bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Diseases-Associated Microglia in the Optic Nerve by Lipoxin B4and Ocular Hypertension
Authors: Maurya Shubham , Lin Maggie , Karnam Shruthi , Singh Tanirika , Kumar Matangi , Ward Emily , Sivak Jeremy , Flanagan John G , Gronert Karsten 
Published: March 2024

AbstractBackgroundThe resident astrocyte-retinal ganglion cell (RGC) lipoxin circuit is impaired during retinal stress, which includes ocular hypertension-induced neuropathy. Lipoxin B4produced by homeostatic astrocytes directly acts on RGCs to increase survival and function in ocular hypertension-induced neuropathy. RGC death in the retina and axonal degeneration in the optic nerve are driven by the complex interactions between microglia and macroglia. Whether LXB4neuroprotective actions include regulation of other cell types in the retina and/or optic nerve is an important knowledge gap.MethodsCellular targets and signaling of LXB4in the retina were defined by single-cell RNA sequencing. Retinal neurodegeneration was induced by injecting silicone oil into the anterior chamber of the mouse eyes, which induced sustained and stable ocular hypertension. Morphological characterization of microglia populations in the retina and optic nerve was established by MorphOMICs and pseudotime trajectory analyses. The pathways and mechanisms of action of LXB4in the optic nerve were investigated using bulk RNA sequencing. Transcriptomics data was validated by qPCR and immunohistochemistry. Differences between experimental groups were assessed by Student’s t-test and one-way ANOVA.ResultsSingle-cell transcriptomics identified microglia as a primary target for LXB4in the healthy retina. LXB4downregulated genes that drive microglia environmental sensing and reactivity responses. Analysis of microglial function revealed that ocular hypertension induced distinct, temporally defined, and dynamic phenotypes in the retina and, unexpectedly, in the distal myelinated optic nerve. Microglial expression of CD74, a marker of disease-associated microglia in the brain, was only induced in a unique population of optic nerve microglia, but not in the retina. Genetic deletion of lipoxin formation correlated with the presence of a CD74 optic nerve microglia population in normotensive eyes, while LXB4treatment during ocular hypertension shifted optic nerve microglia toward a homeostatic morphology and non-reactive state and downregulated the expression of CD74. Furthermore, we identified a correlation between CD74 and phospho-phosphoinositide 3-kinases (p-PI3K) expression levels in the optic nerve, which was reduced by LXB4treatment.ConclusionWe identified early and dynamic changes in the microglia functional phenotype, reactivity, and induction of a unique CD74 microglia population in the distal optic nerve as key features of ocular hypertension-induced neurodegeneration. Our findings establish microglia regulation as a novel LXB4target in the retina and optic nerve. LXB4maintenance of a homeostatic optic nerve microglia phenotype and inhibition of a disease-associated phenotype are potential neuroprotective mechanisms for the resident LXB4pathway.
Identifying leaf anatomy and metabolic regulators that underpin C4photosynthesis inAlloteropsis semialata
Authors: Alenazi Ahmed S , Pereira Lara , Christin Pascal-Antoine , Osborne Colin P , Dunning Luke T 
Published: March 2024

SummaryC4photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4is complicated by the fact that variation in photosynthetic type is usually segregated between species.Here, we perform a genome wide association study (GWAS) using the grassAlloteropsis semialata, the only known species to have C3, intermediate, and C4accessions. We aimed to identify genomic regions associated with the strength of the C4cycle (measured using δ13C), and the development of C4leaf anatomy.Genomic regions correlated with δ13C include regulators of C4decarboxylation enzymes (RIPK), non-photochemical quenching (SOQ1), and the development of Kranz anatomy (SCARECROW-LIKE). Regions associated with the development of C4leaf anatomy in the intermediate accessions contain additional leaf anatomy regulators, including those responsible for vein patterning (GSL8) and meristem determinacy (GRF1).The detection of highly correlated genomic regions with a modest sample size indicates that the emergence of C4photosynthesis inA. semialatarequired a few loci of large effect. The candidate genes could prove to be relevant for engineering C4leaf anatomy in C3species.
NanoPlex: a universal strategy for fluorescence microscopy multiplexing using nanobodies with erasable signals
Authors: Mougios Nikolaos , Cotroneo Elena R. , Imse Nils , Setzke Jonas , Rizzoli Silvio , Simeth Nadja A. , Tsukanov Roman , Opazo Felipe 
Published: March 2024

