bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the dynamics of information exchange in governance networks: Opportunity structures in anti‐corruption multi‐stakeholder partnerships
Authors: Reyes‐Gonzalez Jose Antonio , Agneessens Filip , Esteve Marc 
Published: September 2024

AbstractInformation exchange is critical to the functionality of governance networks. Traditionally, it has been argued that actors within governance networks tend to engage in information exchange with others who share similar beliefs and motivations, as these are deemed catalysts for achieving collective objectives. An alternative viewpoint posits that actors may prioritize strategies aimed at minimizing transaction costs and maximizing returns when selecting their partners. This paper proposes that information exchange predominantly occurs with partners who are easily accessible (i.e., where transaction costs are low) and with partners who are perceived as influential (i.e., where benefits are high). To investigate these alternative propositions, we examine three distinct opportunity structures that actors may utilize, which are based on their preferences for (1) partners with similar participatory motivations, (2) partners who co‐participate in institutional committees, and (3) those perceived as influential. We empirically test these opportunity structures using unique survey data gathered from 10 anti‐corruption multi‐stakeholder partnerships within the public infrastructure domain in countries of Latin America, Africa, and Eurasia. Results from Exponential Random Graph Models suggest that shared participatory motivations do not significantly impact information exchange within our context, whereas the perceived influence of a partner emerges as a critical predictor. In addition, co‐participation in institutional committees significantly facilitates information dissemination, particularly when those committees involve discussions on deliberating about strategies to communicate findings on public‐sector infrastructure discrepancies and formulating recommendations to governments on transparency and accountability. These findings prompt discussions on four network management strategies aimed at restructuring networks and fostering stakeholder involvement and inclusivity.
Relevance of antigen‐induced IL‐6 and mitogen‐induced or spontaneous IFN‐γ secretions in whole blood cultures for detection of Mycobacterium tuberculosis infection and disease
Authors: Sinha Sudhir , Singh Komal , Umam Fareha , Kapoor Prerna , Aggarwal Amita 
Published: September 2024

AbstractFor an effective control of tuberculosis (TB), there is a persistent need for biomarkers that can report true estimates of TB infection (TBI) and predict its progression towards active TB disease. We investigated whether the cell‐mediated immune responses to Mycobacterium tuberculosis (Mtb) antigens could provide such biomarkers. The study subjects (n = 174) comprised a cohort of smear‐positive, drug‐sensitive, HIV‐negative pulmonary TB patients (n = 54) and their household contacts (HC, n = 120). Whole blood cultures, in the presence or absence of Mtb antigens‐ membrane (MtM), purified protein derivative (PPD) and alpha‐crystallin (Acr), or the mitogen PHA were subjected to determinations, by flow cytometry, for T cell proliferative and, by ELISA, for IFN‐γ, TNF‐α, and IL‐6 cytokine responses. Additionally, serum levels of the three cytokines were also estimated. The strongest cell‐proliferative and cytokine responses were induced by MtM and IL‐6 was the most abundantly produced cytokine. While none of the responses induced by Mtb antigens or the serum cytokines levels could discriminate between TB and HC, the ex vivo cytokine responses induced by PHA or ‘spontaneously’ could apparently do so. The concentrations of IFN‐γ induced by PHA in TB blood cultures were significantly lower than in HC cultures (AUC = 0.72). Conversely, the spontaneous IFN‐γ or TNF‐α secretions in TB cultures were significantly higher than in HC cultures (AUC = 0.66). Our results suggest that IL‐6 responses to MtM could be a sensitive indicator of TBI, and low levels of PHA‐induced or high levels of spontaneous IFN‐γ secretions in HC blood cultures may indicate a progressive infection.
Cross‐ratio degrees and triangulations
Authors: Silversmith Rob 
Published: September 2024

