bluuebunny/crossref_metadata_2025 huggingface dataset:
An inducible and reversible system to regulate unsaturated fatty acid biosynthesis inC. elegans
Authors: Battista Bernabe , Cravero Bruno Hernadez , Colaiácovo Monica P , Cochella Luisa , Binolfi Andres , de Mendoza Diego
Published: October 2024

Unsaturated fatty acids (UFAs) play crucial roles in various physiological and pathological processes. In animals, these lipids are synthesized from saturated fatty acids through the action of delta 9 (Δ9) desaturases. InC. elegans, three Δ9 desaturases are encoded by the genesfat-5,fat-6, andfat-7. The presence of multiple Δ9 desaturases has posed a significant challenge in developing a rapid and efficient approach to control UFA production inC. elegansand other model organisms. Utilizing the auxin-inducible degradation system, we specifically targeted theC. elegans fat-7gene, responsible for the major stearoyl-CoA desaturase (SCD), while deletingfat-5andfat-6. This design resulted in a strain that can be reversibly depleted of UFAs in the cells of interest. Conditional depletion in all somatic cells exhibited a pronounced auxin-dependent defect in UFA production. Using this system, we uncovered an essential requirement for de novo UFA production during L1 and L2 stage. Moreover, our results support a direct connection between UFA levels, fat storage and increased lipid turnover. This system will enable further studies exploring the cellular and physiological consequences of impairing UFA biosynthesis at different developmental stages or in specific tissues.

Unsaturated fatty acids (UFAs) are essential for life. In animals, UFAs are synthesized by Δ9 desaturase enzymes.Caenorhabditis eleganspossesses three Δ9 desaturase genes: fat-5, fat-6, and fat-7. We engineered a strain where fat-7 can be reversibly switched off while fat-5 and fat-6 are deleted, allowing precise control of UFA levels throughout the life cycle. Our findings demonstrate the critical role of UFA biosynthesis in early development and its direct link to fat storage and lipid turnover. This strain enables the study of UFA-related physiological and pathological processes in animals.
Filtered Point Processes Tractably Capture Rhythmic And Broadband Power Spectral Structure in Neural Electrophysiological Recordings
Authors: Bloniasz Patrick F. , Oyama Shohei , Stephen Emily P.
Published: October 2024

Abstract

Neural electrophysiological recordings arise from interacting rhythmic (oscillatory) and broadband (aperiodic) biological subprocesses. Both rhythmic and broadband processes contribute to the neural power spectrum, which decomposes the variance of a neural recording across frequencies. Although an extensive body of literature has successfully studied rhythms in various diseases and brain states, researchers only recently have systematically studied the characteristics of broadband effects in the power spectrum. Broadband effects can generally be categorized as 1) shifts in power across all frequencies, which correlate with changes in local firing rates and 2) changes in the overall shape of the power spectrum, such as the spectral slope or power law exponent. Shape changes are evident in various conditions and brain states, influenced by factors such as excitation to inhibition balance, age, and various diseases. It is increasingly recognized that broadband and rhythmic effects can interact on a sub-second timescale. For example, broadband power is time-locked to the phase of <1 Hz rhythms in propofol induced unconsciousness. Modeling tools that explicitly deal with both rhythmic and broadband contributors to the power spectrum and that capture their interactions are essential to help improve the interpretability of power spectral effects. Here, we introduce a tractable stochastic forward modeling framework designed to capture both narrowband and broadband spectral effects when prior knowledge or theory about the primary biophysical processes involved is available. Population-level neural recordings are modeled as the sum of filtered point processes (FPPs), each representing the contribution of a different biophysical process such as action potentials or postsynaptic potentials of different types. Our approach builds on prior neuroscience FPP work by allowing multiple interacting processes and time-varying firing rates and by deriving theoretical power spectra and cross-spectra. We demonstrate several properties of the models, including that they divide the power spectrum into frequency ranges dominated by rhythmic and broadband effects, and that they can capture spectral effects across multiple timescales, including sub-second cross-frequency coupling. The framework can be used to interpret empirically observed power spectra and cross-frequency coupling effects in biophysical terms, which bridges the gap between theoretical models and experimental results.
Artificial lighting affects the predation performance of the predatory bugOrius insidiosus(Say) against the Western flower thripsFrankliniella occidentalis(Pergande)
Authors: Canovas Morgane L. , Abram Paul K. , Cormier Jean-François , Galstian Tigran , Dorais Martine
Published: October 2024

