bluuebunny/crossref_metadata_2025 huggingface dataset:
A gated hydrophobic funnel within BAX binds long-chain alkenals to potentiate pro-apoptotic function
Authors: Gelles Jesse D. , Chen Yiyang , Luna-Vargas Mark P. A. , Follis Ariele Viacava , Bayiokos Stella G. , Mohammed Jarvier N. , Sebastian Tara M. , Al Noman M. Abdullah , Pham Ngoc Dung , Shi Yi , Kriwacki Richard W. , Chipuk Jerry E.
Published: December 2024

Mitochondria maintain a biochemical environment that cooperates with BH3–only proteins (e.g., BIM) to potentiate BAX activation, the key event to initiate physiological and pharmacological forms of apoptosis. The sphingosine-1-phosphate metabolite 2-trans-hexadecenal (2t–hexadecenal) is one such component described to support BAX activation, but molecular mechanisms remain largely unknown. Here, we utilize complementary biochemical and biophysical techniques to reveal that 2t-hexadecenal non-covalently interacts with BAX, and cooperates with BIM to stimulate early-activation steps of monomeric BAX. Integrated structural and computational approaches reveal 2t–hexadecenal binds an undefined region – a hydrophobic cavity formed by core-facing residues of α5, α6, and gated by α8 – we now term the “BAX actuating funnel” (BAF). We define alkenal length and α8 mobility as critical determinants for 2t–hexadecenal synergy with BIM and BAX, and demonstrate that proline 168 allosterically regulates BAF function. Collectively, this work imparts detailed molecular insights advancing our fundamental knowledge of BAX regulation and identifies a regulatory region with implications for biological and therapeutic opportunities.
Investigating the Role of Glyoxalase 1 as a Therapeutic Target for Cocaine and Oxycodone Use Disorder
Authors: Alcantara Elizabeth , Doyle Michelle R. , Ortez Clara A. , Ilustrisimo Anne , Stromberg Bloom , Barkley-Levenson Amanda M. , Palmer Abraham A.
Published: December 2024

Methylglyoxal (MG) is an endogenously produced non-enzymatic side product of glycolysis that acts as a partial agonist at GABAAreceptors. MG that is metabolized by the enzyme glyoxalase-1 (GLO1). Inhibition of GLO1 increases methylglyoxal levels, and has been shown to modulate various behaviors, including decreasing seeking of cocaine-paired cues and ethanol consumption. The goal of these studies was to determine if GLO1 inhibition could alter cocaine-or oxycodone-induced locomotor activation and/or conditioned place preference (CPP) to cocaine or oxycodone. We used both pharmacological and genetic manipulations of GLO1 to address this question. Administration of the GLO1 inhibitor s-bromobenzylglutathione cyclopentyl diester (pBBG) did not alter the locomotor response to cocaine or oxycodone. Additionally, pBBG had no significant effect on place preference for cocaine or oxycodone. Genetic knockdown ofGlo1, which is conceptually similar to pharmacological inhibition, did not have any significant effects on cocaine place preference, nor didGlo1overexpression affect locomotor response to cocaine. In summary, our results show that neither pharmacological nor genetic manipulations of GLO1 influence locomotor response or CPP to cocaine or oxycodone.
Setdb1 and Atf7IP form a hetero-trimeric complex that blocks Setdb1 nuclear export
Authors: Kariapper Leena , Marathe Ila A. , Niesman Ashley B. , Suino-Powell Kelly , Chook Yuh Min , Wysocki Vicki H. , Worden Evan J.
Published: December 2024

Abstract

Histone H3K9 methylation (H3K9me) by Setdb1 silences retrotransposons (rTE) by sequestering them in constitutive heterochromatin. Atf7IP is a constitutive binding partner of Setdb1 and is responsible for Setdb1 nuclear localization, activation and chromatin recruitment. However, structural details of the Setdb1/Atf7IP interaction have not been evaluated. We used Alphafold2 predictions and biochemical reconstitutions to show that one copy of Setdb1 and two copies of Atf7IP form a hetero-trimeric complexin vitroandin cells. We also find that Atf7IP self-associates, forming multimeric complexes that are resolved upon Setdb1 binding. Setdb1 binds to Atf7IP through coiled coil interactions that include both Setdb1 nuclear export signals (NES). Atf7IP directly competes with CRM1 to bind the Setdb1 NES motifs, explaining how Atf7IP prevents CRM1-mediated nuclear export of Setdb1. Setdb1 also forms hetero-trimeric complexes with the Atf7IP paralog Atf7IP2 and we show that Setdb1 can form mixed heterotrimers comprising one copy of each Setdb1, Atf7IP and Atf7IP2. Atf7IP and Atf7IP2 are co-expressed in many tissues suggesting that heterotrimers with different compositions of Atf7IP and Atf7IP2 may differentially regulate H3K9me by fine-tuning Setdb1 localization and activity.
N-Amino Peptide-Graphene Quantum Dot Loaded Small Extracellular Vesicles for Targeted Therapy of Tauopathies
Authors: Zhu Runyao , Kim Gaeun , Rajewski Benjamin H. , Angera Isaac J. , Del Valle Juan R. , Wang Yichun
Published: December 2024