AbstractFluorescence microscopy has long been a transformative technique in biological sciences. Nevertheless, most implementations are limited to a few targets, revealed using primary antibodies (1.Abs) and fluorescently conjugated secondary antibodies. Super-resolution techniques such as Exchange-PAINT and, more recently, SUM-PAINT have increased multiplexing capabilities, but they require specialized equipment, software, and knowledge. To enable multiplexing for any imaging technique in any laboratory, we developed NanoPlex, a streamlined method based on conventional 1.Abs revealed by engineered secondary nanobodies (2.Nbs) that allow to selectively erase the fluorescence signals. We developed three complementary signal removal strategies: OptoPlex (light-induced), EnzyPlex (enzymatic), and ChemiPlex (chemical). We showcase NanoPlex reaching 21 targets for 3D confocal analyses and 5-8 targets fordSTORM and STED super-resolution imaging. NanoPlex has the potential to revolutionize multi-target fluorescent imaging methods, potentially redefining the multiplexing capabilities of antibody-based assays.
Connexin 43 Regulates Intercellular Mitochondrial Transfer from Human Mesenchymal Stromal Cells to Chondrocytes
Authors: Irwin Rebecca M. , Thomas Matthew A. , Fahey Megan J. , Mayán María D. , Smyth James W. , Delco Michelle L. 
Published: March 2024

AbstractBackgroundThe phenomenon of intercellular mitochondrial transfer from mesenchymal stromal cells (MSCs) has shown promise for improving tissue healing after injury and has potential for treating degenerative diseases like osteoarthritis (OA). Recently MSC to chondrocyte mitochondrial transfer has been documented, but the mechanism of transfer is unknown. Full-length connexin43 (Cx43, encoded byGJA1) and the truncated internally translated isoform GJA1-20k have been implicated in mitochondrial transfer between highly oxidative cells, but have not been explored in orthopaedic tissues. Here, our goal was to investigate the role of Cx43 in MSC to chondrocyte mitochondrial transfer. In this study, we tested the hypotheses that (a) mitochondrial transfer from MSCs to chondrocytes is increased when chondrocytes are under oxidative stress and (b) MSC Cx43 expression mediates mitochondrial transfer to chondrocytes.MethodsOxidative stress was induced in immortalized human chondrocytes using tert-Butyl hydroperoxide (t-BHP) and cells were evaluated for mitochondrial membrane depolarization and reactive oxygen species (ROS) production. Human bone-marrow derived MSCs were transduced for mitochondrial fluorescence using lentiviral vectors. MSC Cx43 expression was knocked down using siRNA or overexpressed (GJA1+ and GJA1-20k+) using lentiviral transduction. Chondrocytes and MSCs were co-cultured for 24 hrs in direct contact or separated using transwells. Mitochondrial transfer was quantified using flow cytometry. Co-cultures were fixed and stained for actin and Cx43 to visualize cell-cell interactions during transfer.ResultsMitochondrial transfer was significantly higher in t-BHP-stressed chondrocytes. Contact co-cultures had significantly higher mitochondrial transfer compared to transwell co-cultures. Confocal images showed direct cell contacts between MSCs and chondrocytes where Cx43 staining was enriched at the terminal ends of actin cellular extensions containing mitochondria in MSCs. MSC Cx43 expression was associated with the magnitude of mitochondrial transfer to chondrocytes; knocking down Cx43 significantly decreased transfer while Cx43 overexpression significantly increased transfer. Interestingly, GJA1-20k expression was highly correlated with incidence of mitochondrial transfer from MSCs to chondrocytes.ConclusionsOverexpression of GJA1-20k in MSCs increases mitochondrial transfer to chondrocytes, highlighting GJA1-20k as a potential target for promoting mitochondrial transfer from MSCs as a regenerative therapy for cartilage tissue repair in OA.
Inhibitory Effect of Subthreshold TMS on the Long-Latency Response in the Flexor Carpi Radialis
Authors: Helm Cody A. , Sergi Fabrizio 
Published: March 2024