Protected crops, such as greenhouses and indoor farming environments, using light-emitting diodes (LEDs) enable the modulation of the light spectrum, intensity, and photoperiod for agronomic purposes. This creates dynamic artificial light conditions for insects and arachnids, including predators used in biological control. Despite increasing interest, the effects of LEDs on predator behavior and control performance remain poorly understood. In the laboratory, we examined the locomotion and predation behaviors of the generalist predatorOrius insidiosusagainst the pestFrankliniella occidentalisunder various light spectra and intensities. We tested narrowband blue, green, and red spectra, three ratios of red and blue light, and a spectrum combining all three colors across a gradient of light intensity in microcosms.Orius insidiosuswas active and successfully attacked prey under all lighting conditions, with 70% of individuals engaging in predation during the observation period. The light spectrum significantly influenced all recorded behaviors, while light intensity had negligible effects. Narrowband spectra led to the highest attack probabilities, but the mixed blue-red spectrum with a higher proportion of red light yielded the highest prey capture rates. The spectrum with all three colors showed intermediate capture success. These trends were consistent regarding capture probability in more complex environments with cucumber plants, where thrips were exposed to 24-hour artificial light sequences before and during predator releases. However, thrips survival rates remained similar across all lighting treatments. Our results demonstrated that while lighting treatments affect predator behavior,Orius insidiosusretains its ability to capture prey under various light conditions. This paves the way for developing lighting strategies that balance plant productivity with effective biological control in protected crop environments.
Injury-induced transcription in the planarian outer epithelium is critical for tissue regeneration
Authors: Barai Pallob , Kibtiya Mariya S. , Maggard Nathan G. , Biswas Shishir , Duncan Elizabeth M.
Published: October 2024

Planarian flatworms have an extraordinary regenerative capacity; even a small, asymmetrical fragment of amputated planarian tissue can recreate an entirely new animal. The planarian field has made significant progress in identifying specific genes and cell types required for this complex process, but substantially less is known about the molecular mechanisms that convert a significant physical injury (e.g., head amputation) into the expression of specific genes in particular cell types. One tissue in which this question is particularly relevant is the planarian epidermis, a single-layer, mucociliary epithelium with similarities to the epithelia of mammalian airways. This epithelium plays an essential, early role in planarian regeneration as the cells surrounding the wound site must quickly stretch and extend to cover the wound area after injury. We hypothesized that these injury-induced morphological changes activate the transcription of genes with essential functions in the regenerative process. To best detect these transcriptional changes, we developed a rapid method for isolating the planarian outer epithelium and prepared ribodepleted RNA-sequencing libraries from samples isolated at multiple time points after tissue amputation. One gene we both identified using these methods and found to be functionally important for regeneration is a putative planarian homolog of vertebrateShoc2. SHOC2 is an essential scaffolding protein that mediates specific, context-dependent activation of the ERK1/2 signaling pathway (JangandGalperin2016). Notably, the ERK1/2 pathway is known to be activated after injury and required for regeneration in multiple species (Manuelet al. 2006; Owlarnet al. 2017; Tomassoet al. 2023). These findings suggest that these epithelial datasets have the potential to uncover many functionally relevant and possibly highly conserved genes that play fundamental roles in animal regeneration.
Erbin interacts with NHERF1 and Ezrin to stabilize a membrane ErbB2 signaling complex in HER2-positive breast cancer
Authors: Jeong Jaekwang , Yoo Kwangmin , Lee Jongwon , Shin Jae Hun , Choi Jungmin , Wysolmerski John
Published: October 2024

Approximately 20% of breast cancers overexpress ErbB2/HER2/Neu, a receptor tyrosine kinase. Our previous studies demonstrated that HER2 interacts with the calcium pump, PMCA2, and the scaffolding molecules, NHERF1 and Ezrin to stabilize HER2/HSP90 interactions and contribute to the retention of active HER2 at the plasma membrane. In the normal mammary epithelium where apical/basal polarity is tightly regulated by junctional proteins, HER2 is expressed at the basolateral membrane and interacts with the LAP family member, Erbin, whereas PMCA2, NHERF1, and Ezrin localize to the apical membrane. Here, we show that loss of apical membrane polarity in hyperplastic lesions of MMTV-Neu mammary glands or in human DCIS leads to intermixing of these molecules and allows Erbin to interact with NHERF1, Ezrin and HER2 initially within the basolateral membrane and then more diffusely within the plasma membrane. In SKBR3 cells, Erbin physically interacts with NHERF1, Ezrin and HER2 in actin-rich membrane protrusions that we have previously described to be sites of active HER2 signaling. Knockdown of Erbin in these cells reduced HER2 signaling by disrupting the formation of a HER2/NHERF1/Ezrin/HSP90 protein complex in the membrane protrusions. Furthermore, inhibition of Ezrin or knock-down of NHERF1 expression disrupted the ability of Erbin to interact with HER2. Taken together, our data suggest that Erbin supports HER2 stability, HER2 membrane retention and HER2 transforming ability by interacting with Ezrin and NHERF1 to maintain a multi-protein signaling complex necessary for HER2-mediated transformation.
Unveiling the chemical and behavioural ecology ofTribolium castaneum(Herbst, 1797) in wheat flour: Alterations in flour metabolic content and the role of chemical cues in modulating beetles’ behaviour and regulating population growth
Authors: Das Subhadeep , Manna Sourav , Chatterjee Oishika , Saha Riya , Sarkar Oishee Janet
Published: October 2024

