bluuebunny/crossref_metadata_2025 huggingface dataset:
Chitosan gold nanoparticle-based dot-blot assay for sensitive visual detection of histidine-tagged recombinant proteins
Authors: Mahmoodi Sahar , Pourhassan-Moghaddam Mohammad , Majdi Hasan , Maleki Mohammad Jafar
Published: February 2025

There are various techniques for detecting recombinant proteins such as western blot, SDS-PAGE, ELISA and fluorescence microscopy. However, these methods are difficult to handle, time-consuming and need special tools. We developed a rapid, inexpensive, sensitive, and straightforward approach to address these problems using an Antihistidine biosensor. Colloidal gold nanoparticles (GNPs) were synthesized by chitosan as reducer and stabilizer via the green synthesis method. Then, anti-His tag antibody was immobilized on the Chitosan-gold nanoparticles (CS-GNPs) surface to visually detect spotted target protein on nitrocellulose (NC) membrane. Our results showed that the designed dot-blot immunoassay can detect histidine-tagged recombinant proteins with the limit of detection (LOD) of 1µg/ml without any signal enhancement directly from cell lysate within 5 minutes. In an extra step, we applied HAuCl4 and NH2OH\ HCl as a gold enhancement system and increased the detection sensitivity to 0.1 µg/ml. The results showed that the developed assay can rapidly detect production of recombinant proteins, and it can be used as a screening method in low-resource laboratories.
Mechanism Underlying Carvacrol-induced Alveolar Bone Repair via the Phosphatidylinositol 3-kinase Pathway in Periodontal Disease
Authors: Nian Teng , Zhaoxun Li , Tiantian Gao , Yanrui Xiang , Lulu Zhou , Xiang Gao
Published: February 2025

Background

Conventional antibiotic treatments do not restore the structure of periodontal tissues and can cause antibiotic resistance. This study describes the mechanism by which carvacrol regulates alveolar bone osteoblasts in periodontal disease.

Methods

A rat model of periodontal disease (P group) was created by ligating the first molar and injecting lipopolysaccharide (LPS). Additionally, a control model (C group) was created. The treatment models received low (L group), medium (M group), and high (H group) doses of carvacrol hydrogel. In vitro, rat osteoblast cells were divided into the C, P, L, M, H, and carvacrol + LY294002 (Car+LY group) groups. Immunohistochemical staining analyzed collagen type I and runt-related transcription factor 2 expressions. Western blot analysis detected the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/glycogen synthase kinase 3 beta (GSK-3β) pathway-related and osteoblastic proteins. Quantitative reverse transcription polymerase chain reaction measured the expression of inflammatory factors and osteoblastic proteins. The alkaline phosphatase (ALP) colorimetric kit and Alizarin Red S staining kit assessed the osteogenic ability. Detect the expression of COL1 in osteoblasts by immunofluorescence (IF). Transmission electron microscopy detected cell apoptosis.

Results

Carvacrol hydrogel alleviated periodontal symptoms, upregulated PI3K/AKT/GSK-3β pathway-related and osteoblastic proteins, and increased ALP expression and calcified nodules. However, it decreased cell apoptosis and inflammatory factors. LY294002 inhibited the PI3K/AKT pathway and decreased osteoblastic protein expression, ALP coloration, and calcified nodules.

Conclusion

Carvacrol hydrogel promotes the proliferation and differentiation of alveolar bone osteoblasts by activating the PI3K pathway and inhibiting inflammation-induced bone resorption. This study emphasizes the potential of carvacrol for treating periodontal diseases.
Development of potent humanized TNFα inhibitory nanobodies for therapeutic applications in TNFα-mediated diseases
Authors: Yin Tao , Ramon Aubin , Greenig Matthew , Sormanni Pietro , D’Adamio Luciano
Published: February 2025

Tumor necrosis factor-alpha (TNFα) is a key pro-inflammatory cytokine implicated in the pathogenesis of numerous inflammatory and autoimmune diseases, including rheumatoid arthritis, inflammatory bowel disease, and neurodegenerative disorders such as Alzheimer’s Disease. Effective inhibition of TNFα is essential for mitigating disease progression and improving patient outcomes. In this study, we present the development and comprehensive characterization of potent humanized TNFα inhibitory nanobodies (TNFINbs) derived from camelid single-domain antibodies. In silico analysis of the original camelid nanobodies revealed low immunogenicity, which was further reduced through machine-learning-guided humanization and developability optimization. The two humanized TNFI-Nb variants we developed demonstrated exceptional anti-TNFα activity, achieving IC50values in the picomolar range. Binding assays confirmed their high affinity for TNFα, underscoring robust neutralization capabilities. These TNFI-Nbs present valid alternatives to conventional monoclonal antibodies currently used in human therapy, offering potential advantages in potency, specificity, and reduced immunogenicity. Our findings establish a solid foundation for further preclinical development and clinical translation of TNFα-targeted nanobody therapies in TNFα-mediated diseases.
Driving factors for beta-lactam resistance gene amplification duringde novoresistance evolution inE. coli
Authors: Nong Luyuan , Liu Xinwei , Wang Xinyu , de Leeuw Wim , Jonker Martijs , Brul Stanley , ter Kuile Benno
Published: February 2025

