bluuebunny/crossref_metadata_2025_split huggingface dataset:
ARR1 and ARR12 modulate arsenite toxicity responses in Arabidopsis roots by transcriptionally controlling the actions of NIP1;1 and NIP6;1
Authors: Zhang Ping , Liu Fei , Abdelrahman Mostafa , Song Qianqian , Wu Fei , Li Ruishan , Wu Min , Herrera‐Estrella Luis , Tran Lam‐Son Phan , Xu Jin 
Published: October 2024

SUMMARYCytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Subsequently, we revealed that the cytokinin signaling members ARR1 and ARR12, the type‐B ARABIDOPSIS RESPONSE REGULATORs, participate in cytokinin signaling‐mediated As(III) responses in plants as negative regulators. A comprehensive transcriptome analysis of the arr1 and arr12 single and arr1,12 double mutants was then performed to decipher the cytokinin signaling‐mediated mechanisms underlying plant As(III) stress adaptation. Results revealed important roles for ARR1 and ARR12 in ion transport, nutrient responses, and secondary metabolite accumulation. Furthermore, using hierarchical clustering and regulatory network analyses, we identified two NODULIN 26‐LIKE INTRINSIC PROTEIN (NIP)‐encoding genes, NIP1;1 and NIP6;1, potentially involved in ARR1/12‐mediated As(III) uptake and transport in Arabidopsis. By analyzing various combinations of arr and nip mutants, including high‐order triple and quadruple mutants, we demonstrated that ARR1 and ARR12 redundantly function as negative regulators of As(III) tolerance by acting upstream of NIP1;1 and NIP6;1 to modulate their function in arsenic accumulation. ChIP–qPCR, EMSA, and transient dual‐LUC reporter assays revealed that ARR1 and ARR12 transcriptionally activate the expression of NIP1;1 and NIP6;1 by directly binding to their promoters and upregulating their expression, leading to increased arsenic accumulation under As(III) stress. These findings collectively provide insights into cytokinin signaling‐mediated plant adaptation to excessive As(III), contributing to the development of crops with low arsenic accumulation.
Effectiveness of early childhood education interventions to improve complementary feeding practices in children 4 to 36 months of age: a systematic review protocol
Authors: Cardoso Paloma Sodré , Mori Bruno , Freitas Ronilson Ferreira , Lima Regismeire Viana , Tavares Bruno Mendes , Barcellos Jose Fernando Marques , Lopes Carla Vanessa Alves , Souza Celsa da Silva Moura 
Published: October 2024

Objective:
This review will analyze the effectiveness of early childhood education interventions to improve complementary feeding practices in children aged 4 to 36 months.

Introduction:
Healthy eating habits, which start with food introduction, can influence children’s growth and development. Educational actions carried out at school for children who are beginning to eat, involving families and school staff who attend daycare centers, can serve as strategies to improve complementary feeding practices.

Inclusion criteria:
The review will consider randomized clinical trials, cluster-randomized clinical trials, and controlled clinical trials that evaluate the effectiveness of early childhood education interventions involving children aged 4 to 36 months, their families, or school staff to improve complementary feeding. In their absence, observational cohort, case-control, and cross-sectional studies may be considered.

Methods:
This review will be conducted in line with the JBI methodology for systematic reviews of effectiveness. The search for relevant studies will be conducted in PubMed, Embase (Ovid), BIREME, Scopus, the Cochrane Library (Cochrane Central Register of Controlled Trials CENTRAL and Cochrane Database of Systematic Reviews), CINAHL (EBSCOhost), and the ProQuest Databases (ProQuest Central). No date or language limitations will be applied. Two independent reviewers will select studies by screening titles, abstracts, and keywords against the inclusion criteria. This will be followed by full-text screening. Two independent reviewers will then evaluate the quality of the sources and perform data extraction. GRADEpro will be used to assess the certainty in the findings, which will be reported in the systematic review and, if possible, grouped in a meta-analysis.

