bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracellular Vesicles from Inflammation-Primed Adipose-Derived Stem Cells Enhance Achilles Tendon Repair by Reducing Inflammation and Promoting Intrinsic Healing
Authors: Shen Hua , Lane Ryan A.
Published: February 2023

Achilles tendon rupture is a common sports-related tendon injury. Even with advanced clinical treatments, many patients suffer from long-term pain and reduced function. These unsatisfactory outcomes result primarily from an imbalanced injury response with excessive inflammation and inadequate regeneration. Prior studies showed that extracellular vesicles from inflammation-primed adipose-derived stem cells (iEVs) can attenuate inflammation in the early phase of tendon healing. However, the effect of iEVs on tendon inflammation and regeneration in the later phases of tendon healing and the underlying mechanism remain to be determined. Accordingly, this study investigated the mechanistic roles of iEVs in regulating tendon response to injury using a mouse Achilles tendon injury and repair model in vivo and iEV-macrophage and iEV-tendon cell co-culture models in vitro. Results showed that iEVs promoted tendon anti-inflammatory gene expression and reduced mononuclear cell infiltration in the remodeling phase of tendon healing. iEVs also increased injury site collagen deposition and promoted tendon structural recovery. As such, mice treated with iEVs showed less peritendinous scar formation, much lower incidence of postoperative tendon gap or rupture, and faster functional recovery compared to untreated mice. Further in vitro study revealed that iEVs both inhibited macrophage inflammatory response and increased tendon cell proliferation and collagen production. The iEV effects were partially mediated by miR-147-3p, which blocks the toll-like receptor 4/NF-κB signaling pathway that activates macrophage M1 polarization. The combined results demonstrated that iEVs are a promising therapeutic agent, which can enhance tendon repair by attenuating inflammation and promoting intrinsic healing.

Significance statement

Using a clinically relevant mouse Achilles tendon injury and repair model, this study revealed that iEVs, a biological product generated from inflammation-primed adipose-derived stem cells, can directly target both macrophages and tendon cells and enhance tendon structural and functional recovery by limiting inflammation and promoting intrinsic healing. Results further identified miR-147-3p as one of the active components of iEVs that modulate macrophage inflammatory response by inhibiting toll-like receptor 4/NF-κB signaling pathway. These promising findings paved the road toward clinical application of iEVs in the treatment of tendon injury and other related disorders.
Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics
Authors: Poruthoor Ashlin J. , Sharma Akshara , Grossfield Alan
Published: February 2023

Liquid-liquid phase separation (LLPS) inside the cell often results in biological condensates that can critically impact cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the so-called “lipid raft” hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For this reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation — essentially measuring the sign (but not the amplitude) of the free energy change upon separation — rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from molecular dynamics simulations.

SIGNIFICANCE

Standard molecular dynamics simulations can determine the sign the free energy change upon phase separation, but not the amplitude. We present a new method to determine the phase separation free energy for lipid membranes, based on a enhanced sampling using the weighted ensemble method combined with a novel collective variable, validated using coarse-grained simulations applied to several simple systems. The new method will be valuable as a way to develop models that connect molecular-level structural features to the thermodynamics of phase separation.
The local topology of dynamical network models for biology
Authors: Borriello Enrico
Published: February 2023

The search for motifs –recurrent patterns in the topology of a network– has allowed the identification of universal classes of complex systems from very diverse fields, and has been used as a quantitative tool to highlight unifying properties of evolved and designed networks. This work explores if, and to what extent, network superfamilies previously identified through census of triadic motifs, are represented in the largest data set of dynamic, biological network models. This work presents triad significance profiles of 71 existing biological, and experimentally inspired, network models. The data generated is treated agnostically, and consistently clustered to two classes using several unsupervised techniques. The more populated class correlates with the previously identified superfamily of sensory transmission networks, characterized by the feedforward loop motif typical of signal-processing systems. The other class, surprisingly, better correlates to the superfamily of word-adjacency network. The result is analyzed for varying network size thresholds, and connected to the effect of the model building activity. It is shown that the topology of biological subnetworks starts resembling the topology of “sentences” in word-adjacency networks when the model focuses on smaller portions of the network, coarse-graining the boundary dynamics.
Elamipretide Improves ADP Sensitivity in Aged Mitochondria by Increasing Uptake through the Adenine Nucleotide Translocator (ANT)
Authors: Pharaoh Gavin , Kamat Varun , Kannan Sricharan , Stuppard Rudolph S. , Whitson Jeremy , Martin-Perez Miguel , Qian Wei-Jun , MacCoss Michael J. , Villen Judit , Rabinovitch Peter , Campbell Matthew D. , Sweet Ian R. , Marcinek David J.
Published: February 2023

