bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamical control enables the formation of demixed biomolecular condensates
Authors: Lin Andrew Z. , Ruff Kiersten M. , Jalihal Ameya , Dar Furqan , King Matthew R. , Lalmansingh Jared M. , Posey Ammon E. , Seim Ian , Gladfelter Amy S. , Pappu Rohit V. 
Published: January 2023

AbstractMacromolecular phase separation underlies the regulated formation and dissolution of biomolecular condensates. What is unclear is how condensates of distinct and shared macromolecular compositions form and coexist within cellular milieus. Here, we use theory and computation to establish thermodynamic criteria that must be satisfied to achieve compositionally distinct condensates. We applied these criteria to an archetypal ribonucleoprotein condensate and discovered that demixing into distinct protein-RNA condensates cannot be the result of purely thermodynamic considerations. Instead, demixed, compositionally distinct condensates arise due to asynchronies in timescales that emerge from differences in long-lived protein-RNA and RNA-RNA crosslinks. This type of dynamical control is also found to be active in live cells whereby asynchronous production of molecules is required for realizing demixed protein-RNA condensates. We find that interactions that exert dynamical control provide a versatile and generalizable way to influence the compositions of coexisting condensates in live cells.
How random is the review outcome? A systematic study of the impact of external factors oneLifepeer review
Authors: Liang Weixin , Mahowald Kyle , Raymond Jennifer , Krishna Vamshi , Smith Daniel , Jurafsky Daniel , McFarland Daniel , Zou James 
Published: January 2023

AbstractThe advance of science rests on a robust peer review process. However whether or not a paper is accepted can depend on random external factors--e.g. the timing of the submission, the matching of editors and reviewers--that are beyond the quality of the work. This article systematically investigates the impact of these random factors independent of the paper’s quality on peer review outcomes in a major biomedical journal,eLife. We analyzed all of the submissions toeLifebetween 2016 to 2018, with 23,190 total submissions. We examined the effects of random factors at each decision point in the review process, from the gatekeeping senior editors who may desk-reject papers to review editors and reviewers who recommend the final outcome. Our results suggest that the peer-review process ineLifeis robust overall and that random external factors have relatively little quantifiable bias.
In vitroALPK1 kinase assay reveals new insights into ADP-heptose sensing pathway and kinase activity of disease-associated ALPK1 mutants
Authors: García-Weber Diego , Dangeard Anne-Sophie , Teixeira Veronica , Hauke Martina , Carreaux Alexis , Josenhans Christine , Arrieumerlou Cécile 
Published: January 2023

ABSTRACTAlpha-protein kinase 1 (ALPK1) is a pathogen recognition receptor that detects ADP-heptose (ADPH), a lipopolysaccharide biosynthesis intermediate, recently described as a pathogen-associated molecular pattern in Gram-negative bacteria. ADPH binding to ALPK1 activates its kinase domain and triggers TIFA phosphorylation on threonine 9. This leads to the assembly of large TIFA oligomers called TIFAsomes, activation of NF-κB and pro-inflammatory gene expression. Furthermore, mutations inALPK1are associated with inflammatory syndromes and cancers. While this kinase is of growing medical interest, only few tools are available to characterize its activity. Here, we describe a versatile non-radioactive ALPK1in vitrokinase assay based on protein thiophosphorylation. We confirm that ALPK1 phosphorylates TIFA T9 and show that T2, T12 and T19 are also weakly phosphorylated by ALPK1. Interestingly, we find that ALPK1 itself is phosphorylated in response to ADPH recognition duringShigella flexneriandHelicobacter pyloriinfection and that disease-associated ALPK1 mutants exhibit altered kinase activity. In particular, T237M and V1092A mutations associated with ROSAH syndrome and spiradenoma/spiradenocarcinoma respectively, exhibit enhanced ADPH-induced kinase activity and constitutive assembly of TIFAsomes. Altogether, this study provides new insights into the ADPH sensing pathway and a new tool for measuring the activity of ALPK1.
FAXC Proteins of Vertebrates and Invertebrates: Relationship to Metaxin Proteins
Authors: Adolph Kenneth W. 
Published: January 2023