Review registration:
PROSPERO CRD42022384704
Associations of Working From Home Frequency With Accelerometer-Measured Physical Activity and Sedentary Behavior in Japanese White-Collar Workers: A Cross-Sectional Analysis of the Meiji Yasuda LifeStyle Study
Authors: Kitano Naruki , Fujii Yuya , Wada Aya , Kawakami Ryoko , Yoshiba Kaori , Yamaguchi Daisuke , Kai Yuko , Arao Takashi 
Published: October 2024

Background: The association of working from home (WFH) with physical activity (PA) and sedentary behavior (SB) has been explored; however, this association during periods without stringent measures to combat coronavirus disease 2019 is undercharacterized. Particularly, few studies have evaluated the potential effect modification on its associations. Therefore, this study aimed to investigate the associations of WFH frequency with accelerometer-measured PA and SB, along with its effect modifiers, among Japanese white-collar workers during the later pandemic period. Methods: A cross-sectional study involving 1133 white-collar workers residing in the Tokyo metropolitan area was conducted between April 2022 and March 2023. WFH frequency was evaluated through a self-report questionnaire, while SB and PA during weekdays were measured using a triaxial accelerometer. Linear regression models adjusting for potential confounders were used to examine the association of WFH frequency with PA and SB. Results: Regardless of activity intensity, individuals who worked at home, even for 1 to 2 days per week, demonstrated lower levels of PA and higher levels of SB as compared with those who did not (P < .05). For example, difference between never and ≥5 days per week WFH was approximately 70 minutes/day for total PA and about 4000 steps/day for step counts. Associations between WFH and decreased PA were more pronounced in workers who were older, female, less educated, in sales and service work, nonregular staff, and precontemplating changes in exercise and eating habits. Conclusions: We report that WFH was associated with decreased PA and increased SB in Japanese white-collar workers with pronounced associated in several subgroups.
Variability of macrolide-resistant profile in
Mycobacterium avium
complex pulmonary disease
Authors: Fukushima Kiyoharu , Matsumoto Yuki , Abe Yuko , Hashimoto Kazuki , Motooka Daisuke , Kitada Seigo , Saito Haruko , Komukai Sho , Fukui Eriko , Niitsu Takayuki , Nabeshima Hiroshi , Nagahama Yasuharu , Yamauchi June , Nitta Tadayoshi , Nii Takuro , Matsuki Takanori , Tsujino Kazuyuki , Miki Keisuke , Shintani Yasushi , Kumanogoh Atsushi , Akira Shizuo , Nakamura Shota , Kida Hiroshi 
Published: October 2024

ABSTRACT

This single-center retrospective study aimed to analyze the variability of macrolide resistance (MR) in 68 patients with
Mycobacterium avium
complex pulmonary disease. Among 25 patients treated without macrolides, 13 (52%) reverted to macrolide-susceptible (MS) profiles. Only one (2%) of 43 patients who continued macrolide treatment showed this change. We compared 30 MR isolates with recent specimens. Among them, seven shifted to MS (five attributed to clonally related strains; two resulting from reinfection or polyclonal infection).
Hybrid paper/PDMS microfluidic device integrated with RNA extraction and recombinase polymerase amplification for detection of norovirus in foods
Authors: Lu Yuxiao , Hua Marti Z. , Luo Yuhang , Lu Xiaonan , Liu Qian 
Published: October 2024

ABSTRACT

Human norovirus (HuNoV) is recognized as the leading causative agent of foodborne outbreaks of epidemic gastroenteritis. Consequently, there is a high demand for developing point-of-care testing for HuNoV. We developed an origami microfluidic device that facilitates rapid detection of murine norovirus 1 (MNV-1), a surrogate for HuNoV, encompassing the entire process from sample preparation to result visualization. This process includes RNA absorption
via
a paper strip, RNA amplification using recombinase polymerase amplification (RPA), and a lateral flow assay for signal readout. The on-chip detection of MNV-1 was completed within 35 min, demonstrating 100% specificity to MNV-1 in our settings. The detection limit of this microfluidic device for MNV-1 was 200 PFU/mL, comparable to the in-tube RPA reaction. It also successfully detected MNV-1 in lettuce and raspberries at concentrations of 170 PFU/g and 230 PFU/g, respectively, without requiring extra concentration steps. This device demonstrates high compatibility with isothermal nucleic acid amplification and holds significant potential for detecting foodborne viruses in agri-food products in remote and resource-limited settings.

