bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sanitization of hydroponic farming facilities in Singapore: what, why, and how
Authors: Tham Cliff An Ting , Zwe Ye Htut , Ten Michelle Mei Zhen , Ng Geraldine Shang Ya , Toh Jillinda Yi Ling , Poh Bee Ling , Zhou Weibiao , Li Dan 
Published: June 2024

ABSTRACT

This study performed microbial analysis of nutrient film technique (NFT) hydroponic systems on three indoor farms in Singapore (the “what”). To justify the necessity of sanitizing hydroponic systems, strong biofilm-forming bacteria were isolated from the facility and investigated for their influence on
Salmonella
colonization on polyvinyl chloride (PVC) coupons in hydroponic nutrient solutions (the “why”). Finally, sanitization solutions were evaluated with both laboratory-scale and field-scale tests (the “how”). As a result, the microbiome composition in NFT systems was found to be highly farm specific. The strong biofilm formers
Corynebacterium tuberculostearicum
C2 and
Pseudoxanthomonas mexicana
C3 were found to facilitate the attachment and colonization of
Salmonella
on PVC coupons. When forming dual-species biofilms, the presence of C2 and C3 also significantly promoted the growth of
Salmonella
(
P
< 0.05). Compared with hydrogen peroxide (H
2
O
2
) and sodium percarbonate (SPC), sodium hypochlorite (NaOCl) exhibited superior efficacy in biofilm removal. At 50 ppm, NaOCl reduced the
Salmonella
Typhimurium, C2, and C3 counts to <1 log CFU/cm
2
within 12 h, whereas neither 3% H
2
O
2
nor 1% SPC achieved this effect. In operational hydroponic systems, the concentration of NaOCl needed to achieve biofilm elimination increased to 500 ppm, likely due to the presence of organic matter accumulated during crop cultivation and the greater persistence of naturally formed multispecies biofilms. Sanitization using 500 ppm NaOCl for 12 h did not impede subsequent plant growth, but chlorination byproduct chlorate was detected at high levels in the hydroponic solution and in plants in the sanitized systems without rinsing.

IMPORTANCE
This study’s significance lies first in its elucidation of the necessity of sanitizing hydroponic farming systems. The microbiome in hydroponic systems, although mostly nonpathogenic, might serve as a hotbed for pathogen colonization and thus pose a risk for food safety. We thus explored sanitization solutions with both laboratory-scale and field-scale tests. Of the three tested sanitizers, NaOCl was the most effective and economical option, whereas one must note the vital importance of rinsing the hydroponic systems after sanitization with NaOCl.
Diversity and phage sensitivity to phages of porcine enterotoxigenic
Escherichia coli
Authors: Gambino Michela , Kushwaha Simran Krishnakant , Wu Yi , van Haastrecht Pauline , Klein-Sousa Victor , Lutz Veronika T. , Bejaoui Semeh , Jensen Christoffer Moeskjær C. , Bojer Martin S. , Song Wenchen , Xiao Minfeng , Taylor Nicholas M. I. , Nobrega Franklin L. , Brøndsted Lone 
Published: June 2024

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) is a diverse and poorly characterized
E. coli
pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to
Enterobacteriaceae
phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.

IMPORTANCE

Enterotoxigenic
Escherichia coli
(ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species—
E. coli
.
Absence of farnesol salvage in
Candida albicans
and probably in other fungi
Authors: Voshall Adam , Gutzmann Daniel J. , Verdaguer Ignasi Bofill , Crispim Marcell , Boone Cory H.T. , Atkin Audrey L. , Nickerson Kenneth W. 
Published: June 2024

