Modeling cellular deformations using the level set formalism

BACKGROUND: Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM), in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. RESULTS: We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiration and show how this viscoelastic model can be incorporated into LSM simulations to recreate the observed protrusion of cells into the micropipette faithfully. We also demonstrate the use of our techniques by simulating the cell shape changes elicited by the chemotactic response to an external chemoattractant gradient. CONCLUSION: Our results provide a simple but effective means of incorporating cellular deformations into mathematical simulations of cell signaling. Such methods will be useful for simulating important cellular events such as chemotaxis and cytokinesis

Cellular development and evolution of the mammalian cerebellum

\ua9 2023, The Author(s).The expansion of the neocortex, a hallmark of mammalian evolution 1,2, was accompanied by an increase in cerebellar neuron numbers 3. However, little is known about the evolution of the cellular programmes underlying the development of the cerebellum in mammals. In this study we generated single-nucleus RNA-sequencing data for around 400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse and the marsupial opossum. We established a consensus classification of the cellular diversity in the developing mammalian cerebellum and validated it by spatial mapping in the fetal human cerebellum. Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Global transcriptome profiles, conserved cell-state markers and gene-expression trajectories across neuronal differentiation show that cerebellar cell-type-defining programmes have been overall preserved for at least 160 million years. However, we also identified many orthologous genes that gained or lost expression in cerebellar neural cell types in one of the species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level. In sum, our study unveils shared and lineage-specific gene-expression programmes governing the development of cerebellar cells and expands our understanding of mammalian brain evolution

Tracing silicate weathering processes in the permafrost-dominated Lena River watershed using lithium isotopes

Increasing global temperatures are causing widespread changes in the Arctic, including permafrost thawing and altered freshwater inputs and trace metal and carbon fluxes into the ocean and atmosphere. Changes in the permafrost active layer thickness can affect subsurface water flow-paths and water-rock interaction times, and hence weathering processes. Riverine lithium isotope ratios (reported as δ7Li) are tracers of silicate weathering that are unaffected by biological uptake, redox, carbonate weathering and primary lithology. Here we use Li isotopes to examine silicate weathering processes in one of the largest Russian Arctic rivers: the Lena River in eastern Siberia. The Lena River watershed is a large multi-lithological catchment, underlain by continuous permafrost. An extensive dataset of dissolved Li isotopic compositions of waters from the Lena River main channel, two main tributaries (the Aldan and Viliui Rivers) and a range of smaller sub-tributaries are presented from the post-spring flood/early-summer period at the onset of active layer development and enhanced water-rock interactions. The Lena River main channel (average δ7Lidiss ∼ 19‰) has a slightly lower isotopic composition than the mean global average of 23‰ (Huh et al., 1998a). The greatest range of [Li] and δ7Lidiss are observed in catchments draining the south-facing slopes of the Verkhoyansk Mountain Range. South-facing slopes in high-latitude, permafrost-dominated regions are typically characterised by increased summer insolation and higher daytime temperatures relative to other slope aspects. The increased solar radiation on south-facing catchments promotes repeated freeze-thaw cycles, and contributes to more rapid melting of snow cover, warmer soils, and increased active layer thaw depths. The greater variability in δ7Li and [Li] in the south-facing rivers likely reflect the greater infiltration of melt water and enhanced water-rock interactions within the active layer. A similar magnitude of isotopic fractionation is observed between the low-lying regions of the Central Siberian Plateau (and catchments draining into the Viliui River), and catchments draining the Verkhoyansk Mountain Range into the Aldan River. This is in contrast to global rivers in non-permafrost terrains that drain high elevations or areas of rapid uplift, where high degrees of physical erosion promote dissolution of freshly exposed primary rock typically yielding low δ7Lidiss, and low-lying regions exhibit high riverine δ7Li values resulting from greater water-rock interaction and formation of secondary mineral that fractionates Li isotopes. Overall, the range of Li concentrations and δ7Lidiss observed within the Lena River catchment are comparable to global rivers located in temperate and tropical regions. This suggests that cryogenic weathering features specific to permafrost regions (such as the continual exposure of fresh primary minerals due to seasonal freeze-thaw cycles, frost shattering and salt weathering), and climate (temperature and runoff), are not a dominant control on δ7Li variations. Despite vastly different climatic and weathering regimes, the same range of riverine δ7Li values globally suggests that the same processes govern Li geochemistry – that is, the balance between primary silicate mineral dissolution and the formation (or exchange with) secondary minerals. This has implications for the use of δ7Li as a palaeo-weathering tracer for interpreting changes in past weathering regimes

A phase I randomized therapeutic MVA-B vaccination improves the magnitude and quality of the T cell immune responses in HIV-1-infected subjects on HAART

Trial Design Previous studies suggested that poxvirus-based vaccines might be instrumental in the therapeutic HIV field. A phase I clinical trial was conducted in HIV-1-infected patients on highly active antiretroviral therapy (HAART), with CD4 T cell counts above 450 cells/mm3 and undetectable viremia. Thirty participants were randomized (2:1) to receive either 3 intramuscular injections of MVA-B vaccine (coding for clade B HIV-1 Env, Gag, Pol and Nef antigens) or placebo, followed by interruption of HAART. Methods The magnitude, breadth, quality and phenotype of the HIV-1-specific T cell response were assayed by intracellular cytokine staining (ICS) in 22 volunteers pre- and post-vaccination. Results MVA-B vaccine induced newly detected HIV-1-specific CD4 T cell responses and expanded pre-existing responses (mostly against Gag, Pol and Nef antigens) that were high in magnitude, broadly directed and showed an enhanced polyfunctionality with a T effector memory (TEM) phenotype, while maintaining the magnitude and quality of the pre-existing HIV-1- specific CD8 T cell responses. In addition, vaccination also triggered preferential CD8+ T cell polyfunctional responses to the MVA vector antigens that increase in magnitude after two and three booster doses

