bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanisms underlying exercise intolerance in Long COVID: an accumulation of multi-system dysfunction
Authors: Jamieson Alexandra , Saikhan Lamia Al , Alghamdi Lamis , Howes Lee Hamill , Purcell Helen , Hillman Toby , Heightman Melissa , Treibel Thomas , Orini Michele , Bell Robert , Scully Marie , Hamer Mark , Chaturvedi Nishi , Montgomery Hugh , Hughes Alun D. , Astin Ronan , Jones Siana
Published: December 2023

The pathogenesis of exercise intolerance and persistent fatigue which can follow an infection with the SARS-CoV-2 virus (’Long COVID’) is not fully understood.

Cases were recruited from a Long COVID clinic (N=32; 44±12y; 10(31%)men), and age/sex- matched healthy controls (HC) (N=19; 40±13y; 6(32%)men) from University College London staff and students. We assessed exercise performance, lung and cardiac function, vascular health, skeletal muscle oxidative capacity and autonomic nervous system (ANS) function. Key outcome measures for each physiological system were compared between groups using potential outcome means(95% confidence intervals) adjusted for potential confounders. Long COVID participant outcomes were compared to normative values.

When compared to HC, cases exhibited reduced Oxygen Uptake Efficiency Slope (1847(1679,2016) vs (2176(1978,2373) ml/min, p=0.002) and Anaerobic Threshold (13.2(12.2,14.3) vs 15.6(14.4,17.2) ml/Kg/min, p<0.001), and lower oxidative capacity on near infrared spectroscopy (τ: 38.7(31.9,45.6) vs 24.6(19.1,30.1) seconds, p=0.001). In cases, ANS measures fell below normal limits in 39%.

Long COVID is associated with reduced measures of exercise performance and skeletal muscle oxidative capacity in the absence of evidence of microvascular dysfunction, suggesting mitochondrial pathology. There was evidence of attendant ANS dysregulation in a significant proportion. These multi-system factors might contribute to impaired exercise tolerance in Long COVID sufferers.

Key Points

The pathogenesis of exercise intolerance and persistent fatigue which can follow an infection with the SARS-CoV-2 virus (’Long COVID’) is not fully understood.

We show that Long COVID is associated with reduced measures of exercise performance in line with previous work.

In Long COVID cases, we observed reduced skeletal muscle oxidative capacity in the absence of evidence of microvascular dysfunction, suggesting mitochondrial pathology.

We also observed evidence of attendant autonomic nervous system (ANS) dysregulation in a significant proportion of Long COVID cases.

These multi-system factors might contribute to impaired exercise tolerance in Long COVID sufferers.
Graph-Based Patient Representation for Multimodal Clinical Data: Addressing Data Heterogeneity
Authors: Ghanvatkar Suparna , Rajan Vaibhav
Published: December 2023

Patient data comprises of different modalities like clinical notes, lab results, and radiological investigations. Predictive modeling on this patient data is challenging due to the heterogeneity among patients and modalities captured, such as no ECG recordings for a few patients. Ensuring model applicability to all admitted patients requires addressing three key factors: i) handling modalities at disparate time-scales (e.g., once in a few hours medication and 125 Hz ECG need to be handled by same model), ii) handling missing modality (e.g., ECG not recorded), and iii) modeling temporal interactions between modalities over time (e.g., the ECG fluctuation triggered some lab test order). Existing literature often doesn’t simultaneously address these requirements. Therefore, we propose a novel patient representation approach inspired by clinical workflows, representing each patient as a graph. We categorize patient data into two main components: observations and care team actions, allowing cross-modality temporal interaction when actions consider the previous observations. We define observation nodes to capture modality-specific data within the time between two actions, and action nodes capture data of the actions undertaken, with edges to capture the temporal dependencies. To address missing modalities and time-scale disparities, we define node types for different modalities and use modality-specific representation for the nodes; implying a missing modality is equivalent to a missing node type in the graph. Aligned with clinical workflows, this patient-graph representation aims to enhance the practicality of predictive systems for various healthcare tasks, from mortality risk assessment to medication recommendations, thereby improving clinical decision support.
Using passive telemetry and environmental variables to predict Silver Carp (Hypophthalmichthys molitrix)movement cues on the northwestern edge of their invasion front
Authors: LaBrie Lindsey A. P. , Wesner Jeff S.
Published: December 2023

Silver carpHypophthalmichthys molitrix, are a highly mobile aquatic invasive species in the United States. The James River, South Dakota, USA, is a tributary of the Missouri River and is considered the northwestern leading edge of their invasion front. Understanding silver carp movement patterns on the cusp of this invasion is key to combatting the northwestward expansion of the species. We used passive telemetry to observe large-scale movement patterns of silver carp in the James River, South Dakota. Fifty silver carp were implanted with acoustic transmitter tags in June 2021, and movement data was recorded over a 1.5-year period. Most individuals exhibited site fidelity and stayed within the James River throughout the duration of the study. We used environmental data (i.e., temperature, dissolved oxygen, daily mean discharge, the change in discharge over 24 h and 48 h) and movement data collected from passive telemetry receivers to understand and predict silver carp movement cues in the James River. Daily mean discharge (“flow”) was the most important predictor of silver carp movement in the James River. As flow increased, the probability of movement increased from 59% (95% CrI: 34% to 81%) at 1.5 m3/s to 94% (95% CrI: 80 to 99%) at 100 m3/s. In this study, silver carp exhibited a high propensity for movement within the James River, especially during periods of high flow. To prevent further northwestward expansion of these fish, silver carp movements must continue to be monitored and removal and prevention of further range expansion must be prioritized.
Phospholipase D1 Produces Phosphatidic Acid at Sites of Secretory Vesicle Docking and Fusion
Authors: Bills Broderick L. , Hulser Megan L. , Knowles Michelle K.
Published: December 2023

