Molecular Organization Research Articles

Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex.

The molecular and cellular organization of the primate cerebellum remains poorly characterized. We obtained single-cell spatial transcriptomic atlases of macaque, marmoset, and mouse cerebella and identified primate-specific cell subtypes, including Purkinje cells and molecular-layer interneurons, that show different expression of the glutamate ionotropic receptor Delta type subunit 2 (GRID2) gene. Distinct gene expression profiles were found in anterior, posterior, and vestibular regions in all species, whereas region-selective gene expression was predominantly observed in the granular layer of primates and in the Purkinje layer of mice. Gene expression gradients in the cerebellar cortex matched well with functional connectivity gradients revealed with awake functional magnetic resonance imaging, with more lobule-specific differences between primates and mice than between two primate species. These comprehensive atlases and comparative analyses provide the basis for understanding cerebellar evolution and function.

Variation and Abundance of Resistant Starch in Selected Banana Cultivars in Uganda.

The physiochemical, structural, and molecular characteristics of starch influence its functional properties, thereby dictating its utilization. The study aimed to profile the properties and quantity of resistant starch (RS) from 15 different banana varieties, extracted using a combination of alkaline and enzyme treatments. Granular structure and molecular organization were analyzed using light microscopy, scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR). The physiochemical and functional properties were also investigated. RS content ranged from 49% to 80% without significant relationship to amylose (AM) (r = -0.1062). SEM revealed significant microarchitectural differences on the granules potentially affecting granule digestibility. FTIR and chemometrics identified differences in the crystalline peaks, yielding varying degrees of the molecular order of the RS polymers that aid in differentiating the RS sources. Despite similar solubility and swelling profiles, the pasting profiles varied across varieties, indicating high paste stability in hydrothermal processing. Clarity ranged from 43% to 93%, attributed to amylose leaching. This study highlights that RS from bananas varies in quantity, structure, and functionality, necessitating individualized approaches for processing and utilization.

Ca2+ channel and active zone protein abundance intersects with input-specific synapse organization to shape functional synaptic diversity

Synaptic heterogeneity is a hallmark of nervous systems that enables complex and adaptable communication in neural circuits. To understand circuit function, it is thus critical to determine the factors that contribute to the functional diversity of synapses. We investigated the contributions of voltage-gated calcium channel (VGCC) abundance, spatial organization, and subunit composition to synapse diversity among and between synapses formed by two closely related Drosophila glutamatergic motor neurons with distinct neurotransmitter release probabilities (Pr). Surprisingly, VGCC levels are highly predictive of heterogeneous Pr among individual synapses of either low- or high-Pr inputs, but not between inputs. We find that the same number of VGCCs are more densely organized at high-Pr synapses, consistent with tighter VGCC-synaptic vesicle coupling. We generated endogenously tagged lines to investigate VGCC subunits in vivo and found that the α2δ–3 subunit Straightjacket along with the CAST/ELKS active zone (AZ) protein Bruchpilot, both key regulators of VGCCs, are less abundant at high-Pr inputs, yet positively correlate with Pr among synapses formed by either input. Consistently, both Straightjacket and Bruchpilot levels are dynamically increased across AZs of both inputs when neurotransmitter release is potentiated to maintain stable communication following glutamate receptor inhibition. Together, these findings suggest a model in which VGCC and AZ protein abundance intersects with input-specific spatial and molecular organization to shape the functional diversity of synapses.

Ca2+ channel and active zone protein abundance intersects with input-specific synapse organization to shape functional synaptic diversity.

Synaptic heterogeneity is a hallmark of nervous systems that enables complex and adaptable communication in neural circuits. To understand circuit function, it is thus critical to determine the factors that contribute to the functional diversity of synapses. We investigated the contributions of voltage-gated calcium channel (VGCC) abundance, spatial organization, and subunit composition to synapse diversity among and between synapses formed by two closely related Drosophila glutamatergic motor neurons with distinct neurotransmitter release probabilities (Pr). Surprisingly, VGCC levels are highly predictive of heterogeneous Pr among individual synapses of either low- or high-Pr inputs, but not between inputs. We find that the same number of VGCCs are more densely organized at high-Pr synapses, consistent with tighter VGCC-synaptic vesicle coupling. We generated endogenously tagged lines to investigate VGCC subunits in vivo and found that the α2δ-3 subunit Straightjacket along with the CAST/ELKS active zone (AZ) protein Bruchpilot, both key regulators of VGCCs, are less abundant at high-Pr inputs, yet positively correlate with Pr among synapses formed by either input. Consistently, both Straightjacket and Bruchpilot levels are dynamically increased across AZs of both inputs when neurotransmitter release is potentiated to maintain stable communication following glutamate receptor inhibition. Together, these findings suggest a model in which VGCC and AZ protein abundance intersects with input-specific spatial and molecular organization to shape the functional diversity of synapses.

