bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolutionary history and modern diversity of triterpenoid cyclases
Authors: McShea Hanon , Viens Robb A. , Olagunju Babatunde O. , Giner José-Luis , Welander Paula V. 
Published: November 2024

AbstractCyclic terpenoids are a class of lipid compounds containing immense structural and functional diversity, with many cyclic triterpenoids acting as membrane components, and, for a few well-studied molecules, regulators of membrane physical properties and spatial organization. Cyclic terpenoids are also readily preserved as terpane fossils, such as steranes and hopanes, which form a rich record of the evolution of life on Earth. Formation of the multiple ring structure of all cyclic terpenoids is catalyzed by terpenoid cyclase enzymes, among which are whole clades of proteins – many from environmental metagenomes and uncultured organisms – whose substrates and products are completely unknown. We investigate the function of these divergent cyclases through biochemical assays, and the evolutionary processes that produced them by testing and applying a variety of evolutionary models. We find a deep divergence between the diterpenoid cyclases and all other cyclases. This roots the triterpenoid cyclase tree, demonstrating reciprocal monophyly between squalene-hopene cyclases and sterol cyclases, which is consistent with their simultaneous first occurrence in the geological record. Through a simple test of evolutionary rate shifts, we find positive selection on the enzyme active site on the squalene-hopene cyclase stem. Finally, by testing the activity of divergent cyclases for a variety of substrates, we find a group of stem sterol cyclases from bacteria that synthesize arborinols, two of which produce the molecular precursor to a Permian “orphan biomarker.” Together, our data present an evolutionary framework for triterpenoid cyclases that can inform both the biochemical potential of these proteins and their products’ occurrence in the geological record.
TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads
Authors: Chung George , Piano Fabio , Gunsalus Kristin C 
Published: November 2024

ABSTRACTTelomeres are eukaryotic chromosome end structures that guard against sequence loss and aberrant chromosome fusions. Telomeric repeat motifs (TRMs), the minimal repeating unit of a telomere, vary from species to species, with some evolutionary clades experiencing a rapid sequence divergence. To explore the full scope of this evolutionary divergence, many bioinformatic tools have been developed to infer novel TRMs using repetitive sequence search on short sequencing reads. However, novel telomeric motifs remain unidentified in up to half of the sequencing libraries assayed with these tools. A possible reason may be that short reads, derived from extensively sheared DNA, preserve little to no positional context of the repetitive sequences assayed. On the other hand, if a sequencing read is sufficiently long, telomeric sequences must appear at either end rather than in the middle. The TeloSearchLR algorithm relies on this to help identify novel TRMs on long reads, in many cases where short-read search tools have failed. In addition, we demonstrate that TeloSearchLR can reveal unusually long telomeric motifs not maintained by telomerase, and it can also be used to anchor terminal scaffolds in new genome assemblies.
Alternative splicing modulates chromatin interactome and phase separation of the RIF1 C-terminal domain
Authors: Koo Adenine Si-Hui , Jia Weiyan , Kim Sang Hwa , Scalf Mark , Boos Claire E. , Chen Yuhong , Wang Demin , Voter Andrew F. , Bajaj Aditya , Smith Lloyd M. , Keck James L. , Bakkenist Christopher J. , Guo Lin , Tibbetts Randal S. 
Published: November 2024

ABSTRACTRIF1 (RAP1 interacting factor) fulfills diverse roles in DNA double-strand break repair, DNA replication, and nuclear organization. RIF1 is expressed as two splice variants, RIF1-Long (RIF1-L) and RIF1-Short (RIF1-S), from the alternative splicing (AS) of Exon 32 (Ex32) which encodes a 26 aa Ser/Lys-rich cassette peptide in the RIF1 C-terminal domain (CTD). Here we demonstrate that Ex32 inclusion was repressed by DNA damage and oncogenesis but peaked at G2/M phase of the cell cycle. Ex32 splice-in was catalyzed by positive regulators including SRSF1, which bound to Ex32 directly, and negative regulators such as PTBP1 and SRSF3. Isoform proteomics revealed enhanced association of RIF1-L with MDC1, whose recruitment to IR-induced foci was strengthened by RIF1-L. RIF1-L and RIF1-S also exhibited unique phase separation and chromatin-binding characteristics that were regulated by CDK1-dependent CTD phosphorylation. These combined findings suggest that regulated AS affects multiple aspects of RIF1 function in genome protection and organization.Graphical AbstractHIGHLIGHTSRIF1 AS is dynamically regulated by DNA damage and cell cycle signaling.RIF1-L to RIF1-S isoform switch is associated with primary cancers.SRSF1 acts directly on Exon 32 to promote RIF1-L expression.S/K cassette expanded the RIF1 chromatin interactomes and stabilized phase separation.
The balanced lethal system inTriturusnewts originated in an instantaneous speciation event
Authors: France James , de Visser Manon Chantal , Arntzen Jan W. , Babik Wiesław , Cvijanović Milena , Ivanović Ana , Smith Jeramiah , Vučić Tijana , Wielstra Ben 
Published: November 2024

