bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution and development of a robotic acute care surgery program
Authors: Torres Crisanto M. , Florecki Katherine , Haghshenas Jafar , Manukyan Mariuxi , Kent Alistair , Lawrence Chuck , Sakran Joseph V.
Published: June 2023

BACKGROUND

Acute care surgeons perform more than 850,000 operations annually on emergency general surgery patients in the United States. Emergency general surgery conditions are associated with a disproportionate excess of patient complications and death. Innovative quality improvement strategies have focused on addressing the excess morbidity and mortality among this patient population. Minimally invasive surgical techniques have been shown to reduce the burden experienced by emergency general surgery patients. Still, limited adoption by acute care surgeons has restricted this application’s potential. An institutional robotics acute care surgery program provides acute care surgeons additional opportunities to expand minimally invasive surgery access to emergency general surgery patients irrespective of the time or day of the week.

METHODS

A robotics acute care surgery program was developed and implemented at a high-volume academic institution within the division of trauma and acute care surgery.

RESULTS

Three attending surgeons and two fellows within the trauma and acute care surgery division had successfully completed a defined robotics clinical pathway. As a result, around-the-clock use of a robotic surgical platform for emergency general surgery cases was implemented with routine use by trained robotic acute care surgeons and practicing fellows.

CONCLUSION

The advancement of robotic surgical technology has opened new avenues for surgical application in the emergency setting. The development of a robotic acute care surgery program allows acute care surgeons to diversify their practice while providing greater access to minimally invasive approaches for emergency general surgery patients.
Oncogenic viruses and host lipid metabolism: a new perspective
Authors: Gong Zhiyuan , Yan Zhiyong , Liu Wen , Luo Bing
Published: June 2023

As noncellular organisms, viruses do not have their own metabolism and rely on the metabolism of host cells to provide energy and metabolic substances for their life cycles. Increasing evidence suggests that host cells infected with oncogenic viruses have dramatically altered metabolic requirements and that oncogenic viruses produce substances used for viral replication and virion production by altering host cell metabolism. We focused on the processes by which oncogenic viruses manipulate host lipid metabolism and the lipid metabolism disorders that occur in oncogenic virus-associated diseases. A deeper understanding of viral infections that cause changes in host lipid metabolism could help with the development of new antiviral agents as well as potential new therapeutic targets.
PanGraph: scalable bacterial pan-genome graph construction
Authors: Noll Nicholas , Molari Marco , Shaw Liam P. , Neher Richard A.
Published: June 2023

The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the widespread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. In addition to pangenomic approaches that focus on the variation in the sets of genes present in different genomes, complete assemblies allow investigations of the evolution of genome structure and gene order. This latter problem, however, is computationally demanding with few tools available that shed light on these dynamics. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as a path along vertices, which in turn encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into several common formats for either downstream analysis or immediate visualization.
Top-down Proteomics of 10,000 Single Brain Cells
Authors: Su Pei , Hollas Michael A. R. , Rubakhin Stanislav , Butun Fatma Ayaloglu , Greer Joseph B. , Early Bryan P. , Fellers Ryan T. , Caldwell Michael A. , Sweedler Jonathan V. , Kafader Jared O. , Kelleher Neil L.
Published: June 2023

We introduce single-cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct analysis of intact proteins to process 10,836 single cells from the rat hippocampus. This new platform addresses the throughput bottleneck for single cell proteomics using mass spectrometry, boosting cell processing rates by >20-fold in the field. We identified 169 proteoforms <70 kDa from single brain cells and classified 2758 of them as neurons, astrocytes or microglia cell types.
CULTURAL CONSANGUINITY AS CAUSE OF β-THALASSEMIA PREVALENCE IN POPULATION
Authors: Aslamkhan Muhammad , Qadeer Muhammad Imran , Akhtar Muhammad Shoaib , Chudhary Shafiq Ahmad , Mariam Maida , Ali Zain , Khalid AbdurRauf , Irfan Muhammad , Khan Yasin
Published: June 2023

Background

Some 200 million people worldwide have haemoglobinopathies of some sort. Pakistan, where 80% consanguinity prevails because of marriages within caste groups that are anthropologically same. The study aims to reveal the impact of consanguinity on thalassemia in various castes in Punjab, Pakistan.

Subjects and Methods

262 β-thalassemic patient’s families were studied. Patients were registered in various Thalassemia Blood Transfusion Hospitals/Centers, in the metropolitan city of Lahore, Punjab, Pakistan. Patients and parents were interviewed using structured questionnaire regarding information about name, age, sex, ethnicity (caste), educational status, consanguinity of parents, number of progenies, health status of children, pregnancy wastage and family history.

Results

The 262 (couples) parents of β-thalassemic patients revealed 96% consanguineous marriages with 72% first cousins, 10% distant blood relatives and 14%Bradari. Inter-castes marriages were 4% only. These families produced 1646 children, 582 males and 464 females. Of these, 303 boys and 293 girls are healthy, while 279 boys and 171 girls are thalassemic. In 26 castes, the prevalence of thalassemia varied from 21% to 3%. Rajput tribe on top followed by Arain.