ABSTRACT

Farnesol salvage, a two-step pathway converting farnesol to farnesyl pyrophosphate (FPP), occurs in bacteria, plants, and animals. This paper investigates the presence of this pathway in fungi. Through bioinformatics, biochemistry, and physiological analyses, we demonstrate its absence in the yeasts
Saccharomyces cerevisiae
and
Candida albicans
, suggesting a likely absence across fungi. We screened 1,053 fungal genomes, including 34 from
C. albicans
, for potential homologs to four genes (
Arabidopsis thaliana AtFOLK
,
AtVTE5
,
AtVTE6
, and
Plasmodium falciparum PfPOLK
) known to accomplish farnesol/prenol salvage in other organisms. Additionally, we showed that
3
H-farnesol was not converted to FPP or any other phosphorylated prenol, and exogenous farnesol was not metabolized within 90 minutes at any phase of growth and did not rescue cells from the toxic effects of atorvastatin, but it did elevate the levels of intracellular farnesol (F
i
). All these experiments were conducted with
C. albicans
. In sum, we found no evidence for farnesol salvage in fungi.

IMPORTANCE

The absence of farnesol salvage constitutes a major difference in the metabolic capabilities of fungi. In terms of fungal physiology, the lack of farnesol salvage pathways relates to how farnesol acts as a quorum-sensing molecule in
Candida albicans
and why farnesol should be investigated for use in combination with other known antifungal antibiotics. Its absence is essential for a model (K. W. Nickerson et al., Microbiol Mol Biol Rev 88:e00081-22, 2024), wherein protein farnesylation, protein chaperones, and the unfolded protein response are combined under the unifying umbrella of a cell’s intracellular farnesol (F
i
). In terms of human health, farnesol should have at least two different modes of action depending on whether those cells have farnesol salvage. Because animals have farnesol salvage, we can now see the importance of dietary prenols as well as the potential importance of farnesol in treating neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s disease, and multiple sclerosis.
Dpr-mediated H
2
O
2
resistance contributes to streptococcus survival in a cystic fibrosis airway model system
Authors: Rogers Rendi R. , Kesthely Christopher A. , Jean-Pierre Fabrice , El Hafi Bassam , O'Toole George A. 
Published: June 2024

ABSTRACT

The cystic fibrosis (CF) lung environment is conducive to the colonization of bacteria as polymicrobial biofilms, which are associated with poor clinical outcomes for persons with CF (pwCF).
Streptococcus
spp. are highly prevalent in the CF airway, but its role in the CF lung microbiome is poorly understood. Some studies have shown
Streptococcus
spp. to be associated with better clinical outcomes for pwCF, while others show that high abundance of
Streptococcus
spp. is correlated with exacerbations. Our lab previously reported a polymicrobial culture system consisting of four CF-relevant pathogens that can be used to study microbial behavior in a more clinically relevant setting. Here, we use this model system to identify genetic pathways that are important for
Streptococcus sanguinis
survival in the context of the polymicrobial community. We identified genes related to reactive oxygen species as differentially expressed in
S. sanguinis
monoculture versus growth of this microbe in the mixed community. Genetic studies identified Dpr as important for
S. sanguinis
survival in the community. We show that Dpr, a DNA-binding ferritin-like protein, and PerR, a peroxide-responsive transcriptional regulator of Dpr, are important for protecting
S. sanguinis
from phenazine-mediated toxicity in co-culture with
Pseudomonas aeruginosa
and when exposed to hydrogen peroxide, both of which mimic the CF lung environment. Characterizing such interactions in a clinically relevant model system contributes to our understanding of microbial behavior in the context of polymicrobial biofilm infections.

IMPORTANCE

Streptococcus
spp. are recognized as a highly prevalent pathogen in cystic fibrosis (CF) airway infections. However, the role of this microbe in clinical outcomes for persons with CF is poorly understood. Here, we leverage a polymicrobial community system previously developed by our group to model CF airway infections as a tool to investigate a
Pseudomonas
-
Streptococcus
interaction involving reactive oxygen species (ROS). We show that protection against ROS is required for
Streptococcus sanguinis
survival in a clinically relevant polymicrobial system. Using this model system to study interspecies interactions contributes to our broader understanding of the complex role of
Streptococcus
spp. in the CF lung.
PRRSV GP5 inhibits the antivirus effects of chaperone-mediated autophagy by targeting LAMP2A
Authors: Li Wen , Zhang Mengting , Wang Yueshuai , Zhao Shijie , Xu Pengli , Cui Zhiying , Chen Jing , Xia Pingan , Zhang Yina 
Published: June 2024

