bluuebunny/crossref_metadata_2025_split huggingface dataset:
TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration
Authors: Nam Hangu , Xie Keqiang , Majumdar Ishita , Yang Shaobo , Starzyk Jakob , Lee Danna , Shan Richard , Li Jiahe , Wu Hao 
Published: August 2023

Summary/AbstractNon-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as agenome engineering catalyst(GATALYST) for efficient and safe targeted gene knock-in. However, the engineering efficiency is bottlenecked by the nucleoplasm trafficking and genomic tethering of cssDNA donor, especially for extra-large transgene integration. Here we developed enGager,enhancedGATALYSTassociatedgenomeeditor system by fusion of nucleus localization signal (NLS) peptide tagged Cas9 with various single stranded DNA binding protein modules through a GFP reporter Knock-in screening. The enGager system assembles an integrative genome integration machinery by forming tripartite complex for engineered nuclease editors, sgRNA and ssDNA donors, thereby facilitate the nucleus trafficking of DNA donors and increase their active local concentration at the targeted genomic site. When applied for genome integration with cssDNA donor templates to diverse genomic loci in various cell types, these enGagers outperform unfused editors. The enhancement of integration efficiency ranges from 1.5- to more than 6-fold, with the effect being more prominent for > 4Kb transgene knock-in in primary cells. We further demonstrated that enGager mediated enhancement for genome integration is ssDNA, but less dsDNA dependent. Using one of the mini-enGagers, we demonstrated large chimeric antigen receptor (CAR) transgene integration in primary T cells with exceptional efficiency and anti-tumor function. These tripartiteeditors withssDNAoptimizedgenomeengineering system (TESOGENASETM) add a set of novel endonuclease editors into the gene-editing toolbox for potential cell and gene therapeutic development based on ssDNA mediated non-viral genome engineering.HighlightA reporter Knock-in screening establishes enGager system to identify TESOGENASE editor to improving ssDNA mediated genome integrationMini-TESOGENASEs developed by fusing Cas9 nuclease with novel ssDNA binding motifsmRNA mini-TESOGENASEs enhance targeted genome integration via various non-viral delivery approachesEfficient functional CAR-T cell engineering by mini-TESOGENASE
Model discovery approach enables non-invasive measurement of intra-tumoral fluid transport in dynamic MRI
Authors: Woodall Ryan T. , Esparza Cora C. , Gutova Margarita , Wang Maosen , Cunningham Jessica J. , Brummer Alexander B. , Stine Caleb A. , Brown Christine C. , Munson Jennifer M. , Rockne Russell C. 
Published: August 2023

AbstractDynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a routine method to non-invasively quantify perfusion dynamics in tissues. The standard practice for analyzing DCE-MRI data is to fit an ordinary differential equation to each voxel. Recent advances in data science provide an opportunity to move beyond existing methods to obtain more accurate measurements of fluid properties. Here, we developed a localized convolutional function regression that enables simultaneous measurement of interstitial fluid velocity, diffusion, and perfusion in 3D. We validated the method computationally and experimentally, demonstrating accurate measurement of fluid dynamicsin situandin vivo. Applying the method to human MRIs, we observed tissue-specific differences in fluid dynamics, with an increased fluid velocity in breast cancer as compared to brain cancer. Overall, our method represents an improved strategy for studying interstitial flows and interstitial transport in tumors and patients. We expect that it will contribute to the better understanding of cancer progression and therapeutic response.One-Sentence SummaryA physics-informed computational method enables accurate and efficient measurement of fluid dynamics in individual patient tumors and demonstrates differences between tissues.
Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles
Authors: Somarathne Radha P. , Misra Sandeep K. , Kariyawasam Chathuri S. , Kessl Jacques J. , Sharp Joshua S. , Fitzkee Nicholas C. 
Published: August 2023