Conclusion

Thalassemia is widely spread in Pakistani population. Its prevalence varied in caste groups due to endogamy, a major impact on the prevalence of thalassemia.
Effect of Terpenes fromPoria Cocos: Verifying Modes of Action against Alzheimer’s disease Using Molecular Docking, Drug-induced Transcriptomes and Diffusion Network
Authors: Park Musun , Lee Seo-Young , Lee Haeseung , Yi Jin-Mu
Published: June 2023

Poria cocosis used to treat various diseases because of its unique terpenes. However, no study verifying its modes of action using only its compounds based onin silicoexperiments has been conducted. Here, molecular docking and drug-induced transcriptome analyses were performed to confirm the modes of action ofPoria cocos. Additionally, a diffusion network analysis method was proposed to confirm its modes of action against Alzheimer’s. First,Poria cocosterpenes were collected from standard databases for molecular docking. They were then used for large-scale molecular docking using druggable proteomes, and the modes of action of lanostane and seco-lanostane, unique toPoria cocos, were confirmed. Additionally, the brain cell line was treated withPoria cocosto producePoria cocos-induced transcriptome data, and the transcriptome-based modes of action ofPoria cocoswere confirmed. Finally, a diffusion network was constructed using Alzheimer’s, which acts on both modes of action, and submodules of Alzheimer’s with which terpenes interact were identified. It was confirmed thatPoria cocosacts on the Wnt signaling pathway, Zn-to-anterograde axonal transport, autophagy impairment, insulin and AGE-RAGE signaling pathways, and apoptosis mechanisms. This study identified the modes of action ofPoria cocosusing biological data andin silicomethods.
The senescent mesothelial matrix accentuates colonization by ovarian cancer cells
Authors: Thapa Bharat Vivan , Glimm Tilmann , Saini Deepak K , Bhat Ramray
Published: June 2023

Ovarian cancer is amongst the most morbid of gynecological malignancies due to its diagnosis at an advanced stage, a transcoelomic mode of metastasis, and rapid transition to chemotherapeutic resistance. Like all other malignancies, the progression of ovarian cancer may be interpreted as an emergent outcome of the conflict between metastasizing cancer cells and the natural defense mounted by microenvironmental barriers to such migration. Here, we asked whether senescence in coelom-lining mesothelia, brought about by drug exposure, affects their interaction with disseminated ovarian cancer cells. We observed that cancer cells adhered faster on, senescent human and murine mesothelial monolayers than non-senescent controls. Time-lapse epifluorescent microscopy showed that mesothelial cells were cleared by a host of cancer cells that surrounded the former, even under sub-confluent conditions. A multiscale computational model predicted that such colocalized mesothelial clearance under sub-confluence requires greater adhesion between cancer cells and senescent mesothelia. Consistent with the prediction, we observed that senescent mesothelia expressed extracellular matrix with higher levels of fibronectin, laminins and hyaluronan than non-senescent controls. On senescent matrix, cancer cells adhered more efficiently, spread better, and moved faster and persistently, aiding the spread of cancer. Inhibition assays using RGD cyclopeptides suggested the adhesion was predominantly contributed by fibronectin and laminin. These findings led us to propose that the senescence-associated matrisomal phenotype of peritoneal barriers enhances the colonization of invading ovarian cancer cells and their clearance contributing to the metastatic burden associated with the disease.
Global changes in open reading frame dominance of RNAs during cancer initiation and progression
Authors: Suenaga Yusuke , Kogashi Hiroyuki , Nakatani Kazuma , Lin Jason , Hasegawa Yoshinori , Kugou Kazuto , Kawashima Yusuke , Furukawa Eisaku , Okumura Kazuhiro , Kita Emiri , Wakabayashi Yuichi , Kato Mamoru , Kawazu Masahito , Hippo Yoshitaka
Published: June 2023

Cancer cells express unique RNA transcripts; however, the factors determining their translation have remained unclear. We recently developed open reading frame (ORF) dominance as a measure that correlates with coding potential of RNAs. Upon calculating the ORF dominance of cancer-specific transcripts across 24 human tumor types, 14 exhibited significantly higher ORF dominance in cancer than in normal tissues. In organoid-based mouse genetic models, ORF dominance increased with carcinogenesis. Gene ontology analysis revealed that gene sets with increased ORF dominance were associated with cell proliferation, while those with decreased ORF dominance were linked to DNA damage response. Translatome analyses demonstrated that elevated ORF dominance during carcinogenesis resulted in higher translation frequencies of ribosome-bound RNAs. As cancer progressed, ORF dominance showed that the boundary between coding and noncoding transcripts became blurred prior to distant metastasis, indicating decreased proliferative cell populations and increased generation of RNA isoforms that potentially translate neoantigens before the development of metastatic tumors. These findings suggest that cancer evolution leads to dynamic changes in ORF dominance, resulting in global translational alterations in transcriptomes.
Necessary Role of Acute Ceramide Formation in The Human Microvascular Endothelium During Health and Disease
Authors: SenthilKumar Gopika , Katunaric Boran , Zirgibel Zachary , Lindemer Brian , Jaramillo-Torres Maria J. , Bordas-Murphy Henry , Schulz Mary E. , Pearson Paul J. , Freed Julie K.
Published: June 2023