Regional patterns of human cortex development correlate with underlying neurobiology

Human brain morphology undergoes complex changes over the lifespan. Despite recent progress in tracking brain development via normative models, current knowledge of underlying biological mechanisms is highly limited. We demonstrate that human cortical thickness development and aging trajectories unfold along patterns of molecular and cellular brain organization, traceable from population-level to individual developmental trajectories. During childhood and adolescence, cortex-wide spatial distributions of dopaminergic receptors, inhibitory neurons, glial cell populations, and brain-metabolic features explain up to 50% of the variance associated with a lifespan model of regional cortical thickness trajectories. In contrast, modeled cortical thickness change patterns during adulthood are best explained by cholinergic and glutamatergic neurotransmitter receptor and transporter distributions. These relationships are supported by developmental gene expression trajectories and translate to individual longitudinal data from over 8000 adolescents, explaining up to 59% of developmental change at cohort- and 18% at single-subject level. Integrating neurobiological brain atlases with normative modeling and population neuroimaging provides a biologically meaningful path to understand brain development and aging in living humans.

Polarized ATR-FTIR studies of DPPC/DPPG lipid bilayers doped with PLL

The structural characterization of lipid bilayers is crucial for understanding various biological processes and designing effective systems of drugs. Attenuated Total Reflection Fourier Transformed Infrared (ATR-FTIR) spectroscopy is a powerful technique for probing lipid membrane properties, but conventional methods face challenges in discerning molecular orientation and intermolecular interactions. The polarized ATR-FTIR spectroscopy combined with Principal Component Analysis (PCA) was used to investigate the interactions between positively charged peptide (poly-L-lysine (PLL)) and anionic lipid bilayers (dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylglycerol, DPPC/DPPG). This integrated approach offers deeper insight into mutual interactions between proteins and lipids of membrane, providing a comprehensive understanding of structure of both protein and lipid bilayers components. The findings of this study shed light on the orientational order of lipid molecules in DPPC/DPPG membrane structure as well as secondary strictures of PPL peptides. It was shown that the presence of PLL peptide disrupts lipid molecule ordering within the lipid bilayer, primarily through electrostatic and H-bond interactions. The utility of polarized ATR-FTIR spectroscopy supported by PCA calculations in elucidating molecular organizations within complex membrane systems is emphasized.

Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view.

Spatial transcriptomic techniques offer unprecedented insights into the molecular organization of complex tissues. However, integrating cost-effectiveness, high throughput, a wide field of view and compatibility with three-dimensional (3D) volumes has been challenging. Here we introduce microfluidics-assisted grid chips for spatial transcriptome sequencing (MAGIC-seq), a new method that combines carbodiimide chemistry, spatial combinatorial indexing and innovative microfluidics design. This technique allows sensitive and reproducible profiling of diverse tissue types, achieving an eightfold increase in throughput, minimal cost and reduced batch effects. MAGIC-seq breaks conventional microfluidics limits by enhancing barcoding efficiency and enables analysis of whole postnatal mouse sections, providing comprehensive cellular structure elucidation at near single-cell resolution, uncovering transcriptional variations and dynamic trajectories of mouse organogenesis. Our 3D transcriptomic atlas of the developing mouse brain, consisting of 93 sections, reveals the molecular and cellular landscape, serving as a valuable resource for neuroscience and developmental biology. Overall, MAGIC-seq is a high-throughput, cost-effective, large field of view and versatile method for spatial transcriptomic studies.

Molecular, Cellular, and Developmental Organization of the Mouse Vomeronasal organ at Single Cell Resolution.