AbstractIn biological systems, proteins can bind to nanoparticles to form a “corona” of adsorbed molecules. The nanoparticle corona is of high interest because it impacts the organism’s response to the nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. Ultimately, a residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein fromStaphylococcus epidermidisand is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Through lysine methylation, we observe subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX measurements reveal that certain regions of the R2ab protein undergo faster exchange rates in the presence of PSNPs, suggesting conformational changes upon binding. Both results support a recently proposed “adsorbotope” model, wherein adsorbed proteins consist of unfolded anchor points interspersed with regions of partial structure. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how proteins respond to nanoparticle surfaces, this research emphasizes the need for advanced methods to comprehend these intricate interactions fully at the residue level.TOC ImageLysine methylation and hydrogen-deuterium exchange can reveal useful structural details about protein adsorption to nanoparticle surfaces.
Differentiation of Wharton’s Jelly-derived mesenchymal stem cells into insulin-producing beta cells with the enhanced functional level on electrospun PRP-PVP-PCL/PCL nanofibers scaffold
Authors: Hashemi Seyed Mohammad Javad , Enderami Seyed Ehsan , Barzegar Ali , Mansour ReyhanehNassiri 
Published: August 2023

ABSTRACTDiabetes is a global problem that threatens human health. Cell therapy methods using stem cells and tissue engineering of pancreatic islets as new therapeutic approaches have increased the chances of successful diabetes treatment. In this study, to differentiate Wharton’s Jelly-derived mesenchymal stem cells (WJ-MSCs) into insulin-producing cells (IPCs) with improved maturity and function, platelet-rich plasma (PRP)-Polyvinylpyrrolidone (PVP)-Polycaprolactone (PCL)/PCL nanofiber scaffold was designed and used. WJ-MSCs-derived IPCs on PRP-PVP-PCL/PCL scaffold took round cluster morphology, which is the typical morphology of pancreatic islets. Real-time PCR, immunocytochemistry, and flow cytometry data showed a significant increase in pancreatic marker genes and insulin in WJ-MSCs-derived IPCs on the PRP-PVP-PCL/PCL scaffold compared to the two-dimensional (2D) experimental group. Also, using the ELISA assay, a significant increase in the secretion of insulin and C-peptide was measured in the WJ-MSCs-derived IPCs of the three-dimensional (3D) experimental group compared to the 2D experimental group, which indicated a significant improvement in the functional level of the WJ-MSCs-derived IPCs in the 3D group. The results showed that the PRP-PVP-PCL/PCL scaffold can provide an ideal microenvironment for the engineering of pancreatic islets and the generation of IPCs.
Nanobodies counteract the toxicity of an amyloidogenic light chain by stabilizing a partially open dimeric conformation
Authors: Luca Broggini , Maria Barzago Monica , Valentina Speranzini , Tim Schulte , Federica Sonzini , Matteo Giono , Margherita Romeo , Paolo Milani , Serena Caminito , Giulia Mazzini , Paola Rognoni , Giampaolo Merlini , Carlo Pappone , Luigi Anastasia , Mario Nuvolone , Giovanni Palladini , Luisa Diomede , Stefano Ricagno 
Published: August 2023

ABSTRACTLight chain amyloidosis (AL) is a systemic disease where fibrillar deposition of misfolded immunoglobulin light chains (LCs) severely affects organ function and results in poor prognosis for patients, especially when heart involvement is severe. Particularly relevant in this context is the cardiotoxicity exerted by still uncharacterized soluble LC species. Here, with the final goal of identifying alternative therapeutic strategies to tackle AL amyloidosis, we produced five llama-derived nanobodies (Nbs) specific against H3, a well-characterized amyloidogenic and cardiotoxic LC from an AL patient with severe cardiac involvement. We found that Nbs are specific and potent agents capable of abolishing H3 soluble toxicity inC. elegans in vivomodel. Structural characterization of H3-Nb complexes revealed that the protective effect of Nbs is related to their ability to bind to the H3 VLdomain and stabilise an unexpected partially open LC dimer in which the two VLdomains no longer interact with each other. Thus, while identifying potent inhibitors of LC soluble toxicity, we also describe the first non-native structure of an amyloidogenic LC that may represent a crucial step in toxicity and aggregation mechanisms.
PKC modulator bryostatin-1 therapeutically targets CNS innate immunity to attenuate neuroinflammation and promote remyelination
Authors: Gharibani Payam , Abramson Efrat , Shanmukha Shruthi , Smith Matthew D. , Godfrey Wesley H. , Lee Judy J. , Hu Jingwen , Baydyuk Maryna , Dorion Marie-France , Deng Xiaojing , Guo Yu , Hwang Soonmyung , Huang Jeffrey K. , Calabresi Peter A. , Kornberg Michael D. , Kim Paul M. 
Published: August 2023

