Metabolic Pathway Genes Research Articles

CPTA treatment reveals potential transcription factors associated with carotenoid metabolism in flowers of Osmanthus fragrans

Osmanthus fragrans is one of the top ten traditional flowers in China. It is divided into three different groups according to its color. α-Carotene and β-carotene are the main determinants to distinguish the color differences between three groups. However, the dominant genes and transcription factors involved in carotenoid metabolism remain unclear. CPTA treatment (0.7 mmol · L−1) remarkably promoted lycopene, α-carotene and β-carotene contents in flowers. Transcriptome sequencing analysis revealed that CPTA treatment could trigger chain reactions in carotenoid metabolism pathway genes. Four up-regulated and 10 down-regulated transcription factors which have close association with carotenoid variation were significantly induced by CPTA treatment. The up-regulated TFs such as MYB43, MYB123, HSF, were further subjected to transcript expression determination in different cultivars with drastic colors. Among them, transcript expression of four up-regulated TFs coincided with the carotenoid accumulation in different cultivars. We selected up-regulated OfMYB43 to verify its function, which is related to stress tolerance and transcriptional regulation. Transient overexpression of OfMYB43 in O. fragrans flowers showed that it could remarkably promote the expression of PDS, ZISO, LCYE and CCD4, leading to increased accumulation of β-branch carotenoids. OfMYB43 was a potential positive regulator of carotenoid biosynthesis in O. fragrans flowers. This study provides insight into the molecular mechanism of carotenoid metabolism in O. fragrans.

Biological Behavior and Lipid Metabolism of Colon Cancer Cells are Regulated by a Combination of Sterol Regulatory Element-Binding Protein 1 and ATP Citrate Lyase.

PurposeTo research the effects of ATP citrate lyase (ACLY) and Sterol-regulatory element binding protein 1 (SREBP1) on the biology and lipid metabolism of colorectal cancer cells.MethodsColorectal cancer cells Caco-2 and Lovo were transfected with ACLY or SREBP1 gene knockdown lentiviruses. Four groups were set: ACLY knockdown, SREBP1 knockdown group, empty vector-transfected (negative control), and untreated cells (blank control). Cell proliferation was measured using CCK-8, colony formation, and EdU labeling assays. Apoptosis was detected using Annexin V-APC/7- AAD and JC-1 assay. Transwell migration and wound healing assays analyzed cell migration and invasion. A triglyceride test kit and oil red O stain assessed cell lipid production. Key factors related to lipid metabolism were detected.ResultsACLY and SREBP1 promoted cell proliferation at 48 and 120 h, but there was no significant difference in Caco-2 cells at 24 h, at which point the effect of SREBP1 was more important. ACLY’s effect on cell proliferation was more obvious at 120 h. Colony formation assays in Caco-2 showed similar results to the CCK-8 assay at 120 h, but ACLY knockdown had no effect in Lovo cells. EDU assays showed that ACLY or SREBP1 facilitated DNA reproduction in the two cell lines, in which SREBP1 was more significant. Knockdown of the two genes showed significant differences in Lovo cells. However, ALCY knockdown promoted apoptosis to a greater extent than SREBP1 knockdown in Caco-2 cells. In addition, ACLY and SREBP1 enhanced migration, invasion, and lipid production in both cell lines. Knockdown of ACLY or SREBP1 reduced lipid metabolism pathway gene expression in the two cell lines.ConclusionKnockdown of ACLY and SREBP1 genes inhibit the proliferation, migration, and invasion of colorectal cancer cells, while promoting their apoptosis. Our results identified potential new targets to treat colorectal cancer via lipid synthesis modulation in cancer cells.

