bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others
Authors: Gilbert Donald G. 
Published: December 2023

AbstractSignificant discrepancies in genome sizes measured by cytometric methods versus DNA sequence estimates are frequent, including recent long-read DNA assemblies of plant and animal genomes. A new DNA sequence measure using a baseline of unique conserved genes, Gnodes, finds the larger cytometric measures are often accurate. DNA-informatic measures of size, as well as assembly methods, have errors in methodology that under-measure duplicated genome spans.Major contents of several model and discrepant genomes are assessed here, including human, corn, chicken, insects, crustaceans, and the model plant. Transposons dominate larger genomes, structural repeats are often a major portion of smaller ones. Gene coding sequences are found in similar amounts across the taxonomic spread. The largest contributors to size discrepancies are higher-order repeats, but duplicated coding sequences are a significant missed content, and transposons in some examined species.Informatics of measuring DNA and producing assemblies, including recent long-read telomere to telomere approaches, are subject to mistakes in operation and/or interpretation that are biased against repeats and duplications. Mistaken aspects include alignment methods that are inaccurate for high-copy duplicated spans; misclassification of true repetitive sequence as heterozygosity and artifact; software default settings that exclude high-copy DNA; and overly conservative data processing that reduces duplicated genomic spans. Re-assemblies with balanced methods recover the missing portions of problem genomes including model plant, water fleas and fire ant.
Single cell transcriptomics reveals chondrocyte differentiation dynamicsin vivoandin vitro
Authors: Lawrence John E G , Woods Steven , Roberts Kenny , Sumanaweera Dinithi , Balogh Petra , Predeus Alexander V , He Peng , Li Tong , Polanski Krzysztof , Prigmore Elena , Tuck Elizabeth , Mamanova Lira , Zhou Di , Webb Simone , Jardine Laura , He Xiaoling , Barker Roger A , Haniffa Muzlifah , Flanagan Adrienne M , Young Matthew D , Behjati Sam , Bayraktar Omer , Kimber Susan J , Teichmann Sarah A 
Published: December 2023

SummaryThe consistent production ofin vitrochondrocytes that faithfully recapitulatein vivodevelopment would be of great benefit for musculoskeletal disease modelling and regenerative medicine. Current efforts are often limited by off-target differentiation, resulting in a heterogeneous product. Furthermore, the lack of comparison to human embryonic tissue, precludes detailed evaluation ofin vitrocells. Here, we perform single-cell RNA sequencing of embryonic long bones dissected from first trimester hind limbs from a range of gestational ages. We combine this with publicly available data to form a detailed atlas of endochondral ossification, which we then use to evaluate a series of publishedin vitrochondrogenesis protocols, finding substantial variability in cell states produced by each. We apply single-nuclear RNA sequencing to one protocol to enable direct comparison betweenin vitroandin vivo,and perform trajectory alignment between the two to reveal differentiation dynamics at the single-cell level, shedding new light on off-target differentiationin vitro. Using this information, we inhibit the activity of FOXO1, a transcription factor predicted to be active in embryonic bone development and in chondrogenic cellsin vitro, and increase chondrocyte transcriptsin vitro.This study therefore presents a new framework for evaluating tissue engineering protocols, using single-cell data from human development to drive improvement and bring the prospect of true engineered cartilage closer to reality.
Inactivation of p53 drives breast cancer brain metastasis by altering fatty acid metabolism
Authors: Laue Kathrin , Pozzi Sabina , Cohen-Sharir Yael , Winkler Tom , Eliezer Yonatan , Israeli Dangoor Sahar , Leikin-Frenkel Alicia I. , Lange Katharina , Zerbib Johanna , Ricci Alessia A. , Sacconi Andrea , Berthelet Jean , Schäffer Alexander , Shi Wei , Liao Yang , Barshack Iris , Medyouf Hind , Merino Delphine , Blandino Giovanni , Bertero Luca , Satchi-Fainaro Ronit , Ben-David Uri 
Published: December 2023

