Chip Hybridization Research Articles

Simultaneous detection of eight dairy-derived components using multiplex PCR combined with gene membrane chip

Food adulteration poses a significant risk to food safety, especially in the case of milk and dairy products, which have garnered substantial attention from regulatory authorities. In this study, we developed a method for simultaneous detection of eight animal-derived components in milk and dairy products, employing multiplex PCR combined with gene membrane chip. These components encompass cow, yak, buffalo, goat, sheep, horse, donkey, and camel. Eight dairy-derived animal-specific probes, along with eukaryotic internal reference and plant-derived internal reference probes, were designed and immobilized on nylon membranes for hybridization with PCR products, enabling source identification. Utilizing reverse dot blot hybridization, the gene membrane chip facilitates the determination of eight dairy-derived components and the presence of plant-derived components. The method demonstrated an absolute sensitivity of 0.01 ng in the multiplex PCR and membrane chip hybridization system, with a detection limit of 0.1%, meeting market supervision requirements. Upon analysis of 75 commercially available dairy products, a mislabeling rate of 29.33% was revealed. Comparative analysis with conventional PCR and real-time quantitative PCR demonstrated the method's high specificity, good repeatability, and significantly improved detection throughput, thereby enhancing the screening efficiency for adulterants in dairy products and the targeted detection capability.

Identification of Mycobacterium tuberculosis Resistance to Common Antibiotics: An Overview of Current Methods and Techniques.

Multidrug-resistant tuberculosis (MDR-TB) is an essential cause of tuberculosis treatment failure and death of tuberculosis patients. The rapid and reliable profiling of Mycobacterium tuberculosis (MTB) drug resistance in the early stage is a critical research area for public health. Then, most traditional approaches for detecting MTB are time-consuming and costly, leading to the inappropriate therapeutic schedule resting on the ambiguous information of MTB drug resistance, increasing patient economic burden, morbidity, and mortality. Therefore, novel diagnosis methods are frequently required to meet the emerging challenges of MTB drug resistance distinguish. Considering the difficulty in treating MDR-TB, it is urgently required for the development of rapid and accurate methods in the identification of drug resistance profiles of MTB in clinical diagnosis. This review discussed recent advances in MTB drug resistance detection, focusing on developing emerging approaches and their applications in tangled clinical situations. In particular, a brief overview of antibiotic resistance to MTB was present, referred to as intrinsic bacterial resistance, consisting of cell wall barriers and efflux pumping action and acquired resistance caused by genetic mutations. Then, different drug susceptibility test (DST) methods were described, including phenotype DST,genotype DST and novel DST methods. The phenotype DST includes nitrate reductase assay, RocheTM solid ratio method, and liquid culture method and genotype DST includes fluorescent PCR, GeneXpert, PCR reverse dot hybridization, ddPCR, next-generation sequencing and gene chips. Then, novel DST methods were described, including metabolism testing, cell-free DNA probe, CRISPR assay, and spectral analysis technique. The limitations, challenges, and perspectives of different techniques for drug resistance are also discussed. These methods significantly improve the detection sensitivity and accuracy of multidrug-resistant tuberculosis (MRT) and can effectively curb the incidence of drug-resistant tuberculosis and accelerate the process of tuberculosis eradication.

Chromatin Immunoprecipitation (ChIP) to Study the Transcriptional Regulatory Network that Controls Iron Homeostasis in Arabidopsis thaliana.

In plants, gene expression is orchestrated by thousands of transcription factors (TFs). For instance, a large set of bHLH TFs are involved in the regulation of iron homeostasis in Arabidopsis thaliana. The identification of the direct target genes of TFs through uncovering the interaction between the TFs and cis-regulatory elements has become an essential step toward a comprehensive understanding of the iron homeostasis transcriptional regulatory network in Arabidopsis. Chromatin immunoprecipitation (ChIP) followed by qRT-PCR (ChIP-qPCR), sequencing (ChIP-seq), or chip hybridization (ChIP-chip) is a robust tool to investigate protein-DNA interactions in plants in a physiological context. The procedure generally includes six steps: DNA-protein crosslink, isolation of nuclei, shearing of chromatin, immunoprecipitation, DNA purification, and qRT-PCR analyses. In this protocol, we describe guidelines, experimental setup, and conditions for ChIP experiment in Arabidopsis. This protocol focuses on seedlings grown in control and iron deficiency conditions, but can readily be adapted for use with other Arabidopsis tissues or samples. In addition, the protocol could also be applied to perform ChIP-chip or ChIP-seq experiments.