Background

Elevated plasma ceramides independently predict adverse cardiac events and we have previously shown that exposure to exogenous ceramide induces microvascular endothelial dysfunction in arterioles from otherwise healthy adults (0-1 risk factors for heart disease). However, evidence also suggests that activation of the shear-sensitive, ceramide forming enzyme neutral sphingomyelinase (NSmase) enhances vasoprotective nitric oxide (NO) production. Here we explore a novel hypothesis that acute ceramide formation through NSmase is necessary for maintaining NO signaling within the human microvascular endothelium. We further define the mechanism through which ceramide exerts beneficial effects and discern key mechanistic differences between arterioles from otherwise healthy adults and patients with coronary artery disease (CAD).

Methods

Human arterioles were dissected from otherwise discarded surgical adipose tissue (n=123), and vascular reactivity to flow and C2-ceramide was assessed. Shear-induced NO production was measured in arterioles using fluorescence microscopy. Hydrogen peroxide (H2O2) fluorescence was assessed in isolated human umbilical vein endothelial cells.

Results

Inhibition of NSmase in arterioles from otherwise healthy adults induced a switch from NO to H2O2-mediated flow-induced dilation within 30 minutes. In endothelial cells, NSmase inhibition acutely increased H2O2production. Endothelial dysfunction in both models was prevented by treatment with C2-ceramide, S1P, and an agonist of S1P-receptor 1 (S1PR1), while the inhibition of S1P/S1PR1 signaling axis induced endothelial dysfunction. Ceramide increased NO production in arterioles from healthy adults, an effect that was diminished with inhibition of S1P/S1PR1/S1PR3 signaling. In arterioles from patients with CAD, inhibition of NSmase impaired dilation to flow. This effect was not restored with exogenous S1P. Although, inhibition of S1P/S1PR3 signaling impaired normal dilation to flow. Acute ceramide administration to arterioles from patients with CAD also promoted H2O2as opposed to NO production, an effect dependent on S1PR3 signaling.

Conclusion

These data suggest that despite key differences in downstream signaling between health and disease, acute NSmase-mediated ceramide formation and its subsequent conversion to S1P is necessary for proper functioning of the human microvascular endothelium. As such, therapeutic strategies that aim to significantly lower ceramide formation may prove detrimental to the microvasculature.
VitTCR: A deep learning method for peptide recognition prediction
Authors: Jiang Mengnan , Yu Zilan , Lan Xun
Published: June 2023

The identification of the interaction between T-cell receptors (TCRs) and immunogenic peptides is important for the development of novel cancer immunotherapies and vaccines. However, experimentally determining whether a TCR recognizes a peptide is still time– and labour-consuming. In this study, we introduced VitTCR, a predictive model based on the architecture of the vision transformer (ViT), designed to forecast TCR-peptide interactions. Prior to prediction, VitTCR converts the TCR-peptide interactions into a numerical tensor named AtchleyMaps using Atchley factors. Subsequently, VitTCR takes AtchleyMaps as inputs and predicts whether an interaction between a TCR and a peptide exists. Through comprehensive evaluations, we demonstrate that VitTCR surpasses other published methods in classifying TCR-peptide pairs, exhibiting superior performance in terms of the area under the receiver operating characteristic (AUROC) and the area under the precision-recall curve (AUPR). To determine the focal contact point between TCRs and peptides, we obtained a positional bias weight matrix (PBWM) from the empirical amino acid (AA) contact probabilities derived from 83 structurally resolved pMHC-TCR complexes. The comparison of VitTCR with and without the integration of the PBWM revealed significant enhancements in the performance of the model. Moreover, the predicted probabilities generated by VitTCR exhibit significant correlations with immunological factors such as the clonal expansion and activation percentages of T cells. This further supports the efficacy of VitTCR in capturing biologically meaningful TCR-peptide interactions. In conclusion, VitTCR provides a useful computational tool for the prediction of TCR-peptide interactions, thereby contributing to our understanding in this field.
Cysteine enrichment mediates co-option of uricase in reptilian skin and transition to uricotelism
Authors: Mori Giulia , Liuzzi Anastasia , Ronda Luca , Palma Michele Di , Chegkazi Magda S. , Bui Soi , Garcia-Maya Mitla , Ragazzini Jasmine , Malatesta Marco , Monica Emanuele Della , Rivetti Claudio , Antin Parker , Bettati Stefano , Steiner Roberto A. , Percudani Riccardo
Published: June 2023

Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles) and the end product of purine catabolism in humans and a few other mammals. While uricase is inactivated in mammals unable to degrade urate, the presence of orthologous genes without inactivating mutations in avian and reptilian genomes is unexplained. Here we show that theGallus gallusgene we name cysteine-rich urate oxidase (CRUOX) encodes a functional protein representing a unique case of cysteine enrichment in the evolution of vertebrate orthologous genes. CRUOX retains the ability to catalyze urate oxidation to hydrogen peroxide and 5-hydroxyisourate (HIU), albeit with a 100-fold reduced efficiency. However, differently from all uricases hitherto characterized, it can also facilitate urate regeneration from HIU, a catalytic property which we propose depends on its enrichment in cysteine residues. X-ray structural analysis highlights differences in the active site compared to known orthologs and suggests a mechanism for cysteine-mediated self-aggregation under H2O2-oxidative conditions. Cysteine enrichment was concurrent with transition to uricotelism and a shift in gene expression from the liver to the skin where CRUOX is co-expressed with β-keratins. Therefore, the loss of urate degradation in amniotes has followed opposite evolutionary trajectories: while uricase has been eliminated by pseudogenization in some mammals, it has been repurposed as a redox-sensitive enzyme in the reptilian skin.
Lamivudine (3TC), a nucleoside reverse transcriptase inhibitor, prevents the neuropathological alterations present in mutant tau transgenic mice
Authors: Vallés-Saiz Laura , Ávila Jesús , Hernández Félix
Published: June 2023

The dysregulation of transposable elements contributes to neurodegenerative disorders. Previous studies have reported an increase in retrotransposon transcription inDrosophilamodels, as well as in human tauopathies. In this context, here we tested the possible protective effects of a reverse transcriptase inhibitor, namely lamivudine (also known as 3TC), in P301S mice, an animal model of Alzheimeŕs disease based on FTDP-17-tau overexpression. Transgenic P301S mice administered lamivudine through drinking water showed a decrease in the following histopathological marks typical of tauopathies: tau phosphorylation; inflammation; neuronal death; and hippocampal atrophy. Lamivudine treatment attenuated motor deficits (Rotarod test) and improved short-term memory (Y-maze test). To evaluate the role of tau in retrotransposition, we cotransfected HeLa cells with a plasmid containing a complete LINE-1 sequence and a neomycin reporter cassette designed for retrotransposition assays, and a plasmid with the tau sequence. LINE-1 insertion increased considerably in the cotransfection compared to the transfection without tau. In addition, lamivudine inhibited the insertion of LINE-1. Our data suggest that the progression of the tauopathy can be attenuated by the administration of lamivudine upon the first symptoms of neuropathology.

Highlights

Lamivudine treatment in drinking water inhibited a tau-associated pathology in a mouse model of tauopathy.

Tau promotes the insertion of transposable elements LINE-1in vitro. LINE-1 insertionin vitrois inhibited by lamivudine.

Lamivudine attenuates memory and motor deficits in tau transgenic mice.
Electrochemical biosensor based on NAD(P)H-dependent Quinone Reductase for rapid and efficient detection of vitamin K3
Authors: Khalife Majd , Stankovic Dalibor , Stankovic Vesna , Danicka Julia , Rizzotto Francesco , Costache Vlad , Slama Schwok Anny , Gaudu Philippe , Vidic Jasmina
Published: June 2023

Vitamin K refers to a group of vitamins that play an important role in blood coagulation and regulation of bone and vascular metabolism. However, vitamin K3 may give severe side effects in animal and humans when improperly added to food and feed due to its toxicity. Here, an electrochemical biosensor, based on the YaiB NADPH-dependent quinone reductase fromLactococcus lactis(YaiB), was developed to achieve rapid and redox probe-free detection of vitamin K3. First, we demonstrated the ability of the carbon electrode to distinguish between 1,4-benzoquinone and hydroquinone. Then, we engineered YaiB to work as a bioreceptor immobilized at the electrode and we demonstrated its sensitivity and specificity to reduce vitamin K3. Finally, to demonstrate the practical potential of the biosensor, we tested it directly in spiked milk samples, achieving 15-minute quantification of the vitamin K3. The limit of detection was 0.18μM and 0.86 μM in buffer and milk, respectively.
Near chromosome-level genome assembly of the microsporidiumHamiltosporidium tvaerminnensis
Authors: Angst Pascal , Pombert Jean-François , Ebert Dieter , Fields Peter D.
Published: June 2023

Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents a first near-chromosomal assembly of a large-genome microsporidium,Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences, and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56 % interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism.

