bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H
2
18
O
Authors: Papp Katerina , Hungate Bruce A. , Schwartz Egbert 
Published: February 2018

ABSTRACT

Growing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with H
2
18
O. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with H
2
18
O. The positive correlation between
18
O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA-to-DNA ratios obtained from sequencing libraries and the atom percent excess (APE)
18
O values of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division and suggest that nondividing taxa do not dominate soil metabolic activity.

IMPORTANCE
Using quantitative stable isotope probing of microbial RNA and DNA with H
2
18
O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with
18
O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Additionally, our results indicate that relative sequence abundance-based RNA-to-DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.
Accumulation and Dissolution of Magnetite Crystals in a Magnetically Responsive Ciliate
Authors: Monteil Caroline L. , Menguy Nicolas , Prévéral Sandra , Warren Alan , Pignol David , Lefèvre Christopher T. 
Published: February 2018

ABSTRACT

Magnetotactic bacteria (MTB) represent a group of microorganisms that are widespread in aquatic habitats and thrive at oxic-anoxic interfaces. They are able to scavenge high concentrations of iron thanks to the biomineralization of magnetic crystals in their unique organelles, the so-called magnetosome chains. Although their biodiversity has been intensively studied, their ecology and impact on iron cycling remain largely unexplored. Predation by protozoa was suggested as one of the ecological processes that could be involved in the release of iron back into the ecosystem. Magnetic protozoa were previously observed in aquatic environments, but their diversity and the fate of particulate iron during grazing are poorly documented. In this study, we report the morphological and molecular characterizations of a magnetically responsive MTB-grazing protozoan able to ingest high quantities of MTB. This protozoan is tentatively identified as
Uronema marinum
, a ciliate known to be a predator of bacteria. Using light and electron microscopy, we investigated in detail the vacuoles in which the lysis of phagocytized prokaryotes occurs. We carried out high-resolution observations of aligned magnetosome chains and ongoing dissolution of crystals. Particulate iron in the ciliate represented approximately 0.01% of its total volume. We show the ubiquity of this interaction in other types of environments and describe different grazing strategies. These data contribute to the mounting evidence that the interactions between MTB and protozoa might play a significant role in iron turnover in microaerophilic habitats.

IMPORTANCE
Identifying participants of each biogeochemical cycle is a prerequisite to our understanding of ecosystem functioning. Magnetotactic bacteria (MTB) participate in iron cycling by concentrating large amounts of biomineralized iron minerals in their cells, which impacts their chemical environment at, or below, the oxic-anoxic transition zone in aquatic habitats. It was shown that some protozoa inhabiting this niche could become magnetic by the ingestion of magnetic crystals biomineralized by grazed MTB. In this study, we show that magnetic MTB grazers are commonly observed in marine and freshwater sediments and can sometimes accumulate very large amounts of particulate iron. We describe here different phagocytosis strategies, determined using magnetic particles from MTB as tracers after their ingestion by the protozoa. This study paves the way for potential scientific or medical applications using MTB grazers as magnetosome hyperaccumulators.
A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility
Authors: Fukuto Hana S. , Vadyvaloo Viveka , McPhee Joseph B. , Poinar Hendrik N. , Holmes Edward C. , Bliska James B. 
Published: February 2018

ABSTRACT

Yersinia pestis
, the causative agent of plague, evolved from the closely related pathogen
Yersinia pseudotuberculosis
. During its emergence,
Y. pestis
is believed to have acquired its unique pathogenic characteristics through numerous gene gains/losses, genomic rearrangements, and single nucleotide polymorphism (SNP) changes. One such SNP creates a single amino acid variation in the DNA binding domain of PhoP, the response regulator in the PhoP/PhoQ two-component system.
Y. pseudotuberculosis
and the basal human-avirulent strains of
Y. pestis
harbor glycines at position 215 of PhoP, whereas the modern human-virulent strains (e.g., KIM and CO92) harbor serines at this residue. Since PhoP plays multiple roles in the adaptation of
Y. pestis
to stressful host conditions, we tested whether this amino acid substitution affects PhoP activity or the ability of
Y. pestis
to survive in host environments. Compared to the parental KIM6+ strain carrying the modern allele of
phoP
(
phoP-S215
), a derivative carrying the basal allele (
phoP-G215
) exhibited slightly defective growth under a low-Mg
2+
condition and decreased transcription of a PhoP target gene,
ugd
, as well as an ∼8-fold increase in the susceptibility to the antimicrobial peptide polymyxin B. The
phoP-G215
strain showed no apparent defect in flea colonization, although a
phoP
-null mutant showed decreased flea infectivity in competition experiments. Our results suggest that the amino acid variation at position 215 of PhoP causes subtle changes in the PhoP activity and raise the possibility that the change in this residue have contributed to the evolution of increased virulence in
Y. pestis
.

