bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatal Iatrogenic Cerebral Amyloid-Related Encephalitis in a patient treated with lecanemab for Alzheimer’s disease: neuroimaging and neuropathology
Authors: Solopova Elena , Romero-Fernandez Wilber , Harmsen Hannah , Ventura-Antunes Lissa , Wang Emmeline , Shostak Alena , Maldonado Jose , Donahue Manus , Schultz Daniel , Coyne Thomas M. , Charidimou Andreas , Schrag Matthew
Published: April 2023

We report the case of an elderly woman in good general health aside from early-stage Alzheimer’s disease who was enrolled in a randomized controlled trial of the novel therapeutic monoclonal antibody lecanemab where she was treated with the placebo, and subsequently in the open label extension study where she received lecanemab infusions every two weeks. After the third infusion, she suffered a seizure followed by aphasia and progressively worsening encephalopathy. Magnetic resonance imaging revealed multifocal cerebral edema and an increased burden of cerebral microhemorrhages compared to pre-trial imaging, consistent with Amyloid Related Imaging Abnormality (ARIA). She was treated with an antiepileptic regimen and high-dose intravenous corticosteroids but continued to worsen and expired after five days in the hospital. The family requested an autopsy and consented to evaluation of her brain for research. Post-mortem MRI confirmed extensive microhemorrhagic changes in the temporal, parietal and occipital lobes, some of which were visible on gross inspection of the brain. Autopsy confirmed APOE genotype of E4/E4 and the presence of typical neuropathological features of Alzheimer’s disease along with severe cerebral amyloid angiopathy with inflammatory features, including perivascular lymphocytic infiltrates, reactive macrophages and fibrinoid degeneration of vessel walls. There were deposits of β-amyloid in meningeal vessels and penetrating arterioles with numerous microaneurysms. Cerebral microhemorrhages were associated with arterioles harboring β-amyloid deposits and having degenerative morphologies. We conclude from these results that the patient likely died as a result of severe cerebral amyloid angiopathy with marked microvascular degeneration and meningoencephalitis. Further study of the mechanism of ARIA and the neuropathological changes associated with plaque clearance are needed.
Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence
Authors: Lapalu Nicolas , Lamothe Lucie , Petit Yohann , Genissel Anne , Delude Camille , Feurtey Alice , Abraham Leen N. , Smith Dan , King Robert , Renwick Alison , Appertet Mélanie , Sucher Justine , Steindorff Andrei S. , Goodwin Stephen B. , Kema Gert H.J. , Grigoriev Igor V. , Hane James , Rudd Jason , Stukenbrock Eva , Croll Daniel , Scalliet Gabriel , Lebrun Marc-Henri
Published: April 2023

Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogenZymoseptoria tritici(isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novelab initiogene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5’ and 3’UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining differentab initiogene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape ofZ. tritici, helping develop an increasingly complex picture of its biology.
Easy Removal of Steric Clashes and Entanglements in Macromolecular Systems by Temporary Addition of a Fourth Spatial Dimension
Authors: Elcock Adrian H.
Published: April 2023

When models of complicated macromolecular systems are constructed, it is common to inadvertently include either gross steric clashes or entanglements of extended loop regions. Removing these problems with conventional energy minimization or dynamics algorithms can often be difficult. Here I show that one easy alternative is to temporarily add an extra spatial dimension and to displace atoms or molecules along this fourth dimension such that the distances between atoms, when measured in 4D, are no longer considered clashing. Adding in half-harmonic potential functions to mimic walls in this 4thdimension, and then moving these walls toward each other, has the effect of decreasing the space available in the 4thdimension and drives atoms to avoid each other in 3D. I illustrate the method with three examples: two showing how interlocked ring polymers can be easily disentangled from each other in both 2D and 3D, and one showing how ten identical coarse-grained protein models, all placed at the same point in 3D space, can be separated from each other, without distorting their structures, during the course of a single energy minimization. A sample program implementing the method is available that can be easily adapted to other situations.
Lack of mTORC2 signaling in CD11c+myeloid cells inhibits their migration and ameliorates experimental colitis
Authors: Ignacio Aline , Cipelli Marcella , Takiishi Tatiane , Aguiar Cristhiane Favero , Terra Fernanda Fernandes , Ghirotto Bruno , Silva Eloisa Martins , Castoldi Angela , Magalhães Yuli Thamires , Antonio Tiago , Hiyane Meire Ioshie , Andrade-Oliveira Vinicius , Forti Fabio Luis , Saraiva Camara Niels Olsen
Published: April 2023

