bluuebunny/crossref_metadata_2025 huggingface dataset:
Anex vivoandin vitroinvestigation of extracellular vesicle interactions with B cells ofMacaca nemestrinaand humans
Authors: Pachane Bianca C. , Rodriguez Blanca V. , Shirk Erin N. , Gololobova Olesia , Carlson Bess , Queen Suzanne E. , Erickson Loren D. , Selistre-de-Araujo Heloisa S. , Witwer Kenneth W.
Published: February 2025

Abstract

Extracellular vesicles may modify recipient cell behavior through multiple mechanisms, including interacting with the cell surface or internal membrane components and delivering luminal cargo to the cytoplasm. Here, we use a previously establishedex vivoapproach to investigate the cellular fate of EVs spiked into whole blood samples from nonhuman primate (NHP) and human donors and contrast these findings with results fromin vitroassays. We report that EVs are internalized by NHP and human B cells while also associating to some degree with other PBMCs. EVs exhibit greater association with B cells inex vivowhole blood compared to isolated B cells, suggesting that blood components may promote EV interactions or that cell isolation factors may inhibit this association. Cellular uptake of EVs involves clathrin-dependent endocytosis and may be aided by other pathways, including direct EV-cell membrane fusion. Overall, our data suggest that EV association, including uptake, by B cells occurs in at least two primate species. These findings highlight the potential to develop new strategies to either enhance or inhibit EV tropism toward B cells.

Graphical Abstract
Modeling metabolic disease susceptibility and resilience in genetically diverse mice
Authors: Baker Candice N. , Harder Jeffrey M. , Skelly Daniel A. , Gerdes Gyuricza Isabella , Gaca Margaret , Vincent Matthew , Ingalls Allison , Keller Mark P. , Attie Alan D. , Braun Madeleine , Stitzel Michael , Liu Edison T. , Rosenthal Nadia , Churchill Gary A.
Published: February 2025

Model organisms have provided critical insights into the basic biology of metabolic disorders, however, one of the greatest limitations to translation has been the absence of the genetic heterogeneity that is characteristic of human populations. We examined metabolic health across three genetically diverse mouse strains fed control (low fat, no sucrose) or unhealthy (high fat, high sucrose) diets and observed a wide range of metabolic responses from overt type 2 diabetes in NZO/HlLtJ mice, to obesity and glucose intolerance in C57BL/6J mice, to complete resilience in CAST/EiJ mice. Analysis of multi-tissue gene expression revealed strain- and tissue-specific responses to diet, with strongest responses in white adipose tissue and pancreatic islets. In pancreatic islets, diet response was limited to just NZO mice, which showed high levels of inflammation and associated β cell dysfunction. Adipose tissue was responsive to diet across all three strains and revealed both common and strain-specific changes in inflammatory and metabolic pathways. Using a complementary outbred mouse resource, we mapped genetic loci associated with strain-specific diet responses, including a monocyte regulatory locus on mChr19. This multi-strain approach to modeling metabolic disease revealed a prominent role of white adipose tissue and lipid-associated inflammation in the determination of individual disease risk in response to unhealthy diets.
Tissue- and temperature-dependent expression, enzyme activity, and RNAi knockdown ofCatalasein a freeze-tolerant insect
Authors: Rokosh Sarah E. , Adams Victoria E. , Walter Robyn , Kaiser Grace E. , Gough Amber L. , Toxopeus Jantina
Published: February 2025

Organisms that overwinter in temperate climates may experience freezing and freezing-induced oxidative stress during winter. While many insect species can survive freezing, molecular tools such as RNA interference (RNAi) or CRISPR have not been used to understand the physiological mechanisms underlying freeze tolerance. The spring field cricketGryllus veletiscan survive freezing following a 6-week fall-like acclimation. We used RNAi of an antioxidant enzyme inG. veletisto test the hypothesis that minimizing oxidative stress is important for freeze tolerance. In fat body tissue,CatalasemRNA abundance and enzyme activity increased during the acclimation that induces freeze tolerance. Other tissues such as midgut and Malpighian tubules had more stable or lowerCatalaseexpression and activity during acclimation. In unacclimated (freeze-intolerant) crickets, RNA interference (RNAi) effectively knocked down production of theCatalasemRNA and protein in fat body and midgut, but not Malpighian tubules. In acclimated (freeze-tolerant) crickets, RNAi efficacy was temperature-dependent, functioning well at warm (c. 22°C) but not cool (15°C or lower) temperatures. This highlights a challenge of using RNAi in cold-acclimated organisms, as they may need to be warmed up for RNAi to work, potentially affecting their stress physiology. Knockdown ofCatalasevia RNAi in acclimated crickets also had no effect on the ability of the crickets to survive a mild freeze treatment, suggesting that Catalase may not be necessary for freeze tolerance. Our study is the first to demonstrate that RNAi is possible in a freeze-tolerant insect, but further research is needed to examine whether other genes and antioxidant molecules are important in freeze tolerance ofG. veletis.

