bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of the immunogenicity, efficacy and safety of recombinant RBD
SARS-CoV-2 vaccine with CpG adjuvant in rodent, non-rodent and Maccaca
fascicularis using Indonesian Strain Virus
Authors: Limeilati Nur Amalia , Nidom Reviany V. , Sari Trilokita Tunjung , Kusumarahayu Nurvita P. , Fransiska Siti V. , Indrasari Setyarina , Garmana Afrillia N. , Ayuningtyas Dhyan K. , Nugroho Gembong S. , Darsono  , Maharani  , Wijayadikusumah Acep R. , Yulinah Elin , Adyana I Ketut , Nidom Astria N. , Nurainy Neni , Nidom Chairul A. 
Published: January 2025

Abstract
SARS-CoV-2 is the leading cause of the COVID-19 pandemic that causes acute
respiratory syndrome, emerged in late 2019, and was declared a global pandemic
on March 11th, 2020. A safe and effective vaccine that
prevents SARS-CoV-2 infection or minimize SARS-CoV-2 disease burden is needed.
However, in 2021, Low- and middle-income countries (LMICs) face challenges
regarding supply of COVID-19 vaccines. Indonesia, as a public sector vaccine
manufacturing in developing countries was developed COVID-19 vaccine using a
platform based on recombinant subunit proteins, a Receptor Binding Domain (RBD)
of SARS-CoV-2 formulated with combination of Alhydrogel and CpG
Oligodeoxynucleotides 1018 (CpG). In this study, we report the preclinical study
including immunogenicity, toxicity and efficacy of vaccine in animal models. The
vaccine immunogenicity tested in mice and non-human primates, the toxicity was
done in rodents and non-rodents and challenged study and efficacy was done in
non-human primates (NHPs) model. The animal model was vaccinated intramuscularly
(IM). The serology result in mice and non-human primates showed significant
antibody titers and neutralizing antibody responses compared to the RBD
formulations adjuvanted with Alhydrogel only. Safety study in Wistar rats and
New Zealand rabbits for single-dose (acute toxicity) and repeated-dose
(sub-chronic toxicity) showed no abnormalities in the animal’s organs and
behaviors and no deaths were reported in tested animals. Two doses of
vaccination have been shown to protect NHPs against SARS-CoV-2 infection, as
detected by drastic viral reduction from sample swab in nasal, anal, trachea and
nasal wash in 7 days after virus challenged, also viral load measurement from
lung and BAL tissue showed negative result, which gave better result than
negative control and control vaccine group. No evidence of disease enhancement
was observed. These results support clinical development of SARS-CoV-2 vaccine,
and in 2022 this vaccine has been approved for emergency use in
Indonesia.
G-quadruplexes catalyze protein folding by reshaping the energetic
landscape
Authors: Huang Zijue , Ghosh Kingshuk , Stull Frederick , Horowitz Scott 
Published: January 2025

Abstract

proteins
Many proteins have slow folding timesin
vitrothat are physiologically untenable. To combat this
challenge, ATP-dependent chaperonins are thought to possess the unique
ability to catalyze protein folding. Performing quantitative model selection
using protein folding and unfolding data, we here show that short nucleic
acids containing G-quadruplex (G4) structure can also catalyze protein
folding. Performing the experiments as a function of temperature
demonstrates that the G4 reshapes the underlying driving forces of protein
folding. As short nucleic acids can catalyze protein folding without the
input of ATP, the ability of the cell to fold proteins is far higher than
previously anticipated.

Significance Statement
How folding of proteins occurs en masse in the cell is still a daunting
unsolved problem. Many proteins have complicated and difficult folding
trajectories, within vitrofolding times that are
physiologically untenable. The acceleration of protein folding to
physiologically relevant timescales is a biologically essential function
thought to be accomplished by a small set of ATP-dependent chaperonins. In
this work, we surprisingly show that small nucleic acid sequences containing
G-quadruplexes can catalyze protein folding and reshape protein folding
energy landscapes. As a result, the capacity for accelerating protein
folding in the cells is far higher than previously suggested, potentially
explaining the accommodation of large number of proteins with
physiologically unreasonable folding times.
A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense
system
Authors: Loyo Christian L. , Grossman Alan D. 
Published: January 2025

