bluuebunny/crossref_metadata_2025 huggingface dataset:
“Why would we take men? This is an OB/GYN”: Gender, hysterectomy, and the patriarchal dividend
Authors: Becker Andréa
Published: October 2023

Hysterectomy experiences among transmasculine individuals represent a powerful case to examine gendered dynamics in healthcare, especially given the continued cultural association between the uterus and womanhood. In this paper, I draw on theories from feminist science and technology studies and medical sociology to examine in‐depth interviews with 46 trans or nonbinary individuals who have had, want, or are considering an elective premenopausal hysterectomy. I find that trans men and nonbinary patients must negotiate what I call the structural feminization of gynecology which often leads to poor healthcare experiences. This paper also extends theories of a “patriarchal dividend” in medicine by examining reported differences in medical experiences when patients are perceived as cisgender women versus as trans men or nonbinary. I find a double bind inherent in the patriarchal divided in healthcare: masculinity often leads to better care, but the patriarchal dividend is constrained by the stigma introduced by being a trans patient. In the process, I extend social scientific knowledge of a highly common yet understudied procedure while expanding scholarship on medicine, gender, and embodiment.
Infections after chimeric antigen receptor (CAR)‐T‐cell therapy for hematologic malignancies
Authors: Kampouri Eleftheria , Little Jessica S. , Rejeski Kai , Manuel Oriol , Hammond Sarah P. , Hill Joshua A.
Published: October 2023

Background

Chimeric antigen receptor (CAR)‐T‐cell therapies have revolutionized the management of acute lymphoblastic leukemia, non‐Hodgkin lymphoma, and multiple myeloma but come at the price of unique toxicities, including cytokine release syndrome, immune effector cell‐associated neurotoxicity syndrome, and long‐term “on‐target off‐tumor” effects.

Methods

All of these factors increase infection risk in an already highly immunocompromised patient population. Indeed, infectious complications represent the key determinant of non‐relapse mortality after CAR‐T cells. The temporal distribution of these risk factors shapes different infection patterns early versus late post‐CAR‐T‐cell infusion. Furthermore, due to the expression of their targets on B lineage cells at different stages of differentiation, CD19, and B‐cell maturation antigen (BCMA) CAR‐T cells induce distinct immune deficits that could require different prevention strategies. Infection incidence is the highest during the first month post‐infusion and subsequently decreases thereafter. However, infections remain relatively common even a year after infusion.

Results

Bacterial infections predominate early after CD19, while a more equal distribution between bacterial and viral causes is seen after BCMA CAR‐T‐cell therapy, and fungal infections are universally rare. Cytomegalovirus (CMV) and other herpesviruses are increasingly breported, but whether routine monitoring is warranted for all, or a subgroup of patients, remains to be determined. Clinical practices vary substantially between centers, and many areas of uncertainty remain, including CMV monitoring, antibacterial and antifungal prophylaxis and duration, use of immunoglobulin replacement therapy, and timing of vaccination.

Conclusion

Risk stratification tools are available and may help distinguish between infectious and non‐infectious causes of fever post‐infusion and predict severe infections. These tools need prospective validation, and their integration in clinical practice needs to be systematically studied.

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MINI‐AC: inference of plant gene regulatory networks using bulk or single‐cell accessible chromatin profiles
Authors: Manosalva Pérez Nicolás , Ferrari Camilla , Engelhorn Julia , Depuydt Thomas , Nelissen Hilde , Hartwig Thomas , Vandepoele Klaas
Published: October 2023

Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context‐specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI‐AC (Motif‐Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single‐cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI‐AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI‐AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF–target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC‐based GRNs with MINI‐AC. Finally, we combined MINI‐AC predictions from bulk and single‐cell AC datasets to identify general and cell‐type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI‐AC represents a powerful tool for inferring accurate AC‐derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.
Population genetic structure and implication for adaptive differentiation of the snail (Gastropoda, Provannidae) in deep‐sea chemosynthetic ecosystems
Authors: Zhang Yu , Cheng Jiao , Sha Zhongli , Hui Min
Published: October 2023

The snail Provanna glabra is a dominant species inhabiting both hydrothermal vents and cold seeps of the Northwest Pacific Ocean. The genetic diversity and population structure of the snail from the hydrothermal vents of Okinawa Trough and a methane seep in the South China Sea were investigated using mitochondrial cytochrome c oxidase subunit I (COI) and genome‐wide single nucleotide polymorphisms (SNPs). A total of 28,805 SNPs were screened based on 2b‐RAD sequencing. Substantial genetic differences between vent and seep populations were identified based on the two datasets with FST = 0.753 (COI) and FST = 0.109 (SNPs), respectively. The results of phylogenetic tree, ADMIXTURE and principal component analysis jointly supported the population differentiation. Outlier detection confirmed the local adaptation of P. glabras populations, and the annotation of these outliers revealed that they were closely associated with processes of signal transduction, immunity, DNA repair, transposable elements and biological development. The genetic divergence observed between hydrothermal vent and methane seep P. glabra populations might be induced by the geographic barrier, limited dispersal ability and natural selection imposed by local environmental pressures from different deep‐sea habitats, e.g. chemical composition, temperature and microbes. These results provide a genetic basis for the microevolution of snails inhabiting deep‐sea chemosynthetic ecosystems.
L‐theory of C∗$C^*$‐algebras
Authors: Land Markus , Nikolaus Thomas , Schlichting Marco
Published: October 2023

