bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteolytic Remodeling of 3D Bioprinted Tumor Microenvironments
Authors: Boroojeni Fatemeh Rasti , Naeimipour Sajjad , Lifwergren Philip , Abrahamsson Annelie , Dabrosin Charlotta , Selegård Robert , Aili Daniel 
Published: June 2023

AbstractIn native tissue, remodeling of the pericellular space is essential for cellular activities and is mediated by tightly regulated proteases. Protease activity is dysregulated in many diseases, including many forms of cancer. Increased proteolytic activity is directly linked to tumor invasion into stroma, metastasis, and angiogenesis as well as all other hallmarks of cancer. Here we show how integrated 3D bioprinted structures with distinctly different responses to proteolytic activity can be utilized for systematic investigation of proteolytic remodeling of the extra cellular matrix and the impact of stromal cells on protease driven processes. Bioprinted structures combining non-degradable and degradable hydrogels were designed and demonstrated to be selectively degraded by proteases allowing for protease-mediated material reorganization with high spatial resolution. Bioprinting of tumor microenvironments combining bioinks with different susceptibilities to proteolytic degradation shows that breast cancer cell proliferation, migration into stromal compartments, and spheroid size are significantly increased in protease degradable hydrogels, but only in the presence of fibroblasts. Proteolytic remodeling of the tumor microenvironment has a significant effect on tumor progression and is drastically influenced by the intimate crosstalk between fibroblast and breast cancer cells.
Monitoring norepinephrine releasein vivousing next-generation GRABNEsensors
Authors: Feng Jiesi , Dong Hui , Lischinsky Julieta , Zhou Jingheng , Deng Fei , Zhuang Chaowei , Miao Xiaolei , Wang Huan , Xie Hao , Cui Guohong , Lin Dayu , Li Yulong 
Published: June 2023

SummaryNorepinephrine (NE) is an essential biogenic monoamine neurotransmitter, yet researches using prototype NE sensors were limited by their low sensitivities. Here, we developed next-generation versions of GPCR activation-based NE sensors (GRABNE2mand GRABNE2h) with a superior response, high sensitivity and selectivity to NE bothin vitroandin vivo. Notably, these sensors can detect NE release triggered by either optogenetic or behavioral stimuli in freely moving mice, producing robust signals in the locus coeruleus and hypothalamus. With the development of a novel transgenic mouse line, we recorded both NE release and calcium dynamics with dual-color fiber photometry throughout the sleep-wake cycle; moreover, dual-color mesoscopic imaging revealed cell type‒specific spatiotemporal dynamics of NE and calcium during sensory processing and locomotion. Thus, these new GRABNEsensors are valuable tools for monitoring the precise spatiotemporal release of NEin vivo, providing new insights into the physiological and pathophysiological roles of NE.
Technique for rapidly forming networks of microvessel-like structures
Authors: Hewes Sarah A. , Ahmad Fariha N. , Connell Jennifer P. , Grande-Allen K. Jane 
Published: June 2023

AbstractModelling organ-blood barriers through the inclusion of microvessel networks withinin vitrotissue models could lead to more physiologically accurate results, especially since organ-blood barriers are crucial to the normal function, drug transport, and disease states of vascularized organs. Microvessel networks are difficult to form, since they push the practical limit of most fabrication methods, and it is difficult to coax vascular cells to self-assemble into structures larger than capillaries. Here we present a method for rapidly forming networks of microvessel-like structures using sacrificial, alginate structures. Specifically, we encapsulated endothelial cells within short alginate threads, then embedded them in collagen gel. Following enzymatic degradation of the alginate, the collagen gel contained a network of hollow channels seeded with cells, all surrounding a perfusable central channel. This method uses a 3D printed coaxial extruder and syringe pumps to generate short threads in a way that is repeatable and easily transferrable to other labs. The cell-laden, sacrificial alginate threads can be frozen after fabrication and thawed before embedding without significant loss of cell viability. The ability to freeze the threads enables future scale up and ease of use. Within millifluidic devices that restrict access to media, the threads enhance cell survival under static conditions. These results indicate the potential for use of this method in a range of tissue engineering applications.Impact StatementGenerating microvascular networks is a challenge in tissue engineering. Popular 3D bioprinting techniques use sacrificial structures to generate vascular networks, but those approaches can require expensive equipment and extensive troubleshooting. In this article, a method is presented for easy and rapid generation of centimeter-scale microvascular networks using endothelial cells frozen within sacrificial structures. The method for fabricating and freezing the sacrificial threads of alginate containing cells using a 3D printed coaxial extruder is also described. Experimental results indicate that these microstructures have the potential to enhance cell survival in environments with restricted access to media.
Cell swelling enhances canonical β-adrenergic signaling
Authors: Sirbu Alexei , Bathe-Peters Marc , Kumar Jothi L.M. , Inoue Asuka , Lohse Martin J. , Annibale Paolo 
Published: June 2023