Mammalian target of rapamycin (mTOR) pathway plays a key role in determining immune cells function through modulation of their metabolic status. By specific deletion of Rictor in tissue-resident CD11c+myeloid cells (CD11cRicΔ/Δ), this study investigated the role of mTOR complex 2 (mTORC2) signaling in dendritic cells (DCs) function in mice. We showed that upon DSS-induced colitis, lack of mTORC2 signaling CD11c+cells diminish colonic inflammation, abrogates dendritic cell (DC) migration to the mesenteric lymph nodes (MLN), thereby diminishing the infiltration of T helper (Th) 17 cells in the lamina propria (LP). These findings corroborate with abrogation of cytoskeleton organization and decreased activation of Rac1 and Cdc42 GTPases observed in CD11c+-mTORC2-deficient cells. Meta-analysis on colonic samples from ulcerative colitis (UC) patients revealed increased gene expression of pro-inflammatory cytokines which coincided with augmented expression of mTOR pathway, positive correlation between the DC marker ITGAX, and IL-6, the expression of RICTOR, and CDC42. Together, this work proposes that targeting mTORC2 on DCs offers a key to hamper inflammatory responses and this way, ameliorates the progression and severity of intestinal inflammatory diseases.
Deep Learning for Protein Structure Prediction: Advancements in Structural Bioinformatics
Authors: Szelogowski Daniel
Published: April 2023

Motivation

Accurate prediction of protein structures is crucial for understanding protein function, stability, and interactions, with far-reaching implications in drug discovery and protein engineering. As the fields of structural bioinformatics and artificial intelligence continue to converge, a standardized model for protein structure prediction is still yet to be seen as even large models like AlphaFold continue to change architectures. To this end, we provide a comprehensive literature review highlighting the latest advancements and challenges in deep learning-based structure prediction, as well as a benchmark system for structure prediction and visualization of amino acid protein sequences.

Results

We present ProteiNN, a Transformer-based model for end-to-end single-sequence protein structure prediction, motivated by the need for accurate and efficient methods to decipher protein structures and their roles in biological processes and a system to perform prediction on user-input protein sequences. The model leverages the transformer architecture’s powerful representation learning capabilities to predict protein secondary and tertiary structures directly from integer-encoded amino acid sequences. Our results demonstrate that ProteiNN is effective in predicting secondary structures, though further improvements are necessary to enhance the model’s performance in predicting higher-level structures. This work thus showcases the potential of transformer-based architectures in structure prediction and lays the foundation for future research in structural bioinformatics and related fields.

Availability and implementation

The source code of ProteiNN is available athttps://github.com/danielathome19/ProteiNN-Structure-Predictor.
Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes
Authors: Wu Ling-Yi , Pappas Nikolaos , Wijesekara Yasas , Piedade Gonçalo J. , Brussaard Corina P.D. , Dutilh Bas E.
Published: April 2023

As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training/reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. We compared the performance of ten state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools had highly variable true positive rates (0 – 68%) and false positive rates (0 – 15%). PPR-Meta best distinguished viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identified different subsets of the benchmarking data and all tools, except for Sourmash, found unique viral contigs. Tools performance could be improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. Together, our independent benchmarking provides guidance on choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments for viromics researchers.
Long-Term Oral Tamoxifen Administration Decreases Brain Derived Neurotrophic Factor in the Hippocampus of Female Long-Evans Rats
Authors: Been Laura E. , Halliday Amanda R. , Blossom Sarah M. , Bien Elena M. , Bernhard Anya G. , Roth Grayson E. , Domenech Rosario Karina I. , Pollock Karlie B. , Abramenko Petra E. , Behbehani Leily M. , Pascal Gabriel J. , Kelly Mary Ellen
Published: April 2023

Tamoxifen is a selective estrogen receptor modulator (SERM) that is commonly used as an adjuvant drug therapy for estrogen receptor-positive breast cancers. While this drug is effective at reducing the rate of cancer recurrence, many patients report unwanted cognitive and affective side effects such as brain fog, confusion, memory impairment, anxiety, and depression. Despite this, the impacts of chronic tamoxifen exposure on the brain are poorly understood, and rodent models of tamoxifen exposure do not replicate the chronic oral administration seen in patients. We therefore used long-termad libconsumption of medicated food pellets in adult female rats to model chronic tamoxifen exposure in a clinically-relevant way. Gonadally-intact adult female Long-Evans Hooded rats consumed tamoxifen medicated food pellets for approximately 12 weeks while control animals received standard chow. At the conclusion of the experiment, animals were euthanized, and blood and brain samples were collected for analyses. Blood tamoxifen levels were measured using a novel ultra-performance liquid chromatography-tandem mass spectrometry assay, which found that this administration paradigm produced serum levels of tamoxifen similar to those in human patients. In the brain, brain derived neurotrophic factor (BDNF) was visualized in the hippocampus using immunohistochemistry and quantified using background-subtracted optical densitometry. Chronic oral tamoxifen treatment resulted in a decrease in BDNF expression across several regions of the hippocampus. Together, these findings provide a novel method of modeling and measuring chronic oral tamoxifen exposure, and suggest a putative mechanism by which tamoxifen may cause cognitive and behavioral changes reported by patients.
Anatomically-specific coupling between innate immune gene repertoire and microbiome structure during coral evolution
Authors: Brown Tanya , Sonett Dylan , McMinds Ryan , Pollock F. Joseph , Medina Mónica , Zaneveld Jesse R.
Published: April 2023