Tribolium castaneum(Herbst, 1797) (Coleoptera: Tenebrionidae) is a notorious secondary pest of stored grains and flours, accounting for 10–15% of global annual losses in stored products. This study first evaluated the impact ofT. castaneuminfestation on the nutritional parameters of stored wheat flour. Infested flour exhibited reductions in total soluble sugars, triacylglycerol levels, and unsaturated fatty acids, particularly Oleic and Linoleic acid, while secondary metabolites such as phenolics, flavonoids, and tannins were increased. Behavioural assays revealed that adult beetles were significantly more attracted towards infested flour odour due to the presence of 4,8-Dimethyldecanal (4,8-DMD), an aggregation pheromone of T. castaneum. Another key compound in infested flour, 1-Pentadecene, derived from the beetles’ cuticular wax, was found to influence adult beetle behaviour. At higher concentrations, 1-Pentadecene acted as a repellent for the species. Molecular docking studies suggested that 1-Pentadecene competes with 4,8-DMD for binding to the odorant receptor TcOR1, which could potentially inhibit aggregation behaviour and reduce population growth. The docking analysis revealed that 1-Pentadecene interacts with the same binding pocket on TcOR1, sharing key amino acids (MET49, PHE69, THR72, GLN73, THR134, VAL135, TYR138, LEU154, ILE177, GLY180, ALA181, TYR286) and forming similar intermolecular bonds, such as a pi-alkyl bond, with a binding affinity (ΔG = -5.7) comparable to 4,8-DMD (ΔG = -5.8). Additionally, beetles reared in wheat flour containing higher concentrations of 1-Pentadecene exhibited lower population growth compared to those reared in flour with lower concentrations of this compound.
GLA-3 Mediates Stress Response inCaenorhabditis elegansGerm Cells: A key role of the Tristetraprolin (TTP) Family
Authors: Salinas Laura Silvia , Dámazo-Hernández Angel Armando , Morales-Oliva Enrique , Láscarez-Lagunas Laura Ivón , Navarro Rosa Estela
Published: October 2024

Tristetraprolin or TTP is an RNA-binding protein that possesses two CCCH-like zinc-finger domains that bind AU-rich elements to promote their degradation. One of its targets is the mRNA of tumor necrosis factor alpha (TNF-α). When TTP is absence, the TNF-α factor accumulates causing severe, generalized inflammation in knockout mice. TTP is also considered a tumor suppressor protein because regulates the expression of several mRNAs that encode for proteins involve in cell cycle regulation and it is downregulated in various types of human cancers. Under stress, TTP associates with stress granules (SGs), dynamic cytoplasmic condensates formed by liquid-liquid phase separation (LLPS) that protect mRNAs from harmful conditions. Despite TTP’s important role in mRNA turnover, much remains to explore about its participation in stress resistance in life animals that is why, we explored the role of GLA-3, one of the TTP’s homolog, in the nematodeCaenorhabditis elegans. Nematodes lackinggla-3/TTP exhibit phenotypes such as progressive loss of motility, reduced brood size, and increased embryonic lethality. As well as defects in meiotic progression, and increased germ-cell apoptosis. Here we showed that the GFP::GLA-3 reporter is expressed mainly in theC. elegansgermline, where associates with different condensates like germ granules, processing bodies, and stress granules suggesting that, like TTP, GLA-3 plays an important role in mRNA regulation in theC. elegansgermline. Furthermore we demonstrated that GLA-3 is important for stress granules’ and processing bodies’ formation. We also show that oogenic germ cells of GLA-3 mutant animals that were exposed to heat shock resulted embryos that did not survive showing that GLA-3 plays an important role protecting germ cells from this condition. Our results demonstrate that the role of GLA-3 is conserved inC. elegans, and this model can be very useful for further investigating the role of this protein on the future.
microbetag: simplifying microbial network interpretation through annotation, enrichment tests and metabolic complementarity analysis
Authors: Zafeiropoulos Haris , Michail Delopoulos Ermis Ioannis , Erega Andi , Schneider Aline , Geirnaert Annelies , Morris John , Faust Karoline
Published: October 2024

Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to enhance network annotation. Nodes (taxa) are enriched with phenotypic traits, while edges represent metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 high-quality genomes with detailed annotations. A stand-alone tool allows users to apply microbetag to custom reference genomes/bins/MAGs. Additionally, MGG, a CytoscapeApp, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.
INVESTIGATING TRAIT IMPULSIVITY IN OBSESSIVE-COMPULSIVE DISORDER: A SCOPING REVIEW
Authors: Banwell M.J. , Scheffler F. , Lochner C. , Chamberlain S.R. , Stein D.J.
Published: October 2024

Background/Aims

While obsessive-compulsive disorder (OCD) is specifically characterised by compulsivity, considerable literature suggests impulsivity also plays an important role in the disorder. However, impulsivity is a multi-faceted construct and the exact relationship of trait impulsivity to OCD remains unclear. Therefore, this scoping review aimed to collate and review studies of trait impulsivity in OCD by an investigation of: 1. How trait impulsivity in OCD is measured in the research literature; 2. How people with OCD perform on these measures and compare to healthy and other psychiatric groups; and 3. What correlations with trait impulsivity are observed in OCD.

Methods

This study was pre-registered on PROSPERO (CRD42023481781). Electronic search of PubMed, Scopus, and PsycINFO databases using keywords ‘(impuls*) AND (OCD)’ was undertaken without date restrictions for peer-reviewed articles available in English. After exclusion of duplicates and screening of 1476 abstracts, 114 articles were identified for full-text review.

