bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scrutinizing a
Lactococcus lactis
mutant with enhanced capacity for extracellular electron transfer reveals a unique role for a novel type-II NADH dehydrogenase
Authors: Gu Liuyan , Zhao Shuangqing , Tadesse Belay Tilahun , Zhao Ge , Solem Christian 
Published: April 2024

ABSTRACT

Lactococcus lactis,
a lactic acid bacterium used in food fermentations and commonly found in the human gut, is known to possess a fermentative metabolism.
L. lactis
, however, has been demonstrated to transfer metabolically generated electrons to external electron acceptors, a process termed extracellular electron transfer (EET). Here, we investigated an
L. lactis
mutant with an unusually high capacity for EET that was obtained in an adaptive laboratory evolution (ALE) experiment. First, we investigated how global gene expression had changed, and found that amino acid metabolism and nucleotide metabolism had been affected significantly. One of the most significantly upregulated genes encoded the NADH dehydrogenase NoxB. We found that this upregulation was due to a mutation in the promoter region of NoxB, which abolished carbon catabolite repression. A unique role of NoxB in EET could be attributed and it was directly verified, for the first time, that NoxB could support respiration in
L. lactis
. NoxB, was shown to be a novel type-II NADH dehydrogenase that is widely distributed among gut microorganisms. This work expands our understanding of EET in Gram-positive electroactive microorganisms and the special significance of a novel type-II NADH dehydrogenase in EET.

IMPORTANCE

Electroactive microorganisms with extracellular electron transfer (EET) ability play important roles in biotechnology and ecosystems. To date, there have been many investigations aiming at elucidating the mechanisms behind EET, and determining the relevance of EET for microorganisms in different niches. However, how EET can be enhanced and harnessed for biotechnological applications has been less explored. Here, we compare the transcriptomes of an EET-enhanced
L. lactis
mutant with its parent and elucidate the underlying reason for its superior performance. We find that one of the most significantly upregulated genes is the gene encoding the NADH dehydrogenase NoxB, and that upregulation is due to a mutation in the catabolite-responsive element that abolishes carbon catabolite repression. We demonstrate that NoxB has a special role in EET, and furthermore show that it supports respiration to oxygen, which has never been done previously. In addition, a search reveals that this novel NoxB-type NADH dehydrogenase is widely distributed among gut microorganisms.
Peptidoglycan fragment release and NOD activation by commensal
Neisseria
species from humans and other animals
Authors: Harris-Jones Tiffany N. , Chan Jia Mun , Hackett Kathleen T. , Weyand Nathan J. , Schaub Ryan E. , Dillard Joseph P. 
Published: April 2024

ABSTRACT

Neisseria gonorrhoeae
, a human restricted pathogen, releases inflammatory peptidoglycan (PG) fragments that contribute to the pathophysiology of pelvic inflammatory disease. The genus
Neisseria
is also home to multiple species of human- or animal-associated
Neisseria
that form part of the normal microbiota. Here we characterized PG release from the human-associated nonpathogenic species
Neisseria lactamica
and
Neisseria mucosa
and animal-associated
Neisseria
from macaques and wild mice. An
N. mucosa
strain and an
N. lactamica
strain were found to release limited amounts of the proinflammatory monomeric PG fragments. However, a single amino acid difference in the PG fragment permease AmpG resulted in increased PG fragment release in a second
N. lactamica
strain examined.
Neisseria
isolated from macaques also showed substantial release of PG monomers. The mouse colonizer
Neisseria musculi
exhibited PG fragment release similar to that seen in
N. gonorrhoeae
with PG monomers being the predominant fragments released. All the human-associated species were able to stimulate NOD1 and NOD2 responses.
N. musculi
was a poor inducer of mouse NOD1, but
ldcA
mutation increased this response. The ability to genetically manipulate
N. musculi
and examine effects of different PG fragments or differing amounts of PG fragments during mouse colonization will lead to a better understanding of the roles of PG in
Neisseria
infections. Overall, we found that only some nonpathogenic
Neisseria
have diminished release of proinflammatory PG fragments, and there are differences even within a species as to types and amounts of PG fragments released.
Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II
Authors: Keown Jeremy , Baazaoui Alaa , Šebesta Marek , Štefl Richard , Carrique Loïc , Fodor Ervin , Grimes Jonathan M. 
Published: April 2024