We have generated single cell transcriptomic atlases of vomeronasal organs (VNO) from juvenile and adult mice. Combined with spatial molecular imaging, we uncover a distinct, previously unidentified class of cells that express the vomeronasal receptors and a population of canonical olfactory sensory neurons in the VNO. High resolution trajectory and cluster analyses reveal the lineage relationship, spatial distribution of cell types, and a putative cascade of molecular events that specify the V1r, V2r, and OR lineages from a common stem cell population. The expression of vomeronasal and olfactory receptors follow power law distributions, but there is high variability in average expression levels between individual receptor and cell types. Substantial co-expression is found between receptors across clades, from different classes, and between olfactory and vomeronasal receptors, with nearly half from pairs located on the same chromosome. Interestingly, the expression of V2r, but not V1r, genes is associated with various transcription factors, suggesting distinct mechanisms of receptor choice associated with the two cell types. We identify association between transcription factors, surface axon guidance molecules, and individual VRs, thereby uncovering a molecular code that guides the specification of the vomeronasal circuitry. Our study provides a wealth of data on the development and organization of the accessory olfactory system at both cellular and molecular levels to enable a deeper understanding of vomeronasal system function.

Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.

Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this 'leaflet replacement' model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40-70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.

Protective Effect of Quercetin on Amyloid-Induced Alterations in Lipid Bilayer Integrity

The present study employs molecular dynamics simulations to investigate the interactions between quercetin, amyloid fibrils, and POPC lipid bilayers. The results demonstrate that quercetin does not significantly affect the molecular organization of the bilayer, while IAPP fibrils induce substantial structural changes, particularly in the outer monolayer. Quercetin mitigates these effects by reducing the impact on headgroup and glycerol regions and causing a more superficial positioning of IAPP. Additionally, quercetin slightly decreases the order of sn-2 acyl chains, indicating a disordering effect. In a ternary system with POPC, quercetin, and IAPP, the reduction in the deuterium order parameter of sn-2 acyl chains is less pronounced, underscoring quercetin's protective role. Unlike IAPP, ApoAI and insulin fibrils undergo significant structural reorganization in the membrane-bound state. Quercetin attenuative effects are observed only with ApoAI, highlighting its potential as a protective agent against amyloid-induced membrane disruption. These findings provide valuable insights into the interactions between polyphenols, amyloid fibrils, and lipid membranes, contributing to the understanding of membrane-associated amyloid pathologies.

Selective disruption of synaptic NMDA receptors of the hippocampal trisynaptic circuit in Aβ pathology

Synaptic dysfunction is an early feature in Alzheimer’s disease (AD) pathogenesis and a major morphological correlate of memory deficits. Given the main synaptic location of N-methyl-D-aspartate receptors (NMDARs), their dysregulation has been implicated in these pathological effects. Here, to detect possible alterations in the expression and synaptic localisation of the GluN1 subunit in the brain of amyloidogenic APP/PS1 mice, we employed histoblot and SDS-digested freeze-fracture replica labelling (SDS-FRL) techniques. Histoblots showed that GluN1 expression was significantly reduced in the hippocampus in a layer-dependent manner, in the cortex and the caudate putamen of APP/PS1 transgenic mice at 12 months of age but was unaltered at 1 and 6 months. Using quantitative SDS-FRL, we unravelled the molecular organisation of GluN1 in seven excitatory synapse populations at a high spatial resolution in the CA1 and CA3 fields and the DG of the hippocampus in 12-month-old APP/PS1 mice. In the CA1 field, the labelling density for GluN1 in the excitatory synapses established on spines and interneurons, was significantly reduced in APP/PS1 mice compared to age-matched wild-type mice in the stratum lacunosum-moleculare but unaltered in the stratum radiatum. In the CA3 field, synaptic GluN1 was reduced in mossy fibre-CA3 pyramidal cell synapses but unaltered in the A/C-CA3 pyramidal cell synapses. In the DG, the density of GluN1 in granule cell-perforant pathway synapses was reduced in APP/PS1 mice. Altogether, our findings provide evidence of specific alterations of synaptic GluN1 in the trisynaptic circuit of the hippocampus in Aβ pathology. This differential vulnerability in the disruption of NMDARs may be involved in the mechanisms causing abnormal network activity of the hippocampal circuit and cognitive impairment characteristic of APP/PS1 mice.

Ultraplex microscopy: versatile highly-multiplexed molecular labeling and imaging across scale and resolution.

The molecular organization of cells and tissue is challenging to study due to the inefficiency of multiplexed molecular labeling methods and the limited options for combining microscopy modalities in a single specimen, especially when high spatial resolution is needed. Here we describe ultraplex microscopy, which combines serial multiplexing, ultrathin sectioning, and reversible embedding to circumvent incompatibilities between labeling and imaging techniques, enhance resolution, and expand multiplexing capacity within and across modalities. Samples can be labeled with antibodies, RNA probes, and tissue stains for imaging by brightfield, epifluorescence, super-resolution, and electron microscopy without specialized reagents or materials. We demonstrate applications in brain tissue including molecular profiling of single cells and axonal boutons, high-resolution molecular colocalization, and correlative imaging of fluorescent proteins with confocal and ultraplex microscopy. The power and versatility of ultraplex microscopy will be valuable in addressing currently intractable experimental questions in many systems and contexts.

