bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism
Authors: Fanunza Elisa , Cheng Adam Z. , Auerbach Ashley A. , Stefanovska Bojana , Moraes Sofia N. , Lokensgard James R. , Biolatti Matteo , Dell’Oste Valentina , Bierle Craig J. , Bresnahan Wade A. , Harris Reuben S. 
Published: February 2023

AbstractThe APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses EBV and KSHV and the alpha-herpesviruses HSV-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting involvement of an immediate early or early (IE-E) viral protein. In support of this mechanism, cycloheximide treatment of HCMV-infected cells prevents the expression of viral proteins and simultaneously blocks APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which is a viral DNA synthesis inhibitor affecting late protein expression, still permits A3B relocalization. These results combine to show that the beta-herpesvirus HCMV uses a fundamentally different, RNR-independent molecular mechanism to antagonize APOBEC3B.ImportanceHuman cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses in order to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
Human ovarian ageing is characterized by oxidative damage and mitochondrial dysfunction
Authors: Smits Myrthe A.J. , Schomakers Bauke V. , van Weeghel Michel , Wever Eric J.M. , Wüst Rob C.I. , Dijk Frederike , Janssens Georges E. , Goddijn Mariëtte , Mastenbroek Sebastiaan , Houtkooper Riekelt H. , Hamer Geert 
Published: February 2023

AbstractHuman ovarian ageing encompasses the age-related decline in female fertility. Oxidative stress and mitochondrial dysfunction in oocytes are suggested as causal, but corroborating evidence is limited. Using immunofluorescence imaging on human ovarian tissue, we found oxidative damage by protein and lipid (per)oxidation at the primordial follicle stage. Additionally, using comprehensive metabolomics and lipidomics, a cohort of 150 human germinal vesicles and metaphase I oocytes and 15 corresponding cumulus cell samples displayed a shift in glutathione to oxiglutathione ratio and depletion of phospholipids. Age-related changes in polar metabolites suggested a decrease in mitochondrial function, as demonstrated by NAD+, purine and pyrimidine depletion, while glycolysis substrates and glutamine accumulated with age. Oocytes of advanced maternal age likely used alternative energy sources like glycolysis and the adenosine salvage pathway, and possibly increased ATP production in cumulus cells. These findings indicate that oocytes of advanced maternal age suffer from oxidative damage and mitochondrial dysfunction.Graphical abstract
Perforin-2 is a pore-forming effector of endocytic escape in cross-presenting dendritic cells
Authors: Rodríguez-Silvestre Pablo , Laub Marco , Davies Alexandra K. , Schessner Julia P. , Krawczyk Patrycja A. , Tuck Benjamin J. , McEwan William A. , Borner Georg H.H. , Kozik Patrycja 
Published: February 2023

AbstractDuring initiation of antiviral and antitumour T cell-mediated immune responses, dendritic cells (DCs) cross-present exogenous antigens on MHC class I. Cross-presentation relies on the unique ‘leakiness’ of endocytic compartments in DCs, whereby internalised proteins escape into the cytosol for proteasome-mediated generation of MHC I-binding peptides. Given that type 1 conventional DCs excel at cross-presentation, we searched for cell-type specific effectors of endocytic escape. We devised an escape assay suitable for genetic screening and identified a pore-forming protein, perforin-2, as a dedicated effector exclusive to cross-presenting cells. Perforin-2 is recruited to antigen-containing compartments, where it undergoes maturation, releasing its pore-forming domain.Mpeg1-/-mice fail to efficiently prime CD8+T cells to cell-associated antigens, revealing an important role of perforin-2 in cytosolic entry of antigens during cross-presentation.One-Sentence SummaryPore-forming protein perforin-2 is a dedicated effector of endocytic escape specific to cross-presenting cells
Spatial and compositional variations in fruit characteristics of papaya (Carica papayacv. Tainung No. 2) during ripening
Authors: Chung Sun Woo , Kim Seolah , Kim Seong Cheol 
Published: February 2023