ABSTRACT

Influenza A viruses, causing seasonal epidemics and occasional pandemics, rely on interactions with host proteins for their RNA genome transcription and replication. The viral RNA polymerase utilizes host RNA polymerase II (Pol II) and interacts with the serine 5 phosphorylated (pS5) C-terminal domain (CTD) of Pol II to initiate transcription. Our study, using single-particle electron cryomicroscopy (cryo-EM), reveals the structure of the 1918 pandemic influenza A virus polymerase bound to a synthetic pS5 CTD peptide composed of four heptad repeats mimicking the 52 heptad repeat mammalian Pol II CTD. The structure shows that the CTD peptide binds at the C-terminal domain of the PA viral polymerase subunit (PA-C) and reveals a previously unobserved position of the 627 domain of the PB2 subunit near the CTD. We identify crucial residues of the CTD peptide that mediate interactions with positively charged cavities on PA-C, explaining the preference of the viral polymerase for pS5 CTD. Functional analysis of mutants targeting the CTD-binding site within PA-C reveals reduced transcriptional function or defects in replication, highlighting the multifunctional role of PA-C in viral RNA synthesis. Our study provides insights into the structural and functional aspects of the influenza virus polymerase-host Pol II interaction and identifies a target for antiviral development.

IMPORTANCE
Understanding the intricate interactions between influenza A viruses and host proteins is crucial for developing targeted antiviral strategies. This study employs advanced imaging techniques to uncover the structural nuances of the 1918 pandemic influenza A virus polymerase bound to a specific host protein, shedding light on the vital process of viral RNA synthesis. The study identifies key amino acid residues in the influenza polymerase involved in binding host polymerase II (Pol II) and highlights their role in both viral transcription and genome replication. These findings not only deepen our understanding of the influenza virus life cycle but also pinpoint a potential target for antiviral development. By elucidating the structural and functional aspects of the influenza virus polymerase-host Pol II interaction, this research provides a foundation for designing interventions to disrupt viral replication and transcription, offering promising avenues for future antiviral therapies.
Lack of physiological evidence for cytochrome filaments functioning as conduits for extracellular electron transfer
Authors: Schwarz Ingrid A. , Alsaqri Baha , Lekbach Yassir , Henry Kathryn , Gorman Sydney , Woodard Trevor , Dion Laura , Real Lauren , Holmes Dawn E. , Smith Jessica A. , Lovley Derek R. 
Published: April 2024

ABSTRACT

Extracellular cytochrome filaments are proposed to serve as conduits for long-range extracellular electron transfer. The primary functional physiological evidence has been the reported inhibition of
Geobacter sulfurreducens
Fe(III) oxide reduction when the gene for the filament-forming cytochrome OmcS is deleted. Here we report that the OmcS-deficient strain from that original report reduces Fe(III) oxide as well as the wild-type, as does a triple mutant in which the genes for the other known filament-forming cytochromes were also deleted. The triple cytochrome mutant displayed filaments with the same 3 nm diameter morphology and conductance as those produced by
Escherichia coli
heterologously expressing the
G. sulfurreducens
PilA pilin gene. Fe(III) oxide reduction was inhibited when the pilin gene in cytochrome-deficient mutants was modified to yield poorly conductive 3 nm diameter filaments. The results are consistent with the concept that 3 nm diameter electrically conductive pili (e-pili) are required for
G. sulfurreducens
long-range extracellular electron transfer. In contrast, rigorous physiological functional evidence is lacking for cytochrome filaments serving as conduits for long-range electron transport.

