bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptional analysis of
Candida auris
biofilms following farnesol and tyrosol treatment
Authors: Jakab Ágnes , Kovács Fruzsina , Balla Noémi , Nagy-Köteles Csaba , Ragyák Ágota , Nagy Fruzsina , Borman Andrew M. , Majoros László , Kovács Renátó 
Published: March 2024

ABSTRACT

Candida auris
is frequently associated with biofilm-related invasive infections. The resistant profile of these biofilms necessitates innovative therapeutic options, where quorum sensing may be a potential target. Farnesol and tyrosol are two fungal quorum-sensing molecules with antifungal effects at supraphysiological concentrations. Here, we performed genome-wide transcript profiling with
C. auris
biofilms following farnesol or tyrosol exposure using transcriptome sequencing (RNA-Seq). Since transition metals play a central role in fungal virulence and biofilm formation, levels of intracellular calcium, magnesium, and iron were determined following farnesol or tyrosol treatment using inductively coupled plasma optical emission spectrometry. Farnesol caused an 89.9% and 73.8% significant reduction in the calcium and magnesium content, respectively, whereas tyrosol resulted in 82.6%, 76.6%, and 81.2% decrease in the calcium, magnesium, and iron content, respectively, compared to the control. Genes involved in biofilm events, glycolysis, ergosterol biosynthesis, fatty acid oxidation, iron metabolism, and autophagy were primarily affected in treated cells. To prove ergosterol quorum-sensing molecule interactions, microdilution-based susceptibility testing was performed, where the complexation of farnesol, but not tyrosol, with ergosterol was impeded in the presence of exogenous ergosterol, resulting in a minimum inhibitory concentration increase in the quorum-sensing molecules. This study revealed several farnesol- and tyrosol-specific responses, which will contribute to the development of alternative therapies against
C. auris
biofilms.

IMPORTANCE

Candida auris
is a multidrug-resistant fungal pathogen, which is frequently associated with biofilm-related infections.
Candida
-derived quorum-sensing molecules (farnesol and tyrosol) play a pivotal role in the regulation of fungal morphogenesis and biofilm development. Furthermore, they may have remarkable anti-biofilm effects, especially at supraphysiological concentrations. Innovative therapeutic approaches interfering with quorum sensing may be a promising future strategy against
C. auris
biofilms; however, limited data are currently available concerning farnesol-induced and tyrosol-related molecular effects in
C. auris
. Here, we detected several genes involved in biofilm events, glycolysis, ergosterol biosynthesis, fatty acid oxidation, iron metabolism, and autophagy, which were primarily influenced following farnesol or tyrosol exposure. Moreover, calcium, magnesium, and iron homeostasis were also significantly affected. These results reveal those molecular and physiological events, which may support the development of novel therapeutic approaches against
C. auris
biofilms.
Escherichia coli
possessing the dihydroxyacetone phosphate shunt utilize 5′-deoxynucleosides for growth
Authors: Huening Katherine A. , Groves Joshua T. , Wildenthal John A. , Tabita F. Robert , North Justin A. 
Published: March 2024