AbstractTriturusnewts are afflicted by a balanced lethal system causing the spontaneous death of half of their offspring. How could such a maladaptive trait evolve? We construct genetic maps forTriturusand its sister genusLissotriton, identifying genes involved in the balanced lethal system.Trituruschromosome 1 has diverged into two versions, which each carry a single massive deletion that is compensated for by duplication of the same region in the alternate version – indicating that the balanced lethal system arose instantaneously, in a single macromutation. Simulations show that, counterintuitively, the deleterious nature of the rearranged chromosomes protects them against competition with the ancestral arrangement via reproductive isolation. We conclude that the origin of theTriturusbalanced lethal system also led to instantaneous speciation.
The network structure of cross-feeding impacts microbial community diversity under growth-inhibiting stresses
Authors: Newton Daniel P. , Ho Po-Yi , Huang Kerwyn Casey 
Published: November 2024

AbstractPerturbations such as dietary shifts and drug treatment can reduce gut microbiome diversity, with negative health effects on the host, but predicting changes to community diversity is challenging due to the many mechanisms by which species interact. While both nutrient competition and cross-feeding can play major roles in microbiota assembly, the effect of environmental stresses such as antibiotics is typically studied experimentally in monoculture, and most theoretical studies have focused on communities that interact via nutrient competition alone. To investigate the interplay between nutrient competition, stresses that inhibit growth, and cross-feeding, we introduce a consumer-resource model that includes all three factors and captures a wide range of cross-feeding network architectures with a single parameter. For three-species communities, we found that coexistence during narrow-spectrum growth inhibition was maximal with a cyclic cross-feeding network, while fully connected cross-feeding networks maximized coexistence during broad-spectrum growth inhibition. However, the effects of cyclic cross-feeding were particularly sensitive to community size and the number of targeted species; for communities with more than six species and resources, cyclic cross-feeding can be detrimental to coexistence due to instability. Our findings highlight the complex effects of cross-feeding network architecture on coexistence when growth inhibition reshapes the nutrient competition landscape, with potential applications to microbial communities in all natural environments, where they are often exposed to agents such as drugs, temperature, and pH modulation.
Neutrophil transcriptome diverges into two discrete trajectories in a murine model of severeStreptococcus pneumoniaepneumonia
Authors: Pihl Riley M.F. , Alabdullatif Salam H. , Hiller Bradley E. , Armstrong Elise M.R. , Martins Kevyn R. , Dimbo Ernest L. , Lee Yewoo , Campbell Joshua D. , Gower Adam C. , Mizgerd Joseph P. , Quinton Lee J. , Traber Katrina E. 
Published: November 2024