Tauopathies, a group of neurodegenerative disorders, are characterized by the abnormal aggregation of tau proteins into neurofibrillary tangles (NFTs), driving synaptic dysfunction, neuronal loss, and disease progression through tau aggregate propagation. Graphene quantum dots (GQDs) functionalized withD- cysteine (D-GQDs) have shown promise in inhibiting tau aggregation and transmissionviaπ-π stacking and electrostatic interactions with tau proteins. However, the non-specific binding of GQDs to various proteins in the physiological environment, such as serum albumin, limits their clinical translation. In this study, we aim to enhance the specificity ofD-GQDs toward tau protein by incorporating a tau-targeting N- amino peptide, mxyl-NAP2. The mxyl-NAP2/D-GQD complex demonstrated improved selectivity for tau protein over serum albumin, effectively enhancing the inhibition of tau aggregation. To further minimize off-target effects and optimize therapeutic delivery, we loaded the mxyl-NAP2/D-GQD complex into small extracellular vesicles (sEVs), followed by functionalization of sEVs with neuron targeting ligand, rabies viral glycoprotein peptides. This strategy not only reduced off-target effects, but also enhanced uptake by neuron cells, which further improved inhibition of tau transmission between neurons. Our results indicated that mxyl-NAP2/D-GQD-loaded sEVs hold great promise for overcoming the off-target limitations ofD- GQDs and advancing the development of precision therapeutics for neurodegenerative diseases.
Tumour-derived gliogenesis sustains dedifferentiation-dependent tumour growth in theDrosophilaCNS
Authors: Alvarez-Ochoa Edel , Dong Qian , Truong Hannah , Cheng Louise Y
Published: December 2024

Fate-restricted cells can acquire stem cell-like properties through dedifferentiation, enabling them to gain the plasticity required for differentiation into multiple lineages. Tumour plasticity is prominently observed in brain cancers, where transient cell state changes are linked to resistance to conventional therapies. In this study, we demonstrate that a sub-population of dedifferentiated tumour neural stem cells (NSCs) inDrosophila, induced by the knockdown ofprospero(pros), can generate its own glial niche. Temporal patterning, known to influence oncogenic competence and tumour malignancy, plays a key role in this process. Specifically, we show thatde novogliogenesis occurs in the more differentiated Syncrip+ (Syp+) NSC population. Modulating Syp levels alters the size of the glial niche, subsequently affecting tumour size. Furthermore, the tumour-associated glial niche expands through cell division and fails to cease proliferation on time due to dysregulated ecdysone signalling, contributing to niche expansion. Our findings reveal that tumours arising via dedifferentiation establish their own supportive glial microenvironment, which sustains tumour growth.
Novel interactions within the silent information regulator heterochromatin complex potentiate inter-subunit communication and gene repression
Authors: Kotz Jenna , Martz E. J. , Nelson Maya , Savoie Nicole , Schmitt Lauren , States Jordan , Holton Nathan , Hansen Kirk , Johnson Aaron M.
Published: December 2024

Organisms with smaller genomes often perform multiple functions using one multi-subunit protein complex. TheS. cerevisiaeSilent Information Regulator complex (SIRc) carries out all of the core functions of heterochromatin. SIR complexes first drive the initiation and spreading of histone deacetylation in an iterative manner. Subsequently, the same complexes are incorporated stably with nucleosomes, driving compaction and repression of the underlying chromatin domain. These two distinct functions of SIRc have each been characterized in much detail, but the mechanism by which the dynamic spreading state switches to stable compaction is not well-understood. This incomplete knowledge of intra- complex communication is partly due to a lack of structural information of the complex as a whole; only structures of fragments have been determined to date. Using cross-linking mass spectrometry in solution, we identified a novel inter-subunit interaction that physically connects the two states of SIRc. The Sir2 deacetylase makes direct interactions with the scaffolding subunit Sir4 through its coiled-coil domain, which also interacts with the Sir3 compaction/repression subunit. Within the hub of interactions are conserved residues in Sir2 that can sense deacetylation state, as well as amino acids that likely diverged and co-evolved to interact with Sir4, promoting species-specific functions. Mutation of this interaction hub disrupts heterochromatic repression, potentially by disrupting a conserved mechanism that communicates completion of deacetylation to switch to compaction. Our work highlights how a single multi-functional chromatin regulatory complex can stage a step-wise mechanism that requires a major transition in activities to achieve epigenetic gene repression.
APOE4 Increases Susceptibility to Amyloid, Accelerating Episodic Memory Decline
Authors: Vanderlip Casey R. , Stark Craig E.L. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: December 2024

Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for sporadic Alzheimer’s disease (AD). Individuals with one copy of APOE4 exhibit greater amyloid-beta (Aβ) deposition compared to noncarriers, an effect that is even more pronounced in APOE4 homozygotes. Interestingly, APOE4 carriers not only show more AD pathology but also experience more rapid cognitive decline, particularly in episodic memory. The underlying mechanisms driving this domain-specific vulnerability, however, remain unclear. In this study, we examined whether the accelerated decline in episodic memory among APOE4 carriers is due to increased Aβ deposition or heightened susceptibility to Aβ-related effects. Using data from the Alzheimer’s Disease Research Initiative, we modeled amyloid duration, the estimated number of years an individual has been amyloid-positive, and its impact on cognitive trajectories. Our findings reveal that APOE4 is associated with more rapid episodic memory decline as a function of amyloid duration. This decline was dose-dependent, with APOE4 homozygotes declining more rapidly than heterozygotes, and it was consistently observed across multiple episodic memory tasks and measures. Importantly, this pattern was not observed in other cognitive domains, such as processing speed, executive function, visuospatial skills, language, or crystallized intelligence. These results suggest that cognitive trajectories in AD differ by APOE genotype, with APOE4 conferring increased vulnerability to hippocampal dysfunction early in the disease course. Future research should investigate whether these cognitive differences stem from distinct pathological cascades in APOE4 carriers.
Restoring oxidative phosphorylation enhances osteogenesis in mitochondrial DNA translation defective human bone marrow stromal cells
Authors: Fernandez-Guerra Paula , Kjær Pernille Kirkegaard , Terp Simone Karlsson , Thomsen Jesper S. , Aldana Blanca I. , Renkema Herma , Smeitink Jan , Andersen Per H. , Palmfeldt Johan , Søe Kent , Andersen Thomas L. , Kassem Moustapha , Frost Morten , Frederiksen Anja L.
Published: December 2024