AbstractThe corticospinal pathway and several secondary motor pathways contribute to long-latency responses (LLRs). However, it is unknown if secondary pathways can produce LLRs independently from corticospinal input. Transcranial magnetic stimulation (TMS) can modulate corticospinal excitability during the LLR.SubthresholdTMS would be ideal for inhibition of corticospinal excitability as it would allow to study function of secondary motor pathways using functional imaging methods with low temporal resolution with minimal activation confound. However, thesubthresholdTMS parameters that maximally inhibit corticospinal activity are unknown.In this study, thirty-six healthy participants performed a protocol combining surface electromyography(EMG), robot-evoked wrist perturbations, and single pulse TMS applied to the motor cortex to study the effect of TMS intensity and latency on the LLR amplitude in the flexor carpi radialis. In one experiment, we tested two TMS intensities of 90% and 95% of the active motor threshold and three latencies, defined such that the motor evoked potential (MEP) peak would arrive at 0 ms, 20 ms, or 50 ms prior to perturbation onset (T1, T2, T3, respectively). In a second experiment, we sought to determine whether the inhibitory effect ofsubthresholdTMS was specific to long-latency responses.TMS significantly reduced the LLR amplitude when applied with T3latency, even when restricting the analysis to stimulation modes that did not induce a motor-evoked response (padj= 0.005). However, we found no evidence that TMS inhibition was specific to the LLR. Overall, our findings indicate that single-pulse,subthresholdTMS significantly reduces the corticospinal component of the LLR.NEW & NOTEWORTHYThis study for the first time shows the capability of subthreshold TMS to reduce the long-latency response amplitude in a forearm muscle. We evaluate the effect of the latency between subthreshold TMS and onset of a wrist perturbation using precisely timed TMS pulses, and establish that the inhibition induced by subthreshold TMS is not specific to LLR, but likely resulting from aspecific intracortical inhibition. Insights from this work can be used to design neuroimaging protocols.
A unique and biocompatible approach for corneal collagen crosslinking in vivo
Authors: Gulzar Ayesha , Kaleli Humeyra N , Koseoglu Gulsum D , Hasanreisoglu Murat , Yildiz Ayşe , Sahin Afsun , Kizilel Seda 
Published: March 2024

AbstractCorneal crosslinking (CXL) is a widely applied technique to halt the progression of ectatic diseases by increasing the thickness and mechanical stiffness of the cornea. This study investigated the biocompatibility and efficiency of a novel CXL procedure using ruthenium and blue light in rat corneas and evaluated factors important for clinical application. To perform the CXL procedure, the corneal epithelium of rats was removed under anesthesia, followed by the application of a solution containing ruthenium and sodium persulfate (SPS). The corneas were then exposed to blue light at 430 nm at 3 mW/cm2for 5 minutes. Rat corneas were examined and evaluated for corneal opacity, corneal and limbal neovascularization, and corneal epithelial regeneration at days 0, 1, 3, 6, 8, and 14. On day 28, the corneas were isolated for subsequent tissue follow-up and analysis. CXL with ruthenium and blue light showed rapid epithelial healing, with 100% regeneration of the corneal epithelium and no corneal opacity by day 6. The ruthenium group also exhibited significantly reduced corneal (p<0.01) and limbal neovascularization (p<0.001). Histological analysis revealed no signs of cellular damage or apoptosis, which further confirms the biocompatibility and nontoxicity of our method. Confocal and scanning electron microscopy (SEM) images showed a greater density of collagen fibrils, indicating efficient crosslinking and enhanced structural integrity. This study confirmed the in vivo safety, biocompatibility, and functionality of ruthenium and blue light CXL. This method can prevent toxicity caused by UV-A light and can be a rapid alternative treatment to standard crosslinking procedures.Graphical Abstract
Dedifferentiation of caudate functional organization is linked to reduced D1 dopamine receptor availability and poorer memory function in aging
Authors: Korkki Saana M. , Johansson Jarkko , Nordin Kristin , Pedersen Robin , Bäckman Lars , Rieckmann Anna , Salami Alireza 
Published: March 2024