Phospholipase D1 (PLD1) activity is essential for the stimulated exocytosis of secretory vesicles where it acts as a lipid-modifying enzyme to produces phosphatidic acid (PA). PLD1 localizes to the plasma membrane and secretory vesicles, and PLD1 inhibition or knockdowns reduce the rate of fusion. However, temporal data resolving when and where PLD1 and PA are required during exocytosis is lacking. In this work, PLD1 and production of PA are measured during the trafficking, docking, and fusion of secretory vesicles in PC12 cells. Using fluorescently-tagged PLD1 and a PA-binding protein, cells were imaged using TIRF microscopy to monitor the presence of PLD1 and the formation of PA throughout the stages of exocytosis. Single docking and fusion events were imaged to measure the recruitment of PLD1 and the formation of PA. PLD1 is present on mobile, docking, and fusing vesicles and also colocalizes with Syx1a clusters. Treatment of cells with PLD inhibitors significantly reduces fusion, but not PLD1 localization to secretory vesicles. Inhibitors also alter the formation of PA; when PLD1 is active, PA slowly accumulates on docked vesicles. During fusion, PA is reduced in cells treated with PLD1 inhibitors, indicating that PLD1 produces PA during exocytosis.
Association of Cannabis Legalization with Cannabis Positive Drug Screening in US Veterans
Authors: Fink David S. , Samples Hillary , Malte Carol A. , Olfson Mark , Wall Melanie M. , Alschuler Daniel M. , Saxon Andrew J. , Hasin Deborah S.
Published: December 2023

Background

Although cannabis legalization is associated with increases in self-report cannabis use, biological measures of cannabis use are needed to address potential bias introduced by improved self-reporting of cannabis use in states enacting medical cannabis laws (MCL) and recreational cannabis laws (RCL).

Objective

Quantify the role of MCL and RCL enactment in cannabis positive urine drug screen (UDS) prevalence among Veterans Health Administration (VHA) emergency department (ED) patients from 2008 to 2019.

Design

Staggered-adoption difference-in-difference analysis were used to estimate the role of MCL and RCL in cannabis positive UDS data, fitting adjusted linear binomial regression models to estimate the association between MCL and RCL enactment and prevalence of cannabis positive UDS.

Participants

VHA enrolled veterans aged 18-75 years with ≥1 ED visit in a given year from 2008 to 2019.

Main Measures

Receipt of ≥1 cannabis positive UDS during an ED visit were analyzed.

Key Results

From 2008 to 2019, adjusted cannabis positive UDS prevalences increased from 16.4% to 25.6% in states with no cannabis law, 16.6% to 27.6% in MCL-only enacting states, and 18.2% to 33.8% in RCL-enacting states. MCL-only and MCL/RCL enactment was associated with a 0.8% (95% CI, 0.4-1.0) and 2.9% (95% CI, 2.5-3.3) absolute increase in cannabis positive UDS, respectively. Significant effect sizes were found for MCL and RCL, such that 7.0% and 18.5% of the total increase in cannabis positive UDS prevalence in MCL-only and RCL states could be attributed to MCLs and RCLs.

Conclusions

In this study of VHA ED patients, MCL and RCL enactment played a significant role in the overall increases in cannabis positive UDS. The increase in a biological measure of cannabis use reduces concerns that previously documented increases in self-reported cannabis use from surveys are due to changes in patient willingness to report use as it becomes more legal.
Comprehensive analysis of differentially expressed miRNAs in Hepatocellular carcinoma: prognostic significance and pathway insights
Authors: Smith Kayleigh , Beach Dan , Silva Roger , Balazs Gyorffy , Salani Francesca , Crea Francesco
Published: December 2023

Robust prognostic and predictive factors for hepatocellular carcinoma, a leading cause of cancer-related deaths worldwide, have not yet been identified. Previous studies have identified potential HCC determinants such as genetic mutations, epigenetic alterations, and pathway dysregulation. However the clinical significance of these molecular alterations remains elusive. MicroRNAs are major regulators of protein expression. MiRNA functions are frequently altered in cancer. In this study, we aimed to explore the prognostic value of differentially expressed miRNAs in HCC and elucidate their associated pathways. To this aim, bioinformatics techniques and clinical dataset analyses were employed to identify differentially expressed miRNAs in HCC compared to normal hepatic tissue. We validated known associations and identified novel miRNAs with potential prognostic significance and proposed new targeting pathways based on our comprehensive analysis.
BDNF signaling requires Matrix Metalloproteinase-9 during structural synaptic plasticity
Authors: Legutko Diana , Kuźniewska Bożena , Kalita Katarzyna , Yasuda Ryohei , Kaczmarek Leszek , Michaluk Piotr
Published: December 2023