AbstractIn multiple sclerosis (MS), microglia and macrophages within the central nervous system (CNS) play an important role in determining the balance between myelin repair and demyelination/neurodegeneration. Phagocytic and regenerative functions of these CNS innate immune cells support remyelination, whereas chronic and maladaptive inflammatory activation promotes lesion expansion and disability, particularly in the progressive forms of MS. No currently approved drugs convincingly target microglia and macrophages within the CNS, contributing to the critical lack of therapies promoting remyelination and slowing progression in MS. Here, we found that the protein kinase C (PKC)-modulating drug bryostatin-1 (bryo-1), a CNS-penetrant compound with an established human safety profile, produces a shift in microglia and CNS macrophage transcriptional programs from pro-inflammatory to regenerative phenotypes, both in vitro and in vivo. Treatment of microglia with bryo-1 prevented the activation of neurotoxic astrocytes while stimulating scavenger pathways, phagocytosis, and secretion of factors that promote oligodendrocyte differentiation. In line with these findings, systemic treatment with bryo-1 augmented remyelination following a focal demyelinating injury in vivo. Our results demonstrate the potential of bryo-1 and functionally related PKC modulators as myelin regenerative and neuroprotective agents in MS and other neurologic diseases through therapeutic targeting of microglia and CNS-associated macrophages.One Sentence SummaryPKC modulation in CNS innate immune cells favors the activation of a beneficial phenotype that promotes myelin regeneration and neuroprotection.
Behavioural, physiological, and genetic drivers of coping
Authors: Bhattacharjee Debottam , Guðjónsdóttir Aníta Rut , Chova Paula Escriche , Middelburg Esmee , Jäckels Jana , de Groot Natasja G. , Wallner Bernard , Massen Jorg J.M. , Pflüger Lena S. 
Published: August 2023

AbstractAnimals regularly experience stressful situations, ranging from predation to social stress, yet successfully deal with them on most occasions. This adaptive mechanism, coping, reduces the adverse effects of stressors through behavioural and physiological efforts, failing to which may result in reduced fitness. However, considerable variation in coping is observed. Unlike in humans, coping is often considered a personality trait in non-human animals due to construct similarity, resulting in conceptual ambiguity. Besides, limited multidisciplinary research has rendered comprehending the drivers of coping in animals challenging. We assessed repetitive behavioural coping or coping styles (n=30), emotional arousal (n=12), and consistent inter-individual differences, i.e., personalities (n=32) of long-tailed macaques (Macaca fascicularis) using observations, ecologically relevant experiments, and infrared thermography. We finally investigated the association of coping with a Valine/Methionine polymorphism encoded by the Catechol-O-methyltransferase (COMT) gene (n=26), which is widely known for its involvement in human stress regulation. Our findings suggest that personality and the presence of the human equivalentCOMTVal158Met polymorphism in long-tailed macaques are associated with ‘emotion-focused’ and ‘problem-focused’ coping styles. These coping styles were consistent with emotional arousal as measured with infrared thermography. We discuss these proximate drivers of coping for a better understanding of its evolution in primates.
Large-scale analyses reveal the contribution of adaptive evolution in pathogenic and non-pathogenic fungal species
Authors: Pereira Danilo , Bolton Melvin D , Friesen Timothy L , Stephan Wolfgang , Dutheil Julien Y , Stukenbrock Eva H 
Published: August 2023

