bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functionality of IAV packaging signals depends on site-specific charges within the viral nucleoprotein
Authors: Ciminski Kevin , Flore Viktoria , Jakob Celia , Mues Helen , Smedegaard Frederiksen Anne , Schwemmle Martin , Bolte Hardin , Giese Sebastian 
Published: March 2024

ABSTRACT

The coordinated packaging of the segmented genome of the influenza A virus (IAV) into virions is an essential step of the viral life cycle. This process is controlled by the interaction of packaging signals present in all eight viral RNA (vRNA) segments and the viral nucleoprotein (NP), which binds vRNA via a positively charged binding groove. However, mechanistic models of how the packaging signals and NP work together to coordinate genome packaging are missing. Here, we studied genome packaging in influenza A/SC35M virus mutants that carry mutated packaging signals as well as specific amino acid substitutions at the highly conserved lysine (K) residues 184 and 229 in the RNA-binding groove of NP. Because these lysines are acetylated and thus neutrally charged in infected host cells, we replaced them with glutamine to mimic the acetylated, neutrally charged state or arginine to mimic the non-acetylated, positively charged state. Our analysis shows that the coordinated packaging of eight vRNAs is influenced by (i) the charge state of the replacing amino acid and (ii) its location within the RNA-binding groove. Accordingly, we propose that lysine acetylation induces different charge states within the RNA-binding groove of NP, thereby supporting the activity of specific packaging signals during coordinated genome packaging.

IMPORTANCE
Influenza A viruses (IAVs) have a segmented viral RNA (vRNA) genome encapsidated by multiple copies of the viral nucleoprotein (NP) and organized into eight distinct viral ribonucleoprotein complexes. Although genome segmentation contributes significantly to viral evolution and adaptation, it requires a highly sophisticated genome-packaging mechanism. How eight distinct genome complexes are incorporated into the virion is poorly understood, but previous research suggests an essential role for both vRNA packaging signals and highly conserved NP amino acids. By demonstrating that the packaging process is controlled by charge-dependent interactions of highly conserved lysine residues in NP and vRNA packaging signals, our study provides new insights into the sophisticated packaging mechanism of IAVs.
SP-CHAP, an endolysin with enhanced activity against biofilm pneumococci and nasopharyngeal colonization
Authors: Alreja Adit B. , Appel Amanda E. , Zhu Jinyi C. , Riley Sean P. , Gonzalez-Juarbe Norberto , Nelson Daniel C. 
Published: March 2024

ABSTRACT

Streptococcus pneumoniae
(
Spn
), a Gram-positive bacterium, is responsible for causing a wide variety of invasive infections. The emergence of multi-drug antibiotic resistance has prompted the search for antimicrobial alternatives. Phage-derived peptidoglycan hydrolases, known as endolysins, are an attractive alternative. In this study, an endolysin active against
Spn
, designated SP-CHAP, was cloned, produced, purified, biochemically characterized, and evaluated for its antimicrobial properties. Cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domains are widely represented in bacteriophage endolysins but have never previously been reported for pneumococcal endolysins. Here, we characterize the first pneumococcal endolysin with a CHAP catalytic domain. SP-CHAP was antimicrobial against all
Spn
serovars tested, including capsular and capsule-free pneumococci, and it was found to be more active than the most widely studied pneumococcal endolysin, Cpl-1, while not affecting various oral or nasal commensal organisms tested. SP-CHAP was also effective in eradicating
Spn
biofilms at concentrations as low as 1.56 µg/mL. In addition, a
Spn
mouse nasopharyngeal colonization model was employed, which showed that SP-CHAP caused a significant reduction in
Spn
colony-forming units, even more than Cpl-1. These results indicate that SP-CHAP may represent a promising alternative to combating
Spn
infections.