ABSTRACTFAXC proteins of vertebrates and invertebrates are shown to possess structural features similar to the metaxins, and can therefore be categorized as metaxin-like proteins. A variety of vertebrate and invertebrate species were found to encode FAXC (Failed Axon Connections) proteins. These are predicted proteins. Among the vertebrate species are human, mouse, zebrafish, andXenopus. For invertebrates, FAXC proteins were most common in phyla that include Mollusca, Arthropoda, Cnidaria, and Placozoa. The presence of characteristic GST_N_Metaxin and GST_C_Metaxin protein domains was an important criterion in identifying the FAXCs as metaxin-like. In addition, the Tom37 domain was frequently found, especially in vertebrates. Also important was the possession of segments of α-helical secondary structure in a pattern of eight helices like that of metaxin 1 and other metaxins. Both the domain structures and α-helical structures are characteristic metaxin-like features. But alignment of protein sequences of both vertebrate and invertebrate FAXCs with metaxin proteins demonstrated that FAXCs and metaxins have low percentages of identical amino acids, about 20%. Therefore, FAXCs and metaxins are related, but are not the same protein. As revealed by phylogenetic analysis, vertebrate FAXCs and vertebrate metaxins 1, 2, and 3 constitute separate but related groups of proteins. Distinct phylogenetic groups were also observed for invertebrate FAXCs and invertebrate metaxins 1 and 2. The FAXC genes have neighboring genes that differ from the neighboring genes of metaxins. For vertebrates, the genes adjacent to FAXC genes are highly conserved. For invertebrates, the genes that neighbor FAXC genes are not the same as for vertebrates, but are conserved among different invertebrates. Invertebrates can have multiple FAXC genes, up to at least 12 or 13 genes. In some cases, the multiple FAXC genes exist as a cluster of genes in close proximity.
Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories
Authors: Piovani Laura , Leite Daniel J. , Yañez Guerra Luis Alfonso , Simpson Fraser , Musser Jacob M. , Salvador-Martínez Irepan , Marlétaz Ferdinand , Jékely Gáspár , Telford Maximilian J. 
Published: January 2023

AbstractPelagic larval stages are widespread across animals, yet it is unclear if larvae were present in the last common ancestor of animals or whether they evolved multiple times due to common selective pressures. Many marine larvae are at least superficially similar, they are small, swim through beating of ciliated bands and sense the environment with an apical organ structure. To understand these similarities, we have generated single cell atlases for marine larvae from two animal phyla and have compared their cell types. We found clear similarities among ciliary band cells and neurons of the apical organ in the two larvae pointing to possible homology of these structures suggesting a single origin of larvae within the clade analysed here (Lophotrochozoa). We also find several clade specific innovations in each larva, including distinct myocytes and shell gland cells in the oyster larva. Oyster shell gland cells express many novel genes which have made previous gene age estimates for trochophore larvae too young.
Endophytic fungi related to the ash dieback causal agent encode signatures of pathogenicity on European ash
Authors: Rafiqi Maryam , Kosawang Chatchai , Peers Jessica A. , Jelonek Lukas , Yvanne Hélène , McMullan Mark , Nielsen Lene R. 
Published: January 2023