Abstract

Bacteria
Bacteria contain a diverse array of genes that provide defense against
predation by phages. Anti-phage defense genes are frequently located on
mobile genetic elements and spread through horizontal gene transfer. Despite
the many anti-phage defense systems that have been identified, less is known
about how phages overcome the defenses employed by bacteria. The integrative
and conjugative element
ICEBs1inBacillus
subtiliscontains a gene,spbK,
that confers defense against the temperate phage SPβ through an abortive
infection mechanism. Using genetic and biochemical analyses, we found that
SpbK is an NADase that is activated by binding to the SPβ phage portal
protein YonE. The presence of YonE stimulates NADase activity of the TIR
domain of SpbK and causes cell death. We also found that the SPβ-like phage
Φ3T has a counter-defense gene that prevents SpbK-mediated abortive
infection and enables the phage to produce viable progeny, even in cells
expressingspbK. We made SPβ-Φ3T hybrid phages
that were resistant to SpbK-mediated defense and identified a single gene in
Φ3T (phi3T_120,now
callednipfor NADase inhibitor from phage)
that was both necessary and sufficient to block SpbK-mediated anti-phage
defense. We found that Nip binds to the TIR (NADase) domain of SpbK and
inhibits NADase activity. Our results provide insight into how phages
overcome bacterial immunity by inhibiting enzymatic activity of an
anti-phage defense protein.

Author Summary
Bacterial viruses (bacteriophages or phages) are widespread and abundant
across the planet. Bacteria have a variety of immune systems, often found on
mobile genetic elements, to combat phage predation. Phages can overcome
these immune systems by mutating to avoid recognition or by producing
molecules that prevent the immune system from working. We determined how an
anti-phage defense system encoded by an integrative and conjugative element
recognizes phage infection to cause cell death prior to the generation of
phage progeny. We also identified a phage gene that prevents this defense
system from functioning. The phage-encoded counter-defense protein inhibits
the enzymatic activity of the anti-phage defense protein, enabling evasion
of immunity and production of infectious phage. There are likely many
different phage-encoded counter-defense genes yet to be discovered.
Conditional fusogenic lipid nanocarriers for cytosolic delivery of
macromolecular therapeutics
Authors: Zhong Qian , Tan Edward K.W. , Shyamal Ananth , Ngambenjawong Chayanon , Parisi Tiziana , Ko Henry , Fleming Heather E. , Jacks Tyler , Bhatia Sangeeta N. 
Published: January 2025

Abstract
Macromolecular therapeutics designed for intracellular targets must overcome
systemic delivery barriers, target cell membrane impermeability, and inefficient
endosomal escape. Here, we engineer a class of conditional fusogenic liposomes
(C-FLIPs) that harness the catalytic activity of extracellular proteases present
in the pathological microenvironment. This context-specific activation enables
on-target membrane fusion with cells in diseased tissue, resulting in cytosolic
delivery of therapeutic payloads. We describe the cytoplasmic delivery of three
prototypic macromolecular therapeutic classes: peptide degraders, cytotoxic
proteins, and ribonucleoprotein particles (RNPs). We further develop C-FLIP to
deliver granzyme B (GzmB) to the cytoplasm of cancer cellsin
vivoand induce pyroptosis in immunologically-inert tumors.
Treatment with C-FLIP/GzmB reprograms the immunosuppressive tumor
microenvironment and synergizes with checkpoint blockade to result in the
regression of established tumors and induce immunological memory. This modular,
non-viral, cytosolic delivery platform represents a promising approach to
leverage pathological protease activity for targeted delivery of
biologics.
T cell-derived IFN-γ Suppresses T Follicular Helper Cell Differentiation and Antibody Responses
Authors: Sala Eleonora , Nelli Maria , Laura Chiara , Di Lucia Pietro , Beccaria Cristian Gabriel , Bono Elisa B. , Mangione Marta , Marotta Davide , Grillo Marta , Sperto Valentina , Giustini Leonardo , Tosi Fabio , Nie Jia , Kim Daehong , Furiato Giuliana , Malpighi Chiara , Consolo Eleonora , Becher Burkhard , David Eyal , Cohen Merav , Giladi Amir , Amit Ido , Bosselut Remy , Guidotti Luca G. , Iannacone Matteo , Kuka Mirela 
Published: January 2025