Highlights

Catalaseexpression and activity are elevated in freeze-tolerant cricket fat body

RNAi knocks downCatalasein fat body and midgut at a warm temperature (22°C)

RNAi is not effective at a cool temperature (15°C) that preserves freeze tolerance

Catalaseknockdown has no impact on survival of a mild freeze treatment

The role of antioxidants in freeze tolerance warrants further study

Graphical abstract
Mitotic transcription ensures ecDNA inheritance through chromosomal tethering
Authors: Nichols Ashley , Norman Roshan , Chen Yanyang , Choi Yujin , Striepen Josefine , Salataj Eralda , Toufektchan Eleonore , Koche Richard , Maciejowski John
Published: February 2025

Extrachromosomal DNA (ecDNA) are circular DNA bodies that play critical roles in tumor progression and treatment resistance by amplifying oncogenes across a wide range of cancer types. ecDNA lack centromeres and are thus not constrained by typical Mendelian segregation, enabling their unequal accumulation within daughter cells and associated increases in copy number. Despite intrinsic links to their oncogenic potential, the fidelity and mechanisms of ecDNA inheritance are poorly understood. Here, we show that ecDNA are protected against cytosolic mis-segregation through mitotic clustering and by tethering to the telomeric and subtelomeric regions of mitotic chromosomes. ecDNA-chromosome tethering depends on BRD4 transcriptional co-activation and mitotic transcription of the long non-coding RNAPVT1, which is co-amplified withMYCin colorectal and prostate cancer cell lines. Disruption of ecDNA-chromosome tethering through BRD4 inhibition,PVT1depletion, or inhibiting mitotic transcription results in cytosolic mis-segregation, ecDNA reintegration, and the formation of homogeneously staining regions (HSRs). We propose that nuclear inheritance of ecDNA is facilitated by an RNA-mediated physical tether that links ecDNA to mitotic chromosomes and thus protects against cytosolic mis-segregation and chromosomal integration.
Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes
Authors: Subramanian Vijay , Appadurai Rajeswari , Venkatesh Harikrishnan , Sekhar Ashok , Srivastava Anand
Published: February 2025

Functionally important “fold-switching” proteins, which do not obey the classical folding dogma, are now thought to be widespread. Algorithms that can accurately annotate fold-switching proteins from sequence information can help uncover the true extent of the “metamorphome”. Here, we present Morpheus, a fragment-based classification approach, that works by analysing the diversity of structures within a query protein sequence. Morpheus exhaustively curates and uses fragment structural data from the protein data bank as well as the AlphaFold Protein Structure Database. We employed our algorithm on 57 different proteomes consisting of a total of 601,218 proteins and identified about 10% of these proteins with the ability to fold switch. Additionally, we provide a web server for Morpheus to test for metamorphic propensities for user-defined sequences (http://mbu.iisc.ac.in/∼anand/morpheus). Besides screening for metamorphic behaviour in proteomes, our work will be useful in de novo design and engineering of such proteins through further experimentation.
Investigation of mitochondrial phenotypes in motor neurons derived by direct conversion of fibroblasts from familial ALS subjects
Authors: Woo Evan , Tasnim Faiza , Kawamata Hibiki , Manfredi Giovanni , Konrad Csaba
Published: February 2025

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of motor neurons, leading to fatal muscle paralysis. Familial forms of ALS (fALS) account for approximately 10% of cases and are associated with mutations in numerous genes. Alterations of mitochondrial functions have been proposed to contribute to disease pathogenesis. Here, we employed a direct conversion (DC) technique to generate induced motor neurons (iMN) from skin fibroblasts to investigate mitochondrial phenotypes in a patient-derived disease relevant cell culture system. We converted 7 control fibroblast lines and 17 lines harboring the following fALS mutations, SOD1A4V, TDP-43N352S, FUSR521G, CHCHD10R15L, and C9orf72 repeat expansion. We developed new machine learning approaches to identify iMN, analyze their mitochondrial function, and follow their fate longitudinally. Mitochondrial and energetic abnormalities were observed, but not all fALS iMN lines exhibited the same alterations. SOD1A4V, C9orf72, and TDP-43N352SiMN had increased mitochondrial membrane potential, while in CHCHD10R15Lcells membrane potential was decreased. TDP-43N352SiMN displayed changes in mitochondrial morphology and increased motility. SOD1A4V, TDP-43N352S, and CHCHD10R15LiMN had increased oxygen consumption rates and altered extracellular acidification rates, reflecting a hypermetabolic state similar to the one described in sporadic ALS fibroblasts. FUSR521Gmutants had decreased ATP/ADP ratio, suggesting impaired energy metabolism. We then tested the viability of iMN and found decreases in survival in SOD1A4V, C9orf72, and FUSR521G, which were corrected by small molecules that target mitochondrial stress. Together, our findings reinforce the role of mitochondrial dysfunction in ALS and indicate that fibroblast-derived iMN may be useful to study fALS metabolic alterations. Strengths of the DC iMN approach include low cost, speed of transformation, and the preservation of epigenetic modifications. However, further refinement of the fibroblasts DC iMN technique is still needed to improve transformation efficiency, reproducibility, the relatively short lifespan of iMN, and the senescence of the parental fibroblasts.
Odd-chain dicarboxylic acid feeding recapitulates the biochemical phenotype of glutaric aciduria type 1 in mice
Authors: Richert Adam C. , Zhang Yuxun , Bharathi Sivakama S. , Hernandez Abigail , Dodatko Tetyana , Bons Joanna , Stauffer Brandon , Yu Chunli , Schilling Birgit , Houten Sander M. , Goetzman Eric S.
Published: February 2025