Tropical reef-building corals exist in intimate symbiosis with diverse microbes and viruses. Coral microbiomes are generally much less diverse than their environment, but across studied corals, the biodiversity of these microbiomes varies greatly. It has previously been hypothesized that differences in coral innate immunity in general, and the copy number of TIR-domain containing innate immune genes in particular, may drive interspecific differences in microbiome structure. Despite many existing studies of coral microbiomes, this hypothesis has previously been difficult to test due to a lack of consistently collected cross-species data on coral microbiomes. In this manuscript, we reannotate TIR-domain containing genes across diverse coral genomes, and use phylogenetic comparative methods to compare these innate immune gene copy numbers against 16S rRNA marker gene data on coral mucus, tissue, and skeleton microbiomes from the Global Coral Microbiome Project (GCMP). The copy number of Toll-like receptor (TLRs) and Interleukin-1 receptor (IL-1Rs) gene families, as well as the total genomic count of their constituent domains (LRR and TIR domains; and Ig and TIR domains, respectively), explained most interspecific differences in microbiome richness and beta-diversity among corals with sequenced genomes. We find that these correlations are also anatomically specific, with an especially strong correlation between IL-1R gene copy numbers and microbiome richness in the coral’s endolithic skeleton. Together, these results suggest innate immunity may play a key role in sculpting microbiome structure in corals.
Improved Quality Metrics for Association and Reproducibility in Chromatin Accessibility Data Using Mutual Information
Authors: Roth Cullen , Venu Vrinda , Job Vanessa , Lubbers Nicholas , Sanbonmatsu Karissa Y. , Steadman Christina R. , Starkenburg Shawn R.
Published: April 2023

Background

Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility.

Results

Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson’sRand Spearman’sρcoefficients as well as Kendall’sτand Top-Down correlation. We also test the behavior of association measures, including the coefficient of determinationR2, Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spearman’sρ, Kendall’sτ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, theR2coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships.

Conclusions

Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.
Site effects depth denoising and signal enhancement using dual-projection based ICA model
Authors: Hao Yuxing , Xu Huashuai , Xia Mingrui , Yan Chenwei , Zhang Yunge , Zhou Dongyue , Kärkkäinen Tommi , Nickerson Lisa D. , Li Huanjie , Cong Fengyu
Published: April 2023

Combining magnetic resonance imaging (MRI) data from multi-site studies is a popular approach for constructing larger datasets to greatly enhance the reliability and reproducibility of neuroscience research. However, the scanner/site variability is a significant confound that complicates the interpretation of the results, so effective and complete removal of the scanner/site variability is necessary to realize the full advantages of pooling multi-site datasets. Independent component analysis (ICA) and general linear model (GLM) based denoising methods are the two primary methods used to denoise scanner/site-related effects. Unfortunately, there are challenges with both ICA-based and GLM-based denoising methods to remove site effects completely when the signals of interest and scanner/site-related noises are correlated, which may occur in neuroscience studies. In this study, we propose an effective and powerful denoising strategy that implements dual-projection (DP) theory based on ICA to remove the scanner/site-related effects more completely. This method can separate the signal effects correlated with noise variables from the identified noise effects for removal without losing signals of interest. Both simulations and vivo structural MRI datasets, including a dataset from Autism Brain Imaging Data Exchange II and a traveling subject dataset from the Strategic Research Program for Brain Sciences, were used to test the proposed GLM- and ICA-based denoising methods and our DP-based ICA denoising method. Results show that DP-based ICA
Hyper-Cryptic Radiation of a Tropical Montane Plant Lineage
Authors: Olivares Ingrid , Tusso Sergio , SanÍn MarÍa JosÉ , Kessler Michael , Shimizu Kentaro K.
Published: April 2023

