bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precise genome editing underlines the distinct contributions of mutations in
ERG11
,
ERG3
,
MRR1
, and
TAC1
genes to antifungal resistance in
Candida parapsilosis
Authors: Hartuis Sophie , Ourliac-Garnier Isabelle , Robert Estelle , Albassier Marjorie , Duchesne Léa , Beaufils Clara , Kuhn Joséphine , Le Pape Patrice , Morio Florent 
Published: April 2024

ABSTRACT

Candida parapsilosis
has recently emerged as a major threat due to the worldwide emergence of fluconazole-resistant strains causing clonal outbreaks in hospitals and poses a therapeutic challenge due to the limited antifungal armamentarium. Here, we used precise genome editing using CRISPR-Cas9 to gain further insights into the contribution of mutations in
ERG11
,
ERG3
,
MRR1
, and
TAC1
genes and the influence of allelic dosage to antifungal resistance in
C. parapsilosis
. Seven of the most common amino acid substitutions previously reported in fluconazole-resistant clinical isolates (including Y132F in
ERG11
) were engineered in two fluconazole-susceptible
C. parapsilosis
lineages (ATCC 22019 and STZ5). Each mutant was then challenged
in vitro
against a large array of antifungals, with a focus on azoles. Any possible change in virulence was also assessed in a
Galleria mellonella
model. We successfully generated a total of 19 different mutants, using CRISPR-Cas9. Except for R398I (
ERG11
), all remaining amino acid substitutions conferred reduced susceptibility to fluconazole. However, the impact on fluconazole
in vitro
susceptibility varied greatly according to the engineered mutation, the stronger impact being noted for G583R acting as a gain-of-function mutation in
MRR1
. Cross-resistance with newer azoles, non-medical azoles, but also non-azole antifungals such as flucytosine, was occasionally noted. Posaconazole and isavuconazole remained the most active
in vitro
. Except for G583R, no fitness cost was associated with the acquisition of fluconazole resistance. We highlight the distinct contributions of amino acid substitutions in
ERG11
,
ERG3
,
MRR1
, and
TAC1
genes to antifungal resistance in
C. parapsilosis
.
Warming alters life-history traits and competition in a phage community
Authors: Greenrod Samuel T. E. , Cazares Daniel , Johnson Serena , Hector Tobias E. , Stevens Emily J. , MacLean R. Craig , King Kayla C. 
Published: April 2024

ABSTRACT

Host-parasite interactions are highly susceptible to changes in temperature due to mismatches in species thermal responses. In nature, parasites often exist in communities, and responses to temperature are expected to vary between host-parasite pairs. Temperature change thus has consequences for both host-parasite dynamics and parasite-parasite interactions. Here, we investigate the impact of warming (37°C, 40°C, and 42°C) on parasite life-history traits and competition using the opportunistic bacterial pathogen
Pseudomonas aeruginosa
(host) and a panel of three genetically diverse lytic bacteriophages (parasites). We show that phages vary in their responses to temperature. While 37°C and 40°C did not have a major effect on phage infectivity, infection by two phages was restricted at 42°C. This outcome was attributed to disruption of different phage life-history traits including host attachment and replication inside hosts. Furthermore, we show that temperature mediates competition between phages by altering their competitiveness. These results highlight phage trait variation across thermal regimes with the potential to drive community dynamics. Our results have important implications for eukaryotic viromes and the design of phage cocktail therapies.

IMPORTANCE
Mammalian hosts often elevate their body temperatures through fevers to restrict the growth of bacterial infections. However, the extent to which fever temperatures affect the communities of phages with the ability to parasitize those bacteria remains unclear. In this study, we investigate the impact of warming across a fever temperature range (37°C, 40°C, and 42°C) on phage life-history traits and competition using a bacterium (host) and bacteriophage (parasite) system. We show that phages vary in their responses to temperature due to disruption of different phage life-history traits. Furthermore, we show that temperature can alter phage competitiveness and shape phage-phage competition outcomes. These results suggest that fever temperatures have the potential to restrict phage infectivity and drive phage community dynamics. We discuss implications for the role of temperature in shaping host-parasite interactions more widely.
Polysaccharide intercellular adhesin and proper phospholipid composition are important for aggregation in
Tetragenococcus halophilus
SL10
Authors: Yanagihara Airi , Matsue Kouta , Kobayashi Kurumi , Wakinaka Takura , Mogi Yoshinobu , Watanabe Jun 
Published: April 2024