ABSTRACT

All organisms utilize
S
-adenosyl-
l-
methionine (SAM) as a key co-substrate for the methylation of biological molecules, the synthesis of polyamines, and radical SAM reactions. When these processes occur, 5′-deoxy-nucleosides are formed as byproducts such as
S
-adenosyl-
l
-homocysteine, 5′-methylthioadenosine (MTA), and 5′-deoxyadenosine (5dAdo). A prevalent pathway found in bacteria for the metabolism of MTA and 5dAdo is the dihydroxyacetone phosphate (DHAP) shunt, which converts these compounds into dihydroxyacetone phosphate and 2-methylthioacetaldehyde or acetaldehyde, respectively. Previous work in other organisms has shown that the DHAP shunt can enable methionine synthesis from MTA or serve as an MTA and 5dAdo detoxification pathway. Rather, the DHAP shunt in
Escherichia coli
ATCC 25922, when introduced into
E. coli
K-12, enables the use of 5dAdo and MTA as a carbon source for growth. When MTA is the substrate, the sulfur component is not significantly recycled back to methionine but rather accumulates as 2-methylthioethanol, which is slowly oxidized non-enzymatically under aerobic conditions. The DHAP shunt in ATCC 25922 is active under oxic and anoxic conditions. Growth using 5-deoxy-
d
-ribose was observed during aerobic respiration and anaerobic respiration with Trimethylamine N-oxide (TMAO), but not during fermentation or respiration with nitrate. This suggests the DHAP shunt may only be relevant for extraintestinal pathogenic
E. coli
lineages with the DHAP shunt that inhabit oxic or TMAO-rich extraintestinal environments. This reveals a heretofore overlooked role of the DHAP shunt in carbon and energy metabolism from ubiquitous SAM utilization byproducts and suggests a similar role may occur in other pathogenic and non-pathogenic bacteria with the DHAP shunt.

IMPORTANCE

The acquisition and utilization of organic compounds that serve as growth substrates are essential for
Escherichia coli
to grow and multiply. Ubiquitous enzymatic reactions involving S-adenosyl-
l
-methionine as a co-substrate by all organisms result in the formation of the 5′-deoxy-nucleoside byproducts, 5′-methylthioadenosine and 5′-deoxyadenosine. All
E. coli
possess a conserved nucleosidase that cleaves these 5′-deoxy-nucleosides into 5-deoxy-pentose sugars for adenine salvage. The DHAP shunt pathway is found in some extraintestinal pathogenic
E. coli
, but its function in
E. coli
possessing it has remained unknown. This study reveals that the DHAP shunt enables the utilization of 5′-deoxy-nucleosides and 5-deoxy-pentose sugars as growth substrates in
E. coli
strains with the pathway during aerobic respiration and anaerobic respiration with TMAO, but not fermentative growth. This provides an insight into the diversity of sugar compounds accessible by
E. coli
with the DHAP shunt and suggests that the DHAP shunt is primarily relevant in oxic or TMAO-rich extraintestinal environments.
Whole-genome sequencing-based antimicrobial resistance and shedding dynamics of
Escherichia coli
isolated from calves before and after antimicrobial group treatments
Authors: Bernier Gosselin Véronique , Fernandez Javier E. , Ollagnier Catherine , Morel Isabelle , Siegenthaler Raphael , Collaud Alexandra , Meylan Mireille , Perreten Vincent 
Published: March 2024

ABSTRACT

The fattening of calves is often associated with high antimicrobial use and the selection of antimicrobial resistance (AMR). The objective of this observational longitudinal study was to describe the AMR and strain dynamics, using whole-genome sequencing (WGS), of fecal
Escherichia coli
in a cohort of 22 calves. All calves received antimicrobial group treatments on Day (D) 1 (oxytetracycline, intramuscularly) and on D4 through D12 (doxycycline, in-feed). Additionally, eight calves received individual parenteral treatments between D7 and D59, including florfenicol, amoxicillin, marbofloxacin, and gamithromycin. Rectal swabs were collected from all calves on D1 (prior to treatment), D2, D9, and D82. The swabs were spread onto
Enterobacterales
-selective agar, and three
E. coli
colonies per plate were subjected to WGS. Out of 264 isolates across all calves and sampling times, 80 unique strains were identified, a majority of which harbored genes conferring resistance to tetracyclines, streptomycin, and sulfonamides. The diversity of strains decreased during the in-feed antimicrobial group treatment of the calves. On D82, 90% of isolates were strains that were not isolated at previous sampling times, and the median number per strain of AMR determinants to tetracyclines, florfenicol, β-lactams, quinolones, or macrolides decreased compared to D9. Additionally, clonal dissemination of some strains represented the main transmission route of AMR determinants. In this study, WGS revealed important variations in strain diversity and genotypic AMR of fecal
E. coli
over time in calves subjected to group antimicrobial treatments.