AbstractThe cross‐ratio degree problem counts configurations of points on with prescribed cross‐ratios. Cross‐ratio degrees arise in many corners of combinatorics and geometry, but their structure is not well‐understood in general. Interestingly, examining various special cases of the problem can yield combinatorial structures that are both diverse and rich. In this paper, we prove a simple closed formula for a class of cross‐ratio degrees indexed by triangulations of an ‐gon; these degrees are connected to the geometry of the real locus of , and to positive geometry.
In vivo
and
in vitro
analyses of the role of the Prc protease in inducing mucoidy in
Pseudomonas aeruginosa
Authors: Sommerfield Alexis G. , Wang Michelle , Mamana Julia , Darwin Andrew J. 
Published: September 2024

ABSTRACT

In
Pseudomonas aeruginosa
, alginate biosynthesis gene expression is inhibited by the transmembrane anti-sigma factor MucA, which sequesters the AlgU sigma factor. Cell envelope stress initiates cleavage of the MucA periplasmic domain by site-1 protease AlgW, followed by further MucA degradation to release AlgU. However, after colonizing the lungs of people with cystic fibrosis,
P. aeruginosa
converts to a mucoid form that produces alginate constitutively. Mucoid isolates often have
mucA
mutations, with the most common being
mucA22
, which truncates the periplasmic domain. MucA22 is degraded constitutively, and genetic studies suggested that the Prc protease is responsible. Some studies also suggested that Prc contributes to induction in strains with wild-type MucA, whereas others suggested the opposite. However, missing from all previous studies is a demonstration that Prc cleaves any protein directly, which leaves open the possibility that the effect of a
prc
null mutation is indirect. To address the ambiguities and shortfalls, we reevaluated the roles of AlgW and Prc as MucA and MucA22 site-1 proteases.
In vivo
analyses using three different assays and two different inducing conditions all suggested that AlgW is the only site-1 protease for wild-type MucA in any condition. In contrast, genetics suggested that AlgW or Prc act as MucA22 site-1 proteases in inducing conditions, whereas Prc is the only MucA22 site-1 protease in non-inducing conditions. For the first time, we also show that Prc is unable to degrade the periplasmic domain of wild-type MucA but does degrade the mutated periplasmic domain of MucA22 directly.

IMPORTANCE

After colonizing the lungs of individuals with cystic fibrosis,
Pseudomonas aeruginosa
undergoes mutagenic conversion to a mucoid form, worsening the prognosis. Most mucoid isolates have a truncated negative regulatory protein MucA, which leads to constitutive production of the extracellular polysaccharide alginate. The protease Prc has been implicated, but not shown, to degrade the most common MucA variant, MucA22, to trigger alginate production. This work provides the first demonstration that the molecular mechanism of Prc involvement is direct degradation of the MucA22 periplasmic domain and perhaps other truncated MucA variants as well. MucA truncation and degradation by Prc might be the predominant mechanism of mucoid conversion in cystic fibrosis infections, suggesting that Prc activity could be a useful therapeutic target.
Regulation of bacterial virulence genes by PecS family transcription factors
Authors: Nwokocha George C. , Ghosh Arpita , Grove Anne 
Published: September 2024

ABSTRACT

Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of
pecS
shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the
pecS-pecM
intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for
Dickeya dadantii
PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of
pecS-pecM
. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.
hnRNP H controls alternative splicing of human papillomavirus type 16 E1, E6, E7, and E6^E7 mRNAs via GGG motifs
Authors: Jönsson Johanna , Zhai Qiaoli , Schwartz Stefan , Kajitani Naoko 
Published: September 2024

ABSTRACT

The mRNAs encoding the human papillomavirus type 16 (HPV16) E6 and E7 oncogene mRNAs are subjected to extensive alternative RNA splicing at multiple regulated splice sites. One of the most extensively used 5ʹ-splice sites in the HPV16 genome is named SD880 and is located immediately downstream of the E7 open reading frame. Here, we show that a cluster of three GGG-motifs adjacent to HPV16 SD880 interacts with heterogeneous nuclear ribonucleoprotein (hnRNP) H that cooperates with SD880 to stimulate splicing to the upstream HPV16 3’-splice site SA742. This splice site is located in the E7 coding region and is required for the production of the HPV16 226^742 mRNA that encodes the E6^E7 fusion protein. Enhancement of HPV16 E6^E7 mRNA production by hnRNP H occurred at the expense of the intron-retained E6 mRNAs and the spliced E7 mRNAs, demonstrating that hnRNP H controls the relative levels of E6, E7, and E6^E7 proteins. Unexpectedly, overexpression of hnRNP H also promoted retention of the downstream E1 encoding intron and enhanced E1 protein production. We concluded that hnRNP H plays an important role in the HPV16 gene expression program.

