Regional Subpopulations Research Articles

Landscape of epithelial cell subpopulations in the human esophageal squamous cell carcinoma microenvironment

AimsWe sought to reveal the landscape of epithelial cell subpopulations in the human esophageal squamous cell carcinoma microenvironment and investigate their parts on esophageal squamous carcinoma (ESCC) development. BackgroundEpithelial cells play an important role in the occurrence and development of ESCC through multiple mechanisms. While the landscape of epithelial cell subpopulations in ESCC, remains unclear. ObjectiveExploring the role of epithelial cell subpopulations in ESCC progression. MethodsSeurat R package was used for single-cell RNA sequencing (scRNA-seq) data filtering, dimensionality reduction, clustering and differentially expressed genes analysis. Cellmarker database was adopted for cell cluster annotation. Functional enrichment analysis was carried out by Gene Ontology (GO) analysis. InferCNV package was conducted for copy number variation (CNV) of epithelial cell subpopulations in all chromosomal regions. Pseudotime trajectory analysis was implemented for exploring differentiation trajectory of epithelial cells subgroups during the cancer progression. CellChat analysis was used for probing the interactions between epithelial cells and NK/T cells. cellular experiments were performed using Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR), Wound-Healing Assay and transwell. Results11 major cell subpopulations were identified in ESCC and adjunct tissues. Further reclassification of epithelial cells uncovered 4 subpopulations. Enrichment analysis revealed that highly expressed genes in 4 epithelial cell subpopulations were related to cell proliferation, immune response and angiogenesis. CNV analysis found that UBD + epithelial cells and GAS2L3+ epithelial cells had a higher proportion of CNV. Cell differentiation trajectories disclosed that KRT6C+ and GSTA1+ epithelial cells were in an intermediate state of differentiation, while UBD+ and GAS2L3+ epithelial cells are in an end state of differentiation during ESCC progression. Finally, we found that four epithelial cell subpopulations all inhibited NK/T cells through NECTIN2-TIGIT and CLEC2B-KLRB1. Low ATF3 and DDIT3 mRNA expression inhibited ESCC cell migration and invasion. ConclusionHere, we obtained a through epithelial cell atlas of ESCC at single-cell resolution, explored the role of epithelial cell in ESCC progression, and unveiled immunosuppressive signals to NK/T cells in promoting ESCC. Our findings expand the comprehension of epithelial cells and offer a theoretical guidance for future anti-epithelial cell treatment of ESCC.

Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early Drosophila embryo.

The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3398 and 3433 were differentially regulated, respectively. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail, and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo.

Comprehensive analysis of root canal morphology in maxillary premolars among the Pakistani subpopulation: a CBCT-based study

BackgroundUnderstanding the root canal morphology is essential for the success of root canal treatment. Therefore, this study aimed to evaluate and analyze the root canal configuration of maxillary premolars using Cone Beam Computed Tomography in the Pakistani subpopulation.MethodThis cross-sectional study utilized CBCT scans from two distinct centres: Aga Khan University in Karachi and Jinnah MRI and Body Scans in Lahore. The CBCT images were visualized using GALAXIS version 1.9 (SICAT GmbH and Co. KG, Bonn, Germany), integrated within the Sirona Dental System (D-64625 Bensheim, Germany). The scanning parameters were standardized at 85 kV, 7 mA, with a 15-s exposure time and a voxel size of 0.16 mm. A total of 707 CBCT scans were collected, encompassing 2180 maxillary premolars. Root canal configurations were classified based on (Ahmed et al. Int Endod J. 2017;50(8):761–70). Statistical analyses were performed using SPSS version 26, employing the Chi-square test with a significance level set at p < 0.05.ResultsThe distribution of root canal morphologies varied significantly with age and gender. Among maxillary premolars, 50% exhibited the typical configuration of 2MPMB1 L1 (two roots, single canal in each buccal and lingual root), while 26% of maxillary right second premolars displayed 1MPM1 (one root, one canal). Overall, 1MPM1 accounted for 27.4% of the total cases in the second premolars. There was no statistically significant relationship between age and root canal distribution in either first premolars (p = 0.338) or second premolars (p = 0.833). Regarding gender, a significant difference was observed in the distribution of right maxillary 1st premolars (p = 0.022*), with a higher prevalence among females.ConclusionThis study offers significant insights into the anatomical variations of root canals in maxillary premolars across diverse regional subpopulations in Pakistan. While specific root canal configurations were prevalent, the findings indicate no statistically significant correlation between age and root canal morphology in maxillary premolars. However, a notable gender disparity was observed in the distribution of the right maxillary first premolars.