Long-term exposure ofE. colito non-lethal step-wise increasing concentrations of beta-lactam antibiotics induces high levels of resistance that can be accompanied by amplification of a chromosomal fragment around theampCgene. We compared the amplification of theampCfragment in the wildtype, anampCknockout mutant, a mutant in which theampCgene was replaced by a tetracycline resistance genetet(B)and a strain in which theampChas been translocated. WhenampCwas removed, no amplification occurred at the originalampClocation, but DNA fragments were amplified around the genes coding for efflux pump AcrAB and the multiple antibiotic resistance operon MarRAB. Whentet(B)replacedampC, exposure to tetracycline induced amplification of comparable fragments, while exposure to amoxicillin induced duplication of a larger fragment elsewhere. WhenampCwas translocated, a fragment around it at the new location was amplified. The importance of the presence but not of the location within the chromosome of the resistance genes for the amplification process indicates that the mechanisms are neither gene nor location specific. Without the relatively efficient resistance geneampC, duplication and amplification occur aroundacrABandmarRABthat code for amoxicillin and tetracycline resistance factors. These duplications and amplifications are prevented byampCamplification.
Dimethyl sulfoxide primes induced pluripotent stem cells for more efficient nephron progenitor and kidney organoid differentiation
Authors: Kearney Helen , Rak-Raszewska Aleksandra , Seijas-Gamardo Adrián , Escarda-Castro Enrique , Wieringa Paul , Moroni Lorenzo , Mota Carlos
Published: February 2025

The field of human induced pluripotent stem cells (hiPSCs) has seen significant progress since the discovery of reprogramming somatic cells using the transcription factors Oct4, Sox2, Klf4, and c-Myc. hiPSCs are similar to embryonic stem cells in a primed state of pluripotency and has the potential to differentiate into any adult human cell type, offering a versatile tool for research and potential therapeutic applications. However, the efficiency of differentiation protocols for generating complex structures with multiple cell types, like kidney organoids, remains a challenge. This study investigates the impact of treating hiPSCs with a low-dose dimethyl sulfoxide to enhance kidney organoid differentiation using a well-established protocol from literature. We found that treating hiPSCs with 1-2% DMSO affects gene expression of pluripotent transcription factors, hiPSC colony morphology, and enhances the expression of key metanephric mesenchyme nephron progenitor marker, SIX2 after 9 days of kidney organoid differentiation. Our findings also suggest that DMSO treatment helps improve hiPSC differentiation protocol efficiency toward the development of tubular kidney organoids. Further research is needed to elucidate the mechanisms underlying these effects and to refine the differentiation process for potentialin vitroresearch applications in biomedical research and drug development.
Insect wings arose with a genetic circuit that extends the useful range of a BMP morphogen
Authors: Huang Anqi , Cocconi Luca , Nicholls-Mindlin Ben , Alexandre Cyrille , Salbreux Guillaume , Vincent Jean-Paul
Published: February 2025

Morphogens are produced by a subset of cells to trigger a signalling gradient that provides positional information to surrounding tissues. At increasing distances from the source, the dwindling number of morphogen molecules is expected to constrain the useful range of morphogen gradients. We have identified a genetic circuit that counteracts this limitation in developing wings ofDrosophilaby boosting BMP signalling at the distal end of the gradient without amplifying the signal near the source. This circuit involves Brinker, a transcription factor that represses BMP target genes while itself being repressed by BMP signalling. We suggest that temporal averaging inherent to the production of the inverse Brk gradient contributes to the enhancement of the positional information far from the Dpp source. Despite being a core component of BMP signalling in flies, Brinker is exclusively found in insects, likely in all insect species. Genomic analysis across a wide range of insects and gene expression analysis in limb primordia of the apterygoteThermobia domesticasuggests that Brinker is an insect-specific innovation that was subsequently wired into the BMP signalling network in pterygotes, perhaps to enable wing development.
The CST complex mediates a post-resection non-homologous end-joining repair pathway and promotes local deletions
Authors: Ilioaia Oana , Dudragne Liébaut , Brocas Clémentine , Meneu Léa , Koszul Romain , Dubrana Karine , Xu Zhou
Published: February 2025

Repair of a DNA double-strand break (DSB) by non-homologous end-joining (NHEJ) generally leaves an intact or minimally modified DNA sequence. Resection initiation exposes single-stranded DNA and directs repair towards homology-dependent pathways and away from NHEJ. Therefore, NHEJ is not thought to be an available repair pathway once the DSB is resected. Here, we report that the Cdc13/Stn1/Ten1 (CST) complex, well characterized for its telomere-associated functions, acts after resection initiation to mediate a backup NHEJ repair. We found a CST-specific mutation signature after DSB repair, characterized by deletions of 5-85 bp, mostly dependent on NHEJ. In contrast, NHEJ-mediated small deletions of 1-4 bp and insertions are not affected in CST mutants. The interaction between CST and Polα-primase is critical for these intermediate size deletions, suggesting a role for fill-in synthesis. Consistently, instn1Δand Polα-primase mutant deficient for interaction with CST, resection is increased, leading to larger deletions of several kilobases mediated by microhomologies. Collectively, these results depict a more complex picture of repair pathway choice where CST allows a post-resection NHEJ repair, promoting local deletions but guarding against much larger and potentially more deleterious deletions and rearrangements.
Dissociable effects of LSD and MDMA on striato-cortical connectivity in healthy subjects
Authors: Ertl Natalie , Ashraf Imran , Azizi Lisa , Roseman Leor , Erritzoe David , Nutt David J , Carhart-Harris Robin L , Wall Matthew B
Published: February 2025

