bluuebunny/crossref_metadata_2025 huggingface dataset:
Activation of PKR by a short-hairpin RNA
Authors: Cottrell Kyle A. , Ryu Sua , Donelick Helen , Mai Hung , Pierce Jackson R. , Bass Brenda L. , Weber Jason D.
Published: May 2024

Recognition of viral infection often relies on the detection of double-stranded RNA (dsRNA), a process that is conserved in many different organisms. In mammals, proteins such as MDA5, RIG-I, OAS, and PKR detect viral dsRNA, but struggle to differentiate between viral and endogenous dsRNA. This study investigates an shRNA targeting DDX54’s potential to activate PKR, a key player in the immune response to dsRNA. Knockdown of DDX54 by a specific shRNA induced robust PKR activation in human cells, even when DDX54 is overexpressed, suggesting an off-target mechanism. Activation of PKR by the shRNA was enhanced by knockdown of ADAR1, a dsRNA binding protein that suppresses PKR activation, indicating a dsRNA-mediated mechanism. In vitro assays confirmed direct PKR activation by the shRNA. These findings emphasize the need for rigorous controls and alternative methods to validate gene function and minimize unintended immune pathway activation.
Sexual display behaviour follows consistent sex-specific reaction norms across latitude in response to operational sex-ratio
Authors: Martinossi-Allibert Ivain , Wacker Sebastian , Aparicio Estalella Claudia , Kvarnemo Charlotta , Amundsen Trond
Published: May 2024

Predicting the strength and direction of sexual selection is a challenging task for evolutionary theory, as the effects of ecological factors, social environment, and behavioural plasticity, all need to be taken into account. The Operational Sex Ratio (OSR) is a key variable, which has been shown to (i) affect the strength and direction of mating competition, as a social environment cue, and (ii) be affected itself by ecological conditions through sex-specific environmental effects. Yet, gaining a global view of (i) and (ii) in wild populations represents an arduous but necessary step to further our understanding of sexual selection dynamics in the wild. Here, we address this challenge by using reaction norms. We conducted an extensive field study on the two-spotted gobyPomatoschistus flavescens, monitoring six populations along a latitudinal gradient during an entire breeding season. Doing so, we compared across populations the temporal trajectories in social environment and sexual displays, which is unprecedented. We develop a reaction norm framework based on OSR theory to analyse the data. We show that what appears to be tremendous variation in sexual displays across populations and sampling times, follows consistent rules: sexual display behaviour follows behavioural reaction norms in response to the social environment that are consistent across populations, but social environment fluctuations are specific to each population. Recording behaviour not only over time, but also along a latitudinal gradient where ecological conditions change and in turn affect OSR, was necessary to gain insight into the relationship between social environment and sexual displays, which in turn contributes to sexual selection dynamics.
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm
Authors: Verma Madhulika
Published: May 2024

Lung cancer (LC) remains a significant global health concern, affecting millions worldwide each year. Tumor-infiltrating immune cells (TIICs) play a crucial role in Lung Cancer progression and prognosis, with various immune cell types infiltrating the tumor microenvironment. Traditional methods like immunohistochemistry and flow cytometry have limitations in accurately profiling TIIC subtypes. However, recent advancements in single-cell RNA sequencing and computational algorithms like CIBERSORTx offer a promising approach for characterizing TIICs in bulk tumor samples.

In this study, we undertook the validation of the signature matrix comprising 14 distinct immune cell types and subtypes, which was originally derived from PBMC single-cell RNA-seq data, in our previous work (Verma, 2024). The positive controls included 8 bulk RNA-seq samples of whole blood and specific immune cell bulk RNA-seq samples, while the negative control comprised neuroblastoma cell lines lacking immune content. Subsequently, we applied this signature matrix to deconvolute TCGA-LUAD data (n = 598), and assessed tumor purity and immune-stromal content using the ESTIMATE algorithm.

Our findings indicate that the signature matrix accurately reflected flow cytometry-derived fractions, supported by correlation analysis. Specifically, the second positive control and negative control accurately reflected immune and non-immune sample fractions, respectively, further validating the efficacy of our approach. This study also provide insights into the invasion of immunocytes in lung adenocarcinoma and highlight the potential of computational tools like CIBERSORTx and ESTIMATE in characterizing the immune microenvironment of LC.
The convergent evolution of hummingbird pollination results in repeated floral scent loss through gene downregulation
Authors: Darragh Kathy , Kay Kathleen M , Ramirez Santiago R
Published: May 2024