IMPORTANCE
HuNoV belongs to the family of Caliciviridae and is a leading cause of acute gastroenteritis that can be transmitted through contaminated foods. HuNoV causes around one out of five cases of acute gastroenteritis that lead to diarrhea and vomiting, placing a substantial burden on the healthcare system worldwide. HuNoV outbreaks can occur when food is contaminated at the source (e.g., wild mussels exposed to polluted water), on farms (e.g., during crop cultivation, harvesting, or livestock handling), during packaging, or at catered events. The research outcomes of this study expand the approaches of HuNoV testing, adding value to the framework for routine testing of food products. This microfluidic device can facilitate the monitoring of HuNoV outbreaks, reduce the economic loss of the agri-food industry, and enhance food safety.
Complete genome sequences of three
Pseudomonas aeruginosa
jumbo bacteriophages discovered in Kenya
Authors: Musila Lillian , Bird Jordan T. , Margulieux Katie R. , Kigen Collins , Mzhavia Nino , Filippov Andrey A. , Nikolich Mikeljon P. 
Published: October 2024

ABSTRACT

The genomes of three
Pseudomonas aeruginosa Phikzvirus
bacteriophages isolated in Kenya are described. The genomes of phages vB_PaePAO1-KEN19, vB_Pae3705-KEN49, and vB_Pae10145-KEN51, respectively, had lengths of 278,921, 280,231, and 280,173 bp, with 36.93%, 36.84%, and 36.86% GC content, containing 419, 417, and 417 coding sequences (including seven tRNAs in each genome).
Antibacterial effectors in
Dictyostelium discoideum
: specific activity against different bacterial species
Authors: Munoz-Ruiz Raphael , Lamrabet Otmane , Jauslin Tania , Guilhen Cyril , Bourbon Alixia , Cosson Pierre 
Published: October 2024

ABSTRACT

Dictyostelium discoideum
is a phagocytic amoeba continuously eating, killing, and digesting bacteria. Previous studies have detected in
D. discoideum
cell extracts a bacteriolytic activity effective against
Klebsiella pneumoniae
bacteria. In this study, we characterized bacteriolytic activities found in
D. discoideum
cell extracts against five different bacteria (
K. pneumoniae
,
Escherichia coli
,
Pseudomonas aeruginosa
,
Staphylococcus aureus
, and
Bacillus subtilis
). We first analyzed the bacteriolytic activity against these five bacteria in parallel over a range of pH values. We then measured the remaining bacteriolytic activity in
D. discoideum kil1
and
modA
knockout mutants. We also performed partial fractionation of
D. discoideum
extracts and assessed activity against different bacteria. Together our results indicate that optimal bacteriolytic activity against different bacteria results from the action of different effectors. Proteomic analysis allowed us to propose a list of potential bacteriolytic effectors.

IMPORTANCE

Many antibacterial effectors have been characterized over the past decades, and their biological importance, mode of action, and specificity are often still under study. Here we characterized
in vitro
bacteriolytic activity in
D. discoideum
extracts against five species of Gram-negative and Gram-positive bacteria. Our results reveal that optimal lysis of different bacteria mobilizes different effectors. Proteomic analysis generated a list of potential bacteriolytic effectors. This work opens the way for future analysis of the role of individual effectors in living
D. discoideum
cells.
Comparison of the mechanism of antimicrobial action of the gold(I) compound auranofin in Gram-positive and Gram-negative bacteria
Authors: Quadros Barsé Laísa , Ulfig Agnes , Varatnitskaya Marharyta , Vázquez-Hernández Melissa , Yoo Jihyun , Imann Astrid M. , Lupilov Natalie , Fischer Marina , Becker Katja , Bandow Julia E. , Leichert Lars I. 
Published: October 2024

ABSTRACT

While highly effective at killing Gram-positive bacteria, auranofin lacks significant activity against Gram-negative species for reasons that largely remain unclear. Here, we aimed to elucidate the molecular mechanisms underlying the low susceptibility of the Gram-negative model organism
Escherichia coli
to auranofin when compared to the Gram-positive model organism
Bacillus subtilis
. The proteome response of
E. coli
exposed to auranofin suggests a combination of inactivation of thiol-containing enzymes and the induction of systemic oxidative stress. Susceptibility tests in
E. coli
mutants lacking proteins upregulated upon auranofin treatment suggested that none of them are directly involved in
E. coli
’s high tolerance to auranofin.
E. coli
cells lacking the efflux pump component TolC were more sensitive to auranofin treatment, but not to an extent that would fully explain the observed difference in susceptibility of Gram-positive and Gram-negative organisms. We thus tested whether
E. coli
’s thioredoxin reductase (TrxB) is inherently less sensitive to auranofin than TrxB from
B. subtilis
, which was not the case. However,
E. coli
strains lacking the low-molecular-weight thiol glutathione, but not glutathione reductase, showed a high susceptibility to auranofin. Bacterial cells expressing the genetically encoded redox probe roGFP2 allowed us to observe the oxidation of cellular protein thiols
in situ
. Based on our findings, we hypothesize that auranofin leads to a global disturbance in the cellular thiol redox homeostasis in bacteria, but Gram-negative bacteria are inherently more resistant due to the presence of drug export systems and high cellular concentrations of glutathione.