Glutaric aciduria type-1 (GA1) is an inherited mitochondrial neurometabolic disorder with a poorly understood pathogenesis and unmet medical needs. GA1 can be diagnosed via its hallmark biochemical signature consisting of glutaric aciduria, 3-hydroxyglutaric aciduria, and increased plasma glutarylcarnitine. These glutaryl-CoA-derived metabolites are thought to originate solely in the mitochondria. Here, we demonstrate that wild-type mice fed an 11-carbon odd-chain dicarboxylic acid (undecanedioic acid, DC11) recreates the biochemical phenotype of GA1. Odd-chain dicarboxylic acids like DC11are not present in food but can arise from several endogenous processes, such as lipid peroxidation and fatty acid ω-oxidation. DC11is chain-shortened in peroxisomes to glutaryl (DC5)-CoA, which then gives rise to the GA1-like pattern of DC5metabolites in urine, tissues, and blood. Glutaric acid released from peroxisomes during DC11chain-shortening can enter mitochondria, be activated to CoA by the enzyme succinyl-CoA:glutarate-CoA transferase (SUGCT), and become substrate for glutaryl-CoA dehydrogenase (GCDH), the enzyme that is mutated in GA1. Our data provide proof-of-concept that the generation of dicarboxylic acids by ω-oxidation, which is stimulated during the same catabolic states known to trigger acute encephalopathy in GA1, may exacerbate disease by increasing the glutaryl-CoA substrate load in mitochondria.
Comparative analysis of macrophage feeder systems reveals distinct behaviors and key transcriptional shifts in chronic lymphocytic leukemia cells via coculture
Authors: Kohlhas Viktoria , Jestrabek Hendrik , Rebollido-Rios Rocio , Truong Thanh Tung , Zölzer Rebekka , Schreurs Luca D. , von Lom Anton , vom Stein Alexander F. , Hallek Michael , Nguyen Phuong-Hien
Published: February 2025

In this brief report, we evaluated various macrophage coculture systems for their CLL-feeding potential, phagocytosis capacity, induction of treatment resistance in CLL cells, and their impact on the transcriptional profiles of CLL cells.
Phylogenomics ofMessorharvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns
Authors: Juvé Yannick , Weyna Arthur , Lauroua Elodie , Nidelet Sabine , Khaldi Mourad , Barech Ghania , Lebas Claude , Rasplus Jean-Yves , Cruaud Astrid , Condamine Fabien L. , Romiguier Jonathan
Published: February 2025

As a major abiotic factor, climate change is expected to profoundly alter biological communities. On this basis, identifying how past temperature variations affected species diversification and distribution can help to predict the effects of the ongoing climate change. In this study, we focused on the harvester ant genusMessorwhich is mostly adapted to dry environments dominated by seed-producing plants. The phylogenetic analysis of 2,524 markers obtained from 58Messorspecies/subspecies, supports their emergence in the Irano-Indian area approximately 20 Mya. Phylogenetic relationships uncovered in this study enabled us to redefine historical taxonomic groups, providing a solid basis for future revisions that encompass the entire genus diversity. Their diversification appears to be affected by temperature, with a higher speciation rate during warmer periods. This confirms that the ecological specialization ofMessormakes them strongly dependent on thermal conditions. Our results highlight the importance of abiotic factors on diversification processes, especially for highly specialized species that may exhibit predictable evolutionary responses to climate changes.
Reproductive Adaptation ofAstyanax mexicanusUnder Nutrient Limitation
Authors: Xia Fanning , Santacruz Ana , Wu Di , Bertho Sylvain , Fritz Elizabeth , Morales-Sosa Pedro , McKinney Sean , Nowotarski Stephanie H. , Rohner Nicolas
Published: February 2025

Reproduction is a fundamental biological process for the survival and continuity of species. Examining changes in reproductive strategies offers valuable insights into how animals have adapted their life histories to different environments. Since reproduction is one of the most energy-intensive processes in female animals, nutrient scarcity is expected to interfere with the ability to invest in gametes. Lately, a new model to study adaptation to nutrient limitation has emerged; the Mexican tetraAstyanax mexicanus. This fish species exists as two different morphs, a surface river morph and a cave-dwelling morph. The cave-dwelling morph has adapted to the dark, biodiversity, and nutrient-limited cave environment and consequently evolved an impressive starvation resistance. However, how reproductive strategies have adapted to nutrient limitations in this species remains poorly understood. Here, we compared breeding activities and maternal contributions between laboratory-raised surface fish and cavefish. We found that cavefish produce different clutch sizes of eggs with larger yolk compared to surface fish, indicating a greater maternal nutrient deposition in cavefish embryos. To systematically characterize yolk compositions, we used untargeted proteomics and lipidomics approaches to analyze protein and lipid profiles in 2-cell stage embryos and found an increased proportion of sphingolipids in cavefish compared to surface fish. Additionally, we generated transcriptomic profiles of surface fish and cavefish ovaries using a combination of single cell and bulk RNA sequencing to examine differences in maternal contribution. We found that genes essential for hormone regulation were upregulated in cavefish follicular somatic cells compared to surface fish. To evaluate whether these differences contribute to their reproductive abilities under natural-occurring stress, we induced breeding in starved female fish. Remarkably, cavefish maintained their ability to breed under starvation, whereas surface fish largely lost this ability. We identifiedinsulin-like growth factor 1a receptor(igf1ra) as a potential candidate gene mediating the downregulation of ovarian development genes, potentially contributing to the starvation-resistant fertility of cavefish. Taken together, we investigated the female reproductive strategies inAstyanax mexicanus, which will provide fundamental insights into the adaptations of animals to environments with extreme nutrient deficit.
Shared Lineage, Distinct Outcomes: Yap and Taz Loss Differentially Impact Schwann and Olfactory Ensheathing Cell Development Without Disrupting GnRH-1 Migration
Authors: Taroc Ed Zandro M. , Amato Enrico , Semon Alexis , Dolphin Nikki , Beck Briane , Belin Sophie , Poitelon Yannick , Forni Paolo E.
Published: February 2025

