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.

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.

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

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.

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.

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.

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.

Identification of a candidate elongation related gene in rice induced by GA_3

We identified a gibberellin-induced gene frag-ment in rice elongation by using differentialdisplay(DD)of mRNA.The rice seedlingscarried the eui(elongated)gene,named Zhen-chang A,were used,which were sensitive toGAand elongated rapidly after application of

Autophagy-targeting modulation to promote peripheral nerve regeneration

Nerve regeneration following traumatic peripheral nerve injuries and neuropathies is a complex process modulated by diverse factors and intricate molecular mechanisms.Past studies have focused on factors that stimulate axonal outgrowth and myelin regeneration.However,recent studies have highlighted the pivotal role of autophagy in peripheral nerve regeneration,particularly in the context of traumatic injuries.Consequently,autophagy-targeting modulation has emerged as a promising therapeutic approach to enhancing peripheral nerve regeneration.Our current understanding suggests that activating autophagy facilitates the rapid clearance of damaged axons and myelin sheaths,thereby enhancing neuronal survival and mitigating injury-induced oxidative stress and inflammation.These actions collectively contribute to creating a favorable microenvironment for structural and functional nerve regeneration.A range of autophagyinducing drugs and interventions have demonstrated beneficial effects in alleviating peripheral neuropathy and promoting nerve regeneration in preclinical models of traumatic peripheral nerve injuries.This review delves into the regulation of autophagy in cell types involved in peripheral nerve regeneration,summarizing the potential drugs and interventions that can be harnessed to promote this process.We hope that our review will offer novel insights and perspectives on the exploitation of autophagy pathways in the treatment of peripheral nerve injuries and neuropathies.

Effect of Matrine on Human Ether à go-go Related Gene (HERG) Channels Expressed in Chinese Hamster Ovary Cells

Objective： To observe the effect of matrine on human ether à go-go related gene （HERG） potassium channels expressed in Chinese hamster ovary （CHO） cells and investigate whether HERG channel is a new target of the pharmacological effect of matrine on arrhythmia and tumor. Methods： HERG channel potassium current in CHO cell was recorded using whole-cell patch-clamp technique, and the influence of matrine on the current was explored. Results： Matrine inhibited HERG potassium current in a dose-dependent manner, and the 50% inhibitory concentration （IC50） was 411±23 μmol/L. Matrine had no significant effect on the activation kinetics, and mainly blocked HERG channels in their closed state. Conclusions： The blocking effect of matrine on HERG channels might be one of the mechanisms against arrythmias and tumors. Unlike most other blockers exerting blocking effect at the intracellular sites by entering the cell with the opening of HERG channel, matrine blocked HERG channels at the extracellular sites.

Biofilm-overproducing Bacillus subtilis B12ΔYwcc decreases Cd uptake in Chinese cabbage through increasing Cd-immobilizing related gene abundance and root surface colonization

Biofilm-producing bacteria can decrease Cd uptake in vegetables, but mechanisms underlying this effect are poorly characterized. In this study, two mutant strains B12ΔYwcc and B12ΔSlr R were constructed from a biofilm-producing Bacillus subtilis strain B12. Then, the impacts of strain B12 and its high biofilm-producing mutant strain B12ΔYwcc and low biofilmproducing mutant strain B12ΔSlr R on Cd availability and uptake in Chinese cabbage and the related mechanisms were investigated in the Cd-polluted soil. Strain B12 and its mutants B12ΔYwcc and B12ΔSlr R increased the dry biomasses of edible tissues by 54%–130% compared with the controls. Strain B12 and its mutant B12ΔYwcc reduced the soil available Cd content by 36%–50% and root and edible tissue Cd contents by 23%–50% compared with the controls. Furthermore, the mutant strain B12ΔYwcc reduced the edible tissue Cd content by40% and increased the polysaccharide content by 23%, invertase activity by 139%, and gene copies of the cum A by 4.5-fold, eps A by 7.1-fold, and cad A by 4.3-fold, which were involved in Cd adsorption in the rhizosphere soils, respectively, compared with strain B12. The polysaccharide content and cum A, eps A, and cad A gene copy numbers showed significantly reverse correlations with the available Cd content. Notably, the mutant strain B12ΔYwcc showed better ability to colonize the vegetable root surface than strain B12. These findings demonstrated that the biofilm-overproducing mutant strain B12ΔYwcc increased the polysaccharide production and Cd-immobilizing related cum A, eps A, and cad A gene copies, resulting in lower Cd availability and accumulation in Chinese cabbage in the Cd-polluted soil.

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

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.

Differentially Expressed Genes Related to Fertility Conversion in Thermo-sensitive Genic Male Sterile(TGMS) Lines of Brassica juncea

[Objective] This study was performed to screen functional genes related to the fertility conversion of thermo-sensitive genic male sterile （TGMS） lines of Brassica juncea L. [Method] A B. juncea TGMS line K121S was selected as the experimental material. The total RNAs were isolated from fertile and sterile pollens at different development stages, including mother cell stage, tetrad stage, tricellular pollen stage and maturity stage. DDRT-PCR was carried out to identify differentially expressed genes. [Result] A total of 44 differentially expressed cDNA fragments were identified with Dot blot. And seven candidate genes related to fertility conversion of K121S were screened out by BLASTN, including callose synthase gene, aldehyde dehydrogenase gene and RNA polymerase I transcription factor RRN3 gene which were differentially expressed at the transcriptional level, H＇-ATPase gene, fructose diphosphate aldolase -class I gene, teucine-rich repeat receptor-Jike serine/threonine- protein kinase gene and alkaline/neutral invertase gene, which were differentially expressed at the post-transcriptional level. [Conclusion] The results of this study will help to explain the molecular mechanism of thermo-sensitive genic male sterility of B. juncea.

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-

ASSOCIATION BETWEEN LOW- DENSITY LIPOPROTEIN RECEPTOR- RELATED PROTEIN GENE, BUTYRYLCHOLINESTERASE GENE AND ALZHEIMER'S DISEASE IN CHINESE

Objective. To research the relations between low- density lipoprotein receptor- related protein gene (LRP) polymorphism, butyrylcholinesterase gene (BchE) polymorphism and Alzheimer’s disease (AD) in Chinese. Methods. The gene polymorphisms of LRP and BchE were genotyped in 38 AD cases and 40 controls with polymerase chain reaction- restriction fragment length polymorphism (PCR- RFLP) methods. AD groups were classified according to the LRP C/C genotype and compared with matched controls. Results. AD group had higher frequencies of C/C homozygote (81.6％ vs 60.0％ , P< 0.05) and of C allele (89.5％ vs 76.3％ , P< 0.05),with no significant difference between any of these LRP genotypes classified AD groups and their respective control groups. Conclusions. A positive correlation was found between LRP gene polymorphism and AD, but not between BchE gene polymorphism and AD in Chinese AD cases.

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.

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.