Results

54 articles were reviewed after excluding studies assessing neurocognitive impulsivity only (i.e. no inclusion of trait impulsivity), sub-clinical OCD symptoms, and review articles. The literature reports cross-sectional clinician-rated and self-rated trait impulsivity data, with the Barratt Impulsivity Scale (BIS) being used most frequently. Broadly, people with OCD scored higher than healthy controls on at least one aspect of trait impulsivity. However, comparisons of OCD groups to other psychiatric groups demonstrated equal or lower trait impulsivity in OCD. Individuals with OCD with comorbid diagnoses (ADHD, behavioural addictions, tic disorder, borderline personality disorder, bipolar disorder) had relatively higher levels of trait impulsivity than those without. In OCD, trait impulsivity scores were associated with various psychiatric symptomatology (OCD severity, anxiety, depression, compulsivity, hoarding levels, behavioural addictions, anhedonia, aggressive and sexual impulses). Trait impulsivity did not correlate with neurocognitive measures of impulsivity.

Conclusions

Key findings are that trait impulsivity research in OCD was predominantly observational, with cross-sectional studies using the BIS. While higher levels of trait impulsivity were seen in patients with OCD compared to healthy controls, this finding was not specific to OCD. OCD demonstrated equal or lower trait impulsivity than other psychiatric groups that the literature had examined to date; trait impulsivity in OCD was positively correlated with a number of psychiatric factors; and neurocognitive measures of impulsivity did not correlate with trait impulsivity. Future work on OCD should include interventional and neuroimaging methods that utilise several different measures of impulsivity.
Programmatic diagnostic accuracy and clinical utility of Xpert MTB/XDR in patients with rifampicin-resistant tuberculosis in Georgia
Authors: Pfurtscheller Theresa , Tsutsunava Ana , Maghradze Nino , Gujabidze Mariam , Bablishvili Nino , Yerlikaya Seda , Denkinger Claudia M. , Tukvadze Nestani , Gupta-Wright Ankur
Published: October 2024

Background

Xpert MTB/XDR (Cepheid, USA) is recommended for drug susceptiblity testing in patients with tuberculosis (TB) by the World Health Organization (WHO) with potential for rapid detection of isoniazid and fluoroquinolones resistance. However, diagnostic accuracy and clinical utility in a programmatic setting are unknown.

Methods

We evaluated accuracy and clinical utility of Xpert XDR in patients with rifampicin-resistant pulmonary TB during programmatic implementation in Georgia between July 2022 and August 2024, using phenotypic drug susceptibility testing (pDST) as reference standard.

Results

140 patients were tested with Xpert MTB/XDR and pDST, and 94.9% and 33.8% had isoniazid and fluoroquinolone resistance by pDST respectively. Xpert MTB/XDR showed 99.2% sensitivity (95% CI 95.5-100%) and 100% specificity (95% CI 54.1-100%) for isoniazid resistance. Sensitivity and specificity for fluoroquinolone resistance were 88.4% (95% CI 74.9-96.1%) and 100% (95% CI 95.6-100%). Including indeterminate/invalid Xpert MTB/XDR results, 17.4% (8/46) and 6.4% (8/129) of patients with phenotypic fluoroquinolone and isoniazid resistance were missed, respectively. Median turn-around time for Xpert MTB/XDR was 1 day (IQR 1-3) and median time to treatment was 4 days (IQR 1-7). Phenotypic DST results took a median of 43 days (IQR 29-63) longer than Xpert MTB/XDR results. 95% (115/121, 95% CI 89.5-98.2%) of patients had fluoroquinolones appropriately prescribed based on Xpert XDR result.

Conclusions

Progammatic data confirms high accuracy of Xpert MTB/XDR, although below WHO TPP targets for fluoroquinolones, with significantly faster time-to-results than pDST. However, there is a strong need for rapid tests to detect resistance to bedaquiline and other newer TB drugs.
Spatial analysis of HPV associated cervical intraepithelial neoplastic tissues demonstrate distinct immune signatures associated with cervical cancer progression
Authors: Pavilion Gianna , Vu Hani , Xiong Zherui , Dang Thi Viet Trinh , Walsh Michael , Causer Andrew , Chandra Janin , Nguyen Quan , Frazer Ian H
Published: October 2024

