Bioinformatic analysis and in vivo validation of angiogenesis related genes in inflammatory bowel disease

Angiogenesis plays a significant role in the occurrence and development of inflammatory bowel disease(IBD).The aim of this study is to explore potential angiogenesis related genes(ARGs)in IBD through bioinformatics analysis and in vivo experiments.Methods:GSE57945,GSE87466,and GSE36807 were obtained from the Gene Expression Omnibus database.GSE57945 was used as the training set,while GSE87466 and GSE36807 were used as the validation set.The key ARGs associated with IBD were identified using the least absolute shrinkage and selection operator(LASSO)and random forest methods.These identified ARGs were then utilized to construct a diagnostic model for IBD.The Single-Sample Genome Enrichment Analysis,Cibersort,and Xcell methods were used to evaluate the immune infiltration.Expression of amyloid beta precursor protein(APP)was verified in the IBD mouse model induced by dextran sulfate sodium using immunohistochemistry(IHC).Results:The receiver operating curve area of GSE57945 was 0.948.Two distinct clusters were identified using consensus clustering and non-negative matrix factorization clustering.Subsequent analyses revealed significant differences in immune levels and functional enrichment between the two clusters.The successful construction of the animal model for the IBD was evident by hematoxylin and eosin staining,while IHC results showed a high expression of APP in IBD and a low expression in normal tissues.Conclusion:Our findings provide new insights into the diagnosis of IBD by ARGs,and APP could be a potential novel biomarker for IBD and promising therapeutic targets.

RELATED GENES IN LUNG CANCER TISSUES ASSOCIATED WITH RESIDENTIAL HIGH RADON EXPOSURE

Objective: To investigate the related genes in lung cancer tissues associated with residential high radon exposure. Methods: Differentially expressed gene fragments in lung cancer and normal lung tissues were discovered by differential display and reverse Northern blot hybridization method. The fragments positive in lung cancer and negative in normal lung tissue were determined. Results: Seven differential displayed fragments were sequenced. One of them named NA7 is 95% homologous with AI208667 in EAT of Genbank. Another fragment named NG2 is up to 98% homologous with five fragments. The remained one CA1 may be a new gene fragment. Conclusion: 3 gene fragments were discovered from lung cancer and normal lung tissues of high radon exposure resident.

Genetic Evaluation of Starch Synthesis-Related Genes and Starch Quality Traits in Special Rice Resources

The genetic diversity of 36 rice landraces and 43 breeding materials in the upper reaches of the Yangtze River in China was studied by intragenic molecular markers of 26 starch synthesis-related loci.And research on quality traits such as the amylose content(AC),gel consistency(GC)and alkali spreading value(ASV)to analyze genetic differences in quality traits.The results showed that the number of alleles,average gene diversity and polymorphism information content values of landraces were higher than those of breeding materials.The genetic similarity coefficient(GS)of 79 rice materials ranged from 0.392 to 1,with an average of 0.757.There were significant variations in the quality traits of rice landraces and breeding materials,and the high-quality compliance rates were low,only 6.3%of the varieties have an amylose content that reached grade 1.The results of cluster analysis and population structure analysis are generally consistent;that is,the two resource types are closely related and cannot be clustered independently.This study can provide a basis for genetic improvement of rice starch quality.Make full use of the quality genetic diversity of landraces in modern breeding work,further broaden the genetic base of rice and improve rice quality.

