bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence of
Anaerotignum
sp. strain MB30-C6, isolated from sewage sludge of the wastewater treatment plant at a steel factory
Authors: Feng Fu , Wu Chih-Hung , Shih Chao-Jen , Wu Yen-Chi , Lai Shu-Jung , You Yi-Ting , Chen Sheng-Chung 
Published: March 2024

ABSTRACT

We report the complete genome sequence of
Anaerotignum
sp. strain MB30-C6, which was isolated from the dehydrated sludge collected at the wastewater treatment plant of Sanming Steel Co. Ltd. in Fujian, China. The resulting genome of strain MB30-C6 is a single contig of 3,104,838 bp with 39.49% GC content.
Glycerol metabolism impacts biofilm phenotypes and virulence in
Pseudomonas aeruginosa
via the Entner-Doudoroff pathway
Authors: Pan Somalisa , Underhill Simon A. M. , Hamm Christopher W. , Stover Mylissa A. , Butler Daxton R. , Shults Crystal A. , Manjarrez Jacob R. , Cabeen Matthew T. 
Published: March 2024

ABSTRACT

Pseudomonas aeruginosa
is a ubiquitous bacterium and a notorious opportunistic pathogen that forms biofilm structures in response to many environmental cues. Biofilm formation includes attachment to surfaces and the production of the exopolysaccharide Pel, which is present in both the PAO1 and PA14 laboratory strains of
P. aeruginosa
. Biofilms help protect bacterial cells from host defenses and antibiotics and abet infection. The carbon source used by the cells also influences biofilm, but these effects have not been deeply studied. We show here that glycerol, which can be liberated from host surfactants during infection, encourages surface attachment and magnifies colony morphology differences. We find that glycerol kinase is important but not essential for glycerol utilization and relatively unimportant for biofilm behaviors. Among downstream enzymes predicted to take part in glycerol utilization, Edd stood out as being important for glycerol utilization and for enhanced biofilm phenotypes in the presence of glycerol. Thus, gluconeogenesis and catabolism of anabolically produced glucose appear to impact not only the utilization of glycerol but also glycerol-stimulated biofilm phenotypes. Finally, waxworm moth larvae and nematode infection models reveal that interruption of the Entner-Doudoroff pathway, but not abrogation of glycerol phosphorylation, unexpectedly increases
P. aeruginosa
lethality in both acute and chronic infections, even while stimulating a stronger immune response by
Caenorhabditis elegans
.

IMPORTANCE

Pseudomonas aeruginosa
, the ubiquitous environmental bacterium and human pathogen, forms multicellular communities known as biofilms in response to various stimuli. We find that glycerol, a common carbon source that bacteria can use for energy and biosynthesis, encourages biofilm behaviors such as surface attachment and colony wrinkling by
P. aeruginosa
. Glycerol can be derived from surfactants that are present in the human lungs, a common infection site. Glycerol-stimulated biofilm phenotypes do not depend on phosphorylation of glycerol but are surprisingly impacted by a glucose breakdown pathway, suggesting that it is glycerol utilization, and not its mere presence or cellular import, that stimulates biofilm phenotypes. Moreover, the same mutations that block glycerol-stimulated biofilm phenotypes also impact
P. aeruginosa
virulence in both acute and chronic animal models. Notably, a glucose-breakdown mutant (Δ
edd
) counteracts biofilm phenotypes but shows enhanced virulence and stimulates a stronger immune response in
Caenorhabditis elegans
.
Fatty acids of
Helicobacter pylori
lipoproteins CagT and Lpp20
Authors: McClain Mark S. , Boeglin William E. , Algood Holly M. Scott , Brash Alan R. 
Published: March 2024

