans David , De Mey Fons , Jansen Wouter , Kerstens Robin , Laurijssen Dennis , Lauwers Eline , Schenck Anthony , Schouten Girmi , Simon Ralph , Verellen Thomas , Verreycken Erik , Jorens Philippe , Verhulst Stijn , Daems Walter , Steckel Jan
Published: September 2024

One of the major impacts of the current COVID-19 pandemic is the immense strain that is being put on the intensive care units. As a typical SARS-CoV-2 infection often leads to severe acute respiratory syndromes, one of the most basic essential examinations is lung auscultation. There are different categories of lung sounds that can be assessed with a stethoscope like crackles, wheezes, rhonchi and coarse breath sounds. Each of these malicious lung sounds contribute to a clinical assessment and follow-up of the patient’s airways and lungs and can indicate the development of pneumonia. Therefore, auscultation on a regular basis is essential, but it also takes a lot of time for the physicians. Moreover, because of the risk of infection for health care workers, it is becoming increasingly difficult or sometimes impossible to safely use a stethoscope. Here we introduce a remote stethoscope system that can help to reduce the workload of physicians and nurses, diminishes the risk of contamination and leads to more standardized auscultation, which can also be stored and reevaluated. We provide a detailed description of our system, which consists of parts that are low cost, easily available in most parts of the world, or can be 3D printed. We provide instructions and an open source software stack to run such a system for a large number of patients which can be remotely auscultated from a central computer. We believe that the system described in this paper can allow various institutes to replicate the system, and increase the safety and reduce the overall workload in the intensive care units around the world.
CRISPR editing of candidate host factors that impact influenza A virus infection
Authors: Kyawe Pyae Phyo , Liu Ping , Jiang Zhaozhao , Bradley Evan S. , Cicuto Thomas , Trombly Melanie I. , Silverman Neal , Fitzgerald Katherine A. , McDougall William M. , Wang Jennifer P.
Published: September 2024

Influenza A virus (IAV) is a respiratory pathogen with a segmented negative-sense RNA genome that can cause epidemics and pandemics. The host factors required for the complete IAV infectious cycle have not been fully identified. Here, we examined select host factors that were identified by independent CRISPR screens as candidate contributors to IAV infectivity. We performed CRISPR-mediated knockout of cytidine monophosphate N-acetylneuraminic acid synthetase (CMAS) as well as CRISPR-mediated overexpression of beta-1,4 N-acetylgalactosaminyltransferase 2 (B4GALNT2) and adenosine deaminase acting on RNA 1 (ADAR1) in the human bronchial epithelial A549 cell line and evaluated IAV infectivity. We confirmed that the knockout ofCMASor overexpression ofB4GALNT2restricts IAV infection by diminishing binding to the cell surface but has no effect on vesicular stomatitis virus infection. While ADAR1 overexpression does not significantly inhibit IAV replication, it has a pro-viral effect with coxsackie B virus (CVB) infection. This pro-viral effect is not likely secondary to reduced type I interferon (IFN) production, as the induction of the IFN-stimulated genesISG15andCXCL10is negligible in both parent and ADAR1-overexpressing A549 cells following CVB challenge. In contrast,ISG15andCXCL10production is robust and equal for parent and ADAR1-overexpressing A549 cells challenged with IAV. Taken together, these data provide insight into how host factors identified in CRISPR screens can be further explored to understand the dynamics of pro- and anti-viral factors.

Importance

Influenza A virus (IAV) remains a global threat due to its ability to cause pandemics, making the identification of host factors essential for developing new antiviral strategies. In this study, we utilized CRISPR-based techniques to investigate host factors identified in screens as reducing IAV infectivity. Knockout of CMAS, a key enzyme in sialic acid biosynthesis, significantly reduced IAV binding and infection by disrupting sialic acid production on the cell surface. Overexpression of B4GALNT2 had similar effects, conferring resistance to IAV infection through diminished cell-surface binding. While overexpression of ADAR1, known for its role in RNA editing and immune regulation, slightly reduced IAV replication, it increased coxsackie B virus replication. Such findings reveal the diverse roles of host factors in viral infection, offering insights for targeted therapeutic development against IAV and other pathogens.
Abrogation of presynaptic facilitation at hippocampal mossy fiber synapses impacts neural ensemble activity and spatial memory
Authors: Marneffe Catherine , Grosjean Noelle , Nicolay-Kritter Kyrian , Chatras Cécile , Harrell Evan R. , Kees Ashley , Mulle Christophe
Published: September 2024