ABSTRACT

Autophagy is an important biological process in host defense against viral infection. However, many viruses have evolved various strategies to disrupt the host antiviral system. Porcine reproductive and respiratory syndrome virus (PRRSV) is a typical immunosuppressive virus with a large economic impact on the swine industry. At present, studies on the escape mechanism of PRRSV in the autophagy process, especially through chaperone-mediated autophagy (CMA), are limited. This study confirmed that PRRSV glycoprotein 5 (GP5) could disrupt the formation of the GFAP-LAMP2A complex by inhibiting the MTORC2/PHLPP1/GFAP pathway, promoting the dissociation of the pGFAP-EF1α complex, and blocking the K63-linked polyubiquitination of LAMP2A to inhibit the activity of CMA. Further research demonstrated that CMA plays an anti-PRRSV role by antagonizing nonstructural protein 11 (NSP11)-mediated inhibition of type I interferon (IFN-I) signaling. Taken together, these results indicate that PRRSV GP5 inhibits the antiviral effect of CMA by targeting LAMP2A. This research provides new insight into the escape mechanism of immunosuppressive viruses in CMA.

IMPORTANCE
Viruses have evolved sophisticated mechanisms to manipulate autophagy to evade degradation and immune responses. Porcine reproductive and respiratory syndrome virus (PRRSV) is a typical immunosuppressive virus that causes enormous economic losses in the swine industry. However, the mechanism by which PRRSV manipulates autophagy to defend against host antiviral effects remains unclear. In this study, we found that PRRSV GP5 interacts with LAMP2A and disrupts the formation of the GFAP-LAMP2A complex, thus inhibiting the activity of CMA and subsequently enhancing the inhibitory effect of the NSP11-mediated IFN-I signaling pathway, ultimately facilitating PRRSV replication. Our study revealed a novel mechanism by which PRRSV escapes host antiviral effects through CMA, providing a potential host target, LAMP2A, for developing antiviral drugs and contributing to understanding the escape mechanism of immunosuppressive viruses.
RECON gene disruption enhances host resistance to enable genome-wide evaluation of intracellular pathogen fitness during infection
Authors: Stamm Chelsea E. , McFarland Adelle P. , Locke Melissa N. , Tabakh Hannah , Tang Qing , Thomason Maureen K. , Woodward Joshua J. 
Published: June 2024

ABSTRACT

Transposon sequencing (Tn-seq) is a powerful genome-wide technique to assess bacterial fitness under varying growth conditions. However, screening via Tn-seq
in vivo
is challenging. Dose limitations and host restrictions create bottlenecks that diminish the transposon mutant pool being screened. Here, we have developed a murine model with a disruption in
Akr1c13
that renders the resulting RECON
−/−
mouse resistant to high-dose infection. We leveraged this model to perform a Tn-seq screen of the human pathogen
Listeria monocytogenes in vivo
. We identified 135 genes which were required for
L. monocytogenes
growth in mice including novel genes not previously identified for host survival. We identified organ-specific requirements for
L. monocytogenes
survival and investigated the role of the folate enzyme FolD in
L. monocytogenes
liver pathogenesis. A mutant lacking
folD
was impaired for growth in murine livers by 2.5-log
10
compared to wild type and failed to spread cell-to-cell in fibroblasts. In contrast, a mutant in
alsR,
which encodes a transcription factor that represses an operon involved in D-allose catabolism, was attenuated in both livers and spleens of mice by 4-log
10
and 3-log
10
, respectively, but showed modest phenotypes in
in vitro
models. We confirmed that dysregulation of the D-allose catabolism operon is responsible for the
in vivo
growth defect, as deletion of the operon in the ∆
alsR
background rescued virulence. By undertaking an unbiased, genome-wide screen in mice, we have identified novel fitness determinants for
L. monocytogenes
host infection, which highlights the utility of the RECON
−/−
mouse model for future screening efforts.