ABSTRACTPapaya fruit (Carica papaya) has different degrees of ripening within a fruit, affecting its commercial market value. The fruit characteristics of ‘Tainung No. 2’ papaya was investigated at the stem-end, middle, and calyx-end parts at three ripening stages and categorized based on fruit skin coloration: unripe at ca. 16 weeks after anthesis (WAA), half-ripe at ca. 18 WAA, and full-ripe at ca. 20 WAA. The fruits maintained an elliptical shape during ripening with 2.36 of the ratios of the length to the width. The peel and pulp color changed from green to white to yellow during ripening, regardless of the fruit three parts. In the pulp, soluble solid content increased to about 320% and firmness decreased to about 99% during ripening but did not differ among fruit three parts. Individual nutrient contents, including primary and secondary metabolites, and minerals, changed dynamically between the ripening stages and fruit parts. Total carbohydrates and proteins, N, and K, were more accumulated at the stem-end during ripening, meanwhile fructose, glucose, Mg, and Mn were at the calyx-end. In the principal component analysis, ripening stages and fruit parts were distinctly determined by the first and second principal components, respectively. These results provide fundamental information for improving ripening during papaya cultivation.
Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution
Authors: Feng Xuehuan , Zheng Jinfang , Irisarri Iker , Yu Huihui , Zheng Bo , Ali Zahin , de Vries Sophie , Keller Jean , Fürst-Jansen Janine M.R. , Dadras Armin , Zegers Jaccoline M.S. , Rieseberg Tim P. , Ashok Amra Dhabalia , Darienko Tatyana , Bierenbroodspot Maaike J. , Gramzow Lydia , Petroll Romy , Haas Fabian B. , Fernandez-Pozo Noe , Nousias Orestis , Li Tang , Fitzek Elisabeth , Grayburn W. Scott , Rittmeier Nina , Permann Charlotte , Rümpler Florian , Archibald John M. , Theißen Günter , Mower Jeffrey P. , Lorenz Maike , Buschmann Henrik , von Schwartzenberg Klaus , Boston Lori , Hayes Richard D. , Daum Chris , Barry Kerrie , Grigoriev Igor V. , Wang Xiyin , Li Fay-Wei , Rensing Stefan A. , Ari Julius Ben , Keren Noa , Mosquna Assaf , Holzinger Andreas , Delaux Pierre-Marc , Zhang Chi , Huang Jinling , Mutwil Marek , de Vries Jan , Yin Yanbin 
Published: February 2023

ABSTRACTThe filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains ofZygnema circumcarinatumand one strain ofZ. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model systemZ. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.HIGHLIGHTSGenomes of four filamentous algae (Zygnema) sisters to land plantsZygnemaare rich in genes for multicellular growth and environmental acclimation: signaling, lipid modification, and transportCell wall innovations: diversification of hexameric rosette cellulose synthase in ZygnematophyceaeCo-expression networks reveal conserved modules for balancing growth and acclimation
Being spontaneous has its costs! Characterization of spontaneous phage □D5-resistant mutants ofDickeya solanistrain IPO 2222
Authors: Sokolova Daryna , Smolarska Anna , Bartnik Przemysław , Rabalski Lukasz , Kosinski Maciej , Narajczyk Magdalena , Krzyzanowska Dorota M. , Rajewska Magdalena , Mruk Inez , Czaplewska Paulina , Jafra Sylwia , Czajkowski Robert 
Published: February 2023

AbstractLytic bacteriophages able to infect and killDickeyaspp. can be readily isolated from virtually allDickeyaspp.-containing environments, yet little is known about the selective pressure those viruses exert on their hosts. Here, we identified two spontaneousD. solaniIPO 2222 mutants (0.8% of all obtained mutants), DsR34 and DsR207, resistant to infection caused by lytic phage vB_Dsol_D5 (ΦD5) that expressed a reduced ability to macerate potato tuber tissues compared to the wild-type, phage-susceptibleD. solaniIPO 2222 strain. Genome sequencing revealed that genes encoding: secretion protein HlyD (mutant DsR34) and elongation factor Tu (EF-Tu) (mutant DsR207) were altered in these strains. Both mutations impacted the proteomes of cells grown in both rich and minimal media, including the abundance of the cell envelope and transmembrane transport-associated proteins. Furthermore, features essential for the ecological success of these mutants in a plant environment, including their ability to use various carbon and nitrogen sources, produce plant cell wall degrading enzymes, ability to form biofilms, siderophore production, swimming and swarming motility and virulencein plantawere assessed. Compared to the wild-type strain,D. solanistrain IPO 2222, mutants DsR34 and DsR207 had a reduced ability to macerate chicory leaves and to colonize and cause symptoms in growing potato plants. The implications of the ΦD5 resistance on driving traits affecting the ecological performance ofD. solaniare discussed.
The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after open mitosis in mammalian cells
Authors: Bragulat-Teixidor Helena , Ishihara Keisuke , Szücs Gréta Martina , Otsuka Shotaro 
Published: February 2023