Synaptic plasticity underlies learning and memory processes as well as contributes, in its aberrant form, to neuropsychiatric disorders. One of its major forms is structural long-term potentiation (sLTP), an activity-dependent growth of dendritic spines that harbor excitatory synapses. The process depends on the release of brain-derived neurotrophic factor (BDNF), and activation of its receptor, TrkB. Matrix metalloproteinase-9 (MMP-9), an extracellular protease is essential for many forms of neuronal plasticity engaged in physiological as well as pathological processes. Here, we utilized two-photon microscopy and two-photon glutamate uncaging to demonstrate that MMP-9 activity is essential for sLTP and is rapidly (∼seconds) released from dendritic spines in response to synaptic stimulation. Moreover, we show that either chemical or genetic inhibition of MMP-9 impairs TrkB activation, as measured by fluorescence lifetime imaging microscopy of FRET sensor. Furthermore, we provide evidence for a cell-free cleavage of proBDNF into mature BDNF by MMP-9. Our findings point to the autocrine mechanism of action of MMP-9 through BDNF maturation and TrkB activation during sLTP.
Size photometry and fluorescence imaging of immobilized immersed extracellular vesicles
Authors: Wallucks Andreas , DeCorwin-Martin Philippe , Shen Molly L. , Ng Andy , Juncker David
Published: December 2023

Immunofluorescence analysis of individual extracellular vesicles (EVs) in common fluorescence microscopes is gaining popularity due to its accessibility and high fluorescence sensitivity, however, EV number and size are only measurable using fluorescent stains requiring extensive sample manipulations. Here we introduce highly sensitive label-free EV size photometry (SP) based on interferometric scattering (iSCAT) imaging of immersed EVs immobilized on a glass coverslip. We implement SP on a common inverted epifluorescence microscope with LED illumination and a simple 50:50 beamsplitter, permitting seamless integration of SP with fluorescence imaging (SPFI). We present a high-throughput SPFI workflow recording >10,000 EVs in 7 min over multiple fields of view, pre- and post-incubation imaging to suppress background, along with automated image alignment, aberration correction, spot detection, and EV sizing. We identify the upper sizing limit of SP with 440 nm illumination and extend EVs sizing from ∼37 nm in diameter to >200 nm with dual 440 nm and 740 nm illumination. We benchmark SP to flow cytometry using calibrated silica nanoparticles and demonstrate superior, label-free sensitivity. We showcase SPFI’s potential for EV analysis by experimentally distinguishing surface and volumetric EV dyes, observing the deformation of EVs adsorbed to a surface, and by uncovering distinct subpopulations in <100 nm-in-diameter EVs with fluorescently tagged membrane proteins.
Ultrasound programmable hydrogen-bonded organic frameworks for sono-chemogenetics
Authors: Wang Wenliang , Shi Yanshu , Chai Wenrui , Kevin Tang Kai Wing , Pyatnitskiy Ilya , Xie Yi , Liu Xiangping , He Weilong , Jeong Jinmo , Hsieh Ju-Chun , Lozano Anakaren Romero , Artman Brinkley , Henkelman Graeme , Chen Banglin , Wang Huiliang
Published: December 2023

The precise control of mechanochemical activation within deep tissues via non-invasive ultrasound holds profound implications for advancing our understanding of fundamental biomedical sciences and revolutionizing disease treatments. However, a theory-guided mechanoresponsive materials system with well-defined ultrasound activation has yet to be explored. Here we present the concept of using porous hydrogen-bonded organic frameworks (HOFs) as toolkits for focused ultrasound programmably triggered drug activation to control specific cellular events in the deep brain, through on-demand scission of the supramolecular interactions. A theoretical model is developed to visualize the mechanochemical scission and ultrasound mechanics, providing valuable guidelines for the rational design of mechanoresponsive materials at the molecular level to achieve programmable and spatiotemporal activation control. To demonstrate the practicality of this approach, we encapsulate designer drug clozapine N-oxide (CNO) into the optimal HOF nanoparticles for FUS gated release to activate engineered G-protein-coupled receptors in the mice and rat ventral tegmental area (VTA), and hence achieved targeted neural circuits modulation even at depth 9 mm with a latency of seconds. This work demonstrates the capability of ultrasound to precisely control molecular interaction and develops ultrasound programmable HOFs to minimally invasive and spatiotemporally control cellular events, thereby facilitating the establishment of precise molecular therapeutic possibilities. We anticipate that this research could serve as a source of inspiration for precise and non-invasive molecular manipulation techniques, potentially applicable in programming molecular robots to achieve sophisticated control over cellular events in deep tissues.
New insights into the dynamics ofde novogene origin
Authors: Blair Logan , Cridland Julie , Luo Yige , Begun David , Kopp Artyom
Published: December 2023