Bone formation is critical to maintain bone integrity. Here, we studied the importance of intact energy metabolism for bone formation in humans. The skeletal impact of impaired oxidative phosphorylation (OXPHOS) was investigated in adult individuals with genetically defective mitochondrial DNA translation (m.3243A>G). Although impaired mitochondrial ATP production in m.3243A>G human bone marrow stromal cells (hBMSC) was compensated by increased glycolytic ATP production (unchanged net ATP production), bothin vitroosteoblast differentiation andin vivoectopic bone formation were decreased. The impaired OXPHOS was associated with mitochondrial stress and disruption of the pro-osteogenic transcriptional program characteristic of hBMSC. Supporting OXPHOS pharmacologically in hBMSC restored mitochondrial ATP production, their transcriptional program and metabolism, leading to upregulation of osteogenic genes and restoration of bone formation capacity. These findings demonstrate a mitochondrial regulation mechanism of the osteogenic capacity of hBMSCs and identify OXPHOS as a potential target for increasing bone formation.
RiboTag-based RNA-Seq uncovers oligodendroglial lineage-specific inflammation in autoimmune encephalomyelitis
Authors: Wang Yuhang , Ghimire Sudeep , Mangalam Ashutosh , Kang Zizhen
Published: December 2024

Oligodendroglial lineage cells (OLCs) are critical for neuronal support functions, including myelination and remyelination. Emerging evidence reveals their active roles in neuroinflammation, particularly in conditions like Multiple Sclerosis (MS). This study explores the inflammatory translatome of OLCs during the early onset of experimental autoimmune encephalomyelitis (EAE), an established MS model. Using RiboTag-based RNA sequencing in genetically modified Olig2-Cre RiboTag mice, we identified 1,556 upregulated and 683 downregulated genes in EAE OLCs. Enrichment analysis indicated heightened immune-related pathways, such as cytokine signaling, interferon responses, and antigen presentation, while downregulated genes were linked to neuronal development and myelination. Notably, OLCs expressed cytokines/chemokines, and their receptor, highlighting their active involvement in neuroinflammatory signaling. Functional studies demonstrated that interferon-gamma (IFN-γ) signaling in OLCs exacerbates EAE pathology by enhancing antigen presentation and chemokine production, whereas interferon-beta (IFN-β) signaling showed minimal impact. These findings provide novel insights into the inflammatory role of OLCs in EAE and suggest therapeutic potential in targeting OLC-mediated neuroinflammation for MS and related disorders.
New isolate genomes and global marine metagenomes resolve ecologically relevant units of SAR11
Authors: Freel Kelle C. , Tucker Sarah J. , Freel Evan B. , Giovannoni Stephen J. , Eren A. Murat , Rappé Michael S.
Published: December 2024

The bacterial orderPelagibacterales(SAR11) is among the most abundant and widely distributed microbial lineages across the global surface ocean, where it forms an integral component of the marine carbon cycle. However, the limited availability of high-quality genomes has hampered comprehensive insights into the ecology and evolutionary history of this critical group. Here, we increase the number of complete SAR11 isolate genomes fourfold by describing 81 new SAR11 strains from seven distinct lineages isolated from coastal and offshore surface seawater of the tropical Pacific Ocean. We leveraged comprehensive phylogenomic insights afforded by these isolates to characterize 24 monophyletic, discrete ecotypes with unique spatiotemporal patterns of distribution across the global ocean, which we define as genera. Our data illustrate fine-scale differentiation in patterns of detection with ecologically-relevant gene content variation for some closely related genomes, demonstrating instances of ecological speciation within SAR11 genera. Our study provides unique insight into complex environmental SAR11 populations, and proposes an ecology-informed hierarchy to pave a path forward for the systematic nomenclature for this clade.
LeveragingDrosophilaModels to Explore AI-generated Synthetic Peptide’s Potential in Boosting Honeybee Health and Resilience
Authors: Sun Yanying , Jia Wenjie , Wei Yanan , Zhou Xinyue , Dong Ran , Lee Jihyeon , Bang Jeong Kyu , Ning Fangyong , Kim Woo Jae
Published: December 2024

