Abstract Intercellular communication is important for tissue development and homeostasis, and when dysregulated contributes to a multitude of pathobiological processes. Cells communicate with each other by several mechanisms, including direct cell-cell contacts between membrane-tethered ligands and receptors on the cell surface, through secreted molecules that bind their cognate receptor on the receiving cell, or alternative modalities such as exosomes. The study of cell-cell communication networks using single-cell genomic approaches is now under intensive investigation, and innovative algorithms to interpret the data, infer how cells interact and identify the downstream effectors of a putative binding of a ligand to its cognate receptor are critically needed. Here, we describe a protocol to run CellComm, a data-driven systems biology algorithm that integrates single-cell RNA-sequencing, protein interaction networks, and gene regulatory networks to infer which cells within a heterogeneous tissue are actively communicating, as well as their downstream transcriptional programs. When spatial transcriptomics data is available, CellComm additionally identifies spatially-resolved cell-cell interactions within the tissue. This protocol is associated with our Nature Cell Biology paper describing our algorithm: CellComm infers cellular crosstalk that drives hematopoietic stem and progenitor cell development.
Background The striated muscle Z‐line, a multiprotein complex at the boundary between sarcomeres, plays an integral role in maintaining striated muscle structure and function. Multiple Z‐line‐associated proteins have been identified and shown to play an increasingly important role in the pathogenesis of human cardiomyopathy. Cypher and its close homologue, Enigma homolog protein ( ENH ), are 2 Z‐line proteins previously shown to be individually essential for maintenance of postnatal cardiac function and stability of the Z‐line during muscle contraction, but dispensable for cardiac myofibrillogenesis and development. Methods and Results The current studies were designed to test whether Cypher and ENH play redundant roles during embryonic development. Here, we demonstrated that mice lacking both ENH and Cypher exhibited embryonic lethality and growth retardation. Lethality in double knockout embryos was associated with cardiac dilation and abnormal Z‐line structure. In addition, when ENH was ablated in conjunction with selective ablation of either Cypher short isoforms (CypherS), or Cypher long isoforms (CypherL), only the latter resulted in embryonic lethality. Conclusions Cypher and ENH redundantly play an essential role in sustaining Z‐line structure from the earliest stages of cardiac function, and are redundantly required to maintain normal embryonic heart function and embryonic viability.
Simultaneous and accurate measurements of whole-plant instantaneous carbon-use efficiency (ICUE) and annual total carbon-use efficiency (TCUE) are difficult to make, especially for trees. One usually estimates ICUE based on the net photosynthetic rate or the assumed proportional relationship between growth efficiency and ICUE. However, thus far, protocols for easily estimating annual TCUE remain problematic. Here, we present a theoretical framework (based on the metabolic scaling theory) to predict whole-plant annual TCUE by directly measuring instantaneous net photosynthetic and respiratory rates. This framework makes four predictions, which were evaluated empirically using seedlings of nine Picea taxa: (i) the flux rates of CO2 and energy will scale isometrically as a function of plant size, (ii) whole-plant net and gross photosynthetic rates and the net primary productivity will scale isometrically with respect to total leaf mass, (iii) these scaling relationships will be independent of ambient temperature and humidity fluctuations (as measured within an experimental chamber) regardless of the instantaneous net photosynthetic rate or dark respiratory rate, or overall growth rate and (iv) TCUE will scale isometrically with respect to instantaneous efficiency of carbon use (i.e., the latter can be used to predict the former) across diverse species. These predictions were experimentally verified. We also found that the ranking of the nine taxa based on net photosynthetic rates differed from ranking based on either ICUE or TCUE. In addition, the absolute values of ICUE and TCUE significantly differed among the nine taxa, with both ICUE and temperature-corrected ICUE being highest for Picea abies and lowest for Picea schrenkiana. Nevertheless, the data are consistent with the predictions of our general theoretical framework, which can be used to access annual carbon-use efficiency of different species at the level of an individual plant based on simple, direct measurements. Moreover, we believe that our approach provides a way to cope with the complexities of different ecosystems, provided that sufficient measurements are taken to calibrate our approach to that of the system being studied.
Background: Epithelial barrier disruption is the initial pathogenesis of various diseases. We previously reported that acupoint catgut embedding (AE) improved tight junction proteins in rats with allergic rhinitis. However, whether AE benefits the epithelial barrier in local allergic rhinitis (LAR ) is unknown. Methods: In the present study, we used LAR model rats with or without AE treatment to investigate the effect of AE on nasal mucosal barrier function. Then, the LAR model rats were treated with capsaicin or tunicamycin (TM) to investigate the mechanism of AE on LAR. Results: AE ameliorated symptoms and pathological changes of nasal mucosa in LAR rats. In addition, AE reduced inflammatory factors (IL4, IL5, IL13) and inhibited endoplasmic reticulum stress (ERS) by reducing substance P (SP). Finally, AE improved the epithelial barrier function in LAR by suppressing ERS. Conclusion: the present study strongly confirms that AE is an effective method to improve nasal barrier function and prevent LAR barrier damage.