Presynaptic short-term plasticity is thought to play a major role in the process of spike transfer within local circuits. Mossy fiber synapses between the axons of dentate gyrus (DG) granule cells and CA3 pyramidal cells (Mf-CA3 synapses) display a remarkable extent of presynaptic plasticity which endows these synaptic connections with detonator properties. The pattern of action potential firing, in the form of high frequency bursts in the DG, strongly controls the amplitude of synaptic responses and information transfer to CA3. Here we have investigated the role of presynaptic facilitation at Mf-CA3 synapses in the operation of CA3 circuitsin vivoand in memory encoding. Syt7, a calcium sensor necessary for presynaptic facilitation, was selectively abrogated, in DG granule cells using Syt7 conditional KO mice (DG Syt7 KO mice). In hippocampal slices, we extend previous analysis to show that short-term presynaptic facilitation is selectively suppressed at Mf-CA3 synapses in the absence of Syt7, without any impact on basal synaptic properties and long-term potentiation. Short-term plasticity was found to be crucial for spike transfer between the DG and CA3 in conditions of naturalistic patterns of presynaptic firing. At the network level, in awake head-fixed mice, the abrogation of short-term plasticity largely reduced the co-activity of CA3 pyramidal cells. Finally, whereas DG Syt7 KO mice are not impaired in behavioral tasks based on pattern separation, they show deficits in spatial memory tasks which rely on the process of pattern completion. These results shed new light on the role of the detonator properties of DG-CA3 synapses, and give important insights into how this key synaptic feature translate at the population and behavioral levels.
Distinct input-specific mechanisms enable presynaptic homeostatic plasticity
Authors: Chien Chun , He Kaikai , Perry Sarah , Tchitchkan Elizabeth , Han Yifu , Li Xiling , Dickman Dion
Published: September 2024

Synapses are endowed with the flexibility to change through experience, but must be sufficiently stable to last a lifetime. This tension is illustrated at theDrosophilaneuromuscular junction (NMJ), where two motor inputs that differ in structural and functional properties co-innervate most muscles to coordinate locomotion. To stabilize NMJ activity, motor neurons augment neurotransmitter release following diminished postsynaptic glutamate receptor functionality, termedpresynaptichomeostaticpotentiation (PHP). How these distinct inputs contribute to PHP plasticity remains enigmatic. We have used a botulinum neurotoxin to selectively silence each input and resolve their roles in PHP, demonstrating that PHP is input-specific: Chronic (genetic) PHP selectively targets the tonic MN-Ib, where active zone remodeling enhances Ca2+influx to promote increased glutamate release. In contrast, acute (pharmacological) PHP selectively increases vesicle pools to potentiate phasic MN-Is. Thus, distinct homeostatic modulations in active zone nanoarchitecture, vesicle pools, and Ca2+influx collaborate to enable input-specific PHP expression.
A Novel Maxillofacial Technology for Drug Administration-A Randomized Controlled Trial Using Metronidazole
Authors: Ramachandran Sajani , Kandasamy Ravichandran , Verma Kavita , Murugan Jayahshri , Sudhakar Jishnu , Adiyeri Janardhanan Hridwik , Anoop U.R
Published: September 2024

Aim

To compare the efficacy of a novel maxillofacial drug delivery technology with that of oral administration by analyzing the presence of administered metronidazole in plasma.

Material & Methods

The patients reporting to the Dental outpatient department with acute pulpitis in relation to maxillary molar were examined and recruited for the study. All consenting patients fulfilling the inclusion criteria during the study period were included.

The selected patients were randomly divided into two groups using computer generated sequence of random numbers.

Group I: In the control group patients, a single dose of 400 mg of metronidazole in the form of a tablet was administered through the oral route, after biomechanical preparation of root canals.

Group II: In the experimental group patients, 5mg of metronidazole in the form of an infusion solution was administered into the pulp cavity of a maxillary molar using the maxillofacial route and technology, after biomechanical preparation of root canals.

The blood samples were collected at 15 minutes and 30 minutes after administration of metronidazole. The plasma samples were then analysed for the presence of metronidazole using high performance liquid chromatography (HPLC).