AbstractG protein-coupled receptors’ conformational landscape can be affected by their local, microscopic interactions within the cell plasma membrane. We employ here a pleiotropic stimulus, namely osmotic swelling, to alter the cortical environment within intact cells and monitor the response in terms of receptor function and downstream signaling. We observe that in osmotically swollen cells the β2-adrenergic receptor, a prototypical GPCR, favors an active conformation, resulting in cAMP transient responses to adrenergic stimulation that have increased amplitude. The results are validated in primary cell types such as adult cardiomyocytes, a model system where swelling occurs upon ischemia-reperfusion injury. Our results suggest that receptors’ function is finely modulated by their biophysical context, and specifically that osmotic swelling acts as a potentiator of downstream signaling, not only for the β2-adrenergic receptor, but also for other receptors, hinting at a more general regulatory mechanism.
Repression of Aurora kinase B prevents growth and tissue invasion in medulloblastoma
Authors: Gries Alexandre , Kumar Karthiga Santhana , Kuttler Fabien , Grotzer Michael A. , Baumgartner Martin 
Published: June 2023

AbstractNovel treatment strategies are required to overcome therapy-associated sequelae in survivors of pediatric medulloblastoma (MB) while maintaining therapeutic efficacy. The tissue impact on drug response in MB is not well understood and drug profiling in the physiological context of the tissue may reveal novel therapy targets.To gain insights into the growth and dissemination behavior of the MB tumor cells under treatment, we combined three-dimensional cell culture screening withex vivoorganotypic cerebellum slice co-culture (OCSC), which allowed assessing tumor cell behavior in the tissue context.We screened a panel of 274 kinase inhibitors and identified aurora kinase B (AURKB) as a potential anti-invasion drug target in MB. We validated tumor suppressive activities of the AURKB inhibitor (AURKBi) barasertib and the structurally unrelated compound GSK-1070916 in cerebellum slice culture models for SHH, Grp3 and Grp4 MB at nanomolar concentrations. We confirmed the necessity of AURKB for tumor growth through genetic suppression of AURKB by siRNA in the tissue context. We revealed that the combination of AURKBi with the SRC/BCR-ABL inhibitor dasatinib acts synergistically to repress tumor growth and invasiveness in the SHH MB cell model ONS76, but not in Grp3 MB cells. Finally, we demonstrate that pharmacological repression of AURKB in the tissue context is as effective as X-ray irradiation to repress tumor growth.Our data highlight that AURKBi is equally efficient as irradiation, suggesting that pharmacological targeting of AURKB may constitute a novel means to overcome radiotherapy limitations in patients younger than three years.Importance of the studyOur data demonstrate anti-tumor activity of AURKB inhibitors in the tissue context for MB tumor cells that arein vitroresistant to the treatment. This indication of a tissue component to drug response contributes critical insights for drug response profiling for brain tumors. AURKB inhibitors barasertib and GSK-1070916 block growth and invasiveness of SHH, Grp3 and Grp4 MB tumor cells as well as primary ATRT. Importantly, AURKBi is equally efficient as irradiation. In conclusion, a tissue component contributes to sensitivity to AURKB inhibition and pharmacological targeting of AURKB may constitute a novel means to overcome radiotherapy limitations in patients younger than three years.Key pointsAURKB is essential for in tissue growth of MB.Inactivation of AURKB causes p53 upregulation and decreased in tissue growth and dissemination.AURKB inhibition in the tissue context is as effective as irradiation to restrict tumor cell growth.
Vocabulary Matters: An Annotation Pipeline and Two Deep Learning Algorithms for Enzyme Named Entity Recognition
Authors: Wang Meiqi , Vijayaraghavan Avish , Beck Tim , Posma Joram M. 
Published: June 2023

