bluuebunny/crossref_metadata_2025 huggingface dataset:
Expanding the scope of a catalogue search to bioisosteric fragment merges using a graph database approach
Authors: Wills Stephanie , Sanchez-Garcia Ruben , Roughley Stephen D. , Merritt Andy , Hubbard Roderick E. , von Delft Frank , Deane Charlotte M.
Published: August 2024

The efficiency of fragment-to-lead optimization could be improved by automated workflows for the design of follow-up compounds. Pipelines that are able to fully exploit the interaction opportunities identified from the crystal structures of bound fragments would greatly aid this goal. To do so, these pipelines need to require minimal intervention from the user and be computationally efficient. In this work, we describe an updated version of our fragment merging methodology, which provides several feature enhancements, primarily by expanding the chemical space searched, allowing the identification of more diverse follow-up compounds, thus maximizing the chances of finding successful hits. While the original method focused on finding ‘perfect merges’, meaning compounds that directly incorporate substructures from the original fragments, here we expand the search to what we term ‘bioisosteric merges’, involving the incorporation of substructures that replicate the pharmacophoric features of the original fragments but may not be exactly identical. Unlike existing pharmacophore and shape-based descriptors used for virtual screening, this approach combines the search for these properties with the incorporation of novelty, which is necessary when searching for ways to link together distinct substructures. Compared with ‘perfect merging’, our new approach is able to find compounds that are directly informed by structures within the original fragments but are more chemically diverse. We contrast our approach with the use of a pharmacophore-constrained docking pipeline, run in parallel for select fragment pairs, and show that our method requires between 1.1-45.9-fold less computational time for conformer generation per merging ‘hit’ identified, referring to compounds that show a favourable degree of shape and colour overlap and recapitulation of original fragment interactions. Overall, our results show that our method has potential to be used to generate designs inspired by all fragments within a given pocket.
Spatiotemporal Characterization of Cyclooxygenase Pathway Enzymes During Vertebrate Embryonic Development
Authors: Leathers Tess A. , Ramarapu Raneesh , Rogers Crystal D.
Published: August 2024

Vertebrate development is regulated by several complex well-characterized morphogen signaling pathways, transcription factors, and structural proteins, but less is known about the enzymatic pathways that regulate early development. We have identified that factors from the inflammation-mediating cyclooxygenase (COX) signaling pathway are expressed at early stages of development in avian embryos. UsingGallus gallus(chicken) as a research model, we characterized the spatiotemporal expression of a subset of genes and proteins in the COX pathway during early neural development stages. Specifically, here we show expression patterns of COX1, COX2, and microsomal prostaglandin E synthase-2 (mPGES-2) as well as the genes encoding these enzymes. Unique expression patterns of individual players within the COX pathway suggest that they may play non-canonical/non-traditional roles in the embryo compared to their roles in the adult. Future work should examine the function of the COX pathway in tissue specification and morphogenesis and determine if these expression patterns are conserved across species.

Abstract Figure

Graphical abstract.

Spatiotemporal characterization of cyclooxygenase pathway enzymes during vertebrate embryonic development.
Differential Expression Analysis for Spatially Correlated Data
Authors: Vasconcelos Ana Gabriela , McGuire Daniel , Simon Noah , Danaher Patrick , Shojaie Ali
Published: August 2024

Differential expression is a key application of imaging spatial transcriptomics, moving analysis beyond cell type localization to examining cell state responses to microenvironments. However, spatial data poses new challenges to differential expression: segmentation errors cause bias in fold-change estimates, and correlation among neighboring cells leads standard models to inflate statistical significance. We find that ignoring these issues can result in considerable false discoveries that greatly outnumber true findings. We present a suite of solutions to these fundamental challenges, and implement them in the R package smiDE. spatial transcriptomics, differential expression, segmentation error mitigation, spatial correlation, spatial random effects model
Comprehensive Guide of Epigenetics and Transcriptomics Data Quality Control
Authors: Comendul Arianna , Ruf-zamojski Frederique , Ford Colby T. , Agarwal Pankaj , Zaslavsky Elena , Nudelman German , Hariharan Manoj , Rubenstein Aliza , Pincas Hanna , Nair Venugopalan D. , Michaleas Adam M. , Sealfon Stuart C. , Woods Christopher W. , Claypool Kajal T. , Jaimes Rafael
Published: August 2024

Host response to environmental exposures such as pathogens and chemicals can cause modifications to the epigenome and transcriptome. Analysis of these modifications can reveal signatures with regards to the agent and timing of exposure. Exhaustive interrogation of the cascade of the epigenome and transcriptome requires analysis of disparate datasets from multiple assay types, often at single cell resolution, from the same biospecimen. Improved signature discovery has been enabled by advancements in assaying techniques to detect RNA expression, DNA base modifications, histone modifications, and chromatin accessibility. However, there remains a paucity of rigorous quality control standards of those datasets that reflect quality assurance of the underlying assay. This guide outlines a comprehensive suite of metrics that can be used to ensure quality from 11 different epigenetics and transcriptomics assays. Recommendations on mitigation approaches to address failed metrics and poor quality data are provided. The workflow consists of assessing dataset quality and reiterating benchwork protocols for improved results to generate accurate exposure signatures.
The interplay between motor cost and self-efficacy related to walking across terrain in gaze and walking decisions
Authors: da Eira Silva Vinicius , Marigold Daniel S.
Published: August 2024