Species are seen as the fundamental unit of biotic diversity, and thus their delimitation is crucial for defining measures for diversity assessments and studying evolution. Differences between species have traditionally been associated with variation in morphology. And yet, the discovery of cryptic diversity suggests that the evolution of distinct lineages does not necessarily involve trait differences. Here, we analyze 1,684,987 variant sites and over 4000 genes for more than 400 samples to show how a tropical montane plant lineage (Geonoma undataspecies complex) is composed of numerous unrecognized genetic groups that are not morphologically distinct. We find that 11 to 14 clades do not correspond to the three currently recognized species. Most clades are genetically independent and geographic distance and topography are the most important factors determining this genetic divergence. This lineage does not match the model of an adaptive radiation, but instead, constitutes the first example of a hyper-cryptic plant radiation in tropical mountains.
Mtfp1ablation enhances mitochondrial respiration and protects against hepatic steatosis
Authors: Patitucci Cecilia , Hernández-Camacho Juan Diego , Vimont Elodie , Cokelaer Thomas , Chaze Thibault , Giai Gianetto Quentin , Matondo Mariette , Gazi Anastasia , Nemazanyy Ivan , Stroud David A. , Hock Daniella H. , Donnarumma Erminia , Wai Timothy
Published: April 2023

Hepatic steatosis is the result of an imbalance between nutrient delivery and metabolism in the liver. It is the first hallmark of Non-alcoholic fatty liver disease (NAFLD) and is characterized by the accumulation of excess lipids in the liver that can drive liver failure, inflammation, and cancer. Mitochondria control the fate and function of cells and compelling evidence implicates these multifunctional organelles in the appearance and progression of liver dysfunction, although it remains to be elucidated which specific mitochondrial functions are actually causally linked to NAFLD. Here, we identified Mitochondrial Fission Process 1 protein (MTFP1) as a key regulator of mitochondrial and metabolic activity in the liver. Deletion ofMtfp1in hepatocytes is physiologically benign in mice yet leads to the upregulation of oxidative phosphorylation (OXPHOS) activity and mitochondrial respiration, independently of mitochondrial biogenesis. Consequently, hepatocyte-specific knockout mice are protected against high fat diet-induced hepatic steatosis and metabolic dysregulation. Additionally, we find that deletion ofMtfp1in liver mitochondria inhibits mitochondrial permeability transition pore opening in hepatocytes, conferring protection against apoptotic liver damage in vivo and ex vivo. Our work uncovers novel functions of MTFP1 in the liver, positioning this gene as an unexpected regulator of OXPHOS and a therapeutic candidate for NAFLD.
Mechanism of ozone alleviation of malignant ascites in hepatocellular carcinoma through inhibition of NETs
Authors: Han Feng , Guo Jiayou , Mu Mingchen , Bian Ka , Cui Zhenting , Duan Qiong , Ma Jianxin , Jin Lai , Liu Wentao , Chen Fanghong
Published: April 2023

Malignant ascites in hepatocellular carcinoma is usually a sign of advanced disease and poor prognosis and is also thought to be associated with chronic inflammation mediated by neutrophil extracellular trap networks (NETs). Whereas ozone, a strong oxidant, has significant antibacterial and anti-inflammatory effects, its effectiveness in treating malignant liver ascites is unclear.cOzone showed significant anti-peritoneal fluid production properties in H22 tumor-bearing mice, and ozone reduced peritoneal fluid production by activating AMPK and up-regulating SR-A phagocytosis damage-associated molecular patterns (DAMPs) to reduce the production of NETs. This suggests that ozone could be used as a new drug for the treatment of malignant ascites in hepatocellular carcinoma.
Network inference from temporal phosphoproteomics informed by protein-protein interactions
Authors: Plank Michael
Published: April 2023

Network inference from time-course data holds the promise to overcome challenges associated with other methods for deciphering cell signaling networks. Integration of protein-protein interactions in this process is frequently employed to limit wiring options.

In this study, a graph approach for the analysis of data of high temporal resolution is introduced and applied to a 5 s resolution phosphoproteomics dataset. Steiner trees informed by protein-protein interactions are constructed on individual time slices, which are then stitched together into a temporal signaling network.

Systematic benchmarking against existing knowledge indicates that the approach enriches signaling-relevant edges. The workflow is compatible with future extensions for reliably extracting extended signaling paths.
Computational Insight into Anti-Obesity Effects of Combined Some Phytobiotics to GLP1R (Glucagon-Like Peptide 1 Receptor) Protein inAnas javanica
Authors: Damayanti CA , Harahap MAY , Wibowo S , Sjofjan O , Djunaidi IH
Published: April 2023

Damayanti CA, Harahap MAY, Wibowo S, Sjofjan O, Djunaidi IH. 2023. Computational Insight into Anti-Obesity Effects of Indonesian Phytobiotics to GLP1R (Glucagon-Like Peptide 1 Receptor) Protein inAnas javanica.