The evolution of genesde novofrom ancestrally nongenic sequences is a significant mechanism of gene origin. Many studies have focused on distant evolutionary comparisons, which bias the sample ofde novogenes towards older genes that have acquired important functions and have been refined by selection. In this report, we focus on the earliest steps inde novogene origin by identifying young, polymorphic transcripts that may be missed by other study designs. To accomplish this, we sequenced tissue-specific transcriptomes from a much larger sample of genotypes than have been used in previous analyses ofde novogenes inDrosophila melanogaster. We identified 90 potential species-specificde novogenes expressed in the male accessory glands of 29D melanogasterlines derived from the same natural population. We find that most young, unannotated transcripts are both rare in the population and transcribed at low abundance. Improved sampling of both ingroup and outgroup genotypes reveals that many young genes are polymorphic in more than one species, resulting in substantial uncertainty about the age and phylogenetic distribution ofde novogenes. Among the genes expressed in the same tissue, gene age correlates with proximity to other tissue-specific genes, with the youngest genes being least likely to occur near established tissue-specific genes. This and other lines of evidence suggest thatde novogenes do not commonly evolve by simply reutilizing pre-existing regulatory elements. Together, these results provide new insights into the origin and early evolution ofde novogenes.

Author Summary

Genes may be born and lost without any lasting evidence of their existence. The typical longevity may be especially limited forde novogenes – that is, genes that originate from ancestrally non-genic, untranscribed sequences, since most genomic regions are not expected to be beneficial when transcribed. To better capture the population biology of nascentde novogenes at points close to their origin, we sequenced tissue-specific transcriptomes from a large number ofDrosophila melanogastergenotypes. Mostde novogenes were expressed in very few genotypes, consistent with the expectation of transience and rapid turnover. However, many young genes showed polymorphic transcription in multiple species, suggesting that the combination of low frequency with limited sampling can lead us to underestimate how longde novogenes persist in populations. We identified several features thatde novogenes come to share with established tissue-specific genes the longer they persist. This study highlights important challenges in reconstructingde novogene origin and helps elucidate why some transcripts may survive long enough to acquire selectable functions.
Brain encoding of naturalistic, continuous, and unpredictable tactile events
Authors: Castellani Nicolò , Federici Alessandra , Fantoni Marta , Ricciardi Emiliano , Garbarini Francesca , Bottari Davide
Published: December 2023

Abstract

Studies employing EEG to measure somatosensory responses have been typically optimized to compute event-related potentials in response to discrete events (ERPs). However, tactile interactions involve continuous processing of non-stationary inputs that change in location, duration, and intensity. To fill this gap, this study aims to demonstrate the possibility of measuring the neural tracking of continuous and unpredictable tactile information. Twenty-seven young adults (females = 15) were continuously and passively stimulated with a random series of gentle brushes on single fingers of each hand, which were covered from view. Thus, tactile stimulations were unique for each participant, and stimulated fingers. An encoding model measured the degree of synchronization between brain activity and continuous tactile input, generating a temporal response function (TRF). Brain topographies associated with the encoding of each finger stimulation showed a contralateral response at central sensors starting at 50 ms and peaking at about 140 ms of lag, followed by a bilateral response at about 240 ms. A series of analyses highlighted that reliable tactile TRF emerged after just 3 minutes of stimulation. Strikingly, topographical patterns of the TRF allowed discriminating digit lateralization across hands and digit representation within each hand. Our results demonstrated for the first time the possibility of using EEG to measure the neural tracking of a naturalistic, continuous, and unpredictable stimulation in the somatosensory domain. Crucially, this approach allows the study of brain activity following individualized, idiosyncratic tactile events to the fingers.

Significant Statement

This study expands the current research conducted on neural tracking, opening the exploration of idiosyncratic tactile events and overcoming constraints of laboratory tasks that typically rely on discrete events. We validated a protocol for the ecological investigations of continuous, slow, tactile processing of the hands. The employed approach enriches the possible use of the EEG to characterize somatosensory neural representations of tactile events. Findings unravel coherent neural responses to continuous and naturalistic touch, with sensitivity for digit lateralization and representation.
Generating realistic artificial Human genomes using adversarial autoencoders
Authors: Burnard Callum , Mancheron Alban , Ritchie William
Published: December 2023

A publicly available human genome serves as both a valuable resource for researchers and a potential risk to the individual who provided the genome. Many actors with selfish intentions could exploit it to extract information about the donor’s health or that of their relatives. Recent efforts have employed artificial intelligence models to simulate genomic data, aiming to create synthetic datasets with scientific merit while preserving patient anonymity. However, a major challenge arises in dealing with the vast amount of data that constitutes a complete human genome and the resources required to process it.

We have developed a dimension reduction method that combines artificial intelligence with our knowledge of in vivo mutation association mechanisms. This approach enables the processing of large amounts of data without significant computational resources. Our genome segmentation follows chromosomal recombination hotspots, closely resembling mutation transmission mechanisms. Training data is sourced from the 1000 Genomes Project, which catalogues over 2500 genomes from diverse ethnic groups. Variational autoencoders, utilising neural networks, serve as an extension to the generative model. Wasserstein Generative Adversarial Networks (WGAN) are a benchmark among generation methods for various data types.

