bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gemini NIFS survey of feeding and feedback processes in nearby active galaxies – VI. Stellar populations
Authors: Riffel Rogério , Dahmer-Hahn Luis G , Riffel Rogemar A , Storchi-Bergmann Thaisa , Dametto Natacha Z , Davies Richard , Burtscher Leonard , Bianchin Marina , Ruschel-Dutra Daniel , Ricci Claudio , Rosario David J 
Published: March 2022

ABSTRACT
We use Gemini Near-Infrared Integral Field Spectrograph (NIFS) adaptive optics assisted data cubes to map the stellar population of the inner few hundred parsec of a sample of 18 nearby Seyfert galaxies. The near-infrared light is dominated by the contribution of young to intermediate-age stellar populations, with light-weighted mean ages ‹t›L ≲ 1.5 Gyr. Hot dust (HD) emission is centrally peaked (in the unresolved nucleus), but it is also needed to reproduce the continuum beyond the nucleus in nearly half of the sample. We have analysed the stellar population properties of the nuclear region and their relation with more global properties of the galaxies. We find a correlation between the X-ray luminosity and the contributions from the HD, featureless continuum (FC), and reddening AV. We attribute these correlations to the fact that all these properties are linked to the mass accretion rate to the active galactic nuclei (AGNs). We also find a correlation of the bolometric luminosity log($L_{\rm Bol_{\rm obs}}$) with the mass-weighted mean age of the stellar population, interpreted as due a delay between the formation of new stars and the triggering/feeding of the AGN. The gas reaching the supermassive black hole is probably originated from mass loss from the already somewhat evolved intermediate-age stellar population (‹t›L ≲ 1.5 Gyr). In summary, our results show that there is a significant fraction of young to intermediate-age stellar populations in the inner few 100 pc of active galaxies, suggesting that this region is facing a rejuvenation process in which the AGN, once triggered, precludes further star formation, in the sense that it can be associated with the lack of new star formation in the nuclear region.
Out of the blue: Phototropins of the leaf vascular bundle sheath mediate the regulation of leaf hydraulic conductance by blue light
Authors: Grunwald Yael , Gosa Sanbon Chaka , Torne-Srivastava Tanmayee , Moran Nava , Moshelion Menachem 
Published: March 2022

Abstract
The Arabidopsis (Arabidopsis thaliana) leaf veins bundle-sheath cells (BSCs)—a selective barrier to water and solutes entering the mesophyll—increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs’ expression of phototropins PHOT1 and PHOT2, and the known blue light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs’ phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5 phot2-1, and aha2-4 was lower than that of the wild-type (WT). BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light—ineffective in the phot1-5 mutant—acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts’ water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance.
X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Authors: Macungo Zanildo , Benoit Julien , Fernandez Vincent , Araújo Ricardo M N 
Published: March 2022

AbstractEmydopoidea is one of the major dicynodont subclades and includes some purported fossorial taxa. Various cranial and postcranial adaptations for fossoriality have long been recognized in cistecephalid emydopoids, but anatomical variation of their braincases remains poorly understood. Here, using laboratory and synchrotron X-ray tomography, we provide detailed anatomical descriptions of the basicranial axis of three emydopoids (Myosaurus, Kawingasaurus and a Malawian cistecephalid DMMM-PK-16-1) and compare them to the basal dicynodont Pristerodon. Cistecephalids show the presence of divergent crests on the posterior aspect of the opisthotic and a nuchal crest on their occipital plate, contrasting with the featureless occipital plate of other dicynodonts. These depressions and crests increase the attachment area of the atlanto-occipital muscles, suggesting that cistecephalids were capable of powerful movements of the head during digging. Additionally, Kawingasaurus has a pneumatized braincase and highly co-ossified basicranium, which is probably linked to the auditory system. We corroborate the hypothesis that cistecephalids, in addition to being forelimb diggers, were likely head-lift diggers, and we highlight some derived adaptations consistent with a quasi-obligate fossorial lifestyle. Furthermore, new basicranial phylogenetic characters and a re-evaluation of emydopoid relationships are proposed. We recovered Rastodon as a basal emydopoid, Thliptosaurus as a non-kingoriid emydopoid and novel interrelationships among cistecephalids.
The Olfm4-defined human neutrophil subsets differ in proteomic profile in septic shock
Authors: Lundquist Hans , Andersson Henrik , Chew Michelle S. , Das Jyotirmoy , Turkina Maria V. , Welin Amanda 
Published: March 2022