Movement-related decisions, such as where to step and which path to take, happen throughout each day. Shifts in gaze serve to extract task-relevant information necessary to make these decisions. We are only beginning to appreciate the factors that affect this information-seeking gaze behaviour. Here, we aimed to determine how a person’s belief in their ability to perform an action (i.e., self-efficacy) affected gaze and path choice when choosing between walking paths with different terrains and/or lengths (reflecting different energetic costs). We demonstrated that, when manipulated separately (i.e., paths had different lengths or different terrains), participants looked longer and more frequently and chose the paths with either less expected energetic cost or those for which they had a higher self-efficacy rating. When encountering environments where paths differed in both length and terrain, participants directed gaze progressively more to the longer path as the self-efficacy rating of this path increased and the disparity in rating with the shorter (less costly) path grew; they also chose the higher-rated path more frequently regardless of path length. These results provide evidence for a contribution of self-efficacy and energetic cost in guiding gaze and walking decisions. Interestingly, self-efficacy beliefs appear to play a more dominant role in both behaviours.
A dorsal hippocampus-prodynorphinergic dorsolateral septum-to-lateral hypothalamus circuit mediates contextual gating of feeding
Authors: Goode Travis D. , Alipio Jason Bondoc , Besnard Antoine , Pathak Devesh , Kritzer-Cheren Michael D. , Chung Ain , Duan Xin , Sahay Amar
Published: August 2024

Adaptive regulation of feeding depends on linkage of internal states and food outcomes with contextual cues. Human brain imaging has identified dysregulation of a hippocampal-lateral hypothalamic area (LHA) network in binge eating, but mechanistic instantiation of underlying cell-types and circuitry is lacking. Here, we identify an evolutionary conserved and discrete Prodynorphin (Pdyn)-expressing subpopulation of Somatostatin (Sst)-expressing inhibitory neurons in the dorsolateral septum (DLS) that receives primarily dorsal, but not ventral, hippocampal inputs. DLS(Pdyn) neurons inhibit LHA GABAergic neurons and confer context- and internal state-dependent calibration of feeding. Viral deletion ofPdynin the DLS mimicked effects seen with optogenetic silencing of DLSPdynINs, suggesting a potential role for DYNORPHIN-KAPPA OPIOID RECEPTOR signaling in contextual regulation of food-seeking. Together, our findings illustrate how the dorsal hippocampus has evolved to recruit an ancient LHA feeding circuit module throughPdynDLS inhibitory neurons to link contextual information with regulation of food consumption.

HIGHLIGHTS

DLS(Pdyn) neurons receive dense input from the dorsal but not ventral hippocampus

DLS(Pdyn) neurons inhibit GABAergic neurons in the LHA

Silencing dorsal hippocampus-DLS(Pdyn)-LHA circuit nodes abolishes context-conditioned feeding

Pdynin the DLS is necessary for context-conditioned feeding
Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma
Authors: Goetz Andrew , Shanahan Frances , Brooks Logan , Lin Eva , Mroue Rana , Cruz Darlene Dela , Hunsaker Thomas , Czech Bartosz , Dixit Purushottam , Segal Udi , Martin Scott , Foster Scott A. , Gerosa Luca
Published: August 2024

Purpose: This study explores the potential of preclinicalin vitrocell line response data and computational modeling in identifying optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. Results: In a drug combination screen of 43 melanoma cell lines, we identified unique dosage landscapes of panRAF and MEK inhibitors for NRAS vs BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma. Computational modeling and molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validatedin vivotranslatability ofin vitrodose-response maps by accurately predicting tumor growth in xenografts. Then, we analyzed pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients. Conclusion: Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range.

Simple Summary

Combining drugs is crucial for enhancing anti-cancer responses. However, the potential of pre-clinical data in identifying suitable combinations and dosage is often underutilized. In this study, we leverage preclinicalin vitrocell line drug response data and computational modeling of signal transduction and of pharmacokinetics to elucidate distinct dose requirements for the combination of pan-RAF and MEK inhibitors in melanoma. Our findings reveal a more synergistic, but narrower dosing landscape in NRAS vs BRAF mutant melanoma, which we linked to a mechanism of adaptive resistance through negative feedback. Further, our analysis suggests the importance of drug dosing strategies to optimize synergy based on mutational context, yet highlights the real-world challenges of maintaining a narrow dose range. This approach establishes a framework for translational investigation of drug responses in the refinement of combination therapy, balancing the potential for synergy and practical feasibility in cancer treatment planning.
Reproductive state controls transcription in the murine liver, with implications for breast cancer liver metastasis
Authors: Ozaki Michelle K. , Zhang Yi , Bartlett Alexandra Q. , de Wilde Elise , Guan Xiangnan , Yang Alex , Xia Zheng , Schedin Pepper
Published: August 2024

