bluuebunny/crossref_metadata_2025 huggingface dataset:
TILLCANN: A TILLING platform inCannabis sativafor mutation discovery and crop improvement
Authors: Duarte-Delgado Diana , Alexiou Konstantinos G. , Pujol Marta , Uauy Cristobal , Adamski Nikolai M. , Vidal Victoria , Torres Anthony , Zalewski Christopher , Gaudino Reginald , Monfort Amparo , Argyris Jason
Published: November 2024

Cultivation ofCannabis sativais increasing because of its therapeutic value and recognition as a multi-purpose and sustainable crop. Targeting Induced Local Lesions in Genomes (TILLING) is a versatile reverse genetics approach that unlocks induced variation through mutagenesis to accelerate the development of new cultivars and contribute to the functional validation of genes. Increasingly efficient next-generation sequencing technologies and genomic resources have combined to make TILLING by sequencing (TbyS) an attractive technique that can be applied in cannabis. Here we describe the development of a mutagenesis protocol forC. sativaand the development of the TILLCANN platform composed of 1,633 M2 families. As a demonstration of the functionality of the platform, we used TbyS to perform a high throughput screening of novel mutations in amplicons for genes associated with important agronomic and biochemical traits in a set of 512 M2 families. We confirmed 14 of the identified mutations and calculated an average mutation frequency range of 1/263 to 1/320 kb. We found that heterozygous mutants in the cannabis homologue of Class IITEOSINTE BRANCHED 1/CYCLOIDEA/PCF(TCP4) are linked to alterations in leaf number and morphology. We expect that the novel genetic variability unlocked in the TILLCANN platform for performing forward or reverse genetic screens can significantly boost breeding programs geared toward both medicinal cannabis and industrial hemp.

Gene & accession numbers

Raw sequencing data generated in this study was deposited at the European Nucleotide Archive with accession numbers xxx and xxx. Genes and accession numbers discussed within this manuscript correspond to theCannabis sativacs10 genome assembly deposited in National Center for Biotechnology Information with accession number GCA_900626175.2.
A PI3Kδ-Foxo1-FasL signaling amplification loop rewires CD4+T helper cell signaling, differentiation and epigenetic remodeling
Authors: Golec Dominic P , Gazzinelli-Guimaraes Pedro , Chauss Daniel , Nagashima Hiroyuki , Yu Kang , Hill Tom , Nivelo Luis , Cannons Jennifer L , Perry Jillian , Joshi Ilin , Pereira Nicolas , Oliveira Fabrício Marcus Silva , Cruz Anthony C , Druey Kirk M , Lack Justin B , Nutman Thomas B , Villarino Alejandro V , O’Shea John J , Afzali Behdad , Schwartzberg Pamela L
Published: November 2024

While inputs regulating CD4+T helper cell (Th) differentiation are well-defined, the integration of downstream signaling with transcriptional and epigenetic programs that define Th-lineage identity remain unresolved. PI3K signaling is a critical regulator of T cell function; activating mutations affecting PI3Kδ result in an immunodeficiency with multiple T cell defects. Using mice expressing activated-PI3Kδ, we found aberrant expression of proinflammatory Th1-signature genes under Th2-inducing conditions, bothin vivoandin vitro. This dysregulation was driven by a robust PI3Kδ-IL-2-Foxo1 signaling loop, fueling Foxo1-inactivation, loss of Th2-lineage restriction, altered chromatin accessibility and global impairment of CTCF-DNA interactions. Surprisingly, ablation ofFasl, a Foxo1-repressed gene, restored normal Th2 differentiation, TCR signaling and CTCF expression. BioID revealed Fas interactions with TCR- signaling components, which were supported by Fas-mediated potentiation of TCR signaling. Our results highlight Fas-FasL signaling as a critical intermediate in phenotypes driven by activated-PI3Kδ, thereby linking two key pathways of immune dysregulation.
SenSeqNet: A Deep Learning Framework for Cellular Senescence Detection from Protein Sequences
Authors: Jiang Hanli , Lin Li , Deng Dongliang , Ren Jianyu , Yang Xin , Liu Siyi , Liu Lubin
Published: November 2024