The association of HPV infection and vaginal microbiota of reproductive women in China: A multicenter cohort study protocol

Cervical cancer is a global health concern. Persistent oncogenic human papillomavirus (HPV) infection is a prerequisite for the development of cervical cancer. Emerging research indicates that the vaginal microbiota may play both protective and harmful roles in the acquisition and persistence of HPV and the development of cervical cancer. This multicenter cohort study mainly aims to reveal the association of vaginal microbiota with the outcome of HPV infection in six months in women of reproductive age. We will recruit 50 research centers and enroll a total of about 10,000 female volunteers with a series of strict inclusion and exclusion criteria across China, including HPV positive and HPV negative women. A unified questionnaire will be used to obtain the sociodemographic information, clinical data and lifestyle of all volunteers. Specimens including vaginal secretions swabs and cervical exfoliated cells will be collected at the first visit and follow-up after six months. We will use 16S rRNA sequencing to characterize the vaginal microbiota of volunteers’ vaginal swabs. Twenty-one HPV genotypes and other sexually transmitted pathogens, including Neisseria gonorrhoeae, Chlamydia trachomatis, Ureaplasma urealyticum, Mycoplasma hominis, Mycoplasma genitalium and Herpes simplex virus type Ⅱ will be examined using flow-through hybridization and gene chip. The association of HPV infection and vaginal microbiota will be investigated, and the core microbiota attributes to the persistent HPV infection will be analyzed in this study.

EGFR Amplification Is a Phenomenon of IDH Wildtype and TERT Mutated High-Grade Glioma: An Integrated Analysis Using Fluorescence In Situ Hybridization and DNA Methylome Profiling.

Gliomas are the most common intrinsic brain tumors in adults, and in accordance with their clinical behavior and patients’ outcome, they are graded by the World Health Organization (WHO) classification of brain tumors. One very interesting candidate for targeted tumor therapy may be epidermal growth factor receptor (EGFR) amplification. Here, we performed an integrated comparative analysis of EGFR amplification in 34 glioma samples using standard fluorescence in situ hybridization (FISH) and Illumina EPIC Infinium Methylation Bead Chip and correlated results with molecular glioma hallmarks. We found that the EPIC analysis showed the same power of detecting EGFR amplification compared with FISH. EGFR amplification was detectable in high-grade gliomas (25%). Moreover, EGFR amplification was found to be present solely in IDH wildtype gliomas (26%) and TERT mutated gliomas (27%), occurring independently of MGMT promoter methylation status and being mutually exclusive with 1p/19q codeletion (LOH). In summary, EPIC Bead Chip analysis is a reliable tool for detecting EGFR amplification and is comparable with the standard method FISH. EGFR amplification is a phenomenon of IDH wildtype TERT mutated high-grade gliomas.

Bioinformatics study of the potential therapeutic effects of ginsenoside Rf in reversing nonalcoholic fatty liver disease