AbstractThe specific granule glycoprotein olfactomedin-4 (Olfm4) marks a constitutive subset of neutrophils in humans, where 1-70% of peripheral blood neutrophils produce Olfm4. The proportion of Olfm4-high (Olfm4-H) neutrophils correlates with the severity of paediatric septic shock and could predict mortality in adult septic shock in previous studies, but it is not known whether and how the Olfm4-H neutrophils contribute to sepsis pathogenesis. The aim of this study was to decipher proteomic differences between the Olfm4-H and Olfm4-low (Olfm4-L) human neutrophil subsets at baseline and in the context of septic shock, hypothesizing that Olfm4 marks a neutrophil subset with a distinct proteomic profile, predisposing it for detrimental processes in sepsis. A novel protocol for the preparation of fixed, antibody-stained and sorted neutrophils for LC-MS/MS analysis of proteome was developed. In neutrophil subsets from healthy blood donors, 47 proteins had significantly higher abundance in the Olfm4-H population, and 62 proteins in the Olfm4-L population. Pathway enrichment analysis showed that the differences concerned proteins related to neutrophil degranulation, with e.g. Rab3d and a subunit of the vacuolar ATPase proton pump being more abundant in the Olfm4-H neutrophils, and the alarmin S100-A7, the major neutrophil chemotactic receptor CXCR1 and the antimicrobial peptide defensin alpha-4 being more abundant in the Olfm4-L neutrophils. The data suggest different preparedness to infection in the subsets. In the limited material analysed here, there was no significant correlation between the severity of sepsis and the proportion of Olfm4-H neutrophils, but an increased concentration of Olfm4 in plasma from septic shock patients as compared to healthy blood donors was observed. Furthermore, in neutrophil subsets isolated from septic shock patients, 28 proteins had significantly higher abundance in the Olfm4-H subset and 38 in the Olfm4-L subset, the latter including e.g. Fc receptor proteins and MHC class I molecules, suggesting distinct immunological responses. This is the first report pointing towards differential functions of the Olfm4-defined neutrophil subpopulations in humans and the data are consistent with the idea of distinct responses in the subsets during infection and inflammation.
Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite
Authors: Harrison Mark C. , Dohmen Elias , George Simon , Sillam-Dussès David , Séité Sarah , Vasseur-Cognet Mireille 
Published: March 2022

AbstractThe reproductive castes of eusocial insects are often characterised by extreme lifespans and reproductive output, indicating an absence of the fecundity/longevity trade-off. The role of DNA methylation in the regulation of caste- and age-specific gene expression in eusocial insects is controversial. While some studies find a clear link to caste formation in honeybees and ants, others find no correlation when replication is increased across independent colonies. Although recent studies have identified transcription patterns involved in the maintenance of high reproduction throughout the long lives of queens, the role of DNA methylation in the regulation of these genes is unknown. We carried out a comparative analysis of DNA methylation in the regulation of caste-specific transcription and its importance for the regulation of fertility and longevity in queens of the higher termite, Macrotermes natalensis. We found evidence for significant, well-regulated changes in DNA methylation in mature compared to young queens, especially in several genes related to ageing and fecundity in mature queens. We also found a strong link between methylation and caste-specific alternative splicing. This study reveals a complex regulatory role of fat body DNA methylation both in the division of labour in termites, and during the reproductive maturation of queens.
G-matrix stability in clinally diverging populations of an annual weed
Authors: Henry Georgia Alexandria , Stinchcombe John R 
Published: March 2022

AbstractHow phenotypic and genetic divergence among populations is influenced by the genetic architecture of those traits, and how microevolutionary changes in turn affect the within-population patterns of genetic variation, are of major interest to evolutionary biology. Work on Ipomoea hederacea, an annual vine, has found genetic clines in the means of a suite of ecologically important traits, including flowering time, growth rate, seed mass, and corolla width. Here we investigate the genetic (co)variances of these clinally varying traits in two northern range-edge and two central populations of Ipomoea hederacea to evaluate the influence of the genetic architecture on divergence across the range. We find 1) limited evidence for clear differentiation between Northern and Southern populations in the structure of G, suggesting overall stability of G across the range despite mean trait divergence and 2) that the axes of greatest variation (gmax) were unaligned with the axis of greatest multivariate divergence. Together these results indicate the role of the quantitative genetic architecture in constraining evolutionary response and divergence among populations across the geographic range.
Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?
Authors: Voutsinos Marcos Y. , West-Roberts Jacob A. , Sachdeva Rohan , Moreau John W. , Banfield Jillian F. 
Published: March 2022