The repeated evolution of the same trait in different lineages provides powerful natural experiments to study the phenotypic and genotypic predictability of how traits are gained and lost. A fascinating example of this is the repeated evolution of hummingbird pollination in plant lineages in the Americas, a widespread and often unidirectional phenomenon. The spiral gingers in the genus Costus are ancestrally bee-pollinated, and hummingbird pollination has evolved multiple times independently in the tropical Americas. These pollinator transitions are accompanied by predictable morphological and color changes, but the changes in floral scent have not been described. In this study, we describe the floral scent composition of 30 species of Costus sampled across the phylogeny to understand how floral scent has evolved across the genus with respect to pollinator transitions. We then combine transcriptomics and genomics to identify genetic expression differences and gene family evolution associated with pollinator transitions. We show that hummingbird-pollinated species have mostly lost their floral scent, whereas bee-pollinated species exhibit either floral scent maintenance or in some cases, gains of more diverse scent profiles. We find the floral scent loss appears to be due to gene downregulation rather than pseudogenization. The remarkable consistency of scent loss in hummingbird-pollinated species highlights the shared strong selection pressures experienced by these lineages. Even species with more recent transitions from bee to hummingbird pollination exhibit scent loss, highlighting the rapid breakdown of scent production following pollinator transitions. This research highlights the capacity for rapid changes when selection pressures are strong through downregulation of floral scent genes.
Circulating tumor cell characterization and classification by novel combinatorial dual-color (CoDuCo) in situ hybridization and supervised machine learning
Authors: Bonstingl Lilli , Zinnegger Margret , Sallinger Katja , Pankratz Karin , Pritz Elisabeth , Odar Corinna , Skofler Christina , Ulz Christine , Oberauner-Wappis Lisa , Borrás-Cherrier Anatol , Somođi Višnja , Heitzer Ellen , Kroneis Thomas , Bauernhofer Thomas , El-Heliebi Amin
Published: May 2024

Metastatic prostate cancer is a highly heterogeneous and dynamic disease and practicable tools for patient stratification and resistance monitoring are urgently needed. Liquid biopsy analysis of circulating tumor DNA and circulating tumor cells (CTCs) are promising, but due to the diversity of resistance mechanisms, comprehensive testing is essential. Previously, we demonstrated that CTCs can be characterized by mRNA-based in situ padlock probe hybridization. Now, we have developed a novel combinatorial dual-color (CoDuCo) approach with increased multiplex capacity of up to 15 distinct markers, complemented by semi-automated image analysis and machine learning-assisted CTC classification. Here, we present three exemplary cases of patient samples in which the CoDuCo assay visualized diverse resistance mechanisms (AR-V7, neuroendocrine differentiation (SYP, CHGA, NCAM1)), as well as druggable targets and predictive markers (PSMA, DLL3, SLFN11). The combination of high multiplex capacity and microscopy-based single-cell analysis is a unique and powerful feature of the CoDuCo in situ assay. This synergy enables the identification and characterization of CTCs with epithelial, epithelial-mesenchymal, and neuroendocrine phenotypes, the detection of CTC clusters, and the visualization of CTC heterogeneity. In conclusion, the assay is a promising tool for monitoring the dynamic molecular changes associated with drug response and resistance in prostate cancer.
Fuel buildup shapes post-fire fuel decomposition through soil heating effects on plants, fungi, and soil chemistry
Authors: Hopkins Jacob R. , Semenova-Nelsen Tatiana A. , Huffman Jean M. , Jones Neil J. , Robertson Kevin M. , Platt William J. , Sikes Benjamin A.
Published: May 2024

Forty percent of terrestrial ecosystems require recurrent fires engineered by feedbacks between fire and plant fuels. Fuel loads control fire intensity which alters soil nutrients and shapes soil microbial and plant community responses to fire. Changes to post-fire plant fuel production are well known to feed back to future fires, but post-fire decomposition of new fuels is poorly understood. Our study sought to quantify how pre-fire fuel loading impacted post-fire fuel decomposition through soil abiotic properties, plant and soil fungal communities. In a longleaf pine savanna, both near and away from overstory pines, we manipulated pre-fire plot fuel loads to modify soil heating. We then assessed how fuel load and soil heating influenced post-fire plant fuel decomposition through changes to soil chemistry, vegetation, and fungi. Larger fuel loads, particularly beneath pines, increased soil heating and reduced decomposition of newly deposited fuels during the eight months following fire. Fire intensity effects on soil nutrients had the most consistent effects on decomposition with plant and fungal communities playing secondary roles. This demonstrates how fuel load and soil heating influence post-fire decomposition through fire-driven changes to soil abiotic properties, plant communities, and soil fungi. Further, since fire effects on decomposition and fire-fuel feedbacks were temporally dynamic this illustrates the importance of considering fire-fuel feedbacks across time. Understanding the importance of these feedbacks among ecosystems can help increase our predictive ability to manage fuels and the effects of repeated fires.
Real-time monitoring of attenuated cytomegalovirus using Raman spectroscopy allows non-destructive characterization during flow
Authors: Athalye Shreya Milind , Maruthamuthu Murali K. , Esmaili Ehsan , Boodaghidizaji Miad , Raffaele Jessica , Selvamani Vidhya , Smith Joseph P. , Matos Tiago , Rustandi Richard R. , Ardekani Arezoo M. , Verma Mohit S.
Published: May 2024