Liver biology is functionally linked to lactation, as liver size and metabolic output increase during lactation to support synthesis of breast milk. Upon weaning, the rodent liver returns to baseline homeostasis via hepatocyte cell death, in a process considered liver involution. To explore liver biology changes across a lactation-wean cycle, we employed transcriptomic profiling. We identified elevated hepatocyte proliferation and anabolic metabolism gene signatures during lactation, consistent with the liver being a major producer of substrates needed for milk production. Rapid loss of these capacities upon weaning correlated with catabolic metabolism, lysosomal-mediated cell death, and an influx of immune suppressive cells. Furthermore, we identified that the transcriptional profiles associated with liver involution share similarities with the gene expression patterns of liver pre-metastatic niches. This work identifies features of reproductive control of liver biology that sets a foundation for better understanding the potential role of the liver in maternal health.
A role for YAP-mediated regulation of invadopodia in HNSCC cells
Authors: Jerrell Rachel J. , Marchlewski Dayton D. , Parekh Aron
Published: August 2024

The objective of this study was to determine whether nuclear translocation of the transcriptional coactivator Yes-associated protein (YAP) was sensitive to extracellular matrix (ECM) rigidity and promoted Rho-associated kinase 2 (ROCK2) expression to affect invadopodia maturation and ECM degradation. ECM rigidity mimicking head and neck squamous cell carcinoma (HNSCC) tumor mechanical properties was simulated in vitro using a well-established model based on fibronectin-conjugated polyacrylamide gels (PAAs). The ratio of nuclear to cytoplasmic YAP and overall cellular ROCK2 levels were evaluated in HNSCC cells using quantitative immunofluorescence. YAP-mediated ROCK2 expression in HNSCC cells was determined using nested PCR and Western blot in response to the YAP inhibitor verteporfin. Invadopodia and ECM degradation were evaluated in HNSCC cells with siRNA-mediated inhibition of YAP using quantitative immunofluorescence in invadopodia assays. Both YAP nuclear translocation and ROCK2 cellular levels increased with ECM rigidity. Inhibition of YAP activity with verteporfin decreased ROCK2 gene and protein expression. Knockdown of YAP with siRNA inhibited the formation of mature invadopodia and ECM degradation but not total invadopodia (i.e., mature and immature or not degrading). Our study suggests that tumor-associated ECM rigidity can promote mechanically-induced transcriptional regulation to control proteolytic activity by affecting invadopodia maturation.
Evolution and Diversification of the Aposematic Poison Frog,Oophaga pumilio,in Bocas del Toro
Authors: Aguilar-Gómez Diana , Freeborn Layla , Yuan Lin , Smith Lydia L. , Guzman Alex , Vaughn Andrew H. , Steigerwald Emma , Stuckert Adam , Yang Yusan , Linderoth Tyler , MacManes Matthew , Richards-Zawacki Corinne , Nielsen Rasmus
Published: August 2024

The aposematic strawberry poison frog,Oophaga pumilio, is an iconic model system for studying the evolution and maintenance of color variation. Through most of its range, this frog is red with blue limbs. However, frogs from the Bocas del Toro Province, Panama, show striking variance in color and pattern, both sympatrically and allopatrically. This observation contradicts standard models of the evolution of aposematism and has led to substantial speculation about its evolutionary and molecular causes. Since the enigma ofO. pumiliophenotypic variation is partly unresolved because of its large, ∼ 6.7 Gb genome, we here sequence exomes from 347 individuals from ten populations and map a number of genetic factors responsible for the color and pattern variation. Thekitgene is the primary candidate underlying the blue-red polymorphism in Dolphin Bay, where an increase in melanosomes is correlated with blue coloration. Additionally, thettc39bgene, a known enhancer of yellow-to-red carotenoid conversion in birds, is the primary factor behind the yellow-red polymorphism in the Bastimentos West area. The causal genetic regions show evidence of selective sweeps acting locally to spread the rare phenotype. Our analyses suggest an evolutionary model in which selection is driving the formation of new morphs in a dynamic system resulting from a trade-off between predation avoidance, intraspecific competition, and mate choice.
Expanding the Distribution and Phylogenetic Insights ofChrysobrycon mojicaiin the Peruvian Amazon: Morphological and Molecular Analyses with Taxonomic Corrections
Authors: Chuctaya Junior , Ruiz-Tafur Morgan , Faustino-Fuster Dario , Meza-Vargas Vanessa , Garcia-Davila Carmen , Castro-Ruiz Diana , Angulo Carlos , Vanegas-Ríos James Anyelo
Published: August 2024

