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Advances in Staining Processing of Histological Pathology Images in Deep Learning
LUO Shihuan, LIU Zhiming, YANG Biwen, and GUO Zhouyi
Deep learning allows software to assist in diagnosis to be developed and applied more aggressively and efficiently, whereas the color variability of histopathology images degrades the performance of these algorithms. Stain normalization can address image heterogeneity arising from scanner effects, different staining meDeep learning allows software to assist in diagnosis to be developed and applied more aggressively and efficiently, whereas the color variability of histopathology images degrades the performance of these algorithms. Stain normalization can address image heterogeneity arising from scanner effects, different staining methods, patient’s disease states, staining times, and other factors. Virtual staining can eliminate slide staining and reduce slide preparation steps, reducing sample preparation time for the clinic and saving significant costs. In the absence of annotated training data, pathology image data augmentation is performed by creating artificial samples with realistic texture, color and style to facilitate network training. In this paper, we made a review on staining processing of histological pathology images in deep learning pathology analysis to provide a reference for histological pathology maps in clinical applications and research..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 481 (2022)
Research Progress of CRISPR-Cas9 Gene Editing Technology in Cancer Therapy
DING Yidan, and CHEN Chen
CRISPR-Cas9, which is characterized by simplicity, effectiveness and direct targeting, can be used to treat some incurable genetic diseases by editing DNA sequence. In recent years, Crispr-Cas9 has entered cancer clinical trials and has been used to generate genetically modified animal models and develop drugs, which iCRISPR-Cas9, which is characterized by simplicity, effectiveness and direct targeting, can be used to treat some incurable genetic diseases by editing DNA sequence. In recent years, Crispr-Cas9 has entered cancer clinical trials and has been used to generate genetically modified animal models and develop drugs, which is of great clinical value. This paper reviews the CRISPR-Cas9 system and its application progress in tumor research, including CRISPR screens in the identification of personalized drug targets, delivery systems and adoptive cell therapy. The limitations and prospects of CRISPR-Cas9 in clinical therapy were also discussed, aiming to provide a reference for the future application of this technology for precise cancer therapy..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 488 (2022)
Progresses of Rice Chalkiness Related Genes and Their Functions
TANG Xianyu, XIAO Langtao, and XIA Shitou
Rice is one of the most important food crops in China, whereas the eating and processing quality of rice are seriously compromised by high chalkiness. Rice chalkiness is mainly controlled by heredity but also affected by environmental factors. Reducing rice chalkiness content is an important goal for rice breeding. In Rice is one of the most important food crops in China, whereas the eating and processing quality of rice are seriously compromised by high chalkiness. Rice chalkiness is mainly controlled by heredity but also affected by environmental factors. Reducing rice chalkiness content is an important goal for rice breeding. In recent years, a large number of genetic mechanisms related to chalkiness has been discovered by researchers. The nearest research progress of genes related to rice chalkiness and their genetic characteristics in recent years was reviewed from pathways of energy production, energy material distribution, starch synthesis and amyloplast accumulation structure in the paper, thus providing a reference for mechanism study of rice chalkiness formation and genetic improvement of rice quality..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 498 (2022)
Establishment of Anti-tumor Drug Screening Platform Based on NF-κB Fluorescent Protein Reporter Gene
WANG Ruiping, CHENG Haojie, YU Li, HUANG Mingmin, and TAN Yongjun
Using genetic engineering technology, the green fluorescent protein (GFP) reporter gene plasmid was constructed, which is convenient for live-cell imaging, Western blot (WB), cell flow analysis and live-cell tracing, so as to realize the screening of anti-tumor drugs. The promoter sequence of NF-κB gene and GFP gene frUsing genetic engineering technology, the green fluorescent protein (GFP) reporter gene plasmid was constructed, which is convenient for live-cell imaging, Western blot (WB), cell flow analysis and live-cell tracing, so as to realize the screening of anti-tumor drugs. The promoter sequence of NF-κB gene and GFP gene fragment were amplified by polymerase chain reaction (PCR), cloned into the pGL6-Enhancer vector, and the plasmid construction was proved by colony PCR, digestion identification and sequencing. The successful plasmid is then transfected into HEK-293T cells, and the reported plasmid is normally expressed within the cell based on live-cell fluorescence imaging, WB and flow cytometry. Finally, the anti-tumor drugs rapamycin, paclitaxel, gemcitabine, and the peptide anti-tumor drugs M1-20 and M1-21, which were being developed in our laboratory, were selected to verify that the gene system can respond to the effects of the drug on cells. The establishment of this drug screening platform provides a useful tool for studying the effects of anti-tumor drugs on cells, and also provides materials for building a live cell tracer system..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 506 (2022)