Significance

Microsporidia are a model for genome evolution in response to intracellular parasitism, but we lack high-quality resources from species with large genomes. We present a near complete assembly of a large-genome microsporidium,Hamiltosporidium tvaerminnensis, and obtain high-quality gene annotations through full-length transcripts using Iso-Seq, a novel approach in microsporidia. Our study provides insights into gene regulation and paves the way for comparative genomic analyses aiming to understand the evolution of genome reduction and expansion in these intracellular parasites.
Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes
Authors: Chua Gabriella N. L. , Watters John W. , Olinares Paul Dominic B. , Luo Joshua A. , Chait Brian T. , Liu Shixin
Published: June 2023

Methyl-CpG-binding protein 2 (MeCP2) is an essential chromatin-binding protein whose mutations cause Rett syndrome (RTT), a leading cause of monogenic intellectual disabilities in females. Despite its significant biomedical relevance, the mechanism by which MeCP2 navigates the chromatin epigenetic landscape to regulate chromatin structure and gene expression remains unclear. Here, we used correlative single-molecule fluorescence and force microscopy to directly visualize the distribution and dynamics of MeCP2 on a variety of DNA and chromatin substrates. We found that MeCP2 exhibits differential diffusion dynamics when bound to unmethylated and methylated bare DNA. Moreover, we discovered that MeCP2 preferentially binds nucleosomes within the context of chromatinized DNA and stabilizes them from mechanical perturbation. The distinct behaviors of MeCP2 at bare DNA and nucleosomes also specify its ability to recruit TBLR1, a core component of the NCoR1/2 co-repressor complex. We further examined several RTT mutations and found that they disrupt different aspects of the MeCP2-chromatin interaction, rationalizing the heterogeneous nature of the disease. Our work reveals the biophysical basis for MeCP2’s methylation-dependent activities and suggests a nucleosome-centric model for its genomic distribution and gene repressive functions. These insights provide a framework for delineating the multifaceted functions of MeCP2 and aid in our understanding of the molecular mechanisms of RTT.
Interleukin-21 Drives a Hypermetabolic State and CD4+T Cell-associated Pathogenicity in Chronic Intestinal Inflammation
Authors: Bamidele Adebowale O. , Mishra Shravan K. , Hirsova Petra , Fehrenbach Patrick J. , Valenzuela-Pérez Lucia , Kim Lee Hyun Se
Published: June 2023

BACKGROUND & AIMS

Incapacitated regulatory T cells (Tregs) contribute to immune-mediated diseases. Inflammatory Tregs are evident during human inflammatory bowel disease (IBD); however, mechanisms driving the development of these cells and their function are not well understood. Therefore, we investigated the role of cellular metabolism in Tregs relevant to gut homeostasis.

METHODS

Using human Tregs, we performed mitochondrial ultrastructural studies via electron microscopy and confocal imaging, biochemical and protein analyses using proximity ligation assay, immunoblotting, mass cytometry and fluorescence-activated cell sorting, metabolomics, gene expression analysis, and real-time metabolic profiling utilizing Seahorse XF analyzer. We utilized Crohn’s disease single-cell RNA sequencing dataset to infer therapeutic relevance of targeting metabolic pathways in inflammatory Tregs. We examined the superior functionality of genetically-modified Tregs in CD4+T cell-induced murine colitis models.

RESULTS

Mitochondria-endoplasmic reticulum (ER) appositions, known to mediate pyruvate entry into mitochondria via VDAC1, are abundant in Tregs. VDAC1 inhibition perturbed pyruvate metabolism, eliciting sensitization to other inflammatory signals reversible by membrane-permeable methyl pyruvate (MePyr) supplementation. Notably, IL-21 diminished mitochondria-ER appositions, resulting in enhanced enzymatic function of glycogen synthase kinase 3 β (GSK3β), a putative negative regulator of VDAC1, and a hypermetabolic state that amplified Treg inflammatory response. MePyr and GSK3β pharmacologic inhibitor (LY2090314) reversed IL-21-induced metabolic rewiring and inflammatory state. Moreover, IL-21-induced metabolic genes in Tregsin vitrowere enriched in human Crohn’s disease intestinal Tregs. Adoptively transferredIl21r-/-Tregs efficiently rescued murine colitis in contrast to wild-type Tregs.

CONCLUSIONS

IL-21 triggers metabolic dysfunction associated with Treg inflammatory response. Inhibiting IL-21-induced metabolism in Tregs may mitigate CD4+T cell-driven chronic intestinal inflammation.
A flexible and high-throughput genotyping workflow tracked the emergence of SARS-CoV-2 variants in the UK in 2022
Authors: Lee Suki , Grujic Stefan , Modern Sam , Wann Angela , Fraser Donald , Percival Benita
Published: June 2023

In late 2021, the Omicron SARS-CoV-2 variant spread rapidly worldwide. To track its emergence, and the continued evolution of SARS-CoV-2 while giving actionable epidemiological data that informs public health policy, we developed a high-throughput, automated, genotyping workflow that pairs flexible liquid handling with a re-configurable LIMS system. This workflow facilitated the real-time monitoring of the spread of BA.4 and BA.5, and by the time of its retirement, the system was responsible for typingc. 400,000 SARS-CoV-2 samples. When combined with a population-scale testing program, genotyping assays, can offer a rapid and cost-effective method of determining variants and horizon-scanning for changes in the pool of circulating mutations. Strategies to prepare diagnostics infrastructure for Pathogen X should consider the development of flexible systems with interchangeable components that can be rapidly re-configured to meet uncertain and changing requirements.
A Boltzmann model predicts glycan structures from lectin binding
Authors: Yom Aria , Chiang Austin , Lewis Nathan E.
Published: June 2023

Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88±7% of N-glycans and 87±13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
Cancer drug sensitivity prediction from routine histology images
Authors: Dawood Muhammad , Vu Quoc Dang , Young Lawrence S. , Branson Kim , Jones Louise , Rajpoot Nasir , Minhas Fayyaz ul Amir Afsar
Published: June 2023

Drug sensitivity prediction models can aid in personalising cancer therapy, biomarker discovery, and drug design. Such models require survival data from randomized controlled trials which can be time consuming and expensive. In this proof-of-concept study, we demonstrate for the first time that deep learning can link histological patterns in whole slide images (WSIs) of Haematoxylin & Eosin (H&E) stained breast cancer sections with drug sensitivities inferred from cell lines. We employ patient-wise drug sensitivities imputed from gene expression based mapping of drug effects on cancer cell lines to train a deep learning model that predicts sensitivity to multiple drugs from WSIs. We show that it is possible to use routine WSIs to predict the drug sensitivity profile of a cancer patient for a number of approved and experimental drugs. We also show that the proposed approach can identify cellular and histological patterns associated with drug sensitivity profiles of cancer patients.

Highlights

Predicting drug sensitivity from routine histology images and cell lines

Discovery of histology image patterns linked to drug sensitivity

A novel deep learning pipeline for analysing drug sensitivity profiles
Specific photoreceptor cell fate pathways are differentially altered in NR2E3-associated diseases
Authors: Aísa-Marín Izarbe , Rovira Quirze , Díaz Noelia , Calvo-López Laura , Vaquerizas Juan M. , Marfany Gemma
Published: June 2023

Mutations inNR2E3cause two retinal dystrophies with a distinct phenotype.NR2E3encodes an orphan nuclear transcription factor that contributes to photoreceptor cell fate determination by repressing cone while activating rod genes. To dissect NR2E3 function, we performed scRNA-seq in the retinas of wild type and two differentNr2e3mouse models that show phenotypes similar to patients carryingNR2E3mutations. Our results reveal that rod and cone populations are not homogeneous and can be separated into different sub- classes. We identify a previously unreported cone pathway that generates hybrid cones that co-express both cone- and rod-related genes. In mutant retinas, this hybrid cone subpopulation is more abundant, as it includes a subpopulation of rods transitioning towards a cone cell fate. Hybrid photoreceptors with high misexpression of cone- and rod-related genes are prone to regulated necrosis. Overall, our results shed light on the role of NR2E3 in modulating photoreceptor differentiation towards cone and rod fates and explain how mutations inNR2E3lead to different visual disorders in humans.

GRAPHICAL ABSTRACT

SYNOPSIS

Mutations in the gene encoding the retinal transcription factorNR2E3cause two different inherited retinal dystrophies: retinitis pigmentosa and enhanced S-cone syndrome.

scRNA-seq in retinas of wild type and twoNr2e3mouse models reveal that rod and cone populations are not homogeneous and can be classified into different sub-classes.

A previously unreported cone pathway that generates hybrid cones co- expressing both cone- and rod-related genes is identified.

Hybrid photoreceptors with high misexpression of cone- and rod-related genes are prone to regulated necrosis.

Expression of rod and cone signature genes change in response to differentNR2E3mutations thus providing a frame to understand the molecular basis of distinct NR2E3-associated diseases.
Engineered display of ganglioside-sugars on protein elicits a clonally and structurally constrained B cell response
Authors: Deimel Lachlan P. , Xue Xiaochao , Khan Aziz , Moynie Lucile , Buchanan Charles J. , Sun Guoxuan , McBride Ryan , Schuster Heiko , Gauthier Charles , Saliba Regis , Leonavicus Karolis , Minall Leanne , Bort Guillaume , Russell Rebecca A. , Sezgin Erdinc , Paulson James C. , Anthony Daniel C. , Baldwin Andrew J. , Naismith James , Schiffner Torben , Davis Benjamin G. , Sattentau Quentin J.
Published: June 2023

Ganglioside sugars, as Tumour-Associated Carbohydrate Antigens (TACAs), are long-proposed targets for vaccination and therapeutic antibody production, but their self-like character imparts immunorecessive characteristics that classical vaccination approaches have to date failed to overcome. One prominent TACA, the glycan component of ganglioside GM3 (GM3g), is over-expressed on diverse tumours. To probe the limits of glycan tolerance, we used protein editing methods to display GM3g in systematically varied non-native presentation modes by attachment to carrier protein lysine sidechains using diverse chemical linkers. We report here that such presentation creates glycoconjugates that are strongly immunogenic in mice and elicit robust antigen-specific IgG responses specific to GM3g. Characterisation of this response by antigen-specific B cell cloning and phylogenetic and functional analyses suggests that such display enables the engagement of a highly restricted naïve B cell class with a defined germline configuration dominated by members of theIGHV2subgroup. Strikingly, structural analysis reveals that glycan features appear to be recognised primarily by antibody CDRH1/2, and despite the presence of an antigen-specific Th response and B cell somatic hypermutation, we found no evidence of affinity maturation towards the antigen. Together these findings suggest a ‘reach-through’ model in which glycans, when displayed in non-self formats of sufficient distance from a conjugate backbone, may engage ‘glycan ready’ V-region motifs encoded in the germline. Structural constraints define why, despite engaging the trisaccharide, antibodies do not bind natively-presented glycans, such as when linked to lipid GM3. Our findings provide an explanation for the long-standing difficulties in raising antibodies reactive with native TACAs, and provide a possible template for rational vaccine design against this and other TACA antigens.