Regional patterns of human cortex development correlate with underlying neurobiology.

Human brain morphology undergoes complex changes over the lifespan. Despite recent progress in tracking brain development via normative models, current knowledge of underlying biological mechanisms is highly limited. We demonstrate that human cortical thickness development and aging trajectories unfold along patterns of molecular and cellular brain organization, traceable from population-level to individual developmental trajectories. During childhood and adolescence, cortex-wide spatial distributions of dopaminergic receptors, inhibitory neurons, glial cell populations, and brain-metabolic features explain up to 50% of variance associated with a lifespan model of regional cortical thickness trajectories. In contrast, modeled cortical thickness change patterns during adulthood are best explained by cholinergic and glutamatergic neurotransmitter receptor and transporter distributions. These relationships are supported by developmental gene expression trajectories and translate to individual longitudinal data from over 8,000 adolescents, explaining up to 59% of developmental change at cohort- and 18% at single-subject level. Integrating neurobiological brain atlases with normative modeling and population neuroimaging provides a biologically meaningful path to understand brain development and aging in living humans.

Facile preparation and study of supramolecular architecture of an efficient nanocomposite LB film AHSM/SA based on azo-functionalized hockey stick-shaped mesogen at air-water and air-solid interface

Hockey stick-shaped mesogens are fascinating thermotropic liquid crystal systems owing to their exceptional supramolecular assembly properties and shape anisotropy compared to conventional rod-and bent-shaped mesogens. In this article, we present an investigation of the supramolecular organization of a new azo-functionalized hockey stick-shaped mesogen with stearic acid at the air-water interface and air-solid interfaces by applying the Langmuir-Blodgett film deposition method. The incorporation of stearic acid can change the molecular organization of azo-functionalized hockey stick-shaped mesogen at an aqueous interface through hydrophobic-hydrophobic interactions and form a supramolecular nanostructure at the solid interface. The interfacial nature of the Langmuir monolayer was studied by recording the isotherm (surface pressure area, π–A), which was further analyzed by using Brewster angle microscopy. The significant reduction in molecular area, increased surface pressure, and lower isotherm slope of the AHSM/SA composite mixture indicate the hybrid AHSM/SA monolayer's greater stability compared to pure AHSM. BAM images of the AHSM/SA composite signify nanostructure aggregates formed by the interaction of AHSM and SA molecules at the air-water interface. Field emission scanning electron microscopic analysis of composite films revealed the formation of supramolecular domains. The impact of changing the surface pressure and the number of depositions on the morphology of the composite film surface was monitored using field emission scanning electron microscopy. The supramolecular H-type aggregation of azo-functionalized hockey stick-shaped mesogen and stearic acid molecules in the composite LB film was characterized using UV–visible absorption and steady-state fluorescence spectroscopy. The adsorption of stearic acid onto azo-functionalized hockey stick-shaped mesogen via hydrophobic interactions was confirmed by Fourier transform infrared spectroscopy of the composite Langmuir Blodgett film. Further, Raman spectroscopy of the LB films of the AHSM/SA composites is distinct from the pristine film components due to the merging of signals at similar wave numbers for both SA and AHSM with a lack of typical packing pattern further supported by PXRD studies of the films.

The desmosome comes into focus.

The desmosome is a cell-cell adhesive junction that provides integrity and mechanical resistance to tissues through its attachment to the intermediate filament cytoskeleton. Defects in desmosomes cause diseases impacting the heart, epidermis, and other epithelia. In this review, we provide a historical perspective on the discovery of the desmosome and how the evolution of cellular imaging technologies revealed insights into desmosome structure and function. We also discuss recent findings using contemporary imaging approaches that have informed the molecular order, three-dimensional architecture, and associations of desmosomes with organelles such as the endoplasmic reticulum. Finally, we provide an updated model of desmosome molecular organization and speculate upon novel functions of this cell junction as a signaling center for sensing mechanical and other forms of cell stress.

Optics-free Spatial Genomics for Mapping Mouse Brain Aging.