ObjectiveGinsenoside Rf, a tetracyclic triterpenoid only present in Panax ginseng, has been proven to relieve lipid metabolism and inflammatory reactions, which can be a potential treatment for nonalcoholic fatty liver disease (NAFLD). Therefore, this study aimed to reveal the underlying mechanisms of ginsenoside Rf in the treatment of early-stage NAFLD (NAFL) by using a bioinformatics method and biological experiments. MethodsTarget genes associated with NAFL were screened from the Gene Expression Omnibus (GEO) database, a database repository of high-throughput gene expression data and hybridization arrays, chips, and microarrays. Subsequently, gene set enrichment analysis was performed by using Gene Ontology enrichment analysis tool. Then, the binding capacity between ginsenoside Rf and NAFL-related targets was evaluated by molecular docking. Finally, the FFA-induced HepG2 cell model treated with ginsenoside Rf was adopted to verify the effect of ginsenoside Rf and the related mechanisms. ResultsThere were 41 common differentially expressed genes in the GEO dataset. Gene Ontology and Reactome pathway enrichment analysis of the differentially expressed genes showed that many pathways could be related to the pathogenesis of NAFL, including those participating in the cytokine-mediated signaling pathway, G protein-coupled receptor signaling pathway, and response to lipopolysaccharide. Finally, the qRT–PCR analysis results indicated that ginsenoside Rf therapy could ameliorate the transcription of ANXA2, BAZ1A, DNMT3L and MMP9. ConclusionOur research discovered the relevant mechanisms and basic pharmacological effects of ginsenoside Rf in the treatment of NAFL. These results might facilitate the development of ginsenoside Rf as an alternative medication for NAFL.

Heat maps present the spatial distribution of human papillomavirus infection in Zhejiang Province, China.

Determining the spatial distribution of human papillomavirus (HPV) and performing accurate public health analyses helps to distinguish areas of healthcare that require further research, and enables therapeutic techniques and approaches in healthcare to be focused more accurately. A total of 4,560 women were enrolled in the present study. Flow-through hybridization and gene chip assays were used to detect the genotypes of HPV infection. Heat maps were then generated to present the spatial distribution of HPV infections in Zhejiang Province according to genotype. Of the exfoliated cervical cell samples from the 4,560 women, HPV was detected in 1,886 samples. HPV-16, −58, −52 and −18 were the most prevalently identified genotypes in the population included in the present study. HPV-16 and −58 infections were mainly distributed in the northern and central regions of Zhejiang Province, such as in Hangzhou and Shaoxing, where the prevalence was higher than that in the southern regions (P<0.05). HPV-18 infection was widespread throughout Zhejiang Province, but had a much lower infection rate in Ningbo and Huzhou (P<0.05). High infection rates of HPV-52 were mainly detected in Hangzhou and the eastern coastal areas of Wenzhou, with a relatively low rate of infection in the center of the province (P<0.05). In conclusion, HPV-16, −58, −52 and −18 were the four most prevalent HPV genotypes observed in Zhejiang Province. Heat maps were created to display the spatial distribution of HPV infection according to genotype, which varied by geographical regions. The results indicate that for individuals in Ningbo or Wenzhou, bivalent or quadrivalent vaccines may be suitable, but for those in Hangzhou and Shaoxing, nonavalent vaccines are strongly recommended.

A rime ice-inspired bismuth-based flexible sensor for zinc ion detection in human perspiration.

A nature-inspired special structure of bismuth is newly presented as Zn ion sensing layer for high-performance electrochemical heavy metal detection sensor applications. The rime ice-like bismuth (RIBi) has beensynthesized using an easy ex situ electrodeposition method on the surface of a flexible graphene-based electrode. The flexible graphene-based electrode was fabricated via simple laser-writing and substrate-transfer techniques. The Zn ion sensing performance of the proposed heavy metal sensor was evaluated by square wave anodic stripping voltammetry after investigating the effects of several parameters, such as preconcentration potential, preconcentration time, and pH of acetate buffer. The proposed RIBi-based heavy metal sensor demonstrated a good linear relationship between concentration and current in the range 100-1600ppb Zn ions with an acceptable sensitivity of 106nA/ppb·cm2. The result met the requirements in terms of common human perspiration levels (the average Zn ion concentration in perspiration is 800ppb). In addition, the heavy metal sensor response to Zn ions was successfully performed in human perspiration samples as well, and the results were consistent with those measured by atomic absorption spectroscopy. Besides, the fabricated Zn ion sensor exhibited excellent selectivity, repeatability, and flexibility. Finally, a PANI-LIG-based pH sensor (measurement range: pH4-7) was also integrated with the Zn ion sensor to form a single chip hybrid sensor. These results may provide a great possibility for the use of the proposed flexible sensor to realize wearable perspiration-based healthcare systems. Graphical abstract.

GRB2-associated binding protein 2 regulates multiple pathways associated with the development of prostate cancer.