We establish a formula for the L‐theory spectrum of real ‐algebras from which we deduce a presentation of the L‐groups in terms of the topological K‐groups, extending all previously known results of this kind. Along the way, we extend the integral comparison map obtained in previous work by the first two authors to real ‐algebras and interpret it using topological Grothendieck–Witt theory. Finally, we use our results to give an integral comparison between the Baum–Connes conjecture and the L‐theoretic Farrell–Jones conjecture, and discuss our comparison map in terms of the signature operator on oriented manifolds.
Unsteady Reynolds-Averaged Navier–Stokes Simulations of a Ducted Wind Turbine
Authors: Safford Drew A. , Wang Junfeng , Liang Chunlei , Visser Kenneth
Published: October 2023

An unsteady Reynolds-averaged Navier–Stokes model on body-fitted meshes in a commercial package (SimericsMP+) with a mismatched grid interface is used to study fluid dynamics around a ducted wind turbine. The model is validated by studying turbulent flow past a marine propeller. The nondimensional thrust and torque coefficients are compared against experimental data and results from a large eddy simulation model. Both coefficients are found to be within 3% of experimental results. Following this validation, the impact of different tip speed ratios on the ducted wind turbine's fluid dynamics is assessed. The optimal tip speed ratio is found to be the design value of 3.93 with a maximum power coefficient of 0.465 based on the duct exit area. The corresponding thrust coefficient is found to be 1.02 based on the rotor area. Lower tip speed ratios experience larger flow separation on the duct interior. Higher tip speed ratios decrease the size of the low-velocity region behind the hub. The ducted wind turbine's performance at design conditions is compared to an open rotor. The ducted wind turbine increases the power coefficient by 96% over the open rotor. The impact of hub size on the ducted wind turbine is also studied by simulating a smaller hub with 77% diameter. At the design tip speed ratio, the smaller hub has a power coefficient of 0.417. The maximum power coefficient is found to be 0.446 at a higher tip speed ratio of 4.5.
Comparison of Subspace Identification Methods for Modal Estimation of Bladed Disks
Authors: Jorajuria Corentin , Esteves Cécile , Gibert Claude , Thouverez Fabrice
Published: October 2023

Bladed disks are critical parts of aeronautic turbojet engines requiring numerous dynamic analysis tests to fully achieve their design process. This work presents subspace state-space identification techniques for estimation of modal parameters of bladed disks using realistic although numerically generated test case data. Indeed, modal testing of bladed disks can exhibit high modal density leading to modal estimation issues. This study focuses on subspace state-space identification framework as it is an efficient way to process vector valued time series and thus to estimate modal parameters in a context of high modal density. In order to evaluate the techniques of interest, a versatile modal model has been specifically implemented to simulate data representative of full scale rotating aeronautic fan modal tests. This model is easily adjustable allowing to evaluate the identification methods in a more or less severe estimation context. The performance of the investigated methods is discussed and compared with the prescribed parameters of the model. Moreover, different techniques to estimate the order of the associated state-space model are reviewed and tested over several simulated configurations. Finally, a method to evaluate the uncertainties over the model parameters using covariance of estimator results and pseudospectrum computation is proposed and discussed over the investigated test cases.
Intermittency of Flame Structure and Thermo-Acoustic Behavior in a Staged Multipoint Injector Using Liquid Fuel
Authors: Truffot Marie , Renaud Antoine , Zimmer Laurent , Richecoeur Franck , Cayre Alain , Méry Yoann
Published: October 2023

This study investigates the impact of the staging factor, the ratio between the fuel injected through the pilot stage and the multipoint injection, on the flame dynamic. The BIMER combustor is an atmospheric pressure rig equipped with two corotating swirling air injections (a fixed amount of around 87% of the air goes inside the multipoint stage) and two fuel injection paths for staged combustion. Liquid dodecane is injected with air preheated at 437 K with a global equivalence ratio of 0.6 and a thermal power of around 72 kW. The change of the staging factor from 100% (pilot-only injection) toward 0% (multipoint-only injection) generates changes in the flame-shape which bifurcates from an anchored V-flame into a lifted flame. This flame shape bifurcation appears at a staging of factor around 25%. Around this staging factor, one can witness multistable flames where the flame structure transits randomly between five different states. Processing microphone signals recorded in the chamber provides an understanding of the flame dynamics. The attached flame presents limited pressure fluctuations level at 270 Hz, while the lifted flame features high-pressure fluctuations at 323 Hz. The intermittency between the five states (including the two stable states) is investigated.
Automated Identification of Differential-Variational Equations for Static Systems
Authors: Li Chunjiang , Huang Zhanchao , Huang Zhilong , Wang Yong , Jiang Hanqing
Published: October 2023

