bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of three approaches for accessory lung lobectomy in the canine cadaveric model: Intercostal thoracotomy, median sternotomy, and a transdiaphragmatic approach combined with caudal median sternotomy
Authors: Duvieusart Camille B. , Barbur Laura A. , Burneko Marie F. , Hess Rebecka S. 
Published: October 2024

AbstractObjectiveTo describe a combined transdiaphragmatic and caudal median sternotomy (TDCM) approach to the accessory lung lobe and to compare its accessibility with intercostal thoracotomy (ICT) and median sternotomy (MS).Study designCadaveric study.AnimalsTwelve canine cadavers.MethodsCadavers underwent an accessory lung lobectomy using an articulating EndoGIA stapler via randomly assigned approach: ICT (n = 4), MS (n = 4) or TDCM (n = 4). The percentage of accessory lung tissue removed was measured in surface area and weight. Exposure was measured as area of cavitary or bicavitary exposure at maximal retraction, by tracing a line around the circumference of the exposed cavity using an imaging software. Staple line leak pressures were evaluated to 40 cmH2O.ResultsThe average area of exposure was larger in the TDCM approach (TDCM = 193.5 cm2, MS = 106.5 cm2, ICT = 73.5 cm2); (p = .01). Two of four ICT staple lines leaked at 40 cmH2O or lower, and 1/4 MS resulted in iatrogenic damage to an adjacent lobe. There was no difference in the percentage of the lobe excised by weight or surface area between groups.ConclusionThe transdiaphragmatic and caudal median sternotomy approach provided greater exposure, although the percentage of the lobe excised and the surgical time did not differ between approaches.Clinical significanceAll three approaches allowed for adequate excision of the accessory lung lobe (ALL) with similar surgical times; however, the TDCM approach provided a greater area of exposure, which could increase accessibility to the ALL.
Similarity Analysis to Enhance Transfer Learning for Damage Detection
Authors: de Almeida Estênio Fuzaro , da Silva Samuel , Ritto Thiago G. 
Published: October 2024

Abstract
One significant challenge in machine learning for Structural Health Monitoring (SHM) is reusing previously trained classifiers. A classifier might be suitable for one situation but not for another. Transfer learning techniques try to overcome this difficulty. In SHM, it is common to use the modal parameters as features; however, they are highly influenced by boundary conditions, geometry, and the level of structural damage. This work proposes an innovative approach that performs a similarity analysis to select features before applying transfer learning, aiming at improving classification and damage detection. The reasoning is that a higher similarity leads to a more efficient transfer of learning and, consequently, a better classification. Transfer learning is conducted via the domain adaptation technique known as Transfer Component Analysis (TCA), and cases with low similarity are compared to those with high similarity. Two datasets are analyzed. The first consists of a beam under different boundary conditions, and data are generated through numerical simulations. The second derives from an experimental setup of bolted joints with loosening damage. The proposed strategy, which uses a cosine-type similarity, is shown to improve the transfer learning classification.
A novel methionyl-tRNA synthetase inhibitor targeting gram-positive bacterial pathogens
Authors: Molasky Nora M. R. , Zhang Zhongsheng , Gillespie J. Robert , Domagala John , Reyna Dawn , Lipka Elke , Fan Erkang , Buckner Frederick S. 
Published: October 2024

ABSTRACT

New antibiotics are needed to treat gram-positive bacterial pathogens.
MRS-2541
is a novel inhibitor of methionyl-tRNA synthetase with selective activity against gram-positive bacteria. The minimum inhibitory concentrations (MICs) against
Staphylococcus aureus, Streptococcus pyogenes,
and
Enterococcus
species range from 0.063 to 0.5 µg/mL. Given orally to mice at 50 mg/kg every 8 hours,
MRS-2541
shows sustained plasma levels well above these MICs. In the mouse thigh infection model,
MRS-2541
decreased methicillin-resistant
Staphylococcus aureus
and
Streptococcus pyogenes
bacterial loads to the same degree as linezolid.
MRS-2541
is a promising new antibiotic for development against skin and soft tissue infections.
Effects of wildfire on soil microbial communities in karst forest ecosystems of southern Guizhou Province, China
Authors: Li Xu , Han Yanfeng , Zhang Yunlin , Shao Qiuyu , Dong Chunbo , Li Jianfeng , Ding Bo , Zhang Yanwei 
Published: October 2024