Differences in gene expression of enzymes involved in branched-chain amino acid metabolism of abdominal subcutaneous adipose tissue between pregnant women with and without PCOS

ObjectivePolycystic ovary syndrome (PCOS) appears to be a common endocrine disorder of women in reproductive age. Adipose tissue (AT) is known as an active tissue in the metabolism of branched-chain amino acids (BCAA; Valine, Leucine, and Isoleucine) that they have associated with blood BCAA levels is a prognostic factor for insulin-resistant. Although the crucial roles of AT in women suffering from PCOS was reported, little information exists on the BCAA metabolism in AT of PCOS women. The aim was to assess and compare the expression of BCAAs metabolism pathway genes in abdominal subcutaneous AT of pregnant women with PCOS and non-PCOS pregnant women. Materials and methodsAT samples from 13 PCOS were compared with samples collected from 6 non-PCOS women, all of whom underwent caesarean. Quantitative real-time PCR technique was used for gene expression of branched chain aminotransferase 2 mitochondrial (BCAT2), branched chain ketoacid dehydrogenase E1-alpha (BCKDHA), branched chain ketoacid dehydrogenase E1-Beta (BCKDHB), dihydrolipoamide branched chain transacylase E2 (DBT), dihydrolipoamide dehydrogenase E3 (DLD), branched chain ketoacid dehydrogenase kinase (BCKDK), Data were analyzed using t-test or U-test. ResultsNo significant differences were found in age and body mass index (BMI) between non-PCOS and PCOS women. The mRNA level of BCAT2 and DLD in PCOS group was not significantly different from non-PCOS group whereas mRNA level of BCKDHB and DBT was significantly increased in PCOS group (P < 0.0001). In contrast, mRNA level of BCKDHA (P = 0.0001) and BCKDK (P < 0.0001) was significantly decreased in PCOS group. ConclusionThe alterations in gene expressions involved BCAA metabolism in age-matched and BMI- matched non-PCOS and PCOS pregnant women at delivery day was shown which warrants further studies regards functional activity. More attention should be given to AT of PCOS mothers that was previously ignored.

CRISPR/Cas9-mediated knockout of the NlCSAD gene results in darker cuticle pigmentation and a reduction in female fecundity in Nilaparvata lugens (Hemiptera: Delphacidae)

In insects, cuticular pigmentation genes have been exploited as potential visible markers for constructing genetic manipulation systems. Here, we cloned cysteine sulfinic acid decarboxylase (CSAD), an orthologue of melanin metabolism pathway genes, and performed RNAi experiments in the brown planthopper Nilaparvata lugens (Hemiptera: Delphacidae). The results showed that a decrease in the level of transcription of NlCSAD increased melanin deposition in the body compared to the control group, resulting in darker cuticle pigmentation. Female adults treated with dsNlCSAD and mated with wild-type males laid significantly fewer eggs than the dsGFP-treated group, and lower hatchability of the eggs was also observed. In addition, two melanic mutant N. lugens strains (NlCSAD−/+ and NlCSAD−/−) constructed by the CRISPR/Cas9 genome editing system showed darker cuticular melanisation and a reduced oviposition and hatching rate, but the homozygotes had a darker body colour, fewer eggs and lower hatchability than heterozygotes or individuals after RNAi. Thus, we have provided the first evidence that NlCSAD is required for normal body pigmentation in adults and has a role in the fecundity of females and hatchability of eggs in N. lugens via a combination of RNAi and knockout of target genes based on the CRISPR/Cas9 genome editing system. Our results suggest that NlCSAD is a candidate visual reference gene for genetic manipulation of this important crop pest.

Distinct Genetic Susceptibility Patterns of the Obese and Non-obese South Indian Women with Polycystic Ovary Syndrome

The researchers studied association of 92 SNPs of the metabolic and reproductive pathways genes in the obesity related cohorts of obese PCOS cases and non-obese controls, and non-obese PCOS cases and non-obese controls and observed eleven SNPs to be significantly associated (p &lt; 0.05). While eight of those SNPs, five from FTO and one each from MTCH2, DENNDIA and THADA genes, were found to be associated in the first set involving obese PCOS cases, only three SNPs (IRS2-intronic, LOC107984901-intergenic and SUMO1P1-regulatory variants) showed association in the 2nd set involving non-obese cases. The SNPs associated in the two cohorts were distinct and mutually exclusive. However, all the SNPs associated in either obese or non-obese PCOS cohorts were not only risk-prone but also broadly represented a metabolic pathway, involving mostly obesity and T2DM related genes, prompting one to surmise if the recent spurt in PCOS prevalence is not driven by changes in the lifestyles.