This study focuses on the genusChrysobrycon, particularlyChrysobrycon mojicai, which was initially described in the Amacayacu National Natural Park in Colombia. Here, we document a new geographical record ofC. mojicaiin various locations of the Peruvian Amazon, including the Nanay, Putumayo, Tapiche, and Tigre Rivers basins. Based on morphological, morphometric, and molecular analyses, we confirm the presence ofC. mojicaiin these new locations, expanding its known distribution. Morphological features such as the distinct shape of the hypertrophied scales and the specific arrangement of teeth were used to confirm its identity. Molecular data, obtained through cytochrome oxidase I (COI) gene sequencing, provide additional validation and contribute to understanding its phylogenetic relationships within the Stevardiini tribe. Our phylogenetic analysis reveals unresolved relationships within the tribe, particularly in the genusGephyrocharax, and highlights discrepancies in the current taxonomic framework, withC. mojicaishowing close genetic affinity toC. myersifrom the Pachitea River basin. The study also presents morphometric information of the holotype of C. mojicai, specifically the percentages of measurements relative to the head, which were not included in the original description. It also includes ecological observations of the habitats whereC. mojicaiwas collected, noting its presence in blackwater and mixed water streams characterized by fluctuating water levels and specific physical and chemical parameters. Additionally, the study restricts the distribution ofC. guahibofor Colombia and invalidates the COI sequence ofHysteronotus megalostomusavailable in molecular databases. This research not only expands the known distribution ofC. mojicaibut also underscores the need for further taxonomic and ecological studies to resolve existing ambiguities within the Stevardiini subfamily.
Peucedanol ameliorates LPS-induced inflammation in RAW264.7 cells and CLP-induced sepsis in mice by inhibiting TLR4/myD88/NF-κB pathway
Authors: Yao Qi , Chang Bo-tao
Published: August 2024

Background

Previously, it has reported that Peucedanol (PEU) possesses anti-bacterial activity. However, its effect and mechanism against inflammation remains unclear.

Methods

Isothermal titration calorimetry (ITC) was used to assess binding affinities of PEU to pathogen associated molecular patterns (PAMPs) Kdo2-Lipid A (KLA), oligodeoxynucleotide 1826 (ODN 1826), and peptidoglycan (PGN). A lipopolysaccharide (LPS)-induced RAW264.7 cell inflammation model and a cecum ligation and a puncture (CLP)-induced mouse sepsis model were used to assess efficacy and mechanism of PEUin vitroandin vivo. 16S ribosomal RNA (16S rRNA) sequencing was used to assay characteristics of intestinal flora of the sepsis mice.

Results

PEU had a moderate binding to KLA and ODN 1826. PEU significantly reduced supernatant tumor necrosis factor α (TNF-α) and interleukin 6 (IL-6), and downregulated protein expressions of toll-like receptor 4 (TLR4), myeloid differentiation primary response gene 8 (MyD88), and nuclear factor kappa-B (NF-κB) in the LPS-treated cells. PEU remarkably increased the survival rate, reduced the serum TNF-α and IL-6 levels, attenuated the CLP-induced pathological damage of intestine, increased proliferation-related proteins Bmi1 and Lgr5. Further, the anti-inflammatory effects of PEU were not significantly abolished in the present of chloroquine (CQ). Meanwhile, PEU significantly increased Chao1 index of the intestinal flora at the early stage of sepsis. In addition, PEU significantly changed composition of the flora at both phylum and genus levels. Moreover, PEU significantly affected metabolism-related pathways such as tricarboxylic acid (TCA) cycle, fatty acid degradation, secondary bile acid biosynthesis, and others.

Conclusions

Taken together, PEU significantly inhibits LPS-induced inflammationin vitroand CLP-induced sepsisin vivo. Further, its anti-inflammatory effect is independent of the TLR4/myD88/NF-κB pathway. In addition, PEU improves the intestinal flora imbalance at the early stage of sepsis.
Constraint Induced Movement Therapy Confers only a Transient Behavioral Benefit but Enduring Functional Circuit-Level Changes after Experimental TBI
Authors: Paydar Afshin , Khorasani Laila , Harris Neil G.
Published: August 2024

Although the behavioral outcome of Constraint-Induced Movement Therapy (CIMT) is well known, and that a combination of CIMT and arm use training potentiates the effect, there has been limited study of the brain circuits involved that respond to therapy. An understanding of CIMT from a brain network level would be useful for guiding the duration of effective therapy, the type of training regime to potentiate the outcome, as well as brain regional targets that might be amenable for direct neuromodulation. Here we investigated the effect of CIMT therapy alone unconfounded by additional rehabilitation training in order to determine the impact of intervention at the circuit level. Adult rats were injured by controlled cortical impact injury and studied before and then after 2wks of CIMT or noCIMT at 1-3wks post-injury using a combination of forelimb behavioral tasks and task-based and resting state functional magnetic resonance imaging at 3 and 7wks post-injury and compared to sham rats. There was no difference in behavior or functional imaging between CIMT and noCIMT after injury before intervention so that data are unlikely to be confounded by differences in injury severity. CIMT produced only a transient reduction in limb deficits compared to noCIMT immediately after the intervention, but no difference thereafter. However, CIMT resulted in a persistent reduction in contralesional limb-evoked activation and a corresponding ipsilesional cortical plasticity compared to noCIMT that endured 4wks after intervention. This was associated with a significant amelioration of intra and inter-hemispheric connectivity present in the noCIMT group at 7wks post-injury.
Genomic evolution of pancreatic cancer at single-cell resolution
Authors: Zhang Haochen , Sashittal Palash , Karnoub Elias-Ramzey , Jakatdar Akhil , Umeda Shigeaki , Hong Jungeui , Noronha Anne Marie , Cardenas Agustin , Erakky Amanda , McIntyre Caitlin A. , Hayashi Akimasa , Lecomte Nicolas , Park Wungki , Pan Nan , O'Reilly Eileen M. , Wei Alice C. , Raphael Benjamin J. , Iacobuzio-Donahue Christine A.
Published: August 2024