Cellular senescence, characterized by the irreversible cessation of division in normally proliferating cells due to various stressors, presents a significant challenge in the treatment of age-related diseases. Understanding and accurately detecting cellular senescence is crucial for identifying potential therapeutic targets. However, traditional wet lab assays for detecting cellular senescence are time-consuming and labor-intensive, limiting research and drug development efficiency. There is an urgent need for computational tools allowing swift and accurate detection of cellular senescence from protein sequences. We propose SenSeqNet, a novel deep learning framework for detecting cellular senescence directly from protein sequences. The framework begins with feature extraction using the Evolutionarily Scaled Model (ESM-2), a state-of-the-art protein language model that captures evolutionary information and complex sequence patterns. The extracted embeddings are then passed through a hybrid architecture consisting of long short-term memory (LSTM) networks and convolutional neural networks (CNNs) to further refine and learn from the embedded information. SenSeqNet achieved a final accuracy of 83.55% on independent testing, surpassing various machine learning and deep learning architectures. This performance underscoring the robustness and effectiveness of SenSeqNet for detecting cellular senescence from protein sequences. These results provide a solid foundation for future research on aging and age-related therapeutics.
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

Cyclic 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

Telomeres 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

RIF1 (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 Abstract

HIGHLIGHTS

RIF1 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

Triturusnewts 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

Perturbations 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

Neutrophils 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

Enteroendocrine 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

Background

The 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/Results

Here 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.

Conclusions

The 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

Background

Breast 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.

Methods

We 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).

Results

In 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.

Conclusions

We 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

Strigolactones 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

Reversible 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 Abstract

HIGHLIGHTS

EasyAb, 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

Keel 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.
Neuropsychological and behavioral profiles of patients with chronic trigeminal neuralgia
Authors: Pashkov Anton , Filimonova Elena , Martirosyan Azniv , Moisak Galina , Rzaev Jamil
Published: November 2024

Patients suffering from chronic pain are known to exhibit distinctive personality traits and impaired neuropsychological performance across various cognitive domains. However, there is currently a lack of comprehensive evidence regarding cognitive and behavioral functioning patterns in patients with trigeminal neuralgia. In this study, we aimed to thoroughly characterize a range of psychological and neuropsychological variables in a sample of 80 patients and 34 healthy controls, and to assess their relationship with pain intensity and duration. Our findings revealed that patients with trigeminal pain scored significantly higher on measures of anxiety, depression, perceived stress, alexithymia, pain catastrophizing, harm avoidance and lower on Self-transcendence subscale compared to healthy controls. Additionally, these patients demonstrated lower performance scores on tasks assessing working memory and verbal fluency. These findings may provide valuable insights for the development of personalized treatment plans for patients with trigeminal neuralgia, specifically targeting their unique personality traits and cognitive impairments.
Portable Six-Channel Laser Speckle System for Simultaneous Cerebral Blood Flow and Volume Measurement with Potential Application for Characterization of Brain Injury
Authors: Mahler Simon , Huang Yu Xi , Ismagilov Max , Álvarez-Chou David , Abedi Aidin , Tyszka J. Michael , Lo Yu Tung , Russin Jonathan , Pantera Richard L. , Liu Charles , Yang Changhuei
Published: November 2024

In regional cerebrovascular monitoring, cerebral blood flow (CBF) and cerebral blood volume (CBV) are key metrics. Simultaneous, non-invasive measurement of CBF and CBV at different brain locations would advance cerebrovascular monitoring and pave the way for brain injury detection, as current brain injury diagnostic methods are often constrained by high costs, limited sensitivity, and reliance on subjective symptom reporting. This study’s aim is to develop a multi-channel non-invasive optical system for measuring CBF and CBV at different regions of the brain simultaneously with a cost-effective, reliable, and scalable system capable of detecting potential differences in CBF and CBV across different regions of the brain. The system is based on speckle contrast optical spectroscopy (SCOS) and consists of laser diodes and board cameras which have been both tested and investigated for safe use on the human head. Results on a cohort of five healthy subjects indicated that the dynamics of both CBF and CBV were synchronized and exhibited similar cardiac period waveforms across all six channels. As a preliminary investigation, we also explored the potential use of our six-channel system for detecting the physiological sequela of brain injury, involving a subject with significant structural brain damage compared to another with lesser structural brain damage. The six-point CBF and CBV measurements were compared to MRI scans, revealing that regions with altered blood dynamics closely correlated with the injury sites identified by MRI.
Untangling Empowerment and Contraceptive Use Longitudinally in Five African Settings
Authors: Zimmermann Marita , Myers Cara , Dhar Diva , O’Brien Michelle
Published: November 2024

Objective

Empowerment impacts reproductive health behaviors profoundly. Similarly, contraceptive access and use result in broader social and economic opportunities. We aimed to quantify the directionality of this cyclical relationship.