Real-time monitoring of viral particles can have a crucial impact on vaccine manufacturing and can alleviate public health by supporting continuous supply. Spectroscopic methods such as Raman spectroscopy can provide rapid and non-invasive measurements. Here, we have developed a Raman spectroscopy-based tool to monitor the quality and quantity of viral particles in a continuous flow set-up. The attenuated human cytomegalovirus (CMV) is characterized across a wide range of concentrations (4.50 x 109to 2.90 x 1011particles/mL) and flow rates (100 µm/s to 1000 µm/s) within a square quartz capillary. This process analytical technology (PAT) tool enables the detection of viral particles even at high flow rates such as 1000 µm/s. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and dynamic light scattering (DLS) demonstrated that the samples maintain their integrity even after laser exposure, reiterating the non-invasive nature of Raman spectroscopy. To the best of our knowledge, this is thefirstreport on characterizing CMV particles using Raman spectroscopy. We have also demonstrated the limit of detection (LoD) (2.36 x 1010particles/mL) for CMV particles in continuous flow (via the Raman spectroscopy method) by addressing the effect of flow rate, concentration, and integrity of samples. This technology could enhance our understanding of the quality control in bio-manufacturing processes required in vaccine production.
CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities
Authors: Choi Hongyoon , Park Jeongbin , Kim Sumin , Kim Jiwon , Lee Dongjoo , Bae Sungwoo , Shin Haenara , Lee Daeseung
Published: May 2024

Large-scale single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have transformed biomedical research into a data-driven field, enabling the creation of comprehensive data atlases. These methodologies facilitate detailed understanding of biology and pathophysiology, aiding in the discovery of new therapeutic targets. However, the complexity and sheer volume of data from these technologies present analytical challenges, particularly in robust cell typing, integration and understanding complex spatial relationships of cells. To address these challenges, we developed CELLama (Cell Embedding Leverage Language Model Abilities), a framework that leverage language model to transform cell data into ’sentences’ that encapsulate gene expressions and metadata, enabling universal cellular data embedding for various analysis. CELLama, serving as a foundation model, supports flexible applications ranging from cell typing to the analysis of spatial contexts, independently of manual reference data selection or intricate dataset-specific analytical workflows. Our results demonstrate that CELLama has significant potential to transform cellular analysis in various contexts, from determining cell types across multi-tissue atlases and their interactions to unraveling intricate tissue dynamics.
Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope
Authors: Loretan Morgane , Barella Mariano , Fuchs Nathan , Kocabey Samet , Kołątaj Karol , Stefani Fernando D. , Acuna Guillermo P.
Published: May 2024

We present a novel, low-cost, portable smartphone-based fluorescence microscope capable of directly detecting single molecules without signal amplification. The setup leverages the image sensors and data handling capacity of mass-produced smartphones, making it adaptable to any smartphone and capable of detecting single molecules across the visible spectral range. We showcase this capability through single-molecule measurements on DNA origami models and super-resolution microscopy of biological cells by single-molecule localization microscopy. This development paves the way for biotechnology innovations making use of massively distributed or personalized assays with single-molecule sensitivity with the potential to revolutionize digital bioassays, point-of-care diagnostics, field expeditions, STEM outreach, and life science education.
Concurrent Joint Contact in Anterior Cruciate Ligament Injury induces cartilage micro-injury and subchondral bone sclerosis, resulting in knee osteoarthritis
Authors: Takahata Kei , Lin Yu-Yang , Osipov Benjamin , Arakawa Kohei , Enomoto Saaya , Christiansen Blaine A. , Kokubun Takanori
Published: May 2024

Objective

Anterior Cruciate Ligament (ACL) injury initiates post-traumatic osteoarthritis (PTOA) via two distinct processes: initial direct contact injury of the cartilage surface during ACL injury, and secondary joint instability due to the ACL deficiency. Using the well-established Compression-induced ACL rupture method (ACL-R) and a novel Non-Compression ACL-R model, we aimed to reveal the individual effects of cartilage compression and joint instability on PTOA progression after ACL injury in mice.

Design

Twelve-week-old C57BL/6J male were randomly divided to three experimental groups: Compression ACL-R, Non-Compression ACL-R, and Intact. Following ACL injury, we performed joint laxity testing and microscopic analysis of the articular cartilage surface at 0 days, in vivo optical imaging of matrix-metalloproteinase (MMP) activity at 3 and 7 days, and histological and microCT analysis at 0, 7, 14, and 28 days.

Results

The Compression ACL-R group exhibited a significant increase of cartilage roughness immediately after injury compared with the Non-Compression group. At 7 days, the Compression group exhibited increased MMP-induced fluorescence intensity and MMP-13 positive cell ratio of chondrocytes. Moreover, histological cartilage degeneration was observable in the Compression group at the same time point. Sclerosis of tibial subchondral bone in the Compression group was more significantly developed than in the Non-Compression group at 28 days.

