bluuebunny/crossref_metadata_2025_split huggingface dataset:
CCT39 Transcription Factor Promotes Chlorophyll Biosynthesis and Photosynthesis in Poplar
Authors: Chen Hao , Wu Wenqi , Du Kang , Yang Jun , Kang Xiangyang 
Published: December 2024

ABSTRACTChlorophyll serves as a crucial pigment in plants, essential for photosynthesis, growth, and development. Our previous study has shown that PpnCCT39 can increase leaf chlorophyll content and photosynthesis rate in poplar. However, the underlying molecular mechanisms remain unknown. In this study, we observed that overexpression of PpnCCT39 not only elevates chlorophyll content and photosynthesis, but also induces alterations in leaf morphology, basal diameter, and chloroplast structure. By performing RNA‐seq on terminal buds and leaves at leaf positions 1, 3, 5, and 10, we determined that PpnCCT39 predominantly exerts its effects in young leaves. Chromatin Immunoprecipitation Sequencing (ChIP‐seq) performed on PpnCCT39‐overexpressing poplars identified 17 194 potential regulatory target genes. By integrating RNA‐seq and ChIP‐seq datasets along with validation assays for protein‐DNA interactions, we determined that PpnCCT39 directly stimulated the transcription of three key genes involved in the chlorophyll biosynthesis and photosynthesis pathways: PagHO1, PagLIL3, and PagPYG7. Furthermore, protein interaction assays revealed that PpnCCT39 interacts with PagRD19 and PagATP2, localized in vesicles and mitochondria respectively, with these interactions occurring within chloroplasts. This study elucidates the molecular mechanism by which the PpnCCT39 transcription factor in poplar promotes chlorophyll biosynthesis and photosynthesis. It also highlights the critical role of PpnCCT39 in nucleocytoplasmic interactions. These findings underscore the significance of PpnCCT39 in regulating chlorophyll biosynthesis and enhancing photosynthesis through molecular design.
Optimising Outbreak Investigation, Surveillance and Discovery of Pathogens in Aquaculture Using Unbiased Metatranscriptomics
Authors: Costa Vincenzo A. , Whittington Richard J. , Caraguel Charles , Becker Joy A. , Wiley Kerrie E. , Huynh Christine , Carson Jeremy , Samsing Francisca 
Published: December 2024

ABSTRACTEmerging infectious diseases are a major threat to global aquaculture production and are projected to increase in frequency due to anthropogenic stressors and climate change. Our ability to screen the global aquatic ‘infectome’ is dramatically improving through unbiased metatranscriptomic (i.e., total RNA) sequencing. Despite recent advances in molecular diagnostics and next‐generation sequencing, outbreak investigation in aquaculture often encounters limitations due to the targeted nature of conventional techniques, which may only capture a small portion of the diverse array of disease‐causing agents present in nature, sometimes requiring years to resolve. Here, we propose that unbiased metatranscriptomic sequencing serves as a cost‐effective and powerful technique for characterising pathogens during disease outbreaks and in surveillance programmes. In doing so, we offer a diagnostic framework to mitigate infectious disease threats to global aquaculture. We emphasise the importance of combining rapid metatranscriptomics with traditional techniques for a holistic examination of the causes of unknown aetiologies in aquatic animals, and how it can be used to examine host responses in parallel with pathogen discovery. We suggest that the integration of metatranscriptomics into aquaculture will require upskilling, proficiency testing, user‐friendly bioinformatic tools and open data sharing. Furthermore, it is essential to establish a reporting framework—with analytical guidelines—that ensures the protection of animal industries while safeguarding trade interests.
SARS-CoV-2 S protein disrupts the formation of ISGF3 complex through conserved S2 subunit to antagonize type I interferon response
Authors: Cai Zeng , Ni Wenjia , Li Wenkang , Wu Zhixuan , Yao Xiaoqian , Zheng Yucheng , Zhao Yongliang , Yuan Weifeng , Liang Simeng , Wang Qi , Tang Mingliang , Chen Yu , Lan Ke , Zhou Li , Xu Ke 
Published: December 2024

