bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Weekly Periodization of Top 5 Tour de France General Classification Finishers: A Multiple Case Study
Authors: Gallo Gabriele , Mateo-March Manuel , Gotti Daniel , Maunder Ed , Codella Roberto , Ruggeri Piero , Faelli Emanuela , Filipas Luca 
Published: September 2023

Purpose: The aim of this study was to describe individual training characteristics, racing strategies, and periodization in preparation for the Tour de France in 2 world-class road cyclists finishing in the top 5 of the general classification. Methods: Week‐by‐week power meter training and racing data of 2 (A and B) road cyclists (age: 29 and 23 y; maximum oxygen consumption: 83 and 81 mL·min−1·kg−1; and relative 20‐min record power output: 6.9 and 6.5 W·kg−1) in the preparation phase (December–July/August) leading up to the Tour de France were retrospectively analyzed. Weekly volume and intensity distribution in power zones were considered. Results: Cyclists A and B completed 46 and 19 races, 22.5 (6.3) and 18.2 (5.1) h·wk−1, with a pyramidal intensity distribution of 81.0%–13.3%–5.7%, and 88.8%–7.9%–3.3% in zone 1–zone 2–zone 3. Cyclist B spent 14 days at altitude. Increased high-intensity volume and polarization index occurred during race weeks. During periods without racing, training intensity progressively increased. Strength training was performed during November and December but not during the following months. During tapering, total exercise volume and time at high intensity decreased. Conclusion: These data provide novel insights into the periodization of world-class road cyclists in advance of a top 5 placing in the Tour de France general classification.
Integrative conjugative elements mediate the high prevalence of
tmexCD3-toprJ1b
in
Proteus
spp. of animal source
Authors: Peng Kai , Li Yangfan , Wang Qiaojun , Yang Pengbin , Wang Zhiqiang , Li Ruichao 
Published: September 2023

ABSTRACT

Integrative conjugative elements (ICEs) are important mobile elements that are associated with the dissemination of antibiotic resistance genes (ARGs) in
Proteus
. Recent studies demonstrated that the tigecycline resistance gene cluster
tmexCD-toprJ
has emerged in ICEs of
Proteus
. However, the prevalence of
tmexCD-toprJ
positive
Proteus
from animal sources is unclear. To cover the gap, a total of 762
Proteus
spp. were isolated from animal source from six provinces of China to identify the
tmexCD-toprJ
positive isolates. Eight
tmexCD-toprJ
positive isolates were identified, with the
tmexCD-toprJ
positive rate of 1.05% against all
Proteus
spp. and 2.79% against ICE-bearing
Proteus
spp. The
tmexCD-toprJ
gene cluster in these
Proteus
spp. were
tmexCD3-toprJ1b
and all of them were carried by ICEs. Genetic structure analysis showed that
tmexCD3-toprJ1b
-bearing ICEs were complicated and plastic, but the
tmexCD3-toprJ1b
was specifically integrated into variable region III (VRIII) of ICEs with the help of integrases. Furthermore, we found that the
umuC
gene, which is presented in VRIII of ICEs and other genetic structures of many other bacterial genomes, was a hotspot for the integration of
tmexCD-toprJ
-bearing potential mobile elements. In summary, our results suggested that
Proteus
were important reservoirs for
tmexCD-toprJ
due to the high prevalence of ICEs. Therefore, continuous surveillance of ICEs-associated ARGs in
Proteus
is necessary and significant for controlling their future transmission.