Introduction

Lysergic acid diethylamide (LSD) and 3,4-Methylenedioxymethamphetamine (MDMA) are widely used psychoactive drugs and their potential use in psychiatric medicine is currently generating interest. The mechanism by which these drugs may assist recovery in addiction, mood disorders and post-traumatic stress disorder (PTSD) is still not well understood. Most investigations of the effects of these drugs on brain activity have focussed on cortical resting-state networks, however the striatum is a key reward and motivation hub of the brain and aberrant striatal processing may be part of the pathophysiology of these disorders. Consequently, we investigated striatal connectivity following acute MDMA and LSD administration.

Method

Resting-state fMRI (rs-fMRI) data were acquired, and seed-voxel functional connectivity analyses were used with the striatum subdivided into three seed regions: the associative, limbic, and sensorimotor striatum. Within-network connectivity was measured using group mean network maps and whole-brain connectivity (seed-to-voxel) was also examined.

Results

Neither MDMA nor LSD significantly changed within-network connectivity of any of the three striatal seed regions. However, striatal connectivity with other brain regions was significantly altered with both MDMA and LSD. Most notably, MDMA reduced connectivity between the limbic striatum and the amygdala, while LSD increased connectivity between the associative striatum and the frontal, sensorimotor, and visual cortices.

Conclusion

Changes in connectivity were mostly observed outside the standard striatal networks, consistent with previous findings that psychedelics reduce network modularity or between-network segregation and increase connectivity across standard networks.
Experimentally mimicking 30 years ofMagallana gigasinfections with the OsHV-1 virus reveals evolution through positive selection
Authors: Pelletier Camille , Faury Nicole , Mege Mickaël , Dégremont Lionel , Hattinguais Maelle , Vidal-Dupiol Jeremie , Chevignon Germain , Jacquot Maude , Morga Benjamin
Published: February 2025

Ostreid herpesvirus 1 (OsHV-1) poses a significant threat to the global oyster farming industry, causing substantial economic losses due to mortality outbreaks. While OsHV-1 primarily affects the Pacific oysterMagallana gigas, it has been linked to mortality events in various host species. Despite advancements in understanding OsHV-1 epidemiology, knowledge gaps persist regarding its evolutionary mechanisms and adaptation to host genetic backgrounds. This study employs experimental evolution and extensive genomic analysis to unravel the dynamics of OsHV-1 evolution in response to oyster host genetic variation. Our results show that genetic mutations, particularly transitions and transversions, played a significant role in shaping the viral population, leading to a trend toward genetic homogenization. Stronger positive selection signals were observed in the oyster population with higher susceptibility, suggesting adaptation of viral genotypes to specific host genetic backgrounds. These findings shed light on the complex evolutionary dynamics of OsHV-1 and its interactions with oyster hosts. Understanding how this virus adapts to host genetic diversity is crucial for developing strategies to mitigate its impact on the oyster farming industry and provides valuable insights into the broader mechanisms of viral evolution in response to host variation.
Using single-cell perturbation screens to decode the regulatory architecture of splicing factor programs
Authors: Anglada-Girotto Miquel , Miravet-Verde Samuel , Serrano Luis
Published: February 2025

Splicing factors shape the isoform pool of most transcribed genes, playing a critical role in cellular physiology. Their dysregulation is a hallmark of diseases like cancer, where aberrant splicing contributes to progression. While exon inclusion signatures accurately assess changes in splicing factor activity, systematically mapping disease-driver regulatory interactions at scale remains challenging. Perturb-seq, which combines CRISPR-based perturbations with single-cell RNA sequencing, enables high-throughput measurement of perturbed gene expression signatures but lacks exon-level resolution, limiting its application for splicing factor activity analysis. Here, we show that shallow artificial neural networks (ANNs) can estimate splicing factor activity from gene expression signatures, bypassing the need for exon-level data. As a case study, we map the genetic interactions regulating splicing factors during carcinogenesis, using the shift in splicing program activity –where oncogenic-like splicing factors become more active than tumor suppressor-like factors– as a molecular reporter of a Perturb-seq screen. Our analysis reveals a cross-regulatory loop among splicing factors, involving protein-protein and splicing-mediated interactions, with MYC linking cancer driver mutations to splicing regulation. This network recapitulates splicing factor modulation during development. Altogether, we establish a versatile framework for studying splicing factor regulation and demonstrate its utility for uncovering disease mechanisms.GRAPHICAL ABSTRACT
Bronze AgeYersinia pestisgenome from sheep sheds light on hosts and evolution of a prehistoric plague lineage
Authors: Light-Maka Ian , Hermes Taylor R. , Bianco Raffaela Angelina , Semerau Lena , Kosintsev Pavel , Alekseeva Valeriia , Kim Donghee , Hanage William P. , Herbig Alexander , Jeong Choongwon , Warinner Christina , Key Felix M.
Published: February 2025

