Image2_Highly sensitive and specific responses of shrimp gill cells to high pH stress based on single cell RNA-seq analysis.TIF

High pH is one of the main stressors affecting the shrimp survival, growth, and physiology in aquaculture ponds, but the cellular and molecular mechanism responsible for high pH stress has not been elucidated in shrimp. In this study, the shrimp acid-base disturbance and gill cell alterations were significantly observed and then single cell RNA-sequencing (scRNA-seq) was performed to study the sensitive and specific responses of gill cells to high pH stress. Three main gill cell types, including pillar cells, hemocytes and septal cells were identified. By comparative scRNA-seq analysis between control and pH group, the pillar cell was regarded as the target cell type in response to high pH stress with the down-regulation of ammonia excretion and H+ transport related genes and up-regulation of immune related genes. Notedly, high pH resulted in the emergence of a new immune cell subcluster in pillar cells, with immune activation and stress defense states. Pseudotime analysis also showed that the pillar cells could transform into the functionally inhibited ion cell subclusters and functionally activated immune cell subclusters after high pH stress. Further, the regulatory network of pillar cell population was predicted by WGCNA and two transcription factors were identified. In conclusion, these results provide key insights into the shrimp gill cell-type-specific mechanisms underlying high pH stress response at a single-cell resolution.</p

Image4_Highly sensitive and specific responses of shrimp gill cells to high pH stress based on single cell RNA-seq analysis.TIF

High pH is one of the main stressors affecting the shrimp survival, growth, and physiology in aquaculture ponds, but the cellular and molecular mechanism responsible for high pH stress has not been elucidated in shrimp. In this study, the shrimp acid-base disturbance and gill cell alterations were significantly observed and then single cell RNA-sequencing (scRNA-seq) was performed to study the sensitive and specific responses of gill cells to high pH stress. Three main gill cell types, including pillar cells, hemocytes and septal cells were identified. By comparative scRNA-seq analysis between control and pH group, the pillar cell was regarded as the target cell type in response to high pH stress with the down-regulation of ammonia excretion and H+ transport related genes and up-regulation of immune related genes. Notedly, high pH resulted in the emergence of a new immune cell subcluster in pillar cells, with immune activation and stress defense states. Pseudotime analysis also showed that the pillar cells could transform into the functionally inhibited ion cell subclusters and functionally activated immune cell subclusters after high pH stress. Further, the regulatory network of pillar cell population was predicted by WGCNA and two transcription factors were identified. In conclusion, these results provide key insights into the shrimp gill cell-type-specific mechanisms underlying high pH stress response at a single-cell resolution.</p

Image1_Highly sensitive and specific responses of shrimp gill cells to high pH stress based on single cell RNA-seq analysis.TIF

High pH is one of the main stressors affecting the shrimp survival, growth, and physiology in aquaculture ponds, but the cellular and molecular mechanism responsible for high pH stress has not been elucidated in shrimp. In this study, the shrimp acid-base disturbance and gill cell alterations were significantly observed and then single cell RNA-sequencing (scRNA-seq) was performed to study the sensitive and specific responses of gill cells to high pH stress. Three main gill cell types, including pillar cells, hemocytes and septal cells were identified. By comparative scRNA-seq analysis between control and pH group, the pillar cell was regarded as the target cell type in response to high pH stress with the down-regulation of ammonia excretion and H+ transport related genes and up-regulation of immune related genes. Notedly, high pH resulted in the emergence of a new immune cell subcluster in pillar cells, with immune activation and stress defense states. Pseudotime analysis also showed that the pillar cells could transform into the functionally inhibited ion cell subclusters and functionally activated immune cell subclusters after high pH stress. Further, the regulatory network of pillar cell population was predicted by WGCNA and two transcription factors were identified. In conclusion, these results provide key insights into the shrimp gill cell-type-specific mechanisms underlying high pH stress response at a single-cell resolution.</p

Image3_Highly sensitive and specific responses of shrimp gill cells to high pH stress based on single cell RNA-seq analysis.TIF