The development of prostate cancer is complicated and involves a number of tumor-associated gene expression level abnormalities. Gene chip technology is a high-throughput method that can detect gene expression levels in different tissues and cells on a large scale. In the present study, gene chip technology was used to screen differentially expressed genes in PC-3 human prostate cancer cells following GRB-associated binding protein 2 (GAB2) gene knockdown, and the corresponding biological information was analyzed to investigate the role of GAB2 in prostate cancer. The PC-3 human prostate cancer cell GAB2 gene was knocked out and gene chip hybridization and bioinformatics methods were used to analyze the classical pathway and predict upstream regulatory molecules, disease and function associations and genetic interaction networks. According to the screening conditions |fold change|>1 and P<0.05, 1,242 differential genes were screened; 665 genes were upregulated, and 577 genes were downregulated. Ingenuity Pathway Analysis software demonstrated that GAB2 regulates pathways, such as the superpathway of cholesterol biosynthesis and p53 signaling in cells, and serves a role in diseases and functions such as ‘non-melanoma solid tumors’, ‘viral infections’ and ‘morbidity or mortality’. In the occurrence and development of prostate cancer, factors such as the activation of genes involved in the proliferative cycle, abnormalities in metabolism-associated enzyme gene activities and viral infection play key roles. The present study provides novel research directions and therapeutic targets for prostate cancer.

Recent Advances in Peptide Nucleic Acids for Rapid Detection of Foodborne Pathogens

Peptide nucleic acids (PNAs) are DNA/RNA analogs in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. Since PNA contains a neutral skeleton, there is no electrostatic repulsion, resulting in significant stability of its hybrid structure with complementary oligonucleotides. At present, PNA has taken the place of DNA probe in many studies. There are several disadvantages of cellular uptake of PNA, so modifications in PNA backbone or covalent coupling with cell-penetrating peptides are necessary to improve its delivery inside the cells. In recent years, PNA has been extensively used in the rapid detection of microorganisms, such as fluorescence in situ hybridization, PCR amplification, biosensor, and gene chip. The structure and characteristics of PNA probe, the hybridization method, and the design principle of PNA probes are introduced in this review, and the application progress of PNA probes in the rapid detection of foodborne pathogens is summarized. On this basis, the advantages and disadvantages of PNA probes are analyzed, and the future development trend is prospected.

Hsa_circ_0023642 promotes proliferation, invasion, and migration of gastric cancer by sponging microRNA-223.

BackgroundCircular RNAs (circRNAs) have a closed‐loop structure and are associated with various cellular biological processes, including carcinogenesis and cancer development. However, our knowledge of circRNAs in gastric cancer (GC) remains limited. Thus, this study aimed to investigate the role and underlying molecular mechanisms of hsa_circ_0023642 in GC.Materials and methodsBioinformatic analysis revealed that hsa_circ_0023642 was upregulated in GC. Chromogenic in situ hybridization (CISH) chips was used to explore the relationship between the expression of hsa_circ_0023642 and the malignant degree, clinical stage, and prognosis of patients with GC. The role of hsa_circ_0023642 in GC was assessed in vitro, and biotin‐coupled RNA pull‐down was conducted to evaluate the interaction in between hsa_circ_0023642 and miR‐223.ResultsThe current study showed that hsa_circ_0023642 was upregulated in GC and presented a high positive correlation with the malignant progression of GC. In addition, in vitro experiments showed that the silencing of hsa_circ_0023642 in GC cell lines MKN‐45 and SGC‐7901 significantly reduced the proliferation, invasion, and migration of GC cells. We confirmed that hsa_circ_0023642 could serve as a sponge of miR‐223, subsequently promoting GC progression.ConclusionThis study shows that the upregulation of hsa_circ_0023642 affects the malignant progression, clinical stage, and prognosis of GC which provides a new molecular target for the therapy of GC.