The integration of artificial intelligence (AI) and machine learning (ML) in peptide design has revolutionized the development of antimicrobial peptides (AMPs), which are essential components of innate immunity. In this study, we identified a novel synthetic peptide, PAN4 (GAYTFKIRRK), through genetic screening of AI-generated candidates inDrosophila melanogaster. PAN4 demonstrated robust antimicrobial activity, stress tolerance, and antitumor effects, significantly enhancing survival rates following bacterial infections and improving locomotor behaviors without adversely affecting lifespan. Furthermore, PAN4 expression in intestinal stem cells completely suppressed RasV12-induced tumor progression, indicating its potential role in cancer prevention. The peptide also mitigated gut barrier dysfunction associated with sleep deprivation and reduced inflammation in a dextran sulfate sodium (DSS)-induced colitis model. Mechanistically, PAN4’s antimicrobial activity was linked to its interaction with specific peptidoglycan recognition proteins (PGRPs), particularly PGRP-SC1a, while the Tak1-mediated immune signaling pathway was found to be non-essential for its efficacy. PAN4 showed promising effects on honeybee health, enhancing survival rates under bacterial stress. Furthermore, PAN4 expression demonstrated significant anti-tumor activity in theDrosophilagut tumor model. Our findings suggest that PAN4 serves as a versatile agent with significant implications for enhancing immune responses and combating diseases in honeybee populations, paving the way for future applications in agriculture and medicine.
Coevolution ofDrosophila-type Timeless with Partner Clock Proteins
Authors: Bullo Enrico , Chen Ping , Fiala Ivan , Smýkal Vlastimil , Doležel David
Published: December 2024

Drosophila-type timeless (dTIM) is established key clock protein in fruit flies, regulating the rhythmicity and light-mediated entrainment. However, as indicated by functional experiments, its contribution to the clock differs in various insects. Therefore, we conducted a comprehensive phylogenetic analysis of dTIM across animals, dated its origin, gene duplications, and losses. We identified variable and conserved protein domains, and pinpointed animal lineages that underwent the biggest changes in the dTIM sequence. While dTIM modifications are only mildly affected by changes in the PER protein, even the complete loss of PER in echinoderms had no impact on dTIM. However, changes in dTIM always co-occur with the loss of CRYPTOCHROMES or JETLAG. This is exemplified by the remarkably accelerated evolution of dTIM in phylloxera and aphids. Finally, alternatived-timsplicing, characteristic ofD. melanogastertemperature-dependent function, is conserved at least to some extent in Diptera, albeit with unique alterations. Altogether, this study pinpoints major changes that shaped dTIM origin and evolution.
The natural HLA-Peptidome of Sezary Syndrome: uncovering antigens for T cell-based immunotherapy
Authors: Nyambura Lydon Wainaina , Textoris-Taube Kathrin , Walden Peter
Published: December 2024

Sezary syndrome (SS) is a rare and aggressive form of cutaneous T-cell lymphoma, that has a poor prognosis, with a median overall survival time of less than 3 years. Despite advances in its treatment, SS is a challenge to manage, often characterized by high rates of relapse and limited response to therapy in many patients. The main challenge for treatment, including vaccine development is its heterogeneity. In its molecular and genetic characteristics, clinical presentation, disease progression, and treatment response. Understanding the SS heterogeneity at the omics level is vital in developing T-cell mediated immunotherapeutic. In this study naturally presented HLA-I peptides were isolated from SS patients leukophoresis samples and analyzed using high performance liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and source proteins evaluated for immunotherapy application. The total number of HLA-I–restricted peptides and source proteins identified in SS leukophoresis patient samples was about the same, and they were heterogeneous and individualized. Only a small fraction of HLA-I peptides and source proteins was found to be shared between and among the patients. Peptide lengths were dominated by nanopeptides, with preferred processing by chymotrypsin. The source proteins were predominantly from the cytoplasm, and primarily involved in biosynthesis and regulation. Furthermore, the HLA-I peptides were presented from top 20 genes with somatic mutations in SS that include NCOR1, TRRAP, JAK3, PLCG1, TP53 and STAT3 (SS associated antigens-SAAs). These SAAs had; varying mutation types and frequencies-dominated by missense variant, allele-dependent immunogenicity-highest in HLA-A*11:01 and HLA-A*02:01 and lowest for HLA-A*01:01-with TRRAP showing high affinity peptides, low gene expression levels in normal tissue (except STAT3), significant protein interaction network-including JAK3 and STAT3 at primary level. This study findings, contributes to the overall understanding SS HLA-I peptidome landscape, and highlights potential T-cell mediated immunotherapeutic targets.
Evolution of genetic variance and its consequences on eco-evolutionary response in complex mutualistic networks
Authors: Baruah Gaurav , Wittmann Meike J.
Published: December 2024

Climate change, especially rising temperatures, poses a threat to biodiversity and ecosystem resilience, for example, by disrupting phenological synchrony in plant-pollinator networks. These interactions, essential for ecosystem stability, are highly sensitive to temperature shifts, which can lead to mismatches in plant flowering and pollinator emergence, weakening species interactions and reducing resilience to environmental disturbances. In this study, we model species’ evolutionary responses to an abrupt temperature increase, examining one-dimensional adaptation in mean temperature optimum trait versus adaptation involving both the mean and trait variance. Our results indicate that networks where species can evolve in both dimensions exhibit greater resilience, especially those species with a larger number of interactions that enhance genetic variance and exhibit evolutionary rescue under strong selective pressures. Even specialist species benefit from increased resilience through interactions with highly connected generalists, which help stabilize adaptation of entire mutualistic network to a new environmental optimum. We observed the emergence of opposing selection pressures in such complex networks which consequently promotes increased genetic variance, or “evolvability,” enabling faster adaptation, and thus reducing trait lag, and boosting species survival. These findings highlights the critical role of evolving genetic variance and network architecture in mitigating the impacts of plant-pollinator phenotypic mismatches to rising environmental temperatures. This study provides valuable insights into the adaptive capacity of mutualistic networks, highlighting the importance of dynamical evolution of genetic variance in promoting resilience in the face of accelerating climate change.
Optogenetic actin network assembly on lipid bilayer uncovers the network density-dependent functions of actin-binding proteins
Authors: Yamamoto Kei , Miyazaki Makito
Published: December 2024