ABSTRACT

Wildfires are unpredictable disturbances with profound effects on soil properties and microbial communities within forest ecosystems. However, knowledge of post-fire microbial communities in karst forests remains limited. In this study, microbial amplicon sequencing techniques were employed to investigate the impact of wildfires on the composition, diversity, function, and co-occurrence network of soil microbial communities in karst forest landscapes and to identify the key soil physicochemical factors affecting the post-fire microbial communities. The wildfire affected the fungal community to a greater extent than the bacterial community, with the former shifting from a dominance of Basidiomycota to Ascomycota at the phylum level, while the relative abundance of Actinobacteria increased significantly in the bacterial community. Moreover, the wildfire increased the α-diversity of the microbial community and changed the β-diversity. Network analysis indicated significant reductions in the complexity of microbial community networks and the hub microbiome in burned soils compared to those of unburned soils. Functional predictions indicated an increase in the highly abundant functional taxa of chemoheterotrophic and aerobic chemoheterotrophic bacteria, along with a significant rise in saprotrophic functional fungal taxa following the fire. In addition, soil organic matter, total nitrogen, total phosphorus, and soil water content emerged as key soil physicochemical factors affecting post-fire soil microbial communities in the karst forest. Overall, this study revealed the structural and functional characteristics of soil microbial communities and their key influencing factors after a fire in a karst forest, which will provide a valuable theoretical basis for ecosystem restoration after a wildfire.

IMPORTANCE
Despite the significant impacts of wildfires on forest ecosystems, most existing studies have largely focused on boreal and Mediterranean coniferous forest types, with limited research on the impacts of coniferous and broadleaf forest types in subtropical karst regions. This study reveals the effects of wildfires on soil microbial communities of coniferous and broadleaf forest types in a karst forest. The results of this study not only improve the understanding of the effects of wildfires on the composition, diversity, function, and network of soil microbial communities but also provide a meaningful theoretical basis for post-fire ecosystem restoration in the karst forest.
Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment
Authors: Somboon Kamolrat , Melling Oliver , Lejeune Maylis , Pinheiro Glaucia M. S. , Paquelin Annick , Bardiaux Benjamin , Nilges Michael , Delepelaire Phillippe , Khalid Syma , Izadi-Pruneyre Nadia 
Published: October 2024

ABSTRACT

The envelope of Gram-negative bacteria is composed of two membranes separated by the periplasmic space. This organization imposes geometrical and distance constraints that are key for the mechanism of action of multicomponent systems spanning the envelope. However, consideration of all three compartments by experimental approaches is still elusive. Here, we have used the state-of-the-art molecular dynamics simulation in an
Escherichia coli
envelope model to obtain a dynamic view of molecular interactions between the outer membrane heme transporter HasR and the inner membrane TonB-like protein HasB. Their interaction allows the transfer of the inner membrane proton-motive force derived energy to the transporter for heme internalization. The simulations that incorporate both membranes show the key role of periplasmic domains of both proteins and their dynamics in complex formation and stability. They revealed a previously unidentified network of HasR-HasB protein-protein interactions in the periplasm. Experimental validation (mutations,
in vivo
phenotypic and biophysical assays) provides support for the simulation-predicted interactions. Based on structural and sequence conservation, the network of interaction revealed in this study is expected to occur in other nutrient import systems.

IMPORTANCE
Gram-negative bacteria import scarce nutrients such as metals and vitamins by an energized mechanism involving a multicomponent protein system that spans the cell envelope. It consists of an outer membrane TonB-dependent transporter (TBDT) and a TonB complex in the inner membrane that provides the proton motive force energy for the nutrient entry. Despite the intense research efforts focused on this system (a) from structural and fundamental microbiology perspectives and (b) for the interest in the development of new antibacterial strategies, the molecular mechanism of the system is not at all well understood. The lack of understanding comes from incomplete structural data and the experimental difficulties of studying an inherently flexible multicomponent complex that resides within the heterogeneous environment of the double membrane bacterial cell envelope. To address these challenges and obtain a comprehensive view of the molecular interactions at atomic level, here, we have used the combined power of advanced molecular simulations and complementary microbiology and biochemical experiments. Our results represent a significant step forward in understanding the structural and molecular bases of this vital mechanism.
Suppression of ZBP1-mediated NLRP3 inflammasome by the tegument protein VP22 facilitates pseudorabies virus infection
Authors: Ma Zicheng , Liu Depeng , Cao Wandi , Guo Lei , Liu Kesen , Bai Juan , Li Xingyi , Jiang Ping , Liu Xing 
Published: October 2024

