bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATX1 and HUB1/2 promote recruitment of the transcription elongation factor VIP2 to modulate the floral transition in Arabidopsis
Authors: Lu Qianqian , Shi Wenwen , Zhang Fei , Ding Yong 
Published: March 2024

SUMMARYHistone 2B ubiquitination (H2Bub) and trimethylation of H3 at lysine 4 (H3K4me3) are associated with transcription activation. However, the function of these modifications in transcription in plants remains largely unknown. Here, we report that coordination of H2Bub and H3K4me3 deposition with the binding of the RNA polymerase‐associated factor VERNALIZATION INDEPENDENCE2 (VIP2) to FLOWERING LOCUS C (FLC) modulates flowering time in Arabidopsis. We found that RING domain protein HISTONE MONOUBIQUITINATION1 (HUB1) and HUB2 (we refer as HUB1/2), which are responsible for H2Bub, interact with ARABIDOPSIS TRITHORAX1 (ATX1), which is required for H3K4me3 deposition, to promote the transcription of FLC and repress the flowering time. The atx1‐2 hub1‐10 hub2‐2 triple mutant in FRIGIDIA (FRI) background displayed early flowering like FRI hub1‐10 hub2‐2 and overexpression of ATX1 failed to rescue the early flowering phenotype of hub1‐10 hub2‐2. Mutations in HUB1 and HUB2 reduced the ATX1 enrichment at FLC, indicating that HUB1 and HUB2 are required for ATX1 recruitment and H3K4me3 deposition at FLC. We also found that the VIP2 directly binds to HUB1, HUB2, and ATX1 and that loss of VIP2 in FRI hub1‐10 hub2‐2 and FRI atx1‐2 plants resulted in early flowering like that observed in FRI vip2‐10. Loss of function of HUB2 and ATX1 impaired VIP2 enrichment at FLC, and reduced the transcription initiation and elongation of FLC. In addition, mutations in VIP2 reduced HUB1 and ATX1 enrichment and H2Bub and H3K4me3 levels at FLC. Together, our findings revealed that HUB1/2, ATX1, and VIP2 coordinately modulate H2Bub and H3K4me3 deposition, FLC transcription, and flowering time.
DEFLECTION AND STRAINS PERFORMANCE OF KENAF FIBRE-REINFORCED CONCRETE BEAMS
Authors: Ayeni Ige Samuel , Jamaludin Yatim Mohamad , Abdul Shukor Lim Nor Hasanah Binti 
Published: March 2024

There has been a need to find a lasting means to improve beams' deflection and strain performance without necessarily increasing the beam stirrups. The limitations of steel and other synthetic fibres have reduced their application. Given its tensile strength, renewability, sustainability, and affordability compared to steel and synthetic fibres, kenaf fibre development is of great interest in Malaysia. Therefore, this research work experimentally investigated the deflection and strain performance of Kenaf Fibre Reinforced concrete beams. The volume and length of kenaf fibre used were 0.75% and 25mm, respectively. Kenaf fibre was treated with 5% NaOH to improve its performance. The alkaline-treated and untreated kenaf fibres morphology was observed under a variable-pressure scanning electron microscope. It was discovered inclusion of kenaf fibre reduced the workability of concrete. Also, plain and KFR concrete morphology was observed under a variable-pressure scanning electron microscope. Four beams were designed to study the deflection and strain performance of the KFR concrete beam; one was well reinforced but without kenaf fibre. The stirrups spacings were increased by 25%, 50%, and 75% for the other three beams. The beams were tested under centre loading. Deflection and concrete strain at the centre and along the beam span were measured using LVDTs and concrete strain gauges for the four beams. Furthermore, the strains on the shear and bottom flexural reinforcements at the centre of the beam were measured using steel strain gauges. It was discovered that kenaf fibre enhanced the deflection and strain performance of beams between 25% and 50% stirrups deficiency.
AUTOMATION OF PETROLEUM STORAGE TANK LEAKAGE THROUGH PRODUCT TRANSFER CONTROL USING PROGRAMMABLE LOGIC CONTROLLER
Authors: Bongcales Gian Carlo M. , Cabral Charlotte , Chua Alvin 
Published: March 2024