AbstractEnzymes are indispensable substances in many biological processes. With biomedical literature growing exponentially, it becomes more difficult to review the literature effectively. Hence, text-mining techniques are needed to facilitate and speed up literature review. The aims of this study are to create a corpus with annotated enzymes to train and evaluate enzyme named-entity recognition (NER) models. A novel pipeline was built using a combination of dictionary matching and rulebased keyword searching to automatically annotate enzyme entities in over 4,800 biomedical full texts. Two Bidirectional Long Short-Term Memory (BiLSTM) networks using BioBERT and SciBERT as tokeniser and word embedding layers were trained on this corpus and evaluated on a manually annotated test set of 526 full-text publications. The dictionary- and rule-based annotation pipeline achieved an F1-score of 0.863 (precision 0.996, recall 0.762). The SciBERT-BiLSTM model (F1-score 0.965, precision 0.981, recall 0.954) largely out-performed the BioBERT-BiLSTM model (F1-score 0.955, precision 0.981, recall 0.937). This study contributed a novel dictionary- and rule-based automatic pipeline with almost perfect precision which runs in a matter of seconds on a standard laptop. Both deep learning (DL) models achieved state-of-the-art performance (F1>0.95) for enzyme NER, with the SciBERT-based model outperforming the BioBERT-based model in terms of recall, demonstrating the vocabulary used by models matters. The proposed pipeline with the DL models can facilitate more effective enzyme text-mining and information extraction research for literature review and are the first algorithms specifically for enzyme NER.AvailabilityAll codes are available for automatic annotation and model training (including data), with instructions on how to deploy the model on new text, fromhttps://github.com/omicsNLP/enzymeNER.
Alternative splicing and environmental adaptation in house mice
Authors: Manahan David N. , Nachman Michael W. 
Published: June 2023

AbstractA major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identifycis-acting splicing quantitative trait loci (cis-sQTL), and we identifiedcis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in transcript level, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.
Single neuron analysis of aging associated changes in learning reveals progressive impairments in transcriptional plasticity
Authors: Badal Kerriann K , Sadhu Abhishek , McCracken Carrie , Raveendra Bindu L , Lozano-Villada Sebastian , Shetty Amol C , Gillette Phillip , Zhao Yibo , Stommes Dustin , Fieber Lynne A , Schmale Michael C , Mahurkar Anup , Hawkins Robert D , Puthanveettil Sathyanarayanan V 
Published: June 2023

ABSTRACTMolecular mechanisms underlying aging associated impairments in learning and long-term memory storage are poorly understood. Here we leveraged the single identified motor neuron L7 inAplysia,which mediates a form of non-associative learning, sensitization of the siphon-withdraw reflex, to assess the transcriptomic correlates of aging associated changes in learning. RNAseq analysis of the single L7 motor neuron isolated following short-term or long-term sensitization training of 8,10 and 12 months oldAplysia,corresponding to mature, late mature and senescent stages, has revealed progressive impairments in transcriptional plasticity during aging. Specifically, we observed modulation of the expression of multiple lncRNAs and mRNAs encoding transcription factors, regulators of translation, RNA methylation, and cytoskeletal rearrangements during learning and their deficits during aging. Our comparative gene expression analysis also revealed the recruitment of specific transcriptional changes in two other neurons, the motor neuron L11 and the giant cholinergic neuron R2 whose roles in long-term sensitization were previously not known. Taken together, our analyses establish cell type specific progressive impairments in the expression of learning- and memory-related components of the transcriptome during aging.
Hyperosmolarity-induced suppression of group B1 Raf-like protein kinases modulates drought-growth trade-off inArabidopsis
Authors: Kamiyama Yoshiaki , Katagiri Sotaro , Yamashita Kota , Li Yangdan , Takase Hinano , Umezawa Taishi 
Published: June 2023