AbstractBrain metastasis (BM) is a dire prognosis across cancer types. It is largely unknown why some tumors metastasize to the brain whereas others do not. We analyzed genomic and transcriptional data from clinical samples of breast cancer BM (BCBM) and found that nearly all of them carried p53-inactivating genetic alterations through mutations, copy-number loss, or both. Importantly, p53 pathway activity was already perturbed in primary tumors giving rise to BCBM, often by loss of the entire 17p chromosome-arm. This association was recapitulated across other carcinomas. Experimentally, p53 knockout was sufficient to drastically increase BCBM formation and growthin vivo, providing a causal link between p53 inactivation and brain tropism. Mechanistically, p53-deficient BC cells exhibited altered lipid metabolism, particularly increased fatty acid (FA) synthesis and uptake, which are characteristic of brain-metastasizing cancer cells. FA metabolism was further enhanced by astrocytes in a p53-dependent manner, as astrocyte-conditioned medium increased FASN, SCD1, and CD36 expression and activity, and enhanced the survival, proliferation and migration of p53-deficient cancer cells. Consequently, these cells were more sensitive than p53-competent cells to FA synthesis inhibitors, in isogenic cell cultures, in BCBM-derived spheroids, and across dozens of BC cell lines. Lastly, a significant association was observed between p53 inactivation, astrocyte infiltration, and SCD1 expression in clinical human BCBM samples. In summary, our study identifies p53 inactivation as a driver of BCBM and potentially of BM in general; suggests a p53-dependent effect of astrocytes on BC cell behavior; and reveals FA metabolism as an underlying, therapeutically-targetable molecular mechanism.
Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19
Authors: Lee Jimmy Tsz Hang , Barnett Sam N. , Roberts Kenny , Ashwin Helen , Milross Luke , Cho Jae-Won , Huseynov Alik , Woodhams Benjamin , Aivazidis Alexander , Li Tong , Majo Joaquim , Guerrero Patricia Chaves , Lee Michael , Miranda Antonio M. A. , Jablonska Zuzanna , Arena Vincenzo , Hanley Brian , Osborn Michael , Uhlmann Virginie , Xu Xiao-Ning , McLean Gary R , Teichmann Sarah A. , Randi Anna M. , Filby Andrew , Kaye Paul M. , Fisher Andrew J. , Hemberg Martin , Noseda Michela , Bayraktar Omer Ali 
Published: December 2023

AbstractThe most common cause of death due to COVID-19 remains respiratory failure. Yet, our understanding of the precise cellular and molecular changes underlying lung alveolar damage is limited. Here, we integrate single cell transcriptomic data of COVID-19 donor lungs with spatial transcriptomic data stratifying histopathological stages of diffuse alveolar damage (DAD). We identify changes in cellular composition across progressive DAD, including waves of molecularly distinct macrophages and depleted epithelial and endothelial populations throughout different types of tissue damage. Predicted markers of pathological states identify immunoregulatory signatures, including IFN-alpha and metallothionein signatures in early DAD, and fibrosis-related collagens in organised DAD. Furthermore, we predict a fibrinolytic shutdown via endothelial upregulation ofSERPINE1/PAI-1. Cell-cell interaction analysis revealed macrophage-derivedSPP1/osteopontin signalling as a key regulator during early DAD. These results provide the first comprehensive, spatially resolved atlas of DAD stages, highlighting the cellular mechanisms underlying pro-inflammatory and pro-fibrotic pathways across alveolar damage progression.
Exploration of the intricacies of low light-induced changes in cigar tobacco leaf anticlinal growth: A holistic approach from anatomical and hormonal levels to gene expression
Authors: Ma Xinghua , Yang Jinpeng , Ren Xiaochun , Chen Keling , Yang Chunlei , Gao Huajun , Khan Rayyan 
Published: December 2023

