bluuebunny/crossref_metadata_2025 huggingface dataset:
Oral and cutaneous immune‐related adverse events in cancer patients: Prevalence and overall survival
Authors: de Oliveira Filho Osias Vieira , Gibbons Ivana Lameiras , Medeiros Yuri de Lima , de Oliveira Thiago Bueno , Treister Nathaniel Simon , Alves Fabio Abreu
Published: June 2024

Objectives

To assess the prevalence of cutaneous and oral immune‐related adverse events (irAEs) in cancer patients, risk factors for its development, and overall survival (OS).

Materials and Methods

This retrospective observational study which included 748 medical records of cancer patients who received immune checkpoint inhibitors (ICIs). Demographic and clinicopathological characteristics were collected and analyzed.

Results

Most patients were male (59.4%), with stage IV cancer (65%) and received pembrolizumab (46.7%). Four hundred fourteen (55.34%) patients developed cutaneous lesions, 84 (11.2%) developed oral mucosal lesions, and 70 (9.3%) developed xerostomia. The median time for irAEs development was 11 weeks for cutaneous and oral mucosal lesions, and 21.5 weeks for xerostomia. Patients who received PD‐1 + CTLA‐4 had a higher risk for developing cutaneous irAEs (p = 0.001), while those who underwent ICI and concurrent chemotherapy had a higher risk (p = 0.008) for developing oral mucosal lesions. Patients who presented oral and cutaneous irAEs had better OS than those who did not present (p = 0.0001).

Conclusion

Cutaneous effects affected more than half of the patients, while oral effects and xerostomia were found in around 11% and 9% of patients, respectively. Concurrent chemotherapy and PD‐1 + CTLA‐4 were more associated with oral and cutaneous irAEs, respectively. Patients who developed such irAEs had better overall survival.
Somatosensory game intervention experience among prefrail older adults in the community: A qualitative study
Authors: Wang Xiao , Xu Wanying , Fu Jianying , Wang Xiuhong
Published: June 2024

Background

Somatosensory game interventions have been used to rehabilitate hospitalized older adults. However, their application in prefrail older adults in the community is poorly understood, hindering the development of effective intervention strategies and exercise diversification.

Objectives

This study aimed to explore the experiences of prefrail Chinese older adults engaging in somatosensory gaming interventions and thus develop tailored intervention frameworks and support strategies.

Methods

We conducted semistructured interviews with 12 prefrail older adults who participated in a 12‐week sensory game intervention study from August to September 2022. The interviews were analyzed using Nvivo 11.0 software following Colaizzi's seven‐step analysis method.

Results

Somatosensory game intervention experiences were classified into four main themes and 11 subthemes: health intervention effects (enhanced limb muscle strength, improved reaction capacity, alleviated negative emotions), positive experiences (enhanced self‐achievement, increased exercise motivation, elevated social engagement), negative experiences (frustration from unmet score expectations, initial discomfort), and intervention requirements (sustained interventions, technical support, personalized content).

Conclusion

The findings have implications for somatosensory game interventions targeting prefrail older adults in the community.
Health‐related quality of life instrument with 8 items to measure health‐related quality of life among family caregivers of people with dementia: A pilot validation study
Authors: Choi Eunjeong , Seo Hyun‐Ju , Choo IL Han , Kim Seong Min , Park Jeong Min , Choi Yu Mi
Published: June 2024

Background

The health‐related quality of life instrument with 8 items (HINT‐8) was developed to measure health‐related quality of life (HRQoL) in Korea. However, the HINT‐8 has not yet been validated among the family caregivers of people with dementia (PwD).

Design

A cross‐sectional pilot study.

Objective

The study aimed to examine the convergent and discriminant validity of the HINT‐8 among family caregivers of individuals with dementia.

Sample

Forty‐seven family caregivers of PwD.

Measurements

HINT‐8 was compared with the 5‐level EQ‐5D (EQ‐5D‐5L) to assess its convergent and discriminant validity. Additionally, the association between the two instruments assessing HRQoL was examined using the short‐form Bédard‐Zarit Burden Interview (SZBI).

Results

The HINT‐8 was a promising and valid HRQoL instrument for family caregivers of PwD. There was a significantly high correlation between the overall HINT‐8 and EQ‐5D‐5L indices (r = 0.85, p < .001). The HINT‐8 had acceptable psychometric properties compared to the commonly used EQ‐5D‐5L, as indicated by the subdomains associated with family caregiversʼ burden measured by the SZBI.

Conclusion

Future studies should compare the HINT‐8 with existing dementia carer‐specific QoL instruments among a larger study sample to enhance its statistical power and confirm its reliability and structural validity.
Turgor loss point explains climate‐driven growth reductions in trees in Central Europe
Authors: Kunert N. , Münchinger I. K. , Hajek P.
Published: June 2024

As climate change thrives, and the frequency of intense droughts is affecting many forested regions, a mechanistic understanding of the factors conferring drought tolerance in trees is increasingly important. However, studies linking the observed growth reduction to mechanistic traits are still rare.