ABSTRACT

Viral immunosuppression substantially affects the host immune response of infected patients and the protective efficacy of vaccines. Here, we found that the spike (S) protein, the major vaccine antigen of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), strongly suppresses host innate immunity by inhibiting interferon-stimulated gene (ISG) expression through both S1 and S2 subunits. Mechanistically, the S protein inhibited the formation of the classic interferon-stimulated gene factor 3 (ISGF3) complex composed of STAT1, STAT2, and IRF9 by competing with STAT2 for binding to IRF9, thereby impeding the transcription of ISGs. A strong interaction between S and the STAT1/STAT2 proteins further traps the ISGF3 complex in the endoplasmic reticulum and hinders the nuclear translocation of ISGF3. Notably, the interferon-inhibitory mechanism of the S protein was universal among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, Middle East respiratory syndrome coronavirus (MERS-CoV), human coronavirus 229E (HCoV-229E), human coronavirus NL63 (HCoV-NL63), and human coronavirus HKU1 (HCoV-HKU1), through the most evolutionarily conserved region of S2 subunit. Taken together, the findings of this study reveal a new mechanism by which the coronavirus S protein attenuates the host antiviral immune response and provides new insights into the proper design of coronavirus S-based vaccines to prevent immunosuppressive effects.

IMPORTANCE
This study unveils a new mechanism by which the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein attenuates the host’s antiviral immune response. The interferon-inhibitory mechanism of the S protein was universal among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63, and HCoV-HKU1, through conserved S2 domains. Our study expands the understanding of SARS-CoV-2 and other human coronaviruses in evading antiviral immune strategies, which is very important for the design and optimization of vaccine antigens, thus providing a theoretical basis for human anti-coronavirus immunity and understanding the interaction between the host and coronavirus.
Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample
Authors: Prattico Catherine , Gonzalez Emmanuel , Dridi Lharbi , Jazestani Shiva , Low Kristin E. , Abbott D. Wade , Maurice Corinne F. , Castagner Bastien 
Published: December 2024

ABSTRACT

Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in
Blautia
species not previously reported to be fructan consumers. We therefore validated the ability of different
Blautia
species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE

Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota’s effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among
Blautia
species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.
Development of monoclonal antibodies against
P. gingivalis
Mfa1 and their protective capacity in an experimental periodontitis model
Authors: Cao Mingya , Wang Siyu , Zhou Shengke , Yan Min , Zou Yu , Cui Yuan , Lou Xinyu , Gao Yichang , Chen Ying , Han Zijing , Qian Yi , Chen Jingying , Li Xia 
Published: December 2024

ABSTRACT

Porphyromonas gingivalis
(
P. gingivalis
), a gram-negative, black-pigmented anaerobe, is a major etiological agent and a leading cause of periodontitis. Fimbriae protein Mfa1 is a key virulence factor of
P. gingivalis
and plays a crucial role in bacterial adhesion, colonization, biofilm formation, and persistent inflammation, making it a promising therapeutic target. However, the role of anti-Mfa1 antibodies and the underlying protective mechanisms remain largely unexplored. Here, we developed and characterized the monoclonal antibodies (mAbs) targeting the Mfa1 protein of
P. gingivalis
. Function analysis showed that anti-Mfa1 mAbs mediated bacterial agglutination and inhibited
P. gingivalis
adhesion to saliva-coated hydroxyapatite and host cells. Notably, anti-Mfa1 mAbs significantly reduced bacterial burden and alveolar bone loss in a
P. gingivalis
-induced experimental periodontitis model. These results show that anti-Mfa1 mAbs can be beneficial in alleviating
P. gingivalis
infections, and provide important insights for the development of adequate adjuvant treatment regimens for Mfa1-targeted therapeutics.

IMPORTANCE

Fimbriae (pili) play an important role in bacterial adhesion, invasion of host cells and tissues, and formation of biofilms. Studies have shown that two types of fimbriae of
Porphyromonas gingivalis
, FimA and Mfa1, are important for colonization and infection through their binding to host tissues and other bacteria. While anti-FimA antibodies have been shown to improve periodontitis, the effect of anti-Mfa1 antibodies on
P. gingivalis
infection and periodontitis was previously unknown. In this study, we report for the first time that anti-Mfa1 monoclonal antibodies can reduce
P. gingivalis
infection and improve periodontitis. These findings suggest that Mfa1 represents a promising therapeutic target, and the development of anti-Mfa1 mAbs holds a potential as essential diagnostic and adjunctive therapeutic tools for managing
P. gingivalis
-related diseases.
Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling
Authors: Mottawea Walid , Yousuf Basit , Sultan Salma , Ahmed Tamer , Yeo JuDong , Hüttmann Nico , Li Yingxi , Bouhlel Nour Elhouda , Hassan Hebatoallah , Zhang Xu , Minic Zoran , Hammami Riadh 
Published: December 2024