AbstractCD4+T cells play a critical role in antiviral humoral and cellular immune responses. We have previously reported that subcutaneous lymphocytic choriomeningitis virus (s.c. LCMV) infection is characterized by a stark compartmentalization of CD4+T cells, leading to strong TH1 polarization but virtually absent T follicular helper (TFH) cells, a key driver of humoral immunity. Here, we investigated the mechanisms responsible for this impaired TFHdifferentiation. We found that T-bet+cells induced by s.c. LCMV infection encompass a TH1 subset expressing Granzyme-B (GzmB) and a Tcf-1+subset that retains the potential for TFHdifferentiation without expressing mature TFHmarkers. Interestingly, IFN-γ blockade enables full differentiation of Tcf-1+cells into TFH, formation of germinal centers and increased antibody production. Of note, the suppression of TFHcells by IFN-γ is not directly mediated through CD4+T cells but rather involves another cell type, likely dendritic cells (DCs). Our study provides novel insights into the mechanisms directing early CD4+T cell polarization and affecting humoral responses to viruses, laying a foundation for the development of effective vaccine strategies.
BORC segregates synaptic vesicle and lysosomal proteins through motors UNC-104/KIF1A and UNC-116/KIF5
Authors: Mathew Amal , Seal Sohan , Dandekar Aditee , Chauhan Badal Singh , Sivadasan Sruthi , Nonet Michael L , Koushika Sandhya P. 
Published: January 2025

AbstractWhile synaptic vesicle proteins (SVPs) and lysosomal proteins can be present together in axons, the origin of these compartments is unclear. These SV-lysosomes are however thought to segregate further to SVPs and lysosomal proteins. In this study, we identify genes and characterize a genetic pathway involved in the segregation of SVPs and lysosomal proteins in the neuronal cell body. We identify a novel role for BORC (BLOC-1-related complex) in segregating SVPs and lysosomal proteins in the cell body. BORC subunit SAM-4/Myrlysin acts through ARL-8 and Kinesin motor proteins UNC-116/KIF5 and UNC-104/KIF1A in segregating SVPs and lysosomal proteins. Additionally, we also show that LRK-1/LRRK2 and APB-3/AP-3 (β3), involved in pre-SV biogenesis, regulate the segregation of SVPs and lysosomal proteins in the neuronal cell body. LRK-1 recruits SAM-4 that in turn governs the localisation of APB-3 suggesting a hierarchical pathway of LRK-1-SAM-4-APB-3 for the segregation of SVPs and lysosomal proteins. Additionally, we also observe that the size of lysosomal protein-containing compartments (LPCCs) is smaller in SAM-4 and LRK-1. This size regulation depends on UNC-116. Together, we show that BORC recruited by LRK-1 and in turn via motors and along with AP-3 mediates the segregation of SVPs and lysosomal proteins in the neuronal cell body.
Carbon source, cell density, and the microbial community control inhibition ofV. choleraesurface colonization by environmental nitrate
Authors: James Jamaurie , Santos Renato ERS , Watnick Paula I 
Published: January 2025

AbstractThe intestinal diarrheal pathogenVibrio choleraecolonizes the host terminal ileum, a microaerophilic, glucose-poor, nitrate-rich environment. In this environment,V. choleraerespires nitrate and increases transport and utilization of alternative carbon sources via the cAMP receptor protein (CRP), a transcription factor that is active during glucose scarcity. Here we show thatV. choleraenitrate respiration in aerated cultures is under control of CRP and, therefore, glucose availability.V. choleraenitrate respiration results in extracellular accumulation of nitrite becauseV. choleraedoes not possess the machinery for nitrite reduction. This nitrite inhibitsV. choleraebiofilm formation via an as yet unelucidated mechanism that depends on the high cell density master regulator HapR. The genome ofParacoccus aminovorans, an intestinal microbe shown to enhanceV. choleraebiofilm accumulation in the neonatal mouse gut and predispose household contacts to cholera, encodes enzymes that reduce nitrite to nitrogen gas. We report that, in nitrate-supplemented co-cultures,P. aminovoransmetabolizes the nitrite generated byV. choleraeand, thereby, enhancesV. choleraesurface accumulation. We propose thatV. choleraebiofilm formation in the host intestine is limited by nitrite production but can be rescued by intestinal microbes such asP. aminovoransthat have the capacity to metabolize nitrite. Such microbes increaseV. choleraecolonization of the host ileum and predispose to infection.ImportanceV. choleraecolonizes the terminal ileum where both oxygen and nitrate are available as terminal electron acceptors.V. choleraebiofilm formation is inhibited by nitrate due to its conversion to nitrite duringV. choleraerespiration. When co-cultured with a microbe that can further reduce nitrite,V. choleraesurface accumulation in the presence of nitrate is rescued. The contribution of biofilm formation to ileal colonization depends on the composition of the microbiota. We propose that the intestinal microbiota predisposes mammalian hosts to cholera by consuming the nitrite generated byV. choleraein the terminal ileum. Differences in the intestinal abundance of nitrite-reducing microbes may partially explain the differential susceptibility of humans to cholera and the resistance of non-human mammalian models to intestinal colonization withV. cholerae.
Single-cell mapping of regulatory DNA:Protein interactions
Authors: Chi Wei-Yu , Yoon Sang-Ho , Mekerishvili Levan , Ganesan Saravanan , Potenski Catherine , Izzo Franco , Landau Dan , Raimondi Ivan 
Published: January 2025