ABSTRACT

The interaction between Z-DNA binding protein 1 (ZBP1) and the NLR family pyrin domain-containing 3 (NLRP3) inflammasome has been uncovered in several viral infections. However, the role of this molecular pathway during infection with the alpha-herpesvirus pseudorabies virus (PRV) remains largely elusive. Here, we report that during PRV infection, ZBP1-mediated NLRP3 inflammasome activation is inhibited by the viral tegument protein VP22, thereby facilitating viral infection. Through a combination of RNA sequencing and genetic studies, we demonstrate that PRV VP22 functions as a virus-encoded virulence factor by evading the inhibitory effects of ZBP1 on virus infection. Importantly, the replication and pathogenicity of a recombinant PRV lacking VP22 are significantly increased in ZBP1-deficient cells and mice. Mechanistically, PRV VP22 interacts with ZBP1, impeding the recruitment of receptor-interacting protein kinase 3 and Caspase-8, thereby inhibiting NLRP3 activation. Furthermore, we show that the N-terminal 1–50 amino acid domain of VP22 dominantly destabilizes ZBP1-mediated function. Taken together, these findings identify a functional link between PRV infection and ZBP1-mediated NLRP3 inflammatory response, providing novel insights into the pathogenesis of PRV and other herpesviruses.

IMPORTANCE
Z-DNA binding protein 1 (ZBP1) functions as a pivotal innate immune sensor that regulates inflammatory cell death during viral infections. However, its role in pseudorabies virus (PRV) infection remains unknown. Here, we demonstrate that ZBP1 serves as a restrictive factor by triggering the activation of the NLR family pyrin domain-containing 3 inflammasome, a process counteracted by PRV-encoded protein VP22. Furthermore, VP22 interferes with the interaction between ZBP1 and receptor-interacting protein kinase 3/Caspase-8, particularly through its N-terminal 1–50 amino acids. Importantly, deficiency in ZBP1 enhances the replication and virulence of recombinant viruses lacking VP22 or its N-terminal 1–50 amino acids. These findings reveal how PRV escapes ZBP1-mediated inflammatory responses during infection, potentially informing the rational design of therapeutic interventions.
Elements of dissemination in cryptococcosis
Authors: Bednarek Joseph M. , Brown Jessica C. S. 
Published: October 2024

ABSTRACT

As healthcare improves and our ability to support patients with compromised immune systems increases, such patients become more vulnerable to microbes in the environment. These include fungal pathogens such as
Cryptococcus neoformans
, the primary cause of fungal meningitis and a top priority pathogen on the World Health Organization fungal pathogen list. Like many other environmental pathogens,
C. neoformans
must adapt to and thrive in diverse environments in order to cause disease: (i) the environmental niche, (ii) the lungs following inhalation of infectious particles, (iii) the bloodstream and/or lymphatic system during dissemination, and (iv) the central nervous system (CNS), where it causes a deadly cryptococcal meningoencephalitis. Because CNS infection is the driver of mortality and the presenting illness, understanding the dissemination process from both host and fungal perspectives is important for treating these infections. In this review, we discuss the different stages of dissemination, how fungal cells interact with host cells during disease, and the ability to adapt to different environments within hosts.
Activation of the general stress response sigma factor SigB prevents competence development in
Bacillus subtilis
Authors: Harms Marco , Michalik Stephan , Hildebrandt Petra , Schaffer Marc , Gesell Salazar Manuela , Gerth Ulf , Mäder Ulrike , van Dijl Jan Maarten , Hecker Michael , Völker Uwe , Reder Alexander 
Published: October 2024

ABSTRACT

Seemingly simple bacteria mount intricate adaptive responses when exposed to physical stress or nutrient limitation, and the activation of these responses is governed by complex signal transduction networks. Upon entry into the stationary growth phase, the soil bacterium
Bacillus subtilis
may develop natural competence, form biofilms or stress-resistant cells, or ultimately trigger a cellular differentiation program leading to spore formation. Master regulators, such as Spo0A, ComK, SinR, and SigB, constantly monitor the bacterium’s environment and then determine appropriate adaptive responses. Here, we show that exposure of
B. subtilis
to visible light and other stresses triggers a general stress response-dependent block in competence development. SigB serves as an “emergency system” to silence inappropriate expression of an alternative developmental program in the face of unfavorable conditions. In particular, we document a stress-dependent molecular mechanism that prevents accumulation of the central competence regulator ComK via expression of a SigB-driven antisense RNA (
as-comK
, S365) which is part of a noncontiguous operon.

