bluuebunny/crossref_metadata_2025 huggingface dataset:
Operational Strategies of Two-Spool Micro Gas Turbine With Alternative Fuels: A Performance Assessment
Authors: Gaitanis Aggelos , Tiwari Ravi Nath , De Paepe Ward , Ferrari Mario Luigi , Contino Francesco , Breuhaus Peter
Published: February 2024

Micro gas turbines (mGT) have not yet succeeded in conquering the small-scale combined heat and power (CHP) market. One reason is that their electrical efficiency is not high enough to maintain a cost-effective operation. A two-shaft intercooled mGT has the potential to meet the current market demand. This technology maintains a high electrical efficiency even at part-load and coupled with its fuel-flexible combustion chamber, it is an ideal candidate for CHP concepts in a renewable future. In this paper, performance analysis on two-spool mGT is carried out with various fuel blends. Attention is given to the low-pressure and high-pressure compressors and the variation of surge margin by adding hydrogen and syngas. Two control strategies for the mGT are adopted. In the first scenario, the two shafts have equal rotational speeds while in the second, the speeds are controlled independently. As the engine is operated at equal speeds, the maximum performance with 100 vol. % of syngas is observed at 85% of the nominal load while 100 vol. % of hydrogen shows maximum efficiency at a load of 63.7%. At electric power lower than 60% and for high amounts of syngas in natural gas, the low-pressure compressor (LPC) operates closely to surge line. In the second scenario, the efficiency increases as the load decreases and the LPC runs in an efficient and safe operating region. Additionally, the amount of nitrogen in syngas affects the part-load performance of the two-spool mGT.
Multi-Fidelity Design of Porous Microstructures for Thermofluidic Applications
Authors: Eweis-Labolle Jonathan Tammer , Zhao Chuanning , Won Yoonjin , Bostanabad Ramin
Published: February 2024

As modern electronic devices are increasingly miniaturized and integrated, their performance relies more heavily on effective thermal management. In this regard, two-phase cooling methods which capitalize on thin-film evaporation atop structured porous surfaces are emerging as potential solutions. In such porous structures, the optimum heat dissipation capacity relies on two competing objectives that depend on mass and heat transfer. Optimizing these objectives for effective thermal management is challenging due to the simulation costs and the high dimensionality of the design space which is often a voxelated microstructure representation that must also be manufacturable. We address these challenges by developing a data-driven framework for designing optimal porous microstructures for cooling applications. In our framework, we leverage spectral density functions to encode the design space via a handful of interpretable variables and, in turn, efficiently search it. We develop physics-based formulas to simulate the thermofluidic properties and assess the feasibility of candidate designs based on offline image-based analyses. To decrease the reliance on expensive simulations, we generate multi-fidelity data and build emulators to find Pareto-optimal designs. We apply our approach to a canonical problem on evaporator wick design and obtain fin-like topologies in the optimal microstructures which are also characteristics often observed in industrial applications.
Understanding Thermo-Fluidic Characteristics of a Triangular Solar Air Heater Having W-Shaped Rib-Turbulators: A 3D Computational Fluid Dynamics Study
Authors: Mahanand Yadaba , Senapati Jnana Ranjan
Published: February 2024

A solar air heater duct with W-shaped rib-turbulators on the collector plate disrupts the flow that enhances the heat transfer from the hot surface due to turbulence in the flow. In this analysis, a three-dimensional fluid domain of the W-shaped ribbed triangular solar air heater duct is numerically simulated to analyze the impact of roughness and flow parameters on thermo-fluidic performance; also, the turbulence behavior near the rib surfaces is presented. Roughness variables like non-dimensional pitch and non-dimensional height varied from 6.23 to 17.85 and 0.04 to 0.053, respectively. In contrast, the flow parameter, like the Reynolds number, is kept in the range of 4×103 to 18×103. A maximal performance evaluation criterion of 1.51 is attained for the W-shape ribs with a non-dimensional pitch of 7.14 and a non-dimensional height of 0.047 at a Reynolds number of 15×103. For the W-shaped rib-turbulators with a non-dimensional pitch of 7.14 and a non-dimensional height of 0.047 at a Reynolds number of 15×103, the maximum heat transfer is found to be 1.826 times that of a smooth duct. Accordingly, in the parametric range, the maximum friction penalty is 2.63 times that of a smooth duct. Some useful correlations are established considering the computational data.
Activation of CzcS/CzcR during zinc excess regulates copper tolerance and pyochelin biosynthesis of
Pseudomonas aeruginosa
Authors: Li Ting , Cao Huiluo , Duan Cheng , Chen Shuzhen , Xu Zeling
Published: February 2024