The fate and long-term toxic effects of NiO nanoparticles at environmental concentration in constructed wetland: Enzyme activity, microbial property, metabolic pathway and functional genes

Although the potential threats of metallic oxide nanoparticles (MNPs) to constructed wetland (CW) have been broadly reported, limited information is available regarding the long-term impact of nickel oxide nanoparticles (NiO NPs) on CWs at the environmentally relevant concentrations. Here, we comprehensively elucidated the responses in the treatment performance, enzyme activities, microbial properties, metabolic pathways and functional genes of CWs to chronic exposure of NiO NPs (0.1 and 1 mg/L) for 120 days, with a quantitative analysis on the fate and migration of NiO NPs within CWs. Nitrogen removal evidently declined under the long-term exposure to NiO NPs. Besides, NiO NPs induced a deterioration in phosphorus removal, but gradually restored over time. The activities of dehydrogenase (DHA), phosphatase (PST), urease (URE), ammonia oxygenase (AMO) and nitrate reductase (NAR) were inhibited to some extent under NiO NPs stress. Furthermore, NiO NPs exposure reduced bacterial diversity, shifted microbial composition and obviously inhibited the transcription of the ammonia oxidizing and denitrifying functional genes. The results of nickel mass balance indicated that the major removal mechanism of NiO NPs in CWs was through substrate adsorption and plants uptake. Thus, the ecological impacts of prolonged NiO NPs exposure at environmental concentrations should not be neglected.

Influence of Estrogenic Metabolic Pathway Genes Polymorphisms on Postmenopausal Breast Cancer Risk.

Estrogen metabolism plays an important role in tumor initiation and development. Lifetime exposure to high estrogens levels and deregulation of enzymes involved in estrogen biosynthetic and metabolic pathway are considered risk factors for breast cancer. The present study aimed to evaluate the impact of mutations acquisition during the lifetime in low penetrance genes that codify enzymes responsible for estrogen detoxification. Genotype analysis of GSTM1 and GSTT1 null polymorphisms, CYP1B1 Val432Leu and MTHFR C677T polymorphisms was performed in 157 samples of women with hormone-dependent breast cancer and correlated with the age at diagnosis. The majority of patients with GSTT1 null genotype and with both GSTM1 and GSTT1 null genotypes were 50 years old or more at the diagnosis (p-value = 0.021 and 0.018, respectively). Older women with GSTM1 null genotype were also carriers of the CYP1B1Val allele (p-value = 0.012). As well, GSTT1 null and CYP1B1Val genotypes were correlated with diagnosis at later ages (p-value = 0.022). Similar results were found associating MTHFR C677T and GSTT1 null polymorphism (p-value = 0.034). Our results suggest that estrogen metabolic pathway polymorphisms constitute a factor to be considered simultaneously with models for breast cancer risk assessment.

Metabolic pathways in sporadic colorectal carcinogenesis: A new proposal

Given the reports made about geographical differences in Colorectal Cancer (CRC) occurrence, suggesting a link between dietary habits, genes and cancer risk, we hypothesise that there are four fundamental metabolic pathways involved in diet-genes interactions, directly implicated in colorectal carcinogenesis: folate metabolism; lipid metabolism; oxidative stress response; and inflammatory response. Supporting this hypothesis are the evidence given by the significant associations between several diet-genes polymorphisms and CRC, namely: MTHFR, MTR, MTRR and TS (involved in folate metabolism); NPY, APOA1, APOB, APOC3, APOE, CETP, LPL and PON1 (involved in lipid metabolism); MNSOD, SOD3, CAT, GSTP1, GSTT1 and GSTM1 (involved in oxidative stress response); and IL-1, IL-6, TNF-α, and TGF-β (involved in inflammatory response). We also highlight the association between some foods/nutrients/nutraceuticals that are important in CRC prevention or treatment and the four metabolic pathways proposed, and the recent results of genome-wide association studies, both assisting our hypothesis. Finally, we propose a new line of investigation with larger studies, using accurate dietary biomarkers and investigating the four metabolic pathways genes simultaneously. This line of investigation will be essential to understand the full complexity of the association between nature and nurture in CRC and perhaps in other types of cancers. Only with this in-depth knowledge will it be possible to make personalised nutrition recommendations for disease prevention and management.