Mojosari ducks (Anas javanica) is native Indonesia laying ducks was a egg producing type with quite high egg production, must be maintain body weight to propotional condition as laying duck. If the body weight surpasses normal, it can lead to obesity and reduce the eggs quality. One of the proteins closely related to obesity and hyperglycemia is GLP1R (Glucagon-Like Peptide 1 Receptor). The increase in GLP1R activity by one of the compounds that have been widely researched is loureirin B. Interaction between loureirin B and GLP1R increases insulin production in the body so that hyperglycemia and body weight can be controlled properly. Exploration of phytobiotic compounds from Indonesia is needed to find the substitution of loureirin B as an anti-obesity agent. According to the findings of in silico study (protein modeling and molecular docking), cynaroside (−9.2 kcal/mol), 14-Deoxy-11,12-didehydroandrographolide (−9.1 kcal/mol), rutin (−8.8 kcal/mol), andrographidine E (−8.6 kcal/mol), and cianidanol (−7.8 kcal/mol) had stronger binding affinity than loureirin B (−7.4 kcal/mol). Andrographidine E, derived from the plantAndrographis paniculata, is the best candidate for GLP1R agonist. The binding affinity that Andrographidine E has is lower than control compounds, so it is easier for bonds to occur between proteins and such compounds. In addition, the interacting amino acids do not have unfavourable bonds that make it more stable than other candidates. Results from clinical studies show that the use ofA. paniculatacan reduce glucose levels.
Voluntary muscle activation in people with Multiple Sclerosis is reduced across a wide range of forces following maximal effort fatiguing contractions
Authors: Brotherton Emily J. , Sabapathy Surendran , Heshmat Saman , Kavanagh Justin J.
Published: April 2023

People with Multiple Sclerosis typically exhibit greater levels of exercise-induced fatigue compared to healthy individuals. However, it is unknown if voluntary muscle activation is affected over a range of contraction forces in people with MS who have exercise-induced fatigue. The purpose of this study was to use transcranial magnetic stimulation (TMS) and electrical muscle stimulation to examine muscle activation during exercise-induced fatigue. Ten people with relapsing-remitting MS (39 ± 7 years) and 10 healthy controls (40 ± 5 years) performed elbow flexions at 25%, 50%, 75%, 90%, and 100% MVC while electromyography (EMG) of the biceps brachii was recorded. Sustained elbow flexion MVCs were then performed until force declined to 60% of baseline MVC, and the target contraction intensities of 25%, 50%, 75%, 90%, and 100% MVC were examined again. The Fatigue Severity Scale was higher for the MS group (P< 0.01). Exercise-induced fatigue caused a reduction in biceps EMG amplitude for the MS group across all contraction intensities (P< 0.01), which was not aligned with changes in MEP amplitude (P= 0.25). Exercise-induced fatigue reduced motor cortical voluntary activation in the MS group across all contraction intensities (P< 0.01), as well as increased MS time-to-peak force (P <0.01) and half relaxation time for TMS evoked twitches (P= 0.03). These findings provide evidence that MS-related fatigability during maximal contractions is due to the inability for the motor cortex to drive the muscle, with possible contributions from altered contractile properties in the MS muscle.

NEW & NOTEWORTHY

We use transcranial magnetic stimulation to demonstrate that people with relapsing-remitting Multiple Sclerosis (MS) have a reduced ability to activate muscle following maximal effort fatiguing contractions. Although our MS participants reported greater symptoms of fatigue via the Fatigue Severity Scale, their reduced ability to activate muscle was more associated with the duration of disease.
Similar but distinct: the impact of biomechanical forces and culture age on the production, cargo loading, and biological efficacy of human megakaryocytic extracellular vesicles for applications in cell and gene therapies
Authors: Thompson Will , Papoutsakis Eleftherios Terry
Published: April 2023

