bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters
Authors: Ettinger Cassandra L. , Wu-Woods Jessica , Kurbessoian Tania , Brown Dylan J. , Souza Pacheco Inaiara de , Vindiola Beatriz G. , Walling Linda L. , Atkinson Peter W. , Byrne Frank J. , Redak Richard , Stajich Jason E. 
Published: October 2023

ABSTRACT

The glassy-winged sharpshooter,
Homalodisca vitripennis
Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen,
Xylella fastidiosa
. While studies have focused on
X. fastidiosa
or known symbionts of
H. vitripennis
, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of
H. vitripennis
across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the
H. vitripennis
mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild
H. vitripennis
. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild
H. vitripennis
. This study serves as a foundational look at the
H. vitripennis
mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in
H. vitripennis
management practices.

IMPORTANCE

The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen,
Xylella fastidiosa
, resulting in significant economic damage to California’s agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter’s resistance to insecticides.
Identification of chronic wasting disease prions in decaying tongue tissues from exhumed white-tailed deer
Authors: Soto Paulina , Bravo-Risi Francisca , Benavente Rebeca , Lichtenberg Stuart , Lockwood Mitch , Reed J. Hunter , Morales Rodrigo 
Published: October 2023

ABSTRACT
Chronic wasting disease (CWD) prions cause fatal neuropathies in farmed and free-ranging cervids. The deposition of prions in natural and humanmade environmental components has been implicated as a major mechanism mediating CWD spread in wild and captive populations. Prions can be deposited in the environment through excreta, tissues, and carcasses from pre-clinical and clinical animals. Furthermore, burial of CWD-positive animals may reduce but not completely mitigate prion spread from carcasses into the surrounding environment. Here, we analyzed exhumed, decaying deer carcasses for the presence of CWD prions. By analyzing tongue tissues through the protein misfolding cyclic amplification (PMCA) technique, we were able to identify seven out of 95 exhumed white-tailed deer carcasses as CWD prions carriers. Confirmatory analyses were performed using the real-time quaking-induced conversion (RT-QuIC) technique. In addition, we evaluated the potential contamination of the pens that housed these animals by swabbing feeders and waterers. PMCA analyses of swabs confirmed CWD contamination on farming equipment. This work demonstrates the usefulness of PMCA to detect CWD prions in a variety of contexts, including exhumed/decaying tissues. In addition, this is the first report demonstrating swabbing coupled with PMCA as a method for the detection of prion seeding activity on naturally exposed surfaces. Considering that this study was focused on a single site, further studies should confirm whether prion amplification assays are useful to identify CWD prions not only in animals but also in the environment that contains them.

IMPORTANCE
Environmental contamination is thought to be a major player in the spread of chronic wasting disease (CWD), a fatal prion disease affecting a wide variety of cervid species. At present, there are no officially approved methods allowing for the detection of prion infectivity in environmental components. Importantly, animal as well as anthropogenic activities are thought to contribute to prion environmental contamination. Here, we detected CWD prions in exhumed white-tailed deer carcasses by using the protein misfolding cyclic amplification (PMCA) assay. In addition, we identified CWD prions in feeders used within the infected facility. These results highlight the potential role of PMCA in identifying prion infectivity in a variety of scenarios, ranging from decaying tissues to farming equipment.
SarS and Rot are necessary for the repression of
lukED
and
lukSF-PV
in
Staphylococcus aureus
Authors: Anderson Exene E. , Ilmain Juliana K. , Torres Victor J. 
Published: October 2023

ABSTRACT

Staphylococcus aureus
is an opportunistic pathogen that employs an array of different virulence factors to evade the immune system. The bi-component pore-forming leukocidins are of particular importance for their ability to target and kill phagocytes. The operon of two of these toxins,
lukED
and
lukSF-PV
, are repressed by two proteins, SarS and Rot. However, how these repressors work together to repress these toxins is not completely understood. Here, we determine that repression of leukocidins by SarS and Rot is not additive and that SarS and Rot are able to bind concurrently to the leukocidin promoters. In addition, in a tissue culture model using primary human neutrophils, the deletion of both repressors did not result in increased virulence compared to the single deletions of
sarS
and
rot
. Further experiments revealed that in an
in vivo
mouse infection model, virulence was similar in strains lacking one versus both repressors. Overall, these data show that while the repression of leukocidins by SarS and Rot is not additive, both proteins are critical for the repression of these toxins.