IMPORTANCE
Here, we show that hnRNP H binds to multiple GGG-motifs downstream of human papillomavirus type 16 (HPV16) splice site SD880 and acts in concert with SD880 to promote expression of the HPV16 E6^E7 mRNA. The E6^E7 protein has been shown previously to stabilize the HPV16 E6 and E7 oncoproteins and may as such contribute to the carcinogenic properties of HPV16. In its capacity of major regulator of HPV16 oncogene expression, hnRNP H may be exploited as a target for antiviral drugs to HPV16.
Vascular endothelial growth factor receptor 2 as a potential host target for the inhibition of enterovirus replication
Authors: Zhao Xiaoyu , Qiao Rui , Hao Meng , Xu Longfa , Wang Dong , Lu Yinying , Li Jiayan , Wu Jing , Li Yi , Cheng Tong , Zhang Wenhong , Zhao Jincun , Wang Pengfei 
Published: September 2024

ABSTRACT

Because host kinases are key regulators of multiple signaling pathways in response to viral infections, we previously screened a kinase inhibitor library using rhabdomyosarcoma cells and human intestinal organoids in parallel to identify potent inhibitors against EV-A71 infection. We found that Rho-associated coiled-coil-containing protein kinase (Rock) inhibitor efficiently suppressed the EV-A71 replication and further revealed Rock1 as a novel EV-A71 host factor. In this study, subsequent analysis found that a variety of vascular endothelial growth factor receptor (VEGFR) inhibitors also had potent antiviral effects. Among the hits, Pazopanib, with a selectivity index as high as 254, which was even higher than that of Pirodavir, a potent broad-spectrum picornavirus inhibitor targeting viral capsid protein VP1, was selected for further analysis. We demonstrated that Pazopanib not only efficiently suppressed the replication of EV-A71 in a dose-dependent manner, but also exhibited broad-spectrum anti-enterovirus activity. Mechanistically, Pazopanib probably induces alterations in host cells, thereby impeding viral genome replication and transcription. Notably, VEGFR2 knockdown and overexpression suppressed and facilitated EV-A71 replication, respectively, indicating that VEGFR2 is a novel host dependency factor for EV-A71 replication. Transcriptome analysis further proved that VEGFR2 potentially plays a crucial role in combating EV-A71 infection through the TSAd-Src-PI3K-Akt pathway. These findings expand the range of potential antiviral candidates of anti-enterovirus therapeutics and suggest that VEGFR2 may be a key host factor involved in EV-A71 replication, making it a potential target for the development of anti-enterovirus therapeutics.

IMPORTANCE
As the first clinical case was identified in the United States, EV-A71, a significant neurotropic enterovirus, has been a common cause of hand, foot, and mouth disease (HFMD) in infants and young children. Developing an effective antiviral agent for EV-A71 and other human enteroviruses is crucial, as these viral pathogens consistently cause outbreaks in humans. In this study, we demonstrated that multiple inhibitors against VEGFRs effectively reduced EV-A71 replication, with Pazopanib emerging as the top candidate. Furthermore, Pazopanib also attenuated the replication of other enteroviruses, including CVA10, CVB1, EV-D70, and HRV-A, displaying broad-spectrum anti-enterovirus activity. Given that Pazopanib targets various VEGFRs, we narrowed the focus to VEGFR2 using knockdown and overexpression experiments. Transcriptomic analysis suggests that Pazopanib's potential downstream targets involve the TSAd-Src-PI3K-Akt pathway. Our work may contribute to identifying targets for antiviral inhibitors and advancing treatments for human enterovirus infections.
Identification of novel genetic factors that regulate c-di-AMP production in
Staphylococcus aureus
using a riboswitch-based biosensor
Authors: Kviatkovski Igor , Zhong Qiyun , Vaidya Sanika , Gründling Angelika 
Published: September 2024