ABSTRACT

Aggregating strains of
Tetragenococcus halophilus
tend to be trapped during soy sauce mash-pressing process and are, therefore, critical for clear soy sauce production. However, the precise molecular mechanism involved in
T. halophilus
aggregation remains elusive. In previous studies, we isolated a number of aggregating strains, including
T. halophilus
AB4 and AL1, and showed that a cell surface proteinaceous aggregation factor is responsible for their aggregation phenotype. In the present study, we explored the role of polysaccharide intercellular adhesin (PIA) in aggregate formation in
T. halophilus
SL10, isolated from soy sauce. SL10 exhibited similar aggregation to AB4 and AL1 but formed a non-uniform precipitate with distinctive wrinkles at the bottom of the test tube, unlike AB4 and AL1. Insertion sequence mutations in each gene of the
ica
operon diminished aggregation and PIA production, highlighting the critical role of IcaADBC-mediated PIA production in
T. halophilus
aggregation. Furthermore, two non-aggregating cardiolipin synthase (
cls
) gene mutants with intact
ica
operon did not produce detectable PIA. Phospholipid composition analysis in
cls
mutants revealed a decrease in cardiolipin and an increase in phosphatidylglycerol levels, highlighting the association between phospholipid composition and PIA production. These findings provide evidence for the pivotal role of
cls
in PIA-mediated aggregation and lay the foundation for future studies to understand the intricate networks of the multiple aggregation factors governing microbial aggregation.

IMPORTANCE

Aggregation, commonly observed in various microbes, triggers biofilm formation in pathogenic variants and plays a beneficial role in efficient food production in those used for food production. Here, we showed that
Tetragenococcus halophilus
, a microorganism used in soy sauce fermentation, forms aggregates in a polysaccharide intercellular adhesin (PIA)-mediated manner. Additionally, we unveiled the relationship between phospholipid composition and PIA production. This study provides evidence for the presence of aggregation factors in
T. halophilus
other than the proteinaceous aggregation factor and suggests that further understanding of the coordinated action of these factors may improve clarified soy sauce production.
Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens
Authors: Osborn Lucas J. , Fissel John , Gomez Samantha , Mestas Javier , Flores-Vazquez Jessica , Lee Jaehyeon , Hakimjavadi Hesamedin , Costales Cristina , Dien Bard Jennifer 
Published: April 2024

ABSTRACT

The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive—requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively,
P
= 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively.

IMPORTANCE
To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.
Using augmented reality in molecular case studies to enhance biomolecular structure-function explorations in undergraduate classrooms
Authors: Vardar-Ulu Didem , Ragab Saif Eldeen , Agrawal Swati , Dutta Shuchismita 
Published: April 2024

ABSTRACT

Molecular case studies (MCSs) are open educational resources that use a storytelling approach to engage students in biomolecular structure-function explorations, at the interface of biology and chemistry. Although MCSs are developed for a particular target audience with specific learning goals, they are suitable for implementation in multiple disciplinary course contexts. Detailed teaching notes included in the case study help instructors plan and prepare for their implementation in diverse contexts. A newly developed MCS was simultaneously implemented in a biochemistry and a molecular parasitology course at two different institutions. Instructors participating in this cross-institutional and multidisciplinary implementation collaboratively identified the need for quick and effective ways to bridge the gap between the MCS authors’ vision and the implementing instructor’s interpretation of the case-related molecular structure-function discussions. Augmented reality (AR) is an interactive and engaging experience that has been used effectively in teaching molecular sciences. Its accessibility and ease-of-use with smart devices (e.g., phones and tablets) make it an attractive option for expediting and improving both instructor preparation and classroom implementation of MCSs. In this work, we report the incorporation of ready-to-use AR objects as checkpoints in the MCS. Interacting with these AR objects facilitated instructor preparation, reduced students’ cognitive load, and provided clear expectations for their learning. Based on our classroom observations, we propose that the incorporation of AR in MCSs can facilitate its successful implementation, improve the classroom experience for educators and students, and make MCSs more broadly accessible in diverse curricular settings.
Fluoride export is required for the competitive fitness of pathogenic microorganisms in dental biofilm models
Authors: Banerjee Aditya , Kang Chia-Yu , An Minjun , Koff B. Ben , Sunder Sham , Kumar Anuj , Tenuta Livia M. A. , Stockbridge Randy B. 
Published: April 2024

ABSTRACT

Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species
Streptococcus mutans
and
Candida albicans
extrude intracellular fluoride using a CLC
F
F
-
/H
+
antiporter and FEX fluoride channel, respectively, whereas oral commensal eubacteria, such as
Streptococcus gordonii,
export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using
S. mutans
with the genetic knockout of the CLC
F
transporter, exposure to low fluoride concentrations decreased
S. mutans
counts, synergistically reduced the populations of
C. albicans
, increased the relative proportion of oral commensal
S. gordonii
, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with
C. albicans
with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride but to a lesser degree. Imaging studies indicate that
S. mutans
is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time. Biochemical purification of the
S. mutans
CLC
F
transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms and that
S. mutans
is especially susceptible to fluoride toxicity.