Cervical cancer remains the fourth most common cancer affecting women worldwide, and incidences of other HPV-related cancers continue to rise. For the development of effective prevention strategies in high-risk patients, we aimed to better understand the roles of inflammatory pathways and the tumour microenvironment as the main driver of progression to malignancy in HPV-infected tissues. We analysed the spatial organisation of seven samples of HPV+ high-grade squamous intraepithelial lesion (HSIL) and cervical intraepithelial neoplasia 3 (CIN3), comparing tumour heterogeneity and immune microenvironments between pre-malignant (neoplastic) and adjacent cervical tissues. We observed evidence of immune suppression within the neoplastic regions across all samples and identified distinct immune clusters for each dysplastic lesion. Previous single-cell data analyses in an HPV16 E7 oncoprotein-driven transgenic mouse model suggested a potential role for IL34-CSF1R signalling in immune modulation, where low IL34 expression was associated with Langerhans cell dysfunction, and, in cervical cancer, with poor patient outcome. Here, we observed that IL34-CSF1R co-expression was absent within HPV-associated neoplastic tissues but present in adjacent normal tissue regions. Additionally, we identified enrichment of an M2 gene signature in neoplastic tissue, while adjacent tissue was enriched with a pro-inflammatory M1 gene signature. Our findings provide bio-pathological insights into the spatial cellular and molecular mechanisms underlying HPV-associated cervical cancer immune regulation and suggest a strategy to modulate the immune system in HPV-positive neoplastic cervical and other tissues.
Physiological and injury-induced microglial dynamics across the lifespan
Authors: Tieu Taryn , Cruz Anne-Jolene N. , Weinstein Jonathan R. , Shih Andy Y. , Coelho-Santos Vanessa
Published: October 2024

Microglia are brain’s resident immune cells known for their dynamic responses to tissue and vascular injury. Little is known about how microglial activity differs across the life-stages of early development, adulthood, and aging. Using two-photon live imaging, we show that microglia in the adult cerebral cortex exhibit highly ramified processes and relatively immobile somata under basal conditions. Their responses to injury occur over minutes and are highly coordinated neighboring microglia. In neonates, microglia are denser and more mobile but less morphologically complex. Their responses to focal laser-induced injuries of capillaries or parenchymal tissue are uncoordinated, delayed and persistent over days. In the aged brain, microglia somata remain immobile under basal conditions but their processes become less ramified. Their responses to focal injuries remain coordinated but are slower and less sensitive. These studies confirm that microglia undergo significant changes in their morphology, distribution, dynamics and response to injury across the lifespan.

HIGHLIGHTS

Microglia undergo significant morphological and dynamic changes between life-stages.

Neonatal microglia are highly dynamic, less morphologically complex and mount delayed responses to focal injury compared to adult microglia.

Aged microglia are slightly less ramified and their responses to focal injury are slow and less sensitive than adult microglial.

Maturation of microglial morphology in the developing cortex is disrupted by focal laser injury.

Abstract Figure
Microplate micromilling: A customizable platform to support the prototyping, development and testing of microphysiological culture models
Authors: Reynolds Jacob I. , Adams Meredith , Jimenez Jose , Johnson Brian P.
Published: October 2024

The development of microphysiological cell culture models (MPMs) that align with the throughput demands of drug and chemical testing are needed to help reduce animal testing, aide in the discovery of new drugs, and identify harmful chemical exposures. To address this need, we have developed a process for rapid prototyping MPM devices using computer numerical control (CNC) micromilling of commercially available microplates. Microchannels are cut out of the existing microplate structure and ports are drilled into the bottom of the wells to interface the wells. To test versatility and benchmark to another rapid-prototyping approach, we manufactured common microfluidic features into microplates using four different CNC mills as well as a 3D printer. Cell viability was assessed for polystyrene (PS) well plates and two 3D printed resins (MED610 and VeroClear) with the PS showing >2.5-fold increase in cell growth after three days. Machines were tested on their ability to create common device features including a traditional microfluidic device as well as a custom design incorporating complex geometries. Features were measured by confocal microscopy. We found that features including 1000µm ports, 800µm microchannels, 200µm phase-guides, and 500µm post arrays were machined and the range of CVs for features were 1.02-4.42, 1.32-3.50, 2.34-16.58, 6.25-16.40 respectively, while the 3D printed features exhibited maximal CVs of 20.98, 11.68, 23.60, and 10.01 for the same features. Predictably, more expensive machines generally showed higher accuracy and lower variation, but many features could be created accurately and precisely by inexpensive (<$3000) machines facilitating the broader use of this technology to create a user customizable platform to support the prototyping, development, and testing of human relevant models with broad applications across the life sciences.

Graphical abstract

Multiple CNC mills are assessed on accuracy and precision of microfluidic features of interest for microphysiological model development creation.
Heterogeneity and plasticity of the naïve CD4+T cell compartment
Authors: Sajani Alia , Schaafsma Evelien , Croteau Walburga , ElTanbouly Mohamed , Nowak Elizabeth C. , Cheng Chao , Burns Christopher M. , Turk Mary Jo , Noelle Randolph J. , Lines J. Louise
Published: October 2024

While naïve CD4+T cells have historically been considered a homogenous population, recent studies have provided evidence that functional heterogeneity exists within this population. Using single cell RNA sequencing (scRNAseq), we identify five transcriptionally distinct naïve CD4+T cell subsets that emerge within the single positive stage in the thymus: a quiescence cluster (TQ), a memory-like cluster (TMEM), a TCR reactive cluster (TTCR), an IFN responsive cluster (TIFN), and an undifferentiated cluster (TUND). Elevated expression of transcription factors KLF2, Mx1, and Nur77 within the TQ, TIFN, and TMEMclusters, respectively, allowed enrichment of these subsets for further analyses. Functional studies using sorted cells revealed that naïve T cell subsets have distinctive functional biases upon stimulation. Furthermore, treatment of mice with inflammatory stimuli imparted a state of reduced responsiveness on naïve T cells, evidenced by a reduction in cytokine productionex vivo. In human lupus patients, naïve CD4+T cell cluster frequencies were distorted, with the TIFNcluster expanding proportionately with disease score. Our data show that naïve T cells are influenced by host environment, with functional consequences manifesting upon activation. These findings highlight a need to explore how naïve T cells can become distorted in cancer, autoimmunity, and infectious diseases.