High pH is one of the main stressors affecting the shrimp survival, growth, and physiology in aquaculture ponds, but the cellular and molecular mechanism responsible for high pH stress has not been elucidated in shrimp. In this study, the shrimp acid-base disturbance and gill cell alterations were significantly observed and then single cell RNA-sequencing (scRNA-seq) was performed to study the sensitive and specific responses of gill cells to high pH stress. Three main gill cell types, including pillar cells, hemocytes and septal cells were identified. By comparative scRNA-seq analysis between control and pH group, the pillar cell was regarded as the target cell type in response to high pH stress with the down-regulation of ammonia excretion and H+ transport related genes and up-regulation of immune related genes. Notedly, high pH resulted in the emergence of a new immune cell subcluster in pillar cells, with immune activation and stress defense states. Pseudotime analysis also showed that the pillar cells could transform into the functionally inhibited ion cell subclusters and functionally activated immune cell subclusters after high pH stress. Further, the regulatory network of pillar cell population was predicted by WGCNA and two transcription factors were identified. In conclusion, these results provide key insights into the shrimp gill cell-type-specific mechanisms underlying high pH stress response at a single-cell resolution.</p

Media 1: Electron–hole plasma induced band gap renormalization in ZnO microlaser cavities

Originally published in Optics Express on 17 November 2014 (oe-22-23-28831

CH₃NH₃PbI_3–<i>x</i>Cl_<i>x</i> under Different Fabrication Strategies: Electronic Structures and Energy-Level Alignment with an Organic Hole Transport Material

We report a photoelectron spectroscopy study on the electronic structure of CH₃NH₃PbI_3–<i>x</i>Cl_<i>x</i> thin films fabricated by physical evaporation from CH₃NH₃I and PbCl₂ precursors, including (1) simultaneously evaporation and (2) sequential evaporation. The results are compared with CH₃NH₃PbI_3–<i>x</i>Cl_<i>x</i> made using conventional solution chemistry (i.e., spin-coating). Depending on the fabrication method, CH₃NH₃PbI_3–<i>x</i>Cl_<i>x</i> films show different chemical constituents in the near-surface region, leading to disparities in their energetic levels. The chemical identities of the surface species are revealed by an <i>in situ</i> study on the sequentially evaporated film. Moreover, air-exposure treatment also greatly alters the energetic levels of the film. Using hole transport layer of <i>N</i>,<i>N</i>′-di­(1-naphthyl)-<i>N</i>,<i>N</i>′-diphenyl­benzidine (NPB) as a model system, we find that the energy-level alignment with the spin-coated film after air exposure is most suitable for efficient hole transport

List of DEGs changed for 20 fold and more in <i>Vitis vinifera</i> cv. Muscat of Hamburg.

<p>List of DEGs changed for 20 fold and more in <i>Vitis vinifera</i> cv. Muscat of Hamburg.</p

Genome Wide Transcriptional Profile Analysis of <em>Vitis amurensis</em> and <em>Vitis vinifera</em> in Response to Cold Stress

<div><p>Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. <i>Vitis amurensis</i> is a wild grapevine species with remarkable cold-tolerance, exceeding that of <i>Vitis vinifera</i>, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of <i>V. amurensis</i> remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of <i>V. amurensis</i> under cold treatment. <i>Vitis vinifera</i> cv. Muscat of Hamburg was used as control to help investigate the distinctive features of <i>V. amruensis</i> in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into <i>V. vinifera</i> cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in <i>V. amruensis</i> and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that <i>V. amurensis</i> has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in <i>V. amurensis</i>. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in <i>V. amurensis</i>. Several highly expressed transcripts that were found uniquely accumulated in <i>V. amurensis</i> are discussed in detail. This subset of unique candidate transcripts may contribute to the excellent cold-hardiness of <i>V. amurensis</i>.</p> </div

Differential expressed genes (DEG) in <i>V. amurensis</i> and <i>V. vinifera</i> cv. Muscat of Hamburg during cold treatment.

<p>Differential expressed genes (DEG) in <i>V. amurensis</i> and <i>V. vinifera</i> cv. Muscat of Hamburg during cold treatment.</p

Functional classification of cold stress-related DEGs in <i>V. amurensis</i> and <i>V. vinifera</i> cv. Muscat of Hamburg.

<p>Identified DEGs were classified into functional categories and the percentage of up- or down-regulated functional categories were shown here. The DEGs with BLASTx annotation but that could not be classified into any of the functional categories were clustered into “Other”. Transcripts without any annotation information from BLASTx program were collected into “Unknown”.</p