We compared the median growth anomalies of 16 native tree species, gathered across a network of study plots in Bavaria, with the mean species‐specific turgor loss point (πtlp) measured at five locations in Central Europe

πtlp explained 37% of the growth anomalies observed in response to the intense droughts between 2018 and 2020 compared to the pre‐drought period between 2006 and 2017 across sites.

πtlp constitutes an important leaf drought tolerance trait and influences the growth response of native tree species during extraordinary dry periods. As climate change‐induced droughts intensify, tree species with drought‐tolerant leaves will be less vulnerable to growth reductions. πtlp provides a useful indicator for selecting tree species to adapt forest management systems to climate change.
Illustrating Farmer–Animal Entanglements and Emotions: Drawing Elicitation in Upland Vietnam
Authors: Garber Peter , Turner Sarah
Published: June 2024

While visual methods have been employed in research regarding human‐animal relationships and entanglements, the possible benefits of utilizing drawing elicitation have not been explored to date. Our study utilizes drawing elicitation with Hmong and Mien (Yao) ethnic minority farmers in the northern Vietnamese borderlands. We aim to investigate human‐animal relationships within these communities, considering their longstanding socio‐economic and spiritual entanglements with a number of domesticated animals. Simultaneously, we aim to assess the benefits and drawbacks of employing drawing elicitation in the context of more‐than‐human research in the Global South. Through the drawing exercises, participants not only conveyed important insights into human‐animal entanglements within these rural uplands, resulting in nuanced and at times highly emotive drawings, but they also provided reflections on the drawing activity itself. Despite challenges faced in encouraging drawing within a semiliterate population, our findings, guided by participant feedback, reveal numerous possibilities for employing this approach in more‐than‐human research.
Refined landslide inventory and susceptibility of Weining County, China, inferred from machine learning and Sentinel‐1 InSAR analysis
Authors: Shi Xuguo , Chen Dianqiang , Wang Jianing , Wang Pan , Wu Yunlong , Zhang Shaocheng , Zhang Yi , Yang Chen , Wang Lunche
Published: June 2024

Landslides are widely distributed mountainous geological hazards that threaten economic development and people's daily lives. Interferometric synthetic aperture radar (InSAR) with comprehensive coverage and high‐precision ground displacement monitoring abilities are frequently utilized for regional‐scale active slope detection. Moreover, InSAR measurements that characterize ground dynamics are integrated with conventional topographic, hydrological, and geological landslide conditioning factors (LCFs) for landslide susceptibility mapping (LSM). Weining County in southwest China, with complex geological conditions, steep terrain, and frequent tectonic activities, is prone to catastrophic landslide failures. In this study, we refined the landslide inventory of Weining County using one ascending and one descending Sentinel‐1 dataset acquired during 2015–2021 through a small baseline subset InSAR (SBAS InSAR) analysis. We then combine the LOS measurements from both datasets using multidimensional SBAS to obtain time series two‐dimensional (2D) displacements to characterize the kinematics of active slopes. Hot spot and cluster analysis (HCA) was carried out on 2D displacement rate maps to highlight clustered deformed areas and suppress noisy signals that occurred on single pixels. Two hundred fifty‐eight landslides (including 71 active identified in this study) are used to construct 76,412 positive samples for LSM. In our study, the HCA maps, instead of the 2D displacement maps, are integrated with conventional LCFs to form an LCF_HCA set to feed support vector machine (SVM), Random Forest (RF), extreme Gradient Boosting (XGBoost) and Light Gradient‐Boosting Machine (LightGBM) models. A conventional LCF (LCF_CON) set and an integrated 2D displacement maps (LCF_2D) set have also been adapted for comparison. The performance of the tree‐based ensemble methods distinctly outperforms the SVM model. In the meantime, models' performances using the LCF_HCA set are superior to that of the other 2 LCF sets from all evaluation metrics. The ranks of HCA maps increased compared with 2D displacement maps from feature importance analysis, which might lead to the better performance of models using the LCF_HCA set. With the continuous accumulation of SAR images, ground dynamic characteristics from InSAR can offer us opportunities to understand landslide kinematics and enhance LSM.
Impact of COVID‐19 monoclonal antibodies on outcomes of COVID‐19 infection in hematopoietic stem cell transplant and chimeric antigen receptor therapy recipients
Authors: Hahn Elizabeth H , Li Hong , Sauter Craig S , Mossad Sherif B
Published: June 2024

Background

Hematopoietic stem cell transplant (HSCT) and chimeric antigen receptor T‐cell therapy (CAR‐T) recipients are at higher risk of serious complications of COVID‐19 infection than the general population. Though there is evidence that monoclonal antibodies (MCA) against COVID‐19 reduce the risk of death and hospitalization in the general population, data regarding their efficacy in HSCT and CAR‐T recipients remains scarce.

Methods

We conducted a retrospective review of HSCT and CAR‐T recipients to compare 30‐day outcomes between patients who did and did not receive MCA after their first episode of COVID‐19 between May 1, 2020 and December 31, 2022. Outcomes were defined as the most severe complication experienced out of the following: 30‐day emergency department visit, hospitalization, intensive care unit admission, and death after COVID‐19 infection.

