bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short 2′-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA productionin vitroandin vivo
Authors: Corradi Eloina , Koralewska Natalia , Milewski Marek C. , Masante Linda , Kierzek Ryszard , Figlerowicz Marek , Baudet Marie-Laure , Kurzynska-Kokorniak Anna 
Published: June 2023

ABSTRACTMicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different roles and that this functional divergence might be rooted in their precursors’ sequence. Current knock-down strategies such as antisense oligonucleotides (ASOs) or miRNA sponges cannot distinguish between identical or near identical miRNAs originating from different precursors to allow exploring unique functions of these miRNAs. We now develop a method based on short 2′-OMe/LNA-modified oligonucleotides to selectively target specific precursor molecules and ablate the production of individual members of miRNA familiesin vitroandin vivo. Using the highly conservedXenopusmiR-181a family as a proof-of-concept, we demonstrate that 2′-OMe/LNA-ASOs targeting pre-miRNA apical region elicit a precursor-selective inhibition of mature miRNA-5p production. The levels of miRNAs released from the 3′-arm of these precursors are not reduced, suggesting that our approach is also arm-selective. Overall, we show that this strategy can be successfully appliedin vivoto achieve high target selectivity to study identical or highly similar miRNAs stemming from different precursors.
Coordination of transporter, cargo, and membrane properties during non-vesicular lipid transport
Authors: Koukalova Alena , Eisenreichova Andrea , Różycki Bartosz , Boura Evzen , Humpolickova Jana 
Published: June 2023

AbstractHomeostasis of cellular membranes is maintained by fine-tuning their lipid composition. Yeast lipid transporter Osh6, belonging to the oxysterol-binding protein-related proteins family, was found to participate in the transport of phosphatidylserine (PS). PS synthesized in the endoplasmic reticulum is delivered to the plasma membrane, where it is exchanged for phosphatidylinositol-4 phosphate (PI4P). PI4P provides the driving force for the directed PS transport against its concentration gradient. In this study, we employed an in vitro approach to reconstitute the transport process into the minimalistic system of large unilamellar vesicles to reveal its fundamental biophysical determinants. Our study draws a comprehensive portrait of the interplay between the structure and dynamics of Osh6, the carried cargo lipid, and the physical properties of the involved membranes, with particular attention to their charge and fluidity. Specifically, we address the role of the cargo lipid, which, by occupying the transporter, imposes changes in its dynamics and, consequently, predisposes the cargo to disembark in the correct target membrane.
Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis
Authors: Shiau Carina , Cao Jingyi , Gregory Mark T. , Gong Dennis , Yin Xunqin , Cho Jae-Won , Wang Peter L. , Su Jennifer , Wang Steven , Reeves Jason W. , Kim Tae Kyung , Kim Youngmi , Guo Jimmy A. , Lester Nicole A. , Schurman Nathan , Barth Jamie L. , Weissleder Ralph , Jacks Tyler , Qadan Motaz , Hong Theodore S. , Wo Jennifer Y. , Roberts Hannah , Beechem Joseph M. , Fernandez-del Castillo Carlos , Mino-Kenudson Mari , Ting David T. , Hemberg Martin , Hwang William L. 
Published: June 2023

ABSTRACTIn combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell–cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant chemotherapy/radiotherapy. We developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand–receptor gene expression. Our results uncovered a marked change in ligand–receptor interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by orthogonal datasets, including anex vivotumoroid co-culture system. Overall, this study demonstrates that characterization of the tumor microenvironment using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments.
Effects of destruxin A on the trehalose content, trehalase activity and their gene expression ofBemisia tabaci
Authors: Zhang Can , Guo Jianling , Ali Shaukat , Qiu Bao-Li 
Published: June 2023