Olfactory Ensheathing Cells (OECs) are glial cells originating from the neural crest, critical for bundling olfactory axons to the brain. Their development is crucial for the migration of Gonadotropin-Releasing Hormone-1 (GnRH-1) neurons, which are essential for puberty and fertility. OECs have garnered interest as potential therapeutic targets for central nervous system lesions, although their development is not fully understood.

Our single-cell RNA sequencing of mouse embryonic nasal tissues suggests that OECs and Schwann cells share a common origin from Schwann cell precursors yet exhibit significant genetic differences. The transcription factors Yap and Taz have previously been shown to play a crucial role in Schwann cell development. We usedSox10-Cre mice to conditionally ablateYapandTazin migrating the neural crest and its derivatives. Our analyses showed reduced Sox10+ glial cells along nerves in the nasal region, altered gene expression of SCs, melanocytes, and OECs, and a significant reduction in olfactory sensory neurons and vascularization in the vomeronasal organ. However, despite these changes, GnRH-1 neuronal migration remained unaffected.

Our findings highlight the importance of the Hippo pathway in OEC development and how changes in cranial neural crest derivatives indirectly impact the development of olfactory epithelia.
Using a Novel-Liaison Based Social Media Intervention Utilizing Community Feedback to Improve Organizational Health Literacy in Covid-19 Crisis Communication
Authors: Matangi Nishita , Granillo Cristie , Joachim-Célestin Maud , Fuentes Karla Estudillo , Irani Crissy , Thiruvengadam Nikhil , Montgomery N Susanne
Published: February 2025

The COVID-19 pandemic exposed historical pervasive gaps in information and resources for vulnerable communities. In an academic community partnered response of a consortium of already collaborating community and academic partners, the COVID Care Corps (CCC), was developed to create and disseminate public health information to individuals in the Inland Empire (IE) by including community liaisons to implement a systematic feedback loop to assure community voice. Liaisons made disseminating information and getting community feedback more efficiently in a time of crisis when information needed to be immediate. As a result, it was found that although community was concerned about the pandemic, they also wanted information about other social determinants of health (immigration, finances, housing and job security= often presented as competing priorities to the pandemic. This resulted in a shift in content creation to aligned with community needs and interests. Establishing trust through community relationships and identifying community liaisons should be implemented prior to a crisis to ensure the quick dissemination of information needed for local buy-in and true equitable health communication.
Microbial ecology of acidic, biogenic gypsum: Community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave
Authors: Havlena Zoë E. , Lucero Katherine , Graham Heather V. , Stern Jennifer C. , Wankel Scott D. , Mainiero Maurizio , Jones Daniel S.
Published: February 2025

Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO4•2H2O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help us evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, in order to test hypotheses about how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H2S(g) and other gases in the cave atmosphere. We found that actively-forming gypsum in the lower cave levels was colonized by low diversity communities of sulfide-oxidizing chemolithotrophs and other acidophiles that have few cells compared to other environments in the cave. The most abundant taxa wereAcidithiobacillus, Metallibacterium, Mycobacteria, and three differentThermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. In contrast, deposits in older cave levels had more diverse communities that are dominated by chemoorganotrophic and methanotrophic taxa. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms, and broaden our knowledge of the life associated with terrestrial sulfates.

Importance

Gypsum and other sulfate salts are common on Mars, and many of these deposits are thought to have formed from acidic fluids early in the planet’s history. Understanding the life that survives and thrives in similar environments on Earth is therefore crucial for evaluating whether these Martian sulfates are or ever were habitable. One such environment where acidic gypsum occurs is in sulfuric acid caves, where extremophilic microorganisms drive the precipitation of sulfate minerals by oxidizing hydrogen sulfide gas from the cave atmosphere. Here, we characterized the communities of microorganisms on freshly formed and ancient gypsum in the Frasassi Caves, and found that the gypsum deposits hosted microbial communities that changed based on chemical energy availability and the age of the gypsum. Our findings underscore the importance of chemical and microbiological interactions in shaping habitable niches, and provide context for searching for past or present life in acidic Martian sulfates.
Rostro-caudal TMS mapping of immediate transcranial evoked potentials reveals a pericentral crescendo-decrescendo pattern
Authors: Nuyts Marten , Beck Mikkel Malling , Banach Agata , Thielscher Axel , Meesen Raf , Tomasevic Leo , Siebner Hartwig Roman , Christiansen Lasse
Published: February 2025

Background

We recently demonstrated that single-pulse TMS of the primary sensorimotor hand area (SM1HAND) elicits an immediate transcranial evoked potential (iTEP). This iTEP response appears within 2–7 ms post-TMS, featuring high-frequency peaks superimposed on a slow positive wave. Here, we used a linear TMS-EEG mapping approach to characterize the rostro-caudal iTEP expression and compared it to that of motor-evoked potentials (MEPs).