AbstractGenome studies of fungal pathogens have presented evidence for exceptionally high rates of evolution. It has been proposed that rapid adaptation is a hallmark of pathogen evolution that facilitates the invasion of new host niches and the overcoming of intervention strategies such as fungicide applications and drug treatments. To which extent high levels of genetic variation within and between species correlate with adaptive protein evolution in fungi more generally has so far not been explored. In this study, we addressed the contribution of adaptive evolution relative to genetic drift in 20 fungal species, hereby exploring genetic variation in 2,478 fungal genomes. We reannotated positions of protein-coding genes to obtain a high-quality dataset of 234,427 full-length core gene and 25,612 accessory gene alignments. We applied an extension of the McDonald-Kreitman test that models the distributions of fitness effects to infer the rate of adaptive (ωA) and non-adaptive (ωNA) non-synonymous substitutions in protein-coding genes. To explore the relevance of recombination on local adaptation rates, we inferred the population genomic recombination rate for all 20 species. Our analyses reveal extensive variation in rates of adaptation and show that high rates of adaptation are not a hallmark of a pathogenic lifestyle. Up to 83% of non-synonymous substitutions are adaptive in the speciesParastagonospora nodorum. However, non-synonymous substitutions in other species, including the prominent rice-infecting pathogenMagnaporthe oryzae, are predominantly non-adaptive (neutral or slightly deleterious). Correlating adaptation measures with effective population size and recombination rate, we show that effective population size is a primary determinant of adaptive evolution in fungi. At the genome scale, recombination rate variation explains variation in both ωAand ωNA. Finally, we demonstrate the robustness of our estimates using simulations. We underline the value of population genetic principles in studies of fungal evolution, and we highlight the importance of demographic processes in adaptive evolution of pathogenic and non-pathogenic species.
A viral vector model for circuit-specific synucleinopathy
Authors: Lantheaume Alexia , Schöneberg Nina , Rodriguez-Rozada Silvia , Doll Dennis , Schellenberger Michael , Kobel Konstantin , Katzenberger Kilian , Signoret-Genest Jérémy , Tissone Angela Isabel , Ip Chi Wang , Esposito Maria Soledad , Tovote Philip 
Published: August 2023

ABSTRACTIn Parkinson’s disease (PD), pathomechanisms such as aberrant network dysfunctions can be elucidated by conducting multiscale explorations in animal models. However, the lack of specificity in the existing models limits a restricted targeting of individual network elements and characterization of PD as a “circuitopathy”. We therefore developed a cell-type specific viral vector (AAV2/9-CreON-A53T-αSyn) mouse model that allows to induce synucleinopathy within individual circuit elementsin vivo. When specifically targeted to dopaminergic (DA) neurons of the substantia nigra pars compacta (SNc), our approach recapitulates the main hallmarks of the disease, namely Lewy-body-like aggregation, progressive cellular and nigrostriatal projections loss, together with locomotor impairment. Our strategy is supported by new state-of-the-art analytical approaches for cell quantification and behavior characterization. Altogether, we provide a novel model of synucleinopathy, which offers new opportunities to study the contribution of individual network elements to disease pathomechanisms.
The marmoset default-mode network identified by deactivations in task-based fMRI studies
Authors: Dureux Audrey , Zanini Alessandro , Schaeffer David J. , Johnston Kevin , Gilbert Kyle M. , Everling Stefan 
Published: August 2023

