bluuebunny/crossref_metadata_2025_split huggingface dataset:
EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance
Authors: Zhang Ruizhen , Wang Yan 
Published: November 2023

ABSTRACT

Two-component systems (TCSs) widely exist in bacteria and assist bacteria in adjusting behaviors to adapt to environmental changes after sensing environmental signals and transducing information into cells. As a member of TCSs in
Escherichia coli
, after sensing signals, EvgS/EvgA mainly induces multiple resistances, such as acid and multidrug resistance, and increases bacterial adherence. Notably, the EvgS is one of the five unorthodox sensors in
E. coli
, which has an internal phosphorelay based on the structure with extra domains different from other orthodox sensors. Here, we summarize research on EvgS and EvgA published since 1994. This review includes comprehensive knowledge of EvgS/EvgA and focuses on the EvgS structure and the multiple resistance conferred by EvgS/EvgA. Furthermore, we discuss the unsolved questions of EvgS/EvgA and propose assumptions and inferences on the EvgS structure and the EvgS/EvgA function.

IMPORTANCE

EvgS/EvgA, one of the five unorthodox two-component systems in
Escherichia coli
, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
Impact of surface receptors TLR2, CR3, and FcγRIII on
Rhodococcus equi
phagocytosis and intracellular survival in macrophages
Authors: da Silveira Bibiana Petri , Barhoumi Rola , Bray Jocelyne M. , Cole-Pfeiffer Hannah M. , Mabry Cory J. , Burghardt Robert C. , Cohen Noah D. , Bordin Angela I. 
Published: November 2023

ABSTRACT

The virulence-associated protein A (VapA) produced by virulent
Rhodococcus equi
allows it to replicate in macrophages and cause pneumonia in foals. It is unknown how VapA interacts with mammalian cell receptors, but intracellular replication of avirulent
R. equi
lacking
vapA
can be restored by supplementation with recombinant VapA (rVapA). Our objectives were to determine whether the absence of the surface receptors Toll-like receptor 2 (TLR2), complement receptor 3 (CR3), or Fc gamma receptor III (FcγRIII) impacts
R. equi
phagocytosis and intracellular replication in macrophages, and whether rVapA restoration of virulence in
R. equi
is dependent upon these receptors. Wild-type (WT) murine macrophages with TLR2, CR3, or FcγRIII blocked or knocked out (KO) were infected with virulent or avirulent
R. equi
, with or without rVapA supplementation. Quantitative bacterial culture and immunofluorescence imaging were performed. Phagocytosis of
R. equi
was not affected by blockade or KO of TLR2 or CR3. Intracellular replication of virulent
R. equi
was not affected by TLR2, CR3, or FcγRIII blockade or KO; however, avirulent
R. equi
replicated in TLR2
-/-
and CR3
-/-
macrophages but not in WT and FcγRIII
-/-
. rVapA supplementation did not affect avirulent
R. equi
phagocytosis but promoted intracellular replication in WT and all KO cells. By demonstrating that TLR2 and CR3 limit replication of avirulent but not virulent
R. equi
and that VapA-mediated virulence is independent of TLR2, CR3, or FcγRIII, our study provides novel insights into the role of these specific surface receptors in determining the entry and intracellular fate of
R. equi
.
Identification of
recG
genetic interactions in
Escherichia coli
by transposon sequencing
Authors: Bonde Nina J. , Wood Elizabeth A. , Myers Kevin S. , Place Michael , Keck James L. , Cox Michael M. 
Published: November 2023

ABSTRACT

Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In
Escherichia coli
, the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing to identify
recG
genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the
dam
,
uvrD
,
rnhA
,
radA
, and
rep
genes. The conditional importance of these five genes in cells lacking
recG
was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with
uvrD, rep,
and
radA
, but not
rnhA
or
dam
) were suppressed by deletion of
recF
or
recO
, indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a
recG
deletion when combined with
dam
,
uvrD
,
radA
, or
rnhA
deletions but not with
rep
. The results reinforce the idea of RecG as a general genome guardian. RecG has at least two functions. It plays an important role in the resolution of joint molecules behind the fork, formed during post-replication gap repair. RecG is also required to suppress genome over-replication caused by unscheduled replication initiation at R-loops, at double-strand breaks caused by
dam
inactivation, and during replication termination.