Methods

In 15 healthy young volunteers (9 females), we identified the iTEP hotspot in left SM1HAND. We applied single biphasic TMS pulses at an intensity of 110% of resting motor threshold over six cortical sites along a rostro-caudal axis (2 cm rostral to 3 cm caudal to the SM1HANDhotspot). We analyzed site-specific iTEP and MEP responses.

Results

iTEP magnitude decreased rostrally and caudally from the SM1HANDhotspot. MEPs exhibited a similar rostro-caudal crescendo-decrescendo pattern. While iTEP and MEP response profiles were similar, normalized iTEP amplitudes decayed less rapidly at the first postcentral site.

Discussion

These findings support the idea that pericentral iTEPs reflect a direct response signature of the pericentral cortex, possibly involving a synchronized TMS-induced excitation of cortical pyramidal tract neurons. Similar but non-identical rostro-caudal patterns suggest that iTEPs and MEPs may arise from overlapping but distinct neuronal populations.
Biochemical properties of glycerol kinase from the hypersaline-adapted archaeonHaloferax volcanii
Authors: Sanchez Karol M. , Maupin-Furlow Julie A.
Published: February 2025

Extremophilic microorganisms hold promise to serve as robust biocatalysts in the conversion of glycerol waste into high value products.Haloferax volcaniiis a hypersaline-adapted archaeon that prefers glycerol over glucose and channels this carbon source into central metabolism through glycerol kinase (GK). Here we report the biochemical properties of theH. volcaniiGK and evaluated its potential for biotechnological applications. The N-terminal His-tagged form of GK was found functionalin vivoand was readily purified to homogeneity at 4.5-fold higher yield (3 mg/L culture) than GK fused to a C-terminal StrepII tag. Further analysis of His-GK by size exclusion chromatography revealed the enzyme exhibited a glycerol-induced shift from a homodimer to a homodimer-homotetramer equilibrium. Purified His-GK demonstrated robust activity over a broad pH and salinity range, with optimal activity at 100 mM NaCl and 50-60 °C. The enzyme was catalytically active in organic solvent (5-10 % DMSO) and crude glycerol containing methanol. His-GK was also found to exhibit full activity after freeze-thaw, showed prolonged thermotolerance in 2 M NaCl supplemented buffers, and had a melting temperature (Tm) in the range of 83-84 °C. Kinetic analysis using the Hill equation indicated His-GK displayed positive cooperativity for glycerol, ATP, and magnesium, with manganese and cobalt also found to serve as divalent cation cofactors. These findings underscore the unique and robust enzymatic properties ofH. volcaniiGK, representing the first known GK to exhibit positive cooperativity with glycerol and ATP, and highlighting its potential for biotechnological applications in glycerol conversion.

IMPORTANCE

This study provides new insight into glycerol kinase kinetics through the discovery of an enzyme exhibiting positive cooperativity for glycerol and ATP. By purifying and characterizingH. volcaniiglycerol kinase, this work marks the first isolation of a glycerol kinase from a halophilic archaeon. The enzyme displays unique properties, including resilience to organic solvents, high temperatures, and extreme salinity. It also exhibits sigmoidal kinetics, with Hill coefficients averaging n = 2 for glycerol, ATP, and magnesium, indicating positive cooperativity. This behavior, previously unobserved in other glycerol kinases, aligns with the preference ofH. volcaniifor glycerol over glucose. Given the role of glycerol kinases in converting glycerol waste into value-added products, their efficiency is often a bottleneck in bacterial systems that prefer glucose and struggle under extreme conditions. The distinctive properties ofH. volcaniiglycerol kinase suggest potential for biotechnological applications in harsh environments.
On inputs to deep learning for RNA 3D structure prediction
Authors: Szikszai Marcell , Magnus Marcin , Kadyan Sachin , Rivas Elena
Published: February 2025

Today, there are several effective deep learning models for predicting the 3D structure of proteins. Building on their success, models have been developed for predicting the 3D structure of non-coding RNAs. Unfortunately, these models are much less accurate than their protein counterparts. In this paper, we highlight differences between protein and RNA structure, and demonstrate methods for deep learning targeted at addressing those differences, with the aim of prompting discussion on these topics. We present an RNA-specific pipeline for generating structural Multiple Sequence Alignments (MSAs). Derived from the structural alignments, we introduce engineered evolutionary features that strongly inform RNA structure. Further, from the crystal structure, we derive structural features describing RNA base pairing. These evolutionary and structural features can be used in loss functions at different stages of training. Finally, we discuss different cropping strategies informed by RNA structure.
SLICK: A Sandwich-LIke Culturing Kit forin situCryo-ET Sample Preparation
Authors: Li Qiuye , Zhang Li , Xu Qin , Zhang Peng , Zhu Shiwei
Published: February 2025