COL1A1 as a potential new biomarker and therapeutic target for type 2 diabetes

Type 2 diabetes (T2D) is a public health problem with a rising incidence worldwide. In this study, a potential new biomarker for T2D and mechanisms underlying the hypoglycemic effects of Enteromorpha prolifera oligosaccharide were investigated. Tandem mass tag labeling with LC–MS/MS was used to identify the differentially expressed proteins (DEPs) between the jejunum of diabetic rats and control rats. Correlations between glycometabolic parameters and DEPs were revealed by a network analysis. The expression levels of target genes in key metabolic pathways were further evaluated to identify candidate biomarkers. Among 6810 total proteins, approximately 88 % were quantified, of which 148 DEPs with a fold change of <0.83 or>1.2 and a corrected p-value of <0.05 were identified. A KEGG enrichment analysis indicated that the hypoglycaemic effects of E. prolifera oligosaccharide involved the PI3K/AKT and extracellular matrix receptor interaction signaling pathways. More importantly, Col1a1 was the most significant gene in the extracellular matrix receptor interaction pathway and was linked to hypoglycaemic activity for the first time. Thus, Col1a1 is a novel potential therapeutic target for alleviating T2D.

Sex and Menopause Modify the Effect of Single Nucleotide Polymorphism Genotypes on Fibrosis in NAFLD.

The development of fibrosis in nonalcoholic fatty liver disease (NAFLD) is influenced by genetics, sex, and menopausal status, but whether genetic susceptibility to fibrosis is influenced by sex and reproductive status is unclear. Our aim was to identify metabolism‐related single nucleotide polymorphisms (SNPs), whose effect on NAFLD fibrosis is significantly modified by sex and menopausal status. We performed a cross‐sectional, proof‐of‐concept study of 616 patients in the Duke NAFLD Clinical Database and Biorepository. The primary outcome was nonalcoholic steatohepatitis–Clinical Research Network (NASH–CRN) fibrosis stage. Menopause status was self‐reported; age 51 years was used as a surrogate for menopause in patients with missing menopause data. The Metabochip was used to obtain 98,359 SNP genotypes in known metabolic pathway genes for each patient. We used additive genetic models to characterize sex and menopause‐specific effects of SNP genotypes on NAFLD fibrosis stage. In the main effects analysis, none of the SNPs were associated with fibrosis at P < 0.05 after correcting for multiple comparisons. Twenty‐five SNPs significantly interacted with sex/menopause to affect fibrosis stage (interaction P < 0.0001). After removal of loci in linkage disequilibrium, 10 independent loci were identified. Six were in the following genes: KCNIP4 (potassium voltage‐gated channel interacting protein 4), PSORS1C1 (psoriasis susceptibility 1 candidate 1), KLHL8 (Kelch‐like family member 8), GLRA1 (glycine receptor alpha 1), NOTCH2 (notch receptor 2), and PRKCH (protein kinase C eta), and four SNPs were intergenic. In stratified models, four SNPs were significant in premenopausal and postmenopausal women, three only in postmenopausal women, two in men and postmenopausal women, and one only in premenopausal women. Conclusion: We identified 10 loci with a significant sex/menopause interaction with respect to fibrosis. None of these SNPs were significant in all sex/menopause groups, suggesting modulation of genetic susceptibility to fibrosis by sex and menopause status. Future studies of genetic predictors of NAFLD progression should account for sex and menopause.