A systematic review of the effectiveness of art therapy delivered in school-based settings to children aged 5–12 years

Background: School-based art therapy aims to facilitate children's personal change and growth through the use of visual arts media, such as drawing, painting, sculpture, clay, or digital art. Aims: To identify and synthesise the types of school-based art therapy interventions, and appraise the effectiveness for children aged 5-12. Methods: Systematic searching through ten major electronic databases, grey literature, and contact with experts in the field. Results: Six completed and two on-going studies were identified. Art therapy was delivered to children with asthma, behavioural disorders, oppositional defiant disorders, separation anxiety disorders, learning disorders, and disruptive behaviours. All interventions were delivered over 7-25 sessions, and lasted 40-60' per session. The sample sizes ranged between 20-109 participants, involving 247 participants in total. Conclusions: Art therapy can be effective in improving children's quality of life; anxiety; self-concept; problem-solving skills, attitudes towards school; emotional and behavioural difficulties. The follow-up findings were also promising; though confirmatory evidence is needed. Implications: The risk of bias was high and unclear, highlighting the importance of following standardised reporting guidelines. Future research needs to focus on the identification of primary outcomes and measures that are tailored to art therapy interventions, and explore the (cost-) effectiveness of shorter versus longer durations of treatment

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

Drug discovery: Insights from the invertebrate Caenorhabditis elegans

Therapeutic drug development is a long, expensive, and complex process that usually takes 12–15 years. In the early phases of drug discovery, in particular, there is a growing need for animal models that ensure the reduction in both cost and time. Caenorhabditis elegans has been traditionally used to address fundamental aspects of key biological processes, such as apoptosis, aging, and gene expression regulation. During the last decade, with the advent of large-scale platforms for screenings, this invertebrate has also emerged as an essential tool in the pharmaceutical research industry to identify novel drugs and drug targets. In this review, we discuss the reasons why C. elegans has been positioned as an outstanding cost-effective option for drug discovery, highlighting both the advantages and drawbacks of this model. Particular attention is paid to the suitability of this nematode in large-scale genetic and pharmacological screenings. High-throughput screenings in C. elegans have indeed contributed to the breakthrough of a wide variety of candidate compounds involved in extensive fields including neurodegeneration, pathogen infections and metabolic disorders. The versatility of this nematode, which enables its instrumentation as a model of human diseases, is another attribute also herein underscored. As illustrative examples, we discuss the utility of C. elegans models of both human neurodegenerative diseases and parasitic nematodes in the drug discovery industry. Summing up, this review aims to demonstrate the impact of C. elegans models on the drug discovery pipeline.Fil: Giunti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Bioquímicas de Bahía Blanca. Universidad Nacional del Sur. Instituto de Investigaciones Bioquímicas de Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; ArgentinaFil: Andersen, Natalia Denise. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Bioquímicas de Bahía Blanca. Universidad Nacional del Sur. Instituto de Investigaciones Bioquímicas de Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; ArgentinaFil: Rayes, Diego Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Bioquímicas de Bahía Blanca. Universidad Nacional del Sur. Instituto de Investigaciones Bioquímicas de Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; ArgentinaFil: de Rosa, Maria Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Bioquímicas de Bahía Blanca. Universidad Nacional del Sur. Instituto de Investigaciones Bioquímicas de Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; Argentin

Salmonella Typhi-specific multifunctional CD8+ T cells play a dominant role in protection from typhoid fever in humans.

BACKGROUND: Typhoid fever, caused by the human-restricted organism Salmonella Typhi (S. Typhi), is a major public health problem worldwide. Development of novel vaccines remains imperative, but is hampered by an incomplete understanding of the immune responses that correlate with protection. METHODS: Recently, a controlled human infection model was re-established in which volunteers received ~10(3) cfu wild-type S. Typhi (Quailes strain) orally. Twenty-one volunteers were evaluated for their cell-mediated immune (CMI) responses. Ex vivo PBMC isolated before and up to 1 year after challenge were exposed to three S. Typhi-infected targets, i.e., autologous B lymphoblastoid cell-lines (B-LCL), autologous blasts and HLA-E restricted AEH B-LCL cells. CMI responses were evaluated using 14-color multiparametric flow cytometry to detect simultaneously five intracellular cytokines/chemokines (i.e., IL-17A, IL-2, IFN-g, TNF-a and MIP-1b) and a marker of degranulation/cytotoxic activity (CD107a). RESULTS: Herein we provide the first evidence that S. Typhi-specific CD8+ responses correlate with clinical outcome in humans challenged with wild-type S. Typhi. Higher multifunctional S. Typhi-specific CD8+ baseline responses were associated with protection against typhoid and delayed disease onset. Moreover, following challenge, development of typhoid fever was accompanied by decreases in circulating S. Typhi-specific CD8+ T effector/memory (TEM) with gut homing potential, suggesting migration to the site(s) of infection. In contrast, protection against disease was associated with low or no changes in circulating S. Typhi-specific TEM. CONCLUSIONS: These studies provide novel insights into the protective immune responses against typhoid disease that will aid in selection and development of new vaccine candidates