High dynamic range CdTe mixed-mode pixel array detector (MM-PAD) for kilohertz imaging of hard x-rays

A hard x-ray, high-speed, high dynamic range scientific x-ray imager is described. The imager is based on the mixed-mode pixel array detector (MM-PAD) readout chip coupled to a 750 μm thick cadmium telluride (CdTe) sensor. The full imager is a 2 × 3 tiled array of MM-PAD sensor/readout chip hybrids. CdTe improves detection for high energy x-rays as compared to silicon sensors, enabling efficient x-ray imaging to extend to >100 keV . The detector is capable of 1 kHz imaging and in-pixel circuitry has been designed to allow for well depths of greater than 4 × 106 80 keV x-rays. A charge integrating front-end allows for quantitative measurement of high flux x-ray images beyond the capabilities of photon counting detectors. Detector performance is summarized and experimental measurements are presented.

Intratracheal Transplantation of Amnion-Derived Mesenchymal Stem Cells Ameliorates Hyperoxia-Induced Neonatal Hyperoxic Lung Injury via Aminoacyl-Peptide Hydrolase.

Background and ObjectivesBronchopulmonary dysplasia (BPD) has major effects in premature infants. Although previous literature has indicated that mesenchymal stem cells (MSCs) can alleviate lung pathology in BPD newborns and improve the survival rate, few research have been done investigating significantly differentially expressed genes in the lungs before and after MSCs therapy. The aim of this study is to identify differentially expressed genes in lung tissues before and after hAD-MSC treatment.Methods and ResultsHuman amnion-derived MSCs (hAD-MSCs) were cultured and met the MSCs criteria for cell phenotype and multidirectional differentiation. Then we confirmed the size of hAD-MSCs-EXOs and their expressed markers. An intratracheal drip of living cells showed the strongest effect on NHLI compared to cellular secretions or exosomes, both in terms of ameliorating pulmonary edema and reducing inflammatory cell infiltration. Through gene chip hybridization, PCR, and western blotting, acylaminoacyl-peptide hydrolase (APEH) expression was found to be significantly decreased under hyperoxia, and significantly increased after hAD-MSC treatment.ConclusionsThe intratracheal transplantation of hAD-MSCs ameliorated NHLI in neonatal rats through APEH.

Predictive value of p16INK4a, Ki-67 and ProExC immuno-qualitative features in LSIL progression into HSIL.

The current nested case-control study was conducted to explore the prognostic value of cyclin-dependent kinase inhibitor 2A (p16INK4a), marker of proliferation Ki-67 (Ki-67) and immunohistochemical cocktail containing antibodies directed against topoisomerase IIα (TOP2A) and minichromosome maintenance 2 (MCM2) proteins (ProExC) immuno-qualitative features to predict low-grade squamous intraepithelial lesion (LSIL) progression. A total of 92 LSIL patients were followed-up for 2 years, where those with high-grade squamous intraepithelial lesion (HSIL) or persistent LSIL were designated as the case group and those who spontaneously regressed were designated as the control group. The infection status of human papillomavirus (HPV) was evaluated using flow-through hybridization and gene chip, whilst the expression of p16INK4a, Ki-67 and ProExC were tested in LSIL patient biopsies by immunohistochemistry. All data were collected at the beginning of the follow-up and patient outcomes were diagnosed by histopathological examination. To analyze the risk factors for LSIL progression, sensitivity, specificity, positive-negative predictive value (PPV-NPV), positive-negative likelihood ratio (PLR-NLR), Youden's index (YI) and multinomial logistic regression analysis was performed. The expression rates of p16INK4a, Ki-67, and ProExC were found to be higher in the progression group compared with those in the persistence and regression groups. Only p16INK4a expression significantly associated with high-risk HPV infection. With respect to predicting HSIL, p16INK4a staining was the most sensitive but Ki-67 staining was found to be the most specific. YI was the highest (42.1%) for p16INK4a expression in the present study, followed by ProExC (39.5%) and Ki-67 (28.3%). However, the expression of ProExC was found to be an independent risk factor for LSIL progression into HSIL. In conclusion, whilst immunohistochemical staining for p16INK4a, Ki-67, and ProExC can be used to predict HSIL progression, only ProExC expression can be applied an independent risk factor for LSIL progression.

Association between Vaginal Micro-environment Disorder and Cervical Intraepithelial Neoplasia in a Community Based Population in China.