Study design

This study utilizes data from the Performance Monitoring for Action (PMA) surveys in Kenya, Nigeria (Kano), Burkina Faso, Democratic Republic of Congo (DRC), and Uganda. Using annual longitudinal data (2019-2021), we employed cross-lagged panel models (CLPM) to analyze the bidirectional relationship between women’s empowerment and contraceptive use.

Results

There was a significant positive impact of contraceptive use on women’s empowerment. In Kenya and Kano, contraceptive use was associated with a 10.1% and 12.0% increase in paid work and 14.5% and 14.8% greater control over wages, respectively. In Kenya, women doing paid work with wage control were 5.2% more likely to use contraception the following year. In Kano, control over partner’s wages increased contraceptive use by 9.6%. Additionally, having savings, financial goals, increased financial autonomy, and knowledge of financial information were associated with higher future contraceptive use.

Conclusions

Contraceptive use can act as a catalyst for empowerment, while empowerment, particularly decision-making autonomy over finances, enhances contraceptive use. However, these dynamics vary across different settings, emphasizing the need for context-specific strategies.
Genomics and resistance assays inform the management of two tree species being devastated by the invasive myrtle rust pathogen
Authors: Chen Stephanie H , Yap Jia-Yee S , Viler Veronica , Stehn Craig , Sandhu Karanjeet S , Percival Julie , Pegg Geoff S , Menzies Tracey , Jones Ashley , Guo Karina , Giblin Fiona R , Cohen Joel , Edwards Richard J , Rossetto Maurizio , Bragg Jason G
Published: November 2024

Myrtle rust is a plant disease caused by the invasive fungal pathogenAustropuccinia psidii(G. Winter) Beenken, which has a global host list of 480 species. It was detected in Australia in 2010 and has caused the rapid decline of native Myrtaceae species, including rainforest treesRhodamnia rubescens(Benth.) Miq. (scrub turpentine) andRhodomyrtus psidioides(G.Don) Benth. (native guava).Ex situcollections of these species have been established, with the goal of preserving remaining genetic variation. Analysis of reduced representation sequencing (DArTseq;n= 444 forR.rubescensandn= 301 forR.psidioides) showed genetic diversity is distributed along a latitudinal gradient across the range of each species. A panel of samples of each species (n= 27 forR.rubescensandn= 37 forR.psidioides) were resequenced at genome scale, revealing large historical e]ective population sizes, and little variation among individuals in inferred levels of deleterious load. InRhodamnia rubescens, experimental assays (n= 297) identified individuals that are putatively resistant to myrtle rust. This highlights two important points: there are tangible pathways to recovery for species that are highly susceptible to rust via a genetically informed breeding program, and there is a critical need to act quickly before more standing diversity is lost.
Genetically based variation in fitness and carbon assimilation among bur oak populations
Authors: Rea L.M.S. , Ostrowsky L. , Mohn R. , Garner M. , Worcester L. , Lapadat C. , McCarthy H.R. , Hipp A.L. , Cavender Bares J.
Published: November 2024

Ongoing climate change will negatively impact tree populations unless they are able to acclimate to the changes in their local environment. Effective planning for climate adaptation management requires an understanding of the current state of local adaptation and physiological performance to assess whether populations are at risk of local extinction, determine if assisted migration is appropriate, and to select appropriate seed sources if intervention is needed. We established a new reciprocal transplant experiment (ACE, Adaptation to Climate and Environment) across a latitudinal gradient in North America to examine the impacts of warming on three bur oak (Quercus macrocarpa) populations across much of the species range. We established common gardens in Minnesota, Illinois, and Oklahoma with seedlings grown from seeds collected within 50 km of each of those locations from a total of sixty maternal families. We aimed to 1) assess local adaptation in each of the populations using survival and size as fitness metrics, and 2) evaluate physiological responses to different environments along the latitudinal gradient. We found that northern populations are maladapted to hotter climates as evidenced by their low survival, growth, and photosynthetic rates in the warmest common garden. The southernmost population had the highest survival rate, growth rate, and fitness of the three populations in the southernmost garden, providing evidence for local adaptation to the warmest site. However, conditions in the middle garden resulted in the highest fitness and best physiological performance for all populations. Growth and survival were correlated in the middle garden but were decoupled in the northern and southern gardens. This decoupling is likely due to stress associated with the relatively extreme climates in the gardens at the ends of the gradient that led to greater resource allocation to survival than growth. Our results suggest that southern seed sources may perform well in warmer conditions in the north brought on by climate change, which has important implications for managers assisting broadly ranged tree species in adapting to climate change.
PMAIP1-Mediated Glucose Metabolism and its Impact on the Tumor Microenvironment in Breast Cancer: Integration of Multi-Omics Analysis and Experimental Validation
Authors: Zhang Yidong , Han Xuedan , Yu Qiyi , Zheng Lufeng , Xiao Hua
Published: November 2024