IMPORTANCE

Considering the high rates of pneumococcal resistance reported for several antibiotics, alternatives are urgently needed. In the present study, we report a
Streptococcus pneumoniae
-targeting endolysin with even greater activity than Cpl-1, the most characterized pneumococcal endolysin to date. We have employed a combination of biochemical and microbiological assays to assess the stability and lytic potential of SP-CHAP and demonstrate its efficacy on pneumococcal biofilms
in vitro
and in an
in vivo
mouse model of colonization. Our findings highlight the therapeutic potential of SP-CHAP as an antibiotic alternative to treat
Streptococcus pneumoniae
infections.
Is
Candida auris
the first multidrug-resistant fungal zoonosis emerging from climate change?
Authors: Garcia-Bustos Victor 
Published: March 2024

ABSTRACT

The emergence and evolutionary path of
Candida
auris poses an intriguing scientific enigma. Its isolation from a pet dog’s oral cavity in Kansas, reported by White et al. (T. C. White, B. D. Esquivel, E. M. Rouse Salcido, A. M. Schweiker, et al., mBio 15:e03080-23, 2024,
https://doi.org/10.1128/mbio.03080-23
), carries significant implications. This discovery intensifies concerns about its hypothetical capacity for zoonotic transmission, particularly considering the dog’s extensive human contact and the absence of secondary animal/human cases in both animals and humans. The findings challenge established notions of
C. auris
transmissibility and underscore the need for further investigation into the transmission dynamics, especially zooanthroponotic pathways. It raises concerns about its adaptability in different hosts and environments, highlighting potential role of environmental and animal reservoirs in its dissemination. Critical points include the evolving thermal tolerance and the genetic divergence in the isolate. This case exemplifies the necessity for an integrated One Health approach, combining human, animal, and environmental health perspectives, to unravel the complexities of
C. auris
’s emergence and behavior.
The impact of orphan histidine kinases and phosphotransfer proteins on the regulation of clostridial sporulation initiation
Authors: Mehdizadeh Gohari Iman , Edwards Adrianne N. , McBride Shonna M. , McClane Bruce A. 
Published: March 2024

ABSTRACT

Sporulation is an important feature of the clostridial life cycle, facilitating survival of these bacteria in harsh environments, contributing to disease transmission for pathogenic species, and sharing common early steps that are also involved in regulating industrially important solvent production by some non-pathogenic species. Initial genomics studies suggested that Clostridia lack the classical phosphorelay that phosphorylates Spo0A and initiates sporulation in
Bacillus
, leading to the hypothesis that sporulation in Clostridia universally begins when Spo0A is phosphorylated by orphan histidine kinases (OHKs). However, components of the classical
Bacillus
phosphorelay were recently identified in some Clostridia. Similar
Bacillus
phosphorelay components have not yet been found in the pathogenic Clostridia or the solventogenic Clostridia of industrial importance. For some of those Clostridia lacking a classical phosphorelay, the involvement of OHKs in sporulation initiation has received support from genetic studies demonstrating the involvement of several apparent OHKs in their sporulation. In addition, several clostridial OHKs directly phosphorylate Spo0A
in vitro
. Interestingly, there is considerable protein domain diversity among the sporulation-associated OHKs in Clostridia. Further adding to the emergent complexity of sporulation initiation in Clostridia, several candidate OHK phosphotransfer proteins that were OHK candidates were shown to function as phosphatases that reduce sporulation in some Clostridia. The mounting evidence indicates that no single pathway explains sporulation initiation in all Clostridia and supports the need for further study to fully understand the unexpected and biologically fascinating mechanistic diversity of this important process among these medically and industrially important bacteria.
Redefining development in
Streptomyces venezuelae
: integrating exploration into the classical sporulating life cycle
Authors: Shepherdson Evan M. F. , Elliot Marie A. 
Published: March 2024