There are other factors that contribute to cervical carcinogenesis except HPV infection. This study aimed to investigate the association between vaginal micro-environment factors, including H2O2, vaginal PH value, vagina cleanness, β-glucuronidase, coagulase, neuraminidase and leukocyte esterase and cervical intraeipithelial neoplasia (CIN). In total 1019 participants, including 623 normal cervical (NC) women, 303 patients with low-grade cervical intraepithelial neoplasia (CIN1) and 93 patients with high-grade cervical intraepithelial neoplasia (CIN2/3), were enrolled into the study. HPV genotyping was detected by flow-through hybridization and gene chip. Vaginal H2O2, β-glucuronidase, coagulase, neuraminidase and leukocyte esterase were detected by Aerobic Vaginitis (AV) / Bacterial Vaginal Disease (BV) Five Joint Test Kit. Vaginal PH was measured on the glass slide after microscopy, using color strips with a PH range of 3.8-5.4. Vagina cleanness was determined according to the National Clinical Laboratory Practice Guideline. χ2test and Logistic regression were operated using SPSS 22.0 software. Our results showed that HPV16 infection rate and the abnormal rates of H2O2, PH, vagina cleanness, β-glucuronidase or neuraminidase increased gradually along with the severity of CIN (P<0.05). Abnormities of H2O2, cleanness, β-glucuronidase and neuraminidase were risk factors for CIN regardless of HPV16 infection, furthermore, abnormities of PH value, leukocyte esterase could also increase the risk of CIN in HPV16 positive group. In addition, women with abnormal vaginal micro-environment factors in HPV16 positive group had a significantly higher risk of developing CIN than HPV16 negative group. The results from generalized multifactor dimensionality reduction (GMDR) model showed that there was interaction effect with abnormities of vagina cleanness, H2O2, β-glucuronidase and neuraminidase on CIN2/3 in HPV16 negative group, while, there was interaction effect with abnormities of vagina cleanness, β-glucuronidase and neuraminidase on CIN1 and with abnormities of vagina cleanness, PH, H2O2, β-glucuronidase, neuraminidase and leukocyte esterase on CIN2/3 in HPV16 positive group. Our results suggested that vaginal micro-environment disorder could increase the risk of CIN, especially, the abnormality of H2O2, cleanness, β-glucuronidase and neuraminidase. There were interaction effects with abnormities of H2O2, vagina cleanness, β-glucuronidase and neuraminidase on CIN whether HPV16 was infected or not.

Plasmonic nucleotide hybridization chip for attomolar detection: localized gold and tagged core/shell nanomaterials.

We report a large amplification of surface plasmon signals for a double hybridization microarray chip assembly that bridges localized gold and detection probe-carrying-core/shell Fe3O4@Au nanoparticles for detection of as low as 80 aM miRNA-155 marker in solution. The plasmonic wavelength match of the gold shell with surface localized gold nanoparticles and the additional scattering band of the core/shell material in resonance with the incident 800 nm light source are the underlying factors for the observed remarkable analyte signal at ultra-low (10-18 order) concentrations.

Association of CYP2C19 and UGT1A4 polymorphisms with voriconazole-induced liver injury.

Aim: This study investigated the association between voriconazole-induced liver injury and gene polymorphisms of CYP2C19 and UGT1A4. Materials & methods: Thirty-eight adult patients who received voriconazole therapy were included in the study. Genotype of CYP2C19 was detected using gene chip hybrid analysis. The UGT1A4 142T>G was genotyped using PCR-RFLP analysis. Results: Ten patients (26.3%) had voriconazole-induced liver injury and were considered as the case group There was no significant difference between the two groups in genotype and allele frequencies of CYP2C19*2 and UGT1A4 142T>G (p > 0.05), however, the GA frequency of CYP2C19 *3 in the drug-induced liver injury case group was higher than that in the control group (p < 0.05). Compared with patients carrying *1/*1 or *1/*2, there was no significant difference in voriconazole trough concentration of the patients with *1/*3 (p > 0.05). Conclusion: There was no significant correlation between voriconazole-induced liver injury and gene polymorphisms of CYP2C19 and UGT1A4.

Polygenic risk scores in schizophrenia with clinically significant copy number variants.