The actin cytoskeleton forms a mesh-like network that drives cellular deformations. The network property is defined by the network density and the species of the actin-binding proteins. However, the relationship between the actin network density, the penetration ability of actin-binding proteins into the network, and resulting network dynamics remains elusive. Here, we report anin vitrooptogenetic system, named OptoVCA, which induces Arp2/3-mediated actin network assembly on a lipid membrane. By changing the illumination power, duration, and pattern, the OptoVCA flexibly manipulates the density, thickness, and shape of the actin network. Taking these advantages, we examine the effects of the network density on the two representative actin-binding proteins, myosin and ADF/cofilin. We find that the penetration of myosin filaments into the network is strictly inhibited by only a several-fold increase in network density due to the steric hindrance. Furthermore, penetrated myosin filaments induce directional actin flow when the network has a density gradient. On the other hand, ADF/cofilin penetrates into the network regardless of network density, however, network disassembly is dramatically inhibited by only a several-fold increase in network density. Thus, the OptoVCA contributes to understanding cell mechanics through the examination of the network density-dependent effect on the actin-binding proteins.
Osteoporosis with different causation exhibits different changes in bone tissue mineral and organic matrix
Authors: Lin Jing-Yu , Guo Xu , Sun Ming-Hui , Zhang Yifeng , Lu Jun-Xia
Published: December 2024

Osteoporosis (OP) which is a common skeletal disease with different causation is prevalent in aging population. Postmenopause women generally suffer from OP with bone loss due to estrogen deficiency. Diabetes are also associated with OP by complex metabolic mechanisms. Bone qualities of OP caused by aging were compared with the ovariectomy (OVX) model and the Type 2 diabetic model using Sprague-Dawley (SD) rats in our study. Combining with micro-computed tomography (μ-CT) and solid-state NMR (SSNMR) methods, this research studied bone changes in SD rats from tissue level to the molecular level. The studies revealed bone loss was most significant for cancellous bones, but not for cortical bones in OP rats. However, at the molecular level, the content of HAP in cortical bone increased with aging, contributing to the brittleness of the bone. Triglyceride, as a senescence maker of osteocyte in cortical bone, was also identified to be closely associated with OP in aging and OVX rats, but not in diabetic rats. This research suggests differing bone qualities in molecular level of OP with various causes more objectively reflect the bone tissue reconstruction rather than bone loss inμ-CT analysis.
Mechanistic studies of PFKFB2 reveals a novel inhibitor of its kinase activity
Authors: Eyster Craig , Matsuzaki Satoshi , Pranay Atul , Giorgione Jennifer R. , Faakye Anna , Ahmed Mostafa , Humphries Kenneth M.
Published: December 2024

The 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase (PFKFB) family of proteins are bifunctional enzymes that are of clinical relevance because of their roles in regulating glycolysis in insulin sensitive tissues and cancer. Here, we sought to express recombinant PFKFB2 and develop a robust protocol to measure its kinase activity. These studies resulted in the unexpected finding that bacterially expressed PFKFB2 is phosphorylatedin situon Ser483 but is not a result of autophosphorylation. Recombinant PFKFB2 was used to develop an enzymatic assay to test a library of molecules selected by the Atomwise AtomNet® AI platform. This resulted in the identification of a new inhibitor, B2, that inhibits PFKFB2 (IC503.29 μM) and PFKFB3 (IC5011.89 μM). A-498 cells, which express both PFKFB2 and PFKFB3, were treated with B2. Seahorse XFe analysis revealed B2 inhibited cellular glycolysis and glycolytic capacity. Targeted LC/MS analysis showed B2 decreased fructose-1,6-bisphosphate and downstream glycolytic intermediates but increased fructose-6-phosphate levels, which is consistent with an inhibitory effect on PFK-1 activity. The LC/MS metabolic profile of A-498 cells treated under identical conditions with the known PFKFB3 inhibitor, PFK158, was distinct from that induced by B2. These results thus demonstrate the identification and validation of a new PFKFB kinase inhibitor.
Contribution of glutamatergic projections to neurons in the nonhuman primate lateral substantia nigra pars reticulata for the reactive inhibition
Authors: Yoshida Atsushi , Hikosaka Okihide
Published: December 2024

The basal ganglia play a crucial role in action selection by facilitating desired movements and suppressing unwanted ones. The substantia nigra pars reticulata (SNr), a key output nucleus, facilitates movement through disinhibition of the superior colliculus (SC). However, its role in action suppression, particularly in primates, remains less clear. We investigated whether individual SNr neurons in three male macaque monkeys bidirectionally modulate their activity to both facilitate and suppress actions and examined the role of glutamatergic inputs in suppression. Monkeys performed a sequential choice task, selecting or rejecting visually presented targets. Electrophysiological recordings showed SNr neurons decreased firing rates during target selection and increased firing rates during rejection, demonstrating bidirectional modulation. Pharmacological blockade of glutamatergic inputs to the lateral SNr disrupted saccadic control and impaired suppression of reflexive saccades, providing causal evidence for the role of excitatory input in behavioral inhibition. These findings suggest that glutamatergic projections, most likely from the subthalamic nucleus, drive the increased SNr activity during action suppression. Our results highlight conserved basal ganglia mechanisms across species and offer insights into the neural substrates of action selection and suppression in primates, with implications for understanding disorders such as Parkinson’s disease.