After optimisation of our data simulation strategy our pipeline allows the generation of a simulated population meeting several essential criteria. It demonstrates good diversity, closely resembling that found in the reference dataset. It is plausible, as newly generated combinations of mutations do not disrupt the linkage disequilibria found in humans. It also preserves donor anonymity by synthesising combinations of reference genomes that are distant from reference samples.
Diversity-disease relationships in natural microscopic nematode communities
Authors: van Himbeeck Robbert , Sowa Jessica N. , Jarkass Hala Tamim El , Wu Wenjia , Vrielink Job Oude , Riksen Joost A. G. , Reinke Aaron , van Sluijs Lisa
Published: December 2023

Biodiversity can affect parasite prevalence, a phenomenon widely studied in macroscopic organisms. However, data from microscopic communities is lacking, despite their essential role in ecosystem functioning and the unique experimental opportunities microscopic organisms offer. Here, we study diversity-disease effects in wild nematode communities by profiting from the molecular tools available in the well-studied model nematodeCaenorhabditis elegans. Nanopore sequencing was used to characterize nematode community diversity and composition, whereas parasites were identified using nine distinct experimental assays based on fluorescent staining or fluorescent reporter strains. Our results indicate biotic stress is abundant in wild nematode communities. Moreover, in two assays, diversity-disease relations were observed: microsporidia and immune system activation were more often detected in relatively species-poor communities. Other assays, targeting different parasites, were without diversity-disease relations. Together, this study provides the first demonstration of diversity-disease effects in microbial communities and establishes the use of nematode communities as model systems for disease dilution.
Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis
Authors: Coßmann Jonas , Kos Pavel I. , Varamogianni-Mamatsi Vassiliki , Assenheimer Devin , Bischof Tobias , Kuhn Timo , Vomhof Thomas , Papantonis Argyris , Giorgetti Luca , Gebhardt J. Christof M.
Published: December 2023

The three-dimensional folding of chromosomes is essential for nuclear functions such as DNA replication and gene regulation. The emergence of chromatin architecture is thus an important process during embryogenesis. To shed light on the molecular and kinetic underpinnings of chromatin architecture formation, we characterized biophysical properties of cohesin and CTCF binding to chromatin and their changes upon cofactor depletion using single-molecule imaging in live developing zebrafish embryos. We found that chromatin-bound fractions of both cohesin and CTCF increased significantly between the 1000-cell and shield stages, which we could explain through changes in both their association and dissociation rates. Moreover, increasing binding of cohesin restricted chromatin motion, potentially via loop extrusion, and showed distinct stage-dependent nuclear distribution. Polymer simulations with experimentally derived parameters recapitulated the experimentally observed gradual emergence of chromatin architecture. Our findings suggest a kinetic framework of chromatin architecture formation during zebrafish embryogenesis.
Temporal Complexity of the BOLD-Signal In Preterm Versus Term Infants
Authors: Mella Allison Eve , Vanderwal Tamara , Miller Steven P , Weber Alexander Mark
Published: December 2023

Preterm birth causes alterations in cerebral development. We calculated the Hurst exponent (H) - a measure of temporal complexity - from resting state functional magnetic resonance signal in preterm and term born infants. Anatomical, fMRI, and diffusion weighted imaging data from 716 neonates born between 23-43 weeks gestational age were obtained from the Developing Human Connectome Project. H was assessed in brain tissues and 13 resting state networks. H significantly increased with age, and earlier birth age contributed to lower H values. In most brain regions, H begins below 0.5 at preterm age and crosses 0.5 at term age. Motor and sensory networks demonstrated the greatest increase in H. Correlations between indirect measures of myelination and H were moderate. Overall, H appears to reflect developmental processes in the neonatal brain, as BOLD signal in the preterm infant transforms from anticorrelated to correlated but is reduced compared to term born infants.
NS2B-D55E and NS2B-E65D Variations are Responsible for Differences in NS2B-NS3 Protease Activities Between Japanese Encephalitis Virus Genotype I and III in Fluorogenic Peptide Model
Authors: Wahaab Abdul , Zhang Yan , Rasgon Jason L. , Kang Lei , Hameed Muddassar , Li Chenxi , Anwar Muhammad Naveed , Zhang Yanbing , Shoaib Anam , Liu Ke , Lee Beibei , Wei Jianchao , Qiu Yafeng , Ma Zhiyong
Published: December 2023