We adapted a previously developed targeted single-nucleus DNA sequencing (snDNA-seq) method and constructed a new suite of computational analysis tools to study 137,491 single-nucleus DNA libraries from 24 pancreatic cancers collected under a variety of clinical scenarios including early and late diagnoses, different metastatic sites and before- and after-treatment. We refined the mutational landscape of pancreatic cancer by capturing events missed by bulk sequencing, and validated the evolution pattern of early fixation of driver single-nucleotide variants (SNVs) followed by generation of intratumoral heterogeneity for copy number variations (CNVs). Intertumoral convergent evolution was common, including subclonal inactivation of TGF-β pathway by mutating various components of it; intratumoral convergence was rarely observed, likely due to strong selective force in pancreatic cancer development. Continuous evolution was frequently seen manifesting as CNVs. In the context of non-targeted treatments, no particular pattern was found across metastases or through treatment. In six pancreatic cancers with germline BRCA2 mutation, we discovered varied timing of biallelic inactivation of BRCA2, which sculpted different evolutionary trajectories and could presumably contribute to differential response to treatment. As the first large-scale application of targeted snDNA-seq on pancreatic cancer, this work provides a sample processing and computational analysis pipeline that warrants further clinical utility.
Two distinct chromatin modules regulate proinflammatory gene expression
Authors: Seufert Isabelle , Gerosa Irene , Varamogianni-Mamatsi Vassiliki , Vladimirova Anastasiya , Sen Ezgi , Mantz Stefanie , Rademacher Anne , Schumacher Sabrina , Liakopoulos Panagiotis , Kolovos Petros , Anders Simon , Mallm Jan-Philipp , Papantonis Argyris , Rippe Karsten
Published: August 2024

Various mechanisms have been proposed to explain gene activation and co-regulation, including enhancer-promoter interactions via chromatin looping and the enrichment of transcription factors into hubs or condensates. However, these conclusions often stem from analyses of individual loci, and genome-wide studies exploring mechanistic differences with coupled gene expression are lacking. In this study, we dissected the proinflammatory gene expression program induced by TNFα in primary human endothelial cells using NGS- and imaging-based techniques. Our findings, enabled by our novel RWireX approach for single-cell ATAC-seq analysis, revealed two distinct regulatory chromatin modules: autonomous links of co-accessibility (ACs) between separated sites, and domains of contiguous co-accessibility (DCs) with increased local transcription factor binding. Genes in ACs and DCs exhibited different transcriptional bursting kinetics, highlighting the existence of two structurally and functionally distinct regulatory chromatin modules in the proinflammatory response. These findings provide a novel mechanistic framework for understanding how cells achieve rapid and precise gene expression control.

Graphical abstract

Highlights

Two distinct, non-mutually exclusive chromatin modules, ACs and DCs, that regulate proinflammatory gene expression were identified based on deep scATAC-seq.

ACs represent long-range genomic interactions with regulation occurring more by transcription burst frequency.

DCs are regions of increased local transcription factor binding that can modulate transcription burst size.

The AC/DC model integrates sequencing-based evidence for chromatin looping with microscopy observations of transcription factor hubs/condensates into a unified model.

Our findings provide a novel framework for understanding how cells achieve rapid and precise gene expression control.
Generating Synthetic Task-based Brain Fingerprints for Population Neuroscience Using Deep Learning
Authors: Serin Emin , Ritter Kerstin , Schumann Gunter , Banaschewski Tobias , Marquand Andre , Walter Henrik ,   the environMENTAL consortium
Published: August 2024