Significance Statement

Understanding how the basal ganglia facilitate desired actions while suppressing unwanted ones is fundamental to neuroscience. This study shows that neurons in the primate substantia nigra pars reticulata (SNr) bidirectionally modulate activity to control action, decreasing firing rates to facilitate movements and increasing rates to suppress them. Importantly, we provide causal evidence that glutamatergic inputs to the lateral SNr mediate action suppression. These findings reveal a conserved mechanism of action control in primates and highlight the role of excitatory inputs in behavioral inhibition. This advances our understanding of basal ganglia function and has significant implications for treating movement disorders like Parkinson’s disease.
XhetRel: A Pipeline for X Heterozygosity and Relatedness Analysis in Sequencing Data
Authors: Salman Barış , Bebek Nerses , Uğur İşeri Sibel
Published: December 2024

Motivation

Checking sample sex is one of the preliminary controls performed in genetic studies. Comparing multiple individuals and families in terms of sex and relatedness allows us to eliminate systematic errors in downstream analyses. While developing the pipeline we further delved into the origins of X heterozygosity by analysing the chromosome X variants from the 1000 Genomes Project.

Result

We created an accessible and user-friendly notebook application for X heterozygosity analysis. XhetRel can serve as an initial quality control step in sequencing projects.

Further investigating the source of X heterozygosity reveals the limitations of sequencing and variant calling methods in heterozygosity analysis. Our findings point to specific pseudogenes and gene clusters, such asSLC25A5andGAGEcluster, as key contributors to erroneous variant allele fractions.

Availability and implementation

Source code is availablehttps://github.com/barslmn/XhetRel.

Collab notebook can be accessed athttps://colab.research.google.com/drive/1ep69JvXLwK5ndHUQ8qIGTWvauzsTW9fi.
Ovalbumin-loaded mesoporous silica nanoparticles for allergen specific immunotherapy
Authors: Pérez-Moreno Ana M. , Torres Pablo , Martín-Astorga María del Carmen , Cuevas-Delgado Paula , García-Esteban Irene , Céspedes José A. , Montañez María I. , Torres María José , Aranda Carlos J. , Mayorga Cristobalina , Paris Juan L.
Published: December 2024

Allergic diseases are caused by an unnecessary immune response against harmless external substances (allergens), and they pose an important economic burden for healthcare systems with a large impact on the quality of life of patients. Allergen-specific immunotherapy (AIT) is the only treatment option capable of modifying the natural history of the disease, but current AIT schemes present safety and efficacy limitations. One possible strategy to address these limitations is to encapsulate the allergen in nanoparticle carriers that can deliver it to antigen presenting cells while hiding it from effector cells responsible for the allergic reaction. In this work, we evaluate the use of allergen-loaded mesoporous silica nanoparticles (MSNs) as AIT agents. MSNs of different pore sizes were prepared and characterized, evaluating their capacity to load and release ovalbumin (OVA) as a model allergen. Extra-large pore MSNs (XL-MSNs) showed the optimal loading and release behavior, presenting also enhanced activation of the dendritic cell line DC2.4 and reduced allergenic capacity in pre-sensitized RBL- 2H3 cells, both compared to free OVA. After evaluating their biodistribution following subcutaneous, sublingual or intravenous administration, their therapeutic potential in AIT was further assessed in anin vivomurine model of OVA systemic anaphylaxis. The results showed that intravenous administration of OVA-loaded XL-MSNs significantly protected the mice from anaphylaxis and induced a Th1/Treg-immune profile, while administration through other routes failed to prevent the development of an anaphylactic reaction upon provocation with OVA. These findings establish MSNs, particularly via intravenous administration, as a promising platform to develop safer and more effective AIT.
Seroprevalence and cross-reactivity of neutralizing antibodies to six types of adenoviruses
Authors: Zubkova O.V. , Ozharovskaia T.A. , Popova O. , Vavilova I.V. , Zrelkin D.I. , Goldovskaya P.P. , Voronina D.V. , Dolzhikova I.V. , Grousova D.M. , Shcheblyakov D.V. , Logunov D.Y. , Gintsburg A.L.
Published: December 2024

Background

The use of adenoviral vector vaccines is an effective way to induce an antiviral immune response. Most vaccines used worldwide are based on human adenovirus type 5 (Ad5). Pre-existing natural immunity to Ad5 is a limitation to the frequent use of Ad5-based vectors in gene therapy and vaccination. In the present study, we assessed the seroprevalence and cross-reactivity of neutralizing antibodies to six adenovirus types: Ad1, Ad2, Ad5, Ad19, Ad26, and Ad37.

Methods

The study used immunological and virological research methods. Adenovirus vectors encoding the enhanced green fluorescent protein (EGFP) were developed by the N.F. Gamaleya National Research Center for Epidemiology and Microbiology. For seroprevalence and cross-neutralation study we used a panel of sera from 101 volunteers.

Results

The conducted correlation analysis showed a strong relationship between seropositivity and the geometric mean titer of neutralizing antibodies to adenovirus. An increase in antibody titers indicates the formation of a humoral immune response and population immunity. We determined that there is no cross-reactivity between NtAbs to Ad1, Ad2, Ad5 and Ad26.