Japanese Encephalitis Virus (JEV) NS2B-NS3 is a protein complex composed of NS3 proteases and a NS2B cofactor. The N-terminal protease domain (180 residues) of NS3 (NS3(pro)) interacts directly with a central 40-amino acid hydrophilic domain of NS2B (NS2B(H)) to form an active serine protease. In this study, the recombinant NS2B(H)-NS3(pro) proteases were prepared inE. coliand used to compare the enzymatic activity between genotype I (GI) and III (GIII) NS2B-NS3 proteases. The GI NS2B(H)-NS3(pro) was able to cleave the sites at internal C, NS2A/NS2B, NS2B/NS3 and NS3/NS4A junctions that were identical to the sites proteolytically processed by GIII NS2B(H)-NS3(pro). Analysis of the enzymatic activity of recombinant NS2B(H)-NS3(pro) proteases using a model of fluorogenic peptide substrate revealed that the proteolytical processing activity of GIII NS2B(H)-NS3(pro) was significantly higher than that of GI NS2B(H)-NS3(pro). There were eight amino acid variations between GI and GIII NS2B(H)-NS3(pro), which may be responsible for the difference in enzymatic activities between GI and GIII proteases. Therefore, recombinant mutants were generated by exchanging NS2B(H) and NS3(pro) domains between GI and GIII NS2B(H)-NS3(pro) and subjected to protease activity analysis. Substitution of NS2B(H) significantly altered the protease activities, as compared to the parental NS2B(H)-NS3(pro), suggesting that NS2B(H) played an essential role in regulation of NS3(pro) protease activity. To further identify the amino acids responsible for the difference in protease activities, multiple substitution mutants including the individual and combined mutations at the variant residue 55 and 65 of NS2B(H) were generated and subjected to protease activity analysis. Replacement of NS2B-55 and NS2B-65 of GI to GIII significantly increased the enzymatic activity of GI NS2B(H)-NS3(pro) protease, whereas mutation of NS2B-55 and NS2B-65 of GIII to GI remarkably reduced the enzymatic activity of GIII NS2B(H)-NS3(pro) protease. Overall, these data demonstrated that NS2B-55 and NS2B-65 variations in hydrophilic domain of NS2B co-contributed to the difference in NS2B(H)-NS3(pro) protease activities between GI and GIII. These observations gain an insight into the role of NS2B in regulation of NS3 protease activities, which is useful for understanding the replication of JEV GI and GIII viruses.
What happens with bacteria in the roots affects what happens with fungi in the leaves
Authors: Fernández-Vargas Rachelle , Tabash-Porras Fabiana , Rojas-Jiménez Keilor
Published: December 2023

The impact of plant-bacteria symbioses in roots on plant-fungus interactions in distant tissues, such as leaves, remains a significant knowledge gap, particularly for tropical ecosystems. We employed amplicon metabarcoding of ITS2 sequences to analyze the endophytic fungal communities of eight tropical Fabaceae tree species to determine variations according to the host’s root nodulation capacity and the host’s subfamily affiliation. Nitrogen-fixing bacteria in root nodules significantly impacted the diversity and composition of fungal endophytes, while subfamily affiliation had a less pronounced effect. In non-nodulating plants, leaves harbored a much larger diversity of fungi, with 25 fungal classes and 72 orders compared to 17 classes and 45 orders in nodulating plants. Notably, 40% of the orders were unique to non-nodulating plants, whereas only 5% were exclusive to nodulating species. This pattern was further reflected in the number of fungal ASVs, with non-nodulating plants averaging 130.5 compared to 42.7 in nodulating plants. Similarly, Shannon diversity was significantly higher in non-nodulating plants. This study demonstrates that interactions between Fabaceae plants and nitrogen-fixing root bacteria significantly influence the richness and diversity of the fungal community present in leaves. Our findings contribute valuable insights into the complex interplay between plants and microorganisms, particularly in the context of tropical Fabaceae tree species and their endophytic fungi.
Exploring the accuracy and limits of algorithms for localizing recombination breakpoints
Authors: Cen Shi , Rasmussen David A.
Published: December 2023

Phylogenetic methods are widely used to reconstruct the evolutionary relationships among species and individuals. However, recombination can obscure ancestral relationships as individuals may inherit different regions of their genome from different ancestors. It is therefore often necessary to detect recombination events, locate recombination breakpoints and select recombination-free alignments prior to reconstructing phylogenetic trees. While many earlier studies examined the power of different methods to detect recombination, very few have examined the ability of these methods to accurately locate recombination breakpoints. In this study, we simulated genome sequences based on ancestral recombination graphs and explored the accuracy of three popular recombination detection methods: MaxChi, 3SEQ and GARD. The accuracy of inferred breakpoint locations was evaluated along with the key factors contributing to variation in accuracy across data sets. While many different genomic features contribute to the variation in performance across methods, the number of informative sites consistent with the pattern of inheritance between parent and recombinant child sequences always has the greatest contribution to accuracy. While partitioning sequence alignments based on identified recombination breakpoints can greatly decrease phylogenetic error, the quality of phylogenetic reconstructions depends very little on how breakpoints are chosen to partition the alignment. Our work sheds light on how different features of recombinant genomes affect the performance of recombination detection methods and suggests best practices for reconstructing phylogenies based on recombination-free alignments.
Novel Evolution of the Mineralocorticoid Receptor in Humans compared to Chimpanzees, Gorillas and Orangutans
Authors: Katsu Yoshinao , Zhang Jiawen , Baker Michael E.
Published: December 2023