Results

We identified 166 patients comprised of 53.6% allogeneic HSCT, 35.5% autologous HSCT, and 10.8% CAR‐T recipients; 107 had received a COVID‐19 vaccine >2 weeks prior to testing positive, and 40 were treated with MCA. After adjusting for age, presence of symptoms at the initial positive test, and COVID‐19 vaccination status, patients who did not receive MCA were five times more likely to develop complications after COVID‐19 infection (adjusted odds ratio 5.0 [95% CI, 1.9–12.8], p = .001).

Conclusion

HSCT and CAR‐T recipients who received MCA following COVID‐19 infection were far less likely to develop COVID‐related complications than those who did not receive MCA, regardless of vaccination status. This underscores the potential benefit of developing novel MCA with efficacy against circulating COVID‐19 strains.

image
Reaching new lands: Updating the distribution of Angiostrongylus cantonensis in South America with the first record in Argentina
Authors: Hancke Diego , Guzman Noelia , Tripodi Mariel , Muschetto Emiliano , Suárez Olga Virginia
Published: June 2024

Background

Angiostrongylus cantonensis, commonly known as the rat lungworm, is a metastrongyloid nematode found primarily not only in tropical and subtropical regions but also in temperate areas and considered the leading cause of eosinophilic meningitis in humans. Synanthropic rodents such as Rattus norvegicus and Rattus rattus are the most frequent definitive hosts of this parasite.

Methods and Results

The presence of this parasite was detected in the pulmonary arteries of three specimens of R. norvegicus in the city of Buenos Aires representing the species' southernmost known record in natural hosts. Species confirmation was achieved through partial sequences of 18S and COI genes. By comparing the COI gene sequences with those available in GenBank through the construction of a haplotype network, we obtained that the analysed specimen presents high similarity with those reported in Japan and Southeast Asia.

Conclusions

All infected rats were captured in an area surrounding a port with significant import and export activity, suggesting that A. cantonensis may have been introduced through commercial ships. Specifically, the parasite was detected in a neighbourhood with vulnerable socio‐economic conditions and in a nature reserve, which exhibit biotic and abiotic characteristics conducive to sustaining high‐density rat populations, scattered waste, areas of spontaneous vegetation, debris accumulation and flooded areas or lagoons offering suitable habitats for intermediate hosts such as snails. Thus, the close proximity of the port to these sites creates a favourable ecological context for the establishment of A. cantonensis. This study shows the need to conduct research to detect A. cantonensis in non‐endemic areas but with the characteristics that promote its arrival and development of its life cycle in order to implement control measures to prevent expansion of this parasite and its transmission to humans and other animals.
Exploring Nano-Scale Scratching Induced Tribological Behavior of Graphene Engineered AlCoCrFeNi High-Entropy Alloy
Authors: Barman Subrata , Kumar Gupta Kritesh , Dey Sudip
Published: June 2024

Motivated by the recent discoveries concerning the exceptional surface engineering capabilities offered by high-entropy alloys (HEAs), this article investigates the tribological behavior of pristine and graphene nano-engineered AlxCoCrFeNi HEA. The atomic-scale scratching is performed for different configurations of HEA in a molecular dynamics environment, wherein, at first, aluminum (Al) (x = 0.1, 0.3, and 0.5) concentration-dependent wear behavior of HEA configurations is compared. It is observed that with the increase in Al concentration, the normal and tangential forces, friction coefficients, and wear-rates were significantly reduced, due to the increased plastic deformation and phase transformation. Graphene-engineered HEA surfaces are perceived in two different ways, in the presented investigation: first, the graphene coating is applied directly over the HEA surface, and second, the graphene layers are embedded at a certain depth below the target surface. It is observed that graphene-engineered HEA surfaces exhibit exceptional performance against nano-scratching, wherein, the distribution and height of surface morphology (pile-ups) have seen significant improvement and elastic recovery, especially in the cases of graphene coating over the surface. The findings obtained from this study will be extremely helpful in bringing the bottom-up multi-scale design route for graphene-engineered HEA surfaces to reality. This will enable the development of a novel class of functionally engineered surfaces with enhanced wear and scratch resistance.
Can ultrasonography be used to differentiate parathyroid masses abutting the thyroid gland from thyroid masses extending into the parathyroid area?
Authors: Lee Chae Woon , Yoon Dae Young , Baek Sora , Lee Hyung Jin , Kim Eun Soo , Lim Kyoung Ja , Seo Young Lan , Yun Eun Joo
Published: June 2024

Aim: To determine the ultrasonographic (US) features that could help to distinguish between parathyroid masses abutting the thyroid gland and thyroid masses extending into the parathyroid area.Materials and methods: Two blinded readers retrospectively evaluated the US images of 76 histopathologically confirmed parathyroid masses abutting the thyroid gland and 34 thyroid masses extending into the parathyroid area. Maximal diameter, transverse diameter/anterior-posterior diameter (T/AP) ratio, longitudinal diameter/AP diameter (L/AP) ratio, margin, shape, echogenicity, echotexture, and echogenic interface were evaluated and compared between the two groups.Results: Echogenic interface (p<0.001) and L/AP ratio (p<0.001) were statistically significant US features that differentiated parathyroid and thyroid masses. Other US features did not show any significant differences between the two groups. Interobserver agreement was excellent for all US features. Sensitivity/specificity of the presence of echogenic interface and L/AP ratio >2.0 were 85.5%/100% and 43.2%/82.4% in distinguishing parathyroid from thyroid masses, respectively.Conclusion: The presence of an echogenic interface and L/AP ratio >2.0 were useful US features for differentiating parathyroid masses abutting the thyroid gland from thyroid masses extending into theparathyroid area.
Entropy as a Window Into Behavioral Phase Transitions: Unveiling Contextual Dynamics in Affordance-Based Reaching
Authors: Cooper Dalton S. , Moreira Tarcisio S. , Davis Tehran J.
Published: June 2024

