Protocol for mitochondrial variant enrichment from single-cell RNA sequencing using MAESTER.

Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of cell states but often lacks insights into tissue clonal structures. Here, we present a protocol to probe cell states and clonal information simultaneously by enriching mitochondrial DNA (mtDNA) variants from 3'-barcoded full-length cDNA. We describe steps for input library preparation, mtDNA enrichment, PCR product cleanup, and paired-end sequencing.

Luminance invariant encoding in mouse primary visual cortex.

The visual system adapts to maintain sensitivity and selectivity over a large range of luminance intensities. One way that the retina maintains sensitivity across night and day is by switching between rod and cone photoreceptors, which alters the receptive fields and interneuronal correlations of retinal ganglion cells (RGCs). While these adaptations allow the retina to transmit visual information to the brain across environmental conditions, the code used for that transmission varies.

Antigen affinity and site of immunization dictate B cell recall responses.

Protective antibodies against HIV-1 require unusually high levels of somatic mutations introduced in germinal centers (GCs). To achieve this, a sequential vaccination approach was proposed. Using HIV-1 antibody knockin mice with fate-mapping genes, we examined if antigen affinity affects the outcome of B cell recall responses.

Neuraminidase 1 regulates neuropathogenesis by governing the cellular state of microglia via modulation of Trem2 sialylation.

Neuraminidase 1 (NEU1) cleaves terminal sialic acids from sialoglycoproteins in endolysosomes and at the plasma membrane. As such, NEU1 regulates immune cells, primarily those of the monocytic lineage. Here, we examine how Neu1 influences microglia by modulating the sialylation of full-length Trem2 (Trem2-FL), a multifunctional receptor that regulates microglial survival, phagocytosis, and cytokine production.

Opposing roles of p38α-mediated phosphorylation and PRMT1-mediated arginine methylation in driving TDP-43 proteinopathy.

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder typically characterized by insoluble inclusions of hyperphosphorylated TDP-43. The mechanisms underlying toxic TDP-43 accumulation are not understood. Persistent activation of p38 mitogen-activated protein kinase (MAPK) is implicated in ALS.

Coordination and persistence of aggressive visual communication in Siamese fighting fish.

Outside acoustic communication, little is known about how animals coordinate social turn taking and how the brain drives engagement in these social interactions. Using Siamese fighting fish (Betta splendens), we discover dynamic visual features of an opponent and behavioral sequences that drive visually driven turn-taking aggressive behavior. Lesions of the telencephalon show that it is unnecessary for coordinating turn taking but is required for persistent participation in aggressive interactions.

Coordinated neuron-specific splicing events restrict nucleosome engagement of the LSD1 histone demethylase complex.

Chromatin regulatory proteins are expressed broadly and assumed to exert the same intrinsic function across cell types. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Among them are two components of a histone demethylase complex: LSD1 H3K4 demethylase and the H3K4me0-reader PHF21A.

Probing the functional constraints of influenza A virus NEP by deep mutational scanning.

The influenza A virus nuclear export protein (NEP) is a multifunctional protein that is essential for the viral life cycle and has very high sequence conservation. However, since the open reading frame of NEP largely overlaps with that of another influenza viral protein, non-structural protein 1, it is difficult to infer the functional constraints of NEP based on sequence conservation analysis. In addition, the N-terminal of NEP is structurally disordered, which further complicates the understanding of its function.

ERK activation waves coordinate mechanical cell competition leading to collective elimination via extrusion of bacterially infected cells.

Epithelial cells respond to infection with the intracellular bacterial pathogen Listeria monocytogenes by altering their mechanics to promote collective infected cell extrusion (CICE) and limit infection spread across cell monolayers. However, the underlying biochemical pathways remain elusive. Here, using in vitro (epithelial monolayers) and in vivo (zebrafish larvae) models of infection with L.

Thrombotic Microangiopathy Associated with Systemic Adeno-Associated Virus Gene Transfer: Review of Reported Cases.

Complement-mediated thrombotic microangiopathy (TMA) in the form of atypical hemolytic uremic syndrome (aHUS) has emerged as an immune complication of systemic adeno-associated virus (AAV) gene transfer that was unforeseen based on nonclinical studies. Understanding this phenomenon in the clinical setting has been limited by incomplete data and a lack of uniform diagnostic and reporting criteria. While apparently rare based on available information, AAV-associated TMA/aHUS can pose a substantial risk to patients including one published fatality.

Characterization of Cutaneous Radiation Syndrome in a Mouse Model Using [18F]F- Fluorodeoxyglucose Positron Emission Tomography.

Ionizing radiation on the skin has the potential to cause various sequelae affecting quality of life and even leading to death due to multi-system failure. The development of radiation dermatitis is attributed to oxidative damage to the skin's basal layer and alterations in immune response, leading to inflammation. Past studies have shown that [18F]F-2-fluoro-2-deoxyglucose positron emission tomography-computed tomography ([18F]F-FDG PET/CT) can be used effectively for the detection of inflammatory activity, especially in conditions like hidradenitis suppurativa, psoriasis, and early atherosclerosis.

Single cell derived multicellular meristem: insights into male-to-hermaphrodite conversion and de novo meristem formation in ceratopteris.

Land plants alternate between asexual sporophytes and sexual gametophytes. Unlike seed plants, ferns develop free-living gametophytes. Gametophytes of the model fern Ceratopteris exhibit two sex types: hermaphrodites with pluripotent meristems and males lacking meristems.

Transition of Perovskite Solar Technologies to Being Flexible.