ABSTRACT

Bacterial lipoproteins are post-translationally modified by the addition of acyl chains that anchor the protein to bacterial membranes. This modification includes two ester-linked and one amide-linked acyl chain on lipoproteins from Gram-negative bacteria.
Helicobacter pylori
lipoproteins have important functions in pathogenesis (including delivering the CagA oncoprotein to mammalian cells) and are recognized by host innate and adaptive immune systems. The number and variety of acyl chains on lipoproteins impact the innate immune response through Toll-like receptor 2. The acyl chains added to lipoproteins are derived from membrane phospholipids.
H. pylori
membrane phospholipids have previously been shown to consist primarily of C14:0 and C19:0 cyclopropane-containing acyl chains. However, the acyl composition of
H. pylori
lipoproteins has not been determined. In this study, we characterized the acyl composition of two representative
H. pylori
lipoproteins, Lpp20 and CagT. Fatty acid methyl esters were prepared from both purified lipoproteins and analyzed by gas chromatography-mass spectrometry. For comparison, we also analyzed
H. pylori
phospholipids. Consistent with previous studies, we observed that the
H. pylori
phospholipids contain primarily C14:0 and C19:0 cyclopropane-containing fatty acids. In contrast, both the ester-linked and amide-linked fatty acids found in
H. pylori
lipoproteins were observed to be almost exclusively C16:0 and C18:0. A discrepancy between the acyl composition of membrane phospholipids and lipoproteins as reported here for
H. pylori
has been previously reported in other bacteria including
Borrelia
and
Brucella
. We discuss possible mechanisms.

IMPORTANCE

Colonization of the stomach by
Helicobacter pylori
is an important risk factor in the development of gastric cancer, the third leading cause of cancer-related death worldwide.
H. pylori
persists in the stomach despite an immune response against the bacteria. Recognition of lipoproteins by TLR2 contributes to the innate immune response to
H. pylori
. However, the role of
H. pylori
lipoproteins in bacterial persistence is poorly understood. As the host response to lipoproteins depends on the acyl chain content, defining the acyl composition of
H. pylori
lipoproteins is an important step in characterizing how lipoproteins contribute to persistence.
Genetic and chemical control of tuberculostearic acid production in
Mycobacterium avium
subspecies
paratuberculosis
Authors: Bannantine John P. , Duffy Shannon C. , Colombatti Olivieri María A. , Behr Marcel A. , Biet Franck , Price Neil P. J. 
Published: March 2024

ABSTRACT

Tuberculostearic acid (TBSA) is a fatty acid unique to mycobacteria and some corynebacteria and has been studied due to its diagnostic value, biofuel properties, and role in membrane dynamics. In this study, we demonstrate that TBSA production can be abrogated either by addition of pivalic acid to mycobacterial growth cultures or by a
bfaA
gene knockout encoding a flavin adenine dinucleotide (FAD)-binding oxidoreductase.
Mycobacterium avium
subspecies
paratuberculosis
(
Map
) growth and TBSA production were inhibited in 0.5-mg/mL pivalic acid-supplemented cultures, but higher concentrations were needed to have a similar effect in other mycobacteria, including
Mycobacterium smegmatis
. While
Map
C-type strains, isolated from cattle and other ruminants, will produce TBSA in the absence of pivalic acid, the S-type
Map
strains, typically isolated from sheep, do not produce TBSA in any condition. A SAM-dependent methyltransferase encoded by
bfaB
and FAD-binding oxidoreductase are both required in the two-step biosynthesis of TBSA. However, S-type strains contain a single-nucleotide polymorphism in the
bfaA
gene, rendering the oxidoreductase enzyme vestigial. This results in the production of an intermediate, termed 10-methylene stearate, which is detected only in S-type strains. Fatty acid methyl ester analysis of a C-type
Map bfaA
knockout revealed the loss of TBSA production, but the intermediate was present, similar to the S-type strains. Collectively, these results demonstrate the subtle biochemical differences between two primary genetic lineages of
Map
and other mycobacteria as well as explain the resulting phenotype at the genetic level. These data also suggest that TBSA should not be used as a diagnostic marker for
Map
.

IMPORTANCE

Branched-chain fatty acids are a predominant cell wall component among species belonging to the
Mycobacterium
genus. One of these is TBSA, which is a long-chain middle-branched fatty acid used as a diagnostic marker for
Mycobacterium tuberculosis
. This fatty acid is also an excellent biolubricant. Control of its production is important for industrial purposes as well as understanding the biology of mycobacteria. In this study, we discovered that a carboxylic acid compound termed pivalic acid inhibits TBSA production in mycobacteria. Furthermore,
Map
strains from two separate genetic lineages (C-type and S-type) showed differential production of TBSA. Cattle-type strains of
Mycobacterium avium
subspecies
paratuberculosis
produce TBSA, while the sheep-type strains do not. This important phenotypic difference is attributed to a single-nucleotide deletion in sheep-type strains of
Map
. This work sheds further light on the mechanism used by mycobacteria to produce tuberculostearic acid.
Antibacterial peptide Reg4 ameliorates
Pseudomonas aeruginosa
-induced pulmonary inflammation and fibrosis
Authors: Wan Xiaoyu , Wang Weipeng , Zhu Jing , Xiao Yongtao 
Published: March 2024