Megakaryocytic extracellular vesicles (MkEVs) promote the growth and megakaryopoiesis of hematopoietic stem and progenitor cells (HSPCs) largely through endogenous miR-486-5p and miR-22-3p cargo. Here, we examine the impact of biomechanical force and culture age/differentiation on the formation, properties, and biological efficacy of MkEVs. We applied biomechanical force to Mks using two methods: shake flask cultures and a syringe pump system. Force increased MkEV production in a magnitude-dependent manner, with similar trends emerging regardless of whether flow cytometry or nanoparticle tracking analysis (NTA) was used for MkEV counting. Both methods produced MkEVs that were relatively depleted of miR-486-5p and miR-22-3p cargo. However, while the shake flask-derived MkEVs were correspondingly less effective in promoting megakaryocytic differentiation of HSPCs, the syringe pump-derived MkEVs were more effective in doing so, suggesting the presence of unique, unidentified miRNA cargo components. Higher numbers of MkEVs were also produced by “older” Mk cultures, though miRNA cargo levels and MkEV bioactivity were unaffected by culture age. A reduction in MkEV production by Mks derived from late-differentiating HSPCs was also noted. Taken together, our results demonstrate that biomechanical force has an underappreciated and deeply influential role in MkEV biology, though that role may vary significantly depending on the nature of the force. Given the ubiquity of biomechanical force in vivo and in biomanufacturing, this phenomenon must be grappled with before MkEVs can attain clinical relevance.

Abstract Figure
Exploration of T-cell immune responses by expression of a dominant-negative SHP1 and SHP2
Authors: Taylor Julia , Bulek Anna , Gannon Isaac , Robson Mathew , Kokalaki Evangelia , Grothier Thomas , McKenzie Callum , El-Kholy Mohamed , Stavrou Maria , Traynor-White Charlotte , Lim Wen-Chean , Panagiotou Panagiota , Srivastava Saket , Baldan Vania , Silibourne James , Ferrari Mathieu , Pule Martin , Thomas Simon
Published: April 2023

SHP1 and SHP2 are SH2 domain-containing proteins which have inhibitory phosphatase activity when recruited to phosphorylated ITIMs and ITSMs on inhibitory immune receptors. Consequently, SHP1 and SHP2 are key proteins in the transmission of inhibitory signals within T cells, constituting an important point of convergence for diverse inhibitory receptors. Therefore, SHP1 and SHP2 inhibition may represent a strategy for preventing immunosuppression of T cells mediated by cancers hence improving immunotherapies directed against these malignancies. Both SHP1 and SHP2 contain dual SH2 domains responsible for localization to the endodomain of inhibitory receptors and a protein tyrosine phosphatase domain which dephosphorylates and thus inhibits key mediators of T cell activation. We explored the interaction of the isolated SH2 domains of SHP1 and SHP2 to inhibitory motifs from PD1 and identified strong binding of both SH2 domains from SHP2 and more moderate binding in the case of SHP1. We next explored whether these a truncated form of SHP1/2 comprising only of SH2 domains (dSHP1/2) could act in a dominant negative fashion by preventing docking of the wild type proteins. When co-expressed with CARs we found that dSHP2 but not dSHP1 could alleviate immunosuppression mediated by PD1. We next explored the capacity of dSHP2 to bind with other inhibitory receptors and observed several potential interactions. In vivo we observed that the expression of PDL1 on tumor cells impaired the ability of CAR T cells to mediate tumor rejection and this effect was partially reversed by the co-expression of dSHP2 albeit at the cost of reduced CAR T cell proliferation. Modulation of SHP1 and SHP2 activity in engineered T cells through the expression of these truncated variants may enhance T cell activity and hence efficacy in the context of cancer immunotherapy.
The neurovascular unit of capillary blood vessels in the rat nervous system. A rapid-Golgi electron microscopic study
Authors: Larriva-Sahd Jorge , Martínez-Cabrera Gema , Lozano-Flores Carlos , Concha Luis , Varela-Echavarría Alfredo
Published: April 2023

We describe a pericapillary organ in the rat forebrain and cerebellar cortex. It consists of series of tripartite synapses enveloped by astrocytic endfeet linked to the capillary wall by synaptic extensions. Reciprocal specializations of the pericyte-capillary blood vessel with such specialized synapses suggests a mechanoreceptor role. In Golgi impregnated and 3D reconstructions of cerebral cortex and thalamus, series of tripartite synapses appear sequentially ordered in a tributary dendrite paralleled by synaptic outgrowths termed here golf club-like extensions apposed to a longitudinal crest from the capillary basal lamina. To facilitate identification of principal cell dendrites and arriving axons to these putative mechanosensory structures, we utilized the cerebellar cortex since it has a well known organization and observed that afferent fibers and interneurons display interactions with the capillary wall. Afferent mossy fiber rosettes and ascending granule cell axons and dendrites define pericapillary on passage interactions surrounded by endfeet. The ability of such structures to modulate synaptic transmission is supported by the presence of mRNA of the mechanosensitive channel Piezo 1 in the mossy fiber rosettes, pyramidal isocortical and thalamic neurons. This suggests that ascending impulses to the cerebellar and cortical targets are presynaptically modulated by the reciprocal interaction with the mechanosensory pericapillary organ.
Honey bees (Apis mellifera) decrease the fitness of plants they pollinate
Authors: Travis Dillon J. , Kohn Joshua R.
Published: April 2023