Prior work has demonstrated the presence of hysteresis effects in the control of affordance-guided behavior, in that behavioral transitions around a critical action boundary vary with directions of change in said action boundary. To date, research on this topic has overlooked the influence of the global context on these phenomena. We employ an affordance-based reaching task, whereby participants were asked to move a target to a goal by passing through one of two apertures (size variable or size constant). It was found that the direction of change in the size of the variable aperture influenced the point of behavioral transitions, and this effect interacted with the location of a given goal. In addition, we considered fluctuations in the entropy of participants’ reach trajectories as a window into the nature of the behavioral phase transitions. Differences in the structure of entropy were found depending on the direction of change in the size variable aperture. These results are discussed in light of a dynamical systems approach, and recommendations for future work are made.
Netrin-1–engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair
Authors: Huang Jinsheng , Li Jiangnan , Li Senrui , Yang Xiaoqi , Huo Nianci , Chen Qiang , Wang Wengang , Yang Ningning , Wang Yuanyi , Zhou Nan
Published: June 2024

The formation of vascular niche is pivotal during the early stage of peripheral nerve regeneration. Nevertheless, the mechanisms of vascular niche in the regulation of peripheral nerve repair remain unclear. Netrin-1 (NTN1) was found up-regulated in nerve stump after peripheral nerve injury (PNI). Herein, we demonstrated that NTN1-high endothelial cells (NTN1+ECs) were the critical component of vascular niche, fostering angiogenesis, axon regeneration, and repair-related phenotypes. We also found that NTN1+EC–derived exosomes (NTN1 EC-EXO) were involved in the formation of vascular niche as a critical role. Multi-omics analysis further verified that NTN1 EC-EXO carried a low-level expression of let7a-5p and activated key pathways associated with niche formation including focal adhesion, axon guidance, phosphatidylinositol 3-kinase–AKT, and mammalian target of rapamycin signaling pathway. Together, our study suggested that the construction of a pre-regenerative niche induced by NTN1 EC-EXO could establish a beneficial microenvironment for nerve repair and facilitate functional recovery after PNI.
Climate sensitivity and relative humidity changes in global storm-resolving model simulations of climate change
Authors: Merlis Timothy M. , Cheng Kai-Yuan , Guendelman Ilai , Harris Lucas , Bretherton Christopher S. , Bolot Maximilien , Zhou Linjiong , Kaltenbaugh Alex , Clark Spencer K. , Vecchi Gabriel A. , Fueglistaler Stephan
Published: June 2024

The climate simulation frontier of a global storm-resolving model (GSRM; ork-scale model because of its kilometer-scale horizontal resolution) is deployed for climate change simulations. The climate sensitivity, effective radiative forcing, and relative humidity changes are assessed in multiyear atmospheric GSRM simulations with perturbed sea-surface temperatures and/or carbon dioxide concentrations. Our comparisons to conventional climate model results can build confidence in the existing climate models or highlight important areas for additional research. This GSRM’s climate sensitivity is within the range of conventional climate models, although on the lower end as the result of neutral, rather than amplifying, shortwave feedbacks. Its radiative forcing from carbon dioxide is higher than conventional climate models, and this arises from a bias in climatological clouds and an explicitly simulated high-cloud adjustment. Last, the pattern and magnitude of relative humidity changes, simulated with greater fidelity via explicitly resolving convection, are notably similar to conventional climate models.
Origins of the large piezoelectric response of samarium-doped lead magnesium niobate–lead titanate ceramics
Authors: Arzenšek Matija , Toš Urh , Drnovšek Silvo , Dragomir Mirela , Uršič Hana , Otoničar Mojca , Jankauskas Paulius , Svirskas Šarūnas , Rojac Tadej
Published: June 2024

The recent discovery of the large piezoelectric response of Pb(Mg
1/3
Nb
2/3
)O
3
-PbTiO
3
(PMN-PT) ceramics induced by samarium doping has provided a substantially improved functionality to the group of lead-based relaxor-ferroelectric materials. Different mechanisms have been so far proposed for the large piezoelectricity; however, the explanations are contradictory and focused on a unified description. Here, we use nonlinear harmonic piezoelectric measurements combined with multiscale structural analysis to clarify the origins of the ultrahigh piezoelectric response of samarium-doped PMN-PT. Our methodological approach allowed us to separate the multiple piezoelectric contributions, revealing their quantitative role in the total response. The results show that the ultrahigh piezoelectricity cannot be attributed to a single mechanism but is rather a complex combination of different contributions originating from the multiple effects of samarium doping on the long- and short-range structure of PMN-PT. The study offers a baseline for future engineering of the key material parameters affecting the large piezoelectric response of relaxor-ferroelectric ceramics.
Paleolithic eyed needles and the evolution of dress
Authors: Gilligan Ian , d’Errico Francesco , Doyon Luc , Wang Wei , Kuzmin Yaroslav V.
Published: June 2024