ABSTRACT

Pseudomonas aeruginosa
(
P. aeruginosa
) is a Gram-negative facultative anaerobe that has become an important cause of severe infections in humans, particularly in patients with cystic fibrosis. The development of efficacious methods or mendicants against
P. aeruginosa
is still needed. We previously reported that regenerating islet-derived family member 4 (Reg4) has bactericidal activity against
Salmonella
Typhimurium, a Gram-negative flagellated bacterium. We herein explore whether Reg4 has bactericidal activity against
P. aeruginosa
. In the
P. aeruginosa
PAO1-chronic infection model, Reg4 significantly inhibits the colonization of PAO1 in the lung and subsequently ameliorates pulmonary inflammation and fibrosis. Reg4 recombinant protein suppresses the growth motility and biofilm formation capability of PAO1
in vitro
. Mechanistically, Reg4 not only exerts bactericidal action via direct binding to the
P. aeruginosa
cell wall but also enhances the phagocytosis of alveolar macrophages in the host. Taken together, our study demonstrates that Reg4 may provide protection against
P. aeruginosa
-induced pulmonary inflammation and fibrosis via its antibacterial activity.

IMPORTANCE

Chronic lung infection with
Pseudomonas aeruginosa
is a leading cause of morbidity and mortality in patients with cystic fibrosis. Due to the antibiotic resistance of
Pseudomonas aeruginosa
, antimicrobial peptides appear to be a potential alternative to combat its infection. In this study, we report an antimicrobial peptide, regenerating islet-derived 4 (Reg4), that showed killing activity against clinical strains of
Pseudomonas aeruginosa
PAO1 and ameliorated PAO1-induced pulmonary inflammation and fibrosis. Experimental data also showed Reg4 directly bound to the bacterial cell membrane and enhanced the phagocytosis of host alveolar macrophages. Our presented study will be a helpful resource in searching for novel antimicrobial peptides that could have the potential to replace conventional antibiotics.
Modification of Archean cratons in southern Africa with foundered segments dropped into the shallow lower mantle
Authors: Xi Jiaji , Yu Youqiang , Zhao Dapeng , Hu Jiashun 
Published: March 2024

Abstract
Subducted slabs have been detected in the lower mantle for almost 30 years, yet the presence of foundered cratonic segments in the lower mantle is still unclear and inadequately investigated. We present the first P-wave radial anisotropy tomography of southern Africa (our model SA-RAnis2024), which reveals a contrasting feature of preserved northwest and modified southeast Kalahari cratonic root. Segments from the modified cratonic lithosphere are inferred to have dropped into the shallow lower mantle where seismic evidence of isolated high-velocity anomalies are observed. We detect such a high-velocity anomaly under the southwest margin of the Kalahari craton, which possibly detached from the southeast Zimbabwe craton at ca. 60 Ma based on plate reconstructions. Foundered segments can be partially brought back up to shallow depths, and contribute to the geochemical heterogeneity of younger lithosphere, through large-scale mantle convection.
One-year efficacy of myopia control by the defocus distributed multipoint lens: a multicentric randomised controlled trial
Authors: Chen Xiaoqin , Li Mengdi , Li Jun , Wu Min , Liu Xiaonan , Yu Cui , Guo Xingyi , Wang Yanbo , Wang Yansong , Lu Wenli , Li Lihua , Wang Yan 
Published: March 2024

Aims
To report the 1-year results of the efficacy of a defocus distributed multipoint (DDM) lens in controlling myopia progression in a multicentre, randomised controlled trial.

Methods
Overall, 168 children aged 6–13 years were recruited and randomly assigned to wear a DDM lens (n=84) or single-vision (SV) lens (n=84) in three centres. Cycloplegic autorefraction (spherical equivalent refraction (SER)) and axial length (AL) were measured. Linear mixed model analysis was performed to compare between-group SER and AL changes. Logistic regression analysis was used to analyse the between-group difference in rapid myopia progression (SER increase≥0.75 D per year or AL growth≥0.40 mm per year).