AbstractTree diseases constitute a significant threat to biodiversity worldwide. Pathogen discovery in natural habitats is of vital importance to understanding current and future threats and prioritising efforts towards developing disease management strategies. Ash dieback is a fungal disease of major conservational concern that is infecting common ash trees, Fraxinus excelsior, in Europe. The disease is caused by a non-native fungal pathogen, Hymenoscyphus fraxineus. Other dieback causing-species have not previously been identified in the genus Hymenoscyphus. Here, we discover the pathogenicity potential of two newly identified related species of Asian origin, H. koreanus and H. occultus, and one Europe-native related species, H. albidus. We sequence the genomes of all three Hymenoscyphus species and compare them to that of H. fraxineus. Phylogenetic analysis of core eukaryotic genes identified H. albidus and H. koreanus as sister species, whilst H. occultus diverged prior these and H. fraxineus. All four Hymenoscyphus genomes are of comparable sizes (55-62 Mbp) and GC contents (42–44%) and encode for polymorphic secretomes. Surprisingly, 1,133 predicted secreted proteins are shared between the ash dieback pathogen H. fraxineus and the three related Hymenoscyphus endophytes. Amongst shared secreted proteins are cell death-inducing effector candidates, such as necrosis, and ethylene-inducing peptide 1-like proteins, NLPs, that are upregulated during in planta growth of all Hymenoscyphus species. Indeed, pathogenicity tests showed that all four related Hymenoscyphus species develop pathogenic growth on European ash stems, with native H. albidus being the least virulent. Our results identify the threat Hymenoscypohus species pose to the survival of European ash trees, and highlight the importance of promoting pathogen surveillance in environmental landscapes. Identifying new pathogens and including them in the screening for durable immunity of common ash trees is key to the long-term survival of ash.
Disruption of the standard kinetochore in holocentricCuscutaspecies
Authors: Pavel Neumann , Oliveira Ludmila , Jang Tae-Soo , Novák Petr , Koblížková Andrea , Schubert Veit , Houben Andreas , Macas Jiří 
Published: January 2023

AbstractSegregation of chromosomes depends on the centromere. Most species are monocentric, with the centromere restricted to a single region per chromosome. In some organisms, monocentric organization changed to holocentric, in which the centromere activity is distributed over the entire chromosome length. However, the causes and consequences of this transition are poorly understood. Here, we show that the transition in the genusCuscutawas associated with dramatic changes in the kinetochore, a protein complex that mediates the attachment of chromosomes to microtubules. We found that in holocentricCuscutaspecies the KNL2 genes were lost; the CENP-C, KNL1, and ZWINT1 genes were truncated; the centromeric localization of CENH3, CENP-C, KNL1, MIS12, and NDC80 proteins was disrupted; and the spindle assembly checkpoint (SAC) was degenerated. Our results demonstrate that holocentricCuscutaspecies lost the ability to form a standard kinetochore and do not employ SAC to control the attachment of microtubules to chromosomes.
MitoQuicLy: a high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva
Authors: Michelson Jeremy , Rausser Shannon , Peng Amanda , Yu Temmie , Sturm Gabriel , Trumpff Caroline , Kaufman Brett A. , Rai Alex J. , Picard Martin 
Published: January 2023

AbstractCirculating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy:Mitochondrial DNAQuantification incell-free samples byLysis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 µL of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n=34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.
Loss of NR5A1 in Sertoli cells after sex determination changes their cellular identity and induces their death by anoikis
Authors: Souali-Crespo Sirine , Condrea Diana , Vernet Nadège , Féret Betty , Klopfenstein Muriel , Grandgirard Erwan , Alunni Violaine , Cerciat Marie , Jung Matthieu , Mayere Chloé , Nef Serge , Mark Manuel , Chalmel Frédéric , Ghyselinck Norbert B. 
Published: January 2023