Zinc is an important transition metal that is essential for numerous physiological processes while excessive zinc is cytotoxic.
Pseudomonas aeruginosa
is a ubiquitous opportunistic human pathogen equipped with an exquisite zinc homeostatic system, and the two-component system CzcS/CzcR plays a key role in zinc detoxification. Although an increasing number of studies have shown the versatility of CzcS/CzcR, its physiological functions are still not fully understood. In this study, transcriptome analysis was performed, which revealed that CzcS/CzcR is silenced in the absence of the zinc signal but modulates global gene expression when the pathogen encounters zinc excess. CzcR was demonstrated to positively regulate the copper tolerance gene
ptrA
and negatively regulate the pyochelin biosynthesis regulatory gene
pchR
through direct binding to their promoters. Remarkably, the upregulation of
ptrA
and downregulation of
pchR
were shown to rescue the impaired capacity of copper tolerance and prevent pyochelin overproduction, respectively, caused by zinc excess. This study not only advances our understanding of the regulatory spectrum of CzcS/CzcR but also provides new insights into stress adaptation mediated by two-component systems in bacteria to balance the cellular processes that are disturbed by their signals.

IMPORTANCE

CzcS/CzcR is a two-component system that has been found to modulate zinc homeostasis, quorum sensing, and antibiotic resistance in
Pseudomonas aeruginosa
. To fully understand the physiological functions of CzcS/CzcR, we performed a comparative transcriptome analysis in this study and discovered that CzcS/CzcR controls global gene expression when it is activated during zinc excess. In particular, we demonstrated that CzcS/CzcR is critical for maintaining copper tolerance and iron homeostasis, which are disrupted during zinc excess, by inducing the expression of the copper tolerance gene
ptrA
and repressing the pyochelin biosynthesis genes through
pchR
. This study revealed the global regulatory functions of CzcS/CzcR and described a new and intricate adaptive mechanism in response to zinc excess in
P. aeruginosa
. The findings of this study have important implications for novel anti-infective interventions by incorporating metal-based drugs.
A pleiotropic role of sialidase in the pathogenicity of
Porphyromonas gingivalis
Authors: Pham Christopher , Guo Shuaiqi , Han Xiao , Coleman Laurynn , Sze Ching Wooen , Wang Huizhi , Liu Jun , Li Chunhao
Published: February 2024

As one of the keystone pathogens of periodontitis, the oral bacterium
Porphyromonas gingivalis
produces an array of virulence factors, including a recently identified sialidase (PG0352). Our previous report involving loss-of-function studies indicated that PG0352 plays an important role in the pathophysiology of
P. gingivalis
. However, this report had not been corroborated by gain-of-function studies or substantiated in different
P. gingivalis
strains. To fill these gaps, herein we first confirm the role of PG0352 in cell surface structures (e.g., capsule) and serum resistance using
P. gingivalis
W83 strain through genetic complementation and then recapitulate these studies using
P. gingivalis
ATCC33277 strain. We further investigate the role of PG0352 and its counterpart (PGN1608) in ATCC33277 in cell growth, biofilm formation, neutrophil killing, cell invasion, and
P. gingivalis
-induced inflammation. Our results indicate that PG0352 and PGN1608 are implicated in
P. gingivalis
cell surface structures, hydrophobicity, biofilm formation, resistance to complement and neutrophil killing, and host immune responses. Possible molecular mechanisms involved are also discussed. In summary, this report underscores the importance of sialidases in the pathophysiology of
P. gingivalis
and opens an avenue to elucidate their underlying molecular mechanisms.
Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control
Salmonella enterica
Authors: Acton Luke , Pye Hannah V. , Thilliez Gaëtan , Kolenda Rafał , Matthews Michaela , Turner A. Keith , Yasir Muhammad , Holden Emma , Al-Khanaq Haider , Webber Mark , Adriaenssens Evelien M. , Kingsley Robert A.
Published: February 2024

The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen
Salmonella enterica
. To determine phage host range, a diverse collection of
Enterobacteriaceae
and
Salmonella enterica
was used and genes involved in infection by six SPLA phages were identified using
Salmonella
Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with
S
. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.

IMPORTANCE

As antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse
Salmonella enterica
and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
A novel high-throughput microwell outgrowth assay for HIV-infected cells
Authors: Fenton Anthony D. , Archin Nancie , Turner Anne-Marie , Joseph Sarah , Moeser Matthew , Margolis David M. , Browne Edward P.
Published: February 2024