Regulation Effects of Transcription Factor AP-2α on SOX9 Expression
HUANG Guixiang, LI Zhiwei, and DING Xiaofeng
Hepatocarcinoma is the most common malignant tumor of the liver and the third leading cause of cancer related deaths worldwide. The incidence of hepatocarcinoma is characterized by concealment, cell heterogeneity and drug resistance, and the tumor is prone to invasion, metastasis and recurrence, which makes the clinicaHepatocarcinoma is the most common malignant tumor of the liver and the third leading cause of cancer related deaths worldwide. The incidence of hepatocarcinoma is characterized by concealment, cell heterogeneity and drug resistance, and the tumor is prone to invasion, metastasis and recurrence, which makes the clinical treatment effect of hepatocarcinoma poor. Transcription factor AP-2α plays an important role as a tumor suppressor in hepatocarcinoma, whose expression is positively correlated with the prognosis of hepatocarcinoma patients. SOX9 plays a major role in cell differentiation, sex determination and tumorigenesis. The abnormal increase of SOX9 was found in liver cancer, which promoted the growth of cancer cells. In our study, we used JASPAR software analysis to predict the potential binding sites of AP-2α in the promoter region of the SOX9 gene. The potential binding site of AP-2α was confirmed by luciferase assays and electrophoretic mobility shift assay(EMSA). AP-2α can directly bind to the promoter region of the SOX9 gene and inhibit its transcription activity. We found that AP-2α suppresses the expression of SOX9 at both mRNA and protein levels by real-time quantitative PCR and Western blots. These results revealed that AP-2α binds to the promoter region of the SOX9 gene, and negatively regulates the expression of oncogene SOX9 in hepatocarcinoma cells..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 512 (2022)
Establishment of an Osimertinib-resistant Human Non-small Cell Lung Cancer Cell Line and Study of the Resistance Mechanism
LIU Yiting, WANG Zhe, FENG Jing, GAO Min, ZHANG Xiuwei, and ZHANG Yunlei
Drug resistance remains the key factor that results in the high mortality of lung cancer patients. Therefore, it is very important to explore the mechanisms underlying the lung cancer drug resistance by establishing a third-generation molecular targeting drug-resistant cell line of non-small cell lung cancer (NSCLC). TDrug resistance remains the key factor that results in the high mortality of lung cancer patients. Therefore, it is very important to explore the mechanisms underlying the lung cancer drug resistance by establishing a third-generation molecular targeting drug-resistant cell line of non-small cell lung cancer (NSCLC). This study successfully established an Osimertinib-resistant cell line, HCC827OR, based on HCC827 cell line through combining the methods of intermittent high-dose selection and concentration-increasing. Cytotoxicity of Osimertinib against cancer cells was firstly evaluated through using the CCK8 assay kit, and resistance index (RI) was used to evaluate the sensitivity of cancer cells to Osimertinib; morphological changes of the cancers cells before and after acquiring drug resistance were stained and imaged using an optical microscopy. Western blot was used to detect the expression level of epidermal growth factor receptor (EGFR) and its downstream signaling proteins; mutation of EGFR was measured through using the next generation sequencing (NGS); cell cycle and scratch assays were performed to evaluate cell proliferation and migration ability. The RI of HCC827OR was calculated to be 18.65, demonstrating that HCC827OR was Osimertinib-resistant cells. Compared with the wild-type cells, Osimertinib-resistant cells showed a greater karyoplasmic ratio. Additionally, reduced expression of the p-EGFR and increased expression of cell proliferation-associated p-AKT indicated that the HCC827OR probably acquired the Osimertinib-resistant character through a non-EGFR-dependent signaling pathway. Meanwhile, flow cytometry and scratch assay results demonstrated that HCC827OR cells have significant G2/M cycle arrest and enhanced migration ability in comparison with the HCC827. This study successfully established an Osimertinib-resistant NSCLC cell line, and tentatively demonstrated the acquisition of drug-resistant characteristics by the HCC827OR through a non-EGFR-dependent pathway, thus providing an important in vitro model for lung cancer drug-resistance research..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 518 (2022)