Industrial storage tanks have always been a critical part of the petrochemical industry due to their capacity to either act as a buffer to other plant processes or simply to store enormous amounts of fluids for a long period of time in a controlled environment. These petroleum storage tanks are supposedly constructed to follow specific sets of instructions guided by the American Petroleum Industry from the type of material used up to the welding procedure. But due to inefficient construction, unmaintained and uninspected problems, welding defects, and environmental concerns among others, a leak in a storage tank can occur and will be a major problem as this can cause fire, explosion, and environmental hazards. Additionally, due to tensions between Ukraine and the Russian government and the succeeding Russian ban on oil imports, the cost of 1 barrel of oil rises at an alarming since 2020. With that in mind, an automation procedure is proposed by the researchers, to save as much of this oil from leaking and being unusable and to reduce the causes of further accidents. This paper not only seeks to use an existing tank layout, with currently installed level indicator transmitters, motor-operated control valves, and other equipment, but also to introduce flammable gas detectors that could detect the leaked petroleum on the ground and would initiate the automation procedure. The automation setup was realized by flowcharts, PLC, and ladder logic simulation using Picosoft software. Automation procedures are analyzed wherein the tanks are being filled, the trucks are being loaded, a leaking tank has its contents pumped to another tank, and a leaking tank has its contents pumped to the truck loading station. Results show that a minimum number of 8.89 barrels of oil saved could breakeven the cost of an estimated amount of $80-90 dollars per barrel of oil can be saved by the proposed automation.
Extreme values of L$L$‐functions of newforms
Authors: Gun Sanoli , Lunia Rashi 
Published: March 2024

AbstractIn 2008, Soundararajan showed that there exists a normalized Hecke eigenform of weight and level one such that
for sufficiently large . In this note, we show that for any and for all sufficiently large , the number of normalized Hecke eigenforms of weight and level one for which
is . For an odd fundamental discriminant , let be the set of all cuspidal normalized Hecke eigenforms of weight and level dividing . When the real primitive Dirichlet character satisfies , we investigate the number of for which takes extremal values.
Regulation of phase separation and antiviral activity of Cactin by glycolytic enzyme PGK via phosphorylation in
Drosophila
Authors: Chen Dongchao , Shi Chang , Xu Wen , Rong Qiqi , Wu Qingfa 
Published: March 2024

ABSTRACT

Liquid–liquid phase separation (LLPS) plays a crucial role in various biological processes in eukaryotic organisms, including immune responses in mammals. However, the specific function of LLPS in immune responses in
Drosophila melanogaster
remains poorly understood. Cactin, a highly conserved protein in eukaryotes, is involved in a non-canonical signaling pathway associated with Nuclear factor-κB (NF-κB)-related pathways in
Drosophila
. In this study, we investigated the role of Cactin in LLPS and its implications for immune response modulation. We discovered that Cactin undergoes LLPS, forming droplet-like particles, primarily mediated by its intrinsically disordered region (IDR). Utilizing immunoprecipitation and mass spectrometry analysis, we identified two phosphorylation sites at serine residues 99 and 104 within the IDR1 domain of Cactin. Co-immunoprecipitation and mass spectrometry further revealed phosphoglycerate kinase (PGK) as a Cactin-interacting protein responsible for regulating its phosphorylation. Phosphorylation of Cactin by PGK induced a transition from stable aggregates to dynamic liquid droplets, enhancing its ability to interact with other components in the cellular environment. Overexpression of PGK inhibited
Drosophila
C virus (DCV) replication, while PGK knockdown increased replication. DCV infection also increased Cactin phosphorylation. We also found that phosphorylation enhances the antiviral ability of Cactin by promoting liquid-phase droplet formation. These findings demonstrate the role of Cactin-phase separation in regulating DCV replication and highlight the modulation of its antiviral function through phosphorylation, providing insights into the interplay between LLPS and antiviral defense mechanisms.