AbstractPrior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for the release of phosphate to the biosphere, yet the microorganisms involved, and the genes required for lanthanide metabolism, are poorly understood. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilization and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found gene clusters implicated in lanthanide-based metabolism of methanol (primarily XoxF3 and XoxF5) are surprisingly common in microbial communities in moderately weathered granite where lanthanide phosphate minerals are dissolving. Notably, XoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes, and Alphaproteobacteria. The XoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied XoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilize lanthanide phosphates, it is notable that candidate siderophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. We conclude that the confluence in the zone of moderate weathering of phosphate mineral dissolution, lanthanide utilisation, and methanol oxidation (thus carbonic acid production) may be important during the conversion of granitic rock to soil.
Modeling within-host and aerosol dynamics of SARS-CoV-2: the relationship with infectiousness
Authors: Heitzman-Breen Nora , Ciupe Stanca M. 
Published: March 2022

AbstractThe relationship between transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the amount of virus present in the proximity of a susceptible host is not understood. Here, we developed a within-host and aerosol mathematical model and used it to determine the relationship between viral kinetics in the upper respiratory track, viral kinetics in the aerosols, and new transmissions in golden hamsters challenged with SARS-CoV-2. We determined that infectious virus shedding early in infection correlates with transmission events, shedding of infectious virus diminishes late in the infection, and high viral RNA levels late in the infection is a poor indicator of transmission. We further showed that viral infectiousness increases in a density dependent manner with viral RNA and that their relative ratio is time-dependent. Such information is useful for designing interventions.Author summaryQuantifying the relationship between SARS-CoV-2 dynamics in upper respiratory tract and in aerosols is key to understanding SARS-CoV-2 transmission and evaluating intervention strategies. Of particular interest is the link between the viral RNA measured by PCR and a subject’s infectiousness. Here, we developed a mechanistic model of viral transmission in golden hamsters and used data in upper respiratory tract and aerosols to evaluate key within-host and environment based viral parameters. The significance of our research is in identifying the timing and duration of viral shedding, how long it stays infectious, and the link between infectious virus and total viral RNA. Such knowledge enhances our understanding of the SARS-CoV-2 transmission window.
The therapeutic potential of D-Serine in reducing expression of the cytopathic genotoxin colibactin
Authors: Hallam Jennifer C , O’Boyle Nicky , Turner Natasha C A , Tang-Fichaux Min , Oswald Eric , Roe Andrew J 
Published: March 2022

AbstractSome Escherichia coli strains belonging mainly to the B2 phylogroup harbour the pks island, a 54 kb genomic island encoding the biosynthesis genes for a genotoxic compound named colibactin. In eukaryotic cells, colibactin can induce DNA damage, cell cycle arrest and chromosomal instability. Moreover, production of colibactin has been implicated in the development of colorectal cancer. In this study, we demonstrate the inhibitory effect of D-Serine on the expression of the pks island in two colibactin-producing strains, CFT073 and Nissle 1917, and determine the implications for cytopathic effects on host cells. To investigate the specificity of the inhibitory effect of D-Serine, we also tested a comprehensive panel of proteinogenic L-amino acids and corresponding D-enantiomers for their ability to modulate clbB transcription using RT-qPCR. Several D-amino acids exhibited the ability to inhibit expression of clbB, with D-Serine exerting the strongest repressing activity (3.81-fold in CFT073; 3.80-fold in Nissle 1917) and thus, we focussed additional experiments on D-Serine. To investigate the cellular effect, we investigated if repression of colibactin by D-Serine could reduce the cytopathic responses normally observed during infection of HeLa cells with pks+ strains. Levels of γ-H2AX (a marker of DNA double strand breaks) were reduced 2.75-fold in cells infected with D-Serine treatment. Moreover, exposure of pks+E. coli to D-Serine during infection caused a reduction in cellular senescence that was observable at 72 h post infection. The recent finding of an association between pks-carrying commensal E. coli and CRC, highlights the necessity for the development of colibactin targeting therapeutics. Here we show that D-Serine can reduce expression of colibactin, and inhibit downstream cellular cytopathy, illuminating its therapeutic potential to prevent colibactin-associated disease.
Identification of a new Inovirus in the absence of bacterial infection in the human virome
Authors: Popgeorgiev Nikolay , Krupovic Mart , Hiblot Julien , Fancello Laura , Monteil-Bouchard Sonia , Desnues Christelle 
Published: March 2022