IMPORTANCE
Y. pestis
acquired a single nucleotide polymorphism (SNP) in
phoP
when the highly human-virulent strains diverged from less virulent basal strains, resulting in an amino acid substitution in the DNA binding domain of the PhoP response regulator. We show that
Y. pestis
carrying the modern
phoP
allele has an increased ability to induce the PhoP-regulated
ugd
gene and resist antimicrobial peptides compared to an isogenic strain carrying the basal allele. Given the important roles PhoP plays in host adaptation, the results raise an intriguing possibility that this amino acid substitution contributed to the evolution of increased virulence in
Y. pestis
. Additionally, we present the first evidence that
phoP
confers a survival fitness advantage to
Y. pestis
inside the flea midgut.
Structural Basis of a Thiol-Disulfide Oxidoreductase in the Hedgehog-Forming Actinobacterium Corynebacterium matruchotii
Authors: Luong Truc Thanh , Tirgar Reyhaneh , Reardon-Robinson Melissa E. , Joachimiak Andrzej , Osipiuk Jerzy , Ton-That Hung 
Published: February 2018

ABSTRACT

The actinobacterium
Corynebacterium matruchotii
has been implicated in nucleation of oral microbial consortia leading to biofilm formation. Due to the lack of genetic tools, little is known about basic cellular processes, including protein secretion and folding, in this organism. We report here a survey of the
C. matruchotii
genome, which encodes a large number of exported proteins containing paired cysteine residues, and identified an oxidoreductase that is highly homologous to the
Corynebacterium diphtheriae
thiol-disulfide oxidoreductase MdbA (MdbA
Cd
). Crystallization studies uncovered that the 1.2-Å resolution structure of
C. matruchotii
MdbA (MdbA
Cm
) possesses two conserved features found in actinobacterial MdbA enzymes, a thioredoxin-like fold and an extended α-helical domain. By reconstituting the disulfide bond-forming machine
in vitro
, we demonstrated that MdbA
Cm
catalyzes disulfide bond formation within the actinobacterial pilin FimA. A new gene deletion method supported that
mdbA
is essential in
C. matruchotii
. Remarkably, heterologous expression of MdbA
Cm
in the
C. diphtheriae
Δ
mdbA
mutant rescued its known defects in cell growth and morphology, toxin production, and pilus assembly, and this thiol-disulfide oxidoreductase activity required the catalytic motif CXXC. Altogether, the results suggest that MdbA
Cm
is a major thiol-disulfide oxidoreductase, which likely mediates posttranslocational protein folding in
C. matruchotii
by a mechanism that is conserved in
Actinobacteria
.

IMPORTANCE
The actinobacterium
Corynebacterium matruchotii
has been implicated in the development of oral biofilms or dental plaque; however, little is known about the basic cellular processes in this organism. We report here a high-resolution structure of a
C. matruchotii
oxidoreductase that is highly homologous to the
Corynebacterium diphtheriae
thiol-disulfide oxidoreductase MdbA. By biochemical analysis, we demonstrated that
C. matruchotii
MdbA catalyzes disulfide bond formation
in vitro
. Furthermore, a new gene deletion method revealed that deletion of
mdbA
is lethal in
C. matruchotii
. Remarkably,
C. matruchotii
MdbA can replace
C. diphtheriae
MdbA to maintain normal cell growth and morphology, toxin production, and pilus assembly. Overall, our studies support the hypothesis that
C. matruchotii
utilizes MdbA as a major oxidoreductase to catalyze oxidative protein folding.
Human Papillomaviruses Preferentially Recruit DNA Repair Factors to Viral Genomes for Rapid Repair and Amplification
Authors: Mehta Kavi , Laimins Laimonis 
Published: February 2018