Eyed needles are among the most iconic of Paleolithic artifacts, traditionally seen as rare indicators of prehistoric clothing, particularly tailoring. However, recent finds across Africa and Eurasia show that other technologies like bone awls also facilitated the creation of fitted garments. Nonetheless, the advent of delicate eyed needles suggests a demand for more refined, efficient sewing. This refinement may signify two major developments: the emergence of underwear in layered garment assemblages, and/or a transition in adornment from body modification to decorating clothes, as humans covered themselves more completely for thermal protection. Archaeological evidence for underwear is limited, but the Upper Paleolithic saw an increase in personal ornaments, some sewn onto clothing. Eyed needles may mark a pivotal shift as clothes acquired the social functions of dress, decoupling clothing from climate and ensuring its enduring presence.
Circulating KLRG1
+
long-lived effector memory T cells retain the flexibility to become tissue resident
Authors: Lucas Erin D. , Huggins Matthew A. , Peng Changwei , O’Connor Christine , Gress Abigail R. , Thefaine Claire E. , Dehm Emma M. , Kubota Yoshiaki , Jameson Stephen C. , Hamilton Sara E.
Published: June 2024

KLRG1
+
CD8 T cells persist for months after clearance of acute infections and maintain high levels of effector molecules, contributing protective immunity against systemic pathogens. Upon secondary infection, these long-lived effector cells (LLECs) are incapable of forming other circulating KLRG1
−
memory subsets such as central and effector memory T cells. Thus, KLRG1
+
memory T cells are frequently referred to as a terminally differentiated population that is relatively short lived. Here, we show that after viral infection of mice, effector cells derived from LLECs rapidly enter nonlymphoid tissues and reduce pathogen burden but are largely dependent on receiving antigen cues from vascular endothelial cells. Single-cell RNA sequencing reveals that secondary memory cells in nonlymphoid tissues arising from either KLRG1
+
or KLRG1
−
memory precursors develop a similar resident memory transcriptional signature. Thus, although LLECs cannot differentiate into other circulating memory populations, they still retain the flexibility to enter tissues and establish residency.
Sanitization of hydroponic farming facilities in Singapore: what, why, and how
Authors: Tham Cliff An Ting , Zwe Ye Htut , Ten Michelle Mei Zhen , Ng Geraldine Shang Ya , Toh Jillinda Yi Ling , Poh Bee Ling , Zhou Weibiao , Li Dan
Published: June 2024

This study performed microbial analysis of nutrient film technique (NFT) hydroponic systems on three indoor farms in Singapore (the “what”). To justify the necessity of sanitizing hydroponic systems, strong biofilm-forming bacteria were isolated from the facility and investigated for their influence on
Salmonella
colonization on polyvinyl chloride (PVC) coupons in hydroponic nutrient solutions (the “why”). Finally, sanitization solutions were evaluated with both laboratory-scale and field-scale tests (the “how”). As a result, the microbiome composition in NFT systems was found to be highly farm specific. The strong biofilm formers
Corynebacterium tuberculostearicum
C2 and
Pseudoxanthomonas mexicana
C3 were found to facilitate the attachment and colonization of
Salmonella
on PVC coupons. When forming dual-species biofilms, the presence of C2 and C3 also significantly promoted the growth of
Salmonella
(
P
< 0.05). Compared with hydrogen peroxide (H
2
O
2
) and sodium percarbonate (SPC), sodium hypochlorite (NaOCl) exhibited superior efficacy in biofilm removal. At 50 ppm, NaOCl reduced the
Salmonella
Typhimurium, C2, and C3 counts to <1 log CFU/cm
2
within 12 h, whereas neither 3% H
2
O
2
nor 1% SPC achieved this effect. In operational hydroponic systems, the concentration of NaOCl needed to achieve biofilm elimination increased to 500 ppm, likely due to the presence of organic matter accumulated during crop cultivation and the greater persistence of naturally formed multispecies biofilms. Sanitization using 500 ppm NaOCl for 12 h did not impede subsequent plant growth, but chlorination byproduct chlorate was detected at high levels in the hydroponic solution and in plants in the sanitized systems without rinsing.