Data-driven equation identification for dynamical systems has achieved great progress, which for static systems, however, has not kept pace. Unlike dynamical systems, static systems are time invariant, so we cannot capture discrete data along the time stream, which requires identifying governing equations only from scarce data. This work is devoted to this topic, building a data-driven method for extracting the differential-variational equations that govern static behaviors only from scarce, noisy data of responses, loads, as well as the values of system attributes if available. Compared to the differential framework typically adopted in equation identification, the differential-variational framework, due to its spatial integration and variation arbitrariness, brings some advantages, such as high robustness to data noise and low requirements on data amounts. The application, efficacy, and all the aforementioned advantages of this method are demonstrated by four numerical examples, including three continuous systems and one discrete system.
Unsupervised Anomaly Detection via Nonlinear Manifold Learning
Authors: Yousefpour Amin , Shishehbor Mehdi , Zanjani Foumani Zahra , Bostanabad Ramin
Published: October 2023

Anomalies are samples that significantly deviate from the rest of the data and their detection plays a major role in building machine learning models that can be reliably used in applications such as data-driven design and novelty detection. The majority of existing anomaly detection methods either are exclusively developed for (semi) supervised settings, or provide poor performance in unsupervised applications where there are no training data with labeled anomalous samples. To bridge this research gap, we introduce a robust, efficient, and interpretable methodology based on nonlinear manifold learning to detect anomalies in unsupervised settings. The essence of our approach is to learn a low-dimensional and interpretable latent representation (aka manifold) for all the data points such that normal samples are automatically clustered together and hence can be easily and robustly identified. We learn this low-dimensional manifold by designing a learning algorithm that leverages either a latent map Gaussian process (LMGP) or a deep autoencoder (AE). Our LMGP-based approach, in particular, provides a probabilistic perspective on the learning task and is ideal for high-dimensional applications with scarce data. We demonstrate the superior performance of our approach over existing technologies via multiple analytic examples and real-world datasets.
Elevating nucleic acid delivery via a stable anionic peptide-dextran ternary system
Authors: Cheng Alex , Liu Ying , Song Hai-Qing
Published: October 2023

Nucleic acid-based therapies hold promise for treating previously intractable diseases but require effective delivery vectors to protect the therapeutic agents and ensure efficient transfection. Cationic polymeric vectors are particularly notable for their adaptability, high transfection efficiency, and low cost, but their positive charge often attracts blood proteins, causing aggregation and reduced transfection efficiency. Addressing this, we designed an anionic peptide-grafted dextran (Dex-LipE5H) to serve as a cross-linkable coating to bolster the stability of cationic polymer/nucleic acid complexes. The Dex-LipE5H was synthesized through a Michael addition reaction, combining an anionic peptide (LipE5H) with dextran modified by divinyl sulfone. We demonstrated Dex-lipE5H utility in a novel ternary nucleic acid delivery system, CDex-LipE5H/PEI/nucleic acid. CDex-LipE5H/PEI/nucleic acid demonstrated lower cytotoxicity and superior anti-protein absorption ability compared to PEI/pDNA and Dex-LipE5H/PEI/pDNA. Most notably, the crosslinked CDex-LipE5H/PEI/pDNA demonstrated remarkable transfection performance in HepG2 cells, which poses significant transfection challenges, even in a medium with 20% serum. This system’s effective siRNA interference performance was further validated through a PCSK9 gene knockdown assay. This investigation provides novel insights and contributes to the design of cost-effective, next-generation nucleic acid delivery systems with enhanced blood stability and transfection efficiency.
A Systematic Review of Digital Interventions to Promote Physical Activity in People With Intellectual Disabilities and/or Autism
Authors: Van Biesen Debbie , Van Damme Tine , Morgulec-Adamowicz Natalia , Buchholz Aleksandra , Anjum Momna , Healy Séan
Published: October 2023

This systematic review synthesized the literature on digital health interventions for the promotion of physical activity (PA) among people with intellectual disabilities and/or autism. From an initial screening of 553 records, 10 studies underwent full-text review. Data were extracted relating to study, intervention, and sample characteristics and PA-related findings. Methodological quality was evaluated using the Crowe Critical Appraisal Tool. There were mixed findings pertaining to the effectiveness of digital health interventions for promoting PA among these populations. Positive results were reported for three of five active-video-game interventions, two of three social-media-based interventions, and one of two e-learning/multicomponent interventions. Digital health interventions can potentially be effective for promoting PA among people with intellectual disabilities and/or autism. However, the large variation in the samples and intervention types and a reliance on pre- and quasi-experimental research designs suggest that inferences should be made with caution and additional research is needed.
A Snapshot of Sport Management Courses in Australia
Authors: Hekkema Megan C. , Hall Melinda , Pascoe Deborah A.
Published: October 2023