Highlights

GM3g synthetically coupled via a longer, orthogonal (from backbone) glycoconjugate (LOG) presentation format (thioethyl-lysyl-amidine) display elicits high-titre IgG responses in mice.

The germinal centre experience of LOG glycoconjugate-specific B cell responses is directly influenced by the protein backbone.

Structural characterisation of the antibody response to LOGs reveals highly restricted germline-encoded glycan-engaging motifs that mediate GM3g recognition.

Failure of antibodies to bind the native trisaccharide highlights barriers to be overcome for the rational design of anti-TACA antibodies.
The VR Billboard Paradigm: Using VR and Eye-tracking to Examine the Exposure-Reception-Retention Link in Realistic Communication Environments
Authors: Schmälzle Ralf , Lim Sue , Cho Hee Jung , Wu Juncheng , Bente Gary
Published: June 2023

Exposure is the cornerstone of media and message effects research. If a health, political, or commercial message is not noticed, no effects can ensue. Yet, existing research in communication, advertising, and related disciplines often fails to measure exposure and demonstrate the causal link between quantified exposure to outcomes because actual exposure (i.e., whether recipients were not only exposed to messages but also took notice of them) is difficult to capture. Here, we harness Virtual Reality (VR) technology integrated with eye tracking to overcome this challenge. While eye-tracking technology alone can capture whether people attend to messages in their communication environment, most eye-tracking research is bound by laboratory-based screen-reading paradigms that are not representative of the broader communication environments in which messages are encountered. Emerging eye-tracking field research suffers from an inability to control and experimentally manipulate key variables. Our solution is to measure eye-tracking within an immersive environment in VR that resembles a realistic message reception context. Specifically, we simulate driving down a highway alongside which billboards are placed and use VR-integrated eye-tracking to measure whether the drivers look at individual billboard messages. This allows us to rigorously quantify the nexus between exposure and reception, and to link our measures to subsequent memory, i.e., whether messages were remembered, forgotten, or not even encoded. We further demonstrate that manipulating drivers’ attention directly impacts gaze behavior and memory. We discuss the large potential of this paradigm to quantify exposure and message reception in realistic communication environments and the equally promising applications in new media contexts (e.g., the Metaverse).
Allosteric activation and inhibition of glycogen phosphorylase share common transient structural features
Authors: Kish Monika , Ivory Dylan P. , Phillips Jonathan J.
Published: June 2023

It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme, glycogen phosphorylase is one of the most studied proteins and is a clinical target of much interest to treat type II diabetes and metastatic cancers. However, a lack of understanding of its complex regulation, mediated by dynamic structural changes, hinder its exploitation as a drug target. Here, we precisely locate dynamic structural changes upon allosteric activation and inhibition of glycogen phosphorylase, by developing a time-resolved non-equilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach. We resolved obligate transient changes in localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect at a common structurally dynamic motif. This approach has broad application to determine the structural kinetic mechanisms by which proteins are regulated.
A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism
Authors: Yao Yingjia , Zhang Yunhan , Li Zexu , Chen Zhisong , Wang Xiaofeng , Li Zihan , Yu Li , Cheng Xiaolong , Li Wei , Jiang Wen-Jie , Wu Hua-Jun , Feng Zezhong , Sun Jinfu , Fei Teng
Published: June 2023

The recent outbreak of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a severe threat to the global public health and economy, however, effective drugs to treat COVID-19 are still lacking. Here, we employ a deep learning-based drug repositioning strategy to systematically screen potential anti-SARS-CoV-2 drug candidates that target the cell entry mechanism of SARS-CoV-2 virus from 2,635 FDA-approved drugs and 1,062 active ingredients from Traditional Chinese Medicine herbs.In silicomolecular docking analysis validates the interactions between the top compounds and host receptors or viral spike proteins. Using a SARS-CoV-2 pseudovirus system, we further identify several drug candidates including Fostamatinib, Linagliptin, Lysergol and Sophoridine that can effectively block the cell entry of SARS-CoV-2 variants into human lung cells even at a nanomolar scale. These efforts not only illuminate the feasibility of applying deep learning-based drug repositioning for antiviral agents by targeting a specified mechanism, but also provide a valuable resource of promising drug candidates or lead compounds to treat COVID-19.
Adding Different Exercise Training Volumes to a Diet-Induced Weight Loss Facilitates Fat Loss and Maintains Fat-Free Mass in a Dose-Depending Fashion in Persons with Newly Diagnosed Type 2 Diabetes: Secondary Findings from the DOSE-EX Multi-Arm, Parallel-Group, Randomized Trial
Authors: Lyngbæk Mark P.P. , Legaard Grit E. , Nielsen Nina S. , Durrer Cody , Almdal Thomas P. , Lund Morten Asp Vonsild , Liebetrau Benedikte , Ewertsen Caroline , Lauridsen Carsten , Solomon Thomas P.J. , Karstoft Kristian , Pedersen Bente K. , Ried-Larsen Mathias
Published: June 2023

OBJECTIVE

To assess the dose-response effects of exercise in combination with a diet-induced weight loss on fat mass (FM) percentage (FM%) in persons with diagnosed type 2 diabetes.

