scholarly journals A Cell Atlas of Microbe-Responsive Processes in the Zebrafish Intestine

2020 ◽  
Author(s):  
Reegan J. Willms ◽  
Jennifer C. Hocking ◽  
Edan Foley
Keyword(s):  
Transcriptional Activity ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Host Responses ◽  
Cellular Specificity ◽  
Direct Growth ◽  
A Cell ◽  
Microbe Interactions ◽  
Regulatory Effects ◽  
Host Microbe Interactions

ABSTRACTGut microbial products direct growth, differentiation and development in the animal host. Disruptions to host-microbe interactions have profound health consequences, that include onset of chronic inflammatory illnesses. However, we lack system-wide understanding of cell-specific responses to the microbiome. We profiled transcriptional activity in individual cells from the intestine, and associated tissue, of zebrafish larvae that we raised in the presence, or absence, of a microbiome. We uncovered extensive cellular heterogeneity in the conventional zebrafish intestinal epithelium, including previously undescribed cell types with known mammalian homologs. By comparing conventional to germ-free profiles, we mapped microbial impacts on transcriptional activity in each cell population. We revealed intricate degrees of cellular specificity in host responses to the microbiome, that included regulatory effects on patterning, metabolic and immune activity. For example, we showed that removal of microbes hindered transduction of vascular endothelial growth factor-dependent signals in the developing vasculature, resulting in impaired intestinal vascularization. Our work provides a high-resolution atlas of intestinal cellular composition in the developing fish gut and details the effects of the microbiome on each cell type.

scholarly journals Organoids to Dissect Gastrointestinal Virus–Host Interactions: What Have We Learned?

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 999
Author(s):  
Sue E. Crawford ◽  
Sasirekha Ramani ◽  
Sarah E. Blutt ◽  
Mary K. Estes
Keyword(s):  
Cell Types ◽  
Human Infection ◽  
Viral Pathogens ◽  
Host Interactions ◽  
Complex Interactions ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Human Intestinal Epithelium ◽  
Human Viruses ◽  
Human Infections

Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host–microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens.

scholarly journals Comparative evaluation of the genomes of common bacterial members of the Drosophila intestinal community

2016 ◽  
Author(s):  
Kristina Petkau ◽  
David Fast ◽  
Aashna Duggal ◽  
Edan Foley
Keyword(s):  
Immune Responses ◽  
Intestinal Bacteria ◽  
Lactobacillus Brevis ◽  
Host Responses ◽  
Gene Products ◽  
Starting Point ◽  
Microbe Interactions ◽  
Microbial Products ◽  
Host Microbe Interactions ◽  
Alternative Sources

Drosophila melanogaster is an excellent model to explore the molecular exchanges that occur between an animal intestine and their microbial passengers. For example, groundbreaking studies in flies uncovered a sophisticated web of host responses to intestinal bacteria. The outcomes of these responses define critical events in the host, such as the establishment of immune responses, access to nutrients, and the rate of larval development. Despite our steady march towards illuminating the host machinery that responds to bacterial presence in the gut, we know remarkably little about the microbial products that influence bacterial association with a fly host. To address this deficiency, we sequenced and characterized the genomes of three common Drosophila-associated microbes: Lactobacillus plantarum, Lactobacillus brevis and Acetobacter pasteurianus. In each case, we compared the genomes of Drosophila-associated strains to the genomes of strains isolated from alternative sources. This approach allowed us to identify molecular functions common to Drosophila-associated microbes, and, in the case of A. pasteurianus, to identify genes that are essential for association with the host. Of note, many of the gene products unique to fly-associated strains have established roles in the stabilization of host-microbe interactions. We believe that these data provide a valuable starting point for a more thorough examination of the microbial perspective on host-microbe relationships.

scholarly journals A model symbiosis reveals a role for sheathed-flagellum rotation in the release of immunogenic lipopolysaccharide

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Caitlin A Brennan ◽  
Jason R Hunt ◽  
Natacha Kremer ◽  
Benjamin C Krasity ◽  
Michael A Apicella ◽  
...  
Keyword(s):  
Immune Responses ◽  
Unknown Function ◽  
Vibrio Fischeri ◽  
Host Responses ◽  
Tissue Tropism ◽  
Human Pathogens ◽  
Bacterial Flagella ◽  
Host Immune Responses ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Bacterial flagella mediate host–microbe interactions through tissue tropism during colonization, as well as by activating immune responses. The flagellar shaft of some bacteria, including several human pathogens, is encased in a membranous sheath of unknown function. While it has been hypothesized that the sheath may allow these bacteria to evade host responses to the immunogenic flagellin subunit, this unusual structural feature has remained an enigma. Here we demonstrate that the rotation of the sheathed flagellum in both the mutualist Vibrio fischeri and the pathogen Vibrio cholerae promotes release of a potent bacteria-derived immunogen, lipopolysaccharide, found in the flagellar sheath. We further present a new role for the flagellar sheath in triggering, rather than circumventing, host immune responses in the model squid-vibrio symbiosis. Such an observation not only has implications for the study of bacterial pathogens with sheathed flagella, but also raises important biophysical questions of sheathed-flagellum function.