IMPORTANCE

This study’s significance lies first in its elucidation of the necessity of sanitizing hydroponic farming systems. The microbiome in hydroponic systems, although mostly nonpathogenic, might serve as a hotbed for pathogen colonization and thus pose a risk for food safety. We thus explored sanitization solutions with both laboratory-scale and field-scale tests. Of the three tested sanitizers, NaOCl was the most effective and economical option, whereas one must note the vital importance of rinsing the hydroponic systems after sanitization with NaOCl.
Diversity and phage sensitivity to phages of porcine enterotoxigenic
Escherichia coli
Authors: Gambino Michela , Kushwaha Simran Krishnakant , Wu Yi , van Haastrecht Pauline , Klein-Sousa Victor , Lutz Veronika T. , Bejaoui Semeh , Jensen Christoffer Moeskjær C. , Bojer Martin S. , Song Wenchen , Xiao Minfeng , Taylor Nicholas M. I. , Nobrega Franklin L. , Brøndsted Lone
Published: June 2024

Enterotoxigenic
Escherichia coli
(ETEC) is a diverse and poorly characterized
E. coli
pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to
Enterobacteriaceae
phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.

IMPORTANCE

Enterotoxigenic
Escherichia coli
(ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species—
E. coli
.
Absence of farnesol salvage in
Candida albicans
and probably in other fungi
Authors: Voshall Adam , Gutzmann Daniel J. , Verdaguer Ignasi Bofill , Crispim Marcell , Boone Cory H.T. , Atkin Audrey L. , Nickerson Kenneth W.
Published: June 2024

Farnesol salvage, a two-step pathway converting farnesol to farnesyl pyrophosphate (FPP), occurs in bacteria, plants, and animals. This paper investigates the presence of this pathway in fungi. Through bioinformatics, biochemistry, and physiological analyses, we demonstrate its absence in the yeasts
Saccharomyces cerevisiae
and
Candida albicans
, suggesting a likely absence across fungi. We screened 1,053 fungal genomes, including 34 from
C. albicans
, for potential homologs to four genes (
Arabidopsis thaliana AtFOLK
,
AtVTE5
,
AtVTE6
, and
Plasmodium falciparum PfPOLK
) known to accomplish farnesol/prenol salvage in other organisms. Additionally, we showed that
3
H-farnesol was not converted to FPP or any other phosphorylated prenol, and exogenous farnesol was not metabolized within 90 minutes at any phase of growth and did not rescue cells from the toxic effects of atorvastatin, but it did elevate the levels of intracellular farnesol (F
i
). All these experiments were conducted with
C. albicans
. In sum, we found no evidence for farnesol salvage in fungi.

IMPORTANCE

The absence of farnesol salvage constitutes a major difference in the metabolic capabilities of fungi. In terms of fungal physiology, the lack of farnesol salvage pathways relates to how farnesol acts as a quorum-sensing molecule in
Candida albicans
and why farnesol should be investigated for use in combination with other known antifungal antibiotics. Its absence is essential for a model (K. W. Nickerson et al., Microbiol Mol Biol Rev 88:e00081-22, 2024), wherein protein farnesylation, protein chaperones, and the unfolded protein response are combined under the unifying umbrella of a cell’s intracellular farnesol (F
i
). In terms of human health, farnesol should have at least two different modes of action depending on whether those cells have farnesol salvage. Because animals have farnesol salvage, we can now see the importance of dietary prenols as well as the potential importance of farnesol in treating neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s disease, and multiple sclerosis.
Dpr-mediated H
2
O
2
resistance contributes to streptococcus survival in a cystic fibrosis airway model system
Authors: Rogers Rendi R. , Kesthely Christopher A. , Jean-Pierre Fabrice , El Hafi Bassam , O'Toole George A.
Published: June 2024

The cystic fibrosis (CF) lung environment is conducive to the colonization of bacteria as polymicrobial biofilms, which are associated with poor clinical outcomes for persons with CF (pwCF).
Streptococcus
spp. are highly prevalent in the CF airway, but its role in the CF lung microbiome is poorly understood. Some studies have shown
Streptococcus
spp. to be associated with better clinical outcomes for pwCF, while others show that high abundance of
Streptococcus
spp. is correlated with exacerbations. Our lab previously reported a polymicrobial culture system consisting of four CF-relevant pathogens that can be used to study microbial behavior in a more clinically relevant setting. Here, we use this model system to identify genetic pathways that are important for
Streptococcus sanguinis
survival in the context of the polymicrobial community. We identified genes related to reactive oxygen species as differentially expressed in
S. sanguinis
monoculture versus growth of this microbe in the mixed community. Genetic studies identified Dpr as important for
S. sanguinis
survival in the community. We show that Dpr, a DNA-binding ferritin-like protein, and PerR, a peroxide-responsive transcriptional regulator of Dpr, are important for protecting
S. sanguinis
from phenazine-mediated toxicity in co-culture with
Pseudomonas aeruginosa
and when exposed to hydrogen peroxide, both of which mimic the CF lung environment. Characterizing such interactions in a clinically relevant model system contributes to our understanding of microbial behavior in the context of polymicrobial biofilm infections.