IMPORTANCE

The emergence and spread of
tmexCD-toprJ
have greatly weakened the function of tigecycline. Although studies have demonstrated the significance of
Proteus
as carriers for
tmexCD-toprJ
, the epidemic mechanism and characteristics of
tmexCD-toprJ
in
Proteus
remain unclear. Herein, we deciphered that the
umuC
gene in VRIII of SXT/R391 ICEs was a hotspot for the integration of
tmexCD3-toprJ1b
-bearing mobile genetic elements by genomic analysis. The mobilization and dissemination of
tmexCD3-toprJ1b
in
Proteus
were mediated by highly prevalent ICEs. Furthermore, the co-occurrence of
tmexCD3-toprJ1b
-bearing ICEs with other chromosomally encoded multidrug resistance gene islands warned that the chromosomes of
Proteus
are significant reservoirs of ARGs. Overall, our results provide significant insights for the prevention and control of
tmexCD3-toprJ1b
in
Proteus
.
Interplay between bacterial 5′-NAD-RNA decapping hydrolase NudC and DEAD-box RNA helicase CsdA in stress responses
Authors: Mickutė Milda , Krasauskas Renatas , Kvederavičiūtė Kotryna , Tupikaitė Gytė , Osipenko Aleksandr , Kaupinis Algirdas , Jazdauskaitė Monika , Mineikaitė Raminta , Valius Mindaugas , Masevičius Viktoras , Vilkaitis Giedrius 
Published: September 2023

ABSTRACT

Both prokaryotic and eukaryotic RNAs can be 5′-capped by the metabolite nicotinamide adenine dinucleotide (NAD). Nudix hydrolases, such as bacterial NudC, specifically remove NAD-caps; however, the molecular and cellular functions of these epitranscriptomic modulators remain elusive. Here, we discuss the roles of NudC under stress conditions and the effects of extracellular cues on the NAD epitranscriptome. Our proteome-wide analysis detected the proteins associated with the RNA degradosome as well as ribosomes and stress-responsive proteins in a NudC interactome. Moreover, we confirmed the physical association of NudC with the cold shock DEAD-box RNA helicase CsdA and the RNA chaperone Hfq. Interestingly, knocking out
csdA
similar to ∆
nudC
leads to an increased number of identified 5′-NAD-RNA species compared to wild type, exposing CsdA as a new player in a potentially unexplored layer of NAD-epitranscriptomic landscape. Mass spectrometry analysis also revealed the drastic up-regulation of 5′-NAD-RNA in response to cold. Furthermore, the inactivation of NudC in bacteria changes the levels of sRNA and protein-coding transcripts associated with bacterial chemotaxis and flagellar assembly pathways. We experimentally demonstrate that the decapping hydrolase NudC suppresses the flagellar movement, while CsdA stimulates it. Thus, the interplay between NudC and CsdA regulates bacterial mobility and coordinates stress-avoidance behavior.

IMPORTANCE
Non-canonical 5′-caps removing RNA hydrolase NudC, along with stress-responsive RNA helicase CsdA, is crucial for 5′-NAD-RNA decapping and bacterial movement.
Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant
Klebsiella pneumoniae
isolated in Chile: high-risk ST25 clones and novel mobile elements
Authors: Veloso Marcelo , Arros Patricio , Acosta Joaquin , Rojas Roberto , Berríos-Pastén Camilo , Varas Macarena , Araya Pamela , Hormazábal Juan Carlos , Allende Miguel L. , Chávez Francisco P. , Lagos Rosalba , Marcoleta Andrés E. 
Published: September 2023

ABSTRACT

Multidrug- and carbapenem-resistant
Klebsiella pneumoniae
(CR-
Kp
) are critical threats to global health and key traffickers of resistance genes to other pathogens. Despite the sustained increase in CR-
Kp
infections in Chile, few strains have been described at the genomic level, lacking details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial susceptibility and performed a comparative genomic analysis of 10 CR-
Kp
isolates from the Chilean surveillance of carbapenem-resistant
Enterobacteriaceae
. High resistance was observed among the isolates (five ST25, three ST11, one ST45, and one ST505), which harbored 44 plasmids, most carrying genes for conjugation and resistance to several antibiotics and biocides. Ten plasmids encoding carbapenemases were characterized, including novel plasmids or variants with additional resistance genes, a novel genetic environment for
bla
KPC-2
, and plasmids widely disseminated in South America. ST25 K2 isolates belonging to CG10224, a clone traced back to 2012 in Chile, which recently acquired
bla
NDM-1
,
bla
NDM-7
, or
bla
KPC-2
plasmids stood out as high-risk clones. Moreover, this corresponds to the first report of ST25 and ST45
Kp
producing NDM-7 in South America and ST505 CR-
Kp
producing both NDM-7 and KPC-2 worldwide. Also, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for a detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of CR
-Kp
in Chile and South America.