IMPORTANCE

Listeria monocytogenes
is the gram-positive bacterium responsible for the food-borne disease listeriosis. Although infections with
L. monocytogenes
are limiting in healthy hosts, vulnerable populations, including pregnant and elderly people, can experience high rates of mortality. Thus, understanding the breadth of genetic requirements for
L. monocytogenes in vivo
survival will present new opportunities for treatment and prevention of listeriosis. We developed a murine model of infection using a RECON
−/−
mouse that is restrictive to systemic
L. monocytogenes
infection. We utilized this model to screen for
L. monocytogenes
genes required
in vivo
via transposon sequencing. We identified the liver-specific gene
folD
and a repressor,
alsR
, that only exhibits an
in vivo
growth defect. AlsR controls the expression of the D-allose operon which is a marker in diagnostic techniques to identify pathogenic
Listeria
. A better understanding of the role of the D-allose operon in human disease may further inform diagnostic and prevention measures.
The F plasmid conjutome: the repertoire of
E. coli
proteins translocated through an F-encoded type IV secretion system
Authors: Al Mamun Abu Amar M. , Kissoon Kimberley , Li Yang Grace , Hancock Erin , Christie Peter J. 
Published: June 2024

ABSTRACT

Bacterial conjugation systems pose a major threat to human health through their widespread dissemination of mobile genetic elements (MGEs) carrying cargoes of antibiotic resistance genes. Using the Cre Recombinase Assay for Translocation (CRAfT), we recently reported that the IncFV pED208 conjugation system also translocates at least 16 plasmid-encoded proteins to recipient bacteria. Here, we deployed a high-throughput CRAfT screen to identify the repertoire of chromosomally encoded protein substrates of the pED208 system. We identified 32 substrates encoded by the
Escherichia coli
W3110 genome with functions associated with (i) DNA/nucleotide metabolism, (ii) stress tolerance/physiology, (iii) transcriptional regulation, or (iv) toxin inhibition. The respective gene deletions did not impact pED208 transfer proficiencies, nor did Group 1 (DNA/nucleotide metabolism) mutations detectably alter the SOS response elicited in new transconjugants upon acquisition of pED208. However, MC4100(pED208) donor cells intrinsically exhibit significantly higher SOS activation than plasmid-free MC4100 cells, and this plasmid carriage-induced stress response is further elevated in donor cells deleted of several Group 1 genes. Among 10 characterized substrates, we gained evidence of C-terminal or internal translocation signals that could function independently or synergistically for optimal protein transfer. Remarkably, nearly all tested proteins were also translocated through the IncN pKM101 and IncP RP4 conjugation systems. This repertoire of
E. coli
protein substrates, here termed the F plasmid “conjutome,” is thus characterized by functions of potential benefit to new transconjugants, diverse TSs, and the capacity for promiscuous transfer through heterologous conjugation systems.

IMPORTANCE
Conjugation systems comprise a major subfamily of the type IV secretion systems (T4SSs) and are the progenitors of a second large T4SS subfamily dedicated to translocation of protein effectors. This study examined the capacity of conjugation machines to function as protein translocators. Using a high-throughput reporter screen, we determined that 32 chromosomally encoded proteins are delivered through an F plasmid conjugation system. The translocated proteins potentially enhance the establishment of the co-transferred F plasmid or mitigate mating-induced stresses. Translocation signals located C-terminally or internally conferred substrate recognition by the F system and, remarkably, many substrates also were translocated through heterologous conjugation systems. Our findings highlight the plasticity of conjugation systems in their capacities to co-translocate DNA and many protein substrates.
Geological context and significance of the clay-sulfate transition region in Mount Sharp, Gale crater, Mars: An integrated assessment based on orbiter and rover data
Authors: Meyer Melissa J. , Milliken Ralph E. , Stack Kathryn M. , Edgar Lauren A. , Rampe Elizabeth B. , Turner Madison L. , Lewis Kevin W. , Kite Edwin S. , Caravaca Gwénaël , Vasavada Ashwin R. , Dietrich William E. , Bryk Alexander B. , Gasnault Olivier , Le Mouélic Stéphane , Seeger Christina H. , Sheppard Rachel Y. 
Published: June 2024