Most human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover from original host species. However, we lack direct evidence linking past animal reservoirs and human infections. Here we present aYersinia pestisgenome recovered from a 3rd millennium BCE domesticated sheep from the Eurasian Steppe belonging to the Late Neolithic Bronze Age (LNBA) lineage, until now exclusively identified in ancient humans across Eurasia. We show that this ancient lineage underwent ancestral gene decay paralleling extant lineages, but evolved under distinct selective pressures contributing to its lack of geographic differentiation. We collect evidence supporting a scenario where the LNBA lineage, unable to efficiently transmit via fleas, spread from an unidentified reservoir to humans via sheep and likely other domesticates. Collectively, our results connect prehistoric livestock with infectious disease in humans and showcase the power of moving paleomicrobiology into the zooarcheological record.
Multiple interactions mediate the localization of BLTP2 at ER-PM contacts to control plasma membrane dynamics
Authors: Dai Anbang , Xu Peng , Amos Chase , Fujise Kenshiro , Wu Yumei , Yang Han , Eisen Julia N. , Guillén-Samander Andrés , De Camilli Pietro
Published: February 2025

BLTP2/KIAA0100, a bridge-like lipid transfer protein, was reported to localize at contacts of the endoplasmic reticulum (ER) with either the plasma membrane (PM) or recycling tubular endosomes depending on the cell type. Our findings suggest that mediating bulk lipid transport between the ER and the PM is a key function of this protein as BLTP2 tethers the ER to tubular endosomes only after they become continuous with the PM and that it also tethers the ER to macropinosomes in the process of fusing with the PM. We further identify interactions underlying binding of BLTP2 to the PM, including phosphoinositides, the adaptor proteins FAM102A and FAM102B, and also N-BAR domain proteins at membrane-connected tubules. The absence of BLTP2 results in the accumulation of intracellular vacuoles, many of which are connected to the plasma membrane, pointing to a role of the lipid transport function of BLTP2 in the control of PM dynamics.
ChemEmbed: A deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings
Authors: Faizan-Khan Muhammad , Giné Roger , Badia Josep M. , Pérez-Ribera Maribel , Junza Alexandra , Vinaixa Maria , Sales-Pardo Marta , Guimerà Roger , Yanes Oscar
Published: February 2025

Machine learning tools have become essential for annotating the vast number of unidentified MS/MS spectra in metabolomics, addressing the limitations of current reference spectral libraries. However, these tools often struggle with the high dimensionality and sparsity of MS/MS spectra and metabolite structures. ChemEmbed introduces a novel approach by combining multidimensional and continuous vector representations of chemical structures with enhanced MS/MS spectra. This enhancement is achieved by merging spectra from multiple collision energies and incorporating calculated neutral losses from 38,472 distinct compounds, providing richer input for a convolutional neural network (CNN). ChemEmbed achieves top-ranked candidate annotations in over 42% of cases and identifies the correct compound within the top five in more than 76% of cases in a test dataset. Against external benchmarks such as CASMI 2016 and 2022, ChemEmbed outperforms SIRIUS, the current state-of-the-art in computational metabolomics. In a validation experiment with the Annotated Recurrent Unidentified Spectra (ARUS) dataset— including over 25,000 spectra from human plasma and 68,000 from urine— ChemEmbed successfully identified 24 previously unannotated compounds. By aligning with the advanced capabilities of modern mass spectrometry instrumentation, ChemEmbed balances accuracy, computational efficiency, and scalability, making it a powerful solution for high-throughput metabolomics applications.
Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories
Authors: Glass Madison R. , Matoba Nana , Beltran Alvaro A. , Patel Niyanta K. , Farah Tala M. , Eswar Karthik , Bhargava Shivam , Huang Karen , Curtin Ian , Ahmed Sara , Srivastava Mary , Drake Emma , Davis Liam T. , Yeturi Meghana , Sun Kexin , Love Michael I. , Simon Jeremy M. , St. John Tanya , Marrus Natasha , Pandey Juhi , Estes Annette , Dager Stephen , Schultz Robert T. , Botteron Kelly , Evans Alan , Kim Sun Hyung , Styner Martin , McKinstry Robert C. , Collins D. Louis , Volk Heather , Benke Kelly , Zwaigenbaum Lonnie , Hazlett Heather , Beltran Adriana S. , Girault Jessica B. , Shen Mark D. , Piven Joseph , Stein Jason L. ,   the Infant Brain Imaging Study Network
Published: February 2025