A microfluidic cell-trapping device for single-cell tracking of host–microbe interactions

Lab on a Chip ◽  
2016 ◽  
Vol 16 (17) ◽  
pp. 3276-3285 ◽  
Author(s):  
Matthieu J. Delincé ◽  
Jean-Baptiste Bureau ◽  
Ana Teresa López-Jiménez ◽  
Pierre Cosson ◽  
Thierry Soldati ◽  
...  
Keyword(s):  
Single Cell ◽  
Microfluidic Device ◽  
Cell Tracking ◽  
Bacterial Pathogens ◽  
Host Cells ◽  
Cell Trapping ◽  
A Cell ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Trapping Device

We present a cell-trapping microfluidic device (“InfectChip”) to study the interaction of bacterial pathogens with motile host cells.

scholarly journals Sequence determinants of human gene regulatory elements

2021 ◽  
Author(s):  
Biswajyoti Sahu ◽  
Tuomo Hartonen ◽  
Paivi Pihlajamaa ◽  
Bei Wei ◽  
Kashyap Dave ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Transcriptional Activity ◽  
Cell Types ◽  
Regulatory Elements ◽  
Binding Motif ◽  
Atomic Unit ◽  
Gene Regulatory Elements ◽  
A Cell ◽  
Different Cell Types

DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. To obtain a global and unbiased view of the relative importance of different sequence determinants in gene expression, we measured transcriptional activity of DNA sequences that are in aggregate ~100 times longer than the human genome in three different cell types. We show that enhancers can be classified to three main types: classical enhancers1, closed chromatin enhancers and chromatin-dependent enhancers, which act via different mechanisms and differ in motif content. Transcription factors (TFs) act generally in an additive manner with weak grammar, with classical enhancers increasing expression from promoters by a mechanism that does not involve specific TF-TF interactions. Few TFs are strongly active in a cell, with most activities similar between cell types. Chromatin-dependent enhancers are enriched in forkhead motifs, whereas classical enhancers contain motifs for TFs with strong transactivator domains such as ETS and bZIP; these motifs are also found at transcription start site (TSS)-proximal positions. However, some TFs, such as NRF1 only activate transcription when placed close to the TSS, and others such as YY1 display positional preference with respect to the TSS. TFs can thus be classified into four non-exclusive subtypes based on their transcriptional activity: chromatin opening, enhancing, promoting and TSS determining factors — consistent with the view that the binding motif is the only atomic unit of gene expression.

scholarly journals Spatially Distinct Neutrophil Responses within the Inflammatory Lesions of Pneumonic Plague

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
Nikolas M. Stasulli ◽  
Kara R. Eichelberger ◽  
Paul A. Price ◽  
Roger D. Pechous ◽  
Stephanie A. Montgomery ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Cell Types ◽  
Lung Lesions ◽  
Pneumonic Plague ◽  
Content Type ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Neutrophil Survival

ABSTRACTDuring pneumonic plague, the bacteriumYersinia pestiselicits the development of inflammatory lung lesions that continue to expand throughout infection. This lesion development and persistence are poorly understood. Here, we examine spatially distinct regions of lung lesions using laser capture microdissection and transcriptome sequencing (RNA-seq) analysis to identify transcriptional differences between lesion microenvironments. We show that cellular pathways involved in leukocyte migration and apoptosis are downregulated in the center of lung lesions compared to the periphery. Probing for the bacterial factor(s) important for the alteration in neutrophil survival, we show bothin vitroandin vivothatY. pestisincreases neutrophil survival in a manner that is dependent on the type III secretion system effector YopM. This research explores the complexity of spatially distinct host-microbe interactions and emphasizes the importance of cell relevance in assays in order to fully understandY. pestisvirulence.IMPORTANCEYersinia pestisis a high-priority pathogen and continues to cause outbreaks worldwide. The ability ofY. pestisto be transmitted via respiratory droplets and its history of weaponization has led to its classification as a select agent most likely to be used as a biological weapon. Unrestricted bacterial growth during the initial preinflammatory phase primes patients to be infectious once disease symptoms begin in the proinflammatory phase, and the rapid disease progression can lead to death beforeY. pestisinfection can be diagnosed and treated. Usingin vivoanalyses and focusing on relevant cell types during pneumonic plague infection, we can identify host pathways that may be manipulated to extend the treatment window for pneumonic plague patients.