In situcryo-electron tomography (cryo-ET) has recently been widely used in observing subcellular structures and macromolecules in their native states at high resolution. One of the reasons that it has not been more widely adopted by cell biologists and structural biologists is the difficulties in sample preparation. Here we present the Sandwich-LIke Culturing Kit (SLICK), simplifying the procedure and increasing the throughput for sample preparation forin situcryo-ET (69 words).
A vector-based strategy for olfactory navigation inDrosophila
Authors: Siliciano Andrew F. , Minni Sun , Morton Chad , Dowell Charles K. , Eghbali Noelle B. , Rhee Juliana Y. , Abbott L.F. , Ruta Vanessa
Published: February 2025

Odors serve as essential cues for navigation. Although tracking an odor plume has been modeled as a reflexive process, it remains unclear whether animals can use memories of their past odor encounters to infer the spatial structure of their chemical environment or their location within it. Here we developed a virtual-reality olfactory paradigm that allows head-fixedDrosophilato navigate structured chemical landscapes, offering insight into how memory mechanisms shape their navigational strategies. We found that flies track an appetitive odor corridor by following its boundary, alternating between rapid counterturns to exit the plume and directed returns to its edge. Using a combination of behavioral modeling, functional calcium imaging, and neural perturbations, we demonstrate that this ‘edge-tracking’ strategy relies on vector-based computations within theDrosophilacentral complex in which flies store and dynamically update memories of the direction to return them to the plume’s boundary. Consistent with this, we find that FC2 neurons within the fan-shaped body, which encode a fly’s navigational goal, signal the direction back to the odor boundary when flies are outside the plume. Together, our studies suggest that flies leverage the plume’s boundary as a dynamic landmark to guide their navigation, analogous to the memory-based strategies other insects use for long-distance migration or homing to their nests. Plume tracking thus uses components of a conserved navigational toolkit, enabling flies to use memory mechanisms to navigate through a complex shifting chemical landscape.
Nanopore sequencing-based measurement of paramyxovirus RNA editing reveals virus-specific differences in editing efficiency of mRNA, antigenome and genome
Authors: Masuda Yusuke , Rakib Tofazzal Md. , Akter Lipi , Nakagawa Keisuke , Naitou Kiyotada , Saito Akatsuki , Yamaguchi Ryoji , Matsumoto Yusuke
Published: February 2025

Paramyxovirus polymerase recognizes an RNA editing signal on the viral genome and transcribes mRNA in which guanine nucleotides are inserted in a template-independent manner. This enables the synthesis of multiple proteins from a single gene, which is important for viral growth. We developed a method to quantify RNA editing efficiency using Oxford Nanopore Technologies’ MinION platform. We performed sequence analysis of reverse transcription (RT)-PCR amplicons with the RNA editing sites in cells infected with Sendai virus (SeV) and canine distemper virus (CDV). By modifying RT primers, we simultaneously assessed RNA editing efficiency in mRNA, antigenome and genome. We observed distinct differences in mRNA editing efficiency between SeV and CDV. Notably, while RNA editing in SeV is confined to mRNA, in CDV it is also observed in antigenome/genome. (Anti)genomes harboring extra nucleotides may deviate from a multiple-of-six sequence, suggesting that RNAs not following the “Rule of Six” are produced in CDV-infected cells.

Highlights

A method was established to quantify RNA editing efficiency in RNAs from paramyxovirus-infected cells using the MinION platform.

RNA editing efficiency in mRNA differs between Sendai virus and canine distemper virus.

Although RNA editing is confined to mRNA during Sendai virus infection, it is also observed in the antigenome and genome during canine distemper virus infection.
Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies
Authors: Wang Yuxin , Zuo Shiman , Bao Hanjing , Zhang Zehui , Chen Yijun , Zhang Wenlong , Liu Qi , Lu Yan , Huang Yahong , Zheng Wei , Yang Nanfei , Ye Lupeng , Shen Pingping
Published: February 2025

Chimeric antigen receptor-engineered macrophages (CAR-Ms) hold great promise for solid tumor immunotherapy. The intracellular domains (ICDs) of CARs determine the phenotypic output of therapeutic macrophages but remain largely unexplored. Here, we constructed a CAR library containing 131 unique signaling domains derived from native immune receptors and identified 17 ICDs that enhance macrophage phagocytosis, inflammatory responses, or tumor infiltrationin vitroandin vivo. We further developed a scalable 3’ barcode technology, CARode, to uniquely label and trace ICD variants within large-scale combinatorial CAR library and applied it to single-cell RNA sequencing and single-cell CAR analysis to assess the synergetic effects of ICD combinations on macrophage activation. Our approach uncovered a novel CD40-LY9-FCRL1 chimeric receptor that modulates the tumor microenvironment and improves solid tumor clearance. In conclusion, our findings demonstrate that pooled screening can accelerate the discovery of complex ICD constructs, providing a powerful platform for engineering macrophage-based immunotherapies.
Structure-based analysis unveils co-origin of LPOR and nitrogenase-like proteins
Authors: Sun Xizhe , Ma Lisong , Zeng Fanli , Hong Yiguo , Dixon Ray , Rao Zihe , Zhao Guogang , Zhao Jin , Zhang Chao , Wu Meng , Ma Chukang , Yu Xiaolan , Yang Ji , Purton Saul , Ermilova Elena , Scrutton Nigel , Silva Pedro , Zhao Jianjun , Cheng Qi
Published: February 2025