IMPORTANCE

Dental caries is a globally prevalent condition that occurs when pathogenic species, including
Streptococcus mutans
and
Candida albicans
, outcompete beneficial species, such as
Streptococcus gordonii
, in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic species
S. mutans
and
C. albicans
to fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpaste and mouth rinses. This is a novel strategy to treat dental caries.
HPV oncogenes expressed from only one of multiple integrated HPV DNA copies drive clonal cell expansion in cervical cancer
Authors: Yu Lulu , Majerciak Vladimir , Lobanov Alexei , Mirza Sameer , Band Vimla , Liu Haibin , Cam Maggie , Hughes Stephen H. , Lowy Douglas R. , Zheng Zhi-Ming 
Published: April 2024

ABSTRACT

The integration of HPV DNA into human chromosomes plays a pivotal role in the onset of papillomavirus-related cancers. HPV DNA integration often occurs by linearizing the viral DNA in the E1/E2 region, resulting in the loss of a critical viral early polyadenylation signal (PAS), which is essential for the polyadenylation of the E6E7 bicistronic transcripts and for the expression of the viral E6 and E7 oncogenes. Here, we provide compelling evidence that, despite the presence of numerous integrated viral DNA copies, virus-host fusion transcripts originate from only a single integrated HPV DNA in HPV16 and HPV18 cervical cancers and cervical cancer-derived cell lines. The host genomic elements neighboring the integrated HPV DNA are critical for the efficient expression of the viral oncogenes that leads to clonal cell expansion. The fusion RNAs that are produced use a host RNA polyadenylation signal downstream of the integration site, and almost all involve splicing to host sequences. In cell culture, siRNAs specifically targeting the host portion of the virus-host fusion transcripts effectively silenced viral E6 and E7 expression. This, in turn, inhibited cell growth and promoted cell senescence in HPV16+ CaSki and HPV18+ HeLa cells. Showing that HPV E6 and E7 expression from a single integration site is instrumental in clonal cell expansion sheds new light on the mechanisms of HPV-induced carcinogenesis and could be used for the development of precision medicine tailored to combat HPV-related malignancies.

IMPORTANCE
Persistent oncogenic HPV infections lead to viral DNA integration into the human genome and the development of cervical, anogenital, and oropharyngeal cancers. The expression of the viral E6 and E7 oncogenes plays a key role in cell transformation and tumorigenesis. However, how E6 and E7 could be expressed from the integrated viral DNA which often lacks a viral polyadenylation signal in the cancer cells remains unknown. By analyzing the integrated HPV DNA sites and expressed HPV RNAs in cervical cancer tissues and cell lines, we show that HPV oncogenes are expressed from only one of multiple chromosomal HPV DNA integrated copies. A host polyadenylation signal downstream of the integrated viral DNA is used for polyadenylation and stabilization of the virus-host chimeric RNAs, making the oncogenic transcripts targetable by siRNAs. This observation provides further understanding of the tumorigenic mechanism of HPV integration and suggests possible therapeutic strategies for the development of precision medicine for HPV cancers.
Whole-genome sequence and annotation of
Salmonella enterica
subsp.
enterica
strain QazSL-4
Authors: Barmak Sabyrkhan M. , Mendenhall Ian H. , Sinyavskiy Yuriy A. , Berdygaliev Aidar B. , Sharmanov Turegeldy Sh. , Sultankulova Gulmira T. , Tuigunov Dilyar N. , Zholdybayeva Elena V. 
Published: April 2024

ABSTRACT

Here, we present the whole-genome sequence of
Salmonella enterica
subsp.
enterica
strain QazSL-4 isolated from a chicken fillet in 2018, Almaty, Kazakhstan. The genome obtained using Illumina MiSeq technology consists of 49 contigs with a total length of 4,711,816 bp with a GC content of 52.1%.
Supplemental Material: Alkenone-derived estimates of Cretaceous <i>p</i>CO<sub>2</sub>
Authors: Si Weimin , al. et 
Published: April 2024