IMPORTANCE

Unraveling microbial extracellular electron transfer mechanisms has profound implications for environmental processes and advancing biological applications. This study on
Geobacter sulfurreducens
challenges prevailing beliefs on cytochrome filaments as crucial components thought to facilitate long-range electron transport. The discovery of an OmcS-deficient strain’s unexpected effectiveness in Fe(III) oxide reduction prompted a reevaluation of the key conduits for extracellular electron transfer. By exploring the impact of genetic modifications on
G. sulfurreducens
’ performance, this research sheds light on the importance of 3-nm diameter electrically conductive pili in Fe(III) oxide reduction. Reassessing these mechanisms is essential for uncovering the true drivers of extracellular electron transfer in microbial systems, offering insights that could revolutionize applications across diverse fields.
Annotation of 2,507
Saccharomyces cerevisiae
genomes
Authors: Wang Meng , Li Xuan , Liu Xian , Hou Xiaoping , He Yang , Yu Jun-Hong , Hu Shumin , Yin Hua , Xie Bin-Bin 
Published: April 2024

ABSTRACT

Saccharomyces cerevisiae
(baker’s yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Currently, a huge number of
Saccharomyces cerevisiae
genome sequences are available at the public domain. However, these genomes are distributed at different websites and a large number of them are released without annotation information. To provide one complete annotated genome data resource, we collected 2,507
Saccharomyces cerevisiae
genome assemblies and re-annotated 2,506 assemblies using a custom annotation pipeline, producing a total of 15,407,164 protein-coding gene models. With a custom pipeline, all these gene sequences were clustered into families. A total of 1,506 single-copy genes were selected as marker genes, which were then used to evaluate the genome completeness and base qualities of all assemblies. Pangenomic analyses were performed based on a selected subset of 847 medium-high-quality genomes. Statistical comparisons revealed a number of gene families showing copy number variations among different organism sources. To the authors’ knowledge, this study represents the largest genome annotation project of
S. cerevisiae
so far, providing rich genomic resources for the future studies of the model organism
S. cerevisiae
and its relatives.

IMPORTANCE

Saccharomyces cerevisiae
(baker’s yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Though a huge number of
Saccharomyces cerevisiae
genome sequences are available at the public domain, these genomes are distributed at different websites and most are released without annotation, hindering the efficient reuse of these genome resources. Here, we collected 2,507 genomes for
Saccharomyces cerevisiae
, performed genome annotation, and evaluated the genome qualities. All the obtained data have been deposited at public repositories and are freely accessible to the community. This study represents the largest genome annotation project of
S. cerevisiae
so far, providing one complete annotated genome data set for
S. cerevisiae
, an important workhorse for fundamental biology, biotechnology, and industry.
Protective effect of
Enterococcus faecium
against ethanol-induced gastric injury via extracellular vesicles
Authors: Luo Meiying , Sun Junhang , Li Suqian , Wei Limin , Sun Ruiping , Feng Xin , Zhang Huihua , Chen Ting , Xi Qianyun , Zhang Yongliang , Qi Qien 
Published: April 2024

ABSTRACT

Recently,
Enterococcus
has been shown to have gastric protective functions, and the mechanisms by which
Enterococcus
modulates gastric function are still being investigated. Herein, we investigated how
Enterococcus faecium
(Efm) and
E. faecium
-derived extracellular vesicles (EVs) (EfmEVs) exert protective effect against ethanol-induced gastric injury by investigating the effect of EfmEVs on gastric mucosal ulcer scoring, histological lesion, mucosal glycoprotein production, acidity, anti-oxidative function, and inflammatory responses in rat. Pretreatment with Efm showed significant reduction of ethanol-induced gastric injury, as evidenced by the lowering of ulcer index, histological lesion, gastric pH, and inflammatory responses and the enhancement of mucosal glycoprotein production and anti-oxidative function. Further functional studies on three bioactive components [inactivated Efm, EfmEVs (EVs), and EV-free supernatants] of the bacterial culture showed that EVs are mostly responsible for the gastroprotective effect. Moreover, EV secretion is beneficial for the gastroprotective effect of Efm. Hence, EVs mediated the protective effect of Efm against ethanol-induced gastric injury by lowering inflammatory responses and enhancing anti-oxidative function and may be a potent anti-inflammatory and anti-oxidative strategy to alleviate hyperinflammatory gastrointestinal tract conditions.