Aging muscle experiences functional decline in part mediated by impaired mitochondrial ADP sensitivity. Elamipretide (ELAM) rapidly improves physiological and mitochondrial function in aging and binds directly to the mitochondrial ADP transporter ANT. We hypothesized that ELAM improves ADP sensitivity in aging leading to rescued physiological function. We measured the response to ADP stimulation in young and old muscle mitochondria with ELAM treatment,in vivoheart and muscle function, and compared protein abundance, phosphorylation, and S-glutathionylation of ADP/ATP pathway proteins. ELAM treatment increased ADP sensitivity in old muscle mitochondria by increasing uptake of ADP through the ANT and rescued muscle force and heart systolic function. Protein abundance in the ADP/ATP transport and synthesis pathway was unchanged, but ELAM treatment decreased protein s-glutathionylation incuding of ANT. Mitochondrial ADP sensitivity is rapidly modifiable. This research supports the hypothesis that ELAM improves ANT function in aging and links mitochondrial ADP sensitivity to physiological function.

Abstract Figure

Graphical Abstract.

ELAM Binds Directly to ANT and ATP Synthase and ELAM Treatment Improves ADP Sensitivity, Increases ATP Production, and Improves Physiological Function in Old Muscles.

ADP (adenosine diphosphate), ATP (adenosine triphosphate), VDAC (voltage-dependent anion channel), ANT (Adenine nucleotide translocator), H+(proton), ROS (reactive oxygen species), NADH (nicotinamide adenine dinucleotide), FADH2(flavin adenine dinucleotide), O2(oxygen), ELAM (elamipretide), −SH (free thiol), −SSG (glutathionylated protein).
dGAE(297-391) tau fragment promotes formation of CTE-like full-length tau filaments
Authors: Kitoka Kristine , Lends Alons , Kucinskas Gytis , Bula Anna Lina , Krasauskas Lukas , Smirnovas Vytautas , Zilkova Monika , Kovacech Branislav , Skrabana Rostislav , Hritz Jozef , Jaudzems Kristaps
Published: February 2023

The microtubule-associated protein tau forms disease-specific filamentous aggregates in several different neurodegenerative diseases. In order to understand how tau undergoes misfolding into a specific filament type and to control this process for drug development purposes, it is crucial to studyin vitrotau aggregation methods and investigate the structures of the obtained filaments at the atomic level. Here, we used the tau fragment dGAE, which aggregates spontaneously, to seed the formation of full-length tau filaments. The structures of dGAE and full-length tau filaments were investigated by solid-state MAS NMR, showing that dGAE allows propagation of a chronic traumatic encephalopathy (CTE)-like fold to the full-length tau. The obtained filaments efficiently seeded tau aggregation in HEK293T cells. This work demonstrates thatin vitropreparation of disease-specific types of full-length tau filaments is feasible.
Data-driven filtering for denoising of TCRpMHC single-cell data: a benchmark
Authors: Povlsen Helle Rus , Montemurro Alessandro , Jessen Leon Eyrich , Nielsen Morten
Published: February 2023

Pairing of the T cell receptor (TCR) with its cognate peptide-MHC (pMHC) is a cornerstone in T cell-mediated immunity. Recently, single-cell sequencing coupled with DNA-barcoded MHC multimer staining has enabled high-throughput studies of T cell specificities. However, the immense variability of TCR-pMHC interactions combined with the relatively low signal-to-noise ratio in the data generated using current technologies are complicating these studies. Several approaches have been proposed for denoising single-cell TCR-pMHC specificity data. Here, we present a benchmark evaluating two such denoising methods, ICON and ITRAP. We applied and evaluated the methods on publicly available immune profiling data provided by 10x Genomics. We find that both methods identified approximately 75% of the raw data as noise. We analyzed both internal metrics developed for the purpose and performance on independent data using machine learning methods trained on the raw and denoised 10x data. We find an increased signal-to-noise ratio comparing the denoised to the raw data for both methods, and demonstrate an overall superior performance of the ITRAP method in terms of both data consistency and performance. In conclusion, this study demonstrates that Improving the data quality by optimizing signal yield from high throughput studies of TCRpMHC-specificity is paramount in increasing our understanding of T cell-mediated immunity.
Climate, caribou and human needs linked by analysis of Indigenous and scientific knowledge
Authors: Gagnon Catherine A. , Hamel Sandra , Russell Don E. , Andre James , Buckle Annie , Haogak David , Pascal Jessi , Schafer Esau , Powell Todd , Svoboda Michael Y. , Berteaux Dominique
Published: February 2023