Chromosome abnormalities, Y-chromosome microdeletions, and androgen receptor gene CAG and GGN repeat polymorphisms in infertile Chinese men featuring severe oligospermia and azoospermia were analyzed. Ninety-six fertile men and 189 non-obstructive infertile men, including 125 patients with azoospermia and 64 with severe oligozoospermia, were studied. Seventeen infertile men (9.0%) carried a chromosome abnormality. Twenty (10.6%) carried a Y-chromosome microdeletion. In the remainder of the patients and controls, GGN and CAG repeats were sequenced. Short GGN repeats (n < 23) appeared to be associated with defective spermatogenesis, with the number of GGN repeats strongly correlated with sperm counts. No significant difference in CAG repeats was found between patients and controls, nor were CAG repeats correlated with sperm counts. However, for CAG repeats ranging between 24 and 25, there was a >2.5-fold risk (OR = 2.539, 95%CI = 1.206-5.344, P < 0.05) of severe oligospermia and azoospermia. Our results confirmed the significant role of chromosome abnormalities, Y-chromosome microdeletions, and GGN repeats in Chinese male infertility.
To investigate the regulatory effect of long non-coding RNA (lncRNA) SUMO1P3 on invasion, migration and cell cycle of gastric cancer (GC) cells through Wnt/β-catenin signaling pathway.Tumor tissues and adjacent normal tissues from the GC patients were collected, and human normal gastric epithelial cells GES1 and GC cells SGC-7901, MKN45, HGC-27 and AGS were selected for study. The expression of SUMO1P3 in GC tissues and cells were detected by RT-qPCR. The effects of SUMO1P3 on the proliferation, invasion and migration of SGC-7901 and MKN45 cells were detected by CCK-8, transwell and wound healing assay respectively, and the effects of SUMO1P3 on apoptosis and cycle progression of SGC-7901 and MKN45 cells were detected by flow cytometry. The expressions of Wnt/β-catenin pathway-related and cell cycle-related proteins were detected by Western blot.The expression of SUMO1P3 was significantly upregulated in GC tissues and cell lines. Downregulation of SUMO1P3 significantly inhibited the SGC-7901 and MKN45 cell proliferation, invasion, migration, and cycle progression and promoted the cell apoptosis, while overexpression of SUMO1P3 showed the opposite effect. Further study showed that downregulation of SUMO1P3 significantly reduced the expressions of Wnt1, β-catenin, c-myc, and Cyclin D1 in SGC-7901 and MKN45 cells.SUMO1P3 may promote invasion, migration, and cycle progression of SGC-7901 and MKN45 cells by enhancing the Wnt/β-catenin pathway.
Objective Myocardial ischemia-reperfusion injury (MIRI) is a common problem in heart-related diseases. The aim of this study was to explore the protective effects of STRAP on cardiomyocytes in the MIRI process and its mechanisms. Materials and methods We used SD rats to construct a MIRI model and increased the expression of STRAP in myocardial tissue by Entranster to detect the effect of STRAP on rat myocardial tissue. In addition, we cultured rat cardiomyocyte cell line H9c2 cells and constructed a hypoxia-reoxygenation model to detect the protective effect of STRAP on H9c2 cells. LY294002, an inhibitor of the PI3K/PDK1/Akt signaling pathway, was used to validate the mechanism by which STRAP protects cardiomyocytes. Results Overexpression of STRAP significantly reduced the activity of MDA in myocardial tissue and increased the activity of SOD. STRAP also substantially lowered CK and LDH levels in rat serum and increased Na+-K+-ATPase and Ca2+-Mg2+-ATPase activity. In addition, overexpression of STRAP considerably reduced endoplasmic reticulum stress (ERS) and apoptosis levels in H9c2 cells. However, LY294002 attenuated the protective effect of STRAP on cardiomyocytes. Conclusions STRAP reduces ERS and apoptosis in cardiomyocytes by activating the PI3K/PDK1/Akt signaling pathway, thereby reducing myocardial MIRI.
'/%3e%3cuse xlink:href='%23a' transform='rotate(23.036 .093 25.536)'/%3e%3cuse xlink:href='%23a' transform='rotate(45.87 1.273 16.18)'/%3e%3cuse xlink:href='%23a' transform='rotate(69.945 .996 12.078)'/%3e%3cuse xlink:href='%23a' transform='rotate(20.66 -19.689 31.932)'/%3e%3c/svg%3e)