Results

Out of ten, 5 (50%) samples in the oral route group and all 9 (100%) samples in the maxillofacial route group had the presence of the drug (p = 0.033). There was no statistically significant difference in presence of the drug between 15 minutes and 30 minutes in the oral route (p = 1.0) and in the maxillofacial route (p = 0.687). Further, the mean value of the area under the HPLC curve after 15 minutes was found to be similar in both the groups (p = 0.4). At 30 minutes also the area under the HPLC curve between the groups was not statistically significant (p = 0.156)

Conclusion

The maxillofacial drug delivery technique can be an effective alternate route for painless and controlled drug delivery.
In-hospital stay of anemic patients (70-90 g.L-1) in the ED with/without transfusion: a single-center propensity-matched study
Authors: Coisy Fabien , Anselme Clémence , Goulabchand Radjiv , Grau-Mercier Laura , Markarian Thibaut , Bobbia Xavier , Genre-Grandpierre Romain
Published: September 2024

Background and importance

A quarter of patients presenting to the emergency department (ED) have anemia. Although red blood cell (RBC) transfusion is routinely used in symptomatic anemia, there is no evidence on the benefit of blood transfusion in hemodynamically stable patients in the ED for patients requiring hospitalization.

Objective

The study aimed to compare in-hospital length of stay (LOS) of patients with anemia between 70 and 90 g.L-1transfused or not in ED.

Design

Retrospective single-center study

Settings and participants

All adult patients admitted to the ED of our university hospital with an initial hemoglobin level between 70 and 90 g.L-1, without hemorrhagic shock, who were hospitalized after ED admission.

Outcome measures and analysis

A propensity score, comprising hemoglobin level, Charlson’s comorbidity index, clinical signs of anemia, the chronicity of anemia and hospitalization department was used to compare the LOS of patients transfused versus non-transfused in the ED.

Intervention

RBC transfusion in the ED

Main results

From January 1st to December 31st, 2022, 1 169 patients were screened of whom 569 (49%) were excluded, mostly due to discharge without hospitalization. The remaining 564 (48%) patients had a median age of 77 [68; 85] and 240 (43%) were women. Finally, 127 (23%) patients were transfused in ED. Transfused patients received more units of RBC during the whole hospitalization period (4 [3; 5] versus 2 [1; 3] than non-transfused patients (p< 0.01)). After propensity score matching, median LOS was 9 [5; 19] days for ED transfused patients and 8 [5; 15] days for non-ED transfused patients (median difference= -1 95% CI [-3; 2]; p=0.45).

Conclusion

In patients with non-life-threatening anemia, RBC transfusion in the ED does not appear to reduce in-hospital LOS compared with transfusion in inpatient departments. Further studies are needed to identify patients requiring transfusion in ED.
Computed tomography radiomics-based cross-sectional detection of mandibular osteoradionecrosis in head and neck cancer survivors
Authors:   MD Anderson Head and Neck Cancer Symptom Working Group, Kamel Serageldin , Humbert-Vidan Laia , Kaffey Zaphanlene , Abusaif Abdulrahman , Fuentes David T. A. , Wahid Kareem , Dede Cem , Naser Mohamed A. , He Renjie , Moawad Ahmed W. , Elsayes Khaled M. , Chen Melissa M. , Otun Adegbenga O. , Rigert Jillian , Chambers Mark , Hope Andrew , Watson Erin , Brock Kristy K. , Hutcheson Katherine , van Dijk Lisanne , Moreno Amy C. , Lai Stephen Y. , Fuller Clifton D. , Mohamed Abdallah S. R.
Published: September 2024

Purpose

This study aims to identify radiomic features extracted from contrast-enhanced CT scans that differentiate osteoradionecrosis (ORN) from normal mandibular bone in patients with head and neck cancer (HNC) treated with radiotherapy (RT).

Materials and Methods

Contrast-enhanced CT (CECT) images were collected for 150 patients (80% train, 20% test) with confirmed ORN diagnosis at The University of Texas MD Anderson Cancer Center between 2008 and 2018. Using PyRadiomics, radiomic features were extracted from manually segmented ORN regions and the corresponding automated control regions, the later defined as the contralateral healthy mandible region. A subset of pre-selected features was obtained based on correlation analysis (r > 0.95) and used to train a Random Forest (RF) classifier with Recursive Feature Elimination. Model explainability SHapley Additive exPlanations (SHAP) analysis was performed on the 20 most important features identified by the trained RF classifier.