ABSTRACT
High-risk human papillomaviruses (HPVs) activate the ataxia telangiectasia mutated-dependent (ATM) DNA damage response as well as the ataxia telangiectasia mutated-dependent DNA-related (ATR) pathway in the absence of external DNA damaging agents for differentiation-dependent genome amplification. Through the use of comet assays and pulsed-field gel electrophoresis, our studies showed that these pathways are activated in response to DNA breaks induced by the viral proteins E6 and E7 alone and independently of viral replication. The majority of these virally induced DNA breaks are present in cellular DNAs and only minimally in HPV episomes. Treatment of HPV-positive cells with inhibitors of both ATM and ATR leads to the generation of DNA breaks and the fragmentation of viral episomes, indicating that DNA breaks are introduced into HPV genomes. These breaks, however, are rapidly repaired through the preferential recruitment of homologous recombination repair enzymes, such as RAD51 and BRCA1, to viral genomes at the expense of cellular DNAs. When HPV-positive cells are treated with hydroxyurea, this recruitment of RAD51 and BRCA1 to viral genomes is greatly enhanced with little recruitment to damaged cellular DNAs and with retention of the ability of viral genomes to amplify. Overall, our studies demonstrated that human papillomaviruses induce breaks into cellular and viral DNAs and that the preferential repair of these lesions in viral episomes leads to genome amplification.

IMPORTANCE
High-risk human papillomaviruses (HPVs) are the etiologic agents of cervical cancer and are linked to the development of many other anogenital and oropharyngeal cancers. Replication of high-risk HPVs requires the activation of the ataxia telangiectasia-mutated (ATM) and ATM- and Rad3-related (ATR) DNA repair pathways. Our studies have shown that HPVs activate these pathways by inducing double-strand breaks primarily in cellular DNAs and minimally in viral genomes. Breaks are induced in viral genomes but are rapidly repaired through the preferential recruitment of homologous repair factors such as RAD51 and BRCA1 to HPV episomes. The preferential repair of breaks in viral genomes leads to amplification. Our study identified a novel mechanism by which human papillomaviruses manipulate DNA repair pathways to productively replicate viral genomes. The induction of genetic instability in cellular DNAs likely contributes to the generation of mutations that lead to the development of cancers.
A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and
Mycobacterium avium
Authors: Haig Sarah-Jane , Kotlarz Nadine , LiPuma John J. , Raskin Lutgarde 
Published: February 2018

ABSTRACT

Nontuberculous mycobacteria (NTM) frequently detected in drinking water (DW) include species associated with human infections, as well as species rarely linked to disease. Methods for improved the recovery of NTM DNA and high-throughput identification of NTM are needed for risk assessment of NTM infection through DW exposure. In this study, different methods of recovering bacterial DNA from DW were compared, revealing that a phenol-chloroform DNA extraction method yielded two to four times as much total DNA and eight times as much NTM DNA as two commercial DNA extraction kits. This method, combined with high-throughput, single-molecule real-time sequencing of NTM
rpoB
genes, allowed the identification of NTM to the species, subspecies, and (in some cases) strain levels. This approach was applied to DW samples collected from 15 households serviced by a chloraminated distribution system, with homes located in areas representing short (<24 h) and long (>24 h) distribution system residence times. Multivariate statistical analysis revealed that greater water age (i.e., combined distribution system residence time and home plumbing stagnation time) was associated with a greater relative abundance of
Mycobacterium avium
subsp.
avium
, one of the most prevalent NTM causing infections in humans. DW from homes closer to the treatment plant (with a shorter water age) contained more diverse NTM species, including
Mycobacterium abscessus
and
Mycobacterium chelonae
. Overall, our approach allows NTM identification to the species and subspecies levels and can be used in future studies to assess the risk of waterborne infection by providing insight into the similarity between environmental and infection-associated NTM.