Although antiretroviral therapy (ART) is effective at suppressing HIV replication, a viral reservoir persists that can reseed infection if ART is interrupted. Curing HIV will require elimination or containment of this reservoir, but the size of the HIV reservoir is highly variable between individuals. To evaluate the size of the HIV reservoir, several assays have been developed, including PCR-based assays for viral DNA, the intact proviral DNA assay, and the quantitative viral outgrowth assay (QVOA). QVOA is the gold standard assay for measuring inducible replication-competent proviruses, but this assay is technically challenging and time-consuming. To begin progress toward a more rapid and less laborious tool for quantifying cells infected with replication-competent HIV, we developed the Microwell Outgrowth Assay, in which infected CD4 T cells are co-cultured with an HIV-detecting reporter cell line in a polydimethylsiloxane (PDMS)/polystyrene array of nanoliter-sized wells. Transmission of HIV from infected cells to the reporter cell line induces fluorescent reporter protein expression that is detected by automated scanning across the array. Using this approach, we were able to detect HIV-infected cells from ART-naïve people with HIV (PWH) and from PWH on ART with large reservoirs. Furthermore, we demonstrate that infected cells can be recovered from individual rafts and used to analyze the diversity of viral sequences. Although additional development and optimization will be required for quantifying the reservoir in PWH with small latent reservoirs, this assay may be a useful prototype for microwell assays of infected cells.

IMPORTANCE

Measuring the size of the HIV reservoir in people with HIV (PWH) will be important for determining the impact of HIV cure strategies. However, measuring this reservoir is challenging. We report a new method for quantifying HIV-infected cells that involves culturing cells from PWH in an array of microwells with a cell line that detects HIV infection. We show that this approach can detect rare HIV-infected cells and derive detailed virus sequence information for each infected cell.
Activation of protein kinase receptor (PKR) plays a pro-viral role in mammarenavirus-infected cells
Authors: Witwit Haydar , Khafaji Roaa , Salaniwal Arul , Kim Arthur S. , Cubitt Beatrice , Jackson Nathaniel , Ye Chengjin , Weiss Susan R. , Martinez-Sobrido Luis , de la Torre Juan Carlos
Published: February 2024

Many viruses, including mammarenaviruses, have evolved mechanisms to counteract different components of the host cell innate immunity, which is required to facilitate robust virus multiplication. The double-stranded RNA (dsRNA) sensor protein kinase receptor (PKR) pathway plays a critical role in the cell anti-viral response. Whether PKR can restrict the multiplication of the Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) and the mechanisms by which LCMV may counteract the anti-viral functions of PKR have not yet been investigated. Here we present evidence that LCMV infection results in very limited levels of PKR activation, but LCMV multiplication is enhanced in the absence of PKR. In contrast, infection with a recombinant LCMV with a mutation affecting the 3′−5′ exonuclease (ExoN) activity of the viral nucleoprotein resulted in robust PKR activation in the absence of detectable levels of dsRNA, which was associated with severely restricted virus multiplication that was alleviated in the absence of PKR. However, pharmacological inhibition of PKR activation resulted in reduced levels of LCMV multiplication. These findings uncovered a complex role of the PKR pathway in LCMV-infected cells involving both pro- and anti-viral activities.

IMPORTANCE

As with many other viruses, the prototypic Old World mammarenavirus LCMV can interfere with the host cell innate immune response to infection, which includes the dsRNA sensor PKR pathway. A detailed understanding of LCMV-PKR interactions can provide novel insights about mammarenavirus-host cell interactions and facilitate the development of effective anti-viral strategies against human pathogenic mammarenaviruses. In the present work, we present evidence that LCMV multiplication is enhanced in PKR-deficient cells, but pharmacological inhibition of PKR activation unexpectedly resulted in severely restricted propagation of LCMV. Likewise, we document a robust PKR activation in LCMV-infected cells in the absence of detectable levels of dsRNA. Our findings have revealed a complex role of the PKR pathway during LCMV infection and uncovered the activation of PKR as a druggable target for the development of anti-viral drugs against human pathogenic mammarenaviruses.
Endogenous IL-27 during toxoplasmosis limits early monocyte responses and their inflammatory activation by pathological T cells
Authors: Aldridge Daniel L. , Moodley Devapregasan , Park Jeongho , Phan Anthony T. , Rausch Matthew , White Kerry F. , Ren Yue , Golin Karin , Radaelli Enrico , Kedl Ross , Holland Pamela M. , Hill Jonathan , Hunter Christopher A.
Published: February 2024

Mice that lack the genes for IL-27, or the IL-27 receptor, and infected with
Toxoplasma gondii
develop T cell-mediated pathology. Here, studies were performed to determine the impact of endogenous IL-27 on the immune response to
T. gondii
in wild-type (WT) mice. Analysis of infected mice revealed the early production of IL-27p28 by a subset of Ly6C
hi
, inflammatory monocytes, and sustained IL-27p28 production at sites of acute and chronic infection. Administration of anti-IL-27p28 prior to infection resulted in an early (day 5) increase in levels of macrophage and granulocyte activation, as well as enhanced effector T cell responses, as measured by both cellularity, cytokine production, and transcriptional profiling. This enhanced acute response led to immune pathology, while blockade during the chronic phase of infection resulted in enhanced T cell responses but no systemic pathology. In the absence of IL-27, the enhanced monocyte responses observed at day 10 were a secondary consequence of activated CD4
+
T cells. Thus, in WT mice, IL-27 has distinct suppressive effects that impact innate and adaptive immunity during different phases of this infection.