ABSTRACTBemisia tabaci(Gennadius) (Hemiptera: Aleyrodidae) is a serious pest of agricultural crops in different regions of the world. Destruxin A (DA) is one of 39 derivatives of destruxins, which are secondary metabolites produced by entomopathogenic fungi. Due to the high insecticidal activity, DA have great application potential in biological control ofB. tabaci. In order to understand the impact of destruxin A on the energy substances of the global pestB. tabaci, we measured the changes in energy substance content of theB. tabaciadults treated with DA at LC10and LC50concentrations after 4, 8, and 12 hours. The results revealed that DA caused varying degrees of decline in trehalose, soluble sugars, and glycogen content, indicating its ability to influence the energy substance content of whiteflies. After DA treatment, the content of trehalose inB. tabacidecreased significantly, while the activity of trehalase, a specific hydrolase for trehalose, increased significantly. Further study of the expression levels of two genes (BtTre-1andBtTre-2) encoding trehalases inB. tabaciafter DA treatment showed that the soluble trehalase gene,BtTre-1, was induced in both low and high concentrations of DA, while the membrane-bound trehalase gene,BtTre-2, did not show significant changes in expression level.
Total cell N-glycosylation is altered during neuronal differentiation of iPSC to NSC and is disturbed by trisomy 21
Authors: Cindrić Ana , Vučković Frano , Murray Aoife , Klarić Thomas , Alić Ivan , Petrović Dražen Juraj , Krištić Jasminka , Nižetić Dean , Lauc Gordan 
Published: June 2023

ABSTRACTDown syndrome (DS) is a genetic condition caused by trisomy 21 (T21) and characterized by a range of neurological symptoms including intellectual disability, early onset of neurodegeneration and dementia, some of which can be attributed to accelerated aging. N-glycosylation is a protein modification that plays a critical role in numerous biological processes and its dysregulation is associated with a wide range of diseases, in some even before the onset of symptoms. N-glycosylation of total plasma proteins, as well as specific plasma proteins, such as immunoglobulin G, has been shown to change in DS, displaying an accelerated aging phenotype consistent with the various symptoms of premature aging that occur in DS. However, little is known about how T21 affects the N-glycosylation of other cellular proteins. To better understand how T21 affects N-glycosylation during neural differentiation, we characterized and compared the total released N-glycans of induced pluripotent stem cells (iPSCs) and their neural stem cell (NSC) derivatives. We analyzed six different isogenic clones all derived from a single individual with mosaic DS and thus all sharing the same genetic background; however, three had a normal disomic karyotype (D21), while the other three had an additional copy of chromosome 21 (T21). We characterized the total cell N-glycosylation profiles using ultra high performance liquid chromatography (UHPLC) and subsequent tandem mass spectrometry analysis to determine proposed glycan structures. Our results revealed both qualitative and quantitative differences in the composition of N-glycomes between iPSCs and NSCs, with NSCs showing a higher amount of complex N-glycans and a lower amount of mannosidic N-glycans when compared to iPSCs. Moreover, we found differences in N-glycosylation patterns between D21 and T21 cells. Notably, T21 cells exhibited a significant increase in the amount of pseudohybrid N-glycans. Trisomy 21 also caused a significant decrease in the abundance of a hybrid monoantennary fucosylated glycan (H6N3F1). Our findings define the released N-glycan profile of total cells for both D21 and T21 iPSCs and NSCs and suggest that the presence of a third copy of chromosome 21 impacts N-glycosylation patterns already in the stem cell state.
Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests
Authors: Rando Halie M. , Graim Kiley , Hampikian Greg , Greene Casey S. 
Published: June 2023