IMPORTANCE

This study indicated that
Enterococcus faecium
provided a protective effect against rat gastric injury, which involved improvement of the mucosal glycoprotein production, anti-oxidative function, and inflammatory responses. Furthermore, we confirmed that three bioactive components (inactivated Efm, extracellular vesicles, and EV-free supernatants) of
E. faecium
culture also contributed to the gastroprotective effect. Importantly,
E. faecium
-derived EVs showed an effective impact for the gastroprotective effect.
Approaches for identifying and measuring heteroresistance in azole-susceptible
Candida
isolates
Authors: Gautier Cécile , Maciel Eli I. , Ene Iuliana V. 
Published: April 2024

ABSTRACT

Heteroresistance to antifungal agents poses a significant challenge in the treatment of fungal infections. Currently, the absence of established methods for detecting and measuring heteroresistance impedes progress in understanding this phenomenon in fungal pathogens. In response to this gap, we present a comprehensive set of new and optimized methods designed to detect and quantify azole heteroresistance in
Candida albicans
. Here, we define two primary assays for measuring heteroresistance: population analysis profiling, based on growth on solid medium, and single-cell assays, based on growth in liquid culture. We observe good correlations between the measurements obtained with liquid and solid assays, validating their utility for studying azole heteroresistance. We also highlight that disk diffusion assays could serve as an additional tool for the rapid detection of heteroresistance. These methods collectively provide a versatile toolkit for researchers seeking to assess heteroresistance in
C. albicans
. They also serve as a critical step forward in the characterization of antifungal heteroresistance, providing a framework for investigating this phenomenon in diverse fungal species and in the context of other antifungal agents. Ultimately, these advancements will enhance our ability to effectively measure antifungal drug responses and combat fungal infections.

IMPORTANCE

Heteroresistance involves varying antimicrobial susceptibility within a clonal population. This phenomenon allows the survival of rare resistant subpopulations during drug treatment, significantly complicating the effective management of infections. However, the absence of established detection methods hampers progress in understanding this phenomenon in human fungal pathogens. We propose a comprehensive toolkit to address this gap in the yeast
Candida albicans
, encompassing population analysis profiling, single-cell assays, and disk diffusion assays. By providing robust and correlated measurements through both solid and liquid assays, this work will provide a framework for broader applications across clinically relevant
Candida
species. These methods will enhance our ability to understand this phenomenon and the failure of antifungal therapy.
Genomic analysis of
Salmonella
isolated from canal water in Bangkok, Thailand
Authors: Toyting Jirachaya , Nuanmuang Narong , Utrarachkij Fuangfa , Supha Neunghatai , Thongpanich Yuwanda , Leekitcharoenphon Pimlapas , Aarestrup Frank M. , Sato Toyotaka , Thapa Jeewan , Nakajima Chie , Suzuki Yasuhiko 
Published: April 2024

ABSTRACT

Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria,
Salmonella enterica,
isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was
Salmonella
Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including
mcr-3.1
, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine
S
. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of
S
. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.