IMPORTANCE

Liquid–liquid phase separation (LLPS) plays an integral role in various biological processes in eukaryotic organisms. Although several studies have highlighted its crucial role in modulating immune responses in mammals, its function in immune responses in
Drosophila melanogaster
remains poorly understood. Our study investigated the role of Cactin in LLPS and its implications for immune response modulation. We identified that phosphoglycerate kinase (PGK), an essential enzyme in the glycolytic pathway, phosphorylates Cactin, facilitating its transition from a relatively stable aggregated state to a more dynamic liquid droplet phase during the phase separation process. This transformation allows Cactin to rapidly interact with other cellular components, enhancing its antiviral properties and ultimately inhibiting virus replication. These findings expand our understanding of the role of LLPS in the antiviral defense mechanism, shedding light on the intricate mechanisms underlying immune responses in
D. melanogaster
.
The antagonistic transcription factors, EspM and EspN, regulate the ESX-1 secretion system in
M. marinum
Authors: Nicholson Kathleen R. , Cronin Rachel M. , Prest Rebecca J. , Menon Aruna R. , Yang Yuwei , Jennisch Madeleine K. , Champion Matthew M. , Tobin David M. , Champion Patricia A. 
Published: March 2024

ABSTRACT

Bacterial pathogens use protein secretion systems to transport virulence factors and regulate gene expression. Among pathogenic mycobacteria, including
Mycobacterium tuberculosis
and
Mycobacterium marinum
, the ESAT-6 system 1 (ESX-1) secretion is crucial for host interaction. Secretion of protein substrates by the ESX-1 secretion system disrupts phagosomes, allowing mycobacteria cytoplasmic access during macrophage infections. Deletion or mutation of the ESX-1 system attenuates mycobacterial pathogens. Pathogenic mycobacteria respond to the presence or absence of the ESX-1 system in the cytoplasmic membrane by altering transcription. Under laboratory conditions, the EspM repressor and WhiB6 activator control transcription of specific ESX-1-responsive genes, including the ESX-1 substrate genes. However, deleting the
espM
or
whiB6
gene does not phenocopy the deletion of the ESX-1 substrate genes during macrophage infection by
M. marinum
. In this study, we identified EspN, a critical transcription factor whose activity is masked by the EspM repressor under laboratory conditions. In the absence of EspM, EspN activates transcription of
whiB6
and ESX-1 genes during both laboratory growth and macrophage infection. EspN is also independently required for
M. marinum
growth within and cytolysis of macrophages, similar to the ESX-1 genes, and for disease burden in a zebrafish larval model of infection. These findings suggest that EspN and EspM coordinate to counterbalance the regulation of the ESX-1 system and support mycobacterial pathogenesis.

IMPORTANCE
Pathogenic mycobacteria, which are responsible for tuberculosis and other long-term diseases, use the ESX-1 system to transport proteins that control the host response to infection and promote bacterial survival. In this study, we identify an undescribed transcription factor that controls the expression of ESX-1 genes and is required for both macrophage and animal infection. However, this transcription factor is not the primary regulator of ESX-1 genes under standard laboratory conditions. These findings identify a critical transcription factor that likely controls expression of a major virulence pathway during infection, but whose effect is not detectable with standard laboratory strains and growth conditions.
Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover
Authors: Baumgartner Breanna M. , Bono Kayla A. , McIntosh Dawn R. , Vu Anna M. , Adams Chanel F. , Benik Brooklyn C. , Chavez Jessica , Gresky Samantha J. , Sotelo Andres , Ray Jordan I. , Peister Alexandra , Kimberley Kendra W. , McKenna Chelsey C. , Theoret James R. , Yoon Earl J. , Windsor Erin J. 
Published: March 2024

ABSTRACT

JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium

Mycobacterium smegmatis mc
2
155

. Nibbles and OlgasClover were identified in host bacterium
Gordonia rubripertincta
NRRL B-16540.
Evaluation of three protocols for direct susceptibility testing for Gram-negative rods from flagged positive blood culture bottles
Authors: Khan Salman , Das Arghya , Mishra Anwita , Vidyarthi Ashima Jain , Nandal Mukesh , Yadav Himanshu , Roy Shayak , Singh Mahipal 
Published: March 2024