To prepare sport management students, curricula should align with industry. Given recent changes in sport management, the first step in aligning curricula with industry is to review current curricula. This study reviewed Australian sport management curricula using content analysis of the Common Professional Components based on the Commission on Sport Management Accreditation. From 39 universities, 11 (28%) undergraduate sport management programs were identified. The most common required sport management course was management concepts, followed by sport marketing and finance, budgeting, accounting, and economics. Public relations and ethical aspects were the least common required courses. Technology and sport sales were not offered. Results indicate that the current curricula may not be keeping pace with the sport management industry.
The poleward naturalization of intracontinental alien plants
Authors: Zhang Zhijie , Yang Qiang , Fristoe Trevor S. , Dawson Wayne , Essl Franz , Kreft Holger , Lenzner Bernd , Pergl Jan , Pyšek Petr , Weigelt Patrick , Winter Marten , Fuentes Nicol , Kartesz John T. , Nishino Misako , van Kleunen Mark
Published: October 2023

Plant introductions outside their native ranges by humans have led to substantial ecological consequences. While we have gained considerable knowledge about intercontinental introductions, the distribution and determinants of intracontinental aliens remain poorly understood. Here, we studied naturalized (i.e., self-sustaining) intracontinental aliens using native and alien floras of 243 mainland regions in North America, South America, Europe, and Australia. We revealed that 4510 plant species had intracontinental origins, accounting for 3.9% of all plant species and 56.7% of all naturalized species in these continents. In North America and Europe, the numbers of intracontinental aliens peaked at mid-latitudes, while the proportion peaked at high latitudes in Europe. Notably, we found predominant poleward naturalization, primarily due to larger native species pools in low-latitudes. Geographic and climatic distances constrained the naturalization of intracontinental aliens in Australia, Europe, and North America, but not in South America. These findings suggest that poleward naturalizations will accelerate, as high latitudes become suitable for more plant species due to climate change.
Evidence of immune imprinting or the effect of selection bias?
Authors: Hansen Christian H.
Published: October 2023

People with booster vaccinations appear more prone to reinfection than those with primary series vaccination only; however, selection bias in the study design complicates interpretation.
Multicellular bioprinted skin facilitates human-like skin architecture in vivo
Authors: Jorgensen Adam M. , Gorkun Anastasiya , Mahajan Naresh , Willson Kelsey , Clouse Cara , Jeong Claire G. , Varkey Mathew , Wu Mingsong , Walker Stephen J. , Molnar Joseph A. , Murphy Sean V. , Lee Sang Jin , Yoo James J. , Soker Shay , Atala Anthony
Published: October 2023

Bioprinting is a promising alternative method to generate skin substitutes because it can replicate the structural organization of the skin into biomimetic layers in vitro. In this study, six primary human skin cell types were used to bioprint a trilayer skin construct consisting of epidermis, dermis, and hypodermis. Transplantation of the bioprinted skin with human cells onto full-thickness wounds of nu/nu mice promoted rapid vascularization and formation of epidermal rete ridges analogous to the native human epidermis, with a normal-looking extracellular matrix. Cell-specific staining confirmed the integration of the implanted cells into the regenerated skin. Using a similar approach, a 5 centimeter–by–5 centimeter bioprinted autologous porcine skin graft was transplanted onto full-thickness wounds in a porcine excisional wound model. The bioprinted skin graft improved epithelialization, reduced skin contraction, and supported normal collagen organization with reduced fibrosis. Differential gene expression demonstrated pro-remodeling protease activity in wounds transplanted with bioprinted autologous skin grafts. These results demonstrate that bioprinted skin can support skin regeneration to allow for nonfibrotic wound healing and suggest that the skin bioprinting technology may be applicable for human clinical use.
Found in translation—Fibrosis in metabolic dysfunction–associated steatohepatitis (MASH)
Authors: Wang Shuang , Friedman Scott L. 
Published: October 2023

Metabolic dysfunction–associated steatohepatitis (MASH) is a severe form of liver disease that poses a global health threat because of its potential to progress to advanced fibrosis, leading to cirrhosis and liver cancer. Recent advances in single-cell methodologies, refined disease models, and genetic and epigenetic insights have provided a nuanced understanding of MASH fibrogenesis, with substantial cellular heterogeneity in MASH livers providing potentially targetable cell-cell interactions and behavior. Unlike fibrogenesis, mechanisms underlying fibrosis regression in MASH are still inadequately understood, although antifibrotic targets have been recently identified. A refined antifibrotic treatment framework could lead to noninvasive assessment and targeted therapies that preserve hepatocellular function and restore the liver’s architectural integrity.
Expression of RcrB confers resistance to hypochlorous acid in uropathogenic
Escherichia coli
Authors: Crompton Mary E. , Gaessler Luca F. , Tawiah Patrick O. , Polzer Lisa , Camfield Sydney K. , Jacobson Grady D. , Naudszus Maren K. , Johnson Colton , Meurer Kennadi , Bennis Mehdi , Roseberry Brendan , Sultana Sadia , Dahl Jan-Ulrik
Published: October 2023