IMPORTANCE

Auranofin is an FDA-approved drug for the treatment of rheumatoid arthritis. However, it has also high antibacterial activity, in particular against Gram-positive organisms. In the current antibiotics crisis, this would make it an ideal candidate for drug repurposing. However, its much lower activity against Gram-negative organisms prevents its broad-spectrum application. Here we show that, on the level of the presumed target, there is no difference in susceptibility between Gram-negative and Gram-positive species: thioredoxin reductases from both
Escherichia coli
and
Bacillus subtilis
are equally inhibited by auranofin. In both species, auranofin treatment leads to oxidative protein modification on a systemic level, as monitored by proteomics and the genetically encoded redox probe roGFP2. The single largest contributor to
E. coli
’s relative resistance to auranofin seems to be the low-molecular-weight thiol glutathione, which is absent in
B. subtilis
and other Gram-positive species.
Genomic characterization and clinical evaluation of prosthetic joint infections caused by
Cutibacterium acnes
Authors: Liew-Littorin C. , Davidsson S. , Nilsdotter-Augustinsson Å. , Hellmark B. , Brüggemann H. , Söderquist B. 
Published: October 2024

ABSTRACT

Cutibacterium acnes
is a major skin commensal that may act as an opportunistic pathogen. It is difficult to interpret findings of
C. acnes
in tissue cultures obtained during arthroplasty revision surgery, since they may represent true infection or contamination. This study investigated whether
C. acnes
obtained from prosthetic joint infections (PJIs) were related and shared common genomic traits that might correlate with clinical courses and patient outcomes.
C. acnes
isolates from revision surgery of patients with PJIs of the hip, shoulder, and knee were characterized using molecular methods to determine the sequence type (ST) and the presence of possible virulence determinants (Christie–Atkins–Munch-Peterson factors, dermatan sulfate-binding adhesion 1, hyaluronidase lyase, and linear plasmid). A standardized review of the patients’ medical charts was performed. The study included 37 patients with
C. acnes
culture-positive tissue samples where multiple isolates of
C. acnes
belonged to the same ST. Most of the isolates belonged to phylotype IA
1
. Phylogenetic analysis of virulence determinants revealed no shared pattern among PJI isolates. Seven patients had a polymicrobial infection. Exchange revision was performed in 70% of the patients, and >50% of all patients received antibiotic treatment for ≥3 months. Failure was noted in seven patients. No specific ST or any identifiable unique feature among virulence determinants were found among
C. acnes
isolated from PJIs of hips and shoulders. The majority of patients had low inflammatory markers and were treated successfully, even polymicrobial infections. However, failure was more common among shoulder infections compared with hip infections.

IMPORTANCE

Prosthetic joint infection (PJI) is a rare complication after arthroplasty surgery. The infection seldom resolves without a combination of both surgical and antibiotic treatment and can cause significant suffering among affected patients.
Cutibacterium acnes
is a common skin bacterium that is most often found in shoulder PJIs but can also infect other prostheses. In this study, we conducted a review of patients with previously verified PJIs involving
C. acnes
in hip or shoulder prostheses, along with a genomic analysis of the bacteria causing the infections. The majority of patients had successful outcomes. We did not identify any specific phylogenetic lineage or specific molecular signature of virulence factors among these PJI-associated
C. acnes
isolates that seemed to be associated with increased potential to cause infection among this species. This indicates that
C. acnes
isolated from PJIs originates from the patients’ own skin microbiome and is inoculated during the arthroplasty surgery.
Characterization of
Pseudomonas aeruginosa
from subjects with diffuse panbronchiolitis
Authors: Met Charles M. , Hofstaedter Casey E. , O'Keefe Ian P. , Yang Hyojik , Moustafa Dina A. , Sherman Matthew E. , Doi Yohei , Rasko David A. , Sweet Charles R. , Goldberg Joanna B. , Ernst Robert K. 
Published: October 2024