We identified five distinct full-length human mineralocorticoid receptor (MR) genes containing either 984 amino acids (MR-984) or 988 amino acids (MR-988), which can be distinguished by the presence or absence of Lys, Cys, Ser, Trp (KCSW) in their DNA-binding domain (DBD) and mutations at codons 180 and 241 in their amino terminal domain (NTD). Two human MR-KCSW genes contain either (Val-180, Val-241) or (Ile-180, Val-241) in their NTD and three human MR-984 genes contain either (Ile-180, Ala-241) or (Val-180, Val-241) or (Ile-180, Val-241). Human MR-KCSW with (Ile-180, Ala-241) has not been cloned. In contrast, chimpanzees contain four MRs: two MR-988s with KCSW in their DBD or two MR-984s without KCSW in their DBD. Chimpanzee MRs only contain (Ile180, Val-241) in their NTD. A chimpanzee MR with either (Val-180, Val-241) or (Ile-180, Ala-241) in the NTD has not been cloned. Gorillas and orangutans each contain one MR-988 with KCSW in the DBD and one MR-984 without KCSW, and these MRs only contain (Ile-180, Val-241) in their NTD. A gorilla MR or orangutan MR with either (Val-180, Val-241) or (Ile-180, Ala-241) in the NTD has not been cloned. Together, these data suggest that human MRs with (Val-180, Val-241) or (Ile-180, Ala-241) in the NTD evolved after humans and chimpanzees diverged from their common ancestor. Considering the multiple functions in human development of the MR in kidney, brain, heart, skin, and lungs, as well as MR activity in interaction with the glucocorticoid receptor, we suggest that the evolution of human MRs that are absent in chimpanzees may have been important in the evolution of humans from chimpanzees. Investigation of the physiological responses to corticosteroids mediated by the MR in humans, chimpanzees, gorillas and orangutans may provide insights into the evolution of humans and their closest relatives.
Rendering protein structures inside cells at the atomic level with Unreal Engine
Authors: Chen Muyuan
Published: December 2023

While the recent development of cryogenic electron tomography (CryoET) makes it possible to identify various macromolecules inside cells and determine their structure at near-atomic resolution, it remains challenging to visualize the complex cellular environment at the atomic level. One of the main hurdles in cell visualization is to render the millions of molecules in real time computationally. Here, using a video game engine, we demonstrate the capability of rendering massive biological macromolecules at the atomic level within their native environment. To facilitate the visualization, we also provide tools that help the interactive navigation inside the cells, as well as software that converts protein structures identified using CryoET to a scene that can be explored with the game engine.

Graphical abstract
Stimulus-reward contingencies drive long-lasting alterations in neocortical somatostatin inhibition during learning
Authors: Park Eunsol , Kuljis Dika A. , Zhu Mo , Christian Joseph A. , Barth Alison L.
Published: December 2023

Learning involves the association of discrete events in the world to infer causality, likely through a cascade of changes at input- and target-specific synapses. Transient or sustained disinhibition may initiate cortical circuit plasticity important for association learning, but the cellular networks involved have not been well-defined. Here we show that sensory association learning drives a durable, target-specific reduction in inhibition from somatostatin (SST)-expressing GABAergic neurons onto pyramidal (Pyr) neurons in superficial but not deep layers of mouse somatosensory cortex. Critically, SST-output was not altered when stimulus and rewards were unpaired, indicating that these neurons are not modified by sensory input alone. Depression of SST output onto Pyr neurons could be phenocopied by chemogenetic suppression of SST activity outside of the training context. Thus, neocortical SST neuron output is persistently modified by convergent sensory and reinforcement signals to selectively disinhibit superficial layers of sensory neocortex during learning.
Hydrogel Microneedle Array-Based Transdermal Dressing System for Multiplexed Assessment and Combined Therapy of Chronic Wounds
Authors: Sharifuzzaman Md , Hasabnis Gauri Kishore , Saleh Sheikh Ahmed Abu , Siebert Leonard , Maschkowitz Gregor , Altintas Zeynep
Published: December 2023

Although recent wearable chronic wound (CWO) bandage technologies have opened up exciting opportunities for personalized CWO management, they still face significant obstacles due to the reliance on the wound bed exudate for sensing and delivering therapeutics. Flat, shallow, and desiccated wounds are difficult to collect wound exudate for sensing, and some wounds continuously exude, potentially washing delivered therapeutics out of the wound bed. Herein, we developed a hydrogel-forming microneedles (HFMNs) array-based multimodal transdermal dressing system that continuously monitors the on-site physiological conditions of CWOs in interstitial fluid (ISF) and offers healing capabilities. The unique polar array design enables the integration of six replaceable HFMNs sensing electrodes to target the desired wound-specific analytes in transdermal interstitial fluid (glucose, uric acid, pH, Na+, Cl-, K+, and temperature) based on their significance in reflecting the status of the CWOs. The hydrogel is composed of a biocompatible and swellable polymer - polyvinyl alcohol, and chitosan as a crosslinking agent, while the incorporation of MXene (Ti3C2Tx) nanosheets as conductive nanofillers facilitates the formation of 3D polymer hydrogel networks via hydrogen bonding. Further coating and functionalization of poly(3,4-ethylenedioxythiophene): polystyrene sulfate (PEDOT: PSS) and graphene oxide through a laser-scribed phase separation (LSPS) process improves the electrical conductivity and in-vivo water stability of the HFMNs as a result of the larger and interconnected PEDOT-rich domains. Importantly, anti-inflammatory and antibacterial properties of the hydrogel prevent wound infection and promote skin wound healing. Through the potential correlation between wound-affected ISF and wound bed exudate, this method bridges conventional and implantable dressing systems for commercialization.
The role of mitochondria in sex- and age-specific gene expression in a species without sex chromosomes
Authors: Li Ning , Flanagan Ben A. , Edmands Suzanne
Published: December 2023