ABSTRACT

Nucleotide secondary messengers regulate various processes in bacteria allowing them to rapidly respond to changes in environmental conditions. c-di-AMP is an essential second messenger required for the growth of the human pathogen
Staphylococcus aureus
, regulating potassium, osmolyte uptake, and beta-lactam resistance. Cellular concentrations of c-di-AMP are regulated by the activities of two enzymes, DacA and GdpP, which synthesize and hydrolyze c-di-AMP, respectively. Besides these, only a limited number of other factors are known to regulate c-di-AMP levels. Using a c-di-AMP biosensor consisting of the
Bacillus subtilis
c-di-AMP-binding
kimA
riboswitch and
yfp,
we were able to efficiently detect differences in cellular c-di-AMP levels in
S. aureus
. To identify novel factors that regulate c-di-AMP levels, we introduced the biosensor into a library of
S. aureus
transposon mutants. In this manner, we obtained mutants with increased c-di-AMP levels that contained insertions in
gdpP
coding for the c-di-AMP hydrolase and
ybbR
(
cdaR
) coding for a c-di-AMP cyclase regulator, thus validating our screen. We also identified two high c-di-AMP mutants with insertions upstream of the
nrdIEF
operon coding for the ribonucleotide reductase enzyme. Further analysis revealed that the insertion down-regulated
nrdIEF
expression, indicating that the enzyme is a negative regulator of c-di-AMP production. This negative regulation was dependent on
rsh
, encoding for the synthase of the endogenous GdpP inhibitor (p)ppGpp. The methods established in this work can be readily adapted for use in other bacteria to uncover genetic or environmental factors regulating c-di-AMP levels.

IMPORTANCE

c-di-AMP is an important secondary messenger, produced by many bacterial species including the opportunistic pathogen
Staphylococcus aureus
. In this bacterium, c-di-AMP controls cell wall homeostasis, cell size, and osmotic balance. In addition, it has been shown that strains with high c-di-AMP levels exhibit increased resistance to beta-lactam antibiotics. Here, we developed a biosensor-based method for the rapid detection of c-di-AMP levels in
S. aureus
. We utilized the biosensor in a genetic screen for the identification of novel factors that impact cellular c-di-AMP. In this manner, we identified the ribonucleotide reductase as a novel factor altering cellular c-di-AMP levels and showed that reducing its expression leads to increased cellular c-di-AMP levels. As methicillin-resistant
S. aureus
strains are considered as a global health threat, it is important to study processes that dictate cellular c-di-AMP levels, which are associated with antibiotic resistance.
Differential immunological responses in lamb rumen and colon to alfalfa hay and wheat straw in a concentrate-rich diet: insights into microbe-host interactions
Authors: Gebeyew Kefyalew , Mi Hui , Liu Yong , Liu Yongbin , Wang Biao , Feyera Teka , Zhiliang Tan , He Zhixiong 
Published: September 2024