scholarly journals Identification and characterization of cellular heterogeneity within the developing renal interstitium

Development ◽  
2020 ◽  
Vol 147 (15) ◽  
pp. dev190108 ◽  
Author(s):  
Alicia R. England ◽  
Christopher P. Chaney ◽  
Amrita Das ◽  
Mohita Patel ◽  
Alicia Malewska ◽  
...  
Keyword(s):  
Kidney Development ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Cellular Heterogeneity ◽  
Renal Interstitium ◽  
Collecting Ducts ◽  
A Cell ◽  
Multiple Cell ◽  
Identification And Characterization

ABSTRACTKidney formation requires the coordinated growth of multiple cell types including the collecting ducts, nephrons, vasculature and interstitium. There is a long-held belief that interactions between progenitors of the collecting ducts and nephrons are primarily responsible for kidney development. However, over the last several years, it has become increasingly clear that multiple aspects of kidney development require signaling from the interstitium. How the interstitium orchestrates these various roles is poorly understood. Here, we show that during development the interstitium is a highly heterogeneous patterned population of cells that occupies distinct positions correlated to the adjacent parenchyma. Our analysis indicates that the heterogeneity is not a mere reflection of different stages in a linear developmental trajectory but instead represents several novel differentiated cell states. Further, we find that β-catenin has a cell autonomous role in the development of a medullary subset of the interstitium and that this non-autonomously affects the development of the adjacent epithelia. These findings suggest the intriguing possibility that the different interstitial subtypes may create microenvironments that play unique roles in development of the adjacent epithelia and endothelia.

scholarly journals Microbe-Host Communication by Small RNAs in Extracellular Vesicles: Vehicles for Transkingdom RNA Transportation

2019 ◽  
Vol 20 (6) ◽  
pp. 1487 ◽  
Author(s):  
Heon-Jin Lee
Keyword(s):  
Extracellular Vesicles ◽  
Small Rnas ◽  
Cell Communication ◽  
Cell Types ◽  
Eukaryotic Cells ◽  
Biological Research ◽  
Interspecies Communication ◽  
Microbe Interactions ◽  
Multiple Cell ◽  
Host Microbe Interactions

Extracellular vesicles (EVs) are evolutionary well-conserved nano-sized membranous vesicles that are secreted by both prokaryotic and eukaryotic cells. Recently, they have gained great attention for their proposed roles in cell-to-cell communication, and as biomarkers for human disease. In particular, small RNAs (sRNAs) contained within EVs have been considered as candidate interspecies-communication molecules, due to their demonstrated capacity to modulate gene expression in multiple cell types and species. While research into this field is in its infancy, elucidating the mechanisms that underlie host–microbe interactions and communications promises to impact many fields of biological research, including human health and medicine. Thus, this review discussed the results of recent studies that have examined the ways in which EVs and sRNAs mediate ‘microbe–host’ and ‘host–microbe’ interspecies communication.

Dendritic cells of the human epidermis: immuno-electron microscopic studies of la antigen reactivity

1978 ◽  
Vol 36 (2) ◽  
pp. 644-645
Author(s):  
G. Rowden ◽  
M. G. Lewis ◽  
T. M. Phillips
Keyword(s):  
Dendritic Cells ◽  
Langerhans Cells ◽  
Cell Types ◽  
Cell Type ◽  
Electron Microscopic ◽  
La Antigen ◽  
Microscopic Studies ◽  
A Cell ◽  
C3 Receptors ◽  
Antigen Reactivity

Langerhans cells of mammalian stratified squamous epithelial have proven to be an enigma since their discovery in 1868. These dendritic suprabasal cells have been considered as related to melanocytes either as effete cells, or as post divisional products. Although grafting experiments seemed to demonstrate the independence of the cell types, much confusion still exists. The presence in the epidermis of a cell type with morphological features seemingly shared by melanocytes and Langerhans cells has been especially troublesome. This so called "indeterminate", or " -dendritic cell" lacks both Langerhans cells granules and melanosomes, yet it is clearly not a keratinocyte. Suggestions have been made that it is related to either Langerhans cells or melanocyte. Recent studies have unequivocally demonstrated that Langerhans cells are independent cells with immune function. They display Fc and C3 receptors on their surface as well as la (immune region associated) antigens.

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