To eradicate bacterial pathogens, neutrophils are recruited to the sites of infection, where they engulf and kill microbes through the production of reactive oxygen and chlorine species (ROS/RCS). The most prominent RCS is the antimicrobial oxidant hypochlorous acid (HOCl), which rapidly reacts with various amino acid side chains, including those containing sulfur and primary/tertiary amines, causing significant macromolecular damage. Pathogens like uropathogenic
Escherichia coli
(UPEC), the primary causative agent of urinary tract infections, have developed sophisticated defense systems to protect themselves from HOCl. We recently identified the RcrR regulon as a novel HOCl defense strategy in UPEC. Expression of the
rcrARB
operon is controlled by the HOCl-sensing transcriptional repressor RcrR, which is oxidatively inactivated by HOCl resulting in the expression of its target genes, including
rcrB
. The
rcrB
gene encodes a hypothetical membrane protein, deletion of which substantially increases UPEC’s susceptibility to HOCl. However, the mechanism behind protection by RcrB is unclear. In this study, we investigated whether (i) its mode of action requires additional help, (ii)
rcrARB
expression is induced by physiologically relevant oxidants other than HOCl, and (iii) expression of this defense system is limited to specific media and/or cultivation conditions. We provide evidence that RcrB expression is sufficient to protect
E. coli
from HOCl. Furthermore, RcrB expression is induced by and protects from several RCS but not from ROS. RcrB plays a protective role for RCS-stressed planktonic cells under various growth and cultivation conditions but appears to be irrelevant for UPEC’s biofilm formation.

IMPORTANCE

Bacterial infections pose an increasing threat to human health, exacerbating the demand for alternative treatments. Uropathogenic
Escherichia coli
(UPEC), the most common etiological agent of urinary tract infections (UTIs), are confronted by neutrophilic attacks in the bladder, and must therefore be equipped with powerful defense systems to fend off the toxic effects of reactive chlorine species. How UPEC deal with the negative consequences of the oxidative burst in the neutrophil phagosome remains unclear. Our study sheds light on the requirements for the expression and protective effects of RcrB, which we recently identified as UPEC’s most potent defense system toward hypochlorous acid (HOCl) stress and phagocytosis. Thus, this novel HOCl stress defense system could potentially serve as an attractive drug target to increase the body’s own capacity to fight UTIs.
The
Caulobacter
NtrB-NtrC two-component system bridges nitrogen assimilation and cell development
Authors: North Hunter , McLaughlin Maeve , Fiebig Aretha , Crosson Sean
Published: October 2023

A suite of molecular sensory systems enables
Caulobacter
to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer-binding protein (bEBP) NtrC and its cognate sensor histidine kinase, NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in
Caulobacter
metabolism and development are not well defined. Notably,
Caulobacter
NtrC is an unconventional bEBP that lacks the σ
54
-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of
Caulobacter crescentus ntrC
slows cell growth in complex medium and that
ntrB
and
ntrC
are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of
ntrC
mutant strains by restoring transcription of the
glnBA
operon, revealing a possible role for IS3 transposition in shaping the evolution of
Caulobacter
populations during nutrient limitation. We further identified dozens of direct NtrC-binding sites on the
C. crescentus
chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid-associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in
Caulobacter
.

IMPORTANCE

Bacteria balance cellular processes with the availability of nutrients in their environment. The NtrB-NtrC two-component signaling system is responsible for controlling nitrogen assimilation in many bacteria. We have characterized the effect of
ntrB
and
ntrC
deletion on
Caulobacter
growth and development and uncovered a role for spontaneous IS element transposition in the rescue of transcriptional and nutritional deficiencies caused by
ntrC
mutation. We further defined the regulon of
Caulobacter
NtrC, a bacterial enhancer-binding protein, and demonstrate that it shares specific binding sites with essential proteins involved in cell cycle regulation and chromosome organization. Our work provides a comprehensive view of transcriptional regulation mediated by a distinctive NtrC protein, establishing its connection to nitrogen assimilation and developmental processes in
Caulobacter
.
Bacteriophage steering of
Burkholderia cenocepacia
toward reduced virulence and increased antibiotic sensitivity
Authors: Ruest Marta K. , Supina Brittany S. I. , Dennis Jonathan J.
Published: October 2023

Antibiotic resistance in bacteria is a growing global concern and has spurred increasing efforts to ﬁnd alternative therapeutics, such as the use of bacterial viruses, or bacteriophages. One promising approach is to use phages that not only kill pathogenic bacteria but also select phage-resistant survivors that are newly sensitized to traditional antibiotics, in a process called “phage steering.” Members of the bacterial genus
Burkholderia
, which includes various human pathogens, are highly resistant to most antimicrobial agents, including serum immune components, antimicrobial peptides, and polymixin-class antibiotics. However, the application of phages in combination with certain antibiotics can produce synergistic effects that more effectively kill pathogenic bacteria. Herein, we demonstrate that
Burkholderia cenocepacia
serum resistance is due to intact lipopolysaccharide (LPS) and membranes, and phage-induced resistance altering LPS structure can enhance bacterial sensitivity not only to immune components in serum but also to membrane-associated antibiotics such as colistin.