Results

From a total of 1316 radiomic features extracted, 810 features were excluded due to high collinearity. From a set of 506 pre-selected radiomic features, the optimal subset resulting on the best discriminative accuracy of the RF classifier consisted of 67 features. The RF classifier was well calibrated (Log Loss 0.296, ECE 0.125) and achieved an accuracy of 88% and a ROC AUC of 0.96. The SHAP analysis revealed that higher values of Wavelet-LLH First-order Mean and Median were associated with ORN of the jaw (ORNJ). Conversely, higher Exponential GLDM Dependence Entropy and lower Square First-order Kurtosis were more characteristic of normal mandibular tissue.

Conclusion

This study successfully developed a CECT-based radiomics model for differentiating ORNJ from healthy mandibular tissue in HNC patients after RT. Future work will focus on the detection of subclinical ORNJ regions to guide earlier interventions.
Exploiting the Achilles’ Heel of Viral RNA Processing to Develop Novel Antivirals
Authors: Amiri Ali Zahedi , Ahmed Choudhary , Dahal Subha , Grosso Filomena , Leng Haomin , Stoilov Peter , Mangos Maria , Toutant Johanne , Shkreta Lulzim , Attisano Liliana , Chabot Benoit , Brown Martha , Huesca Mario , Cochrane Alan
Published: September 2024

Viruses continue to pose a significant health burden to the human population, and recent history has shown a concerning surge in viral threats. Treatment options for viral infections are limited, and viruses have proven adept at evolving resistance to many existing therapies, highlighting a significant vulnerability in our defenses. In response to this challenge, we explored the modulation of cellular RNA metabolic processes as an alternative paradigm to antiviral development. Many viruses depend on the host cell’s RNA splicing machinery, and small alterations to this host process results in catastrophic changes in viral protein production, ultimately inhibiting virus replication. Previously, the small molecule 5342191 was identified as a potent inhibitor of HIV-1 replication by altering viral RNA accumulation at doses that minimally affect host gene expression. In this report, we document 5342191 as a potent inhibitor of adenovirus, coronavirus, and influenza replication. In each case, 5342191-mediated reduction in virus replication was associated with altered viral RNA accumulation and loss of viral structural protein expression. Interestingly, while resistant viruses were rapidly isolated for compounds targeting either virus-encoded proteases or polymerases, we have not yet isolated 534219-resistant variants of coronavirus or influenza. As with HIV-1, 5342191’s inhibition of coronaviruses and influenza is mediated through the activation of specific cell signaling networks, including GPCR and/or MAPK signaling pathways that ultimately affect SR kinase expression. Together, these studies highlight the therapeutic potential of compounds that target cellular processes essential for the replication of multiple viruses. Not only do these compounds hold promise as broad-spectrum antivirals, but they also offer the potential of greater resilience in combating viral infections.
Molecular mechanisms of uric acid transport by the native human URAT1 and its inhibition by anti-gout drugs
Authors: Wu Canrong , Zhang Chao , Jin Sanshan , Wang James Jiqi , Dai Antao , Xu Jiuyin , Zhang Heng , Yang Xuemei , He Xinheng , Yuan Qingning , Hu Wen , Xu Youwei , Wang Mingwei , Jiang Yi , Yang Dehua , Xu H. Eric
Published: September 2024

Gout, a common and painful disease, stems from hyperuricemia, where elevated blood uric acid levels lead to urate crystal formation in joints and kidneys. The human urate transporter 1 (hURAT1) plays a critical role in urate homeostasis by facilitating urate reabsorption in the renal proximal tubule, making it a key target for gout therapy. Pharmacological inhibition of hURAT1 with drugs such as dotinurad, benzbromarone, lesinurad, and verinurad promotes uric acid excretion and alleviates gout symptoms. Here we present cryo-electron microscopy structures of native hURAT1 bound with these anti-gout drugs in the inward-open state, and with uric acid in inward-open, outward-open, and occluded states. Complemented by mutagenesis and cell-based assays, these structures reveal the mechanisms of uric acid reabsorption and hURAT1 inhibition. Our findings elucidate the molecular basis of uric acid transport and anti-gout medication action, and provide a structural framework for the rational design of next-generation therapies for hyperuricemia and gout.
A conserved hub protein for coordinating peptidoglycan turnover that activates cell division amidases inAcinetobacter baumannii
Authors: Simpson Brent W. , McLean Amanda B. , Trent M. Stephen
Published: September 2024