AbstractWhen plants are exposed to drought stress, there is a trade-off between plant growth and stress responses. Here, we identified a signaling mechanism for the initial steps of the drought-growth trade-off. Phosphoproteomic profiling revealed that Raf13, a B1 subgroup Raf-like kinase, is dephosphorylated under drought conditions. Raf13 and the related B1-Raf Raf15 are required for growth rather than the acquisition of osmotolerance. We also found that Raf13 interacts with B55-family regulatory subunits of protein phosphatase 2A (PP2A), which mediates hyperosmolarity-induced dephosphorylation of Raf13. In addition, Raf13 interacts with an AGC kinase INCOMPLETE ROOT HAIR ELONGATION HOMOLOG 1 (IREH1), and Raf13 and IREH1 have similar functions in regulating cellular responses that promote plant growth. Overall, our results support a model in which Raf13-IREH1 activity promotes growth under nonstressed conditions, whereas PP2A activity suppresses Raf13-IREH1 during osmotic stress to modulate the physiological “trade-off” between plant growth and stress responses.
Diverse viralcasgenes antagonize CRISPR immunity
Authors: Katz Mark A , Sawyer Edith M , Kozlova Albina , Williams Madison C , Margolis Shally R , Oriolt Luke , Johnson Matthew , Bondy-Denomy Joseph , Meeske Alexander J 
Published: June 2023

ABSTRACTProkaryotic CRISPR-Cas immunity is subverted via anti-CRISPRs (Acrs), small proteins that inhibit Cas protein activities when expressed during the phage lytic cycle or from resident prophages or plasmids. CRISPR-Cas defenses are classified into 6 types and 33 subtypes, which employ a diverse suite of Cas effectors and differ in their mechanisms of interference. As Acrs often work via binding to a cognate Cas protein, inhibition is almost always limited to a single CRISPR type. Furthermore, whileacrgenes are frequently organized together in phage-associated gene clusters, how such inhibitors initially evolve has remained unclear. Here we have investigated the Acr content and inhibition specificity of a collection ofListeriaisolates, which naturally harbor four diverse CRISPR-Cas systems (types I-B, II-A, II-C, and VI-A). We observed widespread antagonism of CRISPR, which we traced to 12 novel and 4 known Acr gene families encoded on endogenous mobile genetic elements. Among these were two Acrs that possess sequence homology to type I-B Cas proteins and assemble into a defective interference complex. Surprisingly, an additional type I-B Cas homolog did not affect type I immunity, but instead inhibited the RNA-targeting type VI CRISPR system through sequestration of crRNA. By probing the IMGVR database of viral genomes, we detected abundant orphancasgenes located within putative anti-defense gene clusters. We experimentally verified the Acr activity of one viralcasgene, a particularly broad-spectrumcas3homolog that inhibits type I-B, II-A, and VI-A CRISPR immunity. Our observations provide direct evidence of Acr evolution viacasgene co-option, and new genes with potential for broad-spectrum control of genome editing technologies.
Robust Homeostasis of Cellular Cholesterol via Antithetic Integral Control
Authors: Scheepers Ronél , Araujo Robyn P. 
Published: June 2023