<div>Sample chronology, detailed analytical and <i>p</i>CO<sub>2</sub> estimate methods, fossil taxon descriptions, supporting data tables, and supplementary figures showing alkenone distributions and mass spectra. </div>
Missing in action: a scoping review of gender as the overlooked component
in decolonial discourses
Authors: Nassiri-Ansari Tiffany , Rhule Emma Louise Margaret 
Published: April 2024

Introduction
Race and gender were intimately intertwined aspects of the colonial
project, used as key categories of hierarchisation within both colonial
and modern societies. As such, true decolonisation is only possible when
both are addressed equally; failure to address the colonial root causes
of gender-based inequalities will allow for the perpetuation of
racialised notions of gender to persist across the global health
ecosystem. However, the authors note with concern the relative
sidelining of gender within the decolonising global health discourse,
especially as it navigates the critical transition from rhetoric to
action.

Methods
A scoping review was conducted to locate where gender does, or does
not, appear within the decolonising global health literature. The
authors reviewed the decolonising global health literature available on
Scopus and PubMed online databases to identify peer-reviewed papers with
the search terms "(decoloni* or de-coloni*) OR (neocolonial or
neo-colonial) AND ‘global health’" in their title, abstract or keywords
published by December 2022.

Results
Out of 167 papers on decolonising global health, only 53 (32%) had
any reference to gender and only 26 (16%) explicitly engaged with gender
as it intersects with (de)coloniality. Four key themes emerged from
these 26 papers: an examination of coloniality’s racialised and gendered
nature; how this shaped and continues to shape hierarchies of knowledge;
how these intertwining forces drive gendered impacts on health
programmes and policies; and how a decolonial gender analysis can inform
action for change.

Conclusion
Historical legacies of colonisation continue to shape contemporary
global health practice. The authors call for the integration of a
decolonial gender analysis in actions and initiatives that aim to
decolonise global health, as well as within allied movements which seek
to confront the root causes of power asymmetries and
inequities.
Preconception counselling in women of reproductive age attending cardiology clinics in Scotland
Authors: Osmanska Joanna , Jackson Alice M , Simpson Joanne , Adamson Carly , Doherty Daniel , Mamet Helene , Moir Lynsey , Walker Niki L , Hogg Duncan , Simpson Maggie 
Published: April 2024

BackgroundGuidelines for the management of cardiovascular disease (CVD) recommend preconception risk stratification and counselling in all women of childbearing age. We assessed the provision of preconception counselling (PCC) among women of reproductive age attending general cardiology outpatient clinics over a 12-month period in two large health boards in Scotland.Methods and resultsElectronic health records were reviewed and data on patient demographics, cardiac diagnoses, medication use and the content of documented discussions regarding PCC were recorded. Women were classified according to the modified WHO (mWHO) risk stratification system. Among 1650 women with a cardiac diagnosis included (1 January 2016–31 December 2016), the mean age was 32.7±8.6 years, and 1574 (95.4%) attended a consultant-led clinic. A quarter (402, 24.4%) were prescribed at least one potentially fetotoxic cardiovascular medication. PCC was documented in 10.3% of women who were not pregnant or were unable to conceive at the time of review (159/1548). The distribution of mWHO classification, and proportion of patients within each mWHO category who received any form of PCC, was 15.0% and 6.0% in mWHO class I, 20.2% and 8.7% in mWHO class II, 22.6% and 10.6% in mWHO class II–III, 9.5% and 15.7% in mWHO class III and 3.9% and 19.7% in mWHO class IV.ConclusionPCC is documented infrequently in women of reproductive age with CVD in the general outpatient setting. Education relating to the risks of cardiac disease in pregnancy for clinicians and patients, and tools to support healthcare providers in delivering PCC, is important.
Dielectric and hydrogen bonding studies of butyronitrile with 1,4-dioxane using a time-domain reflectometry
Authors: Dongre D.G. , Deshmukh A.R. , Garad N.P. , Gubre A.G. , Saknure S.H. , Kumbharkhane A.C. 
Published: April 2024

Using time-domain reflectometry (TDR), the complex permittivity of binary mixture of butyronitrile (BTN) and 1,4-dioxane (1,4-DX) at various temperatures and solvent proportions was determined over the frequency range of 10 MHz to 30 GHz. The complex permittivity spectra (CPS) have been fitted to the Havrilik–Negami equation. The relaxation time (τ) and static dielectric constant (ε0) have been calculated for each concentration using the least squares fit method. The nonlinear behavior of dielectric parameters suggests a change in the molecular size and intermolecular bonding of BTN–1,4-DX mixtures. Theoretical static dielectric constants (ε0) have been determined using hydrogen bonded model suggested by Luzar for all solvent proportions and compared with experimental values obtained from TDR.