AbstractNeutrophils were once considered a homogenous population of transcriptionally static, pathogen-killing cells, however, recent models have demonstrated neutrophil functional and transcriptional plasticity. We performed transcriptomic analyses in a murine model of pneumococcal pneumonia to investigate neutrophil plasticity and demonstrate that neutrophils are highly dynamic, leading to three distinct alveolar neutrophil populations – one immature (early bronchoalveolar lavage neutrophils [BALN]) and two mature (late BALN). Early BALNs produce high levels of inflammatory cytokine transcripts, maturing into late BALNs, including a pro-degranulation and phagocytosis population (late-degranulating BALN) or a population specializing in translation machinery and inflammatory cytokine production (late-cytokine producing BALN). Neutrophil metabolism is also regulated in a stepwise manner – tricarboxylic acid (TCA) cycle and respiratory electron transport chain (ETC) genes are downregulated as neutrophils migrate from the vasculature to the interstitium, lipid and carbohydrate metabolism genes are downregulated during migration from interstitium to the airspace. These transitions may be regulated by aspects of the integrated stress response (ISR), as key regulators includingEif2ak2are upregulated in interstitial neutrophils. Overall, we demonstrate that pneumonic neutrophils are transcriptionally plastic, developing through two distinct transcriptional phenotypes in the airspace, and are metabolically and transcriptionally rewired with potential points of regulation occurring in the interstitial space.
Mapping the druggable targets displayed by human colonic enteroendocrine cells
Authors: Lei Yuxian , Bohl Bettina , Meyer Leah , Jacobs Margot , Haq Naila , Yang Xiaoping , Hayee Bu’ Hussain , Murphy Kevin G , Hashemi Parastoo , Bewick Gavin A 
Published: November 2024

AbstractEnteroendocrine cells (EECs) are specialized intestinal hormone-secreting cells that play critical roles in metabolic homeostasis, digestion, and gut-brain communication. They detect diverse stimuli including endocrine, immune, neuronal, microbial, and dietary signals, through a complex array of receptors, ion channels, and transporters, to modulate the release of over 20 hormones. These molecular sensors serve as potential drug targets to modulate hormone secretion, but until recently, catalogues of such targets in human colonic EECs have not been produced.To address this gap, we performed bulk and single-cell RNA sequencing on fluorescently labelled EECs isolated from human colonic organoids, identifying and cataloguing potential druggable targets. This catalogue includes receptors, orphan GPCRs, transporters, and hormones not previously reported in human colonic EECs. Comparison with murine EECs highlighted interspecies similarities and differences, key data to facilitate the design and optimise the predictive accuracy of pre-clinical models. We also functionally validated two receptors not previously identified in human EECs: IL-13Rα1, was expressed in both peptide-producing EECs and serotonin producing Enterochromaffin cells (ECs), and its ligand IL-13 stimulated the secretion of glucagon-like peptide-1 (GLP-1) and serotonin measured in real-time, and GPR173, which was selectively expressed in ECs and, when activated by its agonist Phoenixin-20, also promoted serotonin release.These analyses provide a valuable resource for therapeutic interventions aimed at modulating gut hormone secretion, with potential applications in treating gastrointestinal, metabolic, and other related disorders.
Electrophysiological comparison of left versus right stellate ganglia neurons
Authors: Verkerk Arie , Remme Carol Ann , O’Reilly Molly 
Published: November 2024

AbstractBackgroundThe stellate ganglia of the peripheral autonomic nervous system innervate the heart and continuously fine-tune cardiac function to meet physiological demands. The right stellate ganglion (RSG) predominantly innervates the sinoatrial node and has functional effects on chronotropy/heart rate, whereas the left stellate ganglion (LSG) has predominance in the ventricular myocardium and impacts inotropy/contractility. Whilst the innervation patterns and functional consequences of block and stimulation are well-documented, basic electrophysiological characterisation and single-cell comparison of RSG and LSG neurons has not been performed. In addition, sex differences in stellate ganglion action potential (AP) parameters may exist, but remain as yet unknown.Methods/ResultsHere we characterise the electrical properties of enzymatically isolated mouse stellate ganglia neurons using the patch clamp technique. Using 500 ms depolarising pulses of varying amplitude, we provide detailed characterisation of basic AP properties and their correlations. We reveal that there are two populations of neurons in terms of their AP firing properties (phasic or tonic firing), with the majority (67%) firing with a phasic pattern. When all recordings were pooled, tonic neurons had a significantly larger AP amplitude (85 ± 3.0 vs 76 ± 2.4 mV) and overshoot (28 ± 1.8 vs 19 ± 1.8 mV) compared to phasic neurons (P<0.05). Moreover, phasic neurons did not fire spontaneously, whereas 50% of tonic neurons did, and more often presented with anodal break excitation (P<0.05). When male vs female neurons were compared, males had a more negative minimum diastolic potential (MDP; -55 ± 1.7 vs -47 ± 3.0 mV, P<0.05). When LSG vs RSG neurons were compared, the RSG had a more negative resting membrane potential (Vrest; -60 ± 1.5 vs -54 ± 1.3 mV, P<0.05). All other AP parameters did not differ significantly between these groups.ConclusionsThe RSG and LSG contain a similar proportion of phasic and tonic firing neurons. A significant difference was observed in the Vrestof RSG vs LSG neurons, and in the MDP of male vs female neurons. However, all other AP parameters were similar. This suggests that the LSG and RSG can be combined irrespective of sex when investigating the electrophysiological properties of these distinct anatomical structures in healthy and disease conditions.
Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites
Authors: Liu Chin-Chih , Grencewicz Dennis , Chakravarthy Karthik , Li Lin , Liepold Ruth , Wolf Matthew , Sangwan Naseer , Tzeng Alice , Hoyd Rebecca , Jhawar Sachin R. , Grobmyer Stephen R. , Al-Hilli Zahraa , Sciallis Andrew P. , Spakowicz Daniel , Ni Ying , Eng Charis 
Published: November 2024