Mitochondria perform an array of functions, many of which involve interactions with gene products encoded by the nucleus. These mitochondrial functions, particularly those involving energy production, can be expected to differ between sexes and across ages. Here we measured mitochondrial effects on sex- and age-specific gene expression in parental and reciprocal F1 hybrids between allopatric populations ofTigriopus californicuswith over 20% mitochondrial DNA divergence. Because the species lacks sex chromosomes, sex-biased mitochondrial effects are not confounded by the effects of sex chromosomes. Using single-individual RNA sequencing, sex differences were found to explain more than 80% of the variance in gene expression. Males had higher expression of mitochondrial genes and mitochondrially targeted proteins (MTPs) involved in oxidative phosphorylation (OXPHOS), while females had elevated expression of non-OXPHOS MTPs, indicating strongly sex-dimorphic energy metabolism at the whole organism level. Comparison of reciprocal F1 hybrids allowed insights into the nature of mito-nuclear interactions, showing both mitochondrial effects on nuclear expression, as well as nuclear effects on mitochondrial expression. Across both sexes, increases in mitochondrial expression with age were associated with longer life. Network analyses identified nuclear components of strong mito-nuclear interactions, and found them to be sexually dimorphic. These results highlight the profound impact of mitochondria and mito-nuclear interactions on sex- and age-specific gene expression.
WRN Inhibition Leads to its Chromatin-Associated Degradation Via the PIAS4-RNF4-p97/VCP Axis
Authors: Pérez Fernando Rodríguez , Natwick Dean , Schiff Lauren , McSwiggen David , Huey Melina , Heckert Alec , Loo Mandy , Miranda Rafael , Morrison Huntly , Ortega Jose , Butler Renee , Cheng Kylie , Filbin John , Zhang Zhengjian , Gonzalez Eric , Miller Rand , Tang Yangzhong , Ho Jaclyn , Anderson Daniel , Bashore Charlene , Basham Steve
Published: December 2023

Synthetic lethality, the concept in which the co-occurrence of two genetic events leads to cell death while either single event alone does not, is an attractive strategy for targeted cancer therapies. A recent example of synthetic lethality as a therapeutic paradigm is the observation that cancer cells with high levels of microsatellite instability (MSI-H) are dependent on the Werner (WRN) RecQ helicase for survival. However, the mechanisms that regulate WRN spatiotemporal dynamics are not fully understood. In this study, we used our single molecule tracking (SMT) platform in combination with a recently disclosed WRN inhibitor to gain insights into WRN’s dynamic localization within the nuclei of live cancer cells. We observe that WRN inhibition results in the helicase becoming trapped on chromatin, requiring p97/VCP for extraction and shuttling to the proteasome for degradation. Interestingly, this sequence of events resulting in WRN degradation appears to be MSI-H dependent. Using a phenotypic screen, we identify the PIAS4-RNF4 axis as the pathway responsible for WRN degradation and show that co-inhibition of WRN and SUMOylation has an additive toxic effect in MSI-H cells. Taken together, our work elucidates a novel regulatory mechanism for WRN. Gaining a deeper understanding into this regulatory pathway for WRN can aid in the identification of new high value targets for targeted cancer therapies.
Lactiplantibacillus plantarum K8lysates regulate hypoxia-induced gene expression
Authors: Jeong Jaehyeon , Kang Byeong-Hee , Ju Sangmin , Park Na Yeon , Kim Deukyeong , Dinh Ngoc Thi Bao , Lee Jeongho , Rhee Chang Yun , Cho Dong-Hyung , Kim Hangeun , Chung Dae Kyun , Bunch Heeyoun
Published: December 2023

Hypoxic responses have been implicated in critical pathologies, including inflammation, immunity, and tumorigenesis. Recently, efforts to identify effective natural remedies and health supplements are increasing. Previous studies have reported that the cell lysates and the cell wall-bound lipoteichoic acids ofLactiplantibacillus plantarum K8(K8) exert anti-inflammatory and immunomodulative effects. However, the effect of K8 on cellular hypoxic responses remains unknown. In this study, we found that K8 lysates had a potent suppressive effect on gene expression under hypoxia. K8 lysates markedly downregulated hypoxia-induced HIF1α accumulation in the human bone marrow and lung cancer cell lines, SH-SY5Y and H460. Consequently, the transcription of known HIF1α target genes, such asp21,GLUT1, andALDOC, was notably suppressed in the K8 lysate supplement and purified lipoteichoic acids of K8, upon hypoxic induction. In addition, K8 lysates decreased the expression of PHD2 and VHL proteins, which are responsible for HIF1α destabilization under normoxic conditions. Overall, our results suggest that K8 lysates desensitize the cells to hypoxic stresses and suppress HIF1α-mediated hypoxic gene activation.
Genome-Wide Profiling of tRNA Using an Unexplored Reverse Transcriptase with High Processivity
Authors: Nakano Yuko , Gamper Howard , McGuigan Henri , Maharjan Sunita , Sun Zhiyi , Krishnan Keerthana , Yigit Erbay , Li Nan-Sheng , Piccirilli Joseph A. , Kleiner Ralph , Nichols Nicole , Hou Ya-Ming
Published: December 2023

Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.