Human induced pluripotent stem cell (iPSC) derived cortical organoids (hCOs) model neurogenesis on an individual’s genetic background. The degree to which hCO phenotypes recapitulate the brain growth of the participants from which they were derived is not well established. We generated up to 3 iPSC clones from each of 18 participants in the Infant Brain Imaging Study, who have undergone longitudinal brain imaging during infancy. We identified consistent hCO morphology and cortical cell types across clones from the same participant. hCO cross-sectional area and production of cortical hem cells were associated within vivocortical growth rates. Cell cycle associated genes expression in early progenitors at the crux of fate decision trajectories were correlated with cortical growth rate from 6-12 months of age, and were enriched in microcephaly and neurodevelopmental disorder genes. Our data suggest the hCOs capture inter-individual variation in cortical cell types influencing infant cortical surface area expansion.
Novel Protein Structure Validation using PDBMine and Data Analytics Approaches
Authors: Pandala Niharika , Brown Katherine G. , Valafar Homayoun
Published: February 2025

Protein structure prediction is essential for understanding biological functions and advancing drug development. Although experimental techniques like NMR, X-ray crystallography, and cryo-EM provide valuable insights, they are expensive and time-consuming, prompting reliance on computational approaches. AlphaFold2 revolutionized protein model predictions accuracy in 2020. However, limitations remain in the prediction of novel proteins, complex conformations, and mutations. To address these challenges, we leverage PDBMine software and machine learning for advanced data analytics. This approach detects and corrects structural inaccuracies, calculates fitness scores, and enhances model reliability, accelerating drug discovery and therapeutic breakthroughs by bridging gaps in current protein prediction capabilities.
Cumulative effects of high temperature and low dissolved oxygen alter the acute thermal tolerance and cellular stress response in lake trout
Authors: Weinrauch Alyssa M , Lazaro-Côté Analisa , Durhack Travis C , Enders Eva C , Jeffries Ken M
Published: February 2025

Lake trout (Salvelinus namaycush) is an important food fish in Northern communities, inhabiting cool, well-oxygenated water. Yet, climate change is reducing available habitat with extended summer stratification of lakes creating an upper thermal barrier (∼15 °C) and lower dissolved oxygen (DO) boundary (4-7 mg L-1). Together, these environmental factors can influence tolerance thresholds and climate change may lead to abiotic factors exceeding these physiological thresholds in lake trout habitats. Thresholds can shift with environmental acclimation in lake trout populations, but the functional basis of this shift has yet to be examined. The abundance of mRNA transcripts offers insight into underlying cellular responses to environmental stressors that can provide an early warning of fitness consequences. Here, we used a stress-response transcriptional profiling chip to investigate a suite of genes involved in thermal and general stress in lake trout acclimated to a range of temperatures (6-18 °C) and DO (normoxia: > 8.5 mg L-1or hypoxia: 5.5-6.5 mg L-1), as well as following an acute thermal stress (i.e., CTmax). Transcriptional profiles were assessed in the gill, liver, and and epidermal mucus. Generally, fish acclimated to the greatest combined stressor (18 °C and hypoxia) had the largest transcriptional response, suggestive of a transition from a routine stress response to an extreme survival response. A noted temperature dependence occurred in liver tissue, which was not evident in gill or mucus tissues. Further, transcriptional responses in the gill and mucus were highly correlated (r= 0.74-0.87), highlighting the potential use of these tissues for non-lethal sampling methods to enhance management and conservation strategies for lake trout across their distribution.
Archaeal lineages related to eukaryotes encode functional diterpenoid cyclases
Authors: McShea Hanon , De Anda Valerie , Brocks Jochen J. , Welander Paula V. , Baker Brett J.
Published: February 2025

The first eukaryotic cell originated through the union of an archaeon (Asgardarchaeota) and a bacterium (Alphaproteobacteria)1–4. Little is known about the molecular basis of eukaryogenesis, but it is likely that lipids played a key role in this process. Modern eukaryotic membranes contain polycyclic triterpenoids (mainly sterols) that are essential for a variety of cellular functions, but these lipids have not been identified in archaea. The lipid composition of Asgardarchaeota including the newly described class Hodarchaeales, which share a common ancestor with eukaryotes, is unknown. Here, we investigated the potential for Asgards to produce cyclic terpenoids. Phylogenomics coupled with structural prediction revealed that Asgards lack the capacity to make sterols, yet organisms from the clades Hodarchaeales and Kariarcheales encode for divergent homologs of sterol cyclases, predicted to produce diterpenoids. We tested the functionality of these enzymesin vitro, showing that they cyclize geranylgeranyl pyrophosphate to form bicyclic halimadienyl pyrophosphate. Halimadienyl lipids have previously been shown to mediate intracellular persistence ofMycobacterium tuberculosisin host endosomes5–7, and may function similarly Asgardarchaeota. This is the first evidence of experimentally validated diterpenoid cyclases in archaea, providing new insights into the biochemistry of these microbes pivotal in the evolution of complex cellular life.
Size switchable DNA origami structure enabled by dynamic crossovers
Authors: Li Xueqiao , Gao Rui , Wang Xiaoxue , Wu Wenna , Liu Huajie , Zhang Tao
Published: February 2025