Migratory tundra caribou are ecologically and culturally critical in the circumpolar North. However, they are declining almost everywhere in North America, likely due to natural variation exacerbated by climate change and human activities. Yet, the interconnectedness between climate, caribou, and human well-being has received little attention. To address this gap, we bridged Indigenous and scientific knowledge in a single model, using as example the Porcupine caribou herd social-ecological system. Our analysis, involving 688 (fall season) and 616 (spring season) interviews conducted over nine years with 405 (fall season) and 390 (spring season) Indigenous hunters from nine communities, demonstrates that environmental conditions, large-scale temporal changes associated with caribou demography, and cultural practices affect hunters’ capacity to meet their needs in caribou. Our quantitative approach bolsters our understanding of the complex relationships between ecosystems and human welfare in environments exposed to rapid climate change, and shows the benefits of long-term participatory research methods implemented by Indigenous and scientific partners.
Three-dimensional spatial quantitative analysis of cardiac lymphatics in the mouse heart
Authors: Phillips Evan H. , Bindokas Vytautas P. , Jung Dahee , Teamer Jay , Kitajewski Jan K. , Solaro R. John , Wolska Beata M. , Lee Steve Seung-Young
Published: February 2023

Objective

3D microscopy and image data analysis are necessary for studying the morphology of cardiac lymphatic vessels (LyVs) and association with other cell types. We aimed to develop a methodology for 3D multiplexed lightsheet microscopy and highly sensitive and quantitative image analysis to identify pathological remodeling in the 3D morphology of LyVs in young adult mouse hearts with familial hypertrophic cardiomyopathy (HCM).

Methods

We developed a 3D lightsheet microscopy workflow providing a quick turn-around (as few as 5-6 days), multiplex fluorescence detection, and preservation of LyV structure and epitope markers. Hearts from non-transgenic (NTG) and transgenic (TG) HCM mice were arrested in diastole, retrograde perfused, immunolabeled, optically cleared, and imaged. We built an image processing pipeline to quantify LyV morphological parameters at the chamber and branch levels.

Results

Chamber-specific pathological alterations of LyVs were identified, but most significantly in the right atrium (RA). TG hearts had a higher volume fraction of ER-TR7+fibroblasts and reticular fibers. In the RA, we found associations between ER-TR7+volume fraction and both LyV segment density and median diameter.

Conclusions

This workflow and study enabled multi-scale analysis of pathological changes in cardiac LyVs of young adult mice, inviting ideas for research on LyVs in cardiac disease.
The eco-evolution and biodiversity in antagonistic and mutualistic interactive populations
Authors: Wang Lingzi , Pontarp Mikael
Published: February 2023

Understanding environmental and ecological effects on ecosystem structure, function, and dynamics is crucial. However, our comprehension of such effects remains challenging due to the complex interplay of abiotic environment, ecological relationships among species, and coevolution within and across trophic levels. Here, we set out to investigate a wide range of combined ecoevolutionary responses in a plant-insect ecosystem. We study ecological population dynamics, coevolution and functional diversity in response to changes in (1) abiotic-biotic interactions, (2) within-trophic-level competitive interactions, and (3) between-trophic-level antagonistic and mutualistic interactions. We developed an eco-evolutionary and functional trait-based model to simulate environmental and ecologically mediated responses to these interactions. We show that mutualistic interactions render a positive feedback loop of increased population sizes followed by selection for even stronger biotic ecological interactions instead of abiotic interactions. Antagonistic interactions have the opposite effect and adaptation to abiotic environment becomes more important. Furthermore, our study reveals that benign conditions (high ecological opportunities, low within-trophic-level competition, and strong interactions between plants and insects) facilitate functional diversity, whereas harsh conditions impede diversity. These findings provide valuable insights into mechanisms that underlie fundamental eco-evolutionary responses to current environmental and ecological changes, offering potential contributions to ecosystem conservation facing urgent challenges.
TheThCre:mTmGmouse has sparse expression in the sympathetic nervous system
Authors: Tian Tina , Ward Patricia J
Published: February 2023

The global double-fluorescent cre-dependent reporter mousemT/mGhas been a valuable tool for differential identification of tissues and cells. This line was previously shown to have EGFP expression in a cre-dependent fashion in single neurons. Here, we demonstrate very sparse labeling in aThCre:mT/mGcross. This is evident in sweat glands, thoracic spinal cord, sciatic nerve, and lumbar sympathetic ganglia. Therefore, this model may be suitable for imaging or electrophysiology studies of postganglionic sympathetic neuron cell bodies but ineffective for visualizing peripheral axons and tissue targets of the sympathetic nervous system.
Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE
Authors: Chongsaritsinsuk Joann , Steigmeyer Alexandra D. , Mahoney Keira E. , Rosenfeld Mia A. , Lucas Taryn M. , Ince Deniz , Kearns Fiona L. , Battison Alexandria S. , Hollenhorst Marie A. , Shon D. Judy , Tiemeyer Katherine H. , Attah Victor , Kwon Catherine , Bertozzi Carolyn R. , Ferracane Michael J. , Amaro Rommie E. , Malaker Stacy A.
Published: February 2023

Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, −3, −4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in terms of glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamics (MD) simulations of TIM-3 and −4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.
Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Authors: Xiao Dongsheng , Yan Yuhao , Murphy Timothy H
Published: February 2023

Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in behaving animals remain limited. Here we present Mesotrode that integrates chronic wide-field mesoscale cortical imaging and compact multi-site cortical/subcortical cellular electrophysiology in head-fixed mice that undergo self-initiated running or orofacial movements. Specifically, we harnessed the flexibility of chronic multi-site tetrode recordings to monitor single-neuron activity in multiple subcortical structures while simultaneously imaging the mesoscale activity of the entire dorsal cortex. A mesoscale spike-triggered averaging procedure allowed the identification of cortical activity motifs preferentially associated with single-neuron spiking. Using this approach, we were able to characterize chronic single-neuron-related functional connectivity maps for up to 60 days post-implantation. Neurons recorded from distinct subcortical structures display diverse but segregated cortical maps, suggesting that neurons of different origins participate in distinct cortico-subcortical pathways. We extended the capability of Mesotrode by implanting the micro-electrode at the facial motor nerve and found that facial nerve spiking is functionally associated with the PTA, RSP, and M2 network, and optogenetic inhibition of the PTA area significantly reduced the facial movement of the mice. These findings demonstrate that Mesotrode can be used to sample different combinations of cortico-subcortical networks over prolonged periods, generating multimodal and multi-scale network activity from a single implant, offering new insights into the neural mechanisms underlying specific behaviors.
B cell repertoire in children with skin barrier dysfunction supports altered IgE maturation associated with allergic food sensitization
Authors: Gill Kirandeep , Moore Carolina , Nwogu Onyekachi , Kroner John W. , Chang Wan-Chi , Stevens Mariana L. , Baatyrbek kyzy Asel , Biagini Jocelyn M. , Devonshire Ashley L. , Kottyan Leah , Schwartz Justin T. , Assa’ad Amal H. , Martin Lisa J. , Andorf Sandra , Khurana Hershey Gurjit K. , Roskin Krishna M.
Published: February 2023

The skin is a major immune organ and skin barrier dysfunction is a major risk factor for the development of the inappropriate immune response seen in allergic disease. Skin barrier disruption alters the landscape of antigens experienced by the immune system and the downstream impacts on the antibody repertoire remain poorly characterized, particularly for the IgE isotype responsible for allergic specificity and in early life, when allergic disease is developing. In this study, we sequenced antibody gene repertoires from a large and well-characterized cohort of children with atopic dermatitis and found that food sensitization was associated with lower mutation frequencies in the IgE compartment. This trend was abrogated in children living with pets during the first year of life. These results elucidate potential molecular mechanisms underlying the protective effects of pet ownership and non-antiseptic environs reported for allergic disease, and the hygiene hypothesis more broadly. We also observed increased IgE diversity and increased isotype-switching to the IgE isotype, suggesting that B cell development, particularly isotype-switching, is heavily altered in the those with food allergen sensitizations relative to those without food allergen sensitizations. Unlike for food antigens, aeroallergen sensitization exhibited no effect on IgE mutation or diversity. Consistent patterns of antibody rearrangement were associated with food allergen sensitization in subjects with atopic dermatitis. Thus, we propose the Immune Repertoire in Atopic Disease (IRAD) score, to quantify this repertoire shift and to aid clinically in patient diagnosis and risk stratification.

One Sentence Summary

Food allergic sensitization is associated with altered B cell development in children with skin barrier dysfunction.
The gene expression classifier ALLCatchR identifies B-precursor ALL subtypes and underlying developmental trajectories across age
Authors: Beder Thomas , Hansen Björn-Thore , Hartmann Alina M. , Zimmermann Johannes , Amelunxen Eric , Wolgast Nadine , Walter Wencke , Zaliova Marketa , Antić Željko , Chouvarine Philippe , Bartsch Lorenz , Barz Malwine , Bultmann Miriam , Horns Johanna , Bendig Sonja , Kässens Jan , Kaleta Christoph , Cario Gunnar , Schrappe Martin , Neumann Martin , Gökbuget Nicola , Bergmann Anke Katharina , Trka Jan , Haferlach Claudia , Brüggemann Monika , Baldus Claudia D. , Bastian Lorenz
Published: February 2023

Current classifications (WHO-HAEM5 / ICC) define up to 26 molecular B-cell precursor acute lymphoblastic leukemia (BCP-ALL) disease subtypes, which are defined by genomic driver aberrations and corresponding gene expression signatures. Identification of driver aberrations by RNA-Seq is well established, while systematic approaches for gene expression analysis are less advanced. Therefore, we developed ALLCatchR, a machine learning based classifier using RNA-Seq expression data to allocate BCP-ALL samples to 21 defined molecular subtypes. Trained on n=1,869 transcriptome profiles with established subtype definitions (4 cohorts; 55% pediatric / 45% adult), ALLCatchR allowed subtype allocation in 3 independent hold-out cohorts (n=1,018; 75% pediatric / 25% adult) with 95.7% accuracy (averaged sensitivity across subtypes: 91.1% / specificity: 99.8%). ‘High confidence predictions’ were achieved in 84.6% of samples with 99.7% accuracy. Only 1.2% of samples remained ‘unclassified’. ALLCatchR outperformed existing tools and identified novel candidates in previously unassigned samples. We established a novel RNA-Seq reference of human B-lymphopoiesis. Implementation in ALLCatchR enabled projection of BCP-ALL samples to this trajectory, which identified shared patterns of proximity of BCP-ALL subtypes to normal lymphopoiesis stages. ALLCatchR sustains RNA-Seq routine application in BCP-ALL diagnostics with systematic gene expression analysis for accurate subtype allocations and novel insights into underlying developmental trajectories.
The Master Database of All Possible RNA Sequences and Its Integration with RNAcmap for RNA Homology Search
Authors: Chen Ke , Litfin Thomas , Singh Jaswinder , Zhan Jian , Zhou Yaoqi
Published: February 2023