Prolonged viral shedding in an immunocompromised Korean patient infected with hMPXV, sub-lineage B.1.3, with acquired drug resistant mutations during tecovirimat treatment.

Following the worldwide surge in mpox (monkeypox) in 2022, cases have persisted in Asia, including South Korea, and sexual contact is presumed as the predominant mode of transmission, with a discernible surge in prevalence among immunocompromised patients. Drugs such as tecovirimat can result in drug-resistant mutations, presenting obstacles to treatment. This study aimed to ascertain the presence of tecovirimat-related resistant mutations through genomic analysis of the monkeypox virus isolated from a reported case involving prolonged viral shedding in South Korea. Here, tecovirimat-resistant mutations, previously identified in the B.1 clade, were observed in the B.1.3 clade, predominant in South Korea. These mutations exhibited diverse patterns across different samples from the same patient and reflected the varied distribution of viral subpopulations in different anatomical regions. The A290V and A288P mutant strains we isolated hold promise for elucidating these mechanisms, enabling a comprehensive analysis of viral pathogenesis, replication strategies, and host interactions. Our findings imply that acquired drug-resistant mutations, may present a challenge to individual patient treatment. Moreover, they have the potential to give rise to transmitted drug-resistant mutations, thereby imposing a burden on the public health system. Consequently, the meticulous genomic surveillance among immunocompromised patients, conducted in this research, assumes paramount importance.

Genetic Diversity and Virulence Variation of Metarhizium rileyi from Infected Spodoptera frugiperda in Corn Fields.

Metarhizium rileyi is an entomopathogenic fungus that naturally infects the larvae of Spodoptera frugiperda, and has biocontrol potential. To explore more natural entomopathogenic fungi resources, a total of 31 strains were isolated from 13 prefectures in Yunnan Province. All the strains were identified using morphology and molecular biology. The genetic diversity of the 31 isolates of M. rileyi was analyzed using inter-simple sequence repeat (ISSR) techniques. Seven primers with good polymorphism were selected, and fifty-four distinct amplification sites were obtained by polymerase chain reaction amplification. Among them, 50 were polymorphic sites, and the percentage of polymorphic sites was 94.44%. The thirty-one strains were divided into eight subpopulations according to the regions. The Nei's gene diversity was 0.2945, and the Shannon information index was 0.4574, indicating that M. rileyi had rich genetic diversity. The average total genetic diversity of the subpopulations in the different regions was 0.2962, the gene diversity within the populations was 0.1931, the genetic differentiation coefficient was 0.3482 (>0.25), and the gene flow was 0.9360 (<1). The individual cluster analysis showed that there was no obvious correlation between the genetic diversity of the strains and their geographical origin, which also indicated that the virulence of the strains was not related to their phylogeny. Thus, the genetic distance of the different populations of M. rileyi in Yunnan Province was not related to the geographical distance. The virulence of those 32 strains against the 3rd-instar larvae of S. frugiperda were varied with the differences in geographical locations. On the 10th day of inoculation, seventeen strains had an insect mortality rate of 70.0%, and seven strains had an insect mortality rate of 100%. The half-lethal times of the M. rileyi SZCY201010, XSBN200920, and MDXZ200803 strains against the S. frugiperda larvae were less than 4 d. Thus, they have the potential to be developed into fungal insecticidal agents.