AbstractAge-related alterations in cortico-striatal function have been highlighted as an important determinant of declines in flexible, higher-order, cognition in older age. However, the mechanisms underlying such alterations remain poorly understood. Computational accounts propose age-related dopaminergic decreases to impoverish neural gain control, possibly contributing to reduced specificity of cortico-striatal circuits, that are modulated by dopamine, in older age. Using multi-modal neuroimaging data (fMRI, PET) from a large lifespan cohort (n= 180), we assessed the relationship between dopamine D1-like receptors (D1DRs) and cortico-striatal function during rest and an n-back working memory task. The results revealed gradual age-related decreases in the specificity of functional coupling between the centrolateral caudate and cortical association networks during both rest and working memory, which in turn was associated with poorer short and long-term memory performance with older age. Critically, reduced D1DR availability in the caudate and the prefrontal cortex predicted less differentiated caudate-cortical coupling across the lifespan, in part accounting for the age-related declines observed on this metric. These findings provide novel empirical evidence for a key role of dopamine in maintaining functional specialization of cortico-striatal circuits as individuals age, aligning with computational models that propose deficient catecholaminergic neuromodulation to underpin age-related dedifferentiation of brain function.
Viral diversity and phloem transcriptional changes in Grapevine Shiraz disease infected vines
Authors: Onetto Cristobal , Nagahatenna Dilrukshi S. K. , Wang Yeniu Mickey , Pagay Vinay , Borneman Anthony 
Published: March 2024

AbstractShiraz disease (SD) is a highly destructive disease of grapevines that is associated with Grapevine Virus A (GVA) infection of vineyards in Australia and South Africa. However, little is known about the transcriptional modifications in grapevine phloem tissues induced by SD. In this study, we explored the viral diversity and transcriptional changes linked to SD. Vines symptomatic for SD exhibited higher viral abundance and were also shown to be co-infected with both GVA and grapevine leafroll-associated virus (GLRaV-4) strain 9. Differential gene (DE) expression analysis revealed physiological responses ofVitis vinifera to the infection. Similar to other plant pathogen infections, SD upregulated genes associated with the systemic acquired resistance (SAR) mechanism and downregulated genes related to vine immunity. Additionally, upregulated genes suggests that callose deposition and the blocking of phloem sieve elements are likely employed byV. viniferaas a defence strategy to limit the internal spread of SD viruses.Grapevine Shiraz disease, Grapevine Virus A, Grapevine Leafroll Associated virus, Systemic Acquired Resistance, Transcriptomics
Manipulating plant development by editing histone methylation with the dCas9 tool: theCUC3boundary gene as a case study
Authors: Fal Kateryna , Masson Marie Le , Berr Alexandre , Carles Cristel C. 
Published: March 2024

SummaryChromatin modifications are deemed to associate with gene expression patterns, yet their causal function on transcription and cell fate remains unestablished. Here, we demonstrate the direct impact of an epigenome editing tool designed to remove a key chromatin modification at a precise locus in living plants, with outcomes from the molecular to the developmental scale.The manipulated mark, H3K27me3, deposited at Lysine 27 of Histone 3 by the methyltransferase Polycomb PRC2 complex, is associated with the repression of developmental genes. As a new approach to investigate this histone mark genuine function, we used a dCas9-derived tool to bring a specific demethylase function at theCUP SHAPED COTYLEDON 3(CUC3)organ frontier gene, aiming to remove the trimethyl mark at H3K27. We show that the removal of H3K27me3 at the locus causally induces activation ofCUC3expression within its regular territory, as well as ectopically. Our precise perturbation strategy reveals that alterations in a chromatin mark lead to changes in transcription and developmental gene expression patterning, with sharp consequences on plant morphogenesis and growth.Our work thus constitutes a proof of concept for the effective use of epigenome editing tools in unveiling the causal role of mark dynamics, supported by both molecular and developmental evidences.
The impact of wildtype SARS-CoV-2 on fatigue and quality of life: prevalence of post COVID-19 condition in a Dutch population-based serosurveillance cohort
Authors: Mutubuki Elizabeth N. , van Hagen Cheyenne C.E. , Vos Eric R.A. , den Hartog Gerco , van der Klis Fiona R.M. , van den Wijngaard Cees C. , de Melker Hester E. , van Hoek Albert Jan 
Published: March 2024