AbstractCigar tobacco stands as a pivotal economic crop, with its leaf growth and development profoundly influenced by light intensity. It specifically aims to investigate how leaf morphology and anticlinal growth respond to varying light intensities, including normal light intensity (NL–300 μmol m−2s−1) and lower light intensity (LL–100 μmol m−2s−1). The research elucidates significant morphological shifts in cigar tobacco leaves under LL, revealing notable alterations in leaf area, leaf length, and leaf width. Early reductions in leaf dimensions, ranging from 30% to 48%, were succeeded by a substantial enhancement in expansion rates from day 9 to day 26, contributing to expanded leaf surfaces at later stages. Upper epidermis thickness declined by 29-19%, with a notably slower expansion rate in the initial 20 days. Palisade cell length consistently decreased by 52-17%, corresponding with upper epidermis trends. Spongy tissue thickness was reduced by 31-12%, with a slower expansion rate in LL for the initial 14 days, and leaf thickness dropped by 34-11%. LL resulted in slower leaf anticlinal expansion, leading to reduced leaf thickness (LT). LL significantly influenced phytohormones in cigar tobacco leaves. Gibberellic acid (41% to 16%) and auxin (20% to 35%) levels were found in higher amounts, while cytokinin levels (19% to 5%) were lowered compared to NL, indicating the intricate regulatory role of light in hormonal dynamics. The observed increase in LT and different cell layers at specific time points (day 8, day 12, day 24, and day 28) under LL, although lower than NL, may be attributed to elevated expression of genes related to cell expansion, includingGRF1,XTH, andSAUR19at those time points. This comprehensive understanding elucidates the intricate mechanisms by which light intensity orchestrates the multifaceted processes governing leaf anatomy and anticlinal expansion in cigar tobacco plants.
Hepatitis B virus neutralization with DNA origami nanoshells
Authors: Willner Elena M. , Kolbe Fenna , Momburg Frank , Protzer Ulrike , Dietz Hendrik 
Published: December 2023

AbstractWe demonstrate the use of DNA origami to create virus-trapping nanoshells that efficiently neutralize hepatitis B virus (HBV) in cell culture. By modifying the shells with a synthetic monoclonal antibody that binds to theHBVenvelope, the effective neutralization potency per antibody is increased by approximately 100 times compared to using free antibodies. The improvements in neutralizing the virus are attributed to two factors: first, the shells act as a physical barrier that block the virus from interacting with host cells; second, the multivalent binding of the antibodies inside the shells lead to stronger attachment to the trapped virus, a phenomenon known as avidity. Pre-incubation of shells withHBVand simultaneous addition of both components separately to cells lead to comparable levels of neutralization, indicating rapid trapping of the virions by the shells. Our study highlights the potential of the DNA shell system to rationally create novel antivirals using components that, when used individually, show little to no antiviral effectiveness.
A common druggable signature of oncogenic CMYC, mutant KRAS and mutant p53 reveals functional redundancy and competition of the oncogenes in cancer
Authors: Grześ Maria , Jaiswar Akanksha , Grochowski Marcin , Wojtyś Weronika , Kaźmierczak Wojciech , Olesiński Tomasz , Lenarcik Małgorzata , Nowak-Niezgoda Magdalena , Kołos Małgorzata , Canarutto Giulia , Piazza Silvano , Wiśniewski Jacek R. , Walerych Dawid 
Published: December 2023

