Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues,providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression...Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues,providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression.In situ sequencing(ISS)is a targeted spatial transcriptomic technique,based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry,for highly multiplexed in situ gene expression profiling.Here,we present improved in situ sequencing(IISS)that exploits a new probing and barcoding approach,combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling.We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation.The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing,while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics.We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis,based on which the developmental trajectory and cell-cell communication networks can also be constructed.展开更多
In inductively coupled plasma mass spectrometry (ICP-MS) analysis, only a few options are available to deal with non-spectroscopic interferences. Considering that diluting the sample is impractical for traces analysis...In inductively coupled plasma mass spectrometry (ICP-MS) analysis, only a few options are available to deal with non-spectroscopic interferences. Considering that diluting the sample is impractical for traces analysis, other alternatives must be employed. Traditionally, the method of standard additions is used to correct the matrix effect but it is a time consuming method. Others methods involves separation techniques. Another way to overcome matrix interferences is to understand the mechanism involved and adjust plasma viewing conditions to reduce or eliminate the effect. In this study, the effect of various concomitant elements in ICP-MS was assessed by measuring the distribution of selected singly charged analyte ions (Al, V, Cr, Mn, Ni, Co, Cu, Zn, As, In, Ba, La, Ce, Pb), doubly charged ions (La, Ce, Ba and Pb) and oxides ions (BaO) in the presence of concomitant elements spanning a mass range from 23 (Na) to 133 (Cs) u.m.a. and different ionization energies. Concomitant elements are alkali metals, alkaline earth metals and Si. Analyte ion suppression was observed while moving the ICP across and away from the sampling interface with or without a single concomitant element. Matrix effect measures were realised, firstly, to highlight the relation between the signal extinction of an analyte and the masse of the concomitant element, and secondly to highlight the relation between the removal of the analyte signal and the first ionization energy of the element of matrix. A dependence upon both the mass of the matrix element and the mass of the analyte was observed. The suppression seems increased with increasing matrix element mass and decreased with increasing analyte mass. The effect of the mass of the matrix element was the more significant of the two factors. If space-charge effects were found to be significant for matrix elements of much lower mass, it seems diffusion also played an active part for heavier matrix elements. Finally, some evidence was found for a shift in ion-atom equilibrium for dications and 展开更多
The results of studies of the peculiarities of formation of phytocenoses in environments contact sites of the western and eastern coasts of the Lake Baikal has been showed in this paper. On the base of geobotanic prof...The results of studies of the peculiarities of formation of phytocenoses in environments contact sites of the western and eastern coasts of the Lake Baikal has been showed in this paper. On the base of geobotanic profiling combined with soil one, the structure and dynamics of phytocenoses forming under the conditions of mutual development of light-coniferous taiga forest and of extra zonal steppes. Edaphic conditions and placement of phytocenoses are main trigger factors determining the ways of plant cover development in this part of Lake Baikal basin. We discuss the characteristics properties inherent in the linkage of the dynamics and spatial variability of the vegetation with the change of climate in the Baikal region. The regional conditions of the physiogeographic environment had given rise to structurally highly contrasting plant communities in this region. The increase in yearly mean summertime amounts of rainfall, combined with the rise of yearly mean winter temperatures over the last years were conducive to changes in the spatial structure of vegetation. The boundary between the types of vegetation undergoes smoothing. The upper boundary of forest is altered because of changes of the environment that are responsible for the zonality and properties of vertical zonality of the vegetation on the mountains surrounding Lake Baikal. Changes in the vegetation serve as indicators of climate change as well as providing diagnostic tools for the genesis of the Baikal region’s natural environment.展开更多
基金supported by the Natural Science Foundation of Fujian Province(2022J06022)the Quanzhou Science and Technology Plan Project(2021C040R)the Scientific Research Funds of Huaqiao University.
文摘Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues,providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression.In situ sequencing(ISS)is a targeted spatial transcriptomic technique,based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry,for highly multiplexed in situ gene expression profiling.Here,we present improved in situ sequencing(IISS)that exploits a new probing and barcoding approach,combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling.We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation.The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing,while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics.We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis,based on which the developmental trajectory and cell-cell communication networks can also be constructed.
文摘In inductively coupled plasma mass spectrometry (ICP-MS) analysis, only a few options are available to deal with non-spectroscopic interferences. Considering that diluting the sample is impractical for traces analysis, other alternatives must be employed. Traditionally, the method of standard additions is used to correct the matrix effect but it is a time consuming method. Others methods involves separation techniques. Another way to overcome matrix interferences is to understand the mechanism involved and adjust plasma viewing conditions to reduce or eliminate the effect. In this study, the effect of various concomitant elements in ICP-MS was assessed by measuring the distribution of selected singly charged analyte ions (Al, V, Cr, Mn, Ni, Co, Cu, Zn, As, In, Ba, La, Ce, Pb), doubly charged ions (La, Ce, Ba and Pb) and oxides ions (BaO) in the presence of concomitant elements spanning a mass range from 23 (Na) to 133 (Cs) u.m.a. and different ionization energies. Concomitant elements are alkali metals, alkaline earth metals and Si. Analyte ion suppression was observed while moving the ICP across and away from the sampling interface with or without a single concomitant element. Matrix effect measures were realised, firstly, to highlight the relation between the signal extinction of an analyte and the masse of the concomitant element, and secondly to highlight the relation between the removal of the analyte signal and the first ionization energy of the element of matrix. A dependence upon both the mass of the matrix element and the mass of the analyte was observed. The suppression seems increased with increasing matrix element mass and decreased with increasing analyte mass. The effect of the mass of the matrix element was the more significant of the two factors. If space-charge effects were found to be significant for matrix elements of much lower mass, it seems diffusion also played an active part for heavier matrix elements. Finally, some evidence was found for a shift in ion-atom equilibrium for dications and
文摘The results of studies of the peculiarities of formation of phytocenoses in environments contact sites of the western and eastern coasts of the Lake Baikal has been showed in this paper. On the base of geobotanic profiling combined with soil one, the structure and dynamics of phytocenoses forming under the conditions of mutual development of light-coniferous taiga forest and of extra zonal steppes. Edaphic conditions and placement of phytocenoses are main trigger factors determining the ways of plant cover development in this part of Lake Baikal basin. We discuss the characteristics properties inherent in the linkage of the dynamics and spatial variability of the vegetation with the change of climate in the Baikal region. The regional conditions of the physiogeographic environment had given rise to structurally highly contrasting plant communities in this region. The increase in yearly mean summertime amounts of rainfall, combined with the rise of yearly mean winter temperatures over the last years were conducive to changes in the spatial structure of vegetation. The boundary between the types of vegetation undergoes smoothing. The upper boundary of forest is altered because of changes of the environment that are responsible for the zonality and properties of vertical zonality of the vegetation on the mountains surrounding Lake Baikal. Changes in the vegetation serve as indicators of climate change as well as providing diagnostic tools for the genesis of the Baikal region’s natural environment.