Recent success of AlphaFold2 in protein structure prediction relied heavily on co-evolutionary information derived from homologous protein sequences found in the huge, integrated database of protein sequences (Big Fantastic Database). In contrast, the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search. Here, we built a comprehensive database by including the noncoding RNA sequences from RNAcentral, the transcriptome assembly and metagenome assembly from MG-RAST, the genomic sequences from Genome Warehouse (GWH), and the genomic sequences from MGnify, in addition to NCBI’s nucleotide database (nt) and its subsets. The resulting MARS database (Master database of All possible RNA sequences) is 20-fold larger than NCBI’s nt database or 60-fold larger than RNAcentral. The new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques. It also yields more accurate and more sensitive multiple sequence alignments (MSA) than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam. The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of noncoding RNAs.
Algae Facade Technology in Improving Air Quality and Building Health: Analysis of Microclimate and Growth ofAspergillus niger
Authors: Algifari Muhammad Haikal , Daniel Ridzik Malky , Nofdianto
Published: February 2023

This research was conducted in response to concerns about room comfort and the Sick Building Syndrome (SBS) phenomenon. The focus of this study was to examine the effect of photobioreactor (PBR) based algae facade on the room microclimate and growth ofAspergillus niger. A glass simulation chamber resembling the letter “U” with a size of 40 cm long, 40 cm wide, and 40 cm high has been used for the experiment. Twenty samples ofAspergillus nigerwere tested for 11 days in four simulation chambers and were given different treatments, two rooms were installed with PBR and the other two rooms were not installed PBR (control). The room with PBR had a relatively lower temperature and humidity in the peak phase with a difference of 4.3°C and 5.5% RH compared to the control room. In addition, three out of ten molds in the PBR chamber had a growth rate of about 0.94 cm2/day and the spore production of 1.9×104CFU/ml. Meanwhile, seven out of ten molds in the control room had a growth rate of 1.4 cm2/day and an average spore production of 5.4×104CFU/ml. These results indicate that the algae facade is able to improve the microclimate of the room and suppress the growth rate ofAspergillus niger. mold in buildings.
An Empirical Study on the Motivation of Helping Behavior in Rats
Authors: Han Shu , Chen Ya-Qin , Zheng Benhuiyuan , Wang Ya-Xin , Yin Bin
Published: February 2023

Using rodent models to explore the motivation of helping behaviors has become a new trend in recent years. Empathy, the alleviation of personal distress, and desire for social contact have been considered motivations for rodents to engage in helping behaviors. We used 108 Sprague-Dawley rats as subjects and modified the two-chambered helping behavior experimental setup in Carvalheiro and colleagues’ study to explore the main motivations of helping behavior in rodents through three experiments. The findings suggest that (1) the desire for social contact and pursuit of an interesting environment are the primary motivations for helping behavior, regardless of the presence of a dark chamber, and (2) the alleviation of personal distress and prior experience of social contact rather than distress experience contribute to the onset and persistence of helping behavior.
PLANET: A Multi-Objective Graph Neural Network Model for Protein–Ligand Binding Affinity Prediction
Authors: Zhang Xiangying , Gao Haotian , Wang Haojie , Chen Zhihang , Zhang Zhe , Chen Xinchong , Li Yan , Qi Yifei , Wang Renxiao
Published: February 2023