IMPORTANCE

The leukocidins play an important role in disarming the host immune system and promoting infection. While both SarS and Rot have been established as repressors of leukocidins, the importance of each repressor in infection is unclear. Here, we demonstrate that repression by SarS and Rot is not additive and show that in addition to upregulating expression of each other, they are also able to bind concurrently to the leukocidin promoters. These findings suggest that both repressors are necessary for maximal repression of
lukED
and
lukSF-PV
and illuminate another complex relationship among
Staphylococcus aureus
virulence regulators.
Bee wisdom: exploring bee control strategies for food microflora by comparing the physicochemical characteristics and microbial composition of beebread
Authors: Wang Ying , Ma Lanting , Xu Baohua 
Published: October 2023

ABSTRACT
Beebread serves not only as a vital food source for bees but also as a significant reservoir of microbes for their intestinal tracts. The distribution of beebread in honeycomb cells is characterized by distinct vertical patterns; however, the vertical distribution patterns of the physicochemical characteristics and microbial composition of beebread remain unclear. In this study, we collected beebread samples from nine colonies in three representative ecosystems (forest, forest-urban, and urban-farmland ecosystems) and systematically assessed the physicochemical characteristics and bacterial diversity in three beebread layers (lower, middle, and upper). We found that upper beebread samples had lower pH; higher proportions of fructose and sucrose; and lower proportions of total solids, crude protein, and ash compared to lower samples. Moreover, 16S rDNA sequencing showed that the dominant bacterial phyla and genera were relatively simple and highly conserved across the three ecosystems. Overall, the microbial community richness of upper beebread was significantly higher than that of lower beebread, and Bacteroidetes and Acidobacteria were significantly decreased in lower compared to upper beebread. Meanwhile, the relative abundance of dominant taxa in the same beebread layer differed by ecosystem types. These findings suggest that bees employ fermentation processes to selectively enrich microbes present in flower pollen, leading to homogenous and relatively stable microbial diversity in beebread. Our study expands on the current understanding of beebread and highlights the significance of fermentation in its production. Furthermore, our findings provide a useful reference for further in-depth exploration of the interactions between food, food microbes, and bee gut microbes.

IMPORTANCE
Bees are a valuable model for investigating the relationship between environmental factors, gut microbiota, and organismal health. Beebread, produced from collected pollen, is a natural food source and a primary reservoir of gut microorganisms. Although pollen typically has diverse bacterial species, beebread has low species richness and bacterial abundance. Consequently, considerable attention has been paid to the adaptive strategies employed by honey bees to cope with the microorganisms within their food environment during co-evolution with plants. This study identified the distribution patterns of beebread's physicochemical characteristics, showing how bees use fermentation to enrich specific microbes. These findings help understand the relationship between environmental and food-associated microbes and bee intestinal microbiota. They also bridge gaps in the literature and provide a valuable reference for studying the complex interplay between these factors.
Salmonella
Derby adaptation to swine and simultaneous attenuation for humans go through decay of
Salmonella
Pathogenicity Island I
Authors: Berni Melissa , Bolzoni Luca , Menozzi Ilaria , Dodi Alessandra , Bracchi Chiara , Morganti Marina , Scaltriti Erika , Pongolini Stefano , Tambassi Martina 
Published: October 2023

ABSTRACT

We report the identification, within the global population of
Salmonella
Derby, of a lineage highly diffused and expanding in swine while being significantly under-represented in humans which carries stop mutations in the Salmonella Pathogenicity Island 1 (SPI-1) genes
sipA
and
hilC
. Single-cell analysis of invasion, vacuolar load, and cytosolic hyper-replication show that these mutations attenuate
S
. Derby virulence in human intestinal cells. Identification of this lineage follows the previous detection of another lineage over-represented in swine compared with humans which carries a loss-of-function mutation in
hilD
, the major SPI-1 regulator, responsible for reduced infection of human cells. Notably, this
hilD
-mutated lineage represents a sub-population of the wider
sipA
and
hilC-
mutated lineages identified in this study, indicating that SPI-1 is subjected to genetic decay in this part of the
Salmonella
Derby population adapted to swine. Virulence assessment on swine intestinal cells showed drastically lower levels for both wild-type and mutant
S
. Derby compared with human cells. Still,
S
. Derby with impaired
sipA
and
hilC
showed further attenuation also in swine cells compared with the wild type. These data suggest that invasion of swine intestinal epithelium is not needed by
S
. Derby to circulate in pigs, leading to the decay of SPI-1, which in turn determines attenuation for humans. Accordingly, a further
S
. Derby lineage under-represented in humans compared with pigs was found carrying truncated or missing SPI-1 genes, indicating that the
S
. Derby population is undergoing converging evolution in its adaptation to swine while attenuating for humans through loss of SPI-1 function.