Distinct Genetic Susceptibility Patterns of the Obese and Nonobese South Indian Women with Polycystic Ovary Syndrome

ABSTRACT The researchers studied association of 92 SNPs of the metabolic and reproductive pathways genes in the obesity related cohorts of obese PCOS cases and non-obese controls, and non-obese PCOS cases and non-obese controls and observed eleven SNPs to be significantly associated (pd” 0.05). While eight of those SNPs, five from FTO and one each from MTCH2, DENNDIA and THADA genes, were found to be associated in the first set involving obese PCOS cases, only three SNPs (IRS2-intronic, LOC107984901-intergenic and SUMO1P1-regulatory variants) showed association in the 2nd set involving non-obese cases. The SNPs associated in the two cohorts were distinct and mutually exclusive. However, all the SNPs associated in either obese or non-obese PCOS cohorts were not only risk-prone but also broadly represented a metabolic pathway, involving mostly obesity and T2DM related genes, prompting one to surmise if the recent spurt in PCOS prevalence is not driven by changes in the lifestyles

1,25-dihydroxyvitamin D3 induces stable and reproducible therapeutic tolerogenic dendritic cells with specific epigenetic modifications

Autologous, antigen-specific, tolerogenic dendritic cells (tolDCs) are presently assessed to reverse and possibly cure autoimmune diseases such as type 1 diabetes (T1D). Good Manufacturing Practice production and clinical implementation of such cell therapies critically depend on their stability and reproducible production from healthy donors and, more importantly, patient-derived monocytes. Here the authors demonstrate that tolDCs (modulated using 1,25-dihydroxyvitamin D3 and dexamethasone) displayed similar features, including protein, transcriptome and epigenome profiles, between two international clinical centers and between T1D and healthy donors, validating reproducible production. In addition, neither phenotype nor function of tolDCs was affected by repeated stimulation with inflammatory stimuli, underscoring their stability as semi-mature DCs. Furthermore, tolDCs exhibited differential DNA methylation profiles compared with inflammatory mature DCs (mDCs), and this was already largely established prior to maturation, indicating that tolDCs are locked into an immature state. Finally, approximately 80% of differentially expressed known T1D risk genes displayed a corresponding differential DNA methylome in tolDCs versus mDCs and metabolic and immune pathway genes were also differentially methylated and expressed. In summary, tolDCs are reproducible and stable clinical cell products unaffected by the T1D status of donors. The observed stable, semi-mature phenotype and function of tolDCs are exemplified by epigenetic modifications representative of immature-stage cells. Together, the authors’ data provide a strong basis for the production and clinical implementation of tolDCs in the treatment of autoimmune diseases such as T1D.

Modulation of hepatic miRNA expression in Atlantic salmon (Salmo salar) by family background and dietary fatty acid composition.

This study finds significant differences in hepatic fatty acid composition between four groups of Atlantic salmon (Salmo salar) consisting of offspring from families selected for high and low capacities to express the delta 6 desaturase isomer b and fed diets with 10% or 75% fish oil. The results demonstrated that hepatic lipid metabolism was affected by experimental conditions (diet/family). The fatty acid composition in the four groups mirrored the differences in dietary composition, but it was also associated with the family groups. Small RNA sequencing followed by RT‐qPCR identified 12 differentially expressed microRNAs (DE miRNAs), with expression associated with family groups (miR‐146 family members, miR‐200b, miR‐214, miR‐221, miR‐125, miR‐135, miR‐137, miR_nov_1), diets (miR‐203, miR‐462) or both conditions. All the conserved DE miRNAs have been reported as associated with lipid metabolism in other vertebrates. In silico predictions revealed 37 lipid metabolism pathway genes, including desaturases, transcription factors and key enzymes in the synthesis pathways as putative targets (e.g., srebp‐1 and 2, Δ6fad_b and c, hmdh, elovl4 and 5b, cdc42). RT‐qPCR analysis of selected target genes showed expression changes that were associated with diet and with family groups (d5fad, d6fad_a, srebp‐1). There was a reciprocal difference in the abundance of ssa‐miR‐203a‐3p and srebp‐1 in one group comparison, whereas other predicted targets did not reveal any evidence of being negatively regulated by degradation. More experimental studies are needed to validate and fully understand the predicted interactions and how the DE miRNAs may participate in the regulation of hepatic lipid metabolism.