Task-based functional magnetic resonance imaging (tb-fMRI) provides valuable insights into individual differences in the neural basis of cognitive functions because it links specific cognitive tasks to their evoked neural responses. Yet, it is challenging to scale to population-level data due to its cognitive demands, variations in task design across studies, and a limited number of tasks acquired in typical large-scale studies. Here, we present DeepTaskGen, a convolutional neural network (CNN) approach that enables us to generate synthetic task-based contrast maps from resting-state fMRI (rs-fMRI) data. Our method outperforms several benchmarks, exhibiting superior reconstruction performance while retaining inter-individual variation essential for biomarker development. We showcase DeepTaskGen by generating synthetic task images from the UK Biobank cohort, achieving competitive or greater performance compared to actual task contrast maps and resting-state connectomes for predicting a wide range of demographic, cognitive, and clinical variables. This approach will facilitate the study of individual differences and the generation of task-related biomarkers by enabling the generation of arbitrary functional cognitive tasks from readily available rs-fMRI data.
High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution
Authors: Eastburn Dennis J. , White Kevin S. , Jayne Nathan D. , Camiolo Salvatore , Montis Gioele , Ha Seungeun , Watson Kendall G. , Yeakley Joanne M. , McComb Joel , Seligmann Bruce
Published: August 2024

We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial-indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000+ cells per run. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC has a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has an observed multiplet rate of less than 1.1% and a cell capture rate of ∼50%. Although the assay can accurately profile the whole transcriptome (19,683 human or 21,400 mouse genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest – thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of 89,722 cells across multiple sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate at least 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies across thousands of samples with high data quality.
Implementation of a Goals-of-Care Communication Priming Intervention Tailored to Outpatient Stroke Survivors: A Pilot Study
Authors: Abedini Nauzley C. , Kross Erin K. , Engelberg Ruth A. , Garzio Gigi , Creutzfeldt Claire J.
Published: August 2024

Background

Goals-of-care conversations (GOCC) are important but infrequent after stroke. Serious illness communication priming guides like the Jumpstart Guide can increase GOCC, but have not been evaluated in the stroke population.

Methods

We conducted a randomized pilot study to evaluate feasibility and acceptability of the Jumpstart Guide adapted for outpatient stroke survivors, their surrogates, and clinicians. We recruited stroke survivors ≥60 years presenting for care at a single academically-affiliated stroke clinic. We enrolled surrogates if the patient had communication or cognitive impairment. Patients/surrogates were randomized to intervention (patient/surrogate and clinician received pre-visit Jumpstart Guide) or control arms. We assessed feasibility of participant enrollment, survey completion and extraction of GOCC documentation from the electronic medical record. We assessed acceptability using patient/surrogate and clinician surveys.

Results

We enrolled 15/24 (63%) eligible patients or surrogates. We randomized 5 patients alone and 3 patients with surrogates to the intervention arm, and 5 patients alone and 2 patients with surrogates to the control arm. Six clinicians were enrolled for the 8 intervention encounters. Patient characteristics in both groups were similar with mean age 74.7 years, 10/15 male, 12/15 white, and 10/15 with acute ischemic stroke. Most patients/surrogates (7/8 intervention vs 7/7 control) and all intervention clinicians completed post-visit surveys. Most intervention participants reported successful pre-visit receipt of the Jumpstart Guide (6/7 patient/surrogates; 6/8 clinicians). Of these, all intervention patients/surrogates and 5/6 clinicians stated they would “definitely” or “probably” recommend it to others. Two intervention vs no control patients had newly documented GOCC post-visit. Intervention patients/surrogates more frequently reported discussing GOCC during their clinic visit (6/7 intervention vs 4/7 control).

Conclusions

Implementation of a stroke-specific GOCC priming guide (Jumpstart Guide) in an outpatient stroke clinic is feasible and acceptable. A large randomized controlled trial is needed to evaluate its efficacy in improving outpatient stroke clinic GOCC.
Regulation of Ferroptosis in Obesity: Muscle Type-Specific Effects of Dietary Restriction and Exercise
Authors: Ji Fujue , Lee Haesung , Kim Jong-Hee
Published: August 2024

Background

Obesity is a significant global health issue and a risk factor for numerous diseases. Ferroptosis, an iron-dependent regulated cell death, is triggered by iron overload and the excessive accumulation of lipid peroxidation mediated by reactive oxygen species. Studies has identified a strong association between ferroptosis and obesity. Additionally, dietary restriction (DR) and DR combined with exercise (DR+Ex) are effective strategies for managing obesity and ferroptosis. However, the regulation of ferroptosis and its signaling pathways in skeletal muscle under conditions of obesity, DR, and DR+Ex remains poorly understood.

Methods

Mice were divided into four groups: normal diet, high-fat diet, high-fat DR, and high-fat DR+Ex. All mice were fed ad libitum with either a normal or high-fat diet for the first 14 weeks, followed by the respective interventions for the subsequent 8 weeks. Mice muscle ferroptosis were examined by immunohistochemistry, Hematoxylin & Eosin, Masson’s trichrome, Prussian blue staining, and Western-Immunoblot.

Results

The high-fat diet resulted in increased inflammatory cell infiltration, fibrosis, and iron accumulation. Red and white muscle showed increased expression of 4-HNE, regulated by GPX4 and NCAO4, respectively. DR and DR+Ex reduced downstream 4-HNE expression by regulating GPX4 in red muscle.