Abstract
On Mars, phyllosilicate (“clay”) minerals are often associated with older terrains, and sulfate minerals are associated with younger terrains, and this dichotomy is taken as evidence that Mars’ surface dried up over time. Therefore, in situ investigation of the Mount Sharp strata in Gale crater, which record a shift from dominantly clay-bearing to sulfate-bearing minerals, as seen in visible–near-infrared orbital reflectance spectra, is a key science objective for the Mars Science Laboratory (MSL) Curiosity rover mission. Here, we present regional (orbiter-based) and in situ (rover-based) evidence for a low-angle erosional unconformity that separates the lacustrine and marginal lacustrine deposits of the Carolyn Shoemaker formation from the dominantly eolian deposits of the lower Mirador formation within the orbitally defined clay-sulfate transition region. The up-section record of wetter (Carolyn Shoemaker formation) to drier (lower Mirador formation) depositional conditions is accompanied by distinct changes in diagenesis. Clay minerals occur preferentially within the Carolyn Shoemaker formation and are absent within the lower members of the Mirador formation. At and above the proposed unconformity, strata are characterized by an increase in diagenetic nodules enriched in X-ray amorphous Mg-sulfate. Early clay formation in the Carolyn Shoemaker formation may have created a hydraulic barrier such that later migrating magnesium- and sulfur-rich fluids accumulated preferentially within the lower members of the Mirador formation. The proposed unconformity may have also acted as a fluid conduit to further promote Mg-sulfate nodule formation at the Carolyn Shoemaker–Mirador formation boundary. These results confirm an association of the clay-sulfate transition with the drying of depositional environments, but they also suggest that at least some orbital sulfate signatures within the region are not time-congruent with the environmental signals extracted from primary sedimentology. Our findings highlight that complex interactions among primary depositional environment, erosion, and diagenesis contribute to the transition in clay-sulfate orbital signatures observed in the stratigraphy of Mount Sharp.
Downward continued ocean bottom seismometer data show continued hydrothermal evolution of mature oceanic upper crust
Authors: Li Lianjun , Collier Jenny , Henstock Tim , Goes Saskia 
Published: June 2024

Abstract
Heat flow measurements indicate hydrothermal activity in oceanic crust continues at least for 65 m.y. after formation. Hydrothermal activity progressively fills cracks and pores with alteration products, which is expected to lead to a trend of increasing seismic velocities with age. Compilations of seismic-P-wave velocity models inverted from ocean bottom seismometer (OBS) data have failed to detect such an aging trend beyond crustal ages of ca. 10 Ma. However, in these models, the velocities of the uppermost crust, where fluid flow would be most concentrated, are poorly resolved. This is because as the oceanic crust matures, the first crustal arrivals on OBS records (which best resolve upper crustal velocities using tomographic inversion), become hidden in the coda of the water wave. This may lead to the masking of any aging trend in the seismic velocities. For the first time, we show how including downward continuation (DC) in the analysis of OBS data collected across 65 Ma seafloor significantly improves measurements of the P-wave velocities of the upper crust. Our new analysis reveals a highly heterogeneous upper crust, with ridge-parallel P-wave velocity variations of 25%, implying local porosity values that are up to double that of global averages. Our new results, combined with other most recent advanced seismic analyses, reveal that seismic velocities indeed evolve with age up to at least 70 Ma, confirming that hydrothermal activity continues in mature oceanic crust.