Gram-negative bacteria produce a multilayered cell envelope in which their peptidoglycan is sandwiched between two membranes, an inner membrane made of glycerophospholipids and an asymmetric outer membrane with glycerophospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet. TheAcinetobacter baumanniiouter membrane contains lipooligosaccharide (LOS), a variant of LPS lacking O-antigen. LPS/LOS is typically essential, butA. baumanniican survive without LOS. Previously, we found that the peptidoglycan biogenesis protein NlpD becomes essential during LOS-deficiency. NlpD is typically redundant and is one of the cell’s amidase activators for regulating peptidoglycan degradation, a process critical for cell division. We found that NlpD is essential under these conditions because a second putative amidase activator, termed WthA (cellwall turnoverhub proteinA), no longer functions in LOS-deficient cells. Mutants lacking WthA had severe cell division defects and were synthetically sick with loss of NlpD. BothAcinetobacterWthA and NlpD were found to activate an amidase activity of Oxa51, a chromosomally encodedβ-lactamase. Further, WthA is homologous toPseudomonasLbcA that impacts two other classes of peptidoglycan degradation enzymes, endopeptidases and lytic transglycosylases. WthA/LbcA homologs were identified across Proteobacteria, Bacteroidota, and Chlorobiota, suggesting they belong to a conserved family involved in regulation of peptidoglycan turnover. WhileAcinetobacterWthA may share functions ofPseudomonasLbcA, we found no evidence that LbcA is an amidase activator. Altogether, we have identified a missing player inAcinetobacterpeptidoglycan biogenesis, a conserved hub protein that regulates multiple peptidoglycan turnover enzymes including cell division amidases.

Significance Statement

Peptidoglycan is a rigid layer that provides structural support to bacterial cells. Peptidoglycan must be degraded to make room for new synthesis and for cells to divide, a process termed turnover. Turnover enzymes are tightly regulated to prevent their activities from lysing the cell. The critical pathogenAcinetobacter baumanniiwas missing known peptidoglycan amidases, a class of turnover enzymes, and the key activator that controls their activity during cell division. We have identified WthA as having a role in cell division most likely as an amidase activator. WthA homologs were widely distributed in bacteria and the closely related LbcA inPseudomonasimpacts two other types of turnover enzymes. We explore the possible functions of this new family of proteins that serves as a hub for impacting peptidoglycan turnover.
Influenza A virus exploits the motility of membrane cytoskeletal actomyosin filaments for its genome packaging in the host cell
Authors: Wang I-Hsuan , Usukura Jiro , Miyake Yasuyuki , Usukura Eiji , Narita Akihiro , Yamauchi Yohei , Kawaoka Yoshihiro
Published: September 2024

Influenza A virus encodes its genome in eight segments of viral ribonucleoproteins (vRNPs) replicated in the host cell nucleus. Our understanding of host factors involved in driving vRNP selective packaging remains incomplete. To address this, we used advanced immuno-freeze-etch electron microscopy to visualise the vRNP packaging process and atomic force live-cell imaging (AFM) to examine the motility of membrane cytoskeletal actin filaments. In the cytoplasm, vRNPs were mainly localised on mottled membrane-like structures, suggesting intracellular trafficking through such structures. After reaching the cytoplasmic side surface of the plasma membrane, vRNPs formed many aggregates while associating with actin filaments. Antibody labelling also detected myosin along actin filaments entangled in vRNPs. Blocking myosin activity with blebbistatin prevented the active movement of membrane cytoskeletal actin filaments just below the plasma membrane visualised by AFM and abrogated proper aggregation of vRNPs. Thus, actomyosin motility appears to be crucial for the selective packaging of vRNPs.
Long-term live imaging, cell identification and cell tracking in regenerating crustacean legs
Authors: Çevrim Çağrı , Laplace-Builhé Béryl , Sugawara Ko , Rusciano Maria Lorenza , Labert Nicolas , Brocard Jacques , Almazán Alba , Averof Michalis
Published: September 2024