Conclusions

Based on the presented data, we assume that Ad1 or Ad2 should be considered the most promising alternative candidates for the development of vaccine vectors.
How suitable are clustering methods for functional annotation of proteins?
Authors: Busi Rakesh , Machingal Pranav , Hemachandra Nandyala , Balaji Petety V.
Published: December 2024

The advent of affordable high-throughput genome sequencing has drastically expanded protein sequence databases, necessitating the development of computational tools to predict protein function from sequence data. Current methods, such as BLASTp and profile HMMs, while effective, are limited by difficulties in detecting remote homologs and uncertainties in multiple sequence alignments. To address this, we explore the use of clustering algorithms for unsupervised protein function annotation, using pseudo-amino acid composition (PAAC) as features.

In this study, we evaluated nine clustering algorithms for their ability to segregate protein sequences based on functional differences using the PAAC feature. Using intrinsic metrics, particularly the silhouette coefficient (SC), we determined the optimal number of clusters (k) for each algorithm. We observed that agglomerative clustering produced results resembling phylogenetic relationships; even k-means clustering, Gaussian mixture model(GMM), and spectral clustering do so but occasionally merge datapoints from distinct original clusters at higherkvalues.

Our findings reveal that k-means clustering, GMM, and agglomerative clustering effectively segregate distinct protein functional families, but effectiveness decreases when distinguishing fine-grained functional differences. Notably, spectral clustering underperformed relative to other methods. Affinity propagation clustering, while effective in some cases, generated more clusters than expected and is prone to false positives. Overall, we find that some of the clustering algorithms are suitable for functional annotation of protein sequences using PAAC as a feature set, even when the number of ground-truth sequences is limited.

The implementation of the clustering method for protein sequences is available in the GitHub repository linked below. It provides comprehensive steps for preprocessing, feature extraction, clustering, and evaluation. All results are presented in a Jupyter Notebook.https://github.com/RakeshBusi/Clustering
Transcontinental patterns in floral pigment frequencies among animal-pollinated species
Authors: Narbona Eduardo , Del Valle Jose C. , Whittall Justen B. , León-Osper Melissa , Buide M. Luisa , Pulgar Iñigo , Camargo Maria Gabriela Gutierrez , Morellato Leonor Patricia Cerdeira , Rodríguez-Castañeda Nancy , Rossi Victor , Conrad Katie , Hernandez-Mena Joey , Ortiz Pedro L. , Arista Montserrat
Published: December 2024

Flower coloration arises primarily from pigments that serve dual functions: attracting pollinators and mitigating environmental stresses. Among major flower pigment groups, anthocyanins and UV-absorbing phenylpropanoids are particularly notable for fulfilling both roles. Their importance suggests that both pigment types should be widespread in flowers. Here, we analyze the UV-Vis absorption profiles of major floral pigments to assess their potential protective role against UV radiation and demonstrate that this protection is largely confined to UV-absorbing phenylpropanoids. We also analyzed the floral pigment composition of 926 animal-pollinated species from California, southern Spain, and southeastern Brazil. UV-absorbing phenylpropanoids were ubiquitous, while anthocyanins occurred in ∼56% of species, carotenoids in ∼37%, and chlorophylls in ∼17%. Pigment frequencies varied with abiotic and biotic factors, such as light environment in Spain, and pollinator type, such as insect versus hummingbird, in California. Despite these local differences, our findings reveal a consistent regional distribution of floral pigments.
“Comparative analysis of red blood cell under real and simulated microgravity conditions”
Authors: Hinge Sarika , Dixit Jyotsana , Vidyasagar Pandit , Kulkarni Gauri
Published: December 2024

Red blood cell is an important role model of microcirculation, gas exchange, drug carrier, and related diseases. There has been an increasing interest in understanding the biochemical and structural changes in Red blood cells (RBC) due to simulated microgravity conditions. In the present work, isolated human red blood cells were exposed to simulated microgravity (SMG) conditions using 2D clinostat. Comparative analysis of normal RBC and RBC in simulated microgravity conditions was performed using UV-visible spectroscopy, FTIR spectroscopy, and single-beam optical tweezer. The change in position of the Soret band absorption peak is observed after the exposure to simulated microgravity. However, biochemical functional groups of RBCs were studied using FTIR spectroscopy with a change in % Transmittance. Power spectrum density (PSD) variations in optically trapped control and SMG exposed single RBC are obtained from position signals acquired by Thorlabs’s OTKBFM-CAL data acquisition software. Microgravity (SMG)-induced stress is responsible for a reduction in haematocrit, haemolysis, change in the morphology, and rigidity of red blood cells. These investigation of the physicochemical properties of RBC in simulated microgravity is useful for improving the health of astronauts during space missions.
Four-dimensional phase space tomography from one-dimensional measurements of a hadron beam
Authors: Hoover Austin
Published: December 2024

In this paper, we use one-dimensional measurements to infer the four-dimensional phase space density of an accumulated proton beam in the Spallation Neutron Source (SNS) accelerator. The reconstruction was performed by maximizing the distribution’s entropy subject to the measurement constraints and thus represents the most conservative inference from the data. The reconstructed distribution reproduces the measured profiles down to the noise level, and simulations indicate that the problem is reasonably well constrained. Similar measurements could serve as benchmarks for beam dynamics simulations in the SNS or hadron accelerators.