Predicting protein-ligand binding affinity is a central issue in drug design. Various deep learning models have been developed in recent years to tackle this issue, but many of them merely focus on reproducing the binding affinity of known binders. In this study, we have developed a graph neural network model called PLANET (Protein-Ligand Affinity prediction NETwork). This model takes the graph-represented 3D structure of the binding pocket on the target protein and the 2D chemical structure of the ligand molecule as input, and it was trained through a multi-objective process with three related tasks, including deriving the protein–ligand binding affinity, protein–ligand contact map, and intra-ligand distance matrix. To serve those tasks, a large number of decoy non-binders were selected and added to the standard PDBbind data set. When tested on the CASF-2016 benchmark, PLANET exhibited a scoring power comparable to other deep learning models that rely on 3D protein–ligand complex structures as input. It also showed notably better performance in virtual screening trials on the DUD-E and LIT-PCBA benchmark. In particular, PLANET achieved comparable accuracy on LIT-PCBA as the conventional docking program Glide. However, it only took less than 1% of the computation time required by Glide to finish the same job because it did not perform exhaustive conformational sampling. In summary, PLANET exhibited a decent performance in binding affinity prediction as well as virtual screening, which makes it potentially useful for drug discovery in practice.
Irreversible inhibition of TRF2TRFHrecruiting functions: a strategy to induce telomeric replication stress in cancer cells
Authors: Sobinoff Alexander P. , Di Maro Salvatore , Low Ronnie R. J. , Benedetti Rosaria , Tomassi Stefano , D’Aniello Antonia , Russo Rosita , Baglivo Ilaria , Chianese Ugo , Pedone Paolo V. , Chambery Angela , Cesare Anthony J. , Altucci Lucia , Pickett Hilda A. , Cosconati Sandro
Published: February 2023

The shelterin component telomeric repeat-binding factor 2 (TRF2) is an essential regulator of telomere homeostasis and genomic stability. Mutations in the TRF2TRFHdomain physically impair t-loop formation and prevent the recruitment of several factors that promote efficient telomere replication, resulting in a telomeric DNA damage response. Here, we design, synthesize, and biologically test covalent cyclic peptides that irreversibly target the TRF2TRFHdomain. We identify APOD53 as our most promising compound. APOD53 forms a covalent adduct with a reactive cysteine residue present in the TRF2TRFHdomain and induces phenotypes consistent with TRF2TRFHdomain mutants. These include induction of a telomeric DNA damage response in the absence of fusions, increased telomeric replication stress, and impaired recruitment of regulator of telomere elongation helicase 1 (RTEL1) and structure-specific endonuclease subunit (SLX4) to telomeres. We demonstrate that APOD53 impairs cell growth in both a telomerase-positive and an ALT cell line, while sparing the viability of non-cancerous cells. Finally, we find that co-treatment with APOD53 and the G4 stabilizer RHPS4 further exacerbates telomere replication stress.
RNA as a component of fibrils from Alzheimer’s disease and other neurodegenerations
Authors: Bridges Leslie R.
Published: February 2023

Fibrils from brains of patients with Alzheimer’s disease1–5, Parkinson’s disease6, amyotrophic lateral sclerosis7and other neurodegenerations3,4,8–18contain unknown molecules. Extra densities (EDs), containing these unknown molecules, are available to examine in electron cryo-microscopy maps from the Electron Microscopy Data Bank19, a public repository. EDs can be visualised in their protein environments using matched atomic models from the Protein Data Bank20, another public repository. Lysine-coordinating EDs from a wide range of neurodegenerative diseases1–6,8–18and EDs from the glycine-rich region of TAR DNA-binding protein 43 (TDP-43) fibrils in amyotrophic lateral sclerosis with frontotemporal lobar degeneration (ALS-FTLD)7were the subject of the present study. EDs ran parallel to the fibril axis and at right angles to protein with a repeat distance matching that of protein. They formed connections with protein consistent with a role in the guided assembly of fibrils. They had a connectivity pattern and estimated molecular weights consistent with ribonucleic acid (RNA). A straight form of RNA (ortho-RNA, oRNA) was modelled into one ED. It fitted other EDs and formed a rich symmetrical network of hydrogen bonds when docked to protein, implicating RNA as a unifying and organising factor in neurodegeneration. A new hypothesis of neurodegeneration (ponc,proteinortho-nucleic acidcomplex, pronounced ponk) is proposed in which RNA is the driver of these diseases. According to the ponc hypothesis, a particular RNA sequence (likely repetitive) enciphers a particular strain of ponc agent with its own protein fold and type of neurodegeneration. Ponc provides an explanation of fibril growth and replication, species barrier and adaptation, inherited neurodegeneration, resistance to chemicals and irradiation, protein-free transmission and co-pathologies. Ponc may also be relevant to other chronic diseases and origins of life. New treatments might be possible, targeting the unique chemical and physical properties of ponc.
Construction of a searchable database for gene expression changes in spinal cord injury experiments
Authors: Rouchka Eric C. , de Almeida Carlos , House Randi B. , Daneshmand Jonah C. , Chariker Julia H. , Saraswat-Ohri Sujata , Gomes Cynthia , Sharp Morgan , Shum-Siu Alice , Cesarz Greta M. , Petruska Jeffrey C. , Magnuson David S.K.
Published: February 2023