IMPORTANCE

The molecule IL-27 is critical in limiting the immune response to the parasite
Toxoplasma gondii
. In the absence of IL-27, a lethal, overactive immune response develops during infection. However, when exactly in the course of infection this molecule is needed was unclear. By selectively inhibiting IL-27 during this parasitic infection, we discovered that IL-27 was only needed during, but not prior to, infection. Additionally, IL-27 is only needed in the active areas in which the parasite is replicating. Finally, our work found that a previously unstudied cell type, monocytes, was regulated by IL-27, which contributes further to our understanding of the regulatory networks established by this molecule.
Inter-species interactions between two bacterial flower commensals and a floral pathogen reduce disease incidence and alter pathogen activity
Authors: Hassani M. Amine , Cui Zhouqi , LaReau Jacquelyn , Huntley Regan B. , Steven Blaire , Zeng Quan
Published: February 2024

Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens.
Erwinia amylovora
is a flower-inhabiting bacterium and a pathogen that infects different plant species, including
Malus × domestica
(apple). Previously, we showed that the co-inoculation of two bacterial strains, members of the genera
Pseudomonas
and
Pantoea,
isolated from apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between the two flower-associated bacteria and
E. amylovora
in field experimentation and
in vitro
co-cultures. The two flower commensal strains did not competitively exclude
E. amylovora
from the stigma habitat, as both bacteria and the pathogen co-existed on the stigma of apple flowers and
in vitro
. This suggests that plant protection might be mediated by other mechanisms than competitive niche exclusion. Using a synthetic stigma exudation medium, ternary co-culture of the bacterial strains led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Importantly, the gene expression profiles for the ternary co-culture were not just additive from binary co-cultures, suggesting that some functions only emerged in multipartite co-culture. Additionally, the ternary co-culture of the strains resulted in a stronger acidification of the growth milieu than mono- or binary co-cultures, pointing to another emergent property of co-inoculation. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their potential impact on plant health and pathogen behavior.

IMPORTANCE

Fire blight, caused by
Erwinia amylovora
, is one of the most important plant diseases of pome fruits. Previous work largely suggested plant microbiota commensals suppressed disease by antagonizing pathogen growth. However, inter-species interactions of multiple flower commensals and their influence on pathogen activity and behavior have not been well studied. Here, we show that co-inoculating two bacterial strains that naturally colonize the apple flowers reduces disease incidence. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen led to the emergence of new gene expression patterns and a strong alteration of the external pH, factors that may modify the pathogen’s behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.
Bacteroides thetaiotaomicron
metabolic activity decreases with polysaccharide molecular weight
Authors: Wong Jeremy P. H. , Chillier Noémie , Fischer-Stettler Michaela , Zeeman Samuel C. , Battin Tom J. , Persat Alexandre
Published: February 2024

The human colon hosts hundreds of commensal bacterial species, many of which ferment complex dietary carbohydrates. To transform these fibers into metabolically accessible compounds, microbes often express a series of dedicated enzymes homologous to the starch utilization system (Sus) encoded in polysaccharide utilization loci (PULs). The genome of
Bacteroides thetaiotaomicron
(
Bt
), a common member of the human gut microbiota, encodes nearly 100 PULs, conferring a strong metabolic versatility. While the structures and functions of individual enzymes within the PULs have been investigated, little is known about how polysaccharide complexity impacts the function of Sus-like systems. We here show that the activity of Sus-like systems depends on polysaccharide size, ultimately impacting bacterial growth. We demonstrate the effect of size-dependent metabolism in the context of dextran metabolism driven by the specific utilization system PUL48. We find that as the molecular weight of dextran increases,
Bt
growth rate decreases and lag time increases. At the enzymatic level, the dextranase BT3087, a glycoside hydrolase (GH) belonging to the GH family 66, is the main GH for dextran utilization, and BT3087 and BT3088 contribute to
Bt
dextran metabolism in a size-dependent manner. Finally, we show that the polysaccharide size-dependent metabolism of
Bt
impacts its metabolic output in a way that modulates the composition of a producer-consumer community it forms with
Bacteroides fragilis
. Altogether, our results expose an overlooked aspect of
Bt
metabolism that can impact the composition and diversity of microbiota.