ABSTRACTBackgroundBreast cancer, the most common cancer type among women, was recently found to contain a specific tumor microbiome, but its impact on host biology remains unclear. CD8+tumor-infiltrating lymphocytes (TILs) are pivotal effectors of anti-tumor immunity that influence cancer prognosis and response to therapy. This study aims to elucidate interactions between CD8+TILs and the breast tumor microbiome and metabolites, as well as how the breast tumor microbiome may affect the tumor metabolome.MethodsWe investigated the interplay among CD8+TILs, the tumor microbiome, and the metabolome in a cohort of 46 breast cancer patients with mixed subtypes (Cohort A). We characterized the tumor metabolome by mass spectrometry and CD8+TILs by immunohistochemistry. Microbiome composition and T cell gene transcript levels were obtained from data from our previous study, which utilized 16S rRNA gene sequencing and a targeted mRNA expression panel. To examine interactions between intratumoralStaphylococcusand specific breast cancer subtypes, we analyzed RNA sequencing data from an independent cohort of 370 breast cancer patients (Cohort B). We explored the functions of the tumor microbiome using mouse models of triple-negative breast cancer (TNBC).ResultsIn tumors from Cohort A, the relative abundance ofStaphylococcuspositively correlated with the expression of T cell activation genes. The abundances of multiple metabolites exhibited significant correlations with CD8+TILs, of which NADH, γ-glutamyltryptophan, and γ-glutamylglutamate displayed differential abundance inStaphylococcus-positive versusStaphylococcus-negative breast tumors. In a larger breast cancer cohort (Cohort B), we observed positive correlations between tumoralStaphylococcusand CD8+TIL activity exclusively in TNBC. Preclinical experiments demonstrated that intratumoral administration ofS. aureus, the predominant species ofStaphylococcusin human breast tumors, resulted in a depletion of total NAD metabolites, and reduced the growth of TNBC tumors by activating CD8+TILs.ConclusionsWe identified specific metabolites and microbial taxa associated with CD8+TILs, delineated interactions between the breast tumor microbiome and metabolome, and demonstrated that intratumoralStaphylococcusinfluences anti-tumor immunity and TIL-associated metabolites. These findings highlight the role of low-biomass microbes in tumor tissues and provide potential biomarkers and therapeutic agents for breast cancer immunotherapy that merit further investigation.
Strigolactones are involved in enhancing iron uptake in maize
Authors: Fili Stavroula , Guan Jiahn-Chou , Koch Karen E. , Walker Elsbeth L. 
Published: November 2024