Most flowering plants require animal pollination and are visited by multiple pollinator species. Historically, the effects of pollinators on plant fitness have been compared using the number of pollen grains they deposit, and the number of seeds or fruits produced following a visit to a virgin flower. While useful, these methods fail to consider differences in pollen quality and the fitness of zygotes resulting from pollination by different floral visitors. Here we show that, for three common native self-compatible plants in Southern California, super-abundant, non-native honey bees (Apis melliferaL.) visit more flowers on an individual before moving to the next plant compared to the suite of native insect visitors. This likely increases the transfer of self-pollen. Offspring produced after honey bee pollination have similar fitness to those resulting from hand self-pollination and both are far less fit than those produced after pollination by native insects or by cross-pollination. Because honey bees often forage methodically, visiting many flowers on each plant, low offspring fitness may commonly result from honey bee pollination of self-compatible plants. To our knowledge, this is the first study to directly compare the fitness of offspring resulting from honey bee pollination to that of other floral visitors.
A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
Authors: Scully Tal , Klein Allon
Published: April 2023

Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicateCiona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.
Differentiation between Descending Thoracic Aortic Diseases using Machine Learning and Plasma Proteomic Signatures
Authors: Momenzadeh Amanda , Kreimer Simion , Guo Dongchuan , Ayres Matthew , Berman Daniel , Chyu Kuang-Yuh , Shah Prediman K , Milewicz Dianna , Azizzadeh Ali , Meyer Jesse G. , Parker Sarah
Published: April 2023

Background

Descending thoracic aortic aneurysms and dissections can go undetected until severe and catastrophic, and few clinical indices exist to screen for aneurysms or predict risk of dissection.

Methods

This study generated a plasma proteomic dataset from 75 patients with descending type B dissection (Type B) and 62 patients with descending thoracic aortic aneurysm (DTAA). Standard statistical approaches were compared to supervised machine learning (ML) algorithms to distinguish Type B from DTAA cases. Quantitatively similar proteins were clustered based on linkage distance from hierarchical clustering and ML models were trained with uncorrelated protein lists across various linkage distances with hyperparameter optimization using 5-fold cross validation. Permutation importance (PI) was used for ranking the most important predictor proteins of ML classification between disease states and the proteins among the top 10 PI protein groups were submitted for pathway analysis.

Results

Of the 1,549 peptides and 198 proteins used in this study, no peptides and only one protein, hemopexin (HPX), were significantly different at an adjusted p-value <0.01 between Type B and DTAA cases. The highest performing model on the training set (Support Vector Classifier) and its corresponding linkage distance (0.5) were used for evaluation of the test set, yielding a precision-recall area under the curve of 0.7 to classify between Type B from DTAA cases. The five proteins with the highest PI scores were immunoglobulin heavy variable 6-1 (IGHV6-1), lecithin-cholesterol acyltransferase (LCAT), coagulation factor 12 (F12), HPX, and immunoglobulin heavy variable 4-4 (IGHV4-4). All proteins from the top 10 most important correlated groups generated the following significantly enriched pathways in the plasma of Type B versus DTAA patients: complement activation, humoral immune response, and blood coagulation.

Conclusions

We conclude that ML may be useful in differentiating the plasma proteome of highly similar disease states that would otherwise not be distinguishable using statistics, and, in such cases, ML may enable prioritizing important proteins for model prediction.
Novel discovery of a lymphatic bridge connecting Schlemm’s canal to limbal and conjunctival lymphatic pathway
Authors: Yang Yujia , Shi Meng , Li Guangyu , Shen Lejun , Chen Lu
Published: April 2023

Purpose

Schlemm’s canal (SC) is a critical structure regulating aqueous humor (AH) drainage and intraocular pressure (IOP). It is known that in the conventional outflow pathway, AH flows from SC to episcleral veins. We recently reported a high-resolution three-dimensional (3D) imaging technology for intact eyeballs, SC and ocular surface. Using this advanced technology, we herein report the discovery of a new structure, termed lymphatic bridge, that directly connects SC to the limbal and conjunctival lymphatic pathway. Further investigation on this novel outflow pathway may provide new mechanisms and therapeutic approaches for glaucoma.

Methods

As reported previously, intact eyeballs were harvested from Prox-1-GFP (green fluorescent protein) mice and processed by a tissue clearing technique with CLARITY. Samples were immunolabeled with specific antibodies for CD31 (pan-endothelial marker) and LYVE-1 (lymphatic vessel endothelial hyaluronan receptor-1) and imaged by light-sheet fluorescent microscopy. The limbal areas were examined to locate connecting channels between SC and limbal and conjunctival lymphatic vessels. Moreover, in vivo anterior chamber dye injection was performed with Texas Red dextran for functional analysis on AH outflow.