ABSTRACT

The impact of a concentrate-rich (CR) diet on the gut microbiome and epithelium homeostasis is well documented. However, it has not been systematically studied whether and how host-microbial interaction contributes to the immune homeostasis in the rumen and colon of lambs fed alfalfa hay and wheat straw, alone or combined, in a CR diet. In all, 63 lambs (initial body weight, 16.69 ± 1.50 kg) were randomly allotted to three dietary groups, each consisting of three pens with seven lambs per pen. Over 14 weeks, the lambs were fed diets as follows: 60% concentrate supplemented with either 40% wheat straw (WG), 20% alfalfa hay combined with 20% wheat straw (MG), or 40% alfalfa hay (AG). The present findings showed that lambs in the AG group had greater (
P
< 0.05) IgG and lower (
P
= 0.067) tumor necrosis factor-alpha concentrations relative to those in the MG and WG groups. The 16S rRNA analysis highlighted that various bacterial phyla and genera in the rumen and colon preferentially degrade fiber and starch derived from alfalfa hay and wheat straw. The weighted gene co-expression network analysis revealed that the bacterial genera from the
Firmicutes
are broadly associated with genes involved in various signaling pathways, underscoring the potential role of
Firmicutes
as key drivers of host-microbial interactions under the present feeding conditions. These findings shed light on the fact that the rumen and colon immune homeostasis is distinctively influenced by diets of alfalfa hay, wheat straw, or their combination in a CR diet. Further studies should examine the prolonged effects of replacing wheat straw with alfalfa hay in a concentrate-rich diet formulated to provide equivalent neutral detergent fiber levels. This could reveal how various forage fibers influence host-microbial interactions and gut health.

IMPORTANCE

In contemporary feedlots, a growing trend is to feed animals a concentrate-rich (CR) diet that could disrupt the synchronized interplay between microbes and host metabolism, leading to altered metabolic functions. Wheat straw and alfalfa hay have different levels of protein and neutral detergent fiber, each with varying rates of digestion. It is unclear how including alfalfa hay and wheat straw, alone or combined in a CR diet, influences the host-microbial consortia and immune homeostasis. Herein, we showed that rumen and colon showed differential immune responses to the alfalfa hay, wheat straw, or both. Bacterial genera preferentially degrade fiber and starch derived from alfalfa hay, wheat straw, or both. Bacterial genera from
Firmicutes
phylum play a pivotal role in driving the host-microbial interactions, as indicated by their extensive association with genes across various signaling pathways.
Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes
Authors: Rappaport H. B. , Senewiratne Nimshika P. J. , Lucas Sarah K. , Wolfe Benjamin E. , Oliverio Angela M. 
Published: September 2024

ABSTRACT

While research on the sourdough microbiome has primarily focused on lactic acid bacteria (LAB) and yeast, recent studies have found that acetic acid bacteria (AAB) are also common members. However, the ecology, genomic diversity, and functional contributions of AAB in sourdough remain unknown. To address this gap, we sequenced 29 AAB genomes, including three that represent putatively novel species, from a collection of over 500 sourdough starters surveyed globally from community scientists. We found variations in metabolic traits related to carbohydrate utilization, nitrogen metabolism, and alcohol production, as well as in genes related to mobile elements and defense mechanisms. Sourdough AAB genomes did not cluster when compared to AAB isolated from other environments, although a subset of gene functions was enriched in sourdough isolates. The lack of a sourdough-specific genomic cluster may reflect the nomadic lifestyle of AAB. To assess the consequences of AAB on the emergent function of sourdough starter microbiomes, we constructed synthetic starter microbiomes, varying only the AAB strain included. All AAB strains increased the acidification of synthetic sourdough starters relative to yeast and LAB by 18.5% on average. Different strains of AAB had distinct effects on the profile of synthetic starter volatiles. Taken together, our results begin to define the ways in which AAB shape emergent properties of sourdough and suggest that differences in gene content resulting from intraspecies diversification can have community-wide consequences on emergent function.

IMPORTANCE
This study is a comprehensive genomic and ecological survey of acetic acid bacteria (AAB) isolated from sourdough starters. By combining comparative genomics with manipulative experiments using synthetic microbiomes, we demonstrate that even strains with >97% average nucleotide identity can shift important microbiome functions, underscoring the importance of species and strain diversity in microbial systems. We also demonstrate the utility of sourdough starters as a model system to understand the consequences of genomic diversity at the strain and species level on multispecies communities. These results are also relevant to industrial and home-bakers as we uncover the importance of AAB in shaping properties of sourdough starters that have direct impacts on sensory notes and the quality of sourdough bread.