ABSTRACT

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. However, their involvement in the gut-brain axis has been poorly investigated. We hypothesize that MEVs cross host cellular barriers and deliver their cargoes of bioactive compounds to the brain. In this study, we aimed to investigate the cargo capacity of MEVs for bioactive metabolites and their interactions with the host cellular barriers. First, we conducted a multi-omics profiling of MEVs’ contents from
ex vivo
and stool samples. Metabolomics analysis identified various neuro-related compounds encapsulated within MEVs, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines. Metaproteomics unveiled an enrichment of enzymes involved in neuronal metabolism, primarily in the glutamine/glutamate/gamma-aminobutyric acid (GABA) pathway. These neuro-related proteins and metabolites were correlated with
Bacteroides
spp. We isolated 18
Bacteroides
strains and assessed their GABA production capacity in extracellular vesicles (EVs) and culture supernatant. A GABA-producing
Bacteroides finegoldii
, released EVs with a high GABA content (4 µM) compared to
Phocaeicola massiliensis
. Upon testing the capacity of MEVs to cross host barriers, MEVs exhibited a dose-dependent paracellular transport and were endocytosed by Caco-2 and hCMEC/D3 cells. Exposure of Caco-2 cells to MEVs did not alter expression of genes related to intestinal barrier integrity, while affected immune pathways and cell apoptosis process as revealed by RNA-seq analyses.
In vivo
, MEVs biodistributed across mice organs, including the brain, liver, stomach, and spleen. Our results highlight the ability of MEVs to cross the intestinal and blood-brain barriers to deliver their cargoes to distant organs, with potential implication for the gut-brain axis.

IMPORTANCE

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. In this study, a multi-level analysis revealed presence of a diverse array of biologically active molecules encapsulated within MEVs, including neuroactive metabolites, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines, and gamma-aminobutyric acid (GABA). Metaproteomics also unveiled an enrichment of neural-related proteins, mainly the glutamine/glutamate/GABA pathway. MEVs were able to cross epithelial and blood-brain barriers
in vitro
. RNA-seq analyses showed that MEVs stimulate several immune pathways while suppressing cell apoptosis process. Furthermore, MEVs were able to traverse the intestinal barriers and reach distal organs, including the brain, thereby potentially influencing brain functionality and contributing to mental and behavior.
Phillyrin ameliorates DSS-induced colitis in mice via modulating the gut microbiota and inhibiting the NF-κB/MLCK pathway
Authors: Li Tong , Hu Guiqiu , Fu Shoupeng , Qin Di , Song Zheyu 
Published: December 2024

ABSTRACT

Phillyrin (PHY), also known as forsythin, is an active constituent isolated from the fruit of
Forsythia suspensa
(Thunb.) Vahl (Oleaceae). It exhibits anti-inflammatory, anti-viral, and antioxidant properties. However, the precise impact of PHY on colitis induced by dextran sodium sulfate (DSS) and its mechanism remain elusive. The present investigation revealed that PHY (12.5, 25.0, and 50.0 mg/kg) exhibited significant therapeutic efficacy in protecting mice against DSS-induced colitis. This effect was manifested as reduced weight loss, a shortened colon, increased secretion of inflammatory factors, increased intestinal permeability, and an enhanced disease activity index in mice with ulcerative colitis (UC). Molecular investigations have determined that PHY mitigates the nuclear translocation of nuclear factor kappa B, thereby downregulating myosin light-chain kinase-driven myosin light-chain phosphorylation. This mechanism results in the preservation of the integrity of the intestinal barrier. The outcomes of 16S rRNA sequencing suggest that PHY (50 mg/kg) augmented the relative abundance of certain probiotic strains, including
Lactobacillaceae
and
Lachnospiraceae
. Additionally, PHY supplementation elevated the short-chain fatty acid contents within the intestinal contents of mice with UC. In conclusion, pre-treatment with PHY may ameliorate the DSS-induced UC in mice by lowering the expression of inflammatory factors, protecting intestinal barrier function, and enhancing the structure of the intestinal flora.