ABSTRACTNR5A1 is an orphan nuclear receptor crucial for gonadal development in mammals. In the mouse testis it is expressed both in Sertoli cells (SC) and Leydig cells (LC). To investigate its role posteriorly to sex determination, we have generated and analysed mice lacking NR5A1 in SC from embryonic day (E) 13.5 onwards (Nr5a1SC−/−mutants). Ablation ofNr5a1impairs the expression of genes characteristic of SC identity (e.g.,Sox9, Amh), makes SC to progressively die from E14.5 by aTrp53-independent mechanism, and induces disorganization of the testis cords, which, together, yields germ cells (GC) to prematurely enter meiosis and die, instead of becoming quiescent. Single-cell RNA-sequencing experiments revealed thatNr5a1-deficient SC acquire a pre-granulosa cell-like identity, and profoundly modify the landscape of the adhesion molecules and extracellular matrix they express. We propose therefore that SC lacking NR5A1 transdifferentiate and die by anoikis. Fetal LC do not display major changes in their transcriptome, indicating that SC are not required beyond E14.5 for their emergence or maintenance. In contrast, adult LC were missing inNr5a1SC−/−postnatal testes. In addition, adult males display Müllerian duct derivatives (i.e., uterus, vagina), as well as a decreased anogenital distance and a shorter penis that can be explained by loss of AMH production and defective HSD17B1- and HSD17B3-mediated synthesis of testosterone in SC during fetal life. Together, our findings indicate thatNr5a1expressed in SC after the period of sex determination safeguards SC identity, which maintains proper seminiferous cord organization and prevents GC to enter meiosis.
Human Brain Endothelial Cell Seeded on Inner Surface of Alginate Hollow Microfibers
Authors: Aykar Saurabh S. , Alimoradi Nima , Petersen Isaac S. , Montazami Reza , Brockman Amanda L. , Hashemi Nicole N. 
Published: January 2023

AbstractBarrier functionality of the blood-brain barrier (BBB) is provided by the tight junctions formed by a monolayer of the human brain endothelial cells (HBECs) internally around the blood capillaries. To mimic such barrier functionality in vitro, replicating the hollow tubular structure of the BBB along with the HBECs monolayer on its inner surface is crucial. Here, we developed an invasive microfluidic technique to obtain the HBECs monolayer on the inner surface of alginate-based hollow microfibers. The HBECs were seeded on the inner surface of these microfibers using a custom-built microfluidic device. The seeded HBECs were monitored for 9 days after manufacturing and cultured to form a monolayer on the inner surface of the alginate hollow microfibers in the maintenance media. A higher cell seeding density of 217 cells/mm length of the hollow microfiber was obtained using our microfluidic technique. Moreover, high accuracy of around 96 % was obtained in seeding cells on the inner surface of alginate hollow microfibers. The microfluidic method illustrated in this study could be extrapolated to obtain a monolayer of different cell types on the inner surface of alginate hollow microfibers with cell-compatible ECM matrix proteins. Furthermore, it will enable us to mimic a range of microvascular systems in vitro by closely replicating the structural attributes of the native structure.
Urban birds become less fearful following COVID-19 reopenings
Authors: Diamant Eleanor S. , MacGregor-Fors Ian , Blumstein Daniel T. , Yeh Pamela J. 
Published: January 2023

AbstractFollowing the COVID-19 pandemic, many people around the world stayed home, drastically altering human activity in cities. This exceptional moment provided researchers the opportunity to test how urban animals respond to human disturbance, in some cases testing fundamental questions on the mechanistic impact of urban behaviors on animal behavior. However, at the end of this “anthropause,” human activity returned to cities. How might each of these strong shifts affect wildlife in the short and long term? We focused on fear response, a trait essential to tolerating urban life. We measured flight initiation distance—at both individual and population-levels—for an urban bird before, during, and after the anthropause to examine if birds experienced longer-term changes after a year of lowered human presence. Dark-eyed juncos did not change fear levels during the anthropause, but they became drastically less fearful afterwards. These surprising and counter-intuitive findings, made possible by following the behavior of individuals over time, has led to a novel understanding that fear response can be driven by plasticity, yet not habituation-like processes. The pandemic-caused changes in human activity have shown that there is great complexity in how humans modify a behavioral trait fundamental to urban tolerance in animals.
High Throughput Viability Assay for Microbiology
Authors: Meyer Christian T. , Lynch Grace K. , Stamo Dana F. , Miller Eugene J. , Chatterjee Anushree , Kralj Joel M. 
Published: January 2023