AbstractThe endoplasmic reticulum (ER) is physically connected to the nucleus by junctions with the outer membrane of the nuclear envelope (NE). The ER–NE junctions are essential for supplying the NE with lipids and proteins synthesized in the ER. However, little is known about the structure of these ER–NE junctions. Here, we systematically studied the ultrastructure of ER–NE junctions in cryo-fixed mammalian cells staged in anaphase, telophase, and interphase by correlating live cell imaging with three-dimensional electron microscopy. Strikingly, our results revealed that ER–NE junctions in interphase cells have a pronounced hourglass shape with a constricted neck of 7–20 nm width. This morphology is significantly distinct from that of junctions among the ER, and it emerges as early as telophase. The highly constricted ER–NE junctions are seen in several mammalian cell types, but not in budding yeast. We speculate that the unique and highly-constricted ER–NE junctions are regulated via novel mechanisms that contribute to ER-to-NE lipid and protein traffic in higher eukaryotes.
A general strategy to develop fluorogenic polymethine dyes for bioimaging
Authors: Martin Annabell , Rivera-Fuentes Pablo 
Published: February 2023

AbstractFluorescence imaging is an invaluable tool to study biological processes and further progress depends on the development of advanced probes. Fluorogenic dyes are crucial to reach intracellular targets and label them with high specificity. Excellent fluorogenic rhodamine dyes have been reported, but they often require a long and low-yielding synthesis and are spectrally limited to the visible range. Here, we present a general strategy to transform polymethine compounds into fluorogenic dyes using an intramolecular ring closure approach. We illustrate the generality of this method by creating both spontaneously blinking and no-wash, turn-on polymethine dyes with emissions across the visible and near-infrared spectrum. These probes are compatible with self-labeling proteins and small-molecule targeting ligands and can be combined with rhodamine-based dyes for multicolor and fluorescence lifetime multiplexing imaging. This strategy provides access to bright, fluorogenic dyes that emit at wavelengths that are significantly more red-shifted than those of existing rhodamine-based dyes.
MPK12 in stomatal CO2signaling: function beyond its kinase activity
Authors: Yeh Chung-Yueh , Wang Yuh-Shuh , Takahashi Yohei , Kuusk Katarina , Paul Karnelia , Arjus Triinu , Yadlos Oleksii , Schroeder Julian I. , Ilves Ivar , Garcia-Sosa Alfonso T. , Kollist Hannes 
Published: February 2023

SummaryProtein phosphorylation by kinases is a major molecular switch mechanism involved in the regulation of stomatal opening and closure. Previous research defined interaction between MAP kinase 12 and Raf-like kinase HT1 as a required step for stomatal movements by changes in CO2concentration. However, whether MPK12 kinase activity is required for regulation of CO2-induced stomatal responses warrants in depth investigation.We apply genetic, biochemical, and structural modeling approaches to examining the non-catalytic role of MPK12 in guard cell CO2signaling that relies on allosteric inhibition of HT1.We show that CO2/HCO3−-enhanced MPK12 interaction with HT1 is independent of its phosphor-transfer activity. By analyzing gas exchange of plant lines expressing various kinase-dead and constitutively active versions of MPK12 in a plant line whereMPK12is deleted, we confirmed that CO2-dependent stomatal responses rely on MPK12’s ability to bind to HT1 but not its kinase activity. We also demonstrate that purified MPK12 and HT1 proteins form a heterodimer in the presence of CO2/HCO3−and present structural modeling that explains the MPK12:HT1 interaction interface.These data add to the model that MPK12 kinase-activity-independent interaction with HT1 functions as a molecular switch by which stomatal guard cells sense changes in atmospheric CO2concentration.
Pitch-size crossmodal correspondence in tortoises (Testudo hermanni)
Authors: Loconsole Maria , Stancher Gionata , Versace Elisabetta 
Published: February 2023