Results

A novel lymphatic bridge structure that expressed both Prox-1 and LYVE-1 was discovered between the SC and limbal lymphatic vessels connected with conjunctival lymphatic pathway. Results from the anterior chamber dye injection showed AH drainage into the conjunctival lymphatic outflow pathway.

Conclusions

This study provides the first evidence on the direct connection between SC and limbal and conjunctival lymphatic pathway. This new pathway is distinctive from the conventional episcleral vein pathway and merits further investigation.
Overexpression of the violaxanthin de-epoxidase confers faster NPQ and photosynthesis induction in rice
Authors: Xin Duanfeng , Chen Faming , Zhou Pengfei , Shi Zai , Tang Qiming , Zhu Xin-Guang
Published: April 2023

Plants in the field experience fluctuations in light conditions. Plants with swift responses to dynamic light conditions usually gain competitive advantage in the field. The dynamic photosynthesis can be reflected in dynamic changes in almost all processes in photosynthesis, with dominant factors being dynamic changes in non-photochemical quenching, Rubisco activation and stomatal dynamics. Each of these dynamic responses is controlled by defined mechanisms. In this study, we showed that overexpression of VDE, an enzyme involved in the xanthophyll cycle and non-photochemical quenching, in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass production by about 11∼16%. This study, demonstrating a previously unnoticed role of VDE in altering the dynamics of photosynthesis induction besides decreasing photoinhibition, offers a potential strategy to improve canopy photosynthesis through capitalizing the ability of plants to use dynamic light.

Highlight

The overexpression of VDE in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass in field.
Emerging viruses are an underestimated cause of undiagnosed febrile illness in Uganda
Authors: Ashraf Shirin , Jerome Hanna , Bugembe Daniel Lule , Ssemwanga Deogratius , Byaruhanga Timothy , Kayiwa John Timothy , Downing Robert , Salazar-Gonzalez Jesus F. , Salazar Maria G. , Shepherd James G. , Davis Chris , Logan Nicola , Vattipally Sreenu B. , Wilkie Gavin S. , da Silva Filipe Ana , Ssekagiri Alfred , Namuwulya Prossy , Bukenya Henry , Kigozi Brian K. , McConnell Weronika Witkowska , Willett Brian J. , Balinandi Stephen , Lutwama Julius , Kaleebu Pontiano , Bwogi Josephine , Thomson Emma C.
Published: April 2023

Background

Viruses that cause acute febrile illness (AFI) in sub-Saharan Africa cause a spectrum of disease from mild to life-threatening. Viral infection is often undiagnosed, as routine diagnostics are insufficient to capture the diversity of circulating pathogens.

Methods

1281 patients with fever of 2-7 days were prospectively recruited from three sites in Uganda as part of the CDC-UVRI AFI Study and screened with enhanced diagnostics. Plasma from 233 undiagnosed patients was analysed using metagenomic next-generation sequencing (mNGS). Confirmatory testing was carried out by PCR and serology.

Findings

Thirty-eight viral pathogens were identified by mNGS in 35/233 (15%) undiagnosed patients including Measles, Hepatitis A/B/E viruses, Human immunodeficiency virus-1, Rhinovirus, Rotavirus-like virus, Human herpesvirus 6B, Human parainfluenza virus 3 and Enteroviruses. Four high-consequence arboviruses were found in six patients; Crimean-Congo haemorrhagic fever virus, Rift Valley fever virus, dengue virus and yellow fever virus. Le Dantec virus, last reported in 1969, was detected and confirmed by serology in one patient (and a contact of that patient). The majority of patients (23/30; 76%) diagnosed with an acute viral infection were treated with antibiotics and/or (12/30; 40%) antimalarials.

Interpretation

AFI in Uganda is commonly associated with undiagnosed viral infection, including high-consequence and rarely reported viruses. This highlights an ongoing risk to public health and the need for improved vigilance. MNGS alongside diagnostic serology is a powerful method for clinical surveillance to investigate circulating viral pathogens. Cost-effective diagnostic assays should be adapted according to regional needs for testing.

Funding

Medical Research Council and Wellcome Trust
Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss
Authors: Lewis Morag A. , Schulte Jennifer , Matthews Lois , Vaden Kenneth I. , Steves Claire J. , Williams Frances M.K. , Schulte Bradley A. , Dubno Judy R. , Steel Karen P.
Published: April 2023

Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease.

Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing.

These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.