Role of PDGFRA+ cells and a CD55+ PDGFRALo fraction in the gastric mesenchymal niche

PDGFRA-expressing mesenchyme supports intestinal stem cells. Stomach epithelia have related niche dependencies, but their enabling mesenchymal cell populations are unknown, in part because previous studies pooled the gastric antrum and corpus. Our high-resolution imaging, transcriptional profiling, and organoid assays identify regional subpopulations and supportive capacities of purified mouse corpus and antral PDGFRA+ cells. Sub-epithelial PDGFRAHi myofibroblasts are principal sources of BMP ligands and two molecularly distinct pools distribute asymmetrically along antral glands but together fail to support epithelial growth in vitro. In contrast, PDGFRALo CD55+ cells strategically positioned beneath gastric glands promote epithelial expansion in the absence of other cells or factors. This population encompasses a small fraction expressing the BMP antagonist Grem1. Although Grem1+ cell ablation in vivo impairs intestinal stem cells, gastric stem cells are spared, implying that CD55+ cell activity in epithelial self-renewal derives from other subpopulations. Our findings shed light on spatial, molecular, and functional organization of gastric mesenchyme and the spectrum of signaling sources for epithelial support.

Sex-dependent endozepinergic regulation of ventromedial hypothalamic nucleus glucose counter-regulatory neuron aromatase protein expression in the adult rat

The hypothalamic brain cell types that produce estradiol from testosterone remain unclear. Aromatase inhibition affects ventromedial hypothalamic nucleus (VMN) glucose-stimulatory nitric oxide (NO) and glucose-inhibitory γ-aminobutyric acid (GABA) transmission during insulin (INS)-induced hypoglycemia (IIH). Pure GABA and NO nerve cell samples acquired by laser-catapult-microdissection from consecutive rostro-caudal segments of the VMN were analyzed by Western blot to investigate whether regional subpopulations of each cell type contain machinery for neuro-estradiol synthesis. Astrocyte endozepinergic signaling governs brain steroidogenesis. Pharmacological tools were used here to determine if the glio-peptide octadecaneuropeptide (ODN) controls aromatase expression in GABA and NO neurons during eu- and/or hypoglycemia. Intracerebroventricular administration of the ODN G-protein coupled-receptor antagonist cyclo(1−8)[DLeu5]OP (LV-1075) decreased (male) or enhanced (female) VMN GABAergic neuron aromatase expression, but increased or reduced this profile in nitrergic neurons in a region-specific manner in each sex. IIH suppressed aromatase levels in GABA neurons located in the middle segment of the male VMN or distributed throughout this nucleus in the female. This inhibitory response was altered by the ODN isoactive surrogate octapeptide (OP) in female, but was refractory to OP in male. NO neuron aromatase protein in hypoglycemic male (middle and caudal VMN) and female (rostral and caudal VMN) rats, but was normalized in OP- plus INS-treated rats of both sexes. Results provide novel evidence that VMN glucose-regulatory neurons may produce neuro-estradiol, and that the astrocyte endozepine transmitter ODN may impose sex-specific control of baseline and/or hypoglycemic patterns of aromatase expression in distinct subsets of nitrergic and GABAergic neurons in this neural structure.

Cellular Diversity in Human Subgenual Anterior Cingulate and Dorsolateral Prefrontal Cortex by Single-Nucleus RNA-Sequencing.

Regional cellular heterogeneity is a fundamental feature of the human neocortex; however, details of this heterogeneity are still undefined. We used single-nucleus RNA-sequencing to examine cell-specific transcriptional features in the dorsolateral PFC (DLPFC) and the subgenual anterior cingulate cortex (sgACC), regions implicated in major psychiatric disorders. Droplet-based nuclei-capture and library preparation were performed on replicate samples from 8 male donors without history of psychiatric or neurologic disorder. Unsupervised clustering identified major neural cell classes. Subsequent iterative clustering of neurons further revealed 20 excitatory and 22 inhibitory subclasses. Inhibitory cells were consistently more abundant in the sgACC and excitatory neuron subclusters exhibited considerable variability across brain regions. Excitatory cell subclasses also exhibited greater within-class transcriptional differences between the two regions. We used these molecular definitions to determine which cell classes might be enriched in loci carrying a genetic signal in genome-wide association studies or for differentially expressed genes in mental illness. We found that the heritable signals of psychiatric disorders were enriched in neurons and that, while the gene expression changes detected in bulk-RNA-sequencing studies were dominated by glial cells, some alterations could be identified in specific classes of excitatory and inhibitory neurons. Intriguingly, only two excitatory cell classes exhibited concomitant region-specific enrichment for both genome-wide association study loci and transcriptional dysregulation. In sum, by detailing the molecular and cellular diversity of the DLPFC and sgACC, we were able to generate hypotheses on regional and cell-specific dysfunctions that may contribute to the development of mental illness.SIGNIFICANCE STATEMENT Dysfunction of the subgenual anterior cingulate cortex has been implicated in mood disorders, particularly major depressive disorder, and the dorsolateral PFC, a subsection of the PFC involved in executive functioning, has been implicated in schizophrenia. Understanding the cellular composition of these regions is critical to elucidating the neurobiology underlying psychiatric and neurologic disorders. We studied cell type diversity of the subgenual anterior cingulate cortex and dorsolateral PFC of humans with no neuropsychiatric illness using a clustering analysis of single-nuclei RNA-sequencing data. Defining the transcriptomic profile of cellular subpopulations in these cortical regions is a first step to demystifying the cellular and molecular pathways involved in psychiatric disorders.