RESEARCH DESIGN AND METHODS

In this secondary analysis of a four-armed randomized trial (Clinicaltrials.govNCT03769883) 82 persons (35% females, mean age and standard deviation (SD) 58.2 (9.8) years) living with type 2 diabetes were randomly allocated to the control group (N=21, CON), diet control (25% energy restriction;N=20, DCON), diet control and exercise three times/week (two sessions of aerobic and one session combining resistance and aerobic training;N=20, MED), or diet control and exercise six times/week (four sessions of aerobic and two sessions combining resistance and aerobic training;N=21, HED) for 16 weeks. The primary outcome was the change in FM percentage points (pp). Secondary outcomes included fat-free mass and visceral adipose tissue volume.

RESULTS

Type 2 diabetes duration was 4.0 years (interquartile range 1.9 to 5.5), body weight (SD) 101.4 kg (14.6), FM% (SD) 39.4 (6.7). FMpp decreased compared to standard care −3.5 pp (95% CI −5.6 to −1.4) p=0.002, −6.3 pp (CI −8.4 to −4.1) p<0.001, and −8.0 pp (95% CI −10.2 to −5.8) p<0.001, for DCON, MED, and HED, respectively. The difference between HED and MED was −1.8 pp [95% CI −3.9 to 0.4]; p=0.11).

CONCLUSIONS

All interventions were superior in reducing FMpp compared to standard care in a dose-dependent manner. Adding three or six sessions of exercise to a low-calorie diet was superior in reducing FM compared to a low-calorie diet alone.

Article Highlights

Why did we undertake this study?

Exercise and weight loss are recommended for persons with type 2 diabetes. It is unclear if adding exercise, and which amount of exercise, to a low-calorie diet supports additional fat mass loss.

What is the specific question(s) we wanted to answer?

What is the dose-response effect of exercise combined with a moderate caloric restriction on changes in fat mass?

What did we find?

Adding exercise to a diet-induced weight loss reduced fat mass and preserved fat-free mass in a dose-dependent manner.

What are the implications of our findings?

Adding exercise to a moderate caloric restriction dose-dependently facilitates reductions in fat mass by enlarging weight loss and fat loss.
Amyloid β Induces Lipid Droplet-Mediated Microglial Dysfunction in Alzheimer’s Disease
Authors: Prakash Priya , Manchanda Palak , Paouri Evi , Bisht Kanchan , Sharma Kaushik , Rajpoot Jitika , Wendt Victoria , Hossain Ahad , Wijewardhane Prageeth R. , Randolph Caitlin E. , Chen Yihao , Stanko Sarah , Gasmi Nadia , Gjojdeshi Anxhela , Card Sophie , Fine Jonathan , Jethava Krupal P. , Clark Matthew G. , Dong Bin , Ma Seohee , Crockett Alexis , Thayer Elizabeth A. , Nicolas Marlo , Davis Ryann , Hardikar Dhruv , Allende Daniela , Prayson Richard A. , Zhang Chi , Davalos Dimitrios , Chopra Gaurav
Published: June 2023

Several microglia-expressed genes have emerged as top risk variants for Alzheimer’s disease (AD). Impaired microglial phagocytosis is one of the main proposed outcomes by which these AD-risk genes may contribute to neurodegeneration, but the mechanisms translating genetic association to cellular dysfunction remain unknown. Here we show that microglia form lipid droplets (LDs) upon exposure to amyloid-beta (Aβ), and that their LD load increases with proximity to amyloid plaques in brains from human patients and the AD mouse model 5xFAD. LD formation is dependent on age and disease progression and is prominent in the hippocampus in mice and humans. Despite differences in microglial LD load between brain regions and sexes in mice, LD-laden microglia exhibited a deficit in Aβ phagocytosis. Unbiased lipidomic analysis identified a decrease in free fatty acids (FFAs) and a parallel increase in triacylglycerols (TGs) as the key metabolic transition underlying LD formation. DGAT2, a key enzyme for converting FFAs to TGs, promotes microglial LD formation and is increased in 5xFAD and human AD brains. Inhibition or degradation of DGAT2 improved microglial uptake of Aβ and drastically reduced plaque load in 5xFAD mice, respectively. These findings identify a new lipid-mediated mechanism underlying microglial dysfunction that could become a novel therapeutic target for AD.