AbstractStrigolactones are plant hormones with roles in a wide range of signaling and developmental processes. A yellow-striped maize mutant, (interveinalyellow)ivy, was determined to have low iron in tissues under normal growth conditions. The gene underlying theivymutation was mapped and identified asZmCCD8, a key enzyme in the biosynthesis of strigolactones. Under iron-replete conditions, comparison of the transcriptomes of wild-type plants and maizeccd8mutants revealed suppression of several iron-regulated genes inccd8. These genes are normally up-regulated during iron deficiency and include the key iron-regulated transcription factorIRO2as well as genes involved in the biosynthesis of iron chelators and transporters. External supply of synthetic strigolactone toivymutants alleviated chlorosis and returned iron-regulated gene expression to wild-type levels. In iron limited conditions, iron-regulated gene expression inccd8mutants responded normally, indicating that strigolactones are not required for response to externally imposed iron deficiency. However, they are required for basal expression of iron-regulated genes when adequate iron is available, highlighting a distinction between iron homeostasis during normal growth, and the iron deficiency response triggered by the lack of external available iron. The connection between strigolactones and iron homeostasis is not limited to maize, as Arabidopsisccd8mutants also show strong chlorosis when grown on medium with moderate levels of iron. This previously unappreciated role may have implications for the use of strigolactones in agricultural contexts.
EasyAb: A High-Throughput Workflow for Antibody-Based PTM Peptide Enrichment Method Coupled to Mass Spectrometry
Authors: Jayavelu Ashok Kumar , Liu Jeffrey J , Schriever Sonja C , Pfluger Paul T , Schwarzer Christoph , Krahmer Natalie , Mann Matthias 
Published: November 2024

SUMMARYReversible post-translational modification (PTMs) is a fundamental mechanism of cellular signal transduction.In vivoandex vivostudies to profile PTMs have greatly advanced our understanding of the complexities of cellular signaling. However, apart from the most commonly studied PTMs, large-scale analysis is still very challenging, limiting our understanding of various cellular processes. PTM-bearing peptides often enriched by antibodies, followed by unbiased mass spectrometry (MS)-based readout of hundreds or thousands of sites. To extend the reach of this powerful technology to in vivo and ex vivo studies with small protein starting amounts, we here developed EasyAb, a streamlined and high throughput MS workflow for antibody-based PTM profiling. Using epidermal growth factor receptor (EGFR) signaling and acute myeloid leukemia (AML) cell systems, we demonstrate that EasyAb increases sensitivity and enables multiple large-scale systems-level studies. Furthermore, EasyAb resolves in vivo brain G protein-coupled receptor-mediated tyrosine kinase activation and reveals the long elusive hypothalamic neuron-specific leptin signaling architecture.Graphical AbstractHIGHLIGHTSEasyAb, a sensitive, rapid and high-throughput method to quantify post translationally modified peptides in diverse cell systems.EasyAb reveals differential tyrosine phosphorylation of mRNA splicing proteins in AML patient samples. Activation of KOR by “G-protein-biased” non-aversive agonist 6’GNTI elicits Src kinase activity in mice. Elucidation ofin vivohypothalamic Leptin induced LEPRb-Jak2 phosphotyrosine signaling architecture.
POSSIBLE MULTIPLE ORIGINS OF SOME IMPORTANT CHARACTERISTICS OF THE KEEL (PAPILIONATE) FLOWERS WITHIN FABALES
Authors: Uluer Deniz Aygören 
Published: November 2024

ABSTRACTKeel flowers are bilaterally symmetrical, pentamerous flowers with the reproductive organs enclosed by keel petals. Within Fabales, keel flowers are dominant in two species-rich lineages, tribe Polygaleae (Polygalaceae) and subfamily Fabaceae (Papilionoideae); however, independent events are also observed, such as in the genusCercis. Before phylogenetic advancements were available (i.e., in contrast to more recent studies), most of the studies hypothesized a non-keeled origin for the Faboideae, although a detailed investigation has never been carried out. In this study, using the results of Aygören Ulueret al. (2020, 2022a), the origin of some important morphological characters of the keel flower are examined, namely floral symmetry, perianth heteromorphism (i.e., three distinct petal/+sepal types), and the presence of enclosed reproductive organs. These characters are analysed within the Fabales using three different ancestral state analyses based on a phylogeny constructed for 678 taxa using publishedmatK,rbcLandtrnLplastid gene regions. The analyses show that symmetry probably originated in the (Fabaceae+Polygalaceae) clade, while the enclosed reproductive organs and three-types of petals appear to have evolved independently multiple times. Interestingly, not only the enclosed reproductive organs but also petal heteromorphism probably did not evolve in the MRCA of the Faboideae, but rather in a very early stage of the evolution of the subfamily. While future homology assessments and/or evolutionary developmental genetic (evo-devo) studies will be required to more clearly elucidate the evolutionary processes, the current study is the first attempt to investigate the origin of some important characteristics of keel flowers within order Fabales.