IMPORTANCE

In the ongoing antimicrobial resistance crisis, carbapenem-resistant strains of
Klebsiella pneumoniae
are critical threats to public health. Besides globally disseminated clones, the burden of local problem clones remains substantial. Although genomic analysis is a powerful tool for improving pathogen and antimicrobial resistance surveillance, it is still restricted in low- to middle-income countries, including Chile, causing them to be underrepresented in genomic databases and epidemiology surveys. This study provided the first 10 complete genomes of the Chilean surveillance for carbapenem-resistant
K. pneumoniae
in healthcare settings, unveiling their resistance and virulence determinants and the mobile genetic elements mediating their dissemination, placed in the South American and global
K. pneumoniae
epidemiological context. We found ST25 with K2 capsule as an emerging high-risk clone, along with other lineages producing two carbapenemases and several other resistance and virulence genes encoded in novel plasmids and genomic islands.
In vivo
gene expression profile of
Haemophilus influenzae
during human pneumonia
Authors: Polland Linnea , Rydén Hanna , Su Yi , Paulsson Magnus 
Published: September 2023

ABSTRACT

Haemophilus influenzae
is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of
H. influenzae
while the bacteria are in the lung during pneumonia (
in vivo
conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (
in vitro
conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018–2020 (
n
= 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with
H. influenzae
(
n
= 8) and colonies from bacterial cultures (
n
= 6) underwent RNA sequencing. The reads were then pseudo-aligned to core and pan genomes created from 15 reference strains. While bacteria cultured
in vitro
clustered tightly by principal component analysis of core genome (
n
= 1067) gene expression, bacteria in the patient samples had more diverse transcriptomic signatures and did not group with their lab-cultured counterparts. In total, 328 core genes were significantly differentially expressed between
in vitro
and
in vivo
conditions. The most highly upregulated genes
in vivo
included
tbpA
and
fbpA
, which are involved in the acquisition of iron from transferrin, and the stress response gene
msrAB
. The biosynthesis of nucleotides/purines and molybdopterin-scavenging processes were also significantly enriched
in vivo
. In contrast, major metabolic pathways and iron-sequestering genes were downregulated under this condition. In conclusion, extensive transcriptomic differences were found between bacteria while in the human lung and bacteria that were cultured
in vitro
.

IMPORTANCE

The human-specific pathogen
Haemophilus influenzae
is generally not well suited for studying in animal models, and most laboratory models are unlikely to approximate the diverse environments encountered by bacteria in the human airways accurately. Thus, we have examined the global gene expression of
H. influenzae
during pneumonia. Extensive differences in the global gene expression profiles were found in
H. influenzae
while in the human lung compared to bacteria that were grown in the laboratory. In contrast, the gene expression profiles of isolates collected from different patients were found to cluster together when grown under the same laboratory conditions. Interesting observations were made of how
H. influenzae
acquires and uses iron and molybdate, endures oxidative stress, and regulates central metabolism while in the lung. Our results indicate important processes during infection and can guide future research on genes and pathways that are relevant in the pathogenesis of
H. influenzae
pneumonia.
Temporal approach to identifying ectomycorrhizal community associated with Mongolian pine in a desert environment, northern China
Authors: Ren Yue , Gao Guanglei , Ding Guodong , Zhang Ying , Zhao Peishan , Wang Jiayuan 
Published: September 2023

ABSTRACT

To date, the ectomycorrhizal (EM) fungi community has been widely investigated with aging plantations affected by the pedologic factors. However, knowledge on the effects of phenology induced by climatic factors across the age range remains poorly understood on an intra-annual scale. Here, we sampled the fine roots of Mongolian pine (
Pinus sylvestris
var.
mongolica
) plantations at different stages of the growing season (from April to September) across three stand ages (27, 34, and 44 yr) in the Mu Us Desert, Northwest China. We aim to disentangle the community composition and structure of EM fungi, as well as the impact of climate on EM fungi. We observed that the 173 distinct EM fungal operational taxonomic units (OTUs) were identified.
Geopora
,
Inocybe
,
Tomentella,
and
Tuber
were the most frequent, and their dominance was maintained as stand aging. The richness and community composition were not significantly different with stand aging (
P
> 0.05). Host phenology and stand age are two important factors that have shaped the EM fungal community. The growing stage affected the beta diversity of the EM fungal community more than stand age, and this variation of the EM fungal community was closely related to seasonal climate, particularly precipitation. This improved information will provide a theoretical basis for the reforestation and rehabilitation of the Mongolian pine plantations using mycorrhizal techniques.