AbstractCounting viable cells is a universal practice in microbiology. The colony forming unit (CFU) assay has remained the gold standard to measure viability across disciplines; however, it is time-intensive and resource-consuming. Herein, we describe the Geometric Viability Assay (GVA) that replicates CFU measurements over 6-orders of magnitude while reducing over 10-fold the time and consumables. GVA computes a sample’s viable cell count based on the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with gram-positive and -negative planktonic bacteria, biofilms, and yeast. Laborious CFU experiments such as checkerboard assays, treatment time-courses, and drug screens against slow-growing cells are simplified by GVA. We therefore screened a drug library against exponential and stationary phaseE. colileading to the discovery of the ROS-mediated, bactericidal mechanism of diphenyliodonium. The ease and low cost of GVA evinces it can accelerate existing viability assays and enable measurements at previously impractical scales.
Phylogenomics reveals patterns of ancient hybridization and differential diversification contributing to phylogenetic conflict inPopulusL. andSalixL
Authors: Sanderson Brian J. , Ghambir Diksha , Feng Guanqiao , Hu Nan , Cronk Quentin C. , Percy Diana M. , Freaner Francisco Molina , Johnson Matthew G. , Smart Lawrence B. , Keefover-Ring Ken , Yin Tongming , Ma Tao , DiFazio Stephen P. , Liu Jianquan , Olson Matthew S. 
Published: January 2023

AbstractDespite the economic, ecological, and scientific importance of the generaPopulusL. (poplars, cottonwoods, and aspens) andSalixL. Salicaceae (willows), we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees.Salixsubgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a ‘spectacular failure’ due to a speculated radiation of the subgeneraVetrixandChamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranchanalysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of theVetrix-Chamaetiaclade inSalix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in bothPopulusandSalixhave played important roles in the diversification and diversity in these two genera.Supplementary data files will be provided by request tomatt.olson@ttu.edu
Vitamin D inhibits osteosarcoma by reprogramming nonsense-mediated RNA decay and SNAI2-mediated epithelial-to-mesenchymal transition
Authors: Capobianco Enrico , McGaughey Vanessa , Seraphin Gerbenn , Heckel John , Rieger Sandra , Lisse Thomas S. 
Published: January 2023

AbstractOsteosarcomas are immune-resistant and metastatic as a result of elevated nonsense-mediated RNA decay (NMD), reactive oxygen species (ROS), and epithelial-to-mesenchymal transition (EMT). Although vitamin D has anti-cancer effects, its effectiveness and mechanism of action against osteosarcomas are poorly understood. In this study, we assessed the impact of vitamin D and its receptor (VDR) on the NMD-ROS-EMT signaling axis inin vitroandin vivoosteosarcoma animal models. Initiation of VDR signaling facilitated the enrichment of EMT pathway genes, after which 1,25(OH)2D, the active vitamin D derivative, inhibited the EMT pathway in osteosarcoma subtypes. The ligand-bound VDR directly downregulated the EMT inducerSNAI2, differentiating highly metastatic from low metastatic subtypes and 1,25(OH)2D sensitivity. Moreover, epigenome-wide motif and putative target gene analysis revealed the VDR’s integration with NMD tumorigenic and immunogenic pathways. In an autoregulatory manner, 1,25(OH)2D inhibited NMD machinery genes and upregulated NMD target genes implicated in anti-oncogenic activity, immunorecognition, and cell-to-cell adhesion. Dicer substrate siRNA knockdown ofSNAI2revealed superoxide dismutase 2 (SOD2)-mediated antioxidative responses and 1,25(OH)2D sensitization via non-canonical SOD2 nuclear-to-mitochondrial translocalization leading to overall ROS suppression. In a mouse xenograft metastasis model, the therapeutically relevant vitamin D derivative calcipotriol inhibited osteosarcoma metastasis and tumor growth shown for the first time. Our results uncover novel osteosarcoma-inhibiting mechanisms for vitamin D and calcipotriol that may be translated to human patients.