ABSTRACT

Bloodstream infections are associated with high mortality, which can be reduced by targeted antibiotic therapy in the early stages of infection. Direct antibiotic susceptibility testing (AST) from flagged positive blood cultures may facilitate the administration of early effective antimicrobials much before the routine AST. This study aimed to evaluate three different direct AST protocols for Gram-negative rods from flagged positive blood culture broths. Blood culture broths showing Gram-negative rods only were subjected to direct AST by Clinical and Laboratory Standards Institute-recommended direct disk diffusion (protocol A). Additionally, automated AST (protocol B) and Kirby-Bauer disk diffusion (protocol C) were performed with standard inoculum prepared from bacterial pellets obtained by centrifuging blood culture broths in serum separator vials. For comparison, conventional AST of isolates from solid media subculture was also performed with Kirby-Bauer disk diffusion (reference standard) and the automated method. Overall, categorical agreements of protocols A, B, and C were 97.6%, 95.7%, and 95.9%, respectively. Among Enterobacterales, minor error, major error, and very major error rates of protocol B were 3.5%, 0.36%, and 0.43%, respectively, whereas minor error, major error, and very major error rates of protocol C were 3.4%, 0.72%, and 0.21%, respectively, and among non-fermenters, protocol B had a minor error rate of 6.5%, and protocol C had a minor error rate of 4.1% and major error rate of 1.9%. All three direct AST protocols demonstrated excellent categorical agreements with the reference method. Performance of protocols B and C between Enterobacterales and non-fermenters was not statistically different.

IMPORTANCE
Bloodstream infections are associated with high mortality that can be reduced by targeted antibiotic therapy in the early stages of infection. Direct antibiotic susceptibility testing (AST) from flagged positive blood cultures may facilitate the administration of early effective antimicrobials much before the routine AST. Clinical and Laboratory Standards Institute-recommended direct AST can be performed with a limited number of antibiotic disks only. On the other hand, using an automated system for direct AST will not only allow effective laboratory workflow with reduced turnaround time but also provide the minimum inhibitory concentration values of tested antibiotics. However, using expensive automated systems for direct AST may not be feasible for resource-limited laboratories. Therefore, in this study, we aimed to evaluate the CLSI-recommended method and two other direct AST protocols (one with an automated system and the other with disk diffusion) for Gram-negative rods from flagged positive blood cultures.
Integrative metabolomics highlights gut microbiota metabolites as novel NAFLD-related candidate biomarkers in children
Authors: Luo Jiayou , Luo Miyang , Kaminga Atipatsa C. , Wei Jia , Dai Wen , Peng Yunlong , Zhao Kunyan , Duan Yamei , Xiao Xiang , Ouyang SiSi , Yao Zhenzhen , Liu Yixu , Pan Xiongfeng 
Published: March 2024

ABSTRACT

Altered gut microbiota and metabolites are important for non-alcoholic fatty liver disease (NAFLD) in children. We aimed to comprehensively examine the effects of gut metabolites on NAFLD progression. We performed integrative metabolomics (untargeted discovery and targeted validation) analysis of non-alcoholic fatty liver (NAFL), non-alcoholic steatohepatitis (NASH), and obesity in children. Fecal samples were collected from 75 subjects in the discovery cohort (25 NAFL, 25 NASH, and 25 obese control children) and 145 subjects in an independent validation cohort (53 NAFL, 39 NASH, and 53 obese control children). Among 2,491 metabolites, untargeted metabolomics revealed a complete NAFLD metabolic map containing 318 increased and 123 decreased metabolites. Then, machine learning selected 65 important metabolites that can distinguish the severity of the NAFLD. Furthermore, precision-targeted metabolomics selected 5 novel gut metabolites from 20 typical metabolites. The functionality of candidate metabolites was validated in hepatocyte cell lines. In the end, this study annotated two novel elevated pathogenic metabolites (dodecanoic acid and creatinine) and a relationship between depleted protective gut microbiota (
Butyricicoccus
and
Alistipes
), increased inflammation (IL-1β), lipid metabolism (TG), and liver function (ALT and AST). This study demonstrates the role of novel gut metabolites (dodecanoic acid and creatinine), as the fatty acid metabolism regulator contributing to NAFLD development through its influence on inflammation and liver function.