ABSTRACT

Two growth modes have been described for the filamentous
Streptomyces
bacteria. Their classic developmental life cycle culminates in the formation of dormant spores, where movement to new environments is mediated through spore dispersal. In contrast, exploratory growth proceeds as a rapidly expanding vegetative mycelium that leads to extensive surface colonization and is associated with the release of volatile compounds that promote alkalinization (and reduced iron bioavailability) of its surrounding environment. Here, we report that exploratory growth in
Streptomyces venezuelae
can proceed in tandem with classic sporulating development in response to specific nutritional cues. Sporulating exploration is not accompanied by a rise in environmental pH but has the same iron acquisition requirements as conventional exploration. We found that mutants that were defective in their ability to sporulate were unaffected in exploration, but mutants undergoing precocious sporulation were compromised in their exploratory growth and this appeared to be mediated through premature activation of the developmental regulator WhiI. Cell envelope integrity was also found to be critical for exploration, as mutations in the cell envelope stress-responsive extracytoplasmic function sigma factor SigE led to a failure to explore robustly under all exploration-promoting conditions. Finally, in expanding the known exploration-promoting conditions, we discovered that the model species
Streptomyces lividans
exhibited exploration capabilities, supporting the proposal that exploration is conserved across diverse streptomycetes.

IMPORTANCE

Streptomyces
bacteria have evolved diverse developmental and metabolic strategies to thrive in dynamic environmental niches. Here, we report the amalgamation of previously disparate developmental pathways, showing that colony expansion via exploration can proceed in tandem with colony sporulation. This developmental integration extends beyond phenotype to include shared genetic elements, with sporulation-specific repressors being required for successful exploration. Comparing this new exploration mode with previously identified strategies has revealed key differences (e.g., no need for environmental alkalinization), and simultaneously allowed us to define unifying requirements for
Streptomyces
exploration. The “reproductive exploration” phenomenon reported here represents a unique bet-hedging strategy, with the
Streptomyces
colony engaging in an aggressive colonization strategy while transporting a protected genetic repository.
Comparison of metagenomic and traditional methods for diagnosis of
E. coli
enteric infections
Authors: Royer C. , Patin N. V. , Jesser K. J. , Peña-Gonzalez A. , Hatt J. K. , Trueba G. , Levy K. , Konstantinidis K. T. 
Published: March 2024

ABSTRACT

Diarrheagenic
Escherichia coli
, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality
E. coli
metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent
E. coli
(DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance.

IMPORTANCE
Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.
Coding-complete genome sequences of rabbit hemorrhagic disease virus type 2 detected in 2023 in Washington State indicate a divergent incursion into the United States
Authors: Pauszek Steven J. , Waters Kaitlyn , Mohamed Fawzi , Lakin Steven M. , Moran Karen , Minor Montariel , Creekmore Lynn , Makhdoomi Muzafar , Faburay Bonto 
Published: March 2024

ABSTRACT

Three rabbit hemorrhagic disease virus type 2 (RHDV2) coding-complete genome sequences were obtained from domestic and wild rabbits in Washington State in June and July 2023. These three RHDV2 sequences are <82% identical to previous RHDV2 sequences in North America and likely indicate a discrete incursion.
Complete genome sequence of plasmid-bearing aerotolerant
Campylobacter jejuni
strain S2-20 isolated from retail chicken meat
Authors: Karki Anand B. , Delaborte Elise , Fakhr Mohamed K. 
Published: March 2024

ABSTRACT

Complete genome sequencing of aerotolerant
Campylobacter jejuni
strain S2-20 revealed the presence of a chromosome of 1,695,449 bp and a plasmid of 49,741 bp that contains predicted antimicrobial resistance and type IV secretion system genes. The chromosome harbored several putative oxidative stress genes with potential roles in aerotolerance.
Whole-genome sequence of
Kosakonia cowanii
strain W006, isolated from seeds of
Triticum aestivum
L.
Authors: Chebotar Vladimir K. , Gancheva Maria S. , Chizhevskaya Elena P. , Keleinikova Oksana V. , Baganova Maria E. , Zaplatkin Alexander N. , Husainov Kharon A. 
Published: March 2024

ABSTRACT

In this study, we sequence, assemble, and annotate
Kosakonia cowanii
strain W006, isolated from seeds of
Triticum aestivum
L. W006 has a single circular chromosome of 4,788,099 bp and 4,466 genes, with a mean G +C content of 56.1%.
Complete genome sequence of
Escherichia coli
MP1
Authors: Pick Kat , Stothard Paul , Raivio Tracy L. 
Published: March 2024