Conclusions

Both Compression and Non-Compression ACL injury initiated PTOA progression due to joint instability. However, joint contact during ACL rupture also caused initial micro-damage on the cartilage surface and initiated early MMP activity, which could accelerate PTOA progression compared to ACL injury without concurrent joint contact.
Multifunctional molecular hybrid for targeted colorectal cancer cells: Integrating doxorubicin, AS1411 aptamer, and T9/U4 ASO
Authors: Jiramitmongkon Kanpitcha , Rotkrua Pichayanoot , Khanchaitit Paisan , Arunpanichlert Jiraporn , Soontornworajit Boonchoy
Published: May 2024

Colorectal cancer (CRC) is one of the public-health concerns worldwide and it requires an effective treatment. However, existing treatment approaches encounter challenges related to specificity and efficacy. To address this issue, a platform for multifunctional drug delivery has been developed, combining bioactive materials with anticancer elements and specific recognition ligands into a single molecule. This study aimed to create a molecular hybrid (MH) containing doxorubicin, AS1411 aptamer, and T9/U4 ASO to regulate SW480 cell proliferation. The AS1411 aptamer targets nucleolin, overexpressed on cancer cell membranes, while T9/U4 ASO inhibits human telomerase RNA activity, further hindering cancer cell proliferation. AS-T9/U4_MH was synthesized via oligonucleotide hybridization, followed by doxorubicin loading and evaluation of its impact on cell proliferation. Binding capability of this MH was verified using fluorescence microscopy and flow cytometry, demonstrating specific recognition of SW480 cells due to nucleolin availability on the cell surface. These findings were corroborated by both microscopy and flow cytometry. AS-T9/U4_MH exhibited anti-proliferative effects, with the doxorubicin-loaded system demonstrating encapsulation and reduced toxicity. Moreover, the presence of Dox within AS-T9/U4_MH led to a notable reduction in hTERT and vimentin expression in SW480 cells. Additionally, examination of apoptotic pathways unveiled a marked decrease in Bcl-2 expression and a simultaneous increase in Bax expression in SW480 cells treated with Dox-loaded AS-T9/U4_MH, indicating its impact on promoting apoptosis. These results suggest that the molecular hybrid holds promise as a system for integrating chemotherapeutic drugs with bioactive materials for cancer treatment delivery.
Predicting MHC-I ligands across alleles and species: How far can we go?
Authors: Tadros Daniel M. , Racle Julien , Gfeller David
Published: May 2024

CD8+T-cell activation is initiated by the recognition of epitopes presented on class I major histocompatibility complex (MHC-I) molecules. Identifying such epitopes is useful for molecular understanding of cellular immune responses and can guide the development of personalized vaccines for various diseases including cancer. Here, we capitalize on high-quality MHC-I peptidomics data available from different species and an expanded architecture of our MHC-I ligand predictor (MixMHCpred) to carefully explore how much predictions can be extrapolated to MHC-I alleles without known ligands. Our results reveal high prediction accuracy for most MHC-I alleles in human and in laboratory mouse strains, but significantly lower accuracy in other species. Our work further outlines some of the molecular determinants of MHC-I ligand predictions accuracy across alleles and species. Robust benchmarking on external data shows that the pan-allele version of MixMHCpred (v3.0) outperforms other state-of-the-art MHC-I ligand predictors and can be used for CD8+T-cell epitope predictions.
mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation
Authors: McCormick Caroline A. , Meseonznik Michele , Qiu Yuchen , Fanari Oleksandra , Thomas Mitchell , Liu Yifang , Bloch Dylan , Klink Isabel N. , Jain Miten , Wanunu Meni , Rouhanifard Sara H.
Published: May 2024

Pseudouridine (psi) is one of the most abundant human mRNA modifications generated via psi synthases, includingTRUB1andPUS7. Nanopore direct RNA sequencing combined with our recently developed tool, Mod-pID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and/or conversion to cDNA. This method is sensitive for detecting differences in the positional occupancy of psi across cell types, which can inform our understanding of the impact of psi on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, we find that conserved psi positions on mRNAs produce higher levels of protein than expected, suggesting a role in translation regulation. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. Finally, we characterize transcripts with multiple psi modifications and found that these psi sites can be conserved or cell type-specific, including examples of multiple psi modifications within the same motif. Our data suggest that psi modifications contribute to regulating translation and that cell type-specific trans-acting factors play a major role in driving pseudouridylation.
A Catalog of the Public T-cell Response to Cytomegalovirus
Authors: May Damon H. , Woodhouse Steven , Howie Bryan , Robins Harlan S.
Published: May 2024

ECOclusters (Exposure Co-Occurrence clusters) are previously described groups of public T-cell receptors (TCRs) that tend to co-occur across T-cell repertoires from tens of thousands of donors. Each ECOcluster putatively represents the public T-cell response to a different prevalent immune exposure. We previously associated a 26,106-member ECOcluster with exposure to cytomegalovirus (CMV) and used it to define a sensitive, specific classifier for CMV seropositivity.