IMPORTANCE
An extraction method for improved recovery of DNA from nontuberculous mycobacteria (NTM), combined with single-molecule real-time sequencing (PacBio) of NTM
rpoB
genes, was used for high-throughput characterization of NTM species and in some cases strains in drinking water (DW). The extraction procedure recovered, on average, eight times as much NTM DNA and three times as much total DNA from DW as two widely used commercial DNA extraction kits. The combined DNA extraction and sequencing approach allowed high-throughput screening of DW samples to identify NTM, revealing that the relative abundance of
Mycobacterium avium
subsp.
avium
increased with water age. Furthermore, the two-step barcoding approach developed as part of the PacBio sequencing method makes this procedure highly adaptable, allowing it to be used for other target genes and species.
Slowdown of Translational Elongation in
Escherichia coli
under Hyperosmotic Stress
Authors: Dai Xiongfeng , Zhu Manlu , Warren Mya , Balakrishnan Rohan , Okano Hiroyuki , Williamson James R. , Fredrick Kurt , Hwa Terence 
Published: February 2018

ABSTRACT

In nature, bacteria frequently experience many adverse conditions, including heat, oxidation, acidity, and hyperosmolarity, which all tend to slow down if not outright stop cell growth. Previous work on bacterial stress mainly focused on understanding gene regulatory responses. Much less is known about how stresses compromise protein synthesis, which is the major driver of cell growth. Here, we quantitatively characterize the translational capacity of
Escherichia coli
cells growing exponentially under hyperosmotic stress. We found that hyperosmotic stress affects bacterial protein synthesis through reduction of the translational elongation rate, which is largely compensated for by an increase in the cellular ribosome content compared with nutrient limitation at a similar growth rate. The slowdown of translational elongation is attributed to a reduction in the rate of binding of tRNA ternary complexes to the ribosomes.

IMPORTANCE
Hyperosmotic stress is a common stress condition confronted by
E. coli
during infection of the urinary tract. It can significantly compromise the bacterial growth rate. Protein translation capacity is a critical component of bacterial growth. In this study, we find for the first time that hyperosmotic stress causes substantial slowdown in bacterial ribosome translation elongation. The slowdown of translation elongation originates from a reduced binding rate of tRNA ternary complex to the ribosomes.
Treatment thresholds for intervention in posthaemorrhagic ventricular dilation: a randomised controlled trial
Authors: de Vries Linda S , Groenendaal Floris , Liem Kian D , Heep Axel , Brouwer Annemieke J , van ’t Verlaat Ellen , Benavente-Fernández Isabel , van Straaten Henrica LM , van Wezel-Meijler Gerda , Smit Bert J , Govaert Paul , Woerdeman Peter A , Whitelaw Andrew 
Published: February 2018

ObjectiveTo compare a low versus a higher threshold for intervention in preterm infants with posthaemorrhagic ventricular dilatation.DesignMulticentre randomised controlled trial (ISRCTN43171322).Setting14 neonatal intensive care units in six countries.Patients126 preterm infants ≤34 weeks gestation with ventricular dilatation after grade III–IV haemorrhage were randomised to low threshold (LT) (ventricular index (VI) >p97 and anterior horn width (AHW) >6 mm) or higher threshold (HT) (VI>p97+4 mm and AHW >10 mm).InterventionCerebrospinal fluid tapping by lumbar punctures (LPs) (max 3), followed by taps from a ventricular reservoir, to reduce VI, and eventually a ventriculoperitoneal (VP) shunt if stabilisation of the VI below the p97+4 mm did not occur.Composite main outcome measureVP shunt or death.Results19 of 64 (30%) LT infants and 23 of 62 (37%) HT infants were shunted or died (P=0.45). A VP shunt was inserted in 12/64 (19%) in the LT and 14/62 (23%) infants in the HT group. 7/12 (58%) LT infants and 1/14 (7%) HT infants required shunt revision (P<0.01). 62 of 64 (97%) LT infants and 36 of 62 (58%) HT infants had LPs (P<0.001). Reservoirs were inserted in 40 of 64 (62%) LT infants and 27 of 62 (43%) HT infants (P<0.05).ConclusionsThere was no significant difference in the primary composite outcome of VP shunt placement or death in infants with posthaemorrhagic ventricular dilatation who were treated at a lower versus a higher threshold for intervention. Infants treated at the lower threshold received more invasive procedures. Assessment of neurodevelopmental outcomes will provide further important information in assessing the risks and benefits of the two treatment approaches.
Effects of changes in eating speed on obesity in patients with diabetes: a secondary analysis of longitudinal health check-up data
Authors: Hurst Yumi , Fukuda Haruhisa 
Published: February 2018