IMPORTANCE

Polysaccharides are complex molecules that are commonly found in our diet. While humans lack the ability to degrade many polysaccharides, their intestinal microbiota contain bacterial commensals that are versatile polysaccharide utilizers. The gut commensal
Bacteroides thetaiotaomicron
dedicates roughly 20% of their genomes to the expression of polysaccharide utilization loci for the broad range utilization of polysaccharides. Although it is known that different polysaccharide utilization loci are dedicated to the degradation of specific polysaccharides with unique glycosidic linkages and monosaccharide compositions, it is often overlooked that specific polysaccharides may also exist in various molecular weights. These different physical attributes may impact their processability by starch utilization system-like systems, leading to differing growth rates and nutrient-sharing properties at the community level. Therefore, understanding how molecular weight impacts utilization by gut microbe may lead to the potential design of novel precision prebiotics.
Unraveling the crystal structure of the HpaA adhesin: insights into cell adhesion function and epitope localization of a
Helicobacter pylori
vaccine candidate
Authors: Martini Cyrielle , Araba Victoria , Beniani Meriem , Armoa Ortiz Paula , Simmons Mimi , Chalbi Mariem , Mellouk Abdelkader , El Bakkouri Majida , Calmettes Charles
Published: February 2024

Helicobacter pylori
is a bacterium that exhibits strict host restriction to humans and non-human primates, and the bacterium is widely acknowledged as a significant etiological factor in the development of chronic gastritis, peptic ulcers, and gastric cancers. The pathogenic potential of this organism lies in its adeptness at colonizing the gastric mucosa, which is facilitated by a diverse repertoire of virulence factors, including adhesins that promote the attachment of the bacteria to the gastric epithelium. Among these adhesins, HpaA stands out due to its conserved nature and pivotal role in establishing
H. pylori
colonization. Moreover, this lipoprotein holds promise as an antigen for the development of effective
H. pylori
vaccines, thus attracting considerable attention for in-depth investigations into its molecular function and identification of binding determinants. Here, we present the elucidation of the crystallographic structure of HpaA at 2.9 Å resolution. The folding adopts an elongated protein shape, which is distinctive to the
Helicobacteraceae
family, and features an apical domain extension that plays a critical role in the cell-adhesion activity on gastric epithelial cells. Our study also demonstrates the ability of HpaA to induce TNF-α expression in macrophages, highlighting a novel role as an immunoregulatory effector promoting the pro-inflammatory response
in vitro
. These findings not only contribute to a deeper comprehension of the multifaceted role of HpaA in
H. pylori
pathogenesis but also establish a fundamental basis for the design and development of structure-based derivatives, aimed at enhancing the efficacy of
H. pylori
vaccines.

IMPORTANCE

Helicobacter pylori
is a bacterium that can cause chronic gastritis, peptic ulcers, and gastric cancers. The bacterium adheres to the lining of the stomach using proteins called adhesins. One of these proteins, HpaA, is particularly important for
H. pylori
colonization and is considered a promising vaccine candidate against
H. pylori
infections. In this work, we determined the atomic structure of HpaA, identifying a characteristic protein fold to the
Helicobacter
family and delineating specific amino acids that are crucial to support the attachment to the gastric cells. Additionally, we discovered that HpaA can trigger the production of TNF-α, a proinflammatory molecule, in macrophages. These findings provide valuable insights into how
H. pylori
causes disease and suggest that HpaA has a dual role in both attachment and immune activation. This knowledge could contribute to the development of improved vaccine strategies for preventing
H. pylori
infections.
Identification of a new export signal that targets early subunits to the flagellar type III secretion export machinery
Authors: Bryant Owain J. , Fraser Gillian M.
Published: February 2024

Type III secretion systems (T3SSs) are essential for motility and virulence in many bacterial pathogens. Proteins destined for the flagellar T3SS contain at least two export signals in their N-terminal D
0
domain. Here, we describe a third carboxy (C)-terminal signal in early flagellar subunits that facilitates subunit targeting to the export machinery. Mutational analysis identified critical residues within the flagellar hook subunit C-terminal export signal. The flagellar ATPase and cytoplasmic ring components were not required for this targeting, indicating that core export machinery components facilitate substrate targeting via the C-terminal export signal. More broadly, these results demonstrate that multiple distinct export signals within type III secretion substrates facilitate distinct export events at the T3SS export machinery. Our data establish key events in the export mechanism of type III secretion systems: targeting of subunits to and their sequential interactions with key components of the export machinery.

IMPORTANCE

Many bacterial pathogens utilize T3SS to inject virulence proteins (effectors) into host cells or to assemble flagella on the bacterial cell surface. Bacterial flagella present a paradigm for how cells build and operate complex cell-surface “nanomachines.” Efficient subunit targeting from the bacterial cytosol to type III secretion systems is essential for rapid assembly and secretion by T3SSs. Subunits are thought to dock at the export machinery before being unfolded and translocated into the export channel. However, little is known about how subunits dock at the export machinery and the events that occur post docking. Here, we identified a new export signal within the C-termini of subunits that is essential for targeting of subunits to the type III export machinery. We show that this new export signal and previously identified export signals are recognized separately and sequentially, revealing a pathway for subunit transit through the type III export machinery in which sequential recognition events carry out different roles at major steps in the export pathway.
Host E3 ubiquitin ligase ITCH mediates
Toxoplasma gondii
effector GRA35-triggered NLRP1 inflammasome activation and cell-autonomous immunity
Authors: Wang Yifan , Hollingsworth L. Robert , Sangaré Lamba Omar , Paredes-Santos Tatiana C. , Krishnamurthy Shruthi , Penn Bennett H. , Wu Hao , Saeij Jeroen P. J.
Published: February 2024