Conclusion

Due to metabolic differences, obesity-induced ferroptosis in skeletal muscle and the regulation by DR+Ex exhibiting fiber type-specificity. Specifically, red and white muscle respond to obesity-induced ferroptosis through different pathways; red muscle can inhibit obesity-induced ferroptosis through DR+Ex by GPX4. This deepens the understanding of mechanisms related to skeletal muscle cell death and provides scientific data support for the personalized treatment of related diseases.
A humanized yeast model for studying TRAPP complex mutations; proof-of-concept using variants from an individual with aTRAPPC1-associated neurodevelopmental syndrome
Authors: Zykaj Erta , Abboud Chelsea , Asadi Paria , Warsame Simane , Greco Brittany , López-Sánchez Marcos , Bratkovic Drago , Kachroo Aashiq , Pérez-Jurado Luis Alberto , Sacher Michael
Published: August 2024

Variants in membrane trafficking proteins are known to cause rare disorders with severe symptoms. The highly conserved transport protein particle (TRAPP) complexes are key membrane trafficking regulators that are also involved in autophagy. Pathogenic genetic variants in specific TRAPP subunits are linked to neurological disorders, muscular dystrophies, and skeletal dysplasias. Characterizing these variants and their phenotypes is important for understanding general and specialized roles of TRAPP subunits as well as for patient diagnosis. Patient-derived cells are not always available, which poses a limitation for the study of these diseases. Therefore, other systems, like the yeastSaccharomyces cerevisiae, can be used to dissect the mechanisms at the intracellular level underlying these disorders. The development of CRISPR/Cas9 technology in yeast has enabled a scar-less editing method that creates an efficient humanized yeast model. In this study, core yeast subunits were humanized by replacing their human orthologs, and TRAPPC1, TRAPPC2, TRAPPC2L, TRAPPC6A, and TRAPPC6B were found to successfully replace their yeast counterparts. This system was used for studying the first reported individual with an autosomal recessive disorder caused by biallelicTRAPPC1variants, a girl with a severe neurodevelopmental disorder and myopathy. We show that the maternal variant (TRAPPC1 p.(Val121Alafs*3)) is non-functional while the paternal variant (TRAPPC1 p.(His22_Lys24del)) is conditional-lethal and affects secretion and non-selective autophagy in yeast. This parallels defects seen in fibroblasts derived from this individual which also showed membrane trafficking defects and altered Golgi morphology, all of which were rescued in the human system by wild typeTRAPPC1. This study suggests that humanized yeast can be an efficient means to study TRAPP subunit variants in the absence of human cells, and can assign significance to variants of unknown significance (VUS). This study lays the foundation for characterizing further TRAPP variants through this system, rapidly contributing to disease diagnosis.
What works to improve species conservation state? An analysis of species whose state has improved and the actions responsible
Authors: Simkins Ashley T. , Sutherland William J. , Dicks Lynn V. , Hilton-Taylor Craig , Grace Molly K. , Butchart Stuart H.M. , Senior Rebecca A. , Petrovan Silviu O.
Published: August 2024

Understanding the consequences of past conservation efforts is essential to inform the means of maintaining and restoring species. Data from the IUCN Red List for 67,217 comprehensively assessed animal species were reviewed and analysed to determine (i) which conservation actions have been implemented for different species, (ii) which types of species have improved in state and (iii) which actions are likely to have driven the improvements. At least 51.8% (34,847) of assessed species have actions reported, mostly comprising protected areas (82.7%), with more actions reported for both terrestrial tetrapods and warm-water reef-building corals and fewer for fish, dragonflies and damselflies and crustaceans. Species at greater risk of extinction have a wider range of species-targeted actions reported compared to less threatened species, reflecting differences in documentation and conservation efforts. Six times more species have deteriorated rather than improved in their Red List category. Almost all species that improved have conservation actions in place; species that improved in state typically were historically at high risk of extinction, have smaller ranges and lacked a range of reported threats, particularly hunting and habitat loss or degradation. All types of conservation action were associated with improvements in state, especially reintroductions and invasive species control, alongside, for amphibians and birds, area management. This suggests a range of conservation interventions have successfully conserved some species at greatest risk but have rarely recovered populations to resilient levels. Scaling up the extent and intensity of conservation interventions, particularly landscape-scale actions that benefit broadly distributed species, is urgently needed to assist the recovery of biodiversity.
Two types of regeneration mechanism in acute liver injury
Authors: Aoyagi Tomomi , Goya Takeshi , Imoto Koji , Azuma Yuki , Hioki Tomonobu , Kohjima Motoyuki , Tanaka Masatake , Oda Yoshinao , Ogawa Yoshihiro
Published: August 2024