IMPORTANCE

Streptococcus
spp. are recognized as a highly prevalent pathogen in cystic fibrosis (CF) airway infections. However, the role of this microbe in clinical outcomes for persons with CF is poorly understood. Here, we leverage a polymicrobial community system previously developed by our group to model CF airway infections as a tool to investigate a
Pseudomonas
-
Streptococcus
interaction involving reactive oxygen species (ROS). We show that protection against ROS is required for
Streptococcus sanguinis
survival in a clinically relevant polymicrobial system. Using this model system to study interspecies interactions contributes to our broader understanding of the complex role of
Streptococcus
spp. in the CF lung.
PRRSV GP5 inhibits the antivirus effects of chaperone-mediated autophagy by targeting LAMP2A
Authors: Li Wen , Zhang Mengting , Wang Yueshuai , Zhao Shijie , Xu Pengli , Cui Zhiying , Chen Jing , Xia Pingan , Zhang Yina
Published: June 2024

Autophagy is an important biological process in host defense against viral infection. However, many viruses have evolved various strategies to disrupt the host antiviral system. Porcine reproductive and respiratory syndrome virus (PRRSV) is a typical immunosuppressive virus with a large economic impact on the swine industry. At present, studies on the escape mechanism of PRRSV in the autophagy process, especially through chaperone-mediated autophagy (CMA), are limited. This study confirmed that PRRSV glycoprotein 5 (GP5) could disrupt the formation of the GFAP-LAMP2A complex by inhibiting the MTORC2/PHLPP1/GFAP pathway, promoting the dissociation of the pGFAP-EF1α complex, and blocking the K63-linked polyubiquitination of LAMP2A to inhibit the activity of CMA. Further research demonstrated that CMA plays an anti-PRRSV role by antagonizing nonstructural protein 11 (NSP11)-mediated inhibition of type I interferon (IFN-I) signaling. Taken together, these results indicate that PRRSV GP5 inhibits the antiviral effect of CMA by targeting LAMP2A. This research provides new insight into the escape mechanism of immunosuppressive viruses in CMA.

IMPORTANCE

Viruses have evolved sophisticated mechanisms to manipulate autophagy to evade degradation and immune responses. Porcine reproductive and respiratory syndrome virus (PRRSV) is a typical immunosuppressive virus that causes enormous economic losses in the swine industry. However, the mechanism by which PRRSV manipulates autophagy to defend against host antiviral effects remains unclear. In this study, we found that PRRSV GP5 interacts with LAMP2A and disrupts the formation of the GFAP-LAMP2A complex, thus inhibiting the activity of CMA and subsequently enhancing the inhibitory effect of the NSP11-mediated IFN-I signaling pathway, ultimately facilitating PRRSV replication. Our study revealed a novel mechanism by which PRRSV escapes host antiviral effects through CMA, providing a potential host target, LAMP2A, for developing antiviral drugs and contributing to understanding the escape mechanism of immunosuppressive viruses.
RECON gene disruption enhances host resistance to enable genome-wide evaluation of intracellular pathogen fitness during infection
Authors: Stamm Chelsea E. , McFarland Adelle P. , Locke Melissa N. , Tabakh Hannah , Tang Qing , Thomason Maureen K. , Woodward Joshua J.
Published: June 2024

Transposon sequencing (Tn-seq) is a powerful genome-wide technique to assess bacterial fitness under varying growth conditions. However, screening via Tn-seq
in vivo
is challenging. Dose limitations and host restrictions create bottlenecks that diminish the transposon mutant pool being screened. Here, we have developed a murine model with a disruption in
Akr1c13
that renders the resulting RECON
−/−
mouse resistant to high-dose infection. We leveraged this model to perform a Tn-seq screen of the human pathogen
Listeria monocytogenes in vivo
. We identified 135 genes which were required for
L. monocytogenes
growth in mice including novel genes not previously identified for host survival. We identified organ-specific requirements for
L. monocytogenes
survival and investigated the role of the folate enzyme FolD in
L. monocytogenes
liver pathogenesis. A mutant lacking
folD
was impaired for growth in murine livers by 2.5-log
10
compared to wild type and failed to spread cell-to-cell in fibroblasts. In contrast, a mutant in
alsR,
which encodes a transcription factor that represses an operon involved in D-allose catabolism, was attenuated in both livers and spleens of mice by 4-log
10
and 3-log
10
, respectively, but showed modest phenotypes in
in vitro
models. We confirmed that dysregulation of the D-allose catabolism operon is responsible for the
in vivo
growth defect, as deletion of the operon in the ∆
alsR
background rescued virulence. By undertaking an unbiased, genome-wide screen in mice, we have identified novel fitness determinants for
L. monocytogenes
host infection, which highlights the utility of the RECON
−/−
mouse model for future screening efforts.

IMPORTANCE

Listeria monocytogenes
is the gram-positive bacterium responsible for the food-borne disease listeriosis. Although infections with
L. monocytogenes
are limiting in healthy hosts, vulnerable populations, including pregnant and elderly people, can experience high rates of mortality. Thus, understanding the breadth of genetic requirements for
L. monocytogenes in vivo
survival will present new opportunities for treatment and prevention of listeriosis. We developed a murine model of infection using a RECON
−/−
mouse that is restrictive to systemic
L. monocytogenes
infection. We utilized this model to screen for
L. monocytogenes
genes required
in vivo
via transposon sequencing. We identified the liver-specific gene
folD
and a repressor,
alsR
, that only exhibits an
in vivo
growth defect. AlsR controls the expression of the D-allose operon which is a marker in diagnostic techniques to identify pathogenic
Listeria
. A better understanding of the role of the D-allose operon in human disease may further inform diagnostic and prevention measures.
The F plasmid conjutome: the repertoire of
E. coli
proteins translocated through an F-encoded type IV secretion system
Authors: Al Mamun Abu Amar M. , Kissoon Kimberley , Li Yang Grace , Hancock Erin , Christie Peter J.
Published: June 2024