AbstractViruses infecting bacteria, known as bacteriophages, represent the most abundant viral particles in the human body. They participate in the control of the human associated bacterial communities and play an important role in the dissemination of virulence genes. Here we present the identification of a new genetic element, named RIP1, in the human virome. RIP1 shares conserved structural genes with the single-stranded DNA viruses of the Inoviridae family. Furthermore structure-function studies identified nuclear subcellular localization of the RIP1 DNA replication/recombination machinery. Additional metagenomics analysis and polymerase chain reaction detected RIP1 in multiple body sites including blood, cerebrospinal pericardial and amniotic fluids, nasal swabs and feces in the absence of concomitant bacterial infection, uncovering inovirus phage persistence in the human virome.
A web-based histology atlas for the freshwater sentinel speciesDaphnia magna
Authors: Ngu Mee S. , Vanselow Daniel J. , Zaino Carolyn R. , Lin Alex Y. , Copper Jean E. , Beaton Margaret J. , Orsini Luisa , Colbourne John K. , Cheng Keith C. , Ang Khai C. 
Published: March 2022

AbstractDaphniaare keystone species of freshwater habitats used as model organisms in ecology and evolutionary biology. Their small size, wide geographic distribution, and sensitivity to chemicals make them useful as environmental sentinels in regulatory toxicology and chemical risk assessment. Biomolecular (-omic) assessments of responses to chemical toxicity, which reveal detailed molecular signatures, become more powerful when correlated with other phenotypic outcomes (such as behavioral, physiological, or histopathological) for comparative validation and regulatory relevance. However, the lack of histopathology or tissue phenotype characterization of this species presently limits our ability to access cellular mechanisms of toxicity. Here, we address the central concept that interpreting aberrant tissue phenotypes requires a basic understanding of species normal microanatomy. We introduce the female and maleDaphniaHistologyReferenceAtlas (DaHRA) for the baseline knowledge ofDaphnia magnamicroanatomy. Additionally, we also included developmental stages of femaleDaphniain this current atlas. This interactive web-based resource of adultDaphniafeatures overlaid vectorized demarcation of anatomical structures whose labels comply with an anatomical ontology created for this atlas. We demonstrate the potential utility of DaHRA for toxicological investigations by presenting aberrant phenotypes of acetaminophen-exposedD. magna. We envision DaHRA to facilitate the effort of integrating molecular and phenotypic data from the scientific community as we seek to understand how genes, chemicals, and environment interactions determine organismal phenotype.
Emergent periodicity in the collective synchronous flashing of fireflies
Authors: Sarfati Raphaël , Joshi Kunaal , Martin Owen , Hayes Julie C. , Iyer-Biswas Srividya , Peleg Orit 
Published: March 2022

AbstractIn isolation from their peers,Photinus carolinusfireflies flash with no intrinsic period between successive bursts. Yet, when congregating into large mating swarms, these fireflies transition into predictability, synchronizing with their neighbors with a rhythmic periodicity. Here we propose a mechanism for emergence of synchrony and periodicity, and formulate the principle in a mathematical framework. Remarkably, with no fitting parameters, analytic predictions from this simple principle and framework agree strikingly well with data. Next, we add further sophistication to the framework using a computational approach featuring groups of random oscillators via integrate-and-fire interactions controlled by a tunable parameter. This agent-based framework ofP. carolinusfireflies interacting in swarms of increasing density also shows quantitatively similar phenomenology and reduces to the analytic framework in the appropriate limit of the tunable coupling strength. We discuss our findings and note that the resulting dynamics follow the style of a decentralized follow-the-leader synchronization, where any of the randomly flashing individuals may take the role of the leader of any subsequent synchronized flash burst.