IMPORTANCE

Bacteria frequently encounter selection pressure from both antibiotics and lytic phages, but little is known about the interactions between antibiotics and phages. This study provides new insights into the evolutionary trade-offs between phage resistance and antibiotic sensitivity. The creation of phage resistance through changes in membrane structure or lipopolysaccharide composition can simultaneously be a major cause of antibiotic sensitivity. Our results provide evidence of synergistic therapeutic efficacy in phage-antibiotic interactions and have implications for the future clinical use of phage steering in phage therapy applications.
Extracellular DNA enhances biofilm integrity and mechanical properties of mucoid
Pseudomonas aeruginosa
Authors: Ferguson Danielle L. , Gloag Erin S. , Parsek Matthew R. , Wozniak Daniel J.
Published: October 2023

Pseudomonas aeruginosa
is one of the most common biofilm-forming pathogens responsible for lung infections of individuals with cystic fibrosis (CF).
P. aeruginosa
becomes tolerant to antimicrobials in the biofilm state and is difficult to treat. Production of extracellular polymeric substances (EPS), such as alginate and extracellular DNA (eDNA), can allow adherence to abiotic and biotic surfaces, antimicrobial evasion, and resilience to environmental pressures. Alginate-producing mucoid variants of
P. aeruginosa
are frequently isolated from CF airway samples and are associated with worsening patient outcomes. While eDNA is a major structural component of nonmucoid
P. aeruginosa
biofilms, the potential role of eDNA in mucoid biofilms is unclear. Here, we investigate how eDNA contributes to clinical mucoid biofilm physiology and integrity. We predicted that eDNA plays a structural and mechanical role in mucoid biofilms. To test this, we quantified biofilm eDNA in mucoid biofilms and used microscopy and rheology to visualize eDNA and detect changes in biofilm structure and mechanics upon DNaseI treatment. We showed that biofilm eDNA abundance is diverse across clinical mucoid strains and observed a temporal increase in foci of eDNA within intact mucoid biofilms. Increased cell dispersal and reduced biomass were also observed following DNaseI treatment of mucoid biofilms. Degradation of eDNA also impacted the mechanical integrity of mucoid biofilms by increasing the stiffness and decreasing the cohesion of the biofilm. These findings advance our understanding of clinical mucoid
P. aeruginosa
biofilms and facilitate the development of new approaches to target biofilms by exploiting the functions of EPS components.

IMPORTANCE

Understanding the role of eDNA in mucoid
Pseudomonas aeruginosa
biofilms will lead to therapeutic strategies that combat the biophysical and structural function of EPS for the eradication of bacteria in mucoid biofilms during chronic infections. This knowledge can be used to further identify unknown matrix component interactions within pathogenic biofilm-forming clinical isolates.
Rapid Aztreonam/Avibactam NP test for detection of aztreonam/avibactam susceptibility/resistance in Enterobacterales
Authors: Viguier Clément , Bouvier Maxime , Sadek Mustafa , Kerbol Auriane , Poirel Laurent , Nordmann Patrice
Published: October 2023

Aztreonam-avibactam (AZA), a newly developed β-lactam/β-lactamase inhibitor combination
,
is a treatment option for infections due to carbapenem-resistant Enterobacterales (CRE), including metallo-ß-lactamase producers, regardless of additional production of broad-spectrum serine-ß-lactamases. However, AZA-resistance has already been reported in Enterobacterales and its early detection could be a valuable tool for faster and more accurate clinical decision-making. We therefore developed a rapid culture-based test for the identification of AZA resistance among multidrug-resistant Enterobacterales. The Rapid Aztreonam/Avibactam NP test is based on resazurin reduction when bacterial growth occurs in the presence of AZA at 8/4 µg/mL (protocol 1) or 12/4 µg/mL (protocol 2). Given the absence of guidelines on AZA susceptibility testing, two tentative breakpoints were indeed used to categorize AZA-susceptible isolates: ≤4 µg/mL in protocol 1 and ≤ 8 µg/mL in protocol 2. Bacterial growth was visually detectable by a blue-to-purple or blue-to-pink color change of the medium. A total of 78 enterobacterial isolates (among which 34 AZA-resistant and 13 AZA-resistant according to protocols 1 and 2, respectively) were used to evaluate the test performance using protocol 1 or protocol 2. The sensitivity and specificity of the test were found to be 100% and 97.7%, respectively, following protocol 1 and 100% and 100%, respectively, following protocol 2, in comparison with broth microdilution. All results were obtained within 4.5 hours corresponding to a time saving of ca. 14 hours compared with currently available methods for AZA susceptibility testing. The Rapid Aztreonam/Avibactam NP test is rapid, highly sensitive, specific, easily interpretable, and easy to implement in routine.
Lockdown!
Learning public health of infectious diseases through gameplay
Authors: Goh Evelyn , Szücs Anna , Loh Victor Weng Keong , Boucher Yann Felix
Published: October 2023

The COVID-19 pandemic has demonstrated the detrimental effects of a lack of understanding of public health measures. During the pandemic, lockdowns, social distancing, and mask mandates introduced by governments were met with skepticism, doubt, and an unwillingness to comply, increasing the extent of negative outcomes as a result. Albeit devastating, the pandemic has offered an invaluable opportunity to observe the correlation between the prevalence of public health education and compliance with public health measures during critical times. In this article, we describe a card game that was developed during the COVID-19 pandemic to educate the public (including children) about how specific public health measures address the pandemic and how global cooperation is essential in addressing even one country’s problems. The game can be used in primary, secondary, or tertiary education classrooms, initiating conversations about the topic and providing a basic understanding before more in-depth learning.
Teaching transferable skills in teamwork, accountability, goal setting, writing, and problem-solving in a non-major microbiology lab: the unknown bacteria experiment redefined
Authors: McKee Felicia , Wolf Josef D. , Simon Samantha , Floyd Jeanetta H.
Published: October 2023