Spatial transcriptomics has revolutionized our understanding of cellular network dynamics in aging and disease by enabling the mapping of molecular and cellular organization across various anatomical locations. Despite these advances, current methods face significant challenges in throughput and cost, limiting their utility for comprehensive studies. To address these limitations, we introduce IRISeq (Imaging Reconstruction using Indexed Sequencing), a optics-free spatial transcriptomics platform that eliminates the need for predefined capture arrays or extensive imaging, allowing for the rapid and cost-effective processing of multiple tissue sections simultaneously. Its capacity to reconstruct images based solely on sequencing local DNA interactions allows for profiling of tissues without size constraints and across varied resolutions. Applying IRISeq, we examined gene expression and cellular dynamics in thirty brain regions of both adult and aged mice, uncovering region-specific changes in gene expression associated with aging. Further cell type-centric analysis further identified age-related cell subtypes and intricate changes in cell interactions that are distinct to certain spatial niches, emphasizing the unique aspects of aging in different brain regions. The affordability and simplicity of IRISeq position it as a versatile tool for mapping region-specific gene expression and cellular interactions across various biological systems.

CS and ZnO Nanoparticles as Fungicides against Potato Fungal Pathogens Alternaria solani and Fusarium solani. Mechanism Underlining Their Antifungal Activity

Fusarium solani (F. solani) and Alternaria solani (A. solani) are among the most destructive pathogenic fungi affecting potatoes, causing significant crop losses in both field and post-harvest conditions. Current control relies heavily on synthetic fungicides which pose serious environmental and health risks. Therefore, there is a growing need to find efficient and environmentally friendly alternatives to combat fungal infections in potatoes. This study offers chitosan (CS) and zinc oxide (ZnO) nanoparticles (NPs) as potential fungicides against A. solani and F. solani. We evaluated their antifungal properties and elucidated the mechanism underlining their activity. Our results revealed that both CS and ZnO NPs exhibited pronounced antifungal activity against the two pathogenic strains by effectively inhibiting the mycelium growth. Furthermore, we discovered that the activity of the NPs involved the induction of oxidative stress in fungal cells and changes in the molecular organization of their membranes.

Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme

Most bacterial, plant and fungal cells possess at their surface a protective layer called the cell wall, conferring strength, plasticity and rigidity to withstand the osmotic pressure. This molecular barrier is crucial for pathogenic microorganisms, as it protects the cell from the local environment and often constitutes the first structural component encountered in the host-pathogen interaction. In pathogenic molds and yeasts, the cell wall constitutes the main target for the development of clinically-relevant antifungal drugs. In the past decade, solid-state NMR has emerged as a powerful analytical technique to investigate the molecular organization of microbial cell walls in the context of intact cells. 13C NMR chemical shift is an exquisite source of information to identify the polysaccharides present in the cell wall, and two-dimensional 13C–13C correlation experiments provide an efficient tool to rapidly access the polysaccharide composition in whole cells. Here we investigate the use of the adiabatic DREAM (for dipolar recoupling enhancement through amplitude modulation) recoupling scheme to improve solid-state NMR analysis of polysaccharides in intact cells. We demonstrate the advantages of two-dimensional 13C–13C experiments using the DREAM recoupling scheme. We report the spectral editing of polysaccharide signals by varying the radio-frequency carrier position. We provide practical considerations for the implementation of DREAM experiments to characterize polysaccharides in whole cells. We demonstrate the approach on intact fungal cells of Neurospora crassa and Aspergillus fumigatus, a model and a pathogenic filamentous fungus, respectively. The approach could be envisioned to efficiently reduce the spectral crowding of more complex cell surfaces, such as cell wall and peptidoglycan in bacteria.

Transcriptomic analysis of the human habenula in schizophrenia.

Transcriptomic analysis of the human habenula and identification of molecular changes associated with schizophrenia risk and illness state.

Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex.

The relation of astrocytic endfeet to the vasculature plays a key functional role in the neuro-glia-vasculature unit. We characterize the spatial organization of astrocytes and the structural aspects that facilitate their involvement in molecular exchanges. Using double transgenic mice, we performed co-immunostaining, confocal microscopy, and three-dimensional digital segmentation to investigate the biophysical and molecular organization of astrocytes and their intricate endfoot network at the micrometer level in the isocortex and hippocampus. The results showed that hippocampal astrocytes had smaller territories, reduced endfoot dimensions, and fewer contacts with blood vessels compared with those in the isocortex. Additionally, we found that both connexins 43 and 30 have a higher density in the endfoot and the former is overexpressed relative to the latter. However, due to the limitations of the method, further studies are needed to determine the exact localization on the endfoot. The quantitative information obtained in this study will be useful for modeling the interactions of astrocytes with the vasculature.