Construction of Zebrafish gpr112a Gene Knockout Line
SUN Luning, YANG Boyu, LIU Ling, ZHU Junwei, YANG Tianle, PENG Zheng, ZHENG Lan, and XIE Huaping
GPR112 protein, as a member of adhesion class G protein-coupled receptors family (aGPCRs), is encoded by GPR112 gene. It contains seven transmembrane domains and interacts with G protein to perform its functions. Zebrafish is an important model organism for studying the development of vertebrates. Its genome contains tGPR112 protein, as a member of adhesion class G protein-coupled receptors family (aGPCRs), is encoded by GPR112 gene. It contains seven transmembrane domains and interacts with G protein to perform its functions. Zebrafish is an important model organism for studying the development of vertebrates. Its genome contains the homologous gene GPR1112a of GPR112, which is expressed in both juvenile and adult fish. To study the role of GPR112 in vertebrate survival and development, CRISPR-Cas9 technology was utilized to construct a gpr112a knockout zebrafish line. First, a pair of sgRNAs targeting the second exon of the gpr112a gene were synthesized and microinjected to obtain F0 generation chimeric zebrafish. Next, the F1 generation zebrafish obtained by mating the chimeras with wild-type zebrafish were genotyped. The gpr112a mutant heterozygotes were screened and the gpr112a mutant alleles were subjected to Sanger sequencing to determine the establishment of gpr112a knockout lines. The gpr112a mutant heterozygous zebrafish were then selfed to obtain gpr112a mutant homozygous zebrafish. After microscopic imaging and observation, the zebrafish homozygous for the gpr112a mutation at 7 days post fertilization did not show a phenotype that was significantly different from that of the wild type, which may be caused by the compensatory mechanism of the zebrafish body. This study laid a foundation for exploring the role of GPR112 gene in vertebrate survival and development..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 526 (2022)
Identification of Pyruvate Kinase Genes and Their Expression Analysis during Cyperus esculentus Tuber Germination and Seedling Establishment
SHI Xianfei, GAO Yu, HUANG Xusheng, ZHOU Yali, LIU Baoling, LI Runzhi, and XUE Jin’ai
Pyruvate kinase (PK) is a key limited enzyme that regulates the glycolysis pathway, which play an important role in biological process including metabolism of basic substances in plants. Cyperus esculentus L. accumulating high levels of nutrients such as lipid/oil, starch, and sugar in tubers is an ideal model for invePyruvate kinase (PK) is a key limited enzyme that regulates the glycolysis pathway, which play an important role in biological process including metabolism of basic substances in plants. Cyperus esculentus L. accumulating high levels of nutrients such as lipid/oil, starch, and sugar in tubers is an ideal model for investigating carbon metabolism and its regulatory mechanisms. A total of 7 CePK genes were identified by mining transcriptome data, including three plastidial CePKp (CePKpα, CePKpβ1 and CePKpβ2) and four cytosolic CePKc (CePKc1, CePKc2, CePKc3 and CePKc4). All CePK proteins encoded by CePK genes have the typical PK and PK_C domains. CePK proteins classified as the same type exhibit the similarity in sequence length, relative molecular weight, stability, and isoelectric point. CePKp proteins are hydrophilic proteins, and predicted to be located in the chloroplast. CePKc proteins are stable hydrophobic proteins, and predicted to be located in the cytoplasm. The tertiary structure prediction indicates that CePK proteins exist in the form of homologous tetramers. During the tuber germination and seedling establishing, the expression patterns of these CePK genes were significantly different, demonstrating that CePK genes may function differentially in regulating nutrient metabolism pathways in the tuber and seedling. The present data provide a new scientific basis for the in-depth analysis of the collaborative regulation mechanism underlying carbon flux and allocation and other biological processes in tuber germination and seedling establishing, as also benefiting breeding of high-yield and high-quality C. esculentus..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 533 (2022)
Effects of Rhizosphere Bacterial Community Structure and Developmental Assembly on Tobacco Root Growth Traits
HOU Jianlin, LI Hongguang, XIAO Yansong, ZHI Qiqi, HU Qi, XU Taosha, YU Fahui, JIN Zhili, and ZHOU Xiangping