Genetic Relationships of Puccinia striiformis f. sp. tritici in Southwestern and Northwestern China.

ABSTRACTWheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China.IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

Potential global distribution of a temperate marine coastal predator: The role of barriers and dispersal corridors on subpopulation connectivity

AbstractPredicting the potential distribution of species and possible dispersal corridors at a global scale can contribute to better understanding the availability of suitable habitat to move between, and the potential connectivity between regional distributions. Such information increases knowledge of ecological and biogeographic processes, but also has management applications at a global scale, for example, for estimating the restocking ability of exploited regional subpopulations. As a case study, we tested the utility of environmental niche modeling to investigate the potential global distribution of a highly mobile temperate marine coastal species, the broadnose sevengill shark (Notorynchus cepedianus). First, we characterized and compared three model variants using global data and regional data from two geographically distant and genetically diverging subpopulations in the Southwest Atlantic and southern Australia. The best performing model was then transferred to the rest of the world to obtain a final global prediction for the species. Predictions revealed broad suitable areas across temperate regions of the Northern and Southern Hemispheres. As a final step, we overlaid underwater seamount data on suitability maps to simulate possible dispersal corridors and regional connectivity. Global subpopulation connectivity and dispersal are discussed in the light of recent genetic evidence, to help explain why unoccupied suitable areas are not currently accessed by the species. This study highlights the potential use of global and regional data for the assessment of habitat suitability of species at a global scale, and provides considerations when applying these models to other highly mobile species.

Diversity of the MHC class II DRB gene in the wolverine (Carnivora: Mustelidae: Gulo gulo) in Finland.

The wolverine (Gulo gulo) in Finland has undergone significant population declines in the past. Since major histocompatibility complex (MHC) genes encode proteins involved in pathogen recognition, the diversity of these genes provides insights into the immunological fitness of regional populations. We sequenced 862 amplicons (242 bp) of MHC class II DRB exon 2 from 32 Finnish wolverines and identified 11 functional alleles and three pseudogenes. A molecular phylogenetic analysis indicated trans-species polymorphism, and PAML and MEME analyses indicated positive selection, suggesting that the Finnish wolverine DRB genes have evolved under balancing and positive selection. In contrast to DRB gene analyses in other species, allele frequencies in the Finnish wolverines clearly indicated the existence of two regional subpopulations, congruent with previous studies based on neutral genetic markers. In the Finnish wolverine, rapid population declines in the past have promoted genetic drift, resulting in a lower genetic diversity of DRB loci, including fewer alleles and positively selected sites, than other mustelid species analyzed previously. Our data suggest that the MHC region in the Finnish wolverine population was likely affected by a recent bottleneck.