Structures of nitrogenases, dark-operative protochlorophyllide oxidoreductases, and light-dependent protochlorophyllide oxidoreductases (LPOR) have been resolved. However, their evolutionary relatedness remains elusive. Here, we show, through structural alignment, that all subunits of nitrogenase-like proteins originated from a co-ancestral archaic one-subdomain precursor. LPOR evolved from the BchX/BchY subunits of nitrogenase-like chlorophyllideaoxidoreductase (COR), and the intermediary retinol dehydrogenase through possible genetic recombination. We thus establish previously unknown structural links among key enzymes involved in biological nitrogen-fixation (BNF) and photosynthesis, unraveling structure-guided functional evolution from a single-subunit iron protein to multi-subunit nitrogenase-like COR, and to the single-subunit LPOR for phototrophic metabolismviabacteriochlorophyll, retinal, and chlorophyll. This work also demonstrates structural similarities are imperative for inferring distant origins of functionally divergent proteins, particularly those lacking primary amino-acid sequence identity. Moreover, our findings coupled with AI may be exploited to design innovative light-driven CORs and/or light-utilizing nitrogenases with enhanced efficacy of photosynthesis and BNF.

Graphical abstract

Video abstract

https://www.youtube.com/watch?v=b0qBE1JMaH0

Highlights

LPOR evolves from BchX and BchY subunits of the nitrogenase-like protein (NGLP) COR

All subunits of NGLPs can be traced back to the ancestral one-subdomain precursor

Retinol dehydrogenase acts as a crucial intermediate in the COR to LPOR evolution

Structure-based design of LUN is showcased to revolutionize protein engineering
Artificial intelligence in action: shaping the future of public sector
Authors: Panda Mahanish , Hossain Munshi Maksud , Puri Roma , Ahmad Anees
Published: February 2025

Purpose

Artificial intelligence (AI) has transformed various sectors, including automotive, finance, media, travel and retail by leveraging new-age technologies. Education, banking, health care, social policy and regulation, within the public sector have witnessed significant AI applications and substantial benefits. The importance of AI in the public sector includes enhanced efficiency, improved decision-making, cost savings, citizen-centric services, etc. Despite these advancements, a mindful discussion on the societal impact of AI in the public sector demands comprehension regarding its subjugation. Therefore, this study aims to analyze the role of AI in transforming the public sector using a bibliometric analysis of recent trends and challenges.

Design/methodology/approach

This study has used bibliometric analysis to trace the intellectual patterns of previous research. It comprises 231 articles from 2000 to 2024 from Scopus through the Scientific Procedures and Rationales for Systematic Literature Reviews protocol. This protocol has adopted a three-step process for identifying articles, i.e. assembling, arranging and assessing.

Findings

The publication trend shows an upward trajectory since 2017, whereas network visualization protrudes with the recent trends and thematic expressions, namely, Global AI ethics and policy challenges in public sectors, AI adoption and governance in public sector, challenges and opportunities of implementing AI in public administration and AI’s role in economic and public transformation.

Research limitations/implications

The findings suggest AI adoption in the public sector enhances transparency and efficiency but demands ethical guidelines, legal frameworks and stakeholder governance to address challenges such as data privacy, algorithmic bias and public trust. Policies should promote responsible AI use, balancing innovation with accountability to improve public service delivery and uphold democratic values.

Originality/value

This paper enhances the limited literature on the integration of AI in the public sector, focusing on emerging themes and trending topics with future research directions to furnish a holistic perspective. It aims to guide researchers and policymakers in exploring areas for further investigation in this domain.
Intercultural sensitivity and sociocultural adaptation among cabin attendants: direct, indirect and interaction effects on organizationally valued job outcomes
Authors: Lee Gyehee , Karatepe Osman M. , Kim Jieun , Olorunsola Victor Oluwafemi , Kim Taegoo Terry
Published: February 2025

Purpose

This paper aimed to propose a research model that investigated job satisfaction (JSAT) and affective organizational commitment (AOC) as the serial mediators linking intercultural sensitivity (IS) to service-oriented organizational citizenship behavior (SOCB). It also explored sociocultural adaptation (SA) as a moderator of the influence of IS on JSAT.

Design/methodology/approach

Data gathered from Korean cabin attendants employed at Middle Eastern airlines were utilized to gauge the aforementioned relationships via structural equation modeling.

Findings

Cabin attendants high on IS were satisfied with their jobs and therefore exhibited affective commitment to their airline company. Such employees in turn displayed heightened SOCB. SA strengthened the positive influence of IS on JSAT.

Practical implications

The presence of interactive training, scenario-based simulations and cross-cultural communication exercises would enable cabin attendants to manage passengers with different cultural background successfully.