Correlation of testicular reproductive tumor related genes in semen of patients with testicular microlithiasis

Objective:To investigate the expression of testicular tumor-related genes in the semen of patients with microlithiasis,as well as the semen concentration in patients with microlithiasis.Methods:Retrospective analysis of 2018/6-2019/6 male in our hospital clinic examination of patients with testicular color to exceed,semen specimen were collected,30 patients with testicular micro stone disease group of 15 cases,control group in 15 cases,the process of semen automatic analyzer to detect sperm concentration,by rt-pcr and Western Blot respectively detect testicular cancer related gene(KITLG KIT ligand(gene),SPRY4(sprouty RTK signaling 4)antagonist)mRNA and protein expression.Results:The semen concentration(17.31±0.92)×10-6/ml in the microstone group was lower than that in the control group(29.26±1.57)×10-6/ml.The mRNA expression of semen(KITLG,SPRY4)in the microstone group was higher than that in the control group,and the difference was statistically significant.The protein expression of semen(KITLG,SPRY4)in the microstone group was higher than that in the control group,and the difference was statistically significant.Conclusion:The semen concentration of testicular microlithiasis decreased,but the expression of seminal testicular tumor genes(KITLG,SPRY4)increased.

Preliminary studies on tin miners’ lung cancer tissue related genes by differential display mRNA

Objective To study the genes related to tin miners' lung cancer tissue Method Differential display mRNA Results Thirty cDNA fragments which differentially expressed in lung cancer tissues and the same patient's normal lung tissues were discovered Among these, 16 expressed in lung cancer tissues, not in normal lung tissues; fourteen expressed on the contrary Six cDNA fragment sequence was determined Five sequences CG2, CG7, CG8, CA5 and CC6 had less than 75% homology with known sequences in GenBank BLAST, so they were believed to be new sequences which we have recorded in Genbank Only one fragment coded CG3 had homology up to 95% with human ribosome protein L27a gene Conclusions mRNA differential display provides a unique and powerful experimental system to study differential gene expression in tin miners' lung cancer tissues and the same patient's normal lung tissues Using the system, differential expression of 30 cDNA fragments was observed Six of them may be used to study the molecular mechanism of miners' radon associated lung cancer

Transcriptome Analysis During Tetrasporogenesis of Gracilariopsis lemaneiformis and Preliminary Study of the Expressions of Its Meiotic Genes

The transcriptomes of three different parts of the fertile tetrasporophyte of Gracilariopsis lemaneiformis,including tip(T),middle(M),and subjacent(S)parts,with a gradual tetrasporangium maturity were analyzed and compared to identify the genes involved in the process of tetrasporogenesis.The number of differentially expressed genes(DEGs)for the Gple-S versus Gple-T comparison was 10296,and the numbers of DEGs for the Gple-S versus Gple-M and Gple-T versus Gple-M comparisons were 7435 and 1337,respectively.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed,and the results showed the enrichment of 132 KEGG pathways(corrected P<0.05).A total of 58 DEGs related to meiosis were screened and blasted against 18 meiosis-related genes(dmc1,mlh1,mnd1,msh4,msh2,msh6,mre11,pds5,pms1,rad21,rad50,rad51,smc1,smc2,smc4,smc5,smc6,and spo11),including four meiosis-specific genes.The transcriptome comparison indicated that in the T part,the meiosis,ribosome,and RNA transport-related genes were mostly up-regulated compared with those in the other two groups.In the M part,the genes related to ribosomes and the endoplasmic reticulum were also up-regulated compared with those in the lower part.Finally,in the S part,the genes associated with photosynthesis were mostly up-regulated,which might be helpful to the recovery from spore formation and release.

Bioinformatics research of CD44 and epithelial cell adhesion molecule related genes and pathways in colorectal cancer

Objective To investigate genes and involved biological processes closely associated with stem cell markers of colorectal cancer-epithelial cell adhesion molecule(EpCAM)+and CD44+.Methods By the bioinformatics method,with microarray data of colorectal cancer from gene expression omnibus(GEO)database and R2 platform,the genes significantly related with CD44 and Ep-

Molecular Cloning and Characterization of Three Novel Genes Related to Fatty Acid Degradation and Their Responses to Abiotic Stresses in Gossypium hirsutum L.