AbstractMajor driver oncogenesCMYC, mutantKRAS and mutantTP53often co-exist and cooperate in promoting human neoplasia. By CRISPR-Cas9-mediated downregulation we determined their proteomics and transcriptomics downstream programs in a panel of cell lines with activated either single or three oncogenes – in cancers of lung, colon and pancreas. This allowed to define and screen the oncogenes’ common functional program for anti-cancer target candidates, and find protocols which efficiently kill cancer cells and organoids by targeting pathways represented by a signature of three genes:RUVBL1, HSPA9andXPO1. We found that these genes were controlled by the driver oncoproteins in a redundant or competitive manner, rather than by cooperation. Each oncoprotein individually was able to upregulate the three target genes, while upon oncogene co-expression each target was controlled preferably by a specific oncoprotein which reduced the influence of the others. Mechanistically this redundancy was mediated by parallel routes of the target gene activation – as in the case of mutant KRAS signaling to C-JUN and GLI-2 transcription factors bypassing CMYC, and by competition – as in the case of mutant p53 and CMYC competing for biding to the target promoters. The transcriptomics data from the cell lines and patient samples indicate that the redundancy of the oncogenic programs is a broad phenomenon which may comprise even a majority of the genes dependent on the oncoprotein, as shown for mutant p53 in colon and lung cancer cell lines. Nevertheless, we demonstrate that the redundant oncogene programs harbor targets of efficient anti-cancer drug combinations, bypassing limitations of a direct oncoprotein inhibition.
The developing pig respiratory microbiome harbours strains antagonistic to common respiratory pathogens
Authors: Vlasblom Abel A. , Duim Birgitta , Patel Shriram , Luiken Roosmarijn E. C. , Crespo-Piazuelo Daniel , Eckenberger Julia , Huseyin Chloe E. , Lawlor Peadar G. , Elend Christian , Wagenaar Jaap A. , Claesson Marcus J. , Zomer Aldert L. 
Published: December 2023

AbstractIn the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until ten weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 time-points on nine farms in three European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as thetufgene for itsStaphylococcaldiscrimination power. The piglets’ age, the farm, and the litter affected the nasal microbiome, with piglets’ age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around two weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and faecal microbiomes shape the piglet nasal microbiome. We identified bacterial Co-Abundance Groups (CAGs) of species that were present in the nasal microbiomes in all three countries over time. Anticorrelation between these species and known bacterial pathogens identified strains that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the longitudinal development and factors influencing the piglet nasal microbiome, providing insights into its role in health and disease.ImportanceOur study on longitudinal analysis of the developing nasal microbiota of piglets in farms in three European countries showed consistent microbiome compositions and that colonization of porcine pathogens occurred in relation with anticorrelating species. These findings enhance our knowledge of co-colonizing species in the nasal cavity, and the identified microbial interactions can be explored for the development of interventions to control pathogens in porcine husbandry.
High Resolution Outdoor Videography of Insects Using Fast Lock-On Tracking
Authors: Vo-Doan T. Thang , Titov Victor V. , Harrap Michael J.M. , Lochner Stephan , Straw Andrew D. 
Published: December 2023

AbstractInsects have significant global impacts on ecology, economy, and health and yet our understanding of their behavior remains limited. Bees, for example, use vision and a tiny brain to find flowers and return home, but understanding how they perform these impressive tasks has been hampered by limitations in recording technology. Here we present Fast Lock-On (FLO) tracking. This method moves an image sensor to remain focused on a retroreflective marker affixed to an insect. Using paraxial infrared illumination, simple image processing can localize the sensor location of the insect in a few milliseconds. When coupled with a feedback system to steer a high magnification optical system to remain focused on the insect, a high spatial-temporal resolution trajectory can be gathered over a large region. As the basis for several robotic systems, we show FLO is a versatile idea which can be employed in combination with other components. We demonstrate that the optical path can be split and used for recording high-speed video. Furthermore, by flying a FLO system on a quadcopter drone, we track a flying honey bee and anticipate tracking insects in the wild over kilometer scales. Such systems have the capability of providing higher resolution information about insects behaving in natural environments and as such will be helpful in revealing the biomechanical and neuroethological mechanisms used by insects in natural settings.One-Sentence SummaryFast Lock-On tracking enables recording trajectories and high-speed videos of insects behaving over large areas in the wild.
Horizontal transfer and recombination fuel Ty4 retrotransposon evolution inSaccharomyces
Authors: Chen Jingxuan , Garfinkel David J. , Bergman Casey M. 
Published: December 2023

AbstractHorizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely-related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genusSaccharomycesusing short- and long-read whole genome sequence data, including new PacBio genome assemblies for twoS. mikataestrains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages ofS. paradoxus,S. cerevisiae,S. eubayanus,S. kudriavzeviiand the ancestor of theS. mikatae/S. jureispecies pair. In bothS. mikataeandS. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally-transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genusSaccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon cladesviarecombination.
Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates
Authors: Rossio Valentina , Paulo Joao A. , Liu Xinyue , Gygi Steven P. , King Randall W. 
Published: December 2023

SummaryDeubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs inXenopusegg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high impact DUBs (USP7, USP9X, USP36, USP15 and USP24) that each reduced ubiquitylation of over ten percent of the isolated proteins. Candidate substrates of high impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.
The endemic plant species of Ebo Forest, Littoral Region, Cameroon with a new Critically Endangered cloud forest shrub,Memecylon ebo(Melastomataceae-Olisbeoideae)
Authors: Stone Robert Douglas , Tchiengué Barthelemy , Cheek Martin 
Published: December 2023

SummaryWe emphasise the urgent need to conserve the Ebo forest (Littoral Region, Cameroon), which holds 10 strict endemic plant species and 15 near endemics for a total of 25, a very high number far exceeding the threshold for its recent status as an Important Plant Area (IPA). We describe a further strict endemic species from the Ebo Forest,Memecylon ebosp. nov. (Melastomataceae-Olisbeoideae) placed in sect.Afzelianadue to its ellipsoid blue-green fruits. The yellow petals and jade green anther-connectives ofM. eboare unique in the genusMemecylonas a whole, among its >400 species ranging overall from Africa to the western Pacific.Memecylon ebois assessed as Critically Endangered (CR) using the 2012 IUCN standard due to the small range size and the extremely high and ongoing threats of logging at Ebo, and also due to subsequent threats of potential oil palm plantation and mining projects. With the addition ofMemecylon ebo, the tally of Critically Endangered plant species recorded from Ebo forest is now the highest of any IPA in Cameroon, equalling that of, Ngovayang with 24 CR species.
Real-time measurements of ATP dynamics via ATeams inPlasmodium falciparumreveal drug-class-specific response patterns
Authors: Springer Eric , Heimsch Kim C. , Rahlfs Stefan , Becker Katja , Przyborski Jude M. 
Published: December 2023

AbstractMalaria tropica, caused by the parasitePlasmodium falciparum(P. falciparum) remains one of the greatest public health burdens for humankind. Due to its pivotal role in parasite survival, the energy metabolism ofP. falciparumis an interesting target for drug design. To this end, analysis of the central metabolite ATP is of great interest. So far, only cell disruptive or intensiometric ATP assays have been available in this system, with various drawbacks for mechanistic interpretation, and partly inconsistent results. To address this, we have established fluorescent probes, based on FRET and known as ATeam, for use in blood stage parasites. ATeams are capable of measuring MgATP2-levels in a ratiometric manner, thereby facilitatingin cellulomeasurements of ATP dynamics in real-time using fluorescence microscopy and plate reader detection, and overcoming many of the obstacles of established ATP analysis methods. Additionally, we established a superfolder variant of the ratiometric pH sensor pHluorin (sfpHluorin) inP. falciparumto monitor pH homeostasis and control for pH fluctuations, which may affect ATeam measurements. We characterized recombinant ATeam and sfpHluorin proteinin vitroand stably integrated the sensors into the genome of theP. falciparumNF54attBcell line. Using these new tools, we found distinct sensor response patterns caused by several different drug classes. Arylamino alcohols increased and redox-cyclers decreased ATP, doxycycline caused first-cycle cytosol alkalization, and 4-aminoquinolines caused aberrant proteolysis. Our results open up a completely new perspective on drugs’ mode of action with possible implications for target identification and drug development.