This study describes the transcriptional heterogeneity of murine and human naïve CD4+T cells as comprising of multiple discrete clusters that impact CD4+T cell fate and trajectories. Naïve CD4+T cells experiencing inflammatory environments exhibit an altered transcriptional state that influences their functional trajectory.
Hierarchical Organization of Visual Feature Attention Control
Authors: Meyyappan Sreenivasan , Ding Mingzhou , Mangun George R
Published: October 2024

Attention can be deployed in anticipation of visual stimuli based on features such as their color or direction of motion. This anticipatory feature-based attention involves top-down neural control signals from the frontoparietal network that bias visual cortex to enhance the processing of attended information and suppress distraction. So, for example, anticipatory attention control can enable effective selection based on stimulus color while ignoring distracting information about stimulus motion. But as well, anticipatory attention can be focused more narrowly, for example, to select specific colors or motion directions that define task-relevant events and objects. One important question that remains open is whether anticipatory attention control first biases broad feature dimensions such as color versus motion before biasing the specific feature attributes (e.g., blue vs. green). To investigate this, we recorded EEG activity during a task where participants were cued to either attend to a color (blue or green) or a motion direction (up or down) on a trial-by-trial basis. Applying multivariate decoding approaches to the EEG alpha band (8-12 Hz) activity during the attention control period (cue-target interval), we observed significant decoding for both the attended dimensions (color vs. motion)andspecific feature attributes (blue vs. green; up vs. down). Importantly, the temporal onset of the dimension-level biasing (color vs. motion) preceded that of the attribute-level biasing (e.g., blue vs. green). These findings demonstrate that the top-down control of feature-based attention proceeds in a hierarchical fashion, first biasing the broad feature dimension, and then narrowing to the specific feature attribute.

Significance Statement

During voluntary feature-based attention, electrophysiological and neuroimaging studies have highlighted the role of anticipatory (top-down) biasing of the sensory cortex in enhancing the selection of attended stimulus attributes, but little is known about how this is achieved. In particular, it is not clear whether attending to an attribute such as a color (blue vs. green) or motion direction (up vs. down)firstbiases all neural structures coding that dimension (color/motion) before biasing the specific attribute, or if the top-down signals directly bias only the attended attribute. Using EEG and multivariate decoding, we report that top-down attention control follows a hierarchical organization: first, the broader attended feature dimension is biased, which is followed by the biasing of the specific feature attribute.
In-gel refolding allows fluorescence detection of fully denatured GFPs after SDS-PAGE
Authors: Shiratori Misa , Tsuyuki Rio , Asanuma Miwako , Kawabata Saki , Yoshioka Hiromasa , Ohgane Kenji
Published: October 2024

Green fluorescent proteins (GFPs) have been widely used as fusion tags, especially to visualize subcellular localization and dynamics of the fused partner proteins. Also, GFPs serve as fluorescent tags in size-exclusion chromatography and native-PAGE, facilitating the evaluation of expression levels and quality of the expressed fusion proteins. However, the fluorescent detection of GFPs is generally incompatible with denaturing SDS-polyacrylamide gel electrophoresis (PAGE), where the samples are heat-denatured before loading. Accordingly, detecting GFP-fused proteins after SDS-PAGE usually relies on western blotting with anti-GFP antibodies. To enable in-gel fluorescence detection of SDS-PAGE-separated GFPs, some protocols employ mild denaturing conditions to keep the GFPs intact. However, such mild denaturation sometimes results in partial denaturation of the proteins and irregular electrophoretic mobility that is not proportional to their molecular weights. Here, we demonstrate that the fully denatured GFPs can be refolded within the gel by cyclodextrin-mediated removal of SDS in the presence of 20% methanol, enabling the in-gel fluorescence detection of the GFP-fused proteins. The protocol is compatible with subsequent total protein staining and western blotting. Although future studies are needed to clarify the scope and generality, the technique developed here would provide a simple, time- and cost-effective alternative to the immunodetection of GFPs.

Highlights

Fully denatured GFPs could be in-gel refolded to enable fluorescence detection.

? cyclodextrin effectively removed SDS to assist in the in-gel refolding of GFPs.

GFPs amenable for in-gel refolding include GFPuv, EGFP, turboGFP, and sfGFP.

Compatible with total protein staining and western blotting.

The in-gel refolding procedure was successfully applied to two turboGFP-fusion proteins.