College to Career is a phrase that we often use to describe the skills and abilities that students should achieve while preparing for college and/or careers. To help prepare our students for their future careers, we developed a microbiology laboratory curriculum based on factors identified to improve college-to-career readiness. These factors include content knowledge, analyzing and interpreting data, accountability, goal setting, and teamwork. At the core of the design are inquiry and problem-based learning. This approach allows students to actively engage in the scientific process while collaborating with classmates and learning technical and transferable career skills. The curriculum includes microbiology laboratory skills, including plating, serial dilutions, and biochemical tests, with integrated opportunities for students to engage in critical thinking, analysis and interpretation of data, teamwork, goal setting, decision-making, and scientific writing.
Chimeric virus-like particles of human norovirus constructed by structure-guided epitope grafting elicit cross-reactive immunity against both GI.1 and GII.4 genotypes
Authors: Hou Ya Nan , Jin Yu Qin , Zhang Xue Feng , Tang Fang , Hou Jun Wei , Liu Zhao Ming , Han Zi Bo , Zhang Hao , Du Li Fang , Shao Shuai , Su Ji Guo , Liang Yu , Zhang Jing , Li Qi Ming
Published: October 2023

Human norovirus (HuNoV) is the main cause of acute non-bacterial gastroenteritis worldwide. There is no vaccine currently available to prevent HuNoV infection. HuNoV is a highly mutated virus, and its genetic diversity and the lack of cross-protection between different genotypes hinder the broadly protective vaccine development. Among various genotypes, GI.1 is the prototype strain, and GII.4 currently predominates the prevalence of HuNoV. In this work, guided by the structural alignment of GI.1 and GII.4 HuNoV capsid proteins, several chimeric virus-like particles (VLPs) were designed to achieve cross-immunity against these two HuNoV genotypes. The neutralizing epitopes of HuNoV have been identified to be mainly located at the loop regions of VP1 protein exposed on the HuNoV surface. In this study, the exposed loops of GII.4 VP1 protein were grafted into the scaffold of GI.1 genotype to produce the chimeric VLPs. The designed chimeric VLPs were recombinantly expressed by the
Hansenula polymorpha
expression system developed by our laboratory. Mice were immunized with the chimeric VLPs plus aluminum adjuvant, and then the antibody responses were detected by using the enzyme-linked immunosorbent assay and the histo-blood group antigen-VLP interaction blocking assay. The experimental results show that two of the designed chimeric VLPs induced cross-reactive IgG and cross-blocking antibodies against both the parental GI.1 and GII.4 genotypes of HuNoV. The results also imply that the transplant site design is important to maintain the immunogenicity of foreign epitopes on the scaffold carrier. Our studies may provide a valuable strategy for the development of cross-reactive HuNoV vaccines.

IMPORTANCE

Human norovirus (HuNoV) is highly infectious and can result in severe illnesses in the elderly and children. So far, there is no effective antiviral drug to treat HuNoV infection, and thus, the development of HuNoV vaccines is urgent. However, NoV evolves rapidly, and currently, at least 10 genogroups with numerous genotypes have been found. The genetic diversity of NoV and the lack of cross-protection between different genotypes pose challenges to the development of broadly protective vaccines. In this study, guided by structural alignment between GI.1 and GII.4 HuNoV VP1 proteins, several chimeric-type virus-like particles (VLPs) were designed through surface-exposed loop grafting. Mouse immunization studies show that two of the designed chimeric VLPs induced cross-immunity against both GI.1 and GII.4 HuNoVs. To our knowledge, this is the first designed chimeric VLPs that can induce cross-immune activities across different genogroups of HuNoV, which provides valuable strategies for the development of cross-reactive HuNoV vaccines.
A viral protein targets mitochondria and chloroplasts by subverting general import pathways and specific receptors
Authors: Sáiz-Bonilla María , Martín-Merchán Andrea , Pallás Vicente , Navarro Jose Antonio
Published: October 2023

Dual targeting is a relatively little explored phenomenon by which some proteins are transported to two different subcellular compartments, such as chloroplasts and mitochondria. We previously showed that the R domain and the arm region of the melon necrotic spot virus coat protein could act as a dual-targeting peptide, which shares many relevant features in structure, amino acid composition, and functionality with that of the Thr-tRNA synthetases, the best-studied dual-targeted proteins by far. Here, we show that a viral coat protein hijacks the general pathways for organellar protein import and identifies the coat protein-interacting organellar translocon receptors. Our findings demonstrate for the first time that an exogenous dual-targeted protein uses the general Toc and Tom import systems to reach mitochondria and chloroplasts because it depends on the availability of NbToc75 and NbTom40. Interaction studies, subcellular localization analysis, and viral infection assays in silenced plants revealed the significance of plant receptors, such as the mitochondrion NbOm64 and chloroplast NbToc159A, in this transport. We also show that chloroplast protein translocation impairment could be interlinked with retrograde communication triggering a JA-based response that incidentally impairs viral infection. Future research may profit from our results to better comprehend cellular communication, protein import mechanisms, how preproteins interact with their receptors, and how plant pathogens manipulate host machinery to their ends.