Toxoplasma gondii
is an intracellular parasite that can activate the NLRP1 inflammasome leading to macrophage pyroptosis in Lewis rats, but the underlying mechanism is not well understood. In this study, we performed a genome-wide CRISPR screen and identified the dense granule proteins GRA35, GRA42, and GRA43 as the
Toxoplasma
effectors mediating cell death in Lewis rat macrophages. GRA35 localizes on the parasitophorous vacuole membrane, where it interacts with the host E3 ubiquitin ligase ITCH. Inhibition of proteasome activity or ITCH knockout prevented pyroptosis in
Toxoplasma
-infected Lewis rat macrophages, consistent with the “NLRP1 functional degradation model.” However, there was no evidence that ITCH directly ubiquitinates or interacts with rat NLRP1. We also found that GRA35-ITCH interaction affected
Toxoplasma
fitness in IFNγ-activated human fibroblasts, likely due to ITCH’s role in recruiting ubiquitin and the parasite-restriction factor RNF213 to the parasitophorous vacuole membrane. These findings identify a new role of host E3 ubiquitin ligase ITCH in mediating effector-triggered immunity, a critical concept that involves recognizing intracellular pathogens and initiating host innate immune responses.

IMPORTANCE

Effector-triggered immunity represents an innate immune defense mechanism that plays a crucial role in sensing and controlling intracellular pathogen infection. The NLRP1 inflammasome in the Lewis rats can detect
Toxoplasma
infection, which triggers proptosis in infected macrophages and eliminates the parasite’s replication niche. The work reported here revealed that host E3 ubiquitin ligase ITCH is able to recognize and interact with
Toxoplasma
effector protein GRA35 localized on the parasite-host interface, leading to NLRP1 inflammasome activation in Lewis rat macrophages. Furthermore, ITCH-GRA35 interaction contributes to the restriction of
Toxoplasma
in human fibroblasts stimulated by IFNγ. Thus, this research provides valuable insights into understanding pathogen recognition and restriction mediated by host E3 ubiquitin ligase.
Activin A levels are raised during human tuberculosis and blockade of the activin signaling axis influences murine responses to
M. tuberculosis
infection
Authors: Nieuwenhuizen Natalie E. , Nouailles Geraldine , Sutherland Jayne S. , Zyla Joanna , Pasternack Arja H. , Heyckendorf Jan , Frye Björn C. , Höhne Kerstin , Zedler Ulrike , Bandermann Silke , Abu Abed Ulrike , Brinkmann Volker , Gutbier Birgitt , Witzenrath Martin , Suttorp Norbert , Zissel Gernot , Lange Christoph , Ritvos Olli , Kaufmann Stefan H. E. ,   the CAPNETZ Study group,   the DZIF TB study group
Published: February 2024

Activin A strongly influences immune responses; yet, few studies have examined its role in infectious diseases. We measured serum activin A levels in two independent tuberculosis (TB) patient cohorts and in patients with pneumonia and sarcoidosis. Serum activin A levels were increased in TB patients compared to healthy controls, including those with positive tuberculin skin tests, and paralleled severity of disease, assessed by X-ray scores. In pneumonia patients, serum activin A levels were also raised, but in sarcoidosis patients, levels were lower. To determine whether blockade of the activin A signaling axis could play a functional role in TB, we harnessed a soluble activin type IIB receptor fused to human IgG1 Fc, ActRIIB-Fc, as a ligand trap in a murine TB model. The administration of ActRIIB-Fc to
Mycobacterium tuberculosis
-infected mice resulted in decreased bacterial loads and increased numbers of CD4 effector T cells and tissue-resident memory T cells in the lung. Increased frequencies of tissue-resident memory T cells corresponded with downregulated T-bet expression in lung CD4 and CD8 T cells. Altogether, the results suggest a disease-exacerbating role of ActRIIB signaling pathways. Serum activin A may be useful as a biomarker for diagnostic triage of active TB or monitoring of anti-tuberculosis therapy.