SUMMARYUnderstanding the default-mode network (DMN) in the common marmoset (Callithrix jacchus) has been challenging due to inconsistencies with human and marmoset DMNs. By analyzing task-negative activation in fMRI studies, we identified medial prefrontal cortical areas, rostral auditory areas, entorhinal cortex, posterior cingulate cortex area 31, hippocampus, hypothalamus, and basomedial amygdala as marmoset DMN components. Notable, medial and posterior parietal areas that were previously hypothesized to be part of the DMN were activated during visual task blocks. Seed analysis using resting-state fMRI showed strong connectivity between task-negative areas, and tracer data supported a structural network aligning with this functional DMN. These findings challenge previous definition of the marmoset DMN and reconcile many inconsistencies with the DMNs observed in humans, macaque monkeys, and even rodents. Overall, these results highlight the marmoset as a powerful model for DMN research, with potential implications for studying neuropsychiatric disorders where DMN activity and connectivity are altered.
Methods for evaluating unsupervised vector representations of genomic regions
Authors: Zheng Guangtao , Rymuza Julia , Gharavi Erfaneh , LeRoy Nathan J. , Zhang Aidong , Sheffield Nathan C. 
Published: August 2023

Representation learning models have become a mainstay of modern genomics. These models are trained to yield vector representations, or embeddings, of various biological entities, such as cells, genes, individuals, or genomic regions. Recent applications of unsupervised embedding approaches have been shown to learn relationships among genomic regions that define functional elements in a genome. Unsupervised representation learning of genomic regions is free of the supervision from curated metadata and can condense rich biological knowledge from publicly available data to region embeddings. However, there exists no method for evaluating the quality of these embeddings in the absence of metadata, making it difficult to assess the reliability of analyses based on the embeddings, and to tune model training to yield optimal results. To bridge this gap, we propose four evaluation metrics: the cluster tendency score (CTS), the reconstruction score (RCS), the genome distance scaling score (GDSS), and the neighborhood preserving score (NPS). The CTS and RCS statistically quantify how well region embeddings can be clustered and how well the embeddings preserve information in training data. The GDSS and NPS exploit the biological tendency of regions close in genomic space to have similar biological functions; they measure how much such information is captured by individual region embeddings in a set. We demonstrate the utility of these statistical and biological scores for evaluating unsupervised genomic region embeddings and provide guidelines for learning reliable embeddings.AvailabilityCode is available athttps://github.com/databio/geniml
Epigenome-wide profiling in the dorsal raphe nucleus highlights cell-type-specific changes inTNXBin Alzheimer’s disease
Authors: Riemens RJM , Pishva E , Iatrou A , Roubroeks J , Nolz J , Lardenoije R , Ali M , Del Sol A , Delgado-Morales R , Esteller M , Kenis G , Rutten BPF , Lesch KP , Ginsberg SD , Coleman P , Mill J , Mastroeni D , Ramirez A , Haaf T , Lunnon K , van den Hove DLA 
Published: August 2023

AbstractRecent studies have demonstrated that the dorsal raphe nucleus (DRN) is among the first brain regions affected in Alzheimer’s disease. Hence, in this study we conducted the first comprehensive epigenetic analysis of the DRN in AD, targeting both bulk tissue and single isolated cells. The Illumina Infinium MethylationEPIC BeadChip array was used to analyze the bulk tissue, assessing differentially modified positions (DMoPs) and regions (DMoRs) associated with Braak stage. The strongest Braak stage-associated DMoR inTNXBwas targeted in a second patient cohort utilizing single laser-capture microdissected serotonin-positive (5-HT+) and -negative (5-HT-) cells isolated from the DRN. Our study revealed previously identified epigenetic loci, includingTNXBandPGLYRP1, and novel loci, includingRBMXL2,CAST,GNAT1,MALAT1, andDNAJB13. Strikingly, we found that the methylation profile ofTNXBdepends both on disease phenotype and cell type analyzed, emphasizing the significance of single cell(-type) neuroepigenetic studies in AD.
Phylloxera and aphids show distinct features of genome evolution despite similar reproductive modes
Authors: Li Zheng , Xue Allen Z. , Maeda Gerald P. , Li Yiyuan , Nabity Paul D. , Moran Nancy A. 
Published: August 2023

AbstractGenomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared to the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid’s life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with one sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids’ patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared to their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.