Patched receptors sense, interpret and establish an epidermal Hedgehog signalling gradient

By using the sensitivity of single-molecule fluorescent in situ hybridization, we have precisely quantified the levels and defined the temporal and spatial distribution of Hedgehog signaling activity during embryonic skin development and discovered that there is a Hedgehog signaling gradient along the proximal-distal axis of developing hair follicles. To explore the contribution of Hedgehog receptors Ptch1 and Ptch2 in establishing the epidermal signaling gradient, we quantitated the level of pathway activity generated in Ptch1- and Ptch1; Ptch2-deficient skin and defined the contribution of each receptor to regulation of the levels of Hedgehog signaling identified in wild-type skin. Moreover, we show that both the cellular phenotype and level of pathway activity featured in Ptch1; Ptch2-deficient cells faithfully recapitulates the Peak level of endogenous Hedgehog signaling detected at the base of developing follicles, where the concentration of endogenous Shh is predicted to be highest. Taken together, these data show that both Ptch1 and Ptch2 play a crucial role in sensing the concentration of Hedgehog ligand and regulating the appropriate dose-dependent response

Analysis of the spatiotemporal fields of chemical soil pollution as a basic component of urban ecosystems

The soil is a depositing medium and an indicator of geochemical load. The fulfillment of important ecosystem functions by urban soils ensures the ecological safety of urban ecosystems as a whole. The purpose of the work is to forecast soil pollution as a basic component of the urban ecosystem with a high level of technogenic load. The calculation of the spatio-temporal fields of chemical pollution of soils in the city of Kolchugino, Vladimir region, was carried out using a balance model based on ecological and analytical data utilizing the results of area surveys of soils and snow cover. The content of heavy metals of hazard classes 1 and 2 in soil and snow samples (solid and liquid phases) was determined by atomic absorption method according to standard methods. The analysis of spatio-temporal fields of soil contamination for each heavy metal is performed on the basis of map diagrams constructed using the INTEGRO GIS software-technological complex. Taking into account aerotechnogenic intake, an assessment of the degree of accumulation of heavy metals in soils and their time to reach the critical level is given. In the soils of Kolchugino, an excess of sanitary and hygienic standards (gross forms) is revealed for all the metals studied. Analysis of the data of spatio-temporal fields of soil pollution with heavy metals in the city of Kolchugino showed that the established level of soil pollution exceeding the MPC is primarily associated with the past economic activity of non-ferrous metallurgy enterprises and will remain at the same level in the near future

Single-molecule transcript counting of stem-cell markers in the mouse intestine

available in PMC 2012 July 1.Determining the molecular identities of adult stem cells requires technologies for sensitive transcript detection in tissues. In mouse intestinal crypts, lineage-tracing studies indicated that different genes uniquely mark spatially distinct stem-cell populations, residing either at crypt bases or at position +4, but a detailed analysis of their spatial co-expression has not been feasible. Here we apply three-colour single-molecule fluorescent in situ hybridization to study a comprehensive panel of intestinal stem-cell markers during homeostasis, ageing and regeneration. We find that the expression of all markers overlaps at crypt-base cells. This co-expression includes Lgr5, Bmi1 and mTert, genes previously suggested to mark distinct stem cells. Strikingly, Dcamkl1 tuft cells, distributed throughout the crypt axis, co-express Lgr5 and other stem-cell markers that are otherwise confined to crypt bases. We also detect significant changes in the expression of some of the markers following irradiation, indicating their potential role in the regeneration process. Our approach can enable the sensitive detection of putative stem cells in other tissues and in tumours, guiding complementary functional studies to evaluate their stem-cell properties.National Institutes of Health (U.S.) (U54CA143874)National Cancer Institute (U.S.) (Physical Sciences Oncology Center at MIT (U54CA143874))National Institutes of Health (U.S.) (NIH Pioneer award (1DP1OD003936))National Cancer Institute (U.S.) (Cancer Center Support (core) grant P30-CA14051)European Molecular Biology Organization (postdoctoral fellowship)Human Frontier Science Program (Strasbourg, France)Machiah FoundationHoward Hughes Medical Institute (Gilliam fellowship

The need for enrichment of meat products with micronutrients

The article discusses the chemical composition of meat according to the main qualitative characteristics to identify the least nutritious product for its subsequent enrichment with various micronutrients. The introduction of dishes and products with an adjusted composition of vitamins, macro- and microelements into the existing diet of an average person is a serious intervention in the traditionally established structure of human nutrition. The need for such an intervention is determined by objective environmental factors associated with changes in the composition and nutritional value of the products that are used in daily nutrition, as well as changes in our lifestyle, with a decrease in physical activity and energy consumption. For these reasons, this intervention should only be carried out in accordance with scientifically sound and proven principles. The choice of micronutrients is quite diverse and, depending on the task of enriching meat products, it is possible to satisfy various physiological needs of the population

Laboratory varietal control as a guarantee of successful work of agribusiness in Russia