Here, we provide the CMV-associated ECOcluster TCRs, describe the ECOcluster and explore some types of analysis that it enables. We assess the CMV specificity of its component HLA-COclusters (subgroups of co-occurring TCRs associated with the same HLA). We use TCR sequence similarity within HLA-ECOclusters to identify groups of TCRs putatively responding to the same antigen, and we find suggestions of different subgroups of CMV-exposed donors responding to different antigens.

The CMV ECOcluster is the most complete catalog of the public T-cell response to CMV to date. We provide the CMV ECOcluster TCRs as a resource for research community use and exploration.
Super-enhancer interactomes from single cells link clustering and transcription
Authors: Le Derek J. , Hafner Antonina , Gaddam Sadhana , Wang Kevin C. , Boettiger Alistair N.
Published: May 2024

Regulation of gene expression hinges on the interplay between enhancers and promoters, traditionally explored through pairwise analyses. Recent advancements in mapping genome folding, like GAM, SPRITE, and multi-contact Hi-C, have uncovered multi-way interactions among super-enhancers (SEs), spanning megabases, yet have not measured their frequency in single cells or the relationship between clustering and transcription. To close this gap, here we used multiplexed imaging to map the 3D positions of 376 SEs across thousands of mammalian nuclei. Notably, our single-cell images reveal that while SE-SE contacts are rare, SEs often form looser associations we termed “communities”. These communities, averaging 4-5 SEs, assemble cooperatively under the combined effects of genomic tethers, Pol2 clustering, and nuclear compartmentalization. Larger communities are associated with more frequent and larger transcriptional bursts. Our work provides insights about the SE interactome in single cells that challenge existing hypotheses on SE clustering in the context of transcriptional regulation.
Individual differences in prefrontal coding of visual features
Authors: Lin Qi , Lau Hakwan
Published: May 2024

Each of us perceives the world differently. What may underlie such individual differences in perception? Here, we characterize the lateral prefrontal cortex’s role in vision using computational models, with a specific focus on individual differences. Using a 7T fMRI dataset, we found that encoding models relating visual features extracted from a deep neural network to brain responses to natural images robustly predict responses in patches of LPFC. We then explored the representational structures and screened for images with high predicted responses in LPFC. We observed more substantial individual differences in the coding schemes of LPFC compared to visual regions. Computational modeling suggests that the amplified individual differences could result from the random projection between sensory and high-level regions underlying flexible working memory. Our study demonstrates the under-appreciated role of LPFC in visual processing and suggests that LPFC may underlie the idiosyncrasies in how different individuals experience the visual world.
DeepES: Deep learning-based enzyme screening to identify orphan enzyme genes
Authors: Hirota Keisuke , Salim Felix , Yamada Takuji
Published: May 2024

Motivation

Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions.

Results

Therefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria.

Availability and implementation

DeepES is available athttps://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).
One size does not fit all: a novel approach for determining the Realised Viewshed Size for remote camera traps
Authors: Carswell B.M. , Avgar T. , Street G.M. , Boyle S.P. , Vander Wal E.
Published: May 2024

1. Camera traps (CTs) have become cemented as an important tool of wildlife research, yet, their utility is now extending beyond academics, as CTs can contribute to more inclusive place-based wildlife management. From advances in analytics and technology, CT-based density estimates of wildlife is an emerging field of research. Most CT-based density methods require an estimate of the size of the viewshed monitored by each CT, a parameter that may be highly variable and difficult to quantify.

2. Here, we developed and tested a standardized field and analytical method allowing us to predict the probability of photographic capture as it varies within CT viewshed. We investigated how capture probability changes due to environmental influences, i.e., vegetation structure, ambient temperature, speed of subject, time of day, in addition to internal factors from CTs themselves, i.e., sensitivity settings, number of photos taken, and CT brand. We then summarize these spatial capture probability kernels into aRealised Viewshed Size(RVS)—the capture-probability corrected size of a CTs viewshed

3. We found that RVS values are heavily influenced by location-specific environmental factors, i.e., vegetation structure, technological delays associated with CTs themselves, i.e., refractory period, and internal CT settings, i.e., sensitivity, number of photographs taken. We also found that the RVS values computed using our methodology are substantially smaller than reported values in the literature.