IMPORTANCE

Tuberculosis remains the leading cause of death by a bacterial pathogen. The etiologic agent of tuberculosis,
Mycobacterium tuberculosis
, can remain dormant in the infected host for years before causing disease. Significant effort has been made to identify biomarkers that can discriminate between latently infected and actively diseased individuals. We found that serum levels of the cytokine activin A were associated with increased lung pathology and could discriminate between active tuberculosis and tuberculin skin-test-positive healthy controls. Activin A signals through the ActRIIB receptor, which can be blocked by administration of the ligand trap ActRIIB-Fc, a soluble activin type IIB receptor fused to human IgG1 Fc. In a murine model of tuberculosis, we found that ActRIIB-Fc treatment reduced mycobacterial loads. Strikingly, ActRIIB-Fc treatment significantly increased the number of tissue-resident memory T cells. These results suggest a role for ActRIIB signaling pathways in host responses to
Mycobacterium tuberculosis
and activin A as a biomarker of ongoing disease.
Genome sequence of bubaline herpesvirus-1 associated with pustular vulvovaginitis in Indian water buffalo
Authors: Yadav Sarita , Boora Ashok , Thomas Prasad , Kaliappan Abinaya , Verma Nisha , Devi Parvina , Dhaka Nishu , Khurana Sandip , Kumar Anil , Balhara Sunesh , Balhara Ashok , Lailer Puran Chand
Published: February 2024

We report here the genome sequence of a bubaline herpesvirus 1 isolated from Indian water buffalo. The bubaline herpesvirus 1 strain S102_1 was isolated in 2021 from a Murrah buffalo heifer with clinical presentation of pustular vulvovaginitis.
Draft genome sequences of
Pseudomonas
strains zfem001–005 isolated from the intestine of larval zebrafish
Danio rerio
Authors: Simbassa Sabona B. , Clark Justin , Salazar Keiko , Maresso Anthony , Krachler Anne- Marie
Published: February 2024

Here, we report the draft genome sequences of
Pseudomonas
strains zfem001–005, five isolates from the intestinal microbiota of healthy larval zebrafish
Danio rerio
at a developmental age of 7 days post fertilization. The isolates have been identified as
Pseudomonas sediminis
,
Pseudomonas japonica
,
Pseudomonas otitidis
,
Pseudomonas sichuanensis
, and
Pseudomonas tohonis
, respectively.
Draft genome sequences of
Arthrobacter
sp. AZCC_0090 and
Mycobacterium
sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona
Authors: Kridler Melanie R. , Viney Isabella A. , Custer Joy M. , Schlottman Bradley , Bartelme Ryan , Carini Paul
Published: February 2024

Here, we present the genomes of two soil actinobacteria:
Arthrobacter
sp. strain AZCC_0090 and
Mycobacterium
sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.
Complete genome sequence of a nucleopolyhedrovirus isolated from
Bombyx mori
in Hakozaki, Japan, obtained using Oxford Nanopore Technologies sequencing
Authors: Tatsuke Tsuneyuki
Published: February 2024

I report the complete genome sequence of an isolate of nucleopolyhedrovirus from
Bombyx mori
, the domesticated silkworm, maintained for the long term at Kyushu University in Hakozaki, Fukuoka Prefecture, Japan. The genome is 127,783 bp long, with a G+C content of 40.3%, and contains 142 open reading frames.
Genome sequence of bacteriophage Djungelskog isolated from an
Arthrobacter globiformis
culture
Authors: Oliveros Abigail M. , McDougall Shelby A. , Snyder Miles A. , Snowden Sara K. , Richard Joseph D. , Rao Christopher M. , Ponce Marybeth , Pitonza Christopher J. , Ozcelik Mira , Mannina Sofia S. , Magna Juliana R. , Lopez Andrew S. , Gustafson Linnea C. , Glackin Brynn K. , Dolge Abigail E. , DeLancy Nate D. , Davis Andrew B. C. , Davis Thomas P. , Blagodar Max , Natale Sydney N. , Dennis Megan K. , Godin Elizabeth A.
Published: February 2024

Actinobacteriophage Djungelskog was isolated from a sample of degraded organic material in Poughkeepsie, NY, using
Arthrobacter globiformis B-2979
. Its genome is 54,512 bp and encodes 86 putative protein-coding genes. Djungelskog has a siphovirus morphology and is assigned to cluster AW based on gene content similarity to actinobacteriophages.
Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils
Authors: Dindhoria Kiran , Kumar Raghawendra , Bhargava Bhavya , Kumar Rakshak
Published: February 2024

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth’s surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%–96.56% and a contamination range of 0%–8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE

The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.
Investigating inhibitors of 1-deoxy-
d
-xylulose 5-phosphate synthase in a mouse model of UTI
Authors: Chen Eric C. , Shapiro Rachel L. , Pal Arindom , Bartee David , DeLong Kevin , Carter Davell M. , Serrano-Diaz Erika , Rais Rana , Ensign Laura M. , Freel Meyers Caren L.
Published: February 2024