DNA nanostructures are formed by many DNA double helices connected via crossovers. If multiple DNA double helices are connected by crossovers at different base positions (different rotational angles), these DNA double helices are stacked together to obtain desired two- or three-dimensional DNA structures. Here we inserted i-motif or hairpin motifs in crossover regions of one layer DNA origami structure and employed dynamic DNA element to implement size-switchablity between expansion and contraction. By changing pH or adding complementary strands to regulate interspacings between DNA double helixes, multiple crossover replacements realize the dynamic size changes between 68 nm and 150 nm as characterized by atomic force microscopy. We further demonstrated dynamic sizes changes enabled or inhibited FRET (fluorescence resonance energy transfer) signals between Cy3 and Cy5 and the controlled distances between protein molecules. The results reveal the feasibility of fabricating size-switchable DNA origami nanostructures via crossover redesign, demonstrating their potential in nano-engineering, proximity enabled chemical reacitons, as well as for biomedical applications.
Suppressed macrophage response to quorum-sensing-activeStreptococcus pyogenesoccurs at the level of the nucleus
Authors: Feldstein Sam F. , Rahbari Kate M. , Leonardo Trevor R. , Alvernaz Suzanne A. , Federle Michael J.
Published: February 2025

Streptococcus pyogenes, or Group A Streptococus (GAS), a significant human pathogen, employs quorum sensing (QS) systems to coordinate its behavior and genetic regulation in order to enhance survival. Our previous research established that one such QS system, the Rgg2/3 system, can suppress macrophage NFκB activity and production of pro-inflammatory cytokines. Yet, the scope of suppression and the mechanism by which it occurs remains unknown. In this study, we used transcriptomic and phosphoproteomic approaches to address these unanswered questions. We found QS-ON GAS broadly suppressed most inflammatory transcriptional pathways including those of NFκB, type I and type II interferon responses, and intracellular stress responses. Yet, we found no alternative transcriptional programs were activated after QS-ON GAS infection. Additionally, phosphoproteomics showed no disruption in typical inflammatory pathways such as those related to NFκB and MAPK activation, which was confirmed by western blotting and translocation assays. Instead, the proteomic data highlighted a potential role for epigenetic mechanisms of inflammatory regulation. To determine if epigenetic regulation was involved in QS-mediated immunomodulation, DNA methylation was measured and studies were performed inhibiting various histone and chromatin modifiers. These studies also showed no dijerence between QS-ON compared with QS-OFF infected macrophages. These findings expand our understanding of QS-mediated suppression and of GAS virulence strategies that appear to employ unusual methods of restricting inflammation. Uncovering this mechanism will ojer invaluable insight into GAS, itself, as well as understudied immunological pathways.

Importance

Streptococcus pyogenesis a ubiquitous pathogen that causes over 600 million infections every year and 500 thousand to 1 million fatalities. While in developed countries it is generally known to cause mild conditions such as pharyngitis, it can also manifest as severe infections such as necrotizing fasciitis, septic arthritis, and lead to post-infectious sequelae including rheumatic heart disease and glomerulonephritis. Elucidating new mechanisms of virulence in this organism, including how it evades and suppresses immune responses can be critical in understanding its pathogenicity, epidemiology, and identification of novel treatment avenues in this era of multi-drug-resistant bacteria. In this study, we characterize the broad spectrum by which GAS modulates the host innate immune response and begin to uncover host pathways that bacteria can use or inhibit for its survival.
DISRUPTION OF TRANSTHALAMIC CIRCUITRY FROM PRIMARY VISUAL CORTEX IMPAIRS VISUAL DISCRIMINATION IN MICE
Authors: McKinnon C. , Mo C. , Sherman S. M.
Published: February 2025

Layer 5 (L5) of the cortex provides strong driving input to higher-order thalamic nuclei, such as the pulvinar in the visual system, forming the basis of cortico-thalamo-cortical (transthalamic) circuits. These circuits provide a communication route between cortical areas in parallel to direct corticocortical connections, but their specific role in perception and behavior remains unclear. Using targeted optogenetic inhibition in mice performing a visual discrimination task, we selectively suppressed the corticothalamic input from L5 cells in primary visual cortex (V1) at their terminals in pulvinar. This suppresses transthalamic circuits from V1; furthermore, any effect on direct corticocortical projections and local V1 circuitry would thus result from transthalamic inputs (e.g., V1 to pulvinar back to V1 (Miller-Hansen and Sherman, 2022). Such suppression of transthalamic processing during visual stimulus presentation of drifting gratings significantly impaired discrimination performance across different orientations. The impact on behavior was specific to the portion of visual space that retinotopically coincided with the V1 L5 corticothalamic inhibition. These results highlight the importance of incorporating L5-initiated transthalamic circuits into cortical processing frameworks, particularly those addressing how the hierarchical propagation of sensory signals supports perceptual decision-making.