Background

Glucose metabolism in breast cancer has a potential effect on tumor progression and is related to the immune microenvironment. Thus, this study aimed to develop a glucose metabolism– tumor microenvironment score to provide new perspectives on breast cancer treatment.

Method

Data were acquired from the Gene Expression Omnibus and UCSC Xena databases, and glucose-metabolism-related genes were acquired from the Gene Set Enrichment Analysis database. Genes with significant prognostic value were identified, and immune infiltration analysis was conducted, and a prognostic model was constructed based on the results of these analyses. The results were validated by in vitro experiments with MCF-7 and MCF-10A cell lines, including expression validation, functional experiments, and bulk sequencing. Single-cell analysis was also conducted to explore the role of specific cell clusters in breast cancer, and Bayes deconvolution was used to further investigate the associations between cell clusters and tumor phenotypes of breast cancer.

Results

Four significant prognostic genes (PMAIP1, PGK1, SIRT7, and SORBS1) were identified, and, through immune infiltration analysis, a combined prognostic model based on glucose metabolism and immune infiltration was established. The model was used to classify clinical subtypes of breast cancer, and PMAIP1 was identified as a potential critical gene related to glucose metabolism in breast cancer. Single-cell analysis and Bayes deconvolution jointly confirmed the protective role of the PMAIP1+ luminal cell cluster.
Screening of potential biomarkers using activity-based protein profiling in a rat model of chemotherapy-induced peripheral neuropathy
Authors: Miao He , Ren Yuxuan , Zhou Yile , Miao Mengmeng , Chen Tong , Ni Feng , Chen Xiaowei
Published: November 2024

Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating condition affecting cancer patients, often resulting from the use of neurotoxic agents, such as paclitaxel. This study aimed to establish a rat model of CIPN through systemic administration of paclitaxel and to identify potential biomarkers using activity-based protein profiling (ABPP) with a desthiobiotin iodoacetamide (DBIA) probe. Male Sprague-Dawley rats received paclitaxel injections at a dosage of 2 mg/kg on Days 0, 2, 4, and 6. Behavioral assessments revealed significant mechanical and thermal pain hypersensitivity in paclitaxel-treated rats compared to control groups. ABPP analysis identified a total of 2,445 proteins and 6,765 peptides, resulting in the identification of 7 candidate proteins as potential biomarkers for CIPN. Notably, 5 proteins were significantly upregulated, while 2 protein including Q63425 (Prx) demonstrated downregulation in response to paclitaxel. These findings suggest that alterations in candidate protein levels may compromise alterations in the spinal cord in the context of CIPN. This study underscores the utility of ABPP in elucidating the proteomic changes associated with CIPN and highlights the potential of identified biomarkers like Prx for enhancing our understanding of chemotherapy-induced neuropathic pain mechanisms.
High-throughput single molecule microscopy with adaptable spatial resolution using exchangeable oligonucleotide labels
Authors: de Zwaan Klarinda , Huo Ran , Hensgens Myron N.F. , Wienecke Hannah Lena , Tekpinar Miyase , Geertsema Hylkje , Grussmayer Kristin
Published: November 2024