SUMMARYGene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibility and histone modifications. These complex networks have been shown to be disrupted during aging, disease, and cancer. However, profiling these networks across diverse cell types and states has been limited due to the technical constraints of existing methods for mapping DNA:Protein interactions in single cells. As a result, a critical gap remains in understanding where TFs or other chromatin remodelers bind to DNA and how these interactions are perturbed in pathological contexts. To address this challenge, we developed a transformative single-cell immuno-tethering DNA:Protein mapping technology. By coupling a species-specific antibody-binding nanobody to a cytosine base editing enzyme, this approach enables profiling of even weak or transient factor binding to DNA, a task that was previously unachievable in single cells. Thus, our Docking & Deamination followed by sequencing (D&D-seq) technique induces cytosine-to-uracil edits in genomic regions bound by the target protein, offering a novel means to capture DNA:Protein interactions with unprecedented resolution. Importantly, this technique can be seamlessly incorporated into common single-cell multiomics workflows, enabling multimodal analysis of gene regulation in single cells. We tested the ability of D&D-seq to record TF binding both in bulk and at the single-cell level by profiling CTCF and GATA family members, obtaining high specificity and efficiency, with clear identification of TF footprint and signal retention in the targeted cell subpopulations. Furthermore, the deamination reaction showed minimal off-target activity, with high concordance to bulk ChIP-seq reference data. Applied to primary human peripheral blood mononuclear cells (PBMCs), D&D-seq successfully identified CTCF binding sites and enabled integration with advanced machine-learning algorithms for predicting 3D chromatin structure. Furthermore, we integrated D&D-seq with single-cell genotyping to assess the impact ofIDH2mutations on CTCF binding in a human clonal hematopoiesis sample, uncovering altered binding and chromatin co-accessibility patterns in mutant cells. Altogether, D&D-seq represents an important technological advance enabling the direct mapping of TF or chromatin remodeler binding to the DNA in primary human samples, opening new avenues for understanding chromatin and transcriptional regulation in health and disease.
Methanogens are associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy
Authors: Dirks Blake , Davis Taylor L. , Carnero Elvis A. , Corbin Karen D. , Smith Steven R. , Rittmann Bruce E. , Krajmalnik-Brown Rosa 
Published: January 2025

AbstractMethanogens are CH4-producing, H2-oxidizing (i.e. hydrogenotrophic) archaea. Numerous studies have associated methanogens with obesity, but these results have been inconsistent. One link to host metabolism may be methanogens’ ability to consume H2, thus reducing H2partial pressure and thermodynamically enhancing fermentation of sugars to short-chain fatty acids (SCFA) that the host can absorb. Because research linking methanogenesis to human metabolism is limited, our goal with this exploratory analysis was to investigate relationships between methanogens and other hydrogenotrophs, and the association of methanogens with human metabolizable energy (ME). Using results from a randomized crossover feeding study with well-characterized human participants and novel continuous methane measurements, we analyzed hydrogenotroph abundance and activity, fecal and serum SCFAs, and host ME between high and low CH4producers. Methanogens were detected in about one-half of participants, and most were high CH4producers. We found no evidence that methanogens’ consumption of H2to produce CH4affected other hydrogenotrophs. High CH4producers had greater serum propionate and host ME irrespective of diet, as well as greater gene and transcript abundance of a key enzyme of the H2-consuming, propionate-producing succinate pathway. Finally, a network analysis revealed positive relationships betweenMethanobrevibacter smithii(the most prevalent methanogen in the human colon) and bacteria capable of degrading fiber and fermenting fiber- degradation products, thus forming a trophic chain to extract additional energy from undigested substrates. Our results show that methanogens in a microbial consortium were linked to host metabolizable energy through enhanced SCFA production and host SCFA absorption.
Structure and Post-Translational Modification of the Prostaglandin Transporter
Authors: Yu Peixuan , Orlando Melanie A. , Orlando Benjamin J. 
Published: January 2025