IMPORTANCE

The continued emergence and spread of antimicrobial resistance (AMR) determinants are serious global concerns. The dynamics of AMR spread and persistence in bacterial and animal host populations are complex and not solely driven by antimicrobial selection pressure. In calf fattening, both antimicrobial use and carriage prevalence of antimicrobial-resistant bacteria are generally recognized as high. This study provides new insights into the short-term, within-farm dynamics and transmission of AMR determinants in
Escherichia coli
from the dominant fecal flora of calves subjected to antimicrobial group treatments during the rearing period. The diversity of
E. coli
strains decreased over time, although, in contrast to previous observations in extended-spectrum β-lactamase-producing
Enterobacterales
, the predominance of a few clones was not observed. The spread of AMR determinants occurred through the dissemination of clonal strains among calves. The median number per strain of AMR determinants conferring resistance to selected antimicrobials decreased toward the end of the rearing period.
Divergent mitochondrial responses and metabolic signal pathways secure the azole resistance in Crabtree-positive and negative
Candida
species
Authors: Zhou Meng , Peng Jingwen , Ren Kun , Yu Yu , Li Dongmei , She Xiaodong , Liu Weida 
Published: March 2024

ABSTRACT

Azole drugs are the main therapeutic drugs for invasive fungal infections. However, azole-resistant strains appear repeatedly in the environment, posing a major threat to human health. Several reports have shown that mitochondria are associated with the virulence of pathogenic fungi. However, there are few studies on the mechanisms of mitochondria-mediated azoles resistance. Here, we first performed mitochondrial proteomic analysis on multiple
Candida
species (
Candida albicans
,
Nakaseomyces glabrata
,
Pichia kudriavzevii,
and
Candida auris
) and analyzed the differentially expressed mitochondrial proteins (DEMPs) between azole-sensitive and azole-resistant
Candida
species. Subsequently, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology analysis, and protein-protein interaction network analysis of DEMPs. Our results showed that a total of 417, 165, and 25 DEMPs were identified in resistant
C. albicans
,
N. glabrata,
and
C. auris
, respectively. These DEMPs were enriched in ribosomal biogenesis at cytosol and mitochondria, tricarboxylic acid cycle, glycolysis, transporters, ergosterol, and cell wall mannan biosynthesis. The high activations of these cellular activities, found in
C. albicans
and
C. auris
(at low scale), were mostly opposite to those observed in two fermenter species—
N. glabrata
and
P. kudriavzevii
. Several transcription factors including Rtg3 were highly produced in resistant
C. albicans
that experienced a complex I activation of mitochondrial electron transport chain (ETC). The reduction of mitochondrial-related activities and complex IV/V of ETC in
N. glabrata
and
P. kudriavzevii
was companying with the reduced proteins of Tor1, Hog1, and Snf1/Snf4.

IMPORTANCE

Candida
spp. are common organisms that cause a variety of invasive diseases. However,
Candida
spp. are resistant to azoles, which hinders antifungal therapy. Exploring the drug-resistance mechanism of pathogenic
Candida
spp. will help improve the prevention and control strategy and discover new targets. Mitochondria, as an important organelle in eukaryotic cells, are closely related to a variety of cellular activities. However, the role of mitochondrial proteins in mediating azole resistance in
Candida
spp. has not been elucidated. Here, we analyzed the mitochondrial proteins and signaling pathways that mediate azole resistance in
Candida
spp. to provide ideas and references for solving the problem of azole resistance. Our work may offer new insights into the connection between mitochondria and azoles resistance in pathogenic fungi and highlight the potential clinical value of mitochondrial proteins in the treatment of invasive fungal infections.
Comparison of the Simplexa GBS Direct and ARIES GBS assays for the detection of
S. agalactiae
in broth-enriched swab specimens
Authors: Sabharwal Lavannya , Faron Matthew L. , Buchan Blake W. 
Published: March 2024