IMPORTANCE

This study integrated population data with
in vitro
assessment of virulence phenotypes to unveil that a considerable part of the global population of
Salmonella
Derby is evolving to enhance its host adaptation to the swine host and that this evolution is simultaneously increasing its attenuation for humans. The study shows that the fixation of deleterious mutations in SPI-1 has a role in this process. This evidence indicates that SPI-1 has a key role for
S
. Derby virulence in humans but not for its circulation in swine. The results show that genes generally considered essential for
Salmonella
pathogenesis do not play the same key role for all
Salmonella
serovars or lineages and/or all hosts. The study helps in understanding the molecular mechanisms underlying the ecology and host adaptation of
Salmonella
showing that the adaptation process can vary for different types of
Salmonella
and hosts.
Mycobacteriophage D29 Lysin B exhibits promising anti-mycobacterial activity against drug-resistant
Mycobacterium tuberculosis
Authors: Singh Amit Kumar , Gangakhedkar Rutuja , Thakur Hemant Singh , Raman Sunil Kumar , Patil Shripad A. , Jain Vikas 
Published: October 2023

ABSTRACT

The emergence of antibiotic resistance in
Mycobacterium tuberculosis
has been the culprit behind the inefficient treatment of tuberculosis (TB). Mycobacteriophages being rapid and specific in their activity against mycobacteria including
M. tuberculosis
are an emerging alternative solution to the antibiotic resistance problem. D29 mycobacteriophage is known as an efficient lytic phage. Its lytic cassette encodes for two lytic proteins, Lysin A (LysA) and Lysin B (LysB), and a holin protein responsible for the translocation of the former two. LysB is a mycolyl-arabinogalactan esterase, which has shown a promising lytic effect on
M. tuberculosis
. In this study, we explored the lytic efficiency of D29 mycobacteriophage LysB protein on drug-resistant strains of
M. tuberculosis
. We demonstrate that LysB effectively lyses multi-drug-resistant
M. tuberculosis
both alone and along with anti-TB drugs. We also report that the surfactant Tween-80, although not vital, potentiates LysB activity. We are able to demonstrate that LysB can eliminate
M. tuberculosis
residing in mouse macrophages. Thus, by combining our
in vitro
and
ex vivo
data, we are able to claim that LysB is a potential phage-derived therapeutic which should undergo pre-clinical and clinical trials.

IMPORTANCE

To combat the rapidly emerging drug-resistant
M. tuberculosis
, it is now essential to look for alternative therapeutics. Mycobacteriophages can be considered as efficient therapeutics due to their natural ability to infect and kill mycobacteria including
M. tuberculosis
. Here, we have exploited the mycolyl-arabinogalactan esterase property of LysB encoded from mycobacteriophage D29. This study is novel in terms of targeting a multi-drug-resistant pathogenic strain of
M. tuberculosis
with LysB and also examining the combination of anti-TB drugs and LysB. All the experiments include external administration of LysB. Therefore, the remarkable lytic activity of LysB overcomes the difficulty to enter the complex cell envelope of mycobacteria. Targeting the intracellularly located
M. tuberculosis
by LysB and non-toxicity to macrophages take the process of the development of LysB as a drug one step ahead, and also, the interaction studies with rifampicin and isoniazid will help to form a new treatment regimen against tuberculosis.
Developing an Interferometric Method for Measuring the Transverse Dimensions of a Particle Beam in Cyclic Accelerators
Authors: Dorokhov V. L. , Meshkov O. I. , Styrin A. I. , Smygachev A. S. 
Published: October 2023

Abstract
This work is devoted to the development of a method for measuring beam sizes in cyclic charged particle accelerators using an interferometer based on the Young scheme with a double-slit diaphragm. We have carried out an experimental verification of the original spectral method for scanning the interference pattern. The results of measurements of the spectrum of low-frequency oscillations of the beam of the storage ring of the Kurchatov Synchrotron Radiation Source (KSRS) obtained by means of the Optical Observation Station (OOS) of the storage ring are presented.
Possible evidence for the production of Ar$$_2^{*-}$$ metastable negative molecular ions in gaseous argon of two-phase detectors for dark matter searches
Authors: Buzulutskov A. , Frolov E. , Borisova E. , Nosov V. , Oleynikov V. , Sokolov A. 
Published: October 2023

AbstractOur recent studies of electroluminescence (EL) properties in two-phase argon detectors for dark matter searches have revealed the presence of unusual delayed pulses in the EL signal in the form of two slow components with time constants of about 5 and 50 $$\upmu \text {s}$$

μ
s

. These components were shown to be present in the charge signal itself, which clearly indicates that drifting electrons are temporarily trapped on two states of metastable negative argon ions which have never been observed before. In this work, using the pressure dependence of the ratio of slow component contributions measured in experiment, it is deduced that these states are those of two types of metastable negative molecular ions, $${{\textrm{Ar}}}_2^{*-}(b \ ^4\varSigma _u^-)$$