IMPORTANCE

DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the
recG
gene, which renders
Escherichia coli
cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported
recG
genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.
Igniting children’s enthusiasm for microbes with an origami paper microscope
Authors: Gardner Joshua , Perry Cynthia , Cervantes Jorge 
Published: November 2023

ABSTRACT

The COVID-19 pandemic has underscored the urgent need for microbiology literacy in society. Microbiology knowledge, and its dissemination, can help inform and increase the objectivity of important decisions, such as treatment or vaccination. A microbiology learning experience titled “What you can’t see can hurt you” was delivered as part of a larger outreach event where children were exposed to various aspects of medicine and health care fields. The activity involved an introduction to and a discussion of bacteria of clinical importance and the use of a smartphone-attachable paper-based foldable microscope. To explore the impact of this activity on participants’ interest in science and microbiology, a pre- and post-activity survey of five questions on an emoji-based Likert scale was completed by the participants. A statistically significant increase in their interest in microbes and where to find them, as well as in microscopy, was observed after the event. Making microbes visible to children and allowing them to capture images of microbes exposes them directly and personally to microscopy and microbiology. An affordable low-cost paper-based microscope can become an alternative approach to teaching and learning to deliver clinical microbiology information to a wide audience range.
Diversity of short linear interaction motifs in SARS-CoV-2 nucleocapsid protein
Authors: Schuck Peter , Zhao Huaying 
Published: November 2023

ABSTRACT

Molecular mimicry of short linear interaction motifs has emerged as a key mechanism for viral proteins binding host domains and hijacking host cell processes. Here, we examine the role of RNA virus sequence diversity in the dynamics of the virus-host interface by analyzing the uniquely vast sequence record of viable SARS-CoV-2 species with focus on the multi-functional nucleocapsid protein. We observe the abundant presentation of motifs encoding several essential host protein interactions, alongside a majority of possibly non-functional and randomly occurring motif sequences absent in subsets of viable virus species. A large number of motifs emerge
ex nihilo
through transient mutations relative to the ancestral consensus sequence. The observed mutational landscape implies an accessible motif space that spans at least 25% of known eukaryotic motifs. This reveals motif mimicry as a highly dynamic process with the capacity to broadly explore host motifs, allowing the virus to rapidly evolve the virus-host interface.

IMPORTANCE
Short linear motifs (SLiMs) are 3–10 amino acid long binding motifs in intrinsically disordered protein regions (IDRs) that serve as ubiquitous protein-protein interaction modules in eukaryotic cells. Through molecular mimicry, viruses hijack these sequence motifs to control host cellular processes. It is thought that the small size of SLiMs and the high mutation frequencies of viral IDRs allow rapid host adaptation. However, a salient characteristic of RNA viruses, due to high replication errors, is their obligate existence as mutant swarms. Taking advantage of the uniquely large genomic database of SARS-CoV-2, here, we analyze the role of sequence diversity in the presentation of SLiMs, focusing on the highly abundant, multi-functional nucleocapsid protein. We find that motif mimicry is a highly dynamic process that produces an abundance of motifs transiently present in subsets of mutant species. This diversity allows the virus to efficiently explore eukaryotic motifs and evolve the host-virus interface.
On the origin of the nucleus: a hypothesis
Authors: Baum Buzz , Spang Anja 
Published: November 2023

SUMMARY
In this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions—emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
Complete genome sequence of
Escherichia
phage iGC_PHA_EC001
Authors: Khan Tahsin , Haider Arefeen , Rahman Sezanur , Moon Shovan Basak , Mahamud Imtiaz , Mondal Shakhinur Islam , Begum Anowara , Biswas Sudhangshu Kumar , Jubair Mohammad , Rahman Mustafizur 
Published: November 2023

ABSTRACT

Antimicrobial resistance (AMR) in bacteria poses a global health emergency due to limited treatment options. Here, we report a lytic bacteriophage belonging to
Stephanstirmvirinae
family against an AMR
Escherichia coli
(ST2089).
Escherichia
phage iGC_PHA_EC001 is of genus
Phapecoctavirus
and 148,445 bp in length, encoding 269 predicted protein-coding sequences and 10 tRNAs. The phage encodes two lytic proteins containing phage_lysozyme (PF00959.22) and cell wall hydrolase_2 (PF07486.15) as catalytic domains, respectively.
Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting
Authors: Ottesen Andrea , Kocurek Brandon , Deaver Christine , Chiesa Oscar , Cohen Rachael , Reed Elizabeth , Commichaux Seth , Mammel Mark , McDermott Patrick , Strain Errol , Myers Michael 
Published: November 2023