Spinal cord injury (SCI) is a debilitating disease resulting in an estimated 18,000 new cases in the United States on an annual basis. Significant behavioral research on animal models has led to a large amount of data, some of which has been catalogued in the Open Data Commons for Spinal Cord Injury (ODC-SCI). More recently, high throughput sequencing experiments have been utilized to understand molecular mechanisms associated with SCI, with nearly 6,000 samples from over 90 studies available in the Sequence Read Archive. However, to date, no resource is available for efficiently mining high throughput sequencing data from SCI experiments. Therefore, we have developed a protocol for processing RNA-Seq samples from high-throughput sequencing experiments related to SCI resulting in both raw and normalized data that can be efficiently mined for comparisons across studies as well as homologous discovery across species. We have processed 1,196 publicly available RNA-seq samples from 50 bulk RNA-Seq studies across nine different species, resulting in an SQLite database that can be used by the SCI research community for further discovery. We provide both the database as well as a web-based front-end that can be used to query the database for genes of interest, differential gene expression, genes with high variance, and gene set enrichments.
PlasmidHunter: Accurate and fast prediction of plasmid sequences using gene content profile and machine learning
Authors: Tian Renmao , Imanian Behzad
Published: February 2023

Plasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions, but they can also carry genes that make bacteria harmful to humans. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be difficult to identify plasmid sequences from chromosomal sequences in genomic and metagenomic data. Here, we have developed a new tool called PlasmidHunter, which uses machine learning to predict plasmid sequences based on gene content profile. PlasmidHunter achieved high accuracies (up to 96.7%) and fast speeds in benchmark tests, outperforming other existing tools.
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms
Authors: Zheng Yiqiao , Sun Chi , Zhang Xiaodong , Ruzycki Philip A. , Chen Shiming
Published: February 2023

Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here we useCone-Rod Homeobox (CRX)as a model to decipher the disease-causing mechanisms of two HD mutations,p.E80Aandp.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidencein vitroand in knock-in mouse models, we uncover two novel gain-of-function mechanisms:p.E80Aincreases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors;p.K88Nalters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
High-Accuracy Machine Learning Techniques for Functional Connectome Fingerprinting and Cognitive State Decoding
Authors: Hannum Andrew , López Mario A. , Blanco Saúl A. , Betzel Richard F.
Published: February 2023

The human brain is a complex network comprised of functionally and anatomically interconnected brain regions. A growing number of studies have suggested that empirical estimates of brain networks may be useful for discovery of biomarkers of disease and cognitive state. A prerequisite for realizing this aim, however, is that brain networks also serve as reliable markers of an individual. Here, using Human Connectome Project data, we build upon recent studies examining brain-based fingerprints of individual subjects and cognitive states based on cognitively-demanding tasks that assess, for example, working memory, theory of mind, and motor function. Our approach achieves accuracy of up to 99% for both identification of the subject of an fMRI scan, and for classification of the cognitive state of a previously-unseen subject in a scan. More broadly, we explore the accuracy and reliability of five different machine learning techniques on subject fingerprinting and cognitive state decoding objectives, using functional connectivity data from fMRI scans of a high number of subjects (865) across a number of cognitive states (8). These results represent an advance on existing techniques for functional connectivity-based brain fingerprinting and state decoding. Additionally, 16 different pre-processing pipelines are compared in order to characterize the effects of different aspects of the production of functional connectomes (FCs) on the accuracy of subject and task classification, and to identify possible confounds.
Variability in Forest Plant Traits along the Western Ghats of India and Their Environmental Drivers at Different Resolutions
Authors: Zheng Ting , Singh Aditya , Desai Ankur R. , Krishnayya N.K. , Townsend Philip A.
Published: February 2023

Identifying key environmental drivers for plant functional traits is an important step to understanding and predicting ecosystem responses to a changing climate. Imaging spectroscopy offers great potential to map plant traits at fine resolution across broad regions and then assess controls on their variation across spatial resolutions. We applied permutational partial least-squares regression to map seven key foliar chemical and morphological traits using NASA’s Airborne Visible/Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) for six sites spanning the Western Ghats of India. We studied the variation of trait space using principal components analysis at spatial resolutions from the plot level (4m), community level (30m and 100m) to the ecosystem level (1000m). We observed a consistent pattern of trait space across different resolutions, with one axis representing the traditional leaf economic spectrum defined by foliar nitrogen concentration and leaf mass per area (LMA) and another axis representing leaf structure and defense defined by fiber, lignin, and total phenolics. We also observed consistent directionality of environment-trait correlations across resolutions with generally higher predictive capacity of our environment-traits models at coarser resolutions. Among the seven traits, total phenolics, fiber, and lignin showed strong environmental dependencies across sites, while calcium, sugar, and nitrogen were significantly affected by site conditions. Models incorporating site as a fixed effect explained more than 50% of the trait variance at 1000m resolution. LMA showed little dependence on both environment and site conditions, implying other factors such as species composition and perhaps site history strongly affect variation in LMA. Our results show that reliable trait-trait relationships can be identified in coarse resolution imagery, but that local scale trait-trait relationships (resolutions finer than 30m) are not sensitive to broad-scale abiotic/biotc factors.
Acute repair of meniscus root tear partially restores joint displacements as measured with MRI and loading in a porcine knee
Authors: Meadows Kyle D. , Peloquin John M. , Markhali Milad I. , Zgonis Miltiadis H. , Schaer Thomas P. , Mauck Robert L. , Elliott Dawn M.
Published: February 2023