Originality/value

This empirical piece contributes to the pertinent literature by investigating the mechanisms underlying the link between IS and organizationally valued behavioral outcomes such as SOCB. It also enhances the understanding about SA which increases the positive impact of IS on JSAT.
Multi-dimensional organizational motivations: the catalyst for interorganizational knowledge sharing in megaprojects
Authors: He Hui , He Qinghua , Chen Yajiao , Wang Ge , Chen Xiaoyan
Published: February 2025

Purpose

Interorganizational knowledge sharing (IKS) is an important strategy for organizations to obtain exterior knowledge resources to enhance innovation and value co-creation in megaprojects. However, little research has deeply investigated multiple attributes of organizational motivations and the combinatorial effects of these motivations on facilitating IKS. Based on resource dependency theory, this study examined the net and combinatorial effects of four types of motivations (i.e. image motivations, reactive motivations, project-based co-creative economic motivations and cross-project co-creative economic motivations).

Design/methodology/approach

Questionnaire surveys were administered to 244 practitioners with over 10 years of experience in construction megaprojects. The collected data were analyzed using a partial least square-structural equation model (PLS-SEM) and fuzzy set qualitative comparative analysis (fsQCA).

Findings

The findings of PLS-SEM support that image and project-based co-creative economic motivations positively drive IKS. The results of fsQCA reveal three types of efficacious configurations, including comprehensive benefits-integrated driven, short-term benefits-dominated driven and long-term benefits-dominated driven configurations.

Originality/value

This study provides insight into broadening the understanding of multidimensional organizational motivations for IKS and fostering the configurational perspective to their effects with the idea that one size does not fit all. Managers should develop effective interventions considering the combination of various motivations and use multi-layered incentive structures that reward both immediate project-specific outcomes and long-term relationship-building efforts.
The impact of exogenous shocks on strategy, business models and product development in the Portuguese footwear industry
Authors: Oliveira Jorge , Pereira Cláudia , Oliveira Ana
Published: February 2025

Purpose

This study aims to investigate the footwear industry’s resilience to external changes in an attempt to provide insights into strategies that can define effective organizational responses to environmental stimuli. In this sense, it is important to understand how companies have adapted to the exogenous shocks. Thus, this paper addresses the impact of the exogenous shocks like COVID-19 pandemic, the Russia–Ukraine war and energy crisis in the European Union and focuses on the potential resilience strategies implemented by the footwear industry.

Design/methodology/approach

Through a qualitative approach, 3 interviews were carried out on the structural basis of the footwear industry, namely at an associative and technological level, and 11 in footwear companies.

Findings

This study shows that the exogenous shocks forced changes in the nature of business, namely: (1) manufacturers entered the B2C segment, shortening the supply chain; (2) it provided changes at the strategic level (greater focus on the development of operational and logistics strategies) and digitization (digital transformation to support the execution of essential activities); (3) development of new products (emergence of a market opportunity that combines the concepts of sporty and classic shoes).

Research limitations/implications

This study is limited to the footwear industry, does not address how cultural, social or behavioral differences in specific markets may impact adaptation to exogenous shocks, and focuses on recent exogenous shocks, without analyzing similar past events for historical comparisons. It also does not explore the direct financial impact of the suggested strategies.

Practical implications

This study focuses on strategic business adaptation in crisis scenarios, showing the importance of flexibility and resilience, suggesting specific practices to improve supply chain resilience. This can help companies reduce vulnerabilities in the face of global disruptions.

Social implications

This study provides an important contribution to contingency theory, by demonstrating that companies need to adjust their structures and strategies in response to exogenous shocks.

Originality/value

This study focuses on the concept of resilience to find out what strategies should be adopted to respond to external changes.
Unveiling excellence in Indian healthcare: a patient-centric PRISMA analysis of hospital service quality, patient satisfaction and loyalty
Authors: Divya Divya , Savita Savita , Kaur Sandeepa
Published: February 2025

Purpose

This paper aims to provide a conceptual framework containing SERVQUAL original dimensions and add two additional dimensions: patient satisfaction and loyalty in the hospital SQ model that demonstrates the relationship between hospital service quality, patient satisfaction and loyalty from patients’ perspective.

Design/methodology/approach

This research conducted a thorough literature review using specific keywords and electronic databases, adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Through analysis, the key dimensions of service quality in Indian hospitals were identified, with the addition of patient satisfaction and loyalty as variables. Of 1,000 initially downloaded papers, 497 were included.

Findings

While many researchers rely on the SERVQUAL model, some introduce new or modified dimensions, often renaming existing ones. This study identifies the RATER factors as the main dimensions patients use to evaluate hospital services. This study finds a positive relationship between service quality, patient satisfaction and loyalty.

Practical implications

An understanding of how health-care service quality dimensions, directly and indirectly, affect patient satisfaction and loyalty is important for hospital marketing managers. This study helps them take action to improve patient satisfaction, which encourages patients to be loyal.

Originality/value

This research provides a comprehensive framework for measuring health-care service quality, combining SERVQUAL dimensions and new variables. This study offers useful insights for academics and health-care professionals, promoting more accurate measurement and enhancement of service quality. The use of PRISMA in this context is also innovative, as it is less common in administrative health-care research.