Ar
2

∗
-

(
b

4

Σ
u
-

)

and $${{\textrm{Ar}}}_2^{*-}(a \ ^4\varSigma _g^+)$$

Ar
2

∗
-

(
a

4

Σ
g
+

)

for the higher and lower energy level respectively.
Multicenter Evaluation of the Feasibility of Clinical Implementation of SPECT Myocardial Blood Flow Measurement: Intersite Variability and Imaging Time
Authors: Wells R. Glenn , Bengel Frank M. , Camoni Luca , Cerudelli Elisabetta , Cuddy-Walsh Sarah G. , Diekmann Johanna , Han Lewis , Kadoya Yoshito , Kawaguchi Naoto , Keng Yung Jih Felix , Miyagawa Masao , Ratner Hagit , Teng Xue Fen , Ruddy Terrence D. 
Published: October 2023

Background:
Single-center studies have shown that single photon emission computed tomography myocardial blood flow (MBF) measurement is accurate compared with MBF measured with microspheres in a porcine model, positron emission tomography, and angiography. Clinical implementation requires consistency across multiple sites. The study goal is to determine the intersite processing repeatability of single photon emission computed tomography MBF and the additional camera time required.

Methods:
Five sites (Canada, Italy, Japan, Germany, and Singapore) each acquired 25 to 35 MBF studies at rest and with pharmacological stress using technetium-99m-tetrofosmin on a pinhole-collimated cadmium-zinc-telluride–based cardiac single photon emission computed tomography camera with standardized list-mode imaging and processing protocols. Patients had intermediate to high pretest probability of coronary artery disease. MBF was measured locally and at a core laboratory using commercially available software. The time a room was occupied for an MBF study was compared with that for a standard rest/stress myocardial perfusion study.

Results:

With motion correction, the overall correlation in MBF between core laboratory and local site was 0.93 (range, 0.87–0.97) at rest, 0.90 (range, 0.84–0.96) at stress, and 0.84 (range, 0.70–0.92) for myocardial flow reserve. The local-to-core difference in global MBF (bias
-MBF
) was 5.4% (−3.8% to 14.8%; median [interquartile range]) at rest and 5.4% (−6.2% to 19.4%) at stress. Between the 5 sites, bias
-MBF
ranged from −1.6% to 11.0% at rest and from −1.9% to 16.3% at stress; the interquartile range in bias
-MBF
was between 9.3% (4.8%–14.0%) and 22.3% (−10.3% to 12.0%) at rest and between 17.0% (−11.3% to 5.6%) and 33.3% (−10.4% to 22.9%) at stress and was not significantly different between most sites. Both bias and interquartile range were like previously reported interobserver variability and less than the SD of the test-retest difference of 30%. The overall difference in myocardial flow reserve was 1.52% (−10.6% to 11.3%). There were no significant differences between with and without motion correction. The average additional acquisition time varied between sites from 44 to 79 minutes.

Conclusions:

The average bias
-MBF
and bias
-MFR
values were small with standard deviations substantially less than the test-retest variability. This demonstrates that MBF can be measured consistently across multiple sites and further supports that this technique can be reliably implemented.

REGISTRATION:

URL:
https://www.clinicaltrials.gov
; Unique identifier: NCT03427749.
The Electrophysiological Markers of Statistically Learned Attentional Enhancement: Evidence for a Saliency-based Mechanism
Authors: Duncan Dock H. , Theeuwes Jan , van Moorselaar Dirk 
Published: October 2023

Abstract
It is well established that attention can be sharpened through the process of statistical learning (e.g., visual search becomes faster when targets appear at high-relative-to-low probability locations). Although this process of statistically learned attentional enhancement differs behaviorally from the well-studied top–down and bottom–up forms of attention, relatively little work has been done to characterize the electrophysiological correlates of statistically learned attentional enhancement. It thus remains unclear whether statistically learned enhancement recruits any of the same cognitive mechanisms as top–down or bottom–up attention. In the current study, EEG data were collected while participants searched for an ambiguous unique shape in a visual array (the additional singleton task). Unbeknownst to the participants, targets appeared more frequently in one location in space (probability cuing). Encephalographic data were then analyzed in two phases: an anticipatory phase and a reactive phase. In the anticipatory phase preceding search stimuli onset, alpha lateralization as well as the Anterior Directing Attention Negativity and Late Directing Attention Positivity components—signs of preparatory attention known to characterize top–down enhancement—were tested. In the reactive phase, the N2pc component—a well-studied marker of target processing—was examined following stimuli onset. Our results showed that statistically learned attentional enhancement is not characterized by any of the well-known anticipatory markers of top–down attention; yet targets at high probability locations did reliably evoke larger N2pc amplitudes, a finding that is associated with bottom–up attention and saliency. Overall, our findings are consistent with the notion that statistically learned attentional enhancement increases the perceptual salience of items appearing at high-probability locations relative to low-probability locations.