IMPORTANCE

Ectomycorrhizal (EM) fungi are particularly important for host plants in a desert ecosystem. With a high degree of plasticity, EM fungi are largely influenced by host plant and environmental variables and fundamentally contribute to the ability of individuals to adapt to environmental changes. Therefore, the EM fungi are important for Mongolian pine (
Pinus sylvestris
var.
mongolica
) plantation in a desert ecosystem. Although previous studies have concluded that multiple endogenous and exogenous processes ultimately lead to species-specific temporal patterns in EM fungal populations. We still neglect the effect of host phenology on EM fungal activity. The significance of our study is the interplay between climate-driven EM fungi and plant phenology.
Canine respiratory coronavirus in Thailand undergoes mutation and evidences a potential putative parent for genetic recombination
Authors: Poonsin Panida , Wiwatvisawakorn Vorapun , Chansaenroj Jira , Poovorawan Yong , Piewbang Chutchai , Techangamsuwan Somporn 
Published: September 2023

ABSTRACT
Canine respiratory coronavirus (CRCoV) is associated with canine infectious respiratory disease complex. Although its detection has been reported worldwide, the genomic characteristics and evolutionary patterns of this virus remain poorly defined. In this study, 21 CRCoV sequences obtained from dogs in Thailand during two episodes (2013–2015, group A; 2021–2022, group B) were characterized and analyzed. The genomic characteristics of Thai CRCoVs changed from 2013 to 2022 and showed a distinct phylogenetic cluster. Phylogenetic analysis of the spike (S) genes divided the analyzed CRCoV strains into five clades. The full-length genome characterization revealed that all Thai CRCoVs possessed a nonsense mutation within the nonstructural gene located between the S and envelope genes, leading to a truncated putative nonstructural protein. Group B Thai CRCoV strains represented the signature nonsynonymous mutations in the S gene that was not identified in group A Thai CRCoVs, suggesting the ongoing evolutionary process of Thai CRCoVs. Although no evidence of recombination of Thai CRCoV strains was found, our analysis identified one Thai CRCoV strain as a potential parent virus for a CRCoV strain found in the United States. Selective pressure analysis of the hypervariable S region indicated that the CRCoV had undergone purifying selection during evolution. Evolutionary analysis suggested that the CRCoV was emerged in 1992 and was first introduced in Thailand in 2004, sharing a common ancestor with Korean CRCoV strains. These findings regarding the genetic characterization and evolutionary analysis of CRCoVs add to the understanding of CRCoVs.

IMPORTANCE
Knowledge of genomic characterization of the CRCoV is still limited and its evolution remains poorly investigated. We, therefore, investigated the full-length genome of CRCoV in Thailand for the first time and analyzed the evolutionary dynamic of CRCoV. Genomic characterization of Thai CRCoV strains revealed that they possess unique genome structures and have undergone nonsynonymous mutations, which have not been reported in previously described CRCoV strains. Our work suggests that the Thai CRCoVs were not undergone mutation through genetic recombination for their evolution. However, one Thai CRCoV strain PP158_THA_2015 was found to be a potential parent virus for the CRCoV strains found in the United States. This study provides an understanding of the genomic characterization and highlights the signature mutations and ongoing evolutionary process of CRCoV that could be crucial for monitoring in the future.
Host-specific adaptation drove the coevolution of leek yellow stripe virus and
Allium
plants
Authors: Kawakubo Shusuke , Kim Hangil , Takeshita Minoru , Masuta Chikara 
Published: September 2023