SIGNIFICANCE STATEMENT

Appreciation of pathways for transthalamic communication between cortical areas, organized in parallel with direct connections, has transformed our thinking about cortical functioning writ large. Studies of transthalamic pathways initially concentrated on their anatomy and physiology, but there has been a shift towards understanding their importance to cognitive behavior. Here, we have used an optogenetic approach in mice to selectively inhibit the transthalamic pathway from primary visual cortex to other cortical areas and back to itself. We find that such inhibition degrades the animals’ ability to discriminate, showing for the first time that specific inhibition of visual transthalamic circuitry reduces visual discrimination. This causal data adds to the growing evidence for the importance of transthalamic signaling in perceptual processing.
Circulating extracellular vesicles from HIV-1 gp120-treated mice act as endogenous algogens, mediating and maintaining HIV-associated chronic pain
Authors: Yuan Subo , Liew Jia Yi , Bei Jiani , Pal Ajay , Qiu Yuan , Shang Junkui , Araya Katherine , Tat Vivian , Hao Haiping , Gamez Isaac , Haines Connor , Chang Qing , Saito Tais B. , Khanipov Kamil , Gong Bin
Published: February 2025

HIV-associated chronic pain (HIV-PAIN) remains prevalent in the post combined antiretroviral therapy era, affecting 30-60% of HIV patients worldwide. The underlying mechanism responsible for the development and maintenance of chronic pain remains unclear. gp120 is a causal factor of the HIV-PAIN and functions as an exogenous algogen. The pain experienced by human HIV-PAIN has been modeled in mice (referred to as mHIV-PAIN) using intrathecal (i.t.) injections of gp120. gp120 is a relatively short-term, static, exogenous algogen that is exhaustiblein vivo. In authentic infection, HIV virions serve as the primary source of exogenous gp120, which initiates the early phase of clinical HIV-PAIN. Interestingly, while the source of replenishing gp120 decreases after antiretroviral therapy by suppressing viremia, the prevalence of chronic HIV-PAIN remains stable. To induce chronic pain in mice, gp120 needs to be repeatedly applied by the i.t. route. This raises a key question: Is an endogenous inexhaustible algogen responsible for maintaining the chronicity of HIV-PAIN?

In the present study, we isolated circulating small extracellular vesicles (sEV) from mice using our mHIV-PAIN model that is i.t. injected with gp120. We refer to such sEV as gp120-sEV herein. We observed that gp120 is absent in gp120-sEV. Following transfusion of gp120-sEV intrathecally, naïve recipient mice exhibit an extensive pain phenotype, including cold pain tested with we newly invented dry ice vapor cold test. RNA-sequence analysis suggests that gp120-sEVs induced expression of genes related to nociception and neuroinflammation pathways. These findings provide direct evidence that circulating sEV function as endogenous long-term “dynamic” algogens that enhance initial pain and extend the chronification of HIV-PAIN in mice, suggesting that chronic HIV-PAIN requires an exogenous algogen (gp120) paired with endogenous algogen (gp120-sEV), and that these components work synchronically to initiate and extend pain chronification. This double algogen concept provides a new insight into the pathogenesis of HIV-PAIN chronification. Our new mechanistic understanding will also assist in identifying new therapeutics to alleviate HIV-PAIN by targeting pathological gp120-sEV.
SynSeg: Generating Synthetic Datasets for Accurate Subcellular Segmentation with U-net
Authors: Guo Zhengyang , Xu Kaiming , Wang Zi , Ke Jingyi , Huang Jingwen , Ye Yuqi , Ou Guangshuo
Published: February 2025

Accurate segmentation of subcellular components is crucial for understanding cellular processes, but traditional methods struggle with noise and complex structures. Convolutional neural networks improve accuracy but require large, time-consuming, and biased manually annotated datasets. Here, we developed SynSeg, a pipeline that generates synthetic training data to train a U-net model for subcellular structure segmentation, eliminating the need for manual annotation. SynSeg leverages synthetic datasets with variations in intensity, morphology, and signal distribution to deliver context-aware segmentations, even in challenging imaging conditions. We demonstrate SynSeg’s superior performance in segmenting vesicles and cytoskeletal filaments from culture cells and liveC. elegans, outperforming traditional methods such as Otsu’s thresholding, ILEE, and FilamentSensor 2.0. Additionally, SynSeg effectively quantified disease-associated microtubule morphology in live cells, uncovering structural defects caused by mutant Tau proteins linked to neurodegenerative diseases. These results highlight the potential of synthetic data-driven approaches to advance biological segmentation and enhance microscopy techniques.

Significance Statement

This study introduces a novel approach for accurately segmenting cellular structures, such as microtubules and vesicles, using synthetic datasets and advanced deep learning techniques. By leveraging a U-Net model trained on thousands of artificially generated images, our method eliminates the need for labor-intensive experimental data and simplifies the data creation process. Importantly, it incorporates noise and variability into the training datasets to make the model more robust and biologically relevant.

Our findings demonstrate that the model can successfully identify cellular components, paving the way for its application in real-world microscopy images. This innovation has the potential to accelerate discoveries in cell biology by providing an efficient, scalable tool for analyzing complex cellular structures, even in challenging imaging conditions.
Machine learning of molecular dynamics simulations provides insights into modulation of viral capsid assembly
Authors: Pavlova Anna , Fan Zixing , Lynch Diane L. , Gumbart James C.
Published: February 2025

An effective approach in the development of novel antivirals is to target the assembly of viral capsids using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nucleocapsid assembly, retaining its structure, or misdirect it into non-capsid-like particles. Previous molecular dynamics (MD) simulations of early capsid-assembly intermediates showed differences in protein conformations for apo and bound states. Here, we have developed and tested several classification machine learning (ML) models to better distinguish between apo-tetramer intermediates and those bound to accelerating or misdirecting CAMs. Models based on tertiary structural properties of the Cp149 tetramers and their inter-dimer orientation, as well as models based on direct and inverse contact distances between protein residues, were tested. All models distinguished the apo states and the two CAM-bound states with high accuracy. Furthermore, tertiary structure models and residue-distance models highlighted different tetramer regions as important for classification. Both models can be used to better understand structural transitions that govern the assembly of nucleocapsids and to assist the development of more potent CAMs. Finally, we demonstrate the utility of classification ML methods in comparing MD trajectories and describe our ML approaches, which can be extended to other systems of interest.