ABSTRACTAlthough cholesterol is essential for cellular viability and proliferation, it is highly toxic in excess. The concentration of cellular cholesterol must therefore be maintained within tight tolerances, and is thought to be subject to a stringent form of homeostasis known as Robust Perfect Adaptation (RPA). While much is known about the cellular signalling interactions involved in cholesterol regulation, the specific chemical reaction network structures that might be responsible for the robust homeostatic regulation of cellular cholesterol have been entirely unclear until now. In particular, the molecular mechanisms responsible for sensing excess whole-cell cholesterol levels have not been identified previously, and no mathematical models to date have been able to capture an integral control implementation that could impose RPA on cellular cholesterol. Here we provide a detailed mathematical description of cholesterol regulation pathways in terms of biochemical reactions, based on an extensive review of experimental and clinical literature. We are able to decompose the associated chemical reaction network structures into several independent subnetworks, one of which is responsible for conferring RPA on several intracellular forms of cholesterol. Remarkably, our analysis reveals that RPA in the cholesterol concentration in the endoplasmic reticulum (ER) is almost certainly due to a well-characterised control strategy known as antithetic integral control which, in this case, involves the high-affinity binding of a multi-molecular transcription factor complex with cholesterol molecules that are excluded from the ER membrane. Our model provides a detailed framework for exploring the necessary biochemical conditions for robust homeostatic control of essential and tightly regulated cellular molecules such as cholesterol.
PARP14 is a writer, reader and eraser of mono-ADP-ribosylation
Authors: Torretta Archimede , Chatzicharalampous Constantinos , Ebenwaldner Carmen , Schüler Herwig 
Published: June 2023

AbstractPARP14/BAL2 is a large multidomain enzyme involved in signaling pathways with relevance to cancer, inflammation, and infection. Inhibition of its mono-ADP-ribosylating PARP homology domain and its three ADP-ribosyl binding macro domains has been regarded as a potential means of therapeutic intervention. Macrodomains-2 and -3 are known to stably bind to ADP-ribosylated target proteins; but the function of macrodomain-1 has remained some-what elusive. Here, we used biochemical assays of ADP-ribosylation levels to characterize PARP14 macrodomain-1 and the homologous macrodomain-1 of PARP9. Our results show that both macrodomains display an ADP-ribosyl glycohydrolase activity that is not directed toward specific protein side chains. PARP14 macrodomain-1 is unable to degrade poly(ADP-ribose), the enzymatic product of PARP1. The F926A mutation of PARP14 and the F244A mutation of PARP9 strongly reduced ADP-ribosyl glycohydrolase activity of the respective macrodomains, suggesting mech-anistic homology to the Mac1 domain of the SARS-CoV-2 Nsp3 protein. This study adds two new enzymes to the previously known six human ADP-ribosyl glycohydrolases. Our results have key implications for how PARP14 and PARP9 will be studied and how their functions will be understood.
Does the OFDI promotion effect of the Belt and Road “crowd in” or “crowd out” domestic investment?
Authors: Ge Pengfei , Wu Xiaoxu , Zhou Bole , Han Xianfeng 
Published: June 2023

PurposeThis study aims to determine how and through what mechanisms the outward foreign direct investment (OFDI) promotion effect of the Belt and Road initiative (BRI-OFDI) affects domestic investment. It is motivated by the context that China is fostering a new development pattern, as well as by the impetus from the Belt and Road initiative for the new pattern.Design/methodology/approachDrawing on data of Chinese-listed companies, this study uses a difference-in-difference method to explore the effect of the BRI-OFDI on domestic investment and a mediation model to illustrate the mechanisms.FindingsThe BRI-OFDI has a significantly positive effect on domestic investment, meaning that the Belt and Road initiative's OFDI promotion effect crowds in domestic investment. The results are heterogeneous: the crowding-in effect mainly exists in non-state-owned and technology-intensive enterprises, while a crowding-out effect is seen in state-owned and labor-intensive enterprises. The easing of corporate financing constraints and the expansion of market demand are two important mechanisms.Originality/valueThis study uses the Belt and Road initiative as an exogenous shock to investigate the impact of the initiative-induced OFDI promotion effect on domestic investment. It addresses the potential endogeneity issue confronting the studies on the relationship between OFDI and domestic investment in the literature. The authors focus on the possible spillover effects of the Belt and Road initiative discussing the impact of the BRI-OFDI on domestic investment from the micro-firm perspective. It offers a new perspective to objectively assess the initiative's policy effect.