The liver has a strong regenerative capacity, but the mechanisms of liver regeneration are not well understood. Furthermore, many previous studies on liver regeneration have been conducted in partial hepatectomy models, which may differ from acute liver injury with inflammation and necrosis, as observed in many clinical cases. In this study, we conducted a single-cell RNA-seq analysis (scRNA-seq) of liver regeneration in mice treated with acetaminophen (APAP) using publicly available data. We discovered that two cell proliferation populations appeared simultaneously during a single regenerative process. The two populations differed significantly in terms of differentiation, localization, proliferation rate, and signal response. Furthermore, one of the populations was induced by contact with necrotic tissue and exhibited a higher proliferative capacity with a dedifferentiated feature. These findings can shed new light on liver regeneration and aid in the development of therapeutic strategies for liver failure.
Identifying Differential Spatial Expression Patterns across Different Slices, Conditions and Developmental Stages with Interpretable Deep Learning
Authors: Cui Yan , Yuan Zhiyuan
Published: August 2024

Spatially resolved transcriptomics technologies enable the mapping of multiplexed gene expression profiles within tissue contexts. To explore the gene spatial patterns in complex tissues, computational methods have been developed to identify spatially variable genes within single tissue slices. However, there is a lack of methods designed to identify genes with differential spatial expression patterns (DSEPs) across multiple slices or conditions, which becomes increasingly common in complex experimental designs. The challenges include the complexity of cross-slice gene expression and spatial information modeling, scalability issues in constructing large-scale cell graphs, and mixed factors of inter-slice heterogeneity. We propose DSEP gene identification as a new task and develop River, an interpretable deep learning-based method, to solve this task. River comprises a two-branch prediction model architecture and a post-hoc attribution method to prioritize DSEP genes that explain condition differences. River’s special design for modeling spatial-informed gene expression makes it scalable to large-scale spatial omics datasets. We proposed strategies to decouple the spatial and non-spatial components of River’s outcomes. We validated River’s performance using simulated datasets and applied it to identify DSEP genes/proteins in diverse biological contexts, including embryo development, diabetes-induced alterations in spermatogenesis, and lupus-induced splenic changes. In a human triple-negative breast cancer dataset, River identified generalizable survival-related DSEPs, validated across unseen patient groups. River does not rely on specific data distribution assumptions and is compatible with various spatial omics data types, making it a versatile method for analyzing complex tissue architectures across multiple biological conditions.
Single component CRISPR-mediated base- editors forAgrobacteriumand their use to develop an improved suite of strains
Authors: Pennetti Vincent J. , LaFayette Peter R. , Parrott Wayne Allen
Published: August 2024

Agrobacterium mediated plant transformation largely depends on two distinct strain lineages – C58 and Ach5. To better serve the plant transformation community, we have created a suite of auxotrophic and auxotrophic recombinant deficient mutants of C58 derivatives EHA105, GV3101::pMP90, and Ach5 derivative LBA4404. While these derivatives are useful, having additional strain backgrounds available would help expand the repertoire for plant transformation even further. Toward that end, two underutilized hypervirulent strains are K599 (NCPPB 2659), and Chry5—but disarmed variants are not easily accessible. To improve availability, we produced disarmed versions ofA. rhizogenesstrain K599 andA. tumefaciensstrain Chry5 and introduced the same desirable mutations as with the other lineages. Each thymidine auxotrophy and recombination deficiency were introduced to existing and newly disarmed Agrobacterium strains via loss of function mutations conferred tothyAandrecA, respectively, through CRISPR-mediated base-editing of codons amenable to nonsense mutation. To streamline the editing process, we created a series of visually marked single component base-editor vectors and a corresponding guide-filtering Geneious Prime wrapper plugin for expedited guide filtering. These new strains, the simplified CRISPR-mediated base-editor plasmids, and streamlined workflow will improve the ease with which futureAgrobacteriumstrain derivatives are created while also supporting plant transformation at large.
Discovery of ICOS-targeted small molecules using affinity selection mass spectrometry screening
Authors: Zhang Longfei , Calvo-Barreiro Laura , de Sousa Batista Victor , Świderek Katarzyna , Gabr Moustafa T.
Published: August 2024

Inducible T cell co-stimulator (ICOS) is a positive immune checkpoint receptor expressed on the surface of activated T cells, which could promote cell function after being stimulated with ICOS ligand (ICOS-L). Although clinical benefits have been reported in the ICOS modulation-based treatment for cancer and autoimmune disease, current modulators are restricted in biologics, whereas ICOS-targeted small molecules are lacking. To fill this gap, we performed an affinity selection mass spectrometry (ASMS) screening for ICOS binding using a library of 15,600 molecules. To the best of our knowledge, this is the first study that utilizes ASMS screening to discover small molecules targeting immune checkpoints. Compound9with a promising ICOS/ICOS-L inhibitory profile (IC50= 29.38 ± 3.41 µM) was selected as the template for the modification. Following preliminary structure-activity relationship (SAR) study and molecular dynamic (MD) simulation revealed the critical role of the ortho-hydroxy group on compound9in the ICOS binding, as it could stabilize the interaction via the hydrogen bond formation with residuals on the glycan, and the depletion could lead to an activity lost. This work validates a promising inhibitor for the ICOS/ICOS-L interaction, and we anticipate future modifications could provide more potent modulators for this interaction.