AbstractObjectiveTo evaluate whether the breed ancestry predictions of direct-to-consumer (DTC) genetic tests for dogs are influenced by the user-provided photograph.AnimalsTwelve pet dogs considered purebred (i.e., registered with a breed organization) representing twelve different breeds.MethodsSix buccal swabs per dog were collected by the owners and submitted to six DTC genetic testing companies. The experimenters registered each sample with the company. For half of the dogs, the registration included a photograph of the DNA donor. For the other half of the dogs, photographs were swapped between dogs. Analysis of the DNA and breed ancestry prediction was conducted by each company. Each company’s breed predictions were evaluated to assess whether the condition (i.e., matching versus shuffled photograph) affected the odds of identifying the DNA donor’s registered breed. A convolutional neural network was also used to predict breed based solely on the photograph as a positive control.ResultsFive of the six tests always produced results that included the registered breed. One test and the convolutional neural network were unlikely to identify the registered breed and frequently returned results that included the breed in the photograph. This result suggests that one test on the market is relying on the photograph more than the DNA sample. Additionally, differences in the predictions made across all tests underscore the challenge of identifying breed ancestry, even in purebred dogs.Clinical RelevanceVeterinarians are likely to encounter patients who have conducted DTC genetic testing and may find themselves in the position of explaining genetic test results that they did not order. This systematic comparison of tests on the market provides context for interpreting unexpected results from consumer-grade DTC genetic testing kits.
Efficient Visual Perception of Human-Robot Walking Environments using Semi-Supervised Learning
Authors: Kuzmenko Dmytro , Tsepa Oleksii , Kurbis Andrew Garrett , Mihailidis Alex , Laschowski Brokoslaw 
Published: June 2023

AbstractConvolutional neural networks trained using supervised learning can improve visual perception for human-robot walking. These advances have been possible due to large-scale datasets like ExoNet and StairNet - the largest open-source image datasets of real-world walking environments. However, these datasets require vast amounts of manually annotated data, the development of which is time consuming and labor intensive. Here we present a novel semi-supervised learning system (ExoNet-SSL) that uses over 1.2 million unlabelled images from ExoNet to improve training efficiency. We developed a deep learning model based on mobile vision transformers and trained the model using semi-supervised learning for image classification. Compared to standard supervised learning (98.4%), our ExoNet-SSL system was able to maintain high prediction accuracy (98.8%) when tested on previously unseen environments, while requiring 35% fewer labelled images during training. These results show that semi-supervised learning can improve training efficiency by leveraging large amounts of unlabelled data and minimize the size requirements for manually annotated images. Future research will focus on model deployment for onboard real-time inference and control of human-robot walking.
A drop dispenser for simplifying on-farm detection of foodborne pathogens
Authors: Ranjbaran Mohsen , Kaur Simerdeep , Wang Jiangshan , Raut Bibek , Verma Mohit S. 
Published: June 2023

AbstractRapid nucleic-acid biosensors are useful for on-farm detection of foodborne pathogens on fresh produce during pre-season and pre-harvest stages. Such tools aim to be user-friendly so that a producer could operate them in a few simple steps and detect multiple targets. Currently, an easy-to-use device for on-farm applications does not exist commercially. One of the bottlenecks is the delivery of a prescribed amount of sample to the reaction sites of the biosensor using a simple and precise approach. Here, we developed drop dispensers using 3D printing and a hydrophilic surface chemistry treatment to generate precise drops (DNA/bacterial samples) of a few micro-liters (∼20 to ∼33 µL). We tested multiple copies of these devices over time of repeated application to estimate their shelf-lives which is about one month. In addition to drop generation tests, we employed these devices in nucleic-acid testing. The tests used loop-mediated isothermal amplification (LAMP) to detect DNA or whole cells of Shiga-toxin-producingEscherichia coliO157:H7. These tests were performed to simulate the on-farm sample collection (using collection flags that we previously designed) and delivery using the drop dispensers. Our results showed that these devices performed similarly to standard commercial pipettors in LAMP assays, providing a limit of detection of 7.8×106cell/mL for whole-cell detection. This drop dispenser will eventually be part of a user-friendly consumable kit that will enable performing LAMP assays by non-specialist users for a cost of USD 4 per test.
Distinct Conformations of Mirabegron Determined by MicroED
Authors: Lin Jieye , Unge Johan , Gonen Tamir 
Published: June 2023