Fatty acid metabolism is responsible not only for oilseed metabolism but also for plant responses to abiotic stresses. In this study, three novel genes related to fatty acid degradation designated GhACX, Gh4CL, and GhMFP, respectively, were isolated from Gossypium hirsutum acc. TM-1. The phylogenetic analysis revealed that amino acid sequences of GhACXand GhMFP have the highest homology with those from Vitis vinifera, and Gh4CL has a closer genetic relationship with that from Camellia sinensis. Tissue- and organ-specific analysis showed that the three genes expressed widely in all the tested tissues, including ovules and fiber at different developing stages, with expressed preferentially in some organs. Among them, GhACX showed the most abundant transcripts in seeds at 25 d post anthesis （DPA）, however, GhMFP and Gh4CL have the strongest expression level in ovules on the day of anthesis. Based on real-time quantitative RT-PCR, the three genes were differentially regulated when induced under wounding, methyl jasmonate （MeJA）, cold, and abscisic acid （ABA） treatments. The characterization and expression pattern of three novel fatty acid degradation related genes will aid both to understand the roles of fatty acid degradation related genes as precursor in stress stimuli and to elucidate the physiological function in cotton oilseed metabolism.

A comparative genomic analysis of plant hormone related genes in different species

Plant hormones are small molecules that play important roles throughout the life span of a plant, known as auxin, gibberellin, cyto- kinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Genetic and molecular studies in the model organism Arabidopsis thaliana have revealed the individual pathways of various plant hormone responses. In this study, we selected 479 genes that were convincingly associated with various hormone actions based on genetic evidence. By using these 479 genes as queries, a genome-wide search for their orthologues in several species （microorganisms, plants and animals） was performed. Meanwhile, a com- parative analysis was conducted to evaluate their evolutionary relationship. Our analysis revealed that the metabolisms and functions of plant hormones are generally more sophisticated and diversified in higher plant species. In particular, we found that several phytohor- mone receptors and key signaling components were not present in lower plants or animals. Meanwhile, as the genome complexity in- creases, the orthologue genes tend to have more copies and probably gain more diverse functions. Our study attempts to introduce the classification and phylogenic analysis of phytohormone related genes, from metabolism enzymes to receptors and signaling components, in different species.

Effects of Manganese on the Antioxidant System and Related Gene Expression Levels in the “Hong Yang” Kiwifruit Seedlings

To explore how manganese affects the antioxidant system and the expression levels of related genes of“Hong yang”seedlings,the leaves of its tissue cultured seedlings were taken as test materials,and single factor treatment was performed by changing the manganese chloride(MnCl_(2)·4H_(2)O)solution concentration when spraying the leaves.The expression levels of Mn-SOD,POD64 and POD27 genes in leaves were quantitatively analyzed by real-time quantitative PCR(qRT-PCR)at different determination times.Meanwhile,the contents of malondial-dehyde(MDA),hydrogen peroxide(H_(2)O_(2)),the activities of antioxidant enzymes,including catalase(CAT),peroxidase(POD),and superoxide dismutase(SOD).The results showed that the SOD,CAT,POD,ascorbate peroxidase(APX),and reduced glutathione(GSH)activities in leaves were the highest at 12 h post-treatment with 50μM MnCl_(2)·4H_(2)O.Furthermore,the contents of MDA and H_(2)O_(2) in leaves also peaked when the concentration of H_(2)O_(2) is 50μM,which is the minimum value.Additionally at 50μM Mn^(2+),the Mn-SOD and POD27 expression was up-regulated as compared to the control,which promoted the expression of their respective enzyme activities.However,POD64 expression increased with the increasing Mn^(2+) concentration.Therefore,50μM is the optimal concentration of Mn when exogenously applied on“Hong yang”,which improve the antioxidant enzyme activity and regulate the plant’s physiological and biochemical functions.