IMPORTANCE

Bacillus subtilis
exhibits a large number of different specific and general adaptation reactions, which need to be well balanced to sustain survival under largely unfavorable conditions. Under specific conditions, natural competence develops, which enables
B. subtilis
to actively take up exogenous DNA to integrate it into its own genome. In contrast to this specific adaptation, the general stress response is induced by a variety of exogenous stress and starvation stimuli, providing comprehensive protection and enabling survival of vegetative
B. subtilis
cells. In the present work, we reveal the molecular basis for the interconnection of these two important responses in the regulatory network. We describe that the master regulator of the general stress response SigB is activated by physiological stress stimuli, including daylight and ethanol stress, leading to the inactivation of the competence master regulator ComK by transcriptional anti-sense regulation, showing a strict hierarchy of adaptational responses under severe stress.
Substrate identification of putative NCS1 and NCS2 nucleobase transporters in
Pseudomonas aeruginosa
Authors: Kennelly Corey , Prindle Arthur 
Published: October 2024

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that can salvage nucleobases from the environment to conserve nutrients that would otherwise be spent on
de novo
nucleotide biosynthesis. However, little is known regarding the substrate specificity of the 13 putative nucleobase transporters in
P. aeruginosa
. Here, using a combination of genetic and chemical approaches, we report substrate identifications for 10 putative nucleobase transporters in
P. aeruginosa
. Specifically, we individually expressed each transporter in a genetic background lacking all 13 putative nucleobase transporters and quantified growth on a panel of 10 nucleobases as sole nitrogen sources. We confirmed these expression-based substrate identifications using targeted genetic knockouts. In a complementary approach, we utilized four toxic nucleobase antimetabolites to characterize antimicrobial activity in these same strains. We identified the sole allantoin transporter as well as transporters for guanine, xanthine, uric acid, cytosine, thymine, uracil, and dihydrouracil. Furthermore, we associated at least five nucleobase transporters with hypoxanthine, which has been recently reported to be an antibiofilm cue in
P. aeruginosa
. These results provide an initial characterization of the putative nucleobase transporters in
P. aeruginosa
, significantly advancing our understanding of nucleobase transport in this clinically relevant organism.

IMPORTANCE

Pseudomonas aeruginosa
is a frequently multidrug-resistant opportunistic pathogen and one of the most common causes of healthcare-acquired infections. While nucleobases are known to support growth in nutrient-limited conditions, recent work showed that adenine and hypoxanthine can also decrease
P. aeruginosa
biofilm formation by disrupting c-di-GMP metabolism. Thus, nucleobase transport may be relevant to multiple aspects of
P. aeruginosa
biology and pathogenesis. However, there is currently little known about the transport of nucleobases in
P. aeruginosa
. Our work reports initial substrate identifications for 10 putative nucleobase transporters in
P. aeruginosa
, providing new tools to address previously difficult-to-test hypotheses relating to nucleobase transport in this organism.
Metabolites augment oxidative stress to sensitize antibiotic-tolerant
Staphylococcus aureus
to fluoroquinolones
Authors: Batchelder Jonathan I. , Taylor Andrew J. , Mok Wendy W. K. 
Published: October 2024