RNA-Seq analysis of resistant and susceptible soybean genotypes in response to stress from soybean cyst nematode (

The soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is a major disease affecting soybean (Glycine max (L.) Merr.) production and yield. Breeding of new SCN-resistant cultivars and understanding their resistance mechanisms are valuable for improving SCN resistance of soybean. However, we still know little about resistance mechanisms to SCN. The purpose of our analysis was to understand the different resistance mechanisms of resistant and susceptible lines to SCN by dissecting their transcriptional changes during infection by SCN HG type 1.2.3.5.7. In this study, 119 recombinant inbred lines derived from a cross of cv. Dongnong L-204 (SCN resistant) and cv. Heinong 37 (SCN susceptible) were identified for resistance status to SCN HG type 1.2.3.5.7. Roots of the lines identified as extremely resistant or susceptible (L5, L89) were sequenced by transcriptome, and we obtained 66.61 Gb of data. Compared with the untreated control, there were 8394 and 6899 differentially expressed genes in SCN-infected roots of L5 and L89, respectively. Genes of metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, and plant–pathogen interaction pathway were significantly expressed in both resistant and susceptible genotypes. The expression of genes of phenylpropanoid biosynthesis, flavonoid biosynthesis, thiamine metabolism, cutin, suberin and wax biosynthesis, and endocytosis pathway was significantly higher in the resistant line than the susceptible line. Transcription factor analysis showed that 88 transcription factors from 18 transcription factor families responded to SCN stress. Nine genes were identified by reverse transcriptase qPCR to be associated with SCN resistance. This study helps us to understand better the mechanism of soybean resistance to SCN.

Metabolic engineering of osmoprotectants to elucidate the mechanism(s) of salt stress tolerance in crop plants.

Previous studies on engineering osmoprotectant metabolic pathway genes focused on the performance of transgenic plants under salt stress conditions rather than elucidating the underlying mechanism(s), and hence, the mechanism(s) remain(s) unclear. Salt stress negatively impacts agricultural crop yields. Hence, to meet future food demands, it is essential to generate salt stress-resistant varieties. Although traditional breeding has improved salt tolerance in several crops, this approach remains inadequate due to the low genetic diversity of certain important crop cultivars. Genetic engineering is used to introduce preferred gene(s) from any genetic reserve or to modify the expression of the existing gene(s) responsible for salt stress response or tolerance, thereby leading to improved salt tolerance in plants. Although plants naturally produce osmoprotectants as an adaptive mechanism for salt stress tolerance, they offer only partial protection. Recently, progress has been made in the identification and characterization of genes involved in the biosynthetic pathways of osmoprotectants. Exogenous application of these osmoprotectants, and genetic engineering of enzymes in their biosynthetic pathways, have been reported to enhance salt tolerance in different plants. However, no clear mechanistic model exists to explain how osmoprotectant accumulation in transgenic plants confers salt tolerance. This review critically examines the results obtained thus far for elucidating the underlying mechanisms of osmoprotectants for improved salt tolerance, and thus, crop yield stability under salt stress conditions, through the genetic engineering of trehalose, glycinebetaine, and proline metabolic pathway genes.

MiR-34a-5p and miR-452-5p: The Novel Regulators of Pancreatic Endocrine Dysfunction in Diabetic Zucker Rats?