A mechanism to improve early diabetic nephropathy by modulating autophagy-related mechanisms with Yuye Decotion

Objective: To investigate the molecular mechanisms of Yuye Decotion in the treatment of diabetic kidney disease using network pharmacology methods and molecular docking techniques. Methods: Obtain the transcriptome gene expression of diabetic nephropathy through GEO database, and extract genes related to autophagy. Screen the active ingredients and corresponding targets of Yuye Decoction through the TCMSP database, and map the drug prediction targets and disease targets to obtain the autophagy-related Yuye treatment targets for diabetic nephropathy point. Use String database combined with Cytoscape 3.7.2 software to construct the "drug-active ingredient-target" network and protein interaction network of Yuyetang for the treatment of diabetic nephropathy. The target point of liquid soup in the treatment of diabetic nephropathy was analyzed by GO biological process enrichment analysis and KEGG pathway enrichment analysis, and finally used Pymol and other software to analyze the core active components of Yuye Decotion and The core target protein undergoes molecular docking verification. Results: (i)100 eligible diabetic nephropathy and autophagy related genes were screened, and the potential targets of Yuye Decoction were 1,428. The acquired genes related to diabetic nephropathy and autophagy were mapped to potential targets of Yuye Decoction, and 22 therapeutic targets were obtained. GO biological process enrichment analysis and KEGG pathway enrichment analysis found that the pathways related to autophagy in the treatment of diabetic nephropathy by Yuye Decoction may include mTOR signaling pathway, phospholipase D signaling pathway, insulin resistance, EGFR tyrosine kinase inhibitor resistance, Apoptosis, PI3K /Akt signaling pathway, NF-κB signaling pathway, etc. (ii)The protein interaction network shows that VEGFA, ERBB2, GASP3, MAPK8, MYC, CDKN1A, EGFR, BCL2L1 may be the key targets of Yuye Decoction in the treatment of diabetic nephropathy. Molecular docking realizes the binding of 4 core active ingredients to 8 core target proteins. Conclusions: The research results show that Yuye Decoction treats diabetic nephropathy through multi-component, multi-target, and multi-pathway action, and provides new theoretical basis for the study of pharmacological effects and clinical application of Yuye Decoction in the treatment of diabetic nephropathy in autophagy-related aspects.

Expression analysis for candidate genes associated with eggshell mechanical property

Damaged eggshells result in losses of eggs.The genetic mechanism of variable eggshell strength is still unclear.The current study was conducted to verify whether the eggshell calcification related genes,CALB1,SPP1,DMP4,BMP2 and SLIT2,were associated with eggshell mechanical property.For this purpose quantitative PCR（q-PCR） analysis was performed to detect gene expression between two groups of hens laying strong and weak eggs.The hens were selected from 360 White Leghorn layers at 60 wk to ensure that the strong and weak eggs differed significantly in breaking strength but not in eggshell thickness and weight.Using this special strong/weak eggshell model,we found that the expression of CALB1 in the uterus of strong shell group was about 3-fold higher（P〈0.05） than that in weak shell group.The DMP4 expression was significantly higher（2-fold,P〈0.05） in the uterus of weak shell group than that in strong shell group.However,no difference was observed for genes of SPP1,SLIT2 and BMP2 between these two groups.The current study provides a new insight to investigate the association of candidate genes with eggshell mechanical property.

The prognostic genes of breast cancer and clinical significance

Breast cancer is one of the most frequent malignant tumors and is receiving more attention due to the increasing incidence and detection rate.Further studies regarding prognosis genes for biology are being conducted.The paper aims to review the prognostic indexes of breast cancer such as p16,Her-2,Ki-67,MCM7.