IMPORTANCE

Bangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant
Salmonella
is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of
Salmonella
strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant
Salmonella
and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of
S
. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.
Magneto-Biological Physics
Authors: Buchachenko A. L. 
Published: April 2024

Abstract
Since the appearance of magneto-biology as an intriguing field of Big Biology, the most significant event, which was happened in it, was the discovery of huge isotope effects, when natural magnesium, calcium and zinc ions in the catalytic sites of enzymes were replaced with nuclear spin magnetic ions 25Mg2+, 43Ca2+, and 67Zn2+ of their stable isotopes. This discovery elucidated physical sense and the origin of numerous magneto-biological effects; it has illuminated all magneto-biology and introduced it as a respectable science. Now the spin concept and radical pair mechanism are generally accepted and overwhelmingly used to interpret experimentally detected magneto-biological effects. In terms of the radical pair mechanism the DNA repair, Hayflick limit and biological longevity under magnetic control are discussed. It is emphasized that magneto-biology is a means to better understand Big Biology itself.
Strength improvement of high organic dredged soil by solidification/oxidization synergistic method
Authors: He Xingxing , Wan Yong , Chen Yijun , Tan Xun , Wang Shiquan , Liu Xiaoli , Xue Qiang 
Published: April 2024

Soil organic matter (SOM) has always been one of the critical factors affecting the solidification of dredged soil. This study proposes a solidification/oxidization synergistic method for treating high organic dredged soil (DS). Three solid oxidants, i.e. , sodium persulfate (PS), sodium percarbonate (PC), and potassium ferrate (PF), were added to DS in cooperation with cement, respectively. The results show that all three oxidants showed a good degradation effect on SOM and had the optimal dosage, which increased gradually with cement content (Ac) when used with cement. Under the optimal dosage of oxidant and Ac = 15%, PS and PC can improve the unconfined compression strength (UCS) of cemented DS (CDS) at 60 days of curing to nearly 4 times compared with that without oxidant, while PF can only increase the 60d-UCS to 1.5 times. In addition, the influence mechanism of different oxidants on the UCS of CDS was analyzed based on microscopic tests, proving that the three oxidants can not only degrade the SOM in CDS but also participate in the hydration reaction of cement. It is feasible to use proper amounts of PC and PS in combination with cement to solidify high organic soil.
Observation of $$K^{+} \rightarrow \pi ^{+}\pi ^{0}\pi ^{0}\gamma $$ decay
Authors: Artamonov A. V. , Bychkov V. N. , Donskov S. V. , Filin A. P. , Filippov S. N. , Gorin A. M. , Gushchin E. N. , Inyakin A. V. , Kekelidze G. D. , Khaustov G. V. , Kholodenko S. A. , Khudyakov A. A. , Kolosov V. N. , Kravtsov V. I. , Kudenko Yu. G. , Kulik A. V. , Kurshetsov V. F. , Lishin V. A. , Lysan V. M. , Medynsky M. V. , Obraztsov V. F. , Okhotnikov A. V. , Polyakov V. A. , Polyarush A. Yu. , Romanovsky V. I. , Rykalin V. I. , Sadovsky A. S. , Samoylenko V. D. , Shapkin M. M. , Tiurin I. S. , Uvarov V. A. , Yushchenko O. P. , Zalikhanov B. Zh. 
Published: April 2024

AbstractThe $$K^{+} \rightarrow \pi ^{+}\pi ^{0}\pi ^{0}\gamma $$

K
+

→

π
+

π
0

π
0

γ

decay is observed by the OKA collaboration. About 60 events of the decay observed with signal:noise $$\approx 1$$

≈
1

. The branching ratio obtained by normalization to $$K^{+} \rightarrow \pi ^{+}\pi ^{0}\pi ^{0}$$

K
+

→

π
+

π
0

π
0

is measured to be $$(3.7 \pm 0.9(stat) \pm 0.3(syst))\times 10^{-6}$$

(
3.7
±
0.9

(
s
t
a
t
)

±
0.3

(
s
y
s
t
)

)

×

10

-
6

for $$E_{\gamma }^*>10\,\textrm{MeV}$$

E

γ

∗

>
10

MeV

. The branching ratio, $$\gamma $$
γ
energy spectrum and angular distribution are consistent with ChPT prediction.