2D Geometric Morphometric Shape Analysis of Casuarius casuarius(Aves: Paleognathae) Cranial Casques

Many vertebrates (e.g., chameleons, bovids, hornbills) possess cranial elaborations; however, studies investigating the morphological variation of these structures are rare. For example, the conspicuous cranial casques of modern cassowaries have long been hypothesized to perform a number of functions (e.g., physical ramming, vocalization, thermoregulation, visual display) despite an absence of quantitative methodologies to determine whether ornament shape variation within the group aligns with proposed biological roles. In order to fill this data gap, we compared casque shape between sexes and native geographic regions in a large sample of adult southern cassowaries (Casuarius casuarius; n = 103). We quantified casque shape in lateral and rostral views using elliptical Fourier analysis, ordinated the shape data, and used multivariate analysis of variance to address specific comparisons. We hypothesized that casques would be sexually dimorphic and regionally specific, consistent with proposed display functions. However, we found no significant differences in casque shape between female and male C. casuariusand few significant shape differences between individuals from specific geographical areas. Much of the intraspecific casque shape variation, particularly from the rostral aspect, is due to asymmetries across the midline. In our sample, casques were 77.5% rightward deviating, 20.7% leftward deviating, and 1.8% non‐deviating. Although it is unclear if this directional casque asymmetry provides a functional advantage, future studies may elucidate this feature. Altogether, two‐dimensional shape analysis does not support a role for the casque as a de factodiscriminator between sexes nor regional sub‐populations in C. casuarius. These findings stand in contrast to those of other ornamented birds (e.g., Numida meleagris) and potentially point towards alternative biological functions.

Role of Cortical Dopamine circuits in regulating Striatal Dopamine dynamics during Reversal Learning

Dopamine is a catecholamine neuromodulator implicated in locomotion, motivation, learning and cognitive behaviors. Although striatal dopamine signaling and circuitry are well established, the role of cortical dopamine projection circuitry in regulating striatal dopamine dynamics and behavior is not clear. Glutamatergic pyramidal neurons in the prefrontal cortex (PFC) are topographically organized and dopamine D1 and D2 receptors are expressed on glutamatergic pyramidal neurons in the PFC. Using a retrograde adeno‐associated virus (AAVRG)‐based approach we show that D1R+ subpopulations in medial orbitofrontal or prelimbic regions project to nucleus accumbens core (NAcc) or dorsal striatum (dSTR), respectively. However, D2R+ subpopulations in medial orbitofrontal, or medial prelimbic PFC, project to NAcc or the midbrain (SNpc/VTA) but not dSTR, respectively. Additionally, D1R+ and D2R+ medial orbitofrontal subpopulations have indirect connections to the medial SNpc through the NAcc core. We next wanted to test which of these topographically organized circuits regulate striatal dopamine dynamics during reversal learning. We used fiber photometry to measure striatal dopamine dynamics in the dorsomedial striatum (DMS) during reversal learning. We were able to measure reward prediction error (RPE) like responses in the DMS during reversal learning. We will next use an intersectional genetic approach to specifically activate or inhibit dopamine receptor cortical projection circuits and test their effect on striatal dopamine dynamics and reversal learning. Our studies will identify previously unappreciated roles for cortical dopamine projection circuits and their regulation of striatal dopamine dynamics.

Genetic diversity of Malagasy baobabs: implications for conservation

Assessing the genetic diversity of species and populations is critical for evaluating extinction vulnerability and provides important information for identifying populations of concern and/or those that should be targeted for breeding material. Baobabs (Adansonia L.) are botanical icons for conservation, with increasing attention regarding their threatened status from both scientists and non-scientists alike. Baobabs are of particular interest especially in Madagascar, where six of the eight species are endemic, and three are listed as Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN). Although A. madagascariensis Baill., A. rubrostipa Jum. & H. Perrier and A. za Baill. are more widespread and classified by IUCN as Least Concern, they show regional variation, which may reflect hidden genetic diversity or even the existence of cryptic species. Here we assess the genetic diversity of the Malagasy baobabs to serve as a basis for future conservation and management planning. Our study used a targeted sequence capture approach (hybrid enrichment) to obtain hundreds of low-copy nuclear loci with phased alleles to assess genetic diversity in the six species and their major regional subpopulations. We discuss the implications of proper delineation of species taxonomy for management issues associated with conservation. We hope such genetic information will guide more targeted population genetic assessments and inform conservation and management efforts, including identification of isolated or disjunct populations that may warrant targeted actions.