The rising rate of antimicrobial resistance continues to threaten global public health. Further hastening antimicrobial resistance is the lack of new antibiotics against new targets. The bacterial enzyme, 1-deoxy-
d
-xylulose 5-phosphate synthase (DXPS), is thought to play important roles in central metabolism, including processes required for pathogen adaptation to fluctuating host environments. Thus, impairing DXPS function represents a possible new antibacterial strategy. We previously investigated a DXPS-dependent metabolic adaptation as a potential target in uropathogenic
Escherichia coli
(UPEC) associated with urinary tract infection (UTI), using the DXPS-selective inhibitor butyl acetylphosphonate (BAP). However, investigations of DXPS inhibitors
in vivo
have not been conducted. The goal of the present study is to advance DXPS inhibitors as
in vivo
probes and assess the potential of inhibiting DXPS as a strategy to prevent UTI
in vivo
. We show that BAP was well-tolerated at high doses in mice and displayed a favorable pharmacokinetic profile for studies in a mouse model of UTI. Further, an alkyl acetylphosphonate prodrug (homopropargyl acetylphosphonate, pro-hpAP) was significantly more potent against UPEC in urine culture and exhibited good exposure in the urinary tract after systemic dosing. Prophylactic treatment with either BAP or pro-hpAP led to a partial protective effect against UTI, with the prodrug displaying improved efficacy compared to BAP. Overall, our results highlight the potential for DXPS inhibitors as
in vivo
probes and establish preliminary evidence that inhibiting DXPS impairs UPEC colonization in a mouse model of UTI.

IMPORTANCE

New antibiotics against new targets are needed to prevent an antimicrobial resistance crisis. Unfortunately, antibiotic discovery has slowed, and many newly FDA-approved antibiotics do not inhibit new targets. Alkyl acetylphosphonates (alkyl APs), which inhibit the enzyme 1-deoxy-
d
-xylulose 5-phosphate synthase (DXPS), represent a new possible class of compounds as there are no FDA-approved DXPS inhibitors. To our knowledge, this is the first study demonstrating the
in vivo
safety, pharmacokinetics, and efficacy of alkyl APs in a urinary tract infection mouse model.
The Linearly Polarized Light Effect on Maize Development
Authors: Kulchin Yu. N. , Kozhanov S. O. , Kholin A. S. , Subbotin E. P. , Kovalevsky K. V. , Subbotina N. I. , Gomolsky A. S.
Published: February 2024

The main purpose of the work was to study the linearly polarized light impact on the maize plants development. The other purpose was to confirm the model proposed earlier. The methods used in this work include the development of LED light sources, the polarization parameter (degree of polarization) assessment and statistical analysis. Maize (Zea mays L.) plants, Hansatech FMS 1+ pulsed fluorimeter and software TXP Series Instrumentation were used. Plants were grown under white light (WW) with intensity of 200 µmol m–2 s–1. The morphometric parameters measured on the 21st day demonstrated that maize plants of different varieties grown under linearly polarized light developed better than under non-polarized light conditions. In addition, the fact was confirmed by chlorophyll fluorescence measurements. The mechanism has been proposed to explain significant polarized radiation impact on maize, according to which this impact depends on the shape and arrangement of the leaf epidermal cells. The monocotyledonous maize plants have leaves with an ordered arrangement of epidermal cells in comparison with dicotyledonous plants, which cells placed in chaotic order and have no certain shape. Thus, the maize cells layer can transform linearly polarized radiation into elliptically polarized radiation, thus latter should be more efficiently absorbed by the chiral chromophores of photosensitive structures in underlying photosynthetic cells.
Economic impact on local businesses of road safety improvements in Seattle: implications for Vision Zero projects
Authors: Osterhage Daniel R , Acolin Jessica , Fishman Paul A , Dannenberg Andrew L
Published: February 2024

Background

Local transportation agencies implementing Vision Zero road safety improvement projects often face opposition from business owners concerned about the potential negative impact on their sales. Few studies have documented the economic impact of these projects.

Methods

We examined baseline and up to 3 years of postimprovement taxable sales data for retail, food and service-based businesses adjacent to seven road safety projects begun between 2006 and 2014 in Seattle. We used hierarchical linear models to test whether the change in annual taxable sales differed between the 7 intervention sites and 18 nearby matched comparison sites that had no road safety improvements within the study time frame.

Results

Average annual taxable sales at baseline were comparable at the 7 intervention sites (US$44.7 million) and the 18 comparison sites (US$56.8 million). Regression analysis suggests that each additional year following baseline was associated with US$1.20 million more in taxable sales among intervention sites and US$1.14 million more among comparison sites. This difference is not statistically significant (p=0.64). Sensitivity analyses including a random slope, using a generalised linear model and an analysis of variance did not change conclusions.

Discussion

Results suggest that road safety improvement projects such as those in Vision Zero plans are not associated with adverse economic impacts on adjacent businesses. The absence of negative economic impacts associated with pedestrian and bicycle road safety projects should reassure local business owners and may encourage them to work with transportation agencies to implement Vision Zero road safety projects designed to eliminate traffic-related injuries.