High resolution live imaging of regeneration presents unique challenges, due to the nature of the specimens (large mobile animals), the duration of the process (spanning days or weeks), and the fact that cellular resolution must be achieved without damage caused by lengthy exposures to light. Here, we develop a method for live imaging that captures the entire process of leg regeneration, spanning up to 10 days, at cellular resolution, in the crustaceanParhyale hawaiensis. Our method allows (1) mounting and long-term live imaging of regenerating legs under conditions that yield high spatial and temporal resolution but minimise photodamage, (2) fixing andin situstaining of the regenerated legs that were imaged, to identify cell fates, and (3) computer-assisted cell tracking to determine the cell lineages and progenitors of identified cells. The method is optimised to limit light exposure while maximising tracking efficiency. Combined with appropriate cell-type-specific markers, this method may allow the description of cell lineages for every regenerated cell type in the limb.
gilgamesh, Drosophila casein kinase 1g, is required for myosin-dependent junction strengthening and epithelial folding
Authors: Gu Lingkun , Koran Reina , Brar Jasneet , Weng Mo
Published: September 2024

Adherens junctions, which serve as the primary physical link between cells, undergo remodeling in response to tension forces to maintain tissue integrity and promote tissue shape changes. However, the in vivo mechanisms driving this process remain poorly understood. Here, we identified Gilgamesh (Gish), the conserved fly homolog of casein kinase 1g as essential for myosin-dependent junction strengthening and tissue folding during apical constriction of Drosophila mesoderm. We show that Gish is recruited to spot adherens junctions in a contractile myosin-dependent manner. During apical constriction, Gish is required for junction strengthening by promoting growth and merging of small junction puncta, as well as stabilizing junction puncta at cell edges. The junction defects in Gish-depleted mesoderm result in breakage of the tissue-scale apical actomyosin network during apical constriction, and ultimately failure in mesoderm infolding. Our data show that Gish is a mechanosensitive kinase required for the integrity of adherens junctions during apical constriction.
ATG9 vesicles are a subtype of intracellular nanovesicle
Authors: Fesenko Mary , Moore Daniel J. , Ewbank Peyton , Courthold Elizabeth , Royle Stephen J.
Published: September 2024

Cells are filled with thousands of vesicles, which mediate protein transport and ensure homeostasis of the endomembrane system. Distinguishing these vesicles functionally and molecularly represents a major challenge. Intracellular nanovesicles (INVs) are a large class of transport vesicles that likely comprises of multiple subtypes. Here, we define the INV proteome and find that it is molecularly heterogeneous, and enriched for transmembrane cargo molecules including integrins, transporters, and ATG9A, a lipid scramblase associated with autophagy. ATG9A is known to reside in ‘ATG9 vesicles’: small vesicles that contribute to autophagosome formation. Using in-cell vesicle capture assays we found that ATG9A, as well as other ATG9 vesicle cargos, were in INVs. Quantitative analysis showed that virtually all ATG9 vesicles are INVs, but that only ∼20% of INVs are ATG9 vesicles, suggesting that ATG9 vesicles are in fact a subtype of INV, which we term ATG9A-flavor INVs. Finally, we show that perturbing ATG9A-flavor INVs impaired the autophagy response induced by starvation.
Developmental regulation of dermal adipose tissue by BCL11b
Authors: Traynor Sarah , Bhattacharya Shashwati , Batmanov Kirill , Cheng Lan , Weller Angela , Moore Natalie , Flesher Carmen , Merrick David
Published: September 2024

The distinct anatomic environment in which adipose tissues arise during organogenesis is a principle determinant of their adult expansion capacity. Metabolic disease results from a deficiency in hyperplastic adipose expansion within the dermal/subcutaneous depot; thus, understanding the embryonic origins of dermal adipose is imperative. Using single-cell transcriptomics throughout murine embryogenesis, we characterized cell populations, includingBcl11b+cells, that regulate the development of dermal white adipose tissue (dWAT). We discovered that BCL11b expression modulates the Wnt signaling microenvironment to enable adipogenic differentiation in the dermal compartment. Subcutaneous and visceral adipose arises from a distinct population ofNefl+cells during embryonic organogenesis, whereasPi16+/Dpp4+fibroadipogenic progenitors support obesity-stimulated hypertrophic expansion in the adult. Together, these results highlight the unique regulatory pathways used by anatomically distinct adipose depots, with important implications for human metabolic disease.
Quantum sensing of ultralow temperature in biwire ultracold polar molecules
Authors: Boudjemâa Abdelâali , Abbas Karima , Taiba Asma Tahar , Tan Qing-Shou
Published: September 2024