ABSTRACT

If left unchecked, infections involving antibiotic-refractory bacteria are expected to cause millions of deaths per year in the coming decades. Beyond genetically resistant bacteria, persisters, which are genetically susceptible cells that survive antibiotic doses that kill the rest of the clonal population, can potentially contribute to treatment failure and infection relapse. Stationary-phase bacterial cultures are enriched with persisters, and it has been shown that stimulating these populations with exogenous nutrients can reduce persistence to different classes of antibiotics, including topoisomerase-targeting fluoroquinolones (FQs). In this study, we show that adding glucose and amino acids to nutrient-starved
Staphylococcus aureus
cultures enhanced their sensitivity to FQs, including delafloxacin (Dela)—a drug that was recently approved for treating staphylococcal infections. We found that while the added nutrients increased nucleic acid synthesis, this increase was not required to sensitize
S. aureus
to FQs. We further demonstrate that addition of these nutrients increases membrane potential and the ability to generate harmful reactive oxygen species (ROS) during FQ treatment. Chelating iron, scavenging hydroxyl radicals, and limiting oxygenation during FQ treatment and during recovery following FQ treatment rescued nutrient-stimulated
S. aureus
. In all, our data suggest that while nutrient stimulation increases the activity of FQ targets in stationary-phase
S. aureus
, the resulting generation of ROS, presumably made possible through metabolic upregulation, is the primary driver of increased sensitivity to these drugs.

IMPORTANCE

Staphylococcus aureus
causes many chronic and relapsing infections because of its ability to endure host immunity and antibiotic therapy. While several studies have focused on the nutrient requirements for the formation and maintenance of staphylococcal infections, the effects of the nutrient environment on bacterial responses to antibiotic treatment remain understudied. Here, we show that adding nutrients to starved
S. aureus
activates biosynthetic processes, including DNA synthesis, but it is the generation of harmful reactive oxidants that sensitizes
S. aureus
to DNA topoisomerase-targeting FQs. Our results suggest that the development of approaches aimed at perturbing metabolism and increasing oxidative stress can potentiate the bactericidal activity of FQs against antibiotic-tolerant
S. aureus
.
Complete genome sequences of five bacteria isolated from rice plants in a paddy field in Sekinchan, Selangor, Malaysia
Authors: Abdul Malek Ahmad Zuhairi , Hashim Amalia Mohd , Khairil Mokhtar Nur Fadhilah , Saidi Noor Baity , Abu Bakar Mohd Faizal , Singaram Nallamai 
Published: October 2024

ABSTRACT

This study examines the genome sequences of five endophytic bacterial isolates from the
Oryza sativa
microbiome to assess their potential as plant bio-inoculants. The five complete bacterial genomes from the genera
Pseudomonas, Burkholderia, Sphingobacterium, Stenotrophomonas,
and
Pantoea
were sequenced using Nanopore long-read sequencing technology.
Complete genome sequence of the saprophytic actinomycete
Rhodococcus (Prescottella) soli
DSD51W
T
, closely related to the multi-host pathogen
Rhodococcus (Prescottella) equi
Authors: Yerlikaya Zeynep , Miranda-CasoLuengo Raúl , Ó Gaora Peadar , Meijer Wim G. 
Published: October 2024

ABSTRACT

Rhodococcus (Prescottella) soli
strain DSD51W
T
is an aerobic, non-spore-forming, non-motile actinomycete isolated previously from soil collected from Kyoto Park, Japan, using a resuscitative technique. Here, we report the complete, circular genome sequence of
R. soli
DSD51W
T
. We employed a hybrid approach using Illumina and Oxford Nanopore platforms.
Complete genome sequence of strain KD-1
T
, the type strain of
Sulfurisphaera javensis
, isolated from an Indonesian hot spring
Authors: Sakai Hiroyuki D. , Nur Naswandi , Suwanto Antonius , Kurosawa Norio 
Published: October 2024

ABSTRACT

Sulfurisphaera javensis
KD-1
T
, originally isolated from an Indonesian acidic hot spring, is a hyperthermophilic, acidophilic, and facultatively anaerobic archaeon. Here, we report the 2.6 Mb complete genome sequence of KD-1
T
. Genes related to sulfur metabolism were found in the genome, indicating that KD-1
T
is involved in the sulfur cycle in its habitat.
Complete genome of the opportunistic pathogen
Nocardia vulneris
strain LPB4002 and its biosynthetic potential
Authors: González-Nava Janette , Salinas-Virgen Leilani I. , Sandoval-Trujillo Horacio , Torre-Hernández Ma. Eugenia de la , Ramírez-Saad Hugo 
Published: October 2024

ABSTRACT

The complete genome sequence of the opportunistic pathogen
Nocardia vulneris
is reported. The strain
N. vulneris
LPB4002 was isolated from a clinical sample of a patient with actinomycetoma. The reported genome comprises a single 9,489-Kb closed chromosome, with 8,584 protein-coding genes and 68% GC content.