Perovskite technologies has taken giant steps on its advances in only a decade time, from fundamental science to device engineering. The possibility to exploit this technology on a thin flexible substrate gives an unbeatable power to weight ratio compares to similar photovoltaic systems, opening new possibilities and new integration concepts, going from building integrated and applied photovoltaics (BIPV, BAPV) to internet of things (IoT). In this perspective, the recent progress of perovskite solar technologies on flexible substrates are summarized, focusing on the challenges that researchers face upon using flexible substrates.

ICD-11 posttraumatic stress disorder (PTSD) and complex PTSD in a sample of prison staff: A latent profile approach.

Although empirical support for the International Statistical Classification of Diseases and Related Health Problems (11th ed.; ICD-11) distinction between posttraumatic stress disorder (PTSD) and complex PTSD (CPTSD) is growing, research into the ICD-11 CPTSD model in prison staff is lacking. This study used latent profile analysis (LPA) to (a) determine if there are distinct groups of trauma-exposed prison governors (i.

Therapeutic impacts of recalling and processing positive autobiographical memories on posttrauma health: An open-label study.

The processing of positive memories technique (PPMT) entails detailed narration and processing of specific positive autobiographical memories (AM) and has shown promise in improving posttraumatic stress disorder (PTSD) symptoms. We examined whether participants receiving PPMT reported decreases in PTSD and depressive symptom severity, negative affect levels/reactivity, posttrauma cognitions, and positive emotion dysregulation, as well as increases in positive affect levels/reactivity and the number of retrieved positive AMs across four PPMT sessions. Individuals (N = 70) recruited from the community completed surveys at baseline (pre-PPMT), each PPMT session, and after completing all four PPMT sessions.

Community-Partnered Training in Trauma-Informed Primary Care for Patients Experiencing Reentry From Incarceration: A Pilot Training Study.

Introduction/objectives: Patients returning to the community from incarceration (ie, reentry) are at heightened risk of experiencing trauma when interacting with the healthcare system. Healthcare professionals may not recognize patients' trauma reactions or know how to effectively respond. This paper describes the development and pilot evaluation of a single-session training to prepare primary care teams to deliver trauma-informed care (TIC) to patients experiencing reentry.

Overview of point-of-care diagnostic options for detection of : current technology and implementation considerations.

Introduction Chlamydia Trachomatis: continues to be the most common bacterial infection worldwide and rates continue to increase despite long-standing control efforts. Point of care (POC) testing options may offer improvements in case finding that lead to improved control of this sexually transmitted infection (STI).

Areas Covered: This review will provide information on the three tests that have US Food and Drug Administration (FDA) clearance and describe assays in the developmental pipeline.

Macrolide resistance due to (55).

Unlabelled: Antimicrobial resistance (AMR) is a global threat. The identification and characterization of novel resistance genes is integral to AMR surveillance. The (55) gene was originally identified through whole genome sequencing of macrolide-resistant strains of .

Molecular identification and antibiotic clearance of and from cell cultures infected with or species.

Mycoplasma (Class: Mollicutes) contamination in cell cultures is a universal concern for research laboratories. Some estimates report contamination in up to 35% of continuous cell lines. Various commercial antibiotic treatments can successfully decontaminate clean cell lines ; however, decontamination of bacterial cultures remains challenging.

Paranoia and unusual sensory experiences in Parkinson's disease.

Objectives: There has been limited exploration into the nature and development of psychotic experiences (PEs) in Parkinson's disease (PD). We aimed to comprehensively assess the frequency, severity, and associated distress of paranoia and unusual sensory experiences (USEs) in PD, and to assess what variables are significantly associated with these experiences, focussing on psychological processes central to understanding PEs in non-PD groups.

Method: A questionnaire battery was completed by 369 individuals with PD with a mean age of 66 years and mean time since diagnosis of 5 years.

Vaccination against SARS-CoV-2 provides low-level cross-protection against common cold coronaviruses in mouse and non-human primate animal models.

The common cold coronaviruses are a source of ongoing morbidity and mortality particularly among elderly and immunocompromised individuals. While cross-reactive immune responses against multiple coronaviruses have been described following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination, it remains unclear if these confer any degree of cross-protection against the common cold coronaviruses. A recombinant fowl adenovirus vaccine expressing the SARS-CoV-2 spike protein (FAdV-9-S19) was generated, and protection from SARS-CoV-2 challenge was shown in K18-hACE2 mice.

Resistance mutations that distinguish HIV-1 envelopes with discordant VRC01 phenotypes from multi-lineage infections in the HVTN703/HPTN081 trial: implications for cross-resistance.

The Antibody Mediated Prevention (AMP) trials showed that passively infused VRC01, a broadly neutralizing antibody (bNAb) targeting the CD4 binding site (CD4bs) on the HIV-1 envelope protein (Env), protected against neutralization-sensitive viruses. We identified six individuals from the VRC01 treatment arm with multi-lineage breakthrough HIV-1 infections from HVTN703, where one variant was sensitive to VRC01 (IC < 25 ug/mL) but another was resistant. By comparing Env sequences of resistant and sensitive clones from each participant, we identified sites predicted to affect VRC01 neutralization and assessed the effect of their reversion in the VRC01-resistant clone on neutralization sensitivity.

Vaccinia growth factor-dependent modulation of the mTORC1-CAD axis upon nutrient restriction.

The molecular mechanisms by which vaccinia virus (VACV), the prototypical member of the poxviridae family, reprograms host cell metabolism remain largely unexplored. Additionally, cells sense and respond to fluctuating nutrient availability, thereby modulating metabolic pathways to ensure cellular homeostasis. Understanding how VACV modulates metabolic pathways in response to nutrient signals is crucial for understanding viral replication mechanisms, with the potential for developing antiviral therapies.