IMPORTANCE

Many plant proteins and some proteins from plant pathogens are dually targeted to chloroplasts and mitochondria, and are supposed to be transported along the general pathways for organellar protein import, but this issue has not been explored yet. Moreover, organellar translocon receptors exist as families of several members whose functional specialization in different cargos is supposed but not thoroughly studied. This article provides novel insights into such topics showing for the first time that an exogenous protein, the melon necrotic spot virus coat protein, exploits the common Toc/Tom import systems to enter both mitochondria and chloroplasts while identifying the involved specific receptors.
Genome sequence ofHemileia vastatrixBerk. and Br. (Race I), the causal agent of coffee leaf rust, isolate from Risaralda, Colombia
Authors: Ángel C. Carlos A. , Marín-Ramírez Gustavo A. , Maldonado Carlos E.
Published: October 2023

Coffee leaf rust, caused by the fungusHemileia vastatrix(Basidiomycota; Pucciniomycota),is a devastating disease spread worldwide. To improve the available genomes, we use PacBio HiFi sequencing enhanced by Dovetail Omni-C chromatin conformation capture to assemble a highly contiguous 747.98 Mb genome of an isolate collected fromCoffea arabica.
Volatile profiling distinguishes
Streptococcus pyogenes
from other respiratory streptococcal species
Authors: Berna Amalia Z. , Merriman Joseph A. , Mellett Leah , Parchment Danealle K. , Caparon Michael G. , Odom John Audrey R.
Published: October 2023

Sore throat is one of the most common complaints encountered in the ambulatory clinical setting. Rapid, culture-independent diagnostic techniques that do not rely on pharyngeal swabs would be highly valuable as a point-of-care strategy to guide outpatient antibiotic treatment. Despite the promise of this approach, efforts to detect volatiles during oropharyngeal infection have yet been limited. In our research study, we sought to evaluate for specific bacterial volatile organic compounds (VOC) biomarkers in isolated cultures
in vitro
, in order to establish proof-of-concept prior to initial clinical studies of breath biomarkers. A particular challenge for the diagnosis of pharyngitis due to
Streptococcus pyogenes
is the likelihood that many metabolites may be shared by
S. pyogenes
and other related oropharyngeal colonizing bacterial species. Therefore, we evaluated whether sufficient metabolic differences are present, which distinguish the volatile metabolome of Group A streptococci from other streptococcal species that also colonize the respiratory mucosa, such as
Streptococcus pneumoniae
and
Streptococcus intermedius
. In this work, we identified 27 discriminatory VOCs (
q
-values < 0.05), composed of aldehydes, alcohols, nitrogen-containing compounds, hydrocarbons, ketones, aromatic compounds, esters, ethers, and carboxylic acid. From this group of volatiles, we identify candidate biomarkers that distinguish
S. pyogenes
from other species and establish highly produced VOCs that indicate the presence of
S. pyogenes in vitro
, supporting future breath-based diagnostic testing for streptococcal pharyngitis.

IMPORTANCE

Acute pharyngitis accounts for approximately 15 million ambulatory care visits in the United States. The most common and important bacterial cause of pharyngitis is
Streptococcus pyogenesis
, accounting for 15%–30% of pediatric pharyngitis. Distinguishing between bacterial and viral pharyngitis is key to management in US practice. The culture of a specimen obtained by a throat swab is the standard laboratory procedure for the microbiologic confirmation of pharyngitis; however, this method is time-consuming, which delays appropriate treatment. If left untreated,
S. pyogenes
pharyngitis may lead to local and distant complications. In this study, we characterized the volatile metabolomes of
S. pyogenes
and other related oropharyngeal colonizing bacterial species. We identify candidate biomarkers that distinguish
S. pyogenes
from other species and provide evidence to support future breath-based diagnostic testing for streptococcal pharyngitis.
Chronic inflammatory pulmonary artery lesion causing right pulmonary artery stenosis 15 years post Blalock-Taussig shunt ligation
Authors: Bayfield Nicholas , Wang Edward , Andrews David
Published: October 2023

Discrete central endovascular pulmonary arterial lesions raise clinical concern for malignancy such as primary pulmonary artery sarcoma. We present a case of a female in her late teens who had an obstructive mid right pulmonary artery lesion found on follow-up imaging 15 years after Tetralogy of Fallot repair. The lesion was in the vicinity of a previously ligated Blalock-Taussig shunt and causing right PA stenosis with delayed perfusion to the right lung, and a flow-related distal left PA aneurysm. The lesion was excised and confirmed histologically to be inflammatory in nature. Intraoperative microbiology demonstrated growth of the Kytococcus species, and she was managed with 6 weeks of intravenous antibiotics, with a full recovery.