AbstractBackgroundOur aim was to assess the relationship between (time since) wild-type SARS-CoV-2 infection and health-related quality of life (HRQoL) and fatigue as endpoints linked to Post COVID-19 condition (PCC).MethodsParticipants ≥15 years were selected from the February 2021 round of the population-based PIENTER Corona study. We investigated the association between (time since) SARS-COV-2 infection and health outcomes: HRQoL (health utility (SF-6D); physical health and mental health (both SF-12)) and fatigue (CIS-fatigue) using multivariable logistic regression analyses adjusted for age, sex, educational level, number of comorbidities, COVID-19 vaccination status, and the intensity of restrictions. For each outcome, multivariable logistic regression models were fitted at cut-off points selected based on the cumulative distribution of those uninfected.ResultsResults shown correspond to the cut-off point related to the worst off 15% of each outcome. Significant differences between those uninfected (n=4,614) and cases infected ≤4 months ago (n=368) were observed for health utility (OR [95%CI]: 1.6 [1.2-2.2]), physical health (OR [95%CI]: 1.7 [1.3-2.3]) and fatigue (OR [95%CI]: 1.6 [1.2-2.0]), but not for mental health. There were no significant differences between uninfected and cases infected >4 months ago (n=345) for all outcomes.ConclusionsIn a Dutch population-based cohort of seroconverted individuals, those infected with wild-type SARS-CoV-2 ≤4 months ago more often reported poor health utility and physical health and were more often severely fatigued compared to those uninfected (at the 15% cut-off). HRQoL and fatigue remained below the detection limit for those infected >4 months ago, suggesting a relatively low prevalence of PCC.
Synapse specific and plasticity-regulated AMPAR mobility tunes synaptic integration
Authors: Nowacka Agata , Getz Angela M. , Zieger Hanna L. , Bessa-Neto Diogo , Breillat Christelle , Daburon Sophie , Lemoigne Cécile , Marais Sébastien , Ducros Mathieu , Penn Andrew C. , Sainlos Matthieu , Choquet Daniel 
Published: March 2024

AbstractSynaptic responses adapt to fast repetitive inputs during bursts of neuronal network activity over timescales of milliseconds to seconds, either transiently facilitating or depressing. This high-frequency stimulus-dependent short-term synaptic plasticity (HF-STP) relies on a number of molecular processes that collectively endow synapses with filtering properties for information processing, optimized for the transmission of certain input frequencies and patterns in distinct circuits1–3. Changes in HF-STP are traditionally thought to stem from changes in pre-synaptic transmitter release1,2, but post-synaptic modifications in receptor biophysical properties or surface diffusion also regulate HF-STP4–11. A major challenge in understanding synapse function is to decipher how pre- and post-synaptic mechanisms synergistically tune synaptic transmission efficacy during HF-STP, and to determine how neuronal activity modifies post-synaptic signal computation and integration to diversify neuronal circuit function. Here, taking advantage of new molecular tools to directly visualize glutamate release12and specifically manipulate the surface diffusion of endogenous AMPAR in intact circuits13, we define the respective contributions of pre-synaptic glutamate release, AMPAR desensitization and surface mobility to frequency-dependent synaptic adaptation. We demonstrate that post-synaptic gain control and signal integration capacity in synaptic networks is influenced by synapse-specific differences in AMPAR desensitization and diffusion-trapping characteristics that are shaped by molecular signaling events recruited during LTP.