Published by the American Physical Society
2024
In situ
x-ray absorption and photoelectron spectroscopy on epitaxial
FexTe
thin films with a wide range of Fe/Te compositions
Authors: Liu C. E. , Wu C. N. , Falke J. , Chang C. F. , Kuo C.-Y. , Yang S. , Juang J. Y. , Koz C. , Schwarz U. , Chen C. T. , Tjeng L. H. , Altendorf S. G.
Published: December 2024

FexTe thin films were prepared on SrTiO3 (001) substrates by molecular beam epitaxy in a well-ordered epitaxial layer-by-layer fashion. The composition of the films was varied by adjusting the Te flux in a Te-limited growth regime. Changes in the electronic structure were systematically studied using x-ray absorption spectroscopy at the Fe L2,3 and Te M4,5 edges and x-ray photoelectron spectroscopy of core levels and valence band. We found that FeTe with optimized composition (Fe/Te ratio ≈ 1) provides the sharpest spectral features, indicating that Fe1.00Te can be synthesized as a thin film, although it is not possible in bulk.

Published by the American Physical Society
2024
Magnetized neutral 2SC color superconductivity and possible origin of the inner magnetic field of magnetars
Authors: Yuan Shuai , Feng Bo , Ferrer Efrain J. , Pinero Alejandro
Published: December 2024

In this paper, the neutral 2SC phase of color superconductivity is investigated in the presence of a magnetic field and for diquark coupling constants and baryonic densities that are expected to characterize neutron stars. Specifically, the behavior of the charged gluons Meissner masses is investigated in the parameter region of interest, taking into account, in addition, the contribution of a rotated magnetic field. It is found that up to moderately high diquark coupling constants the mentioned Meissner masses become tachyonic independently of the applied magnetic-field amplitude, hence signalizing the chromomagnetic instability of this phase. To remove the instability, the restructuring of the system ground state is proposed, which now will be formed by vortices of the rotated charged gluons. These vortices boost the applied magnetic field, having the most significant increase for relatively low applied magnetic fields. Finally, considering that with the stellar rotational frequency observed for magnetars a field of the order of 108  G can be generated by dynamo effect, we show that by the boosting effect just described the field can be amplified to 1017  G that is in the range of inner core fields expected for magnetars. Thus, we conclude that the described mechanism could be the one responsible for the large fields characterizing magnetars if the cores of these compact objects are formed by neutral 2SC matter.

Published by the American Physical Society
2024
Critical look at the cosmological neutrino mass bound
Authors: Naredo-Tuero Daniel , Escudero Miguel , Enrique Fernandez-Martinez  , Marcano Xabier , Poulin Vivian
Published: December 2024

Cosmological neutrino mass bounds are becoming increasingly stringent. The latest limit within ΛCDM from Planck 2018+ACT lensing+DESI is ∑mν<0.072  eV at 95% CL, very close to the minimum possible sum of neutrino masses (∑mν>0.06  eV), hinting at vanishing or even “negative” cosmological neutrino masses. In this context, it is urgent to carefully evaluate the origin of these cosmological constraints. In this paper, we investigate the robustness of these results in three ways: (i) we check the role of potential anomalies in Planck CMB and DESI BAO data; (ii) we compare the results for frequentist and Bayesian techniques, as very close to physical boundaries subtleties in the derivation and interpretation of constraints can arise; (iii) we investigate how deviations from ΛCDM, potentially alleviating these anomalies, can alter the constraints. From a profile likelihood analysis, we derive constraints in agreement at the ∼10% level with Bayesian posteriors. We find that the weak preference for negative neutrino masses is mostly present for Planck 18 data, affected by the well-known “lensing anomaly.” It disappears when the new Planck 2020 HiLLiPoP is used, leading to significantly weaker constraints. Additionally, the pull toward negative masses in DESI data stems from the z=0.7 bin, which contains a BAO measurement in ∼3σ tension with Planck expectations. Without this bin, and in combination with HiLLiPoP, the bound relaxes to ∑mν<0.11  eV at 95% CL. The recent preference for dynamical dark energy alleviates this tension and further weakens the bound. As we are at the dawn of a neutrino mass discovery from cosmology, it will be very exciting to see if this trend is confirmed by future data.

Published by the American Physical Society
2024
W
-boson exotic decay into three charged leptons at the LHC
Authors: Fei Yifan , Li Peiran , Liu Zhen , Lyu Kun-Feng , Pospelov Maxim
Published: December 2024

We investigate the W boson’s exotic decay channel, W→ℓℓℓν, at the LHC. Although the four-body final states suppress the decay branching ratio, the large production of W bosons makes detecting and precisely measuring this decay probability entirely feasible. Our simulation study indicates that this tiny branching ratio can be measured with subpercent precision at the HL-LHC. This decay channel can also constrain Standard Model extensions. Using the Lμ−Lτ model as a benchmark, we find that the current bound on the gauge coupling for Z′ mass in the range of [4, 75] GeV can significantly improve.

Published by the American Physical Society
2024
Fast Quantum Control of Cavities Using an Improved Protocol without Coherent Errors
Authors: Landgraf Jonas , Flühmann Christa , Fösel Thomas , Marquardt Florian , Schoelkopf Robert J.
Published: December 2024

The selective number-dependent arbitrary phase gates form a powerful class of quantum gates, imparting arbitrarily chosen phases to the Fock states of a cavity. However, for short pulses, coherent errors limit the performance. Here, we demonstrate in theory and experiment that such errors can be completely suppressed, provided that the pulse times exceed a specific limit. The resulting shorter gate times also reduce incoherent errors. Our approach needs only a small number of frequency components, the resulting pulses can be interpreted easily, and it is compatible with fault-tolerant schemes.

Published by the American Physical Society
2024