Objective: The pancreatic endocrinal system dominates the regulation of blood glucose levels in vivo, and the dysfunction of pancreatic endocrine β-cells is a major cause of the occurrence and development of Type 2 diabetes (T2D). Although microRNA (miRNA) have been found to be key regulators of pancreatic β-cells proliferation, differentiation and apoptosis, the underlying mechanism remains enigmatic. The aim of this study was to identify several novel miRNAs which might be involved in the etiopathogenesis of diabetic β-cells dysfunction.Methods: The miRNA expression profiles in the pancreas of high-fat diet (HFD) fed Zucker diabetic fatty (ZDF) rats and Zucker lean (ZL) rats feed with normal-fat diet (NFD) were detected by using miRNA microarray chip, and individually verified the most significant factors by quantitative real-time polymerase chain reaction (qRT-PCR) assay. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to predict the target genes related to each of the identified miRNAs and the functions of these target genes in different metabolic signaling pathways.Results: Compared with the ZL rats, a total of 24 differentially expressed miRNAs were detected in ZDF rats. Among which miR-34a-5p and miR-452-5p were the most significantly up-regulated and down-regulated respectively. These miRNAs have not been reported in rats' pancreas before. By GO and KEGG enrichment analyses, we found that miR-34a-5p could negatively regulate pancreatic β-cell proliferation through the involvement of Wnt signaling pathway. In addition, it was also found to regulate insulin secretion through the insulin signaling pathway to modulate blood glucose levels. At the same time, miR-452-5p was found to positively regulate the activity of the key rate-limiting enzyme branched-chain α-keto acid dehydrogenase-β (BCKDHB) in the catabolism of branched chain amino acids (BCAA), leading to mitochondrial dysfunction in pancreatic β-cells.Conclusions: miR-34a-5p and miR-452-5p were identified as the novel regulators of pancreatic endocrine dysfunction. These miRNAs might have the potential to be utilized as the new predictive biomarkers for the diagnosis of the occurrence and development of T2D, as well as the therapeutic targets for T2D treatment.

Genomics and molecular analysis of RPL9 and LIAS in lung cancer: Emerging implications in carcinogenesis

Abstract Worldwide, lung cancer is a leading cause of cancer-related deaths and is the most commonly diagnosed form of cancer. A major characteristic of lung cancer is its profound clinical, histological and molecular heterogeneity. This heterogeneity is not only spatial but also temporal thus stressing the need for personalized patient-tailored treatment planning. The current optimal treatment planning is currently based on real-time monitoring of the evolving molecular profiling of the tumour throughout the course of the disease and treatment. In the current work, we will investigate the emerging role that that RPL9 and LIAS could have in carcinogenesis. While the aberrant expression of RPL9 has already been shown to occur in colorectal cancer its role in lung cancer is not yet known. In a similar manner, the role of LIAS, as a metabolism-linked gene, in cancer biology and especially in lung cancer is still unknown. Emerging research reveals both RPL9 and LIAS as interacting partners and apoptosis resistance genes. The aim of this study is to determine the differential expression of the rpl9 and lias genes in both normal lung tissue and lung cancer samples. This was achieved by using in situ hybridization (ISH) and quantitative Real-time PCR (qPCR). Further data on the role played by RPL9 in lung cancer was established through the use of in silico bioinformatic analysis. This was done in order to map biological pathways enriched by the expression of these genes. Both the KEGG pathway and Reactome analysis confirmed the role of these genes in RNA metabolic pathways. Furthermore, RPL9 was shown to play a role in signal transduction, autophagy, and cellular response to stress pathways. The function of these two proteins overlapped with regard to protein metabolism. STRING analysis also demonstrated an interaction between RPL9 and LIAS. Here we propose that the aberrant expression of RPL9 and LIAS may contribute to lung carcinogenesis and can be targeted for molecular therapy.

Identification and Analysis of &lt;I&gt;PGM&lt;/i&gt; and &lt;I&gt;SUS&lt;/i&gt; Gene Families in Leymus Chinensis Seed Transcriptome