Spatial transcriptomics of human middle temporal gyrus reveals layer‐specific gene expression in early Alzheimer’s disease

In many neurodegenerative diseases including Alzheimer's disease (AD), specific subpopulations of cells and brain regions are more sensitive to dysfunction and degeneration than others. For example, excitatory neurons in the layer 2/3 of middle temporal gyrus (MTG) is particularly vulnerable to degeneration in early AD. The mechanisms underpinning this selective cellular and regional vulnerability, however, are unclear. Recently, the spatially resolved transcriptomics has been used in AD-like mouse models to identify genes altered in the vicinity of amyloid plaques and genes differentially expressed in those vulnerable regions in AD. Here we report that spatial transcriptomics of human postmortem MTG reveals differential gene expression in layer 2/3 of early AD compared to non-AD cases. Human MTG frozen sections from 2 non-AD and 2 early AD cases were mounted over the capture areas with poly T probes on the 10x Visium Gene Expression slide. The cDNA libraries were generated by following the 10x Visium Spatial Gene Expression Reagent Kits user guide. Then cDNA libraries from 4 samples were pooled in a NovaSeq6000 SP v1.0 flowcell and paired end sequencing were performed on an Illumina NovaSeq6000 sequencer. The sequence data were analyzed via 10x Genomics software (Space Ranger v 4.0.0 and Loupe Browser v 4.1.0) and Seurat (v 3.2.2). Uniform Manifold Approximation and Projection (UMAP) analysis of spatial transcriptomics data generated seven cell clusters, which correspond to the cortical layers 1-6 and the white matter in MTG. In the identified differentially expressed genes (DEGs) in layer 2/3, we found many signatures associated with AD including plaque-induced genes, disease associated microglia genes, oligodendrocyte response genes, A1 astrocyte genes, as well as tangle-associated genes. GO enrichment analysis of these DEGs revealed important functional pathways that may be implicated in the pathogenesis of AD, such as synapse structure or activity, protein folding and stability, neuronal apoptosis, autophagy, ER stress, oxidative stress, response to amyloid-beta, microglial activation, neuroinflammatory response, regulation of chemotaxis, and myelination. Taken together, we demonstrate that the genome-wide the spatially resolved transcriptomics provide an unprecedented and unbiased approach to untangle the selective cellular and regional vulnerability in early AD.

Maternal Deprivation in Rats Decreases the Expression of Interneuron Markers in the Neocortex and Hippocampus.

Early life stress has profound effects on the development of the central nervous system. We exposed 9-day-old rat pups to a 24 h maternal deprivation (MD) and sacrificed them as young adults (60-day-old), with the aim to study the effects of early stress on forebrain circuitry. We estimated numbers of various immunohistochemically defined interneuron subpopulations in several neocortical regions and in the hippocampus. MD rats showed reduced numbers of parvalbumin-expressing interneurons in the CA1 region of the hippocampus and in the prefrontal cortex, compared with controls. Numbers of reelin-expressing and calretinin-expressing interneurons were also reduced in the CA1 and CA3 hippocampal areas, but unaltered in the neocortex of MD rats. The number of calbinin-expressing interneurons in the neocortex was similar in the MD rats compared with controls. We analyzed cell death in 15-day-old rats after MD and found no difference compared to control rats. Thus, our results more likely reflect the downregulation of markers than the actual loss of interneurons. To investigate synaptic activity in the hippocampus we immunostained for glutamatergic and inhibitory vesicular transporters. The number of inhibitory synapses was decreased in the CA1 and CA3 regions of the hippocampus in MD rats, with the normal number of excitatory synapses. Our results indicate complex, cell type-specific, and region-specific alterations in the inhibitory circuitry induced by maternal deprivation. Such alterations may underlie symptoms of MD at the behavioral level and possibly contribute to mechanisms by which early life stress causes neuropsychiatric disorders, such as schizophrenia.

The diversity of adult lung epithelial stem cells and their niche in homeostasis and regeneration.