Graphical abstract
BioLLMNet: Enhancing RNA-Interaction Prediction with a Specialized Cross-LLM Transformation Network
Authors: Tahmid Md Toki , Abir Abrar Rahman , Bayzid Md. Shamsuzzoha
Published: October 2024

Existing computational methods for the prediction of RNA related interactions often rely heavily on manually crafted features. Language model features for bio-sequences has gain significant popularity in proteomics and genomics. However, during interaction prediction, how language model features from different modalities should be combined to extract the most representative features is yet to be explored. We introduce BioLLMNet, a novel framework that introduces an effective combination approach for multi-modal bio-sequences. BioLLMNet provides a way to transform feature space of different molecule’s language model features and uses learnable gating mechanism to effectively fuse features. Rigorous evaluations show that BioLLMNet achieves state-of-the-art performance in RNA-protein, RNA-small molecule, and RNA-RNA interactions, outperforming existing methods in RNA-associated interaction prediction.
Regeneration of Sensory Hair Cells and Restoration of Vestibular Function by Notch Inhibition
Authors: Lahlou Hanae , Zhu Hong , Zhou Wu , Edge Albert S.B.
Published: October 2024

Sensory hair cell loss in the vestibular organs of the inner ear causes balance disorders which are essentially irreversible due to the lack of significant hair cell regeneration. Here, we administered a γ-secretase inhibitor to an adult mouse model of vestibular hair cell loss. The treatment resulted in complete regeneration of type II and partial restoration of type I hair cells after one month and restored vestibuloocular reflexes across all frequencies of rotational and linear acceleration. Further recovery was apparent at 8 months. Genetic deletion ofNotch1in supporting cells identified Notch1 as the target of the drug. The results demonstrate that a single injection of a γ-secretase inhibitor is a viable therapy for functional restoration of the vestibular system in patients with balance disorders.
Spectral estimation at the edge
Authors: Patel Shivangi , Psarou Eleni , Mönke Gregor , Fries Pascal
Published: October 2024

Cognitive functions depend on neuronal communication, which is subserved by the synchronization of neuronal rhythms. Rhythms are characterized by their frequency, power and phase. If the phase of a rhythm just preceding an input is predictive of the neuronal or behavioral response to the input, this provides strong evidence for a functional role of the rhythm. Yet, this requires estimating the phase of a rhythm at the edge of the epoch. This is challenging, because any phase estimation that is spectrally specific requires a finite window length often combined with tapers that de-emphasize the signal close to the edge. To overcome this, we propose a method that builds on previously described approaches based on autoregressive modeling of the data and corresponding extrapolation beyond the edge. In contrast to related previous approaches, the modeling is based on the broadband signals, avoiding filtering-related group delays, and the extrapolation is performed multiple times, allowing averaging and thereby the reduction of extrapolation noise. The new method provided more accurate phase estimation at the edge for most simulated datasets, and for an empirical dataset from awake macaque area V4. We propose that the enhanced phase estimation accuracy at the edge might help to investigate the functional roles of brain rhythms and potentially also to improve phase-specific stimulation for clinical applications.
Combined Nanodrops Imaging and Ultrasound Localization Microscopy for Detecting Intracerebral Hemorrhage
Authors: Lin Bing-Ze , Fan Alexander Changyu , Wang Yike , Lowerison Matthew R. , Dong Zhijie , You Qi , Sekaran Nathiya Vaithiyalingam Chandra , Llano Daniel , Borden Mark , Song Pengfei
Published: October 2024

Objective

Advanced imaging methods are crucial for understanding stroke mechanisms and discovering effective treatments to reduce bleeding and enhance recovery. In preclinicalin vivostroke imaging, MRI, CT, and optical imaging are commonly used to evaluate stroke outcomes in rodent models. However, MRI and CT have limited spatial resolution for rodent brains, and optical imaging is hindered by limited imaging depth of penetration. Here we introduce a novel contrast-enhanced ultrasound imaging method to overcome these challenges and characterize intracerebral hemorrhage with unique insights.

Methods

We combined microbubble (MB)-based ultrasound localization microscopy (ULM) and nanodrop (ND)- based vessel leakage imaging to achieve simultaneous microvascular imaging and hemorrhage detection. ULM maps brain-wide cerebral vasculature with high spatial resolution and identifies microvascular impairments around hemorrhagic areas. NDs are sub-micron liquid-core particles which can extravasate due to blood-brain barrier (BBB) breakdown, serving as positive contrast agents to detect hemorrhage sites.

Results

Our findings demonstrate that NDs could effectively accumulate in the hemorrhagic site and reveal the location of the bleeding areas upon activation by focused ultrasound beams. ULM further reveals the microvascular damage manifested in the form of reduced vascularity and decreased blood flow velocity across areas affected by the hemorrhagic stroke.