AbstractThe prostaglandin transporter (PGT) is a member of the Organic Anion Transporting Polypeptide (OATP) family of membrane transporters. PGT mediates the uptake of prostaglandins from the extracellular environment to enable intracellular enzymatic degradation and termination of signaling. In addition to importing prostaglandins, PGT is also an essential core component of the Maxi-Cl channel, which facilitates cellular release of ATP and other small organic anions. Despite progress on understanding the (patho)physiological roles of PGT, and development of small molecules to inhibit this transporter, molecular details of the overall structure and transport mechanism remain elusive. Here we determined the cryo-EM structure of human PGT, which demonstrates an overall topology consistent with other OATPs despite possessing a dual transporter/channel functionality. We additionally investigated the role of eight potential disulfide bonds found in the extracellular loops of PGT and paralogous transporters. Through biochemical and functional characterization we demonstrate that six intra-loop disulfide bonds (C420-C511, C450-C470, C492-C474, C459-C507, C444-C494, C580-C594) are essential for proper N-glycosylation, plasma membrane trafficking, and prostaglandin import activity of PGT. In contrast, two inter-loop disulfides (C155-C587 and C143-C448) were found to restrict maximal prostaglandin uptake, suggesting a possible regulatory role in modulating PGT activity. In total, our studies provide a fresh molecular perspective on the structure, post-translational modification, and overall function of PGT.Significance StatementThe prostaglandin transporter (PGT) is essential for cellular uptake of prostaglandins and serves as a core component of the Maxi-Cl channel. Using cryo-EM we resolved the structure of human PGT, revealing a similar overall topology as other OATP transporters. Extensive site-directed mutagenesis and functional assays identified eight disulfide bonds in PGT’s extracellular domain as key regulators of glycosylation, trafficking, and transport activity. These findings provide a structural basis for PGT function and lay a foundation to further explore substrate recognition and inhibitor design for this biologically significant transporter.
Biochemical and physiological characterization ofAedes aegyptimidgut chymotrypsin
Authors: Ramirez Abigail G. , Isoe Jun , Serafim Mateus Sá M , Fong Daniel , Le My Anh , Nguyen James T. , Burata Olive E. , Lucero Rachael M. , Rascón Alberto A. 
Published: January 2025

ABSTRACTTheAedes aegyptimosquito is a vector of dengue, Zika, and chikungunya. The mosquito’s reliance on blood facilitates the transmission of these viral pathogens to humans. Digestion of blood proteins depends on the biphasic expression of serine proteases, with trypsin-like activity contributing to most of the activity in the midgut. Other proteases found (serine collagenase- and chymotrypsin-like) are thought to contribute to digestion, but their roles are largely understudied. Thus, elucidating the activity and specific roles of all midgut proteases will help understand the complexity of the digestion process and help validate them as potential targets for the development of a new vector control strategy. Herein, we focused on characterizing the activity profile and role ofAe. aegyptichymotrypsin (AaCHYMO). Knockdown studies resulted in elimination and significant reduction of chymotrypsin-like activity in blood fed midgut extracts, whilein vitrofluorescent and blood protein digestion assays revealed important substrate specificity differences. Interestingly, knockdown of AaCHYMO did not impact fecundity, indicating the presence of an intricate network of proteases working collectively to degrade blood proteins. Further, knockdown of the ecdysone receptor (EcR) led to a decrease in overall AaCHYMO expression and activity in the mosquito, which may play an important regulatory role.