4. Imprecision surrounding CT viewshed areas can create propagating bias when implementing CT-based density estimators. Our method can change how practitioners consider photographs for use in CT density estimators thus increasing the reliability of CT-based density estimation, and contribute to more accessible wildlife management practices.
MYB68 regulates radial endodermal differentiation and suberin patterning
Authors: Kraska Leonie , Mercadal Melia Josep , Nakano Ryohei Thomas , Molina David , Formosa-Jordan Pau , Ragni Laura , Andersen Tonni Grube
Published: May 2024

Roots are composed of concentric tissue layers that embrace the centrally localized vasculature. Of these layers, particularly the endodermis stands out as it contains barriers that facilitate selective uptake across the plasma membrane. In mature root regions, endodermal cells undergo additional differentiation and become coated with suberin, a hydrophobic polymer that blocks membrane transport and seals off the inner root parts. Intriguingly, individual cells adjacent to the water-conducting xylem remain unsuberized. These are termed “passage cells”, based on the assumption that they facilitate radial vascular access in a zone which is otherwise impenetrable. The identity of passage cells remain unknown, but their existence suggests that distinct identities and developmental trajectories exist within the second differentiation of the endodermis. In this study, we investigate this in the model plantArabidopsis thaliana. Our work identifies a genetic regulator that controls pole-specific endodermal differentiation and tissue-forming divisions connected to passage cells. Through a number of analyses, we provide spatiotemporal insights into suberization, establish a framework for radial organization of the endodermis and highlight putative function(s) of passage cells. Combined our findings illustrate how multi-dimensional developmental proceses integrate with environmental inputs in order to provide distinct cellular functions within root tissues.
Maximising the translational potential of neurophysiology in amyotrophic lateral sclerosis: a study on compound muscle action potentials
Authors: McKinnon Scott , Qiang Zekai , Keerie Amy , Wells Tyler , Shaw Pamela J. , Alix James J.P. , Mead Richard J.
Published: May 2024

Transgenic mouse models of amyotrophic lateral sclerosis, such as the widely used SOD1G93Amouse, enable investigation of disease mechanisms and testing of novel therapeutic interventions. However, treatments that have been considered successful in mice have often failed to translate into human benefit in clinical trials, particularly when relying on the so-called ‘survival’ read-out. Compound muscle action potentials (CMAPs), are a simple neurophysiological test that measures the summation of muscle fibre depolarisation in response to maximal stimulation of the innervating nerve. CMAPs can be measured in both mice and humans and decline with motor axon loss in ALS, making them a potential translational read-out of disease progression which could help bridge the preclinical and clinical divide. Herein we assess the translational potential of CMAPs and ascertain at what time points human and mouse data aligned most closely. We extracted data from 18 human studies and compared with results generated from SOD1G93Aand control mice at different ages across different muscles. We found that the relative CMAP amplitude difference between SOD1G93Aand control mice in tibialis anterior and gastrocnemius muscles at 70 days of age was most similar to the relative difference between baseline ALS patient CMAP measurements and healthy controls in the abductor pollicis brevis (APB) muscle. We also found that the relative decline in SOD1G93Atibialis anterior CMAP amplitude between 70-140 days was similar to that observed in 12 month human longitudinal studies in APB. Our findings suggest CMAP amplitudes can provide a ‘translational window’, from which to make comparisons between the SOD1G93Amodel and human ALS patients. CMAPs are easy to perform and can help determine the most clinically relevant starting/end points for preclinical studies and provide a basis for predicting potential clinical effect sizes.
Characterization of BioID tagging systems in budding yeast and exploring the interactome of the Ccr4-Not complex
Authors: Pfannenstein J. , Tyryshkin M. , Gulden M.E , Doud E.H. , Mosley A. L. , Reese J.C.
Published: May 2024

The modified E. coli biotin ligase BirA* was the first developed for proximity labeling of proteins (BioID). However, it has low activity at temperatures below 37°C, which reduces its effectiveness in organisms growing at lower temperatures, such as budding yeast. Multiple derivatives of the enzymes have been engineered, but a comparison of these variations of biotin ligases has not been reported in Saccharomyces cerevisiae. Here, we designed a suite of vectors to compare the activities of biotin ligase enzymes in yeast. We found that the newer TurboID versions were the most effective at labeling proteins, but they displayed low constitutive activity from biotin contained in the culture medium. We describe a simple strategy to express free BioID enzymes in cells that can be used as an appropriate control in BioID studies to account for the promiscuous labeling of proteins caused by random interactions between bait-BioID enzymes in cells. We also describe chemically-induced BioID systems exploiting the rapamycin-stabilized FRB-FKBP interaction. Finally, we used the TurboID version of the enzyme to explore the interactome of different subunits of the Ccr4-Not gene regulatory complex. We find that Ccr4-Not predominantly labeled cytoplasmic mRNA regulators, consistent with its function in mRNA decay and translation quality control in this cell compartment.
Emerging neurodevelopmental mechanisms in patient induced pluripotent stem cells-derived spheroids modellingSCN1ADravet Syndrome
Authors: Mattei Cristiana , Mao Miaomiao , Byars Sean , Syazwan Erlina Mohamed , Oliva Megan , Karle Timothy , Richards Kay , Scheffer Ingrid , Petrou Steven , Maljevic Snezana
Published: May 2024