AbstractHumans spontaneously match information coming from different senses, what we call crossmodal associations. For instance, high pitch sounds are preferentially associated with small objects, and low pitch sounds with larger ones. While previous studies reported crossmodal associations in mammalian species, evidence for other taxa is scarce, hindering an evolutionary understanding of this phenomenon. Here we provide evidence of pitch-size correspondence in a reptile, the tortoiseTestudo hermanni. Tortoises showed a spontaneous preference to associate a small disc (i.e., visual information about size) to a high pitch sound (i.e., auditory information), and a larger disc to a low pitch sound. These results suggest that crossmodal associations may be an evolutionary ancient phenomenon, potentially an organising principle of the vertebrate brain.
Cross-domain interactions induce community stability to benthic biofilms in proglacial streams
Authors: Busi Susheel Bhanu , Peter Hannes , Brandani Jade , Kohler Tyler J. , Fodelianakis Stilianos , Pramateftaki Paraskevi , Bourquin Massimo , Ezzat Leïla , Michoud Grégoire , Lane Stuart , Wilmes Paul , Battin Tom J. 
Published: February 2023

AbstractCross-domain interactions are an integral part of the success of complex biofilms in natural environments. Here, we report on cross-domain interactions in biofilms of streams draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterized by multiple environmental gradients and stability that depend on the time since deglaciation. We estimate co-occurrence of prokaryotic and eukaryotic communities along this gradient and show that key community members have disproportionate effects on the stability of co-occurrence networks. The topology of the networks was similar independent of environmental gradients and stability. However, network stability was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that both pro- and eukaryotes are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. These ‘keyplayers’ are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.
Tubular Mitochondrial Pyruvate Carrier Disruption Elicits Redox Adaptations that Protect from Acute Kidney Injury
Authors: Rauckhorst Adam J. , Martinez Gabriela Vasquez , Andrade Gabriel Mayoral , Wen Hsiang , Kim Ji Young , Simoni Aaron , Mapuskar Kranti A. , Rastogi Prerna , Steinbach Emily J , McCormick Michael L. , Allen Bryan G. , Pabla Navjot S. , Jackson Ashley R. , Coleman Mitchell C. , Spitz Douglas R. , Taylor Eric B. , Zepeda-Orozco Diana 
Published: February 2023

ABSTRACTEnergy-intensive kidney reabsorption processes essential for normal whole-body function are maintained by tubular epithelial cell metabolism. Tubular metabolism changes markedly following acute kidney injury (AKI), but which changes are adaptive versus maladaptive remain poorly understood. In publicly available data sets, we noticed a consistent downregulation of the mitochondrial pyruvate carrier (MPC) after AKI, which we experimentally confirmed. To test the functional consequences of MPC downregulation, we generated novel tubular epithelial cell-specificMpc1knockout (MPC TubKO) mice.13C-glucose tracing, steady-state metabolomic profiling, and enzymatic activity assays revealed that MPC TubKO coordinately increased activities of the pentose phosphate pathway and the glutathione and thioredoxin oxidant defense systems. Following rhabdomyolysis-induced AKI, MPC TubKO decreased markers of kidney injury and oxidative damage and strikingly increased survival. Our findings suggest that decreased mitochondrial pyruvate uptake is a central adaptive response following AKI and raise the possibility of therapeutically modulating the MPC to attenuate AKI severity.
Wolbachia-infected pharaoh ant colonies have higher egg production, metabolic rate, and worker survival
Authors: Singh Rohini , Suresh Sachin , Fewell Jennifer H. , Harrison Jon F. , Linksvayer Timothy A. 
Published: February 2023

AbstractWolbachiais a widespread endosymbiotic bacteria with diverse phenotypic effects on its insect hosts.Wolbachiaalso commonly infects social insects, where it faces unique challenges associated with its hosts’ caste-based reproductive division of labor and colony living. Here we dissect the benefits and costs ofWolbachiainfection on life-history traits of pharaoh ants,Monomorium pharaonis. Pharaoh ants are relatively short-lived and show natural variation inWolbachiainfection between colonies, thereby making them an ideal model system for this study. We quantified effects on the lifespan of queen and worker castes, the egg-laying rate of queens across queen lifespan, and the metabolic rates of whole colonies and colony members. Newly-infected queens laid more eggs than uninfected queens but had similar metabolic rates and lifespans. Surprisingly, infected workers outlived uninfected workers. Infected colonies were more productive due to increased queen egg-laying rates and worker longevity, and infected colonies had higher metabolic rates during peak colony productivity. While some effects of infection, such as elevated colony-level metabolic rates may be detrimental in more stressful conditions, we did not find any costs of infection under laboratory conditions. Overall, our study emphasizes the beneficial effects ofWolbachiaon colony-level growth and metabolism in this species.