ABSTRACT

Diffuse panbronchiolitis (DPB) is a rare, idiopathic inflammatory disease primarily diagnosed in East Asian populations. DPB is characterized by diffuse pulmonary lesions, inflammation of the respiratory bronchioles, and bacterial infections of the airway. Historically, sputum cultures reveal
Pseudomonas aeruginosa
in 22% of DPB patients, increasing to 60% after 4 years from disease onset. Although DPB patients have a known susceptibility to respiratory
P. aeruginosa
infections, as is observed in other chronic lung diseases such as cystic fibrosis (CF), the characterization of DPB
P. aeruginosa
strains is limited. In this study, we characterized 24 strains obtained from a cohort of DPB patients for traits previously associated with virulence, including growth, motility, antibiotic susceptibility, lipopolysaccharide structure, and genomic diversity. Our cohort of DPB
P. aeruginosa
strains exhibits considerable genomic variability when compared with isolates from people with cystic fibrosis chronically colonized with
P. aeruginosa
and acute
P. aeruginosa
infection isolates. Similar to CF, DPB
P. aeruginosa
strains produce a diverse array of modified lipid A structures. Antibiotic susceptibility testing revealed increased resistance to erythromycin, a representative agent of the macrolide antibiotics used to manage DPB patients. Differences in the O-antigen type among
P. aeruginosa
strains collected from these different backgrounds were also observed. Ultimately, the characterization of DPB
P. aeruginosa
strains highlights several unique qualities of
P. aeruginosa
strains collected from chronically diseased airways, underscoring the challenges in treating DPB, CF, and other obstructive respiratory disease patients with
P. aeruginosa
infections.

IMPORTANCE

Diffuse panbronchiolitis (DPB), a chronic lung disease characterized by persistent
P. aeruginosa
infection, serves as an informative comparator to more common chronic lung diseases, such as cystic fibrosis (CF). This study aimed to better address the interplay between
P. aeruginosa
and chronically compromised airway environments through the examination of DPB
P. aeruginosa
strains, as existing literature regarding DPB is limited to case reports, case series, and clinical treatment guidelines. The evaluation of these features in the context of DPB, in tandem with prevailing knowledge of
P. aeruginosa
strains collected from more common chronic lung diseases (e.g., CF), can aid in the development of more effective strategies to combat respiratory
P. aeruginosa
infections in patients with chronic lung diseases.
Transcriptomics identify the triggering of citrate export as the key event caused by manganese deficiency in
Aspergillus niger
Authors: Fekete Erzsébet , Bíró Vivien , Márton Alexandra , Bakondi-Kovács István , Sándor Erzsébet , Kovács Béla , Geoffrion Nicholas , Tsang Adrian , Kubicek Christian P. , Karaffa Levente 
Published: October 2024

ABSTRACT

For over a century, the filamentous Ascomycete fungus
Aspergillus niger
has played a pivotal role in the industrial production of citric acid. A critical fermentation parameter that sustains high-yield citric acid accumulation is the suboptimal concentration of manganese(II) ions in the culture broth at the early stages of the process. However, the requirement for this deficiency has not been investigated on a functional genomics level. In this study, we compared the transcriptome of the citric acid hyper-producer
A. niger
NRRL2270 strain grown under citric acid-producing conditions in 6-L scale bioreactors at Mn
2+
ion-deficient (5 ppb) and Mn
2+
ion-sufficient (100 ppb) conditions at three early time points of cultivation. Of the 11,846 genes in the genome, 963 genes (8.1% of the total) were identified as significantly differentially expressed under these conditions. Disproportionately high number of differentially regulated genes encode predicted extracellular and membrane proteins. The most abundant gene group that was upregulated in Mn
2+
ion deficiency condition encodes enzymes acting on polysaccharides. In contrast, six clusters of genes encoding secondary metabolites showed downregulation under manganese deficiency. Mn
2+
deficiency also triggers upregulation of the
cexA
gene, which encodes the citrate exporter. We provide functional evidence that the upregulation of
cexA
is caused by the intracellular accumulation of citrate or acetyl-CoA and is a major factor in triggering citrate overflow.

IMPORTANCE

Citric acid is produced on industrial scale by batch fermentation of the filamentous fungus
Aspergillus niger
. High-yield citric acid production requires a low (<5 ppb) manganese(II) ion concentration in the culture broth. However, the requirement for this deficiency has not been investigated on a functional genomics level. Here, we compared the transcriptome of a citric acid hyper-producer
A. niger
strain grown under citric acid-producing conditions in 6-L scale bioreactors at Mn
2+
ion-deficient (5 ppb) and Mn
2+
ion-sufficient (100 ppb) conditions at three early time points of cultivation. We observed that Mn
2+
deficiency triggers an upregulation of the citrate exporter gene cexA and provides functional evidence that this event is responsible for citrate overflow. In addition to the industrial relevance, this is the first study that examined the role of Mn
2+
ion deficiency in a heterotrophic eukaryotic cell on a genome-wide scale.