ABSTRACT

Host adaptation plays a crucial role in virus evolution and is a consequence of long-term interactions between virus and host in a complex arms race between host RNA silencing and viral RNA silencing suppressor (RSS) as counterdefense. Leek yellow stripe virus (LYSV), a potyvirus causing yield loss of garlic, infects several species of
Allium
plants. The unexpected discovery of an interspecific hybrid of garlic, leek, and great-headed (GH) garlic motivated us to explore the host-adaptive evolution of LYSV. Here, using Bayesian phylogenetic comparative methods and a functional assay of viral RSS activity, we show that the evolutionary context of LYSV has been shaped by the host adaptation of the virus during its coevolution with
Allium
plants. Our phylogenetic analysis revealed that LYSV isolates from leek and their taxonomic relatives (
Allium ampeloprasum
complex; AAC) formed a distinct monophyletic clade separate from garlic isolates and are likely to be uniquely adapted to AAC. Our comparative studies on viral accumulation indicated that LYSV accumulated at a low level in leek, whereas LYSVs were abundant in other
Allium
species such as garlic and its relatives. When RSS activity of the viral P1 and HC-Pro of leek LYSV isolate was analyzed, significant synergism in RSS activity between the two proteins was observed in leek but not in other species, suggesting that viral RSS activity may be important for the viral host-specific adaptation. We thus consider that LYSV may have undergone host-specific evolution at least in leek, which must be driven by speciation of its
Allium
hosts.

IMPORTANCE

Potyviruses are the most abundant plant RNA viruses and are extremely diversified in terms of their wide host range. Due to frequent host switching during their evolution, host-specific adaptation of potyviruses may have been shaped by numerous host factors. However, any critical determinants for viral host range remain largely unknown, possibly because of the repeated gain and loss of virus infectivity of plants. Leek yellow stripe virus (LYSV) is a species of the genus
Potyvirus
, which has a relatively narrow host range, generally limited to hosts in the genus
Allium
. Our investigations on leek and leek relatives (
Allium ampeloprasum
complex), which must have been generated through interspecies hybridization, revealed that LYSV accumulation remained low in leek as a result of viral host adaptation in competition with host resistance such as RNA silencing. This study presents LYSV as an ideal model to study the process of host-adaptive evolution and virus-host coevolution.
Eugenol works synergistically with colistin against colistin-resistant
Pseudomonas aeruginosa
and
Klebsiella pneumoniae
isolates by enhancing membrane permeability
Authors: Kong Jingchun , Wang Yue , Yao Zhuocheng , Lin Yishuai , Zhang Yi , Han Yijia , Zhou Tieli , Ye Jianzhong , Cao Jianming 
Published: September 2023

ABSTRACT

Colistin is a potent antibiotic for the treatment of carbapenem-resistant Gram-negative bacteria and is considered a last-resort drug. Unfortunately, the incidence of colistin-resistant bacteria isolated from patients is continuously growing due to clinical reuse of colistin. In this study, we found that the combination of colistin and eugenol has a significant synergistic antibacterial effect and reverses the sensitivity of colistin-resistant
Pseudomonas aeruginosa
and
Klebsiella pneumoniae
against colistin, as confirmed by checkerboard and time-kill assays. Crystal violet staining and scanning electron microscopy revealed colistin and eugenol’s synergistic antibiofilm action. Concerning the synergy mechanism, the results revealed that the combination of eugenol and colistin increases membrane permeability and causes considerable membrane damage, further inhibiting bacteria synergistically. Meanwhile, up to 500 µg/mL of eugenol is non-toxic to RAW 264.7 cells, and the colistin/eugenol combination is also efficacious
in vivo
, as demonstrated by the
Galleria mellonella
infection model. Our findings indicate that the colistin/eugenol combination is a viable treatment option for colistin-resistant
P. aeruginosa
and
K. pneumoniae
clinical infections.

IMPORTANCE

Colistin is used as a last resort for severe infections caused by multidrug-resistant Gram-negative bacteria, however, colistin resistance is increasing. As a result, we investigated the synergistic effect of eugenol/colistin combination, and the results revealed significant antibacterial and antibiofilm action. Eugenol may help clinical colistin-resistant
Pseudomonas aeruginosa
and
Klebsiella pneumoniae
recover their susceptibility. These findings suggest that combining eugenol and colistin may be a viable treatment option for colistin-resistant pathogen clinical infections.