ABSTRACT

We conducted a comparative evaluation of the FDA-cleared Simplexa GBS Direct and ARIES GBS molecular assays for the detection of
Streptococcus agalactiae
(Group B
Streptococcus
, GBS) in 386 prospectively collected, broth-enriched vaginal/rectal swab specimens. The sensitivity of each test was 96.2% and specificity was ≥98.7% when compared to a combined direct and enriched culture method using chromogenic culture medium. A total of four specimens were called positive by both molecular assays but negative by culture, likely representing specimens with a low burden of GBS in these specimens. Two specimens were reported positive by culture but negative by both molecular assays. One of these specimens demonstrated atypically colored colonies on chromogenic agar; the other yielded typically colored colonies only observed after broth enrichment. Our data demonstrate equivalent performance of Simplexa and ARIES molecular assays for the detection of GBS in clinical specimens.

IMPORTANCE
Clinical laboratories often face decisions regarding which of the multiple available molecular platforms would best fit their needs based on cost, workflow, menu, and diagnostic performance. Therefore, objective clinical comparisons of similar molecular tests are valuable resources to aid these decisions. We provide a clinical comparison of two FDA-cleared tests to routine culture and to each other that can be used by clinical laboratories when determining which of the available molecular platforms would best fit their laboratory in terms of workflow, cost, and performance.
Nutrition counsellors’ recommended eating patterns for individuals with type 2 diabetes in the USA
Authors: Khosrovaneh Katherine , Hisamatsu Rina , Reiss Jacob , Rau Jacqueline , Oshman Lauren , Diez Heidi L , Lee Joyce M , Aikens James E , Richardson Caroline , Griauzde Dina H 
Published: March 2024

IntroductionMultiple eating patterns can promote glycaemic control and weight loss among patients with type 2 diabetes mellitus (T2D). Clinical practice guidelines for T2D management encourage health professionals to guide patients’ selection of a patient-centred eating pattern. This study aims to characterise beliefs about and recommendations for and against practice guideline-concordant eating patterns among registered dietitians (RDs) and other healthcare professionals who provide nutrition counselling to patients with T2D.MethodsThis was a cross-sectional online survey. We invited 82 RDs affiliated with an academic health system in the midwestern USA to participate. We also invited health professionals who provide nutrition counselling to patients with T2D and are affiliated with 264 primary care practices within the Michigan Collaborative for Type 2 Diabetes. Participants were asked to select the eating pattern(s) that they commonly recommend or avoid for patients with T2D and why.ResultsSurvey respondents (n=81) most commonly recommend low-carbohydrate (77.8%); Mediterranean-style (52.8%) and energy-modified/calorie-restricted (36.1%) eating patterns. Survey respondents most commonly recommend avoiding very low-carbohydrate (51.0%) and very low-calorie (49.0%) eating patterns. Respondents who did not recommend very low-carbohydrate were most concerned about the eating pattern being too restrictive (93.0%).ConclusionsSurvey respondents recommend a range of guideline-adherent eating patterns to patients with T2D but tend to recommend against very low-carbohydrate and very low-calorie eating patterns. Additional strategies are needed to increase patient-centred use of these evidence-based options in clinical practice settings.
‘One Is Too Many’ preventing self-harm and suicide in military veterans: a quantitative evaluation
Authors: Finnegan Alan , Salem K , Ainsworth-Moore L 
Published: March 2024