A new direction of agribusiness has been formed in the modern agricultural industry. This is expressed in the appearance of highly specialized enterprises working in the field of production of high-quality seeds of agricultural crops. The use of electrophoresis method in varietal identification is a new technology in domestic agribusiness. The purpose of the research was to study the electrophoresis role of prolamins in varietal identification of crops for high-quality seed material. The laboratory of varietal identification of seeds analyzed 47 varieties of oats Russian selection. On the basis of data on the component composition of avenin, varieties with a high level of intersort genetic differences were identified: Megion, Fobos, Local (K-8427), Uspekh, Otrada, Pushkinskij. Groups of samples with identical component composition of prolamins were found. Their genetic formulas of avenin have the following form: Avn A2B4C2, Avn A4B4C2, Avn A2B4C1 or Avn A2B1C3. It is established that the method of electrophoresis of oat prolamins allows effectively distinguish varieties belonging to the same variety and indistinguishable by morphological features. Implementation of a system of regular laboratory control of purity and compliance of original and reproductive oats seeds by electrophoresis of prolamins is necessary to improve the competitiveness of Russian grain production in the world market

Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient

By using the sensitivity of single-molecule fluorescent in situ hybridization, we have precisely quantified the levels and defined the temporal and spatial distribution of Hedgehog signaling activity during embryonic skin development and discovered that there is a Hedgehog signaling gradient along the proximal-distal axis of developing hair follicles. To explore the contribution of Hedgehog receptors Ptch1 and Ptch2 in establishing the epidermal signaling gradient, we quantitated the level of pathway activity generated in Ptch1- and Ptch1;Ptch2-deficient skin and defined the contribution of each receptor to regulation of the levels of Hedgehog signaling identified in wild-type skin. Moreover, we show that both the cellular phenotype and level of pathway activity featured in Ptch1;Ptch2-deficient cells faithfully recapitulates the Peak level of endogenous Hedgehog signaling detected at the base of developing follicles, where the concentration of endogenous Shh is predicted to be highest. Taken together, these data show that both Ptch1 and Ptch2 play a crucial role in sensing the concentration of Hedgehog ligand and regulating the appropriate dose-dependent response

Mapping the physical network of cellular interactions

A cell's function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network based on physical cell interaction and single-cell mRNA sequencing, and show that it can be used to discover new preferential cellular interactions without prior knowledge of component cell types. ProximID found specific interactions between megakaryocytes and mature neutrophils and between plasma cells and myeloblasts and/or promyelocytes (precursors of neutrophils) in mouse bone marrow, and it identified a Tac1+ enteroendocrine cell-Lgr5+ stem cell interaction in small intestine crypts. This strategy can be used to discover new niches or preferential interactions in a variety of organs

A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche

Adult neurogenesis in the murine dentate gyrus occurs in a specialized microenvironment that sustains the generation of neurons during life. To fully understand adult neurogenesis, it is essential to determine the neural stem cell (NSC) and progenitor developmental stages, their molecular determinants, and the niche cellular and molecular composition. We report on a single-cell RNA sequencing study of the hippocampal niche, performed by isolating all the non-neuronal cell populations. Our analysis provides a comprehensive description of the dentate gyrus cells, and it allows the identification of exclusive cell-type-specific markers. We define the developmental stages and transcriptional dynamics of NSCs and progenitors, and we find that, while NSCs represent a heterogeneous cellular continuum, progenitors can be grouped into distinct subtypes. We determine the oligodendrocyte lineage and transcriptional dynamics, and we describe the microglia transcriptional profile and activation state. The combined data constitute a valuable resource to understand regulatory mechanisms of adult neurogenesis. Artegiani et al. perform single-cell sequencing analysis of the dentate gyrus, and they identify molecular features and lineage relations of the cell types present in the niche

A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche

Adult neurogenesis in the murine dentate gyrus occurs in a specialized microenvironment that sustains the generation of neurons during life. To fully understand adult neurogenesis, it is essential to determine the neural stem cell (NSC) and progenitor developmental stages, their molecular determinants, and the niche cellular and molecular composition. We report on a single-cell RNA sequencing study of the hippocampal niche, performed by isolating all the non-neuronal cell populations. Our analysis provides a comprehensive description of the dentate gyrus cells, and it allows the identification of exclusive cell-type-specific markers. We define the developmental stages and transcriptional dynamics of NSCs and progenitors, and we find that, while NSCs represent a heterogeneous cellular continuum, progenitors can be grouped into distinct subtypes. We determine the oligodendrocyte lineage and transcriptional dynamics, and we describe the microglia transcriptional profile and activation state. The combined data constitute a valuable resource to understand regulatory mechanisms of adult neurogenesis. Artegiani et al. perform single-cell sequencing analysis of the dentate gyrus, and they identify molecular features and lineage relations of the cell types present in the niche

Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution

Summary: Organoid evolution models complemented with integrated single-cell sequencing technology provide a powerful platform to characterize intra-tumor heterogeneity (ITH) and tumor evolution. Here, we conduct a parallel evolution experiment to mimic the tumor evolution process by evolving a colon cancer organoid model over 100 generations, spanning 6 months in time. We use single-cell whole-genome sequencing (WGS) in combination with viral lineage tracing at 12 time points to simultaneously monitor clone size, CNV states, SNV states, and viral lineage barcodes for 1,641 single cells. We integrate these measurements to construct clonal evolution trees with high resolution. We characterize the order of events in which chromosomal aberrations occur and identify aberrations that recur multiple times within the same tumor sub-population. We observe recurrent sequential loss of chromosome 4 after loss of chromosome 18 in four unique tumor clones. SNVs and CNVs identified in our organoid experiments are also frequently reported in colorectal carcinoma samples, and out of 334 patients with chromosome 18 loss in a Memorial Sloan Kettering colorectal cancer cohort, 99 (29.6%) also harbor chromosome 4 loss. Our study reconstructs tumor evolution in a colon cancer organoid model at high resolution, demonstrating an approach to identify potentially clinically relevant genomic aberrations in tumor evolution