ABSTRACT

Here, we report the complete genome sequence of
Escherichia coli
strain MP1, consisting of one circular chromosome and one circular plasmid. Long-read assembly was performed using a consensus approach, followed by long- and short-read polishing, and gene annotation.
Complete genome sequence of
Paraburkholderia
sp. strain 22B1P capable of utilizing 3-chlorobenzoate as a carbon source
Authors: Moriuchi Ryota , Sano Rion , Fujii Shuma , Suzuki Yuito , Makita Miyune , Kawashima Yo , Shirakawa Takumi , Shindo Renki , Shinkai Tatsumi , Miura Kaede , Hirose Moka , Nakajima Momiji , Kurokawa Asahi , Chetia Rituparna , Hirokawa Chiharu , Suzuki Tomoko , Ito Yukiko , Murano Hiroki , Dohra Hideo , Ogawa Naoto , Kanesaki Yu 
Published: March 2024

ABSTRACT

Paraburkholderia
sp. strain 22B1P utilizes 3-chlorobenzoate as a carbon source. Complete genome sequencing of strain 22B1P revealed two chromosomes and two plasmids. The genes involved in the conversion of 3-chlorobenzoate to 3-chlorocatechol and those involved in the conversion of 3-chlorocatechol to 3-oxoadipate were located on chromosomes 2 and 1, respectively.
Complete genome sequence of
Acidovorax temperans
strain LMJ isolated from a contaminated
Chlamydomonas reinhardtii
Tris-Acetate-Phosphate medium culture plate
Authors: Mitra Mautusi , Stanescu Ana 
Published: March 2024

ABSTRACT

A heavy metal and xenobiotic-tolerant strain of
Acidovorax temperans
strain LMJ was isolated from a contaminated Tris-Acetate-Phosphate medium plate of a green micro-alga,
Chlamydomonas reinhardtii
. Here, we report the complete genome sequence of this strain to provide insights into its survival strategies and nearest taxonomic neighbor.
Diaphorobacter nitroreducens
synergize with oxaliplatin to reduce tumor burden in mice with lung adenocarcinoma
Authors: Ni Yalan , Li Rui , Shen Xiaoyu , Yi Deli , Ren Yilin , Wang Fudong , Geng Yan , You Qingjun 
Published: March 2024

ABSTRACT

Lung adenocarcinoma (LADC) is the most common lung cancer and the leading cause of cancer-related deaths globally. Accumulating evidence suggests that the gut microbiota regulates the host response to chemotherapeutic drugs and can be targeted to reduce the toxicity of current chemotherapeutic agents. However, the effect of
Diaphorobacter nitroreducens
synergized with oxaliplatin on the gut microbiota and their impact on LADC have never been explored. This study aimed to evaluate the anti-cancer effects of
D. nitroreducens
, oxaliplatin, and their combined treatment on tumor growth in tumor-bearing mice. The composition of gut microbiota and the immune infiltration of tumors were evaluated by using 16S rRNA gene high-throughput sequencing and immunofluorescence, respectively. The inhibitory effect of the combination treatment with
D. nitroreducens
and oxaliplatin was significantly stronger than that of oxaliplatin alone in tumor-bearing mice. Furthermore, we observed that the combination treatment significantly increased the relative abundance of
Lactobacillus
and
Akkermansia
in the gut microbiota. Meanwhile, the combination treatment significantly increased the proportions of macrophage but decreased the proportion of regulatory T cells in the LADC tumor tissues of mice. These findings underscored the relationship between
D. nitroreducens
and the gut microbiota-immune cell-LADC axis, highlighting potential therapeutic avenues for LADC treatment.