TOC Graphic
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases
Authors: Malik Ashar J. , Ascher David B.
Published: February 2025

The increasing availability of protein structures presents new opportunities for detecting homologous proteins. While global alignment methods are widely used and generally effective, they often struggle to identify related structures obscured by differences in protein size and domain architecture. To address this limitation, we introduce Structome-TM, a web server for protein structure comparison and phylogenetic analysis using TM-score as a metric. By emphasizing local structural alignments, Structome-TM improves the detection of homologous proteins that global methods might overlook. With a user-friendly interface and efficient pairwise comparisons, Structome-TM expands the structural neighbourhood landscape and facilitates phylogenetic reconstruction.

Availability and implementation

The Structome-TM web server is available athttps://biosig.lab.uq.edu.au/structometm/
The power of the content of the influencers in inducing impulse buying: mediating role of trust
Authors: Shamim Komal , Azam Muhammad
Published: February 2025

Purpose

The present research examines an underlying mechanism outlining how features of the influencers’ content influence the consumers’ urge to buy impulsively through the mediation of trust. Moreover, the moderating role of persuasion knowledge is also investigated in this study.

Design/methodology/approach

By employing persuasion theory and social capital theory, this study develops a framework that is tested on 251 social media users. The PLS-SEM modeling technique is employed for data analysis.

Findings

Results indicate that vicarious expressions and informational value are the two main characteristics of the influencer’s content, which develop trust in influencers’ posts and instigate an UBI. In addition, trust in influencer posts serves as a mediator between content characteristics and UBI. However, no moderating role of persuasion knowledge was found.

Originality/value

The present study offers an inclusive understanding of how marketers can strategically use influencers by leveraging the influential power of their content.
Exploring information needed in maintenance backlog-related decision-making in the Finnish road network
Authors: Hamalainen Anne Kristiina , Vaismaa Kalle , Kolisoja Pauli Juhani
Published: February 2025

Purpose

Road maintenance backlog (MB) is increasing rapidly in many countries, partly as a result of the changing climate conditions, increasing traffic volumes and insufficient funding for maintenance. This study aims to identify the type of information used and needed when making decisions concerning the MB of the road network.

Design/methodology/approach

This qualitative study involved 21 semi-structured interviews with experts in Finland, including road authorities (7), politicians (3), maintenance specialists (4) and business representatives (7). Participants were selected using purposive sampling based on criteria such as professional designation, knowledge and experience in the field. The data were analyzed using content analysis.

Findings

At the operational level, most information pertains to the technical condition of the road network. At higher decision-making levels, MB is used more as a monetary value and a basis for budgeting. More information is required on the impact of changes in road conditions in terms of safety, the social economy, companies’ operational capabilities, logistics and CO2 emissions. These impacts need to be quantified in monetary terms for society as a whole.

Research limitations/implications

This research covers the years 2018–2022. Although Finland served as the target country for this study, we believe that the results, presented at the political decision-making level, can be adopted and modified for countries with similar governmental decision principles and where further justifications for funding decisions are required. Additionally, insights from the asset owner perspective can assist road authorities in developed countries, while operational-level findings can be applied to other developed countries with similar geographical characteristics. The results of this study were collected from an industrialized country for the years 2018–2022. Consequently, the applicability of these findings to different time periods and countries may be limited.

Practical implications

With the help of these findings, road authorities will be able to make decisions in a more data-driven way, which has long-term economic implications.

Originality/value

The results of this study will provide information that can be utilized by decision-makers at various levels. The research has scientific value, and in addition, the results presented in the study can lead to changes in practical applications in the field, which in turn have societal and economic impact.
Two decades of climate change discourse: a systematic review of top communication journals
Authors: Shrivastava Archana , Swartz Stephanie
Published: February 2025

Purpose

In a globalized world where environmental sustainability is a critical success factor, effective environmental communication takes precedence. The purpose of the present study is to analyse the evolution of climate change research, primarily in communication focussed journals, over the last decade.

Design/methodology/approach

Employing the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) protocol, a comprehensive analysis was conducted using research protocol on 374 studies in top ten high-ranking communication journals.

Findings

The results suggest that though effective communication strategies are crucial for generating climate awareness, contributions in communication-focussed journals remain limited. Most publications on this theme originate from the USA, Europe and Australia, with a notable lack of contributions from Asian publications. Five major themes, emerged representing the types of discussions taking place: “Green Advocacy in Corporate Communication”, “Green and sustainable IT infrastructure”, “Climate Narratives”, “Scientific discourses” and “Framing climate change”.

Originality/value

The research is original in the way it provides valuable insights for researchers, policymakers and practitioners aiming to enhance the impact of environmental communication.