SCN1Aencodes Naᵥ1.1, a voltage-gated sodium channel preferentially expressed in GABAergic interneurons, and it is the major cause of Dravet Syndrome (DS), a rare condition of developmental and epileptic encephalopathy (DEE). Among over 1000 DS mutations reported to date, almost all causeSCN1Aloss-of function (LoF). A reduction in NaV1.1 function in inhibitory neurons would subsequently cause an over-excitation of glutamatergic neurons resulting in seizures, which are exacerbated by the use of sodium channel blocking common anti-seizure medications (ASM). In this study we generated and assessed 3D spheroids enriched with GABAergic neurons fromSCN1ADS patient to establish a 3D human-derived DS model. To investigate developmental disruptions in DS pathophysiology we profiled the transcriptome of patient-derived spheroids and subsequently, tested the capability of this 3Din vitromodel to reveal the cellular mechanisms of DS and predict drug response. In summary, our patient iPSC-derived neuronal model ofSCN1ADS revealed a profound dysregulation of developmental processes which correlated with functional disruption in GABAergic neurons and predicted response to fenfluramine, an ASM increasingly used for the treatment of DS.
Optimal AAV capsid/promoter combinations to target specific cell types in the common marmoset cerebral cortex
Authors: Matsuzaki Yasunori , Fukai Yuuki , Konno Ayumu , Hirai Hirokazu
Published: May 2024

To achieve cell type-specific gene expression, using target cell-tropic AAV capsids is advantageous. However, their tropism across brain cell types remains unexplored in non-human primates. We assessed the tropism of nine AAV serotype capsids (AAV1, 2, 5, 6, 7, 8, 9, rh.10 (rh10), and DJ) on marmoset cerebral cortical cell types. Marmoset cerebral cortex was injected with different serotype AAVs expressing enhanced GFP (EGFP) by the ubiquitous chicken β-actin hybrid (CBh) promoter. After 4 weeks, all nine AAV capsid vectors, especially AAV9 and AAVrh10, caused highly neuron-selective EGFP expression. Some AAV capsids, including AAV5, caused EGFP expression in oligodendrocytes to a lesser extent, with minimal or no expression in astrocytes and microglia. Different ubiquitous CMV and CAG promoters showed similar neuron-predominant transduction. Conversely, all nine AAV capsid vectors with the astrocyte-specific hGFA(ABC1D) promoter selectively transduced astrocytes, except AAV5, which transduced oligodendrocytes modestly. Oligodendrocyte-specific mouse myeline basic protein (mMBP) promoter in AAV5 vectors transduced oligodendrocytes specifically and efficiently. Our results suggest optimal combinations of capsids and promoters for cell type-specific expression: AAV9 or AAVrh10 and ubiquitous CBh, CMV, or CAG promoter for neuron-specific transduction; AAV2 or 7 and hGFA(ABC1D) promoter for astrocyte-specific transduction; and AAV5 and mMBP promoter for oligodendrocyte-specific transduction.
Abundant and metabolically flexible lineages within the SAR324 and gammaproteobacteria dominate the potential for rubisco-mediated carbon fixation in the dark ocean
Authors: Jaffe Alexander L. , Salcedo Rebecca S. R. , Dekas Anne E.
Published: May 2024

Background: Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that employ it for carbon fixation are still emerging, particularly in unlit ecosystems like the deep sea. Results: Here, we generate fifteen deeply-sequenced metagenomes along a spatially-resolved transect off the California coast, and combine them with globally-distributed public data to examine the diversity, distribution, and metabolic features of rubisco-encoding organisms from the dark water column. Organisms with rubisco were detected in the vast majority of all samples, spanning over 1,000 species groups and together comprising up to ~20% of the total microbial community. At 150 meters and below, potential for carbon fixation via rubisco was dominated by just two orders of gammaproteobacteria and SAR324, encoding either the form I or II rubisco. Many of these organisms also possessed genes for the oxidation of reduced sulfur compounds, which may energetically support carbon fixation. Transcriptomic profiling in the epi- and mesopelagic suggested that all major forms of rubisco can be highly expressed in the deep water column, but are not done so constitutively, consistent with metabolic flexibility. Conclusion: Our results demonstrate that the genetic potential to fix carbon via rubisco is significant and spatially widespread in the dark ocean. We identify several rubisco-encoding species groups that are particularly abundant and cosmopolitan, highlighting the key role they may play in deep-sea chemoautotrophy and the global marine carbon cycle.
Circulatory dietary and gut-derived metabolites predict preclinical Alzheimer’s disease
Authors: Connell Emily , Sami Saber , Khondoker Mizanur , Minihane Anne-Marie , Pontifex Matthew G. , Müller Michael , McArthur Simon , Gall Gwenaelle Le , Vauzour David
Published: May 2024