Leymus chinensis ( Leymus chinensis &nbsp;(Trin.) Tzvel.)&nbsp;is a good perennial forage with good palatability, high yield and high feeding value. In addition, because of its strong resistance, Leymus chinensis can improve the disadvantaged environment such as poor land, and it is an important species to protect grassland ecology in China.&nbsp;Therefore, in order to promote the germination of leymus chinensis seeds and explore the mechanism of Germination, this study used sterile water treatment of leymus chinensis seeds as control, exogenous GA3 as treatment conditions. Based on the analysis of pre-transcriptome data, it was determined that&nbsp; PGM &nbsp;and&nbsp; SUS &nbsp;genes in sucrose and starch metabolic pathways play a significant role in seed Germination.&nbsp;Members identification, conserved domains, and evolutionary trees were analyzed for both gene families using the bioinformatics method. The expression pattern of&nbsp; PGM &nbsp;and&nbsp; SUS &nbsp;genes were analyzed with FPKM value. The results showed that 7 members were selected from each of the the&nbsp; PGM &nbsp;and&nbsp; SUS &nbsp;families based on the data of Leymus Chinensis seeds transcriptome. The molecular weight of&nbsp; PGM &nbsp;genes ranged from 15 471.3 to 67 912.9 Da, and the isoelectric point value ranged from 4.45 to 6.31, showing weak acidity.&nbsp; PGM &nbsp;family in Leymus Chinensis seeds are hydrophilic stable proteins. The molecular weight of&nbsp; SUS &nbsp;genes ranged from 30 421.5 to 110 262.9 Da. The isoelectric point of&nbsp; SUS &nbsp;genes were neutral except&nbsp; LcSUS1,5 &nbsp;and&nbsp; 7 , while the other four genes were weak acidic.&nbsp; LcSUS4 , 6 &nbsp;were stable hydrophilic proteins, the rest were unstable hydrophilic proteins. The&nbsp; PGM and&nbsp; SUS &nbsp;gene families in Leymus chinensis seeds play an enzyme role in promoting sucrose and starch synthesis in sucrose and starch metabolism pathways. The expression pattern analysis of Leymus chinensis seeds showed that the genes of&nbsp; PGM &nbsp;and&nbsp; SUS &nbsp;gene families in GA3-treated Leymus chinensis seeds promoted the germination of&nbsp;Leymus chinensis&nbsp;seeds by regulating the sucrose and starch pathways with different expression levels.

Cell size: a key determinant of meristematic potential in plant protoplasts.

Metabolic pathway reconstruction and gene edits for native natural product synthesis in single plant cells are considered to be less complicated when compared to the production of non-native metabolites. Being an efficient eukaryotic system, plants encompass suitable post-translational modifications. However, slow cell division rate and heterogeneous nature is an impediment for consistent product retrieval from plant cells. Plant cell synchrony can be attained in cultures developed in vitro. Isolated plant protoplasts capable of division, can potentially enhance the unimpaired yield of target bioactives, similar to microbes and unicellular eukaryotes. Evidence from yeast experiments suggests that 'critical cell size' and division rates for enhancement machinery, primarily depend on culture conditions and nutrient availability. The cell size control mechanisms in Arabidopsis shoot apical meristem is analogous to yeast notably, fission yeast. If protoplasts isolated from plants are subjected to cell size studies and cell cycle progression in culture, it will answer the underlying molecular mechanisms such as, unicellular to multicellular transition states, longevity, senescence, 'cell-size resetting' during organogenesis, and adaptation to external cues.

A comprehensive association analysis between homocysteine metabolic pathway gene methylation and ischemic stroke in a Chinese hypertensive population.

BackgroundIschemic stroke (IS) is a serious global health burden. In order to improve our understanding of the risk factors associated with IS, we investigated the combined effect of the methylation of five genes related to the metabolism of homocysteine on developing IS.MethodsQuantitative methylation‐specific PCR was used to measure the levels of promoter methylation in hypertensive and stroke patients. The cutoff value calculated by the maximum Youden index was used to classify the levels of gene methylation as hypomethylation and hypermethylation. Logistic regression was used to explore the relationship between gene methylation and IS.ResultsThe methylation levels of the genes encoding methylenetetrahydrofolate dehydrogenase 1 [MTHFD1], cystathionine β‐synthase [CBS], and dihydrofolate reductase [DHFR] in hypertensive patients were higher than those in stroke patients (all p < 0.01). MTHFD1 hypermethylation, CBS hypermethylation, and DHFR hypermethylation were protective factors for stroke after adjustment for confounding factors. Compared with individuals carrying none of the biomarkers, the ORs [95% CIs] for stroke of those with 1 and 2 elevated biomarkers were 4.068 [1.670–9.913] and 15.345 [6.198–37.994] after adjustment for confounding factors. The participants with a larger number of biomarkers had an increased risk of stroke (p for trend <0.001). For the combination biomarkers, the area under the curve of the receiver operating characteristic was 0.716.ConclusionA significant linear relationship between the number of elevated biomarkers and the risk of stroke has been observed, suggesting that elevations of these biomarkers could be used for potentially predicting the disease.