The Experimental Study on the Effect Calcitonin Gene related Peptide on Bone Resorption Mediated by Interleukin-1

To investigate the effect of calcitonin gene related peptide (CGRP) on bone resorption mediated by interleukin 1β(IL 1β) in vitro , the osteoclasts isolated from the long bones of newborn SD rats were co cultured with osteoblasts on ivory slices placed in 24 well plates . 24 h later, conditioned media containing CGRP and/or IL 1β were added to the wells respectively, and continued culturing for 48 h. After the cells were stripped off by ultrasonication, the ivory slices were stained in toludine blue. The number and the total area of resorption lacunae on each slice were measured by computer imaging analysis system. Our results showed that IL 1β significantly stimulated bone resorption, but CGRP inhibited the effect mediated by IL 1β in a dose dependent manner. It is suggested that CGRP may inhibit osteoclastic bone resorption through two ways: One is that CGRP functions directly on osteoclasts to block their activation; the other is that CGRP regulates the release of cytokines by osteoblasts and indirectly affects the function of osteoclasts.

Identification of a LMNA (c.646C>T) variant by whole-exome sequencing in combination with a dilated cardiomyopathy (DCM) related gene filter in a family with familiar DCM

Dilated cardiomyopathy（DCM）is characterized by the dilated heart chambers and reduced systolic function in the absence of specific aetiology[1].Approximately one third of DCM cases are hereditary.In recent years,DCM concomitant with arrhythmias and sudden death resulting from gene mutation has been widely

IDENTIFICATION OF DRUG RESISTANT RELATED cDNA IN LUNG ADENOCARCINOMA CELL LINES

Objective: To clone multidrug resistance (MDR) related genes in lung adenocarcinoma cell lines. Methods: The differentially expressed cDNA fragments between A549 and A549 DDP cells were analyzed by mRNA differential display PCR(DD RT-PCR). The fragments thus obtained were further analyzed by DNA sequencing and Northern blotting. Results: Three differentially expressed cDNA fragments were obtained and confirmed by Northern blot. Sequence analysis revealed that two of them were novel and one was 100% identical with ICE gene. Conclusion: Analyzing differentially expressed fragment between A549 and A549 DDP cells may be helpful for finding new MDR related genes. The drug resistance of A549 DDP cells may be related to the inhibition or down-regulation of ICE gene.

Prokaryotic Expression and Preparation of Polyantibody of Human Histydyl-tRNA Synthetase Related Gene

Summary: The aim of this study was to express and purify human histydyl-tRNA synthetase related gene and to prepare its polyantibody. The open reading frame was amplified by PCR, and then recombined into prokaryotic expression vector pQE30 and transformed into E. coli M15 for expression. The expressed products were induced by IPTG after the reconstructed pQE30 was transferred into M15. After purified by Ni affinity chromatography, the product was identified to be a single band by SDS-PAGE. The rabbits were inoculated with purified products. High-titer polyantibody was successfully prepared. Highly-purified expression product and prepared polyantibody may provide a good basis for further study.

Controlling N-methyl-D-aspartate receptor subunit 1 with calcitonin gene related peptide after cerebral ischemic injury