AbstractMirabegron, commonly known as “Myrbetriq”, has been widely prescribed as a medicine for overactive bladder syndrome for over a decade. However, the structure of the drug and what conformational changes it may undergo upon binding its receptor remain unknown. In this study, we employed microcrystal electron diffraction (MicroED) to reveal its elusive three-dimensional (3D) structure. We find that the drug adopts two distinct conformational states (conformers) within the asymmetric unit. Analysis of hydrogen bonding and packing demonstrated that the hydrophilic groups were embedded within the crystal lattice, resulting in a hydrophobic surface and low water solubility. Structural comparison revealed the presence oftrans- andcis-forms in conformers1and2, respectively. Comparison of the structures of Mirabegron alone with that of the drug bound to its receptor,1the beta 3 adrenergic receptor (β3AR) suggests that the drug undergoes major conformational change to fit in the receptor agonist binding site. This research highlights the efficacy of MicroED in determining the unknown and polymorphic structures of active pharmaceutical ingredients (APIs) directly from powders.
Decoding the comprehensive substrate-specificity and evidence of altered site-specific collagen prolyl-3-hydroxylation, lysyl-hydroxylation, and lysyl O-glycosylation in P4ha1 and P4ha2 deleted mutant mice
Authors: Sarohi Vivek , Basak Trayambak 
Published: June 2023

AbstractCollagens, the most abundant proteins in mammals, play pivotal roles in the maintenance of tissue structure, functions, cell-to-cell communication, cellular migration, behavior, and growth. Collagens are highly complex in structure due to the dynamic post-translational modifications (PTMs) such as hydroxylations (on prolines and lysine residues) and O-glycosylation (on hydroxylysines) enzymatically catalyzed during biosynthesis. The most prevalent modification in fibrillar collagens is prolyl 4-hydroxylation catalyzed by collagen prolyl 4-hydroxylases (C-P4hs). Prolyl 4-hydroxylation on collagens plays a critical role in collagen biosynthesis, thermostability, and cell-collagen interactions. However, the site-specificity of prolyl 4-hydroxylase 1 (P4ha1) and P4ha2 is not comprehensively studied yet. Further, the effect of P4ha1 and P4ha2 on the plethora of other site-specific collagen PTMs is not known to date. In-depth mass-spectrometry data (PXD008802) analysis of mice skin collagen I extracted from wild-type and different deletion mutants of C-P4hs revealed that partial or full deletion of prolyl 4-hydroxylases (P4ha1 and P4ha2) significantly decreases collagen deposition in ECM hinting towards perturbed biosynthesis. A total of421site-specific PTMs on fibrillar collagen chains (Col1a1, Col1a2, and Col3a1) were identified. Further, novel23P4ha1 specific,8P4ha2 specific, and18C-P4hs promiscuous sites on fibrillar collagen chains were identified. Partial deletion of P4ha1 and full deletion of P4ha2 also resulted in altered levels of the site-specific prolyl-3-hydroxylation occupancy in collagen I. Surprisingly, an increased level of site-specific lysyl hydroxylation (Col1a1-K731, Col1a2-K183,315) was documented upon partial deletion of P4ha1 and full deletion of P4ha2. Our findings showcased that the activity of prolyl 4-hydroxylases is not limited to 4-hydroxylation of specific proline sites, but simultaneously can perturb the entire biosynthetic network by modulating prolyl 3-hydroxylation and lysyl hydroxylation occupancy levels in the fibrillar collagen chains in a site-specific manner.
Comprehensive profiling of the human intestinal DNA virome and prediction of disease-associated bacterial hosts in severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
Authors: Hsieh Shen-Yuan , Savva George M. , Telatin Andrea , Tiwari Sumeet K. , Tariq Mohammad A. , Newberry Fiona , Seton Katharine A. , Booth Catherine , Bansal Amolak S. , Wileman Thomas , Adriaenssens Evelien M. , Carding Simon R. 
Published: June 2023

AbstractMyalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling disorder of unknown etiology with severely affected patients being house- and/or bedbound. A historical association with chronic virus infection and subsequent recent reports correlating intestinal microbial dysbiosis with disease pathology prompted us to analyze the intestinal virome in a small cohort of severely-affected ME/CFS patients and same household healthy controls (SHHC). Datasets from whole metagenomic sequencing (WMS) and sequencing of virus-like particles (VLP)-enriched metagenomes from the same fecal sample yielded diverse, high-quality vOTUs with high read coverage and high genome completeness. The core intestinal virome was largely composed of tailed phages in the classCaudoviriceteswith no significant differences in alpha diversity between ME/CFS and SHHC groups. However, the WMS dataset had a higher Shannon measure than the VLP dataset (p< 0.0001), with VLP- and WMS-derived sequences indicating differential abundances within several viral families and different viral compositions in beta diversity. This confirms that combining different isolation methodologies identifies a greater diversity of viruses including extracellular phages and integrated prophages. DNA viromes and bacteriomes from ME/CFS and SHHC groups were comparable with no differences in any alpha or beta diversity measures. One vOTU derived from the VLP-derived dataset was assigned to ssDNA human virus smacovirus 1. Using anin-silicoapproach to predict cohort-based bacterial hosts, we identified members of theAnaerotruncusgenus interacting with unique viruses present in ME/CFS microbiomes; this may contribute to the GI microbial dysbiosis described in ME/CFS patients.
Nanoparticle endocytosis is driven by monocyte phenotype rather than nanoparticle size under high shear flow conditions
Authors: Aldarondo Dasia A. , Huynh Chris , Dickey Leah , Bilynsky Colette , Lee Yerim , Wayne Elizabeth C. 
Published: June 2023

AbstractMonocytes are members of the mononuclear phagocyte system involved in pathogen clearance and nanoparticle pharmacokinetics. Monocytes play a critical role in the development and progression of cardiovascular disease and, recently, in SARS-CoV-2 pathogenesis. While studies have investigated the effect of nanoparticle modulation on monocyte uptake, their capacity for nanoparticle clearance is poorly studied. In this study, we investigated the impact ofACE2deficiency, frequently observed in individuals with cardiovascular complications, on monocyte nanoparticle endocytosis. Moreover, we investigated nanoparticle uptake as a function of nanoparticle size, physiological shear stress, and monocyte phenotype. Our Design of Experiment (DOE) analysis found that the THP-1ACE2-cells showed a greater preference for 100nm particles under atherosclerotic conditions than THP-1 wild-type cells. Observing how nanoparticles can modulate monocytes in the context of disease can inform precision dosing.
The Antitumor Activities of Anti-CD47 Antibodies Require Fc-FcγR interactions
Authors: Osorio Juan C. , Smith Patrick , Knorr David A. , Ravetch Jeffrey V. 
Published: June 2023

SummaryWhile anti-CD47 antibodies hold promise for cancer immunotherapy, early phase clinical trials have shown limited signs of clinical benefit, suggesting that blockade of CD47 alone may not be sufficient for effective tumor control. Here, we investigate the contributions of the Fc domain of anti-CD47 antibodies required for optimal in vivo antitumor activity across multiple species-matched models, providing new insights into the mechanisms underlying the efficacy of this emerging class of therapeutic antibodies. Using a novel mouse model humanized for CD47, SIRPα and FcγRs, we demonstrate that local administration of an Fc-engineered anti-CD47 antibody with enhanced binding to activating FcγRs modulates myeloid and T-cell subsets in the tumor microenvironment, resulting in improved long-term systemic antitumor immunity and minimal on-target off-tumor toxicity. Our results highlight the importance of Fc optimization in the development of effective anti-CD47 therapies and provide a novel approach for enhancing the antitumor activity of this promising immunotherapy.Highlights-Engagement of activating FcγRs augments the in vivo antitumor activity of CD47 blocking antibodies-Humanized mice for CD47, SIRPα and FcγRs allow assessment of hFcγRs contribution to the activity of anti-hCD47 Abs-Fc-optimized anti-hCD47 ab promotes systemic antitumor immunity with abscopal effect and minimal on-target toxicityGraphical Abstract