A key component of disease prevention is the identification of at-risk individuals. Microbial dysbiosis and microbe-derived metabolites (MDM) can influence the central nervous system, but their role in disease progression and as prognostic indicators is unknown. To identify preclinical factors associated with Alzheimer’s disease (AD), we compared gut microbiome and metabolome profiles of cognitively healthy subjects, subjective cognitive impairment (SCI) participants and mild cognitive impairment (MCI) participants (n=50 per group, matched for age, BMI and sex), targeting metabolites previously associated with cognitive health (TMAO, bile acids, tryptophan,p-cresol and their derivatives). 16S rRNA bacterial microbiome sequencing and targeted LC-MS/MS were employed for faecal microbiome speciation and serum MDM quantification. Microbiome beta diversity differed between healthy controls and SCI participants. Multiple linear regression modelling highlighted five serum metabolites (indoxyl sulfate, choline, 5-hydroxyindole acetic acid, indole-3-propionic acid (IPA) and kynurenic acid) significantly altered in preclinical AD. Neuroprotective metabolites, including choline, 5-hydroxyindole acetic acid and IPA, exhibited lower concentrations in SCI and MCI in comparison to controls, while the cytotoxic metabolite indoxyl sulfate had higher levels. A Random Forest algorithm with multiclass classification confirmed and extended our results, identifying six metabolites (indoxyl sulfate, choline, 5-hydroxyindole acetic acid, IPA, kynurenic acid, kynurenine) as predictors of early cognitive decline, with an area under the curve of 0.74. In summary, a combined statistical and machine learning approach identified MDM as a novel composite risk factor for the early identification of future dementia risk.
Genotype-specific effects of physical activities on self-harm behavior in depressed patients: findings from the UK Biobank
Authors: Jung Jaegyun , Lee Sangyeon , Lee Jeong Ho , Lee Doheon
Published: May 2024

Background

Physical activities are widely implemented for non-pharmacological intervention in depression. However, there is little evidence supporting their genotype-specific effectiveness in reducing the risk of intentional self-harm in midlife and late-life depression patients.

Aims

To assess whether the specific type and amount of physical activity is associated with the risk of intentional self-harm behavior among patients with depression phenotype.

Method

We developed the bidirectional analytic model to investigate the genotype-specific effectiveness (BAIGE) on UK Biobank. After the genetic stratification on the depression phenotype cohort using hierarchical clustering, multivariable logistic regression models and Cox proportional hazard models were built to investigate the associations between physical activity and the risk of intentional self-harm behavior.

Results

A total of 28,923 subjects with depression phenotype were included in the study. In retrospective cohort analysis, the moderate and highly active groups were at lower risk of hospitalizations (moderate: adjusted odds ratio [OR], 0.77 [95% CI, 0.61-0.98], high: OR, 0.76 [95% CI, 0.60-0.97]). In the follow-up prospective cohort analysis, light-intensity physical activity (LIPA) was associated with a lower risk of hospitalizations in one genetic cluster (adjusted hazard ratio [HR], 0.26 [95% CI, 0.08 – 0.88]), which was distinguished by three genetic variants: rs1432639, rs4543289, and rs11209948. Compliance with the guideline-level moderate-to-vigorous physical activities was not significantly related to the risk of hospitalizations.

Conclusions

Physical activities, particularly a certain amount of light-intensity physical activity, mitigate the risk of hospitalizations due to self-harm in depression patients with a specific genotype.
25-hydroxycholesterol promotes brain endothelial dysfunction by remodelling cholesterol metabolism
Authors: Tapia Victor S. , Withers Sarah E. , Zhou Ran , Bennington Abigail , Hedley Frances , El Khouja Adam , Luka Nadim , Massimo Marco , Crilly Siobhan , Long Katherine R. , Lawrence Catherine B. , Kasher Paul R.
Published: May 2024

The antiviral enzyme cholesterol 25-hydroxylase (CH25H) and its metabolite 25-hydroxycholesterol (25HC), which modulates cholesterol metabolism during infection, have been previously associated with vascular pathology. Viral infections have been linked to risk of intracerebral haemorrhage (ICH) but the molecular mechanisms leading to brain vessel rupture via antiviral responses remain unknown. We hypothesised that the CH25H/25HC pathway may impact neuroendothelial integrity in the context of infection-associated ICH. Here, using a SARS-CoV-2-spike-induced zebrafish ICH model and foetal human SARS-CoV-2-associated cortical tissue containing microbleeds, we identified an upregulation of CH25H in infection-associated cerebral haemorrhage. Using zebrafish ICH models and human brain endothelial cells, we asked whether 25HC may promote neurovascular dysfunction by modulating cholesterol metabolism. We found that 25HC and pharmacological inhibition ofHMGCRby atorvastatin interacted to exacerbate brain bleeding in zebrafish larvae andin vitrobrain endothelial dysfunction.In vitro25HC-induced dysfunction was also rescued by cholesterol supplementation. These results demonstrate that the antiviral factor 25HC can dysregulate brain endothelial function by remodelling cholesterol metabolism. We propose that the CH25H/25HC pathway represents an important component in the pathophysiology of brain vessel dysfunction associated with infection and cholesterol dysregulation in the context of ICH.

Summary Statement

The antiviral metabolite 25-hydroxycholesterol dysregulates brain endothelial function by remodelling cholesterol metabolism, thereby providing a mechanistic link between viral infection and brain endothelial dysfunction in conditions such as intracerebral haemorrhage.