IntroductionIn 2021, the Armed Forces Covenant Fund Trust allocated over £2 million to programmes designed to have a clear and demonstrable impact on suicide prevention. Four grant holders delivered a combination of psychotherapeutic interventions, group activities, social prescribing, peer support mentoring, life skills coaching, educational courses and practical help with housing and employment. The evaluation was completed between August 2021 and July 2023.MethodsA survey was completed by 503 participants at entry and 423 at exit. It captured data regarding demographic and military-specific details, health status, situational stressors, predisposing symptoms, help-seeking behaviour, social engagement, housing, living arrangements and employment status. The questionnaire included a number of validated psychometric questionnaires.ResultsThis evaluation revealed reductions in situational stressors, symptoms and mental health illnesses. Seventy-six per cent of participants had completed an Operational Tour, and 77% were exposed to a traumatic event during service. It was the negative impact of unresolved traumatic effects that influenced service-users to require support. Forty-nine per cent delayed seeking help, and 36% self-referred to the One Is Too Many programme which demonstrates the importance of this option. There were improvements in the participants’ social networking, social activities, club membership and having people to rely on. Only 4% of participants were women which reinforces the requirement to explore initiatives to engage with female veterans.ConclusionsTimely therapeutic and social prescribing interventions in a safe environment lowered depression, anxiety and the associated situational stressors leading to self-harming and may have reduced suicide. It presented another option to veterans and their families regarding where they can obtain support, care and therapeutic interventions. The programme provided a strong foundation for delivery organisations to forge lasting collaborative partnerships that can be extended to working with other authorities and institutes. The results highlight pathways for prevention and intervention strategies to inform policymakers, healthcare professionals and third-sector organisations.
The relative influence of landscape features on maternity roost and hibernaculum selection in temperate bats
Authors: Legros Jade , McGuire Liam P. , Elliott Kyle H. , Simard Anouk 
Published: March 2024

Many animal life-history stages center around residences (nests, roosts, etc.) where the availability of resources within an optimal range can affect fitness. Understanding factors influencing residence selection is fundamental for efficient management or recovery plans. Many bat species use permanent roosts during different periods of the year, and while most conservation plans aim to protect these roosts, the availability of suitable habitat near the roosts (e.g., foraging habitat) is also critical to consider. We evaluated the importance of landscape features at multiple scales surrounding seasonal bat roosts in two regions (north and south) of Québec (Canada), using data from participatory science and government databases. In the human-altered environment of south Québec, bats selected maternity roosts with high anthropogenic cover and water edge density at the 150 m and 2 km scales, respectively. Conversely, roost selection in north Québec, a forested area, could not be explained by any landscape features. In winter, fewer bats used hibernacula located in heavily human-modified landscapes—opposite to the trend observed with maternity roost selection. Our study demonstrates how considering landscape features at the appropriate temporal and spatial scales can promote more efficient conservation for bats.
The dynamic hadronization of charm quarks in heavy-ion collisions
Authors: Bierlich Christian , Gustafson Gösta , Lönnblad Leif , Shah Harsh 
Published: March 2024

AbstractThePythia8/Angantyr model for heavy ion collisions was recently updated with a mechanism forglobal colour reconnection. The colour reconnection model used is QCD colour algebra inspired and enhances baryon production due to the formation of string junctions. In this paper, we present updates to the junction formation and string fragmentation mechanisms, connected to heavy quark fragmentation. This allows for the simulation of heavy quark fragmentation, using junction formation, in heavy ion collisions. The framework is validated for proton collisions, and we show results for charm baryon production in proton-lead collisions.
Generalized time-bin quantum random number generator with uncharacterized devices
Authors: Tebyanian Hamid , Zahidy Mujtaba , Müller Ronny , Forchhammer Søren , Bacco Davide , Oxenløwe Leif. K. 
Published: March 2024

AbstractRandom number generators (RNG) based on quantum mechanics are captivating due to their security and unpredictability compared to conventional generators, such as pseudo-random number generators and hardware-random number generators. This work analyzes evolutions in the extractable amount of randomness with increasing the Hilbert space dimension, state preparation subspace, or measurement subspace in a class of semi-device-independent quantum-RNG, where bounding the states’ overlap is the core assumption, built on the prepare-and-measure scheme. We further discuss the effect of these factors on the complexity and draw a conclusion on the optimal scenario. We investigate the generic case of time-bin encoding scheme, define various input (state preparation) and outcome (measurement) subspaces, and discuss the optimal scenarios to obtain maximum entropy. Several input designs were experimentally tested and analyzed for their conceivable outcome arrangements. We evaluated their performance by considering the device’s imperfections, particularly the after-pulsing effect and dark counts of the detectors. Finally, we demonstrate that this approach can boost the system entropy, resulting in more extractable randomness.