ABSTRACT

Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast
in vivo
versus
in vitro
bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.
Complete genome sequence of
Bordetella parapertussis
strain 400431-b, isolated from a protracted course of whooping cough in Austria, 2023
Authors: Cardoso Maria João , Rouhani David , Cabal Rosel Adriana , Daza Prieto Beatriz , Hopfgartner Miriam , Stöger Anna , Hasenberger Petra , Stadlbauer Silke , Moesenbacher Tobias , Hyden Patrick , Wiedermann Ursula , Schmid Daniela , Ruppitsch Werner 
Published: November 2023

ABSTRACT

Here, we report the complete genome of
Bordetella parapertussis
strain 400431-b isolated from a nasopharyngeal swab from a 4-year-old patient presenting with a protracted course of whooping cough, vaccinated with three doses of diphtheria-tetanus-acellular pertussis-hepatitis B-poliomyelitis-
Haemophilus influenzae
type b vaccine.
Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system
Authors: Freeman Claire N. , Russell Jennifer N. , Yost Chris K. 
Published: November 2023

ABSTRACT

The biological removal of nitrogen using natural microbial metabolic processes can be a valuable component of wastewater treatment that helps reduce downstream eutrophication of receiving water ecosystems. Biological nutrient removal (BNR) is a well-established component of wastewater treatment due to its recognized environmental benefits. The composition and diversity of these microbial communities are an important consideration, as disruptions to or instability in the microbial community can negatively impact N cycling and reduce treatment efficiency. To characterize the bacterial community and associated nitrogen cycling genes within a cold-acclimated BNR facility, metagenomic sequencing combined with a read-based quantification strategy and metagenomic assembled genome (MAG) generation was used on samples collected from a Canadian prairie wastewater treatment plant. Generally, this system had a high abundance of Proteobacteria and Actinobacteria throughout the year, including the genera
Thiomonas, Tetrasphaera, Afipia,
and
Hyphomicrobium
. Communities remained stable throughout the different bioreactors in this system, while diversity varied between sampling months, demonstrating seasonal effects on the population dynamics. Genes involved in the denitrification pathway were abundant and distributed widely across different MAGs, while genes involved in nitrification were absent. Additionally, these genes remained stable across all sampling months, suggesting that the efficacy and robustness of this system rely on more than the taxonomic composition of the microbial community.

IMPORTANCE
Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.
CRISPR-Cas9-mediated IncF plasmid curing in extraintestinal pathogenic
Escherichia coli
Authors: Chen Liang , Peirano Gisele , Yen Kelly , Wang Bingjie , Terlecky Austin , DeVinney Rebekah , Kreiswirth Barry N. , Pitout Johann D. D. 
Published: November 2023

ABSTRACT

IncF plasmids are commonly found in extra-intestinal pathogenic
Escherichia coli
(ExPEC) strains, serving as reservoirs for antimicrobial resistance (AMR) genes and virulence factors, persistently coexisting with ExPEC lineages. Multidrug-resistant (MDR) high-risk ExPEC clones, particularly ST131, ST1193, and ST410, have acquired diverse IncF plasmids over time, containing various AMR determinants, contributing significantly to their global success. However, the broader roles of these IncF plasmids in the success of MDR ExPEC clones, beyond AMR, remain elusive. In this study, we employed a novel clustered regularly interspaced short palindromic repeats–CRISPR-associated protein-9 nuclease (CRISPR-Cas9)-mediated pCasCure plasmid-curing system to precisely remove specific IncF plasmids among ExPEC clones (ST1193, ST131, and ST410). Antibiotic-resistant parent strains reverted to antibiotic-susceptible states post-curing; however, IncF plasmid curing did not show significant impact on bacterial
in vitro
growth and had little impact on other
in vitro
phenotypes, including survival in water, dry environment and biofilm production. In addition, IncF plasmid curing did not affect the conjugation frequency of KPC-producing pKpQIL plasmid. This study represents a pivotal initial step in understanding the precise roles of IncF plasmids in the success of ExPEC. Future research will be crucial in investigating their influence on cell invasion and
in vivo
fitness, thereby providing a more comprehensive perspective on the functions of IncF plasmids in MDR ExPEC clones.