IMPORTANCE
The protective effect of phillyrin on DSS-induced colitis was explained for the first time, and the anti-inflammatory effect of phillyrin was demonstrated by fecal microbiota transplantation experiments mainly through intestinal flora.
Effect of colistin-tigecycline combination on colistin-resistant and carbapenem-resistant
Klebsiella pneumoniae
and
Acinetobacter baumannii
Authors: Park Suyeon , Jin Yanhong , Ko Kwan Soo 
Published: December 2024

ABSTRACT

There is a critical need for treatment strategies to combat carbapenem-resistant Gram-negative pathogens. This study investigates the efficacy of combining low concentrations of colistin with tigecycline against colistin- and carbapenem-resistant
Klebsiella pneumoniae
and
Acinetobacter baumannii
strains. We used two strains of KPC-2-producing
K. pneumoniae
and OXA-23-producing
A. baumannii
, both of which are highly colistin-resistant. In the
in vitro
time-killing assays, monotherapy with colistin (2 mg/L) and tigecycline (4 or 8 mg/L) was ineffective against all strains. However, the combination of colistin (2 mg/L) and tigecycline (4 or 8 mg/L) inhibited bacterial growth. Survival analysis of
Galleria mellonella
larvae also demonstrated the efficacy of low concentrations of colistin and tigecycline against colistin- and carbapenem-resistant strains. All larvae survived when treated with a combination of colistin and tigecycline, whereas monotherapy with either colistin or tigecycline did not increase larval survival rates. This study proposes using a combination of tigecycline and colistin at clinical concentrations to treat carbapenem-resistant
K. pneumoniae
and
A. baumannii,
regardless of colistin resistance.

IMPORTANCE
Colistin resistance in carbapenem-resistant Gram-negative pathogens is a serious challenge in clinical settings. Our study showed that low concentration of colistin can be effective when combined with tigecycline. It presents the possibility of an available treatment option for antibiotic-resistant pathogens.
(Invited) The Potential of Pulsed Low Temperature Plasmas for the Controlled Deposition of Plasma Polymer Ultrathin Films and Composite Nanomaterials (Invited)
Authors: Berndt Johannes 
Published: December 2024

Low temperature discharges with their unique non-equilibrium properties are often used in industrial processes for the deposition of ultra-thin (plasma) polymer films. Applications for this type of thin films range from protective coatings to their use in membranes, biosensors and batteries. However, the properties of these thin films are highly dependent on the choice of discharge parameters, both in terms of their surface topography and their chemical composition. This paper deals with the great potential of pulsed discharges for the controlled deposition of plasma polymer films. The influence of pulse frequency and duty cycle on the deposition process and the properties of the resulting thin films is discussed from a theoretical point of view and is illustrated by experimental results. The latter concern examples of experiments carried out with discharges operated with acetylene or aniline, as well as functional coatings on top of MoS2, 2D graphene or CNTs.
The work was supported by the project PEGASUS (Plasma Enabled and Graphene Allowed Synthesis of Unique nano-structures), funded by the European Union’s Horizon research innovation program under Grant Agreement No. 766894; EU Graphene Flagship FLAG-ERA III JTC 2021 project VEGA (No. PR-11938) Project-ANR-21-GRF1-0004. Further support was obtained via ARD MATEX Centre-Val de Loire Region (projects Carbon2 and Carbon3) and project Orleans Metropole (both France).
Pd-Based Metal-Support Heterostructure Catalyst for High Performance Electrocatalytic N2 Reduction Reaction
Authors: Song Ji-Yoon , Park Jaehyun , Jung Hee-Tae 
Published: December 2024

Electrocatalytic nitrogen (N2) reduction reaction (eNRR) is of great interest to produce the green ammonia (NH3). However, the competitive side reaction of hydrogen (H2) evolution reaction (HER) and slow proton-couple electron transfer (PCET) step still become a bottleneck where resulting in poor N2 selectivity and yield of NH3 production. The heterostructures of metal and boron nitride (BN) analogs have been computatively demonstrated and suggested as a potential eNRR catalyst to improve eNRR performance as both suppressing HER and accelerating PCET step. However, experimental demonstration is still challenging due to the complex synthetic method required to achieve a uniform and dense distribution of metal catalysts on the BN surface.
Here, we present the facile and uniform formation of the Pd nanoparticles (NPs) on defective boron nitride (BN) using ultrafast radiative Joule-heating within short time (~0.5 s), which is the first-time demonstration on the BN family. Especially, thanks to the strong electronic metal-to-support interaction (EMSI) effect between the defect site of BN surface and Pd NPs, the electron-deficient state of Pd NPs facilitates the significant reduce of free energy during the PCET step which is beneficial to interact with N2 molecules. In particular, we observe that Pd NPs on defective BN support exhibit the high NH3 selectivity of 68% in the neutral aqueous electrolyte and 59% of NH3 selectivity and 53.3 µg/h/cm2 of NH3 yield rate in the acidic media, respectively, which are the highest values of the selectivity and NH3 yield rate among existing Pd-based eNRR catalysts.