Bacterial conjugation systems pose a major threat to human health through their widespread dissemination of mobile genetic elements (MGEs) carrying cargoes of antibiotic resistance genes. Using the Cre Recombinase Assay for Translocation (CRAfT), we recently reported that the IncFV pED208 conjugation system also translocates at least 16 plasmid-encoded proteins to recipient bacteria. Here, we deployed a high-throughput CRAfT screen to identify the repertoire of chromosomally encoded protein substrates of the pED208 system. We identified 32 substrates encoded by the
Escherichia coli
W3110 genome with functions associated with (i) DNA/nucleotide metabolism, (ii) stress tolerance/physiology, (iii) transcriptional regulation, or (iv) toxin inhibition. The respective gene deletions did not impact pED208 transfer proficiencies, nor did Group 1 (DNA/nucleotide metabolism) mutations detectably alter the SOS response elicited in new transconjugants upon acquisition of pED208. However, MC4100(pED208) donor cells intrinsically exhibit significantly higher SOS activation than plasmid-free MC4100 cells, and this plasmid carriage-induced stress response is further elevated in donor cells deleted of several Group 1 genes. Among 10 characterized substrates, we gained evidence of C-terminal or internal translocation signals that could function independently or synergistically for optimal protein transfer. Remarkably, nearly all tested proteins were also translocated through the IncN pKM101 and IncP RP4 conjugation systems. This repertoire of
E. coli
protein substrates, here termed the F plasmid “conjutome,” is thus characterized by functions of potential benefit to new transconjugants, diverse TSs, and the capacity for promiscuous transfer through heterologous conjugation systems.

IMPORTANCE

Conjugation systems comprise a major subfamily of the type IV secretion systems (T4SSs) and are the progenitors of a second large T4SS subfamily dedicated to translocation of protein effectors. This study examined the capacity of conjugation machines to function as protein translocators. Using a high-throughput reporter screen, we determined that 32 chromosomally encoded proteins are delivered through an F plasmid conjugation system. The translocated proteins potentially enhance the establishment of the co-transferred F plasmid or mitigate mating-induced stresses. Translocation signals located C-terminally or internally conferred substrate recognition by the F system and, remarkably, many substrates also were translocated through heterologous conjugation systems. Our findings highlight the plasticity of conjugation systems in their capacities to co-translocate DNA and many protein substrates.
Geological context and significance of the clay-sulfate transition region in Mount Sharp, Gale crater, Mars: An integrated assessment based on orbiter and rover data
Authors: Meyer Melissa J. , Milliken Ralph E. , Stack Kathryn M. , Edgar Lauren A. , Rampe Elizabeth B. , Turner Madison L. , Lewis Kevin W. , Kite Edwin S. , Caravaca Gwénaël , Vasavada Ashwin R. , Dietrich William E. , Bryk Alexander B. , Gasnault Olivier , Le Mouélic Stéphane , Seeger Christina H. , Sheppard Rachel Y.
Published: June 2024

On Mars, phyllosilicate (“clay”) minerals are often associated with older terrains, and sulfate minerals are associated with younger terrains, and this dichotomy is taken as evidence that Mars’ surface dried up over time. Therefore, in situ investigation of the Mount Sharp strata in Gale crater, which record a shift from dominantly clay-bearing to sulfate-bearing minerals, as seen in visible–near-infrared orbital reflectance spectra, is a key science objective for the Mars Science Laboratory (MSL) Curiosity rover mission. Here, we present regional (orbiter-based) and in situ (rover-based) evidence for a low-angle erosional unconformity that separates the lacustrine and marginal lacustrine deposits of the Carolyn Shoemaker formation from the dominantly eolian deposits of the lower Mirador formation within the orbitally defined clay-sulfate transition region. The up-section record of wetter (Carolyn Shoemaker formation) to drier (lower Mirador formation) depositional conditions is accompanied by distinct changes in diagenesis. Clay minerals occur preferentially within the Carolyn Shoemaker formation and are absent within the lower members of the Mirador formation. At and above the proposed unconformity, strata are characterized by an increase in diagenetic nodules enriched in X-ray amorphous Mg-sulfate. Early clay formation in the Carolyn Shoemaker formation may have created a hydraulic barrier such that later migrating magnesium- and sulfur-rich fluids accumulated preferentially within the lower members of the Mirador formation. The proposed unconformity may have also acted as a fluid conduit to further promote Mg-sulfate nodule formation at the Carolyn Shoemaker–Mirador formation boundary. These results confirm an association of the clay-sulfate transition with the drying of depositional environments, but they also suggest that at least some orbital sulfate signatures within the region are not time-congruent with the environmental signals extracted from primary sedimentology. Our findings highlight that complex interactions among primary depositional environment, erosion, and diagenesis contribute to the transition in clay-sulfate orbital signatures observed in the stratigraphy of Mount Sharp.