Results
After 1 year, mean changes in SER were significantly lower in the DDM group (−0.47±0.37 D) than in the SV group (−0.71±0.42 D) (p<0.001). Similarly, mean changes in AL were significantly lower in the DDM group (0.21±0.17 mm) than in the SV group (0.34±0.16 mm) (p<0.001). After adjusting for age, sex, daily wearing time and parental myopia, rapid myopia progression risk was higher in the SV group than in the DDM group (OR=3.51, 95% CI: 1.77 to 6.99), especially for children who wore a lens for >12 hours per day, boys and younger children (6–9 years) with ORs (95% CIs) of 10.82 (3.22 to 36.37), 5.34 (1.93 to 14.78) and 8.73 (2.6 to 29.33), respectively.

Conclusions
After 1 year, DDM lenses effectively retarded myopia progression in children. Longer daily wearing time of DDM lens improved the efficacy of myopia control. Future long-term studies are needed for validation.

Trial registration number

NCT05340699
.
Towards global elimination of lymphatic filariasis: a systematic review of the application of spatial epidemiological methods to enhance surveillance and support elimination programmes
Authors: Martin Beatris Mario , Cadavid Restrepo Angela , Mayfield Helen J , Lau Colleen L 
Published: March 2024

BackgroundIn recent decades, spatial epidemiology has increasingly been used to study neglected tropical diseases (NTDs). Spatial methods are particularly relevant when transmission is strongly driven by sociodemographic and environmental factors, resulting in heterogeneous disease distribution. We use lymphatic filariasis (LF)—an NTD targeted for global elimination—as a case study to examine how spatial epidemiology has been used to enhance NTD surveillance.MethodsWe conducted a systematic literature review of spatial analytical studies of LF published in English across PubMed, Embase, Web of Science and Scopus databases, before 15 November 2022. Additional papers were identified from experts’ suggestions. Studies that employed spatial analytical methods were included, but those that applied only visualisation tools were excluded.FindingsSixty-one eligible studies published between 1997 and 2023 were identified. The studies used a wide range of spatial methods. Thirty-one (50.8%) studies used spatial statistical modelling, with model-based geostatistics being the most common method. Spatial autocorrelation and hotspot analysis were applied in 30 studies (49.2%). The most frequent model outputs were prevalence maps (17 studies, 27.9%), followed by risk maps based on environmental suitability (7 studies, 11.5%) and maps of the odds of seroprevalence being above a predetermined threshold (7 studies, 11.5%).InterpretationBy demonstrating the applicability of spatial methods for investigating transmission drivers, identifying clusters and predicting hotspots, we highlight innovative ways in which spatial epidemiology has provided valuable evidence to support LF elimination. Spatial analysis is particularly useful in low-prevalence settings for improving hotspot detection and enhancing postelimination surveillance.PROSPERO registration numberCRD42022333804.
Changes in fertility intention among married Chinese couples with two children during COVID-19: a cross-sectional study
Authors: Ning Ni , Tan Xiangmin , Li Ying , Tang Jingfei , Lommel Lisa , Sun Mei 
Published: March 2024

BackgroundA three-child policy was implemented in China to stimulate a rise in fertility levels and coincided with the COVID-19 pandemic. Data suggested that COVID-19 has a negative impact on fertility intention.AimTo describe married couples’ changes in intention to have a third child during the COVID-19 pandemic and determine factors associated with altered intentions.MethodsAn online survey was conducted in October 2021, including sociodemographic characteristics, change of intention to have a third child after the COVID-19 pandemic outbreak, reasons for increased or decreased intention, and the Fertility Intention Scale (FIS). Bivariate and multivariable logistic regression were used to test the potential factors associated with changes in intention.ResultsA total of 1308 participants provided responses. Following the COVID-19 outbreak, 35.8% of participants decreased their third-child intention, while 2.8% of participants increased their third-child intention. Males (aOR 1.90, 95% CI 1.42 to 2.54), youngsters (aOR 1.77, 95% CI 1.08 to 2.93) and those living in Estern China (aOR 2.12, 95% CI 1.13 to 3.98) were more likely to decrease their third-child intention. Perceived risk (aOR 1.07, 95% CI 1.03 to 1.10) and policy support (aOR 1.06, 95% CI 1.03 to 1.09) as measured on the FIS decreased couples’ intention to have a third child. Social support (aOR 0.94, 95% CI 0.91 to 0.98) as measured on the scale protected participants from decreased intention.ConclusionsDuring severe public health emergencies, strong prevention and control policies, together with enhancing support from partners and healthcare professionals for women, are necessary to improve intentions to give birth.
Understanding the impact of COVID-19 on women’s access to and experiences of contraceptive services in England: a qualitative study
Authors: McMillan Lauren , Gadsby Erica , Howell Rebecca , Ussher Michael , Hunt Kate , Ford Allison 
Published: March 2024