The adult lung, a workhorse for gas exchange, is continually subjected to a barrage of assaults from the inhaled particles and pathogens. Hence, homeostatic maintenance is of paramount importance. Epithelial stem cells interact with their particular niche in the adult lung to orchestrate both natural tissue rejuvenation and robust post-injury regeneration. Advances in single-cell sequencing, lineage tracing, and living tissue imaging have deepened our understanding about stem cell heterogeneities, transition states, and specific cell lineage markers. In this review, we provided an overview of the known stem/progenitor cells and their subpopulations in different regions of the adult lung, and explored the regulatory networks in stem cells and their respective niche which collectively coordinated stem cell quiescence and regeneration states. We finally discussed relationships between dysregulated stem cell function and lung disease.

Association between HSPA1B, S100B, and TNF genes polymorphisms and risks of chronic mercury poisoning

We examined association between HSPA1B (+1267A/G, rs1061581), TNF-α (–308G/A, rs1800629), and S100B (C/T, rs9722) genes polymorphisms and chronic mercury poisoning (CMP). PCR-RFLP analysis was used to examine a cohort consisting of 128 workers who were chronically exposed to mercury vapor; workers were distributed into two groups. The group 1 was made up of workers with long working experience who didn’t have CMP (n = 46), the group 2 included patients with long-term CMP period (n = 82). In addition, we estimated frequencies of rs1061581genotypes in 298 practically healthy men from regional sub-population (group 3). HSPA1B (+1267A/G) polymorphic variant was established to have more frequent carriage of both minor G allele (р = 0.003) and a rare GG homozygote (р = 0.005) in the group 2 against the group 1. 23.2 % patients from the group 2 turned out to have GG genotype and CMP was diagnosed in 95 % people who had it. We didn’t detect any differences in genotypes distribution among people from the examined occupational cohort (groups 1 and 2) against the group 3. GG-HSP1AB (+1267A/G) homozygous genotype was shown to be associated with CMP risks (OR = 13.57, p &lt; 0.0001, recessive model). Haplotype G–G (rs1061581–rs1800629) carriers were established to run 2.6 higher risks of CMP occurrence (р = 0.0098), and there was a significant linkage disequilibrium D' = 0.459 (р = 0.0004) between a pair of the abovementioned polymorphic loci. These data indicate that there is genetic interaction between HSPA1B (+1267A/G) and TNF-α (–308G/A) loci in the examined cohort. Overall, these results indicate that carriers of GG-HSPA1B (+1267A/G) genotype run high predictive risks of CMP occurrence.

Ассоциация полиморфизмов HSPA1B, S100B и TNF генов с риском развития хронической ртутной интоксикации

We examined association between HSPA1B (+1267A/G, rs1061581), TNF-α (–308G/A, rs1800629), and S100B (C/T, rs9722) genes polymorphisms and chronic mercury poisoning (CMP). PCR-RFLP analysis was used to examine a cohort consisting of 128 workers who were chronically exposed to mercury vapor; workers were distributed into two groups. The group 1 was made up of workers with long working experience who didn’t have CMP (n = 46), the group 2 included patients with long-term CMP period (n = 82). In addition, we estimated frequencies of rs1061581genotypes in 298 practically healthy men from regional sub-population (group 3). HSPA1B (+1267A/G) polymorphic variant was established to have more frequent carriage of both minor G allele (р = 0.003) and a rare GG homozygote (р = 0.005) in the group 2 against the group 1. 23.2 % patients from the group 2 turned out to have GG genotype and CMP was diagnosed in 95 % people who had it. We didn’t detect any differences in genotypes distribution among people from the examined occupational cohort (groups 1 and 2) against the group 3. GG-HSP1AB (+1267A/G) homozygous genotype was shown to be associated with CMP risks (OR = 13.57, p &lt; 0.0001, recessive model). Haplotype G–G (rs1061581–rs1800629) carriers were established to run 2.6 higher risks of CMP occurrence (р = 0.0098), and there was a significant linkage disequilibrium D' = 0.459 (р = 0.0004) between a pair of the abovementioned polymorphic loci. These data indicate that there is genetic interaction between HSPA1B (+1267A/G) and TNF-α (–308G/A) loci in the examined cohort. Overall, these results indicate that carriers of GG-HSPA1B (+1267A/G) genotype run high predictive risks of CMP occurrence.

Statistical analysis in support of maintaining a healthy traditional Siamese cat population

BackgroundFor many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression.ResultsOur cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved.ConclusionIn principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.