The meniscus serves important load-bearing functions and protects the underlying articular cartilage. Unfortunately, meniscus tears are common and impair the ability of the meniscus to distribute loads, greatly increasing the risk for developing osteoarthritis. Therefore, surgical repair of the meniscus is a frequently performed procedure; however, this repair does not always prevent osteoarthritis. This is hypothesized to be due to altered joint loading post injury and repair, where the functional deficit of the meniscus prevents it from performing its role of distributing forces. However, many studies of meniscus function required opening the joint, which alters kinematics. The objective of this study was to use novel MRI methods to image the intact joint under axial load and measure the acute meniscus and femur displacements in an intact joint, after a meniscus root tear, and after suture repair in the porcine knee, a frequently used in vivo model. We found that anterior root tear led to large meniscus and femur displacements under physiological axial loading, and that suture anchor repair reduced these displacements, but did not fully restore intact joint kinematics. After tear and repair, the anterior region of the meniscus moved posteriorly and medially as it was forced out of the joint space under loading, while the posterior region had small displacements as the posterior attachment acted as a hinge about which the meniscus rotated in the axial plane. This technique can be applied to evaluate the effect of knee injuries and to develop improved repair strategies to restore joint kinematics.
SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses
Authors: Chen Liyun , Shi Victoria , Wang Songyan , Freeman Rebecca , Ruiz Fiona , Jayachandran Kay , Zhang Jin , Cosper Pippa , Sun Lulu , Luke Clifford J. , Spina Catherine , Grigsby Perry W. , Schwarz Julie K. , Markovina Stephanie
Published: February 2023

Radiotherapy is a commonly used cancer treatment; however, patients with high serum squamous cell carcinoma antigen (SCCA1/SERPINB3) are associated with resistance and poor prognosis. Despite being a strong clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We investigated the microenvironment of SERPINB3 high tumors through RNAseq of primary cervix tumors and found thatSERPINB3was positively correlated withCXCL1/8, S100A8/A9and myeloid cell infiltration. Induction of SERPINB3in vitroresulted in increased CXCL1/8 and S100A8/A9 production, and supernatants from SERPINB3-expressing cultures attracted monocytes and MDSCs. In murine tumors, the orthologuemSerpinB3apromoted MDSC, TAM, and M2 macrophage infiltration contributing to an immunosuppressive phenotype, which was further augmented upon radiation. Radiation-enhanced T cell response was muted in SERPINB3 tumors, whereas Treg expansion was observed. A STAT-dependent mechanism was implicated, whereby inhibiting STAT signaling with ruxolitinib abrogated suppressive chemokine production. Patients with elevated pre-treatment serum SCCA and high pSTAT3 had increased intratumoral CD11b+ myeloid cell compared to patients with low SCCA and pSTAT3 cohort that had overall improved cancer specific survival after radiotherapy. These findings provide a preclinical rationale for targeting STAT signaling in tumors with high SERPINB3 to counteract the immunosuppressive microenvironment and improve response to radiation.
Adipocyte lipin 1 is positively associated with metabolic health in humans and regulates systemic metabolism in mice
Authors: LaPoint Andrew , Singer Jason M. , Ferguson Daniel , Shew Trevor M. , Renkemeyer M. Katie , Palacios Hector , Field Rachael , Shankaran Mahalakshmi , Smith Gordon I. , Yoshino Jun , He Mai , Patti Gary J. , Hellerstein Marc K. , Klein Samuel , Brestoff Jonathan R. , Finck Brian N. , Lutkewitte Andrew J.
Published: February 2023

Dysfunctional adipose tissue is believed to promote the development of hepatic steatosis and systemic insulin resistance, but many of the mechanisms involved are still unclear. Lipin 1 catalyzes the conversion of phosphatidic acid to diacylglycerol (DAG), the penultimate step of triglyceride synthesis, which is essential for lipid storage. Herein we found that adipose tissueLPIN1expression is decreased in people with obesity compared to lean subjects and lowLPIN1expression correlated with multi-tissue insulin resistance and increased rates of hepatic de novo lipogenesis. Comprehensive metabolic and multi-omic phenotyping demonstrated that adipocyte-specificLpin1-/-mice had a metabolically-unhealthy phenotype, including liver and skeletal muscle insulin resistance, hepatic steatosis, increased hepatic de novo lipogenesis, and transcriptomic signatures of nonalcoholic steatohepatitis that was exacerbated by high-fat diets. We conclude that adipocyte lipin 1-mediated lipid storage is vital for preserving adipose tissue and systemic metabolic health and its loss predisposes mice to nonalcoholic steatohepatitis.