BackgroundThe COVID-19 pandemic response prompted rapid changes to how contraceptive services were delivered in England. Our aim was to examine women’s experiences of accessing contraceptive services since March 2020 and to understand any inequalities of access.MethodsWe conducted telephone interviews with 31 women aged 17–54 years who had accessed contraceptive services in England since March 2020. The sample was skewed to include participants with lower educational attainment and higher deprivation. Interview transcripts were thematically analysed using inductive and deductive approaches.ResultsFew differences were found regarding educational attainment. Participants using contraceptive injections (all living in areas in the most deprived quintile) reported the greatest access challenges. Some switched method or stopped using contraception as a result. More general barriers reported by participants included service closures, unclear booking processes, and lack of appointment availability. Many participants welcomed the flexibility and convenience of remote contraceptive services. However, telephone appointments posed challenges for those at school or living with parents, and some described them as rushed and inconducive to asking questions or raising concerns. Those accessing contraception for the first time or nearing menopause felt they were unable to access sufficient support and guidance during the pandemic. Some participants voiced concerns around the lasting effects of COVID-19 on appointment availability and inadequate service delivery.ConclusionsWomen’s experiences of accessing contraceptive services in England since March 2020 are diverse. While remote services were suitable for some, COVID-19 restrictions unequally impacted women depending on their method of contraception and life stage.
Presence and utility of electrocardiographic abnormalities in long-term childhood cancer survivors
Authors: de Baat Esmée C , Merkx Remy , Leerink Jan M , Boerhout Coen , van der Pal Heleen J H , van Dalen Elvira C , Loonen Jacqueline , Bresters Dorine , van Dulmen-den Broeder Eline , van der Heiden-van der Loo Margriet , van den Heuvel Marry M , Kok Judith L , Louwerens Marloes , Neggers Sebastian J C M M , Ronckers Cecline M , Teepen Jop C , Tissing Wim J E , de Vries Andrica C , Kapusta Livia , Kremer Leontien C M , Mavinkurve-Groothuis Annelies M C , Kok Wouter E M , Feijen Elizabeth A M 
Published: March 2024

BackgroundWe assessed the prevalence and diagnostic value of ECG abnormalities for cardiomyopathy surveillance in childhood cancer survivors.MethodsIn this cross-sectional study, 1381 survivors (≥5 years) from the Dutch Childhood Cancer Survivor Study part 2 and 272 siblings underwent a long-term follow-up ECG and echocardiography. We compared ECG abnormality prevalences using the Minnesota Code between survivors and siblings, and within biplane left ventricular ejection fraction (LVEF) categories. Among 880 survivors who received anthracycline, mitoxantrone or heart radiotherapy, logistic regression models using least absolute shrinkage and selection operator identified ECG abnormalities associated with three abnormal LVEF categories (<52% in male/<54% in female, <50% and <45%). We assessed the overall contribution of these ECG abnormalities to clinical regression models predicting abnormal LVEF, assuming an absence of systolic dysfunction with a <1% threshold probability.Results16% of survivors (52% female, mean age 34.7 years) and 14% of siblings had major ECG abnormalities. ECG abnormalities increased with decreasing LVEF. Integrating selected ECG data into the baseline model significantly improved prediction of sex-specific abnormal LVEF (c-statistic 0.66 vs 0.71), LVEF <50% (0.66 vs 0.76) and LVEF <45% (0.80 vs 0.86). While no survivor met the preset probability threshold in the first two models, the third model used five ECG variables to predict LVEF <45% and was applicable for ruling out (sensitivity 93%, specificity 56%, negative predictive value 99.6%). Calibration and internal validation tests performed well.ConclusionA clinical prediction model with ECG data (left bundle branch block, left atrial enlargement, left heart axis, Cornell’s criteria for left ventricular hypertrophy and heart rate) may aid in ruling out LVEF <45%.