We present a systematic study of quantum sensing of ultralow temperature in biwire ultracold polar molecules of a quasi-one-dimensional (1D) trap by exploring the dynamics of two physically different qubit models. The two models consist of a trapped impurity atom that act as a temperature quantum sensor interacting with polar molecules reservoir, where dipole moments are aligned head-to-tail across the wires. Our model takes advantage of the adjustable interwire distance to accurately control the precision ultralow temperatures measurement. We show that the system undergoes a transition from Markovian to non-Markovian dynamics, which can be controlled by changing the interwire separation, the dipole-–dipole interaction (DDI), and the temperature. We characterize the thermometric performance using the quantum signal-to-noise ratio for both models and demonstrate that such a quantity exhibits a higher peak at ultralow temperature. We therefore emphasize that ultracold polar molecules are crucial for revolutionizing temperature sensing.

Published by the American Physical Society
2024
New constraints on
CPT
symmetry violation in charm mesons
Authors: Krzemień Wojciech , Kmieć Mateusz , Szabelski Adam , Wiślicki Wojciech
Published: September 2024

Small CPT-violating effects are admissible in several theories beyond the Standard Model of interactions. We analyze experimental data obtained with neutral flavored meson mixing and place bounds on the scale of such phenomena. The constraints on the CPT-violating parameter z are derived by reinterpreting the LHCb measurement of the time-dependent asymmetry in the Cabbibo-favored D0→K−π+ and D0¯→K+π− decay rates. The bounds provided in this paper are 2 orders of magnitude stricter compared to the results obtained by the FOCUS Collaboration. Among other constraints, we report bounds on the differences in the decay widths and masses of the neutral D meson flavor states at a 95% confidence level. The decay width difference is bounded by (−4.7<δΓD<2.1)×10−16  GeV. The mass difference lies within (−2.0<δmD<2.0)×10−15  GeV for 95% of arg(z) values. The paper includes an assessment of the influence of CP violation on the results and a discussion of the future prospects.

Published by the American Physical Society
2024
Evidence for universal flow and characteristics of early time thermalization in a scalar field model for heavy ion collisions
Authors: Carrington Margaret E. , Cowie Wade N. , Kunstatter Gabor , Phillips Christopher D.
Published: September 2024

We study numerically the evolution of an expanding strongly self-coupled real scalar field. We use a conformally invariant action that gives a traceless energy-momentum tensor and is better suited to model the early time behavior of a system such as QCD, whose action is also conformally invariant. We consider asymmetric initial conditions and observe that when the system is initialized with nonzero spatial eccentricity, the eccentricity decreases and the elliptic flow coefficient increases. This behavior is characteristic of a hydrodynamic system in which pressure gradients are converted into fluid velocities, and therefore spatial anisotropy decreases while momentum anisotropy is generated. We look at a measure of transverse pressure asymmetry that has been shown to behave similarly to the elliptic flow coefficient in hydrodynamic systems and show that in our system their behavior is strikingly similar. We show that the derivative of the transverse velocity is proportional to the gradient of the energy in Milne coordinates and argue that this result means that transverse velocity initially develops in the same way that it does in hydrodynamic systems. We conclude that some aspects of the early onset of hydrodynamic behavior that has been observed in quark-gluon plasmas are seen in our numerical simulation of strongly coupled scalar fields.