ObjectiveFew studies have examined the causal relationships between lifestyle habits and obesity. With a focus on eating speed in patients with type 2 diabetes, this study aimed to analyse the effects of changes in lifestyle habits on changes in obesity using panel data.MethodsPatient-level panel data from 2008 to 2013 were generated using commercially available insurance claims data and health check-up data. The study subjects comprised Japanese men and women (n=59 717) enrolled in health insurance societies who had been diagnosed with type 2 diabetes during the study period. Body mass index (BMI) was measured, and obesity was defined as a BMI of 25 or more. Information on lifestyle habits were obtained from the subjects’ responses to questions asked during health check-ups. The main exposure of interest was eating speed (‘fast’, ‘normal’ and ‘slow’). Other lifestyle habits included eating dinner within 2 hours of sleeping, after-dinner snacking, skipping breakfast, alcohol consumption frequency, sleep adequacy and tobacco consumption. A generalised estimating equation model was used to examine the effects of these habits on obesity. In addition, fixed-effects models were used to assess these effects on BMI and waist circumference.ResultsThe generalised estimating equation model showed that eating slower inhibited the development of obesity. The ORs for slow (0.58) and normal-speed eaters (0.71) indicated that these groups were less likely to be obese than fast eaters (P<0.001). Similarly, the fixed-effects models showed that eating slower reduced BMI and waist circumference. Relative to fast eaters, the coefficients of the BMI model for slow and normal-speed eaters were −0.11 and −0.07, respectively (P<0.001).DiscussionChanges in eating speed can affect changes in obesity, BMI and waist circumference. Interventions aimed at reducing eating speed may be effective in preventing obesity and lowering the associated health risks.
Ready-made and custom-made eyeglasses in India: a cost-effectiveness analysis of a randomised controlled trial
Authors: Angell Blake , Ali Ferhina , Gandhi Monica , Mathur Umang , Friedman David S , Jan Stephen , Keay Lisa 
Published: February 2018

ObjectiveReady-made spectacles have been suggested as a less resource-intensive treatment for the millions of people living with uncorrected refractive error (URE) in low-income environments. In spite of this interest, there have been no published economic evaluations examining the cost-effectiveness of ready-made spectacles. This study aims to determine the relative cost-effectiveness of offering ready-made spectacles (RMS) relative to no intervention as well as the relative cost-effectiveness of custom-made spectacles (CS) relative to RMS to treat URE.Methods and analysisThe relative cost-effectiveness of RMS relative to CS and no intervention was tested through a cost-effectiveness analysis from the health service provider perspective conducted alongside a double-masked randomised controlled trial in an urban hospital in Delhi, India. Participants were adults aged 18–45 years with ≥1 dioptre (D) of URE.ResultsThere was no significant difference between the effectiveness of the CS and RMS interventions in improving visual acuity, but the CS was over four times the price of the RMS per patient (204 INR (US$2.42) and 792 INR (US$11.22)). The cost per unit improvement in logarithm of the minimum angle of resolution (logMAR) relative to baseline with the RMS intervention was 407 INR (US$4.35). Existing estimates of utility resulting from improvements in visual acuity result in incremental cost per quality-adjusted life years gained of between 212 INR and 1137 INR (US$0.44–US$23.74) depending on the source of the utility estimate and assumed expected life of the spectacles.ConclusionRMS represent a significantly cost-effective option for spectacle provision in low-resource settings. The RMS programme was substantially cheaper than an equivalent CS intervention while being effective in improving visual acuity for the majority of adults with refractive error in this setting. These findings provide further support for including RMS in programmes to address URE.Trial registration numberNCT00657670, Results.