Plant rhizosphere microbes are closely related to plant growth, whereas how the rhizosphere microbial community affects root development remains poorly understood. In this study, 16S rRNA gene high-throughput sequencing technology was used to detect the bacterial community of tobacco rhizosphere, and to explore the assPlant rhizosphere microbes are closely related to plant growth, whereas how the rhizosphere microbial community affects root development remains poorly understood. In this study, 16S rRNA gene high-throughput sequencing technology was used to detect the bacterial community of tobacco rhizosphere, and to explore the association mechanism between different developmental conditions of tobacco roots and differences in rhizosphere microbial community. The results showed that the species richness and diversity of rhizosphere bacteria in the well-developed root system (WDR) were higher than those in the undeveloped root system (UDR), with the genera Gallionella and Luteimona significantly increased, while the genera Edaphobaculum, PLTA13 and Rhodobacter significantly increased. Abundance significantly reduced (P<0.05). The molecular ecological network of UDR is more complex, and the interaction between species is strong, especially the cooperative behavior. The number of key nodes in the WDR network is more, and its carbon cycle related network modules increase. In addition, the WDR rhizosphere bacterial community assembly tends to be more developmentally aggregated, and environmental filtering plays a more important role in it. Overall, the results of this study emphasize that the structural composition, network changes and community assembly of the rhizosphere microbial community play an important role in the development of plant roots, and provide a theoretical basis for regulating the rhizosphere microbial community to promote plant root growth..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 542 (2022)
A Histological Study on the Tongues of Wild and Domesticated Rana nigromaculata
WANG Xuejing, CHEN Zhinan, CHEN Jiayan, HUANG Zhen, FU Wen, PENG Liangyue, LIU Jinhui, XU Yongfu, WANG Dongwu, XIAO Yamei, and LIU Wenbin
Due to environmental pollution and artificial hunting and other factors, the number of wild Rana nigromaculata has been far from meeting the needs of people, hence the artificial training of domesticated Rana nigromaculata is gradually emerging. Nevertheless, to ensure the production of domesticated Rana nigromaculata,Due to environmental pollution and artificial hunting and other factors, the number of wild Rana nigromaculata has been far from meeting the needs of people, hence the artificial training of domesticated Rana nigromaculata is gradually emerging. Nevertheless, to ensure the production of domesticated Rana nigromaculata, the first step is to solve the food intake related problems. The tongue is an important feeding and taste organ, which directly affects its food intake function. In this study, optical microscopy, scanning electron microscopy and transmission electron microscopy were used to study the ultrastructure of the dorsal surface and interior of the tongue of wild and domesticated Rana nigromaculata. The paraffin section study showed that both wild and domesticated Rana nigromaculata had keratinized filamentous papillae and bacteriform papillae. Filamentous papillae were distributed throughout the dorsal surface of the tongue and were composed of primary and secondary papillae. The bacteriform papillae were round, located at the tip of tongue and tongue margin. When the epithelium was removed, the epithelium of the bacteriform papilla was volcanically shaped with a taste bud cavity at the top. However, there were some differences in the histological structure of the tongue: the filamentous papillae on the tongue surface of wild Rana nigromaculata are more developed, and the degree of keratinization was more obvious than that of domesticated Rana nigromaculata. By comparing the ultrastructure of scanning electron microscopy, it was found that both wild and domesticated Rana nigromaculata could be observeed that there were large size circumvallate papilla on the lingual side of the dorsal surface caudal region, and foliated papilla composed of epithelial folds separated by parallel grooves. There were some differences in the scanning submicrostructure of tongue tissue between the two species. The filamentous papillae on the tongue surface of wild Rana nigromaculata were more developed and the degree of keratinization was greater than that of domesticated Rana nigromaculata. This was consistemt with the results of paraffin section study. The comparative observation of ultrastructure by transmission electron microscopy showed that the tongue heart of wild and domesticated Rana nigromaculata was composed of skeletal muscle fibers, connective tissue and tongue glands. The muscle fibers crossed over in three planes. The lamina propria and submucosa contain blood vessels and nerve fibers and were surrounded by thin connective tissue fibers. The salivary glands were confined to the back of the tongue and consist of many serous and mucous cells. Therefore, it can be inferred that the tongue structure is closely related to its food intake. The results of this study not only can enrich the study of tongue histological structure of Rana nigromaculata and amphibians, but also provide experimental basis for the conservation of wild germplasm resources of Rana nigromaculata, the improvement of diet formula of domesticated Rana nigromaculata and the development of industrial production..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 550 (2022)
Effects of Nitrification Inhibitors on Soybean Soil Inorganic Nitrogen and N2O Emissions under Elevated Atmospheric CO2 Concentration and Temperature