IMPORTANCE

Oxaliplatin is widely used as an effective chemotherapeutic agent in cancer treatment, but its side effects and response rate still need to be improved. Conventional probiotics potentially benefit cancer chemotherapy by regulating gut microbiota and tumor immune infiltration. This study was novel in reporting a more significant inhibitory effect of
Diaphorobacter nitroreducens
on lung adenocarcinoma (LADC) cells compared with common traditional probiotics and validating its potential as an adjuvant therapy for LADC chemotherapy in mice. This study investigated the impact of
D. nitroreducens
combined with oxaliplatin on the gut microbiota and immune infiltration of tumors as a potential mechanism to improve anticancer effects.
Revisiting the dynamics of interacting vector-like dark energy
Authors: Rodriguez-Benites Carlos , Gonzalez-Espinoza Manuel , Otalora Giovanni , Alva-Morales Manuel 
Published: March 2024

AbstractWe revise the dynamics of interacting vector-like dark energy, a theoretical framework proposed to explain the accelerated expansion of the universe. By investigating the interaction between vector-like dark energy and dark matter, we analyze its effects on the cosmic expansion history and the thermodynamics of the accelerating universe. Our results demonstrate that the presence of interaction significantly influences the evolution of vector-like dark energy, leading to distinct features in its equation of state and energy density. We compare our findings with observational data and highlight the importance of considering interactions in future cosmological studies.
Single field inflation in the light of Pulsar Timing Array Data: quintessential interpretation of blue tilted tensor spectrum through Non-Bunch Davies initial condition
Authors: Choudhury Sayantan 
Published: March 2024

AbstractIn this work, we present a quintessential interpretation of having a blue-tilted tensor power spectrum for canonical single-field slow-roll inflation to explain the recently observed Pulsar Timing Array (NANOGrav 15-year and EPTA) signal of Gravitational Waves (GW). We formulate the complete semi-classical description of cosmological perturbation theory in terms of scalar and tensor modes using the Non-Bunch Davies initial condition. We found that the existence of the blue tilt $$(n_t)$$

(

n
t

)

within the favoured range $$1.2<n_t<2.5$$

1.2
<

n
t

<
2.5

can be explained in terms of a newly derived consistency relation. Further, we compute a new field excursion formula using the Non-Bunch Davies initial condition, that validates the requirement of Effective Field Theory in the sub-Planckian regime, $$|\Delta \phi |\ll M_{\textrm{pl}}$$

|
Δ
ϕ
|

≪

M
pl

for the allowed value of the tensor-to-scalar ratio, $$r<0.06$$

r
<
0.06

from CMB observations. In our study, we refer to this result as Anti Lyth bound as it violates the well-known Lyth bound originally derived for Bunch Davies initial condition. Further, we study the behaviour of the spectral density of GW and the associated abundance with the frequency, which shows that within the frequency domain $$10^{-9}~{\textrm{Hz}}<f<10^{-7}~{\textrm{Hz}}$$

10

-
9

Hz
<
f
<

10

-
7

Hz

the outcome obtained from our analysis is completely consistent with the Pulsar Timing Array (NANOGrav 15-year and EPTA) signal. Also, we found that the behaviour of GW spectra satisfies the CMB constraints at the low frequency, $$f_*\sim 7.7\times 10^{-17}~{\textrm{Hz}}$$

f

∗

∼
7.7
×

10

-
17

Hz

corresponding to the pivots scale wave number, $$k_*\sim 0.05~{\textrm{Mpc}}^{-1}.$$

k

∗

∼
0.05

Mpc

-
1

.

Finally, the sharp falling behaviour of the GW spectra within the frequency domain $$10^{-7}~{\textrm{Hz}}<f<1~{\textrm{Hz}}$$

10

-
7

Hz
<
f
<
1

Hz

validates our theory in the comparatively high-frequency regime as well.
Electric and dilatonic fields of a charged massive particle at rest in the field of a charged dilaton black hole
Authors: Kan Nahomi , Shiraishi Kiyoshi 
Published: March 2024

AbstractWe study linear-perturbation equations for the two-body system of a charged dilaton black hole, of which dilaton coupling constant is $$\alpha $$
α
, and a static particle with mass m, electric charge q, and dilatonic charge $$\beta m$$

β
m

. We find that a consistent condition for the coupled equations corresponds to the equilibrium condition of the test particle. The expressions of classical fields are given in closed analytical formulas in the most interesting case with $$\beta =\alpha $$

β
=
α

. We examine the electrical field around a charged dilaton black hole especially in the limit of the maximum electric charge and we find the electric Meissner effect which has been found for the Reissner–Nordström black hole in the Einstein–Maxwell system.