Super-resolution microscopy facilitates the visualization of cellular structures at resolutions approaching the molecular level. Especially, super-resolution techniques based on the localization of single-molecules have relatively modest instrument requirements and are thus good candidates for adoption in bioimaging. However, their low throughput nature hampers their applicability in biomolecular research and screening. Here, we propose a workflow for more efficient data collection, starting with scanning of large areas using fast fluctuation based imaging, followed by single-molecule localization microscopy of selected cells. To achieve this workflow, we exploit the versatility of DNA oligo hybridization kinetics with DNA-PAINT probes to tailor the fluorescent blinking towards high-throughput and high-resolution imaging. Additionally, we employ super-resolution optical fluctuation imaging (SOFI) to analyze statistical fluctuations in the DNA-PAINT binding kinetics, thereby tolerating much denser blinking and facilitating accelerated imaging speeds. Thus, we demonstrate 30-300-fold faster imaging of different cellular structures compared to conventional DNA-PAINT imaging, albeit at a lower resolution. Notably, by tuning image medium and data processing though, we can flexibly switch between high-throughput SOFI (scanning a FOV of 0.65mm× 0.52mmwithin 4 minutes of total acquisition time) and super-resolution DNA-PAINT microscopy and thereby demonstrate that combining DNA-PAINT and SOFI enables to adapt image resolution and acquisition time based to the imaging needs. We envision this approach to be especially powerful when combined with multiplexing and 3D imaging.
Graph-Regularized Optimal Transport for Single-Cell Data Integration
Authors: Wang Zexuan , Zhan Qipeng , Shen Li
Published: November 2024

Recent advancements in single-cell omics technologies have enabled comprehensive analyses of cellular processes. However, due to the lack of co-assay sequencing technologies, single-cell omics datasets often comprise unpaired observations with varying feature dimensions. In this study, we present Graph-Regularized Optimal Transport for Single-Cell Data Integration (GROT), a computational method that aligns different multi-omics datasets without requiring correspondence information. GROT achieves global alignment through optimal transport while preserving local structure via graph regularization. We demonstrate its effectiveness on four simulated datasets and two real-world datasets, achieving superior performance compared to current state-of-the-art unsupervised alignment methods. The software is available athttps://github.com/PennShenLab/GROT.
A quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs
Authors: Subbanna Mythili S. , Winters Matthew J. , Örd Mihkel , Davey Norman E. , Pryciak Peter M.
Published: November 2024

Transient protein-protein interactions play key roles in controlling dynamic cellular responses. Many examples involve globular protein domains that bind to peptide sequences known as Short Linear Motifs (SLiMs), which are enriched in intrinsically disordered regions of proteins. Here we describe a novel functional assay for measuring SLiM binding, called Systematic Intracellular Motif Binding Analysis (SIMBA). In this method, binding of a foreign globular domain to its cognate SLiM peptide allows yeast cells to proliferate by blocking a growth arrest signal. A high-throughput application of the SIMBA method involving competitive growth and deep sequencing provides rapid quantification of the relative binding strength for thousands of SLiM sequence variants, and a comprehensive interrogation of SLiM sequence features that control their recognition and potency. We show that multiple distinct classes of SLiM-binding domains can be analyzed by this method, and that the relative binding strength of peptides in vivo correlates with their biochemical affinities measured in vitro. Deep mutational scanning provides high-resolution definitions of motif recognition determinants and reveals how sequence variations at non-core positions can modulate binding strength. Furthermore, mutational scanning of multiple parent peptides that bind human tankyrase ARC or YAP WW domains identifies distinct binding modes and uncovers context effects in which the preferred residues at one position depend on residues elsewhere. The findings establish SIMBA as a fast and incisive approach for interrogating SLiM recognition via massively parallel quantification of protein-peptide binding strength in vivo.
A mathematical model informs optimal fungicide use against Sclerotinia stem rot to maximize profits in soybean production
Authors: Byer Tanner , Hatfield Tad , Kadelka Claus
Published: November 2024

Sclerotinia sclerotiorum, the causative agent of stem rot (SR), is a significant yield-limiting disease affecting soybean crops in the temperate climates around the globe. Effective disease management practices rely on fungicides to mitigate the growth and spread of the disease. To infer optimal, profit-maximizing fungicide application rates, this study develops a mathematical model of mold and soybean growth with a requisite profit function. Sensitivity of the optimal fungicide application rate was computed against profit parameters (fungicide cost and soybean bushel price), and model parameters (mold growth rate, maximal SR damage to crops and fungicide efficiency). Expectantly, higher soybean bushel prices, rates of mold growth, and maximal mold damage to crops return elevated optimal fungicide rates. In contrast, higher levels of fungicide efficiency motivate lower optimal fungicide rates. The model also reveals a discontinuity in the optimal fungicide application rates for elevated fungicide costs; in this economic context, it becomes more profitable to apply no fungicide rather than low, ineffectual amounts that still allow mold to reach near-maximal outbreak levels in a finite time period. Future refinements of the model will incorporate variable mold growth rates modeled on annual weather patterns, crop rotation practices, and further exploring the relationships that soybean densities and row spacing have on mold growth, in order to build a more robust system to analyze the long-term effect of disease behavior on soybean crop yield.