IMPORTANCE

Altered gut microbiota and metabolites are a major cause of non-alcoholic fatty liver disease (NAFLD) in children. This study demonstrated a complete gut metabolic map of children with NAFLD, containing 318 increased and 123 decreased metabolites by untargeted metabolomic. Multiple validation approaches (machine learning and targeted metabolomic) selected five novel gut metabolites for targeted metabolomics, which can distinguish NAFLD status and severity. The gut microbiota (
Butyricicoccus
and
Alistipes
) and metabolites (creatinine and dodecanoic acid) were novel biomarkers associated with impaired liver function and inflammation and validated by experiments of hepatocyte cell lines. The data provide a better understanding of the importance of gut microbiota and metabolite alterations in NAFLD, which implies that the altered gut microbiota and metabolites may represent a potential target to prevent NAFLD development.
Middle–Late Jurassic subduction erosion caused by intra-oceanic arc subduction in central Tibet
Authors: Zhang Bo-Chuan , Fan Jian-Jun , Luo An-Bo , Sun Si-Lin , Bai Jia-Wei 
Published: March 2024

Abstract
Subduction erosion is crucial in crustal material recycling. However, subduction erosion caused by intra-oceanic arc subduction has not been sufficiently investigated. In this study, we provide new geological, geochronological, geochemical, and isotopic data from Dongco granodiorites in the central Bangong–Nujiang suture zone of central Tibet to explore subduction erosion caused by intra-oceanic arc subduction. Analysis shows that the ca. 158–155 Ma Dongco granodiorites originated from the subducted oceanic plate, and they were contaminated with accretionary wedge when they intruded the Dongco ophiolite. This suggests that the Dongco ophiolite was emplaced in the subducted accretionary wedge before the Late Jurassic. Based on the intra-oceanic arc affinity and lack of volcanic rocks of Middle Jurassic Dongco ophiolite and other regional data, we believe that the main body of the central intra-oceanic arcs and a portion of the western intra-oceanic arcs in the Meso-Tethys Ocean subducted beneath the southern Qiangtang terrane during the Middle–Late Jurassic. In addition, the different degree absence of the Jurassic accretionary wedge, forearc region, and arc magmatic rocks in the southern Qiangtang terrane indicate that the central and western parts of the southern Qiangtang terrane experienced both vigorous and relatively weak subduction erosion during the Middle–Late Jurassic, respectively. Thus, there is a significant spatiotemporal coupling between subduction erosion of the southern Qiangtang terrane and intra-oceanic arc subduction. Based on these studies and the research on subduction erosion, we suggest that subduction of the main body of the central intra-oceanic arcs and partial subduction of the western intra-oceanic arcs in the Meso-Tethys Ocean caused both vigorous and relatively weak subduction erosion of the southern Qiangtang terrane during the Middle–Late Jurassic, respectively. In addition, the increase in subduction rate also promoted Middle–Late Jurassic subduction erosion of the southern Qiangtang terrane.
An ongoing lithospheric dripping process beneath northeast China and its impact on intraplate volcanism
Authors: Lin Feiyu , Qi Liang , Zhang Nan , Guo Zhen 
Published: March 2024

Abstract
Unique intraplate volcano eruptions and westward volcano migration since the Oligocene have been observed in northeast China, where an overriding continental zone is tectonically controlled by the subduction of the northwestern Pacific plate and the opening of Japan Sea. Interestingly, these intraplate magmatic events occur around a subsiding basin (the Songliao Basin), but no volcanic activity has been observed within the Songliao Basin. The geodynamic mechanism responsible for these volcanoes remains unclear. To address the geodynamic process beneath northeast China, we conducted numerical models constrained by data from regional reconstruction and seismic and volcanic studies. The vertical velocity field of mantle convection and lithospheric partial melting structures derived from our models show that mantle upwelling and melting centers migrate from east to west in northeast China with the westward propagation of the sub-horizontal slab in the transition zone, leading to the observed volcano migration. Also, with the subduction retreat of the northwestern region of the Pacific plate and the opening of the Japan Sea, significant lithospheric thickness differences developed between the Changbaishan-Mudanjiang region and the Songliao Basin, leading to lithospheric unstable dripping. This dripping structure prevents the partial melting of the lithosphere but facilitates the subsidence of the Songliao Basin. Moreover, the lithospheric dripping model successfully predicts upper mantle structures consistent with the proposed tomography model, the observed Moho depth, and surface topography variations. Thus, lithospheric dripping induced by lithospheric thickness differences and the retreating subduction of the Pacific slab provides a robust mechanism for the unique geodynamic processes in northeast China.