Published by the American Physical Society
2024
Automatic generation of helicity amplitudes in the Feynman-diagram gauge
Authors: Hagiwara Kaoru , Kanzaki Junichi , Mattelaer Olivier , Mawatari Kentarou , Zheng Ya-Juan
Published: September 2024

We develop a method to calculate helicity amplitudes of an arbitrary tree-level process in the Feynman-diagram (FD) gauge for an arbitrary gauge model with adraph5_a@. We start from the ’t Hooft–Feynman gauge Lagrangian in eynules and generate scattering amplitudes by identifying the Goldstone boson as the 5th component of each weak boson. All the vertices of the 5-component weak bosons are then created automatically by assembling the relevant weak boson and Goldstone boson vertices in the Feynman gauge. The 5-component weak boson vertices are then connected by the 5×5 matrix propagator in the FD gauge. As a demonstration of the method we calculate the cross section for the process μ−μ+→νμν¯μtt¯H with complex top Yukawa coupling, which can be obtained by adding a gauge invariant dimension-6 operator to the Standard Model (SM) Lagrangian. The FD gauge and the unitary (U) gauge amplitudes give exactly the same cross section, and subtle gauge theory cancellation among diagrams in the U gauge at high energies is absent in the FD gauge, as has been observed for various SM processes. In addition, we find that the total cross sections at high energies are dominated by a single, or a set of nonvanishing Feynman amplitudes with the higher dimensional vertices in the FD gauge.

Published by the American Physical Society
2024
Sensitivity floor for primordial black holes in neutrino searches
Authors: Liu Qishan , Ng Kenny C. Y.
Published: September 2024

Primordial black holes (PBHs) formed in the early Universe are well-motivated dark matter (DM) candidates over a wide range of masses. These PBHs could emit detectable signals in the form of photons, electrons, and neutrinos through Hawking radiation. We consider the null observations of astrophysical ν¯e flux from several neutrino detectors and set new constraints on the PBHs as the dominant DM component to be above 6.4×1015  g. We also estimate the expected constraints with JUNO for the prospects in the near future. Lastly, we note that the diffuse supernova neutrino background (DSNB) is an unavoidable isotropic background. We thus estimate the sensitivity floor for PBH parameter space due to the DSNB and show that it is challenging for neutrino detectors to identify PBHs as they constitute 100% of the DM above a mass of 9×1015  g.

Published by the American Physical Society
2024
Quantum chaos on edge
Authors: Altland Alexander , Kim Kun Woo , Micklitz Tobias , Rezaei Maedeh , Sonner Julian , Verbaarschot Jacobus J. M.
Published: September 2024

Recently, the physics of many-body quantum chaotic systems close to their ground states has come under intensified scrutiny. Such studies are motivated by the emergence of model systems exhibiting chaotic fluctuations throughout the entire spectrum [the Sachdev-Ye-Kitaev (SYK) model being a renowned representative] as well as by the physics of holographic principles, which likewise unfold close to ground states. Interpreting the edge of the spectrum as a quantum critical point, here we combine a wide range of analytical and numerical methods to the identification and comprehensive description of two different universality classes: the near edge physics of “sparse” and the near edge of “dense” chaotic systems. The distinction lies in the ratio between the number of a system's random parameters and its Hilbert space dimension, which is exponentially small or algebraically small in the sparse and dense case, respectively. Notable representatives of the two classes are generic chaotic many-body models (sparse) and invariant random matrix ensembles or chaotic gravitational systems (dense). While the two families share identical spectral correlations at energy scales comparable to the level spacing, the density of states and its fluctuations near the edge are different. Considering the SYK model as a representative of the sparse class, we apply a combination of field theory and exact diagonalization to a detailed discussion of its edge spectrum. Conversely, Jackiw-Teitelboim gravity is our reference model for the dense class, where an analysis of the gravitational path integral and random matrix theory reveal universal differences to the sparse class, whose implications for the construction of holographic principles we discuss.

Published by the American Physical Society
2024
Quantum-metric-induced quantum Hall conductance inversion and reentrant transition in fractional Chern insulators
Authors: Wu Ang-Kun , Sarkar Siddhartha , Wan Xiaohan , Sun Kai , Lin Shi-Zeng
Published: September 2024

The quantum metric of single-particle wave functions in topological flat bands plays a crucial role in determining the stability of fractional Chern insulating (FCI) states. Here, we unravel that the quantum metric causes the many-body Chern number of the FCI states to deviate sharply from the expected value associated with partial filling of the single-particle topological flat band. Furthermore, the variation of the quantum metric in momentum space induces band dispersion through interactions, affecting the stability of the FCI states. This causes a reentrant transition into the Fermi liquid from the FCI phase as the interaction strength increases.

Published by the American Physical Society
2024