BACKGROUND: Activation of N-methyl-D-aspartate receptor (NMDAR) is a key link of exitotoxicity at the phase of cerebral ischemic injury. Because NMDAR is a main way to mediate internal flow of Ca2+ among glutamic acid receptors, over-excitation can cause neuronal apoptosis. Calcitonin gene related peptide has a strongly biological activity. On one hand, it can protect ischemic neurons through inhibiting the expression of NMDAR1 mRNA; on the other hand, it can play the protective effect through down-regulating the expression of NMDAR1 mRNA by exogenous calcitonin gene related peptide. OBJECTIVE: To observe the expression of NMDAR1 and the regulatory effect of calcitonin gene related peptide on the expression of NMDAR1 mRNA and protein in the cerebral cortex of rats with focal cerebral ischemia/reperfusion (I/R). DESIGN: Randomized controlled animal study. SETTING: China Medical University. MATERIALS: A total of 216 healthy male Wistar rats, general grade, weighing 250-280 g, were selected in this study. Twelve rats were randomly selected to regard as control group; meanwhile, other 204 rats were used to establish middle cerebral artery occlusion/reperfusion (MACO) models. The main reagents were detailed as follows: calcitonin gene related peptide (Sigma Company); calcitonin gene related peptide kit (Boster Company); antibody Ⅰ, Ⅱ and antibody β-actin Ⅰ, Ⅱ of NMDAR1 mRNA and chemiluminescence reagent (Santa Cruz Company, USA). METHODS: The experiment was carried out in the Laboratory of Neurobiology of China Medical University from August 2005 to June 2006. ① Right MCAO models of rats were established to cause focal ischemia and scored based on Zea Longa five-grade scale. If the scores were 1, 2 and 3 after wakefulness, the MACO models were established successfully and involved in the experiment. A total of 120 rats with successful modeling were randomly divided into I/R group and administration group with 60 in each group. All rats in the both groups were observed at five time points, including 6, 12, 24, 48 and 72 hours after reperfusion and after 2-hour ischemia, with 12 experimental animals at each time point. Six rats were prepared for detection of hybridization in situ, and the other 6 were used for Western blotting histochemical detection. Rats in the control group were opened their skin to separate common carotid artery and not treated with line and drugs. In addition, rats in the I/R group were treated with 1 mL saline at 2 hours after focal cerebral ischemia, and then, rats in the administration group were treated with 1 mL (1 g/L) calcitonin gene related peptide at 2 hours after focal cerebral ischemia. ② The expression of NMDAR1 mRNA was detected with hybridization in situ at various time points; moreover, the expression of NMDAR1 protein was measured with Western blotting method at various time points. The results were analyzed with Metamoph imaging analytical system. MAIN OUTCOME MEASURES: The expression of NMDAR1 mRNA and its protein in cortical neurons of rats at various time points. RESULTS: A total of 84 rats were excluded because of non-symptoms, exanimation or death; and then, 132 rats were involved in the final analysis. The expression of NMDAR1 mRNA and its protein in cortical neurons of rats in the control group was 0.205±0.001 and 0.184±0.001, respectively; after I/R, expression of NMDAR1 mRNA and its protein was up-regulated, especially, expression of mRNA at 6, 12, 24, 48 and 72 hours was 0.245±0.003, 0.287±0.004, 0.354±0.008, 0.284±0.002 and 0.217±0.006, respectively; moreover, expression of protein at 6, 12, 24, 48 and 72 hours was 0.222±0.003, 0.261±0.028, 0.311±0.004, 0.259±0.013 and 0.210±0.008, respectively. There was significant difference between the two groups (0.205±0.001, P < 0.01). The expression was up-related in the former 24 hours, reached peak at 24 hours, down-regulated, and decreased to the level of control group at 72 hours. Except 72 hours, the expression of NMDAR1 mRNA and its protein was lower in administration group than that in I/R group at other four time points. In addition, the expression of mRNA at 6, 12, 24, 48 and 72 hours was 0.223±0.005, 0.243±0.001, 0.292±0.002, 0.250±0.003 and 0.213±0.003, respectively; moreover, the expression of protein at 6, 12, 24, 48 and 72 hours was 0.216±0.006, 0.245±0.025, 0.276±0.003, 0.241±0.045 and 0.202±0.013, respectively. There was significant difference at various time points (P < 0.05). CONCLUSION: The expressions of NMDAR1 mRNA and its protein of peripheral cortical neurons are up-related in ischemic area after focal cerebral I/R. Meanwhile, exogenous calcitonin gene related peptide can protect cortical neurons through inhibiting expression of NMDAR1 mRNA and its protein after focal cerebral I/R.

Heat Stress Related Gene Expression in Gossypium hirsutum L.

Abiotic stress is a major limiting factor to crop productivity,and heat stress is one of the important elements for reduced crop production.Plants respond to heat stress at molecular and cellular levels as well as physiological level.Heat stress alters expression patterns of numerous genes in plants.