Conclusion

The results demonstrate that sequential ULM combined with ND imaging is a useful imaging tool for basicin vivoresearch in stroke with rodent models where brain-wide detection of active bleeding and microvascular impairment are essential.
Afternoon to early evening bright light exposure reduces later melatonin production in adolescents
Authors: Lazar Rafael , Fazlali Fatemeh , Dourte Marine , Epple Christian , Stefani Oliver , Spitschan Manuel , Cajochen Christian
Published: October 2024

Whether light exposure during the day reduces non-visual light effects later in the evening has not been studied in adolescents. We investigate whether afternoon-early evening (AEE) light interventions (130 lx, 2500 lx, 4.5 hours, compared to 6.5 lx) would increase melatonin levels during later evening light exposure (130 lx) in a counterbalanced crossover study with 22 adolescents (14-17 years, 11 female). Contrary to our hypothesis, evening melatonin levels decreased after AEE bright light exposure, while sleepiness and vigilance were unaffected, and skin temperature showed no clear changes. The AEE light had acute alerting effects and bright light exposure in the 32 hours before laboratory entry was associated with higher evening melatonin and sleepiness. These findings suggest that bright AEE light increases alertness but may delay melatonin production by interfering with circadian rhythms. The study highlights the complex effects of light timing and its implications for managing adolescents' light exposure.
Mitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDecon
Authors: Wang Zirui , Xu Ke , Liu Yang , Xu Yu , Zhang Lu
Published: October 2024

The advent of spatially resolved transcriptomics (SRT) has revolutionized our understanding of tissue molecular microenvironments by enabling the study of gene expression in its spatial context. However, many SRT platforms lack single-cell resolution, necessitating cell-type deconvolution methods to estimate cell-type proportions in SRT spots. Despite advancements in existing tools, these methods have not addressed biases occurring at three scales: individual spots, entire tissue samples, and discrepancies between SRT and reference scRNA-seq datasets. These biases result in overbalanced cell-type proportions for each spot, mismatched cell-type fractions at the sample level, and data distribution shifts across platforms. To mitigate these biases, we introduce HarmoDecon, a novel semi-supervised deep learning model for spatial cell-type deconvolution. HarmoDecon leverages pseudo-spots derived from scRNA-seq data and employs Gaussian Mixture Graph Convolutional Networks to address the aforementioned issues. Through extensive simulations on multi-cell spots from STARmap and osmFISH, HarmoDecon outperformed 11 state-of-the-art methods. Additionally, when applied to legacy SRT platforms and 10x Visium datasets, HarmoDecon achieved the highest accuracy in spatial domain clustering and maintained strong correlations between cancer marker genes and cancer cells in human breast cancer samples. These results highlight the utility of HarmoDecon in advancing spatial transcriptomics analysis.
Cross-catalytic enhancement of peptides and RNA from a common prebiotic activated intermediate
Authors: Roy Raya , Sawant Anupam A. , Rajamani Sudha
Published: October 2024

Previous origin of life studies have demonstrated the presence of amino acids and nucleotides in the same prebiotic milieu. In this study, we set out to understand the interplay of amino acids with linear or cyclic nucleotides under prebiotically pertinent reaction conditions, especially for its implications for biomolecular evolution. We characterized the cross-catalytic effect of oligomerization, potentially stemming from the simultaneous presence of these two biochemically important monomers. Qualitative and quantitative analysis indicated the formation of longer AMP oligomers and peptides, with 8-10 fold increase in specific reaction scenarios, when compared to reactions that evaluated the monomer oligomerization in isolation. The reason behind such an increase in yield and length, in case of both the oligomers, was the formation of a reactive intermediate. This aminoacylated-AMP (AMP-aa) resulted from a condensation reaction between the nucleotide and the amino acid. We extended this to other amino acids with different R chain characteristics, to comprehend the properties required for the formation of AMP-aa under our reaction conditions. The nonenzymatic formation of these aminoacylated AMP, which in turn resulted in longer oligomers, indicates the plausibility of the emergence of initial steps involved in a primordial translation system.
Symptom-modulating satRNAs of cucumoviruses affect the orientation and feeding behaviour ofMyzus persicae
Authors: Wrzesińska-Krupa Barbara , Strażyński Przemysław , Frąckowiak Patryk , Obrępalska-Stęplowska Aleksandra
Published: October 2024

Plant viruses evolved mechanisms to manipulate host plants to replicate and be efficiently transmitted by insect vectors. In the context of non-persistently transmitted viruses, an important strategy is to change the plant’s metabolism to attract the vectors, and subsequently repel viruliferous insects from the infected plants to facilitate the virus transmission to neighbouring plants. The presence of satellite RNAs (satRNAs), which accompany certain plant RNA virus species and strains, leads to changes in the host plants, such as alterations in the virus-induced infection symptoms, either exacerbating or attenuating them. This study aimed to analyse the influence of satRNAs on the orientation and feeding behaviour of the cucumovirus insect vector –Myzus persicae, which might consequently contribute to the virus transmission efficiency. The hypothesis behind this study was that satRNAs of cucumoviruses alter these insect activities toward virus-infected plants, and strongly symptom-deteriorating satRNAs might negatively affect the attractiveness of the infected plants for aphids. Using two cucumoviruses, peanut stunt virus (PSV) and cucumber mosaic virus (CMV), and their satRNAs, which induce divergent infection symptoms, olfactometry and electrical penetration graph (EPG) monitoring analyses were performed. The results showed that satRNAs which presence leads to disease symptom exacerbation might alter the orientation behaviour of aphids by reducing the attractiveness of the plants and discouraging aphids from feeding. This phenomenon may contribute to the better persistence in the environment of satRNAs alleviating disease symptoms compared to the worsening ones, benefiting the virus by not destroying the plant and prolonging the virus’ exposure to insect vectors.