IMPORTANCE

Understanding the role of IncF plasmids in the success of drug-resistant bacteria has far-reaching implications for tackling antibiotic resistance. The study's use of a novel CRISPR-Cas9-mediated plasmid-curing system provides a precision tool for dissecting the specific impact of IncF plasmids on ExPEC clones, especially high-risk, multidrug-resistant strains like ST131, ST1193, and ST410. The study offers a crucial stepping stone for future research into understanding how these plasmids influence more complex aspects of bacterial behavior, such as cell invasion and
in vivo
fitness.
Late Miocene to present synchronous extension and contraction in the eastern Pamir: Insights from inversion of thermochronologic data across the southern Muztaghata dome
Authors: Chen Shenqiang , Fellin Maria Giuditta , Willett Sean D. , Maden Colin , Guillong Marcel , Chen Hanlin , Chen Yaguang 
Published: November 2023

Abstract
Late Cenozoic gneiss domes cover ~30% of the surface of the Pamir salient in the northwestern end of the India–Asia collision zone. The highest peaks of the Pamir are in the east, where the ~250-km-long, ~N–S-trending Kongur Shan extensional system controls the topography. We combined 115 new apatite (U-Th-Sm)/He and zircon (U-Th)/He single-grain dates from 18 samples and previous thermochronologic data with three-dimensional thermokinematic models to constrain the thermo-tectonic history of the southern portion of the Muztaghata dome, one of the largest gneiss domes in the eastern Pamir. The new cooling dates from the western boundary of the southern Muztaghata dome generally increase with distance from the southern Kongur Shan fault and are related to normal faulting along the fault at near-surface levels over the last 6.5 m.y. The new dates across the central–eastern portion of the dome outline the previously recorded U-shaped date pattern at a higher spatial resolution. The modeling indicates that this pattern is most likely the result of uplift and erosion above a flat-ramp-flat thrust fault at depth over the last 7 m.y. Modeling does not resolve how topographic changes may have affected the observed distribution of cooling dates, but it indicates a faster thrust-slip rate associated with an increase in relief and a slower one associated with steady-state topography. Our results suggest that the modern topography along the southern Muztaghata dome, similar to the rest of the eastern Pamir salient, is shaped by normal faulting at shallow depth, but its growth may still be governed by contraction and crustal thickening at depth.
Effectiveness of prevention programmes on the rate of burn injuries in children: a systematic review
Authors: van Balen Nina I M , Simon Myrthe H , Botman Matthijs , Bloemers Frank W , Schoonmade Linda J , Meij-de Vries Annebeth 
Published: November 2023

IntroductionBurns are a frequent injury in children and can cause great physical and psychological impairment. Studies have identified positive effects of prevention measures based on increase in knowledge or reduction in hazards. The main goal of burn prevention campaigns, however, is to prevent burns. Therefore, this review is focused on the effectiveness of prevention programmes on the rates of burns in children.MethodsA literature search was performed on PubMed, Embase, CINAHL, Web of Science, Google Scholar and Scopus, including a reference-check. Included were studies which evaluated burn prevention programmes in terms of burn injury rate in children up to 19 years old. Studies specifically focused on non-accidental burns were excluded as well as studies with only outcomes such as safety knowledge or number of hazards.ResultsThe search led to 1783 articles that were screened on title and abstract. 85 articles were screened in full text, which led to 14 relevant studies. Nine of them reported a significant reduction in burn injury rate. Five others showed no effect on the number of burn injuries. In particular, studies that focused on high-risk populations and combined active with passive preventive strategies were successful.ConclusionSome prevention programmes appear to be an effective manner to reduce the number of burn injuries in children. However, it is essential to interpret the results of the included studies cautiously, as several forms of biases may have influenced the observed outcomes. The research and evidence on this subject is still very limited. Therefore, it is of great importance that future studies will be evaluated on a decrease in burns and bias will be prevented. Especially in low-income countries, where most of the burns in children occur and the need for effective prevention campaigns is vital.
Ancestry, race and ethnicity: the role and relevance of language in clinical genetics practice
Authors: Redman Melody Grace , Horton Rachel Helen , Carley Helena , Lucassen Anneke 
Published: November 2023

BackgroundThe terms ancestry, race and ethnicity are used variably within the medical literature and within society and clinical care. Biological lineage can provide an important context for the interpretation of genomic data, but the language used, and practices around when to ascertain this, vary.MethodsUsing a fictional case scenario we explore the relevance of questions around ancestry, race and ethnicity in clinical genetic practice.ResultsIn the UK, data on ‘ethnicity’ are routinely collected by those using genomic medicine, as well as within the wider UK National Health Service, although the reasons for this are not always clear to practitioners and patients. Sometimes it is requested as a proxy for biological lineage to aid variant interpretation, refine estimations of carrier frequency and guide decisions around the need for pharmacogenetic testing.ConclusionThere are many challenges around the use and utility of these terms. Currently, genomic databases are populated primarily with data from people of European descent, and this can lead to health disparities and poorer service for minoritised or underserved populations. Sensitivity and consideration are needed when communicating with patients around these areas. We explore the role and relevance of language around biological lineage in clinical genetics practice.