LI Chao, HAO Xingyu, LI Ping, ZONG Yuzheng, ZHANG Dongsheng, and SHI Xinrui
To investigate the effects of nitrification inhibitors applied in the wheat season on the soil inorganic nitrogen (N), N2O emissions and related enzyme activities in the soybean season for the wheat-soybean rotation system under the background of climate change, different atmospheric CO2 concentration (400 and 600 μmolTo investigate the effects of nitrification inhibitors applied in the wheat season on the soil inorganic nitrogen (N), N2O emissions and related enzyme activities in the soybean season for the wheat-soybean rotation system under the background of climate change, different atmospheric CO2 concentration (400 and 600 μmol/mol) and air temperature (ambient temperature T and T+2℃) were set in the control air chamber. The contents of soybean soil nitrate and ammonium N, nitrification and denitrification-related enzyme activities and N2O emissions were measured when nitrification inhibitors were added in the wheat season. The results showed that the addition of nitrification inhibitor combined with wheat straw returning to the field in wheat season increased soil nitrate N and ammonium N in soybean season, whereas it had little effect on the enzyme activities of soil nitrification-denitrification. Elevated air temperature (ET) significantly increased the content of nitrate N in soybean soil, while the content of ammonium N significantly decreased. At the conditions of increased atmospheric CO2 concentration (EC) or simultaneously increased air temperature and CO2 concentration (ECT), soil nitrate N and ammonium N content both increased, whereas there were no significantly difference with the inorganic N content under ambient temperature and CO2 concentration (CK). The enzyme activities of soil nitrification-denitrification under different environmental conditions showed no obvious regularity. Under ET and ECT conditions, the total amount of N2O emission in soybean growing season was significantly higher than that in CK treatment, and the addition of nitrification inhibitors reduced N2O emission. The difference of N2O emissions between EC and CK conditions was small, whereas the N2O emission of nitrification inhibitor treatment was significantly higher than that of common urea treatment under CK condition. To sum up, under the background of rising air temperature and CO2 concentration in the future, reasonable application of nitrification inhibitors is beneficial to the increase of available N in soybean soil, whereas the increase of air temperature (ET and ECT) may increase N2O emissions, and adding nitrification inhibitors can reduce N2O emissions. The changes in N2O emissions are not obvious when the CO2 concentration (EC) increased alone. This study can provide a theoretical support for fertilization management and farmland N2O emission reduction under the wheat-soybean crop rotation system under the background of future climate change..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 559 (2022)
An Exploration of the Correlation between Immune Genes FGF13, GZMB, FLT3 plus CRLF3, and the Prognosis of Acute Myeloid Leukemia Patients
LIU Qiongzhi, and HUANG Wenli
In order to build a prognostic risk model for patients with acute myeloid leukemia (AML), this study extracted immune genes through IMMPORT database, the Gene Expression Omnibus (GEO) database was used to search and download AML-related transcriptome RNA sequencing datasets, and the differentially expressed immune geneIn order to build a prognostic risk model for patients with acute myeloid leukemia (AML), this study extracted immune genes through IMMPORT database, the Gene Expression Omnibus (GEO) database was used to search and download AML-related transcriptome RNA sequencing datasets, and the differentially expressed immune genes in AML were searched and analyzed. And we downloaded the AML related expression profile dataset (TCGA-LAML) and clinical data based on the Cancer Genome Atlas (TCGA) database, the differentially expressed immune genes were further analyzed by constructing the prognostic risk model through univariate COX regression analysis and multivariate COX regression analysis. The key immune genes were finally determined, and the single gene prognosis analysis and immune infiltration analysis were carried out according to the immune genes. The results of analysis showed that compared with the normal control group, 55 immune genes were significantly up-regulated or down-regulated in the bone marrow samples of AML patients. The risk model based on four immune genes (FGF13, GZMB, FLT3 and CRLF3) could accurately predict the prognosis of AML patients [in which the area under the curve (AUC) = 0.741]. There were significant differences in the content of immune cells in high/low-risk groups. FGF13 and CRLF3 were low-risk genes, GZMB and FLT3 were high-risk genes. We constructed a risk model based on four immune genes (FGF13, GZMB, FLT3, CRLF3), which provides a theoretical basis for monitoring the prognosis and immune infiltration of AML patients..
Acta Laser Biology Sinica
- Publication Date: Mar. 06, 2023
- Vol. 31, Issue 6, 568 (2022)