AimsRecent studies have revealed that the interplay between polygenic risk scores (PRS) and large copy number variants (CNV; >500kb) is essential for the etiology of schizophrenia (SCZ). To replicate previous findings, including those for smaller CNV (>10kb), the PRS between SCZ patients with and without CNV were compared.MethodsThe PRS were calculated for 724 patients with SCZ and 1178 healthy controls (HC), genotyped using array‐based comparative genomic hybridization and single nucleotide polymorphisms chips, and comparisons were made between cases and HC, or between subjects with and without ‘clinically significant’ CNV.ResultsFirst, we replicated the higher PRS in patients with SCZ compared to that in HC (without taking into account the CNV). For clinically significant CNV, as defined by the American College of Medical Genetics (‘pathogenic’ and ‘uncertain clinical significance, likely pathogenic’ CNV), 66 patients with SCZ carried clinically significant CNV, whereas 658 SCZ patients had no such CNV. In the comparison of PRS between cases with/without the CNV, despite no significant difference in PRS, significant enrichment of the well‐established risk CNV (22q11.2 deletion and 47,XXY/47,XXX) was observed in the lowest decile of PRS in SCZ patients with the CNV.ConclusionAlthough the present study failed to replicate the significant difference in PRS between SCZ patients with and without clinically significant CNV, SCZ patients with well‐established risk CNV tended to have a lower PRS. Therefore, we speculate that the CNV in SCZ patients with lower PRS may contain ‘genuine’ risk; PRS is a possible tool for prioritizing clinically significant CNV because the power of the CNV association analysis is limited due to their rarity.

Genome-wide identification, classification, expression profiling and DNA methylation (5mC) analysis of stress-responsive ZFP transcription factors in rice (Oryza sativa L.)

Cytosine DNA methylation (5mC) is an epigenetic mark that regulates gene expression in plant responses to environmental stresses. Zinc-finger protein (ZFP) is the largest family of DNA-binding transcription factors that also plays an essential role in eukaryote. In plant we have already identified and characterized different useful ZFP-genes. While, the main objective of this research was to observe and identify more targeted stress responsive genes of ZFPs epigenetically throughout genome in rice for the first time. A comprehensive correlation analysis was performed through methylated DNA immunoprecipitation (MeDIP)-chip hybridization in rice under salt and osmotic stresses. High salinity and drought are two major abiotic hazards that are destroying the crop world-wide. As a result, Through-out genome 14 unique stress responsive transcription factors of ZFP-genes with varying level of methylation and expression under two conditions (control vs. stress) were isolated. All the identified genes were confirmed from different databases for their specific structure, cis-regulatory elements, phylogenetic analysis, and synteny analysis. Moreover, the tissue-specific expression patterns, and expression under abiotic and phytohormones stresses were also investigated. Phylogenetically all the genes were divided into 6 distinct subgroups with Arabidopsis and orthologous proteins were find-out through synteny analysis. Available RNA-seq data in response to various phytohormones provided hormone inducible gene expression profile. Through Reverse Transcriptase qPCR (RT-qPCR) analysis tissue-specific expression in shoot and root over various time points against salt and osmotic stresses exhibited the diverse expression patterns of identified genes. Overall, the present study providing a foundation for in-depth characterization of identified genes and to further understand the epigenetic role of DNA methylation for genes expression and environmental stresses regulation in higher plant.

Identification of Key Genes Potentially Related to Intervertebral Disk Degeneration by Microarray Analysis

Aims: This study was designed to investigate differentially expressed genes (DEGs) in the annulus fibrosus (AF), nucleus pulposus (NP), and whole blood (WB) of intervertebral disk degeneration (IDD) patients. Materials and Methods: We retrieved microarray data set GSE70362, which contains the gene expression profiles of 24 AF and 24 NP samples from the Gene Expression Omnibus and identified DEGs in degenerative AF (AF-DEGs) and NP (NP-DEGs) samples compared with nondegenerative samples. We also examined gene expression profiles in WB from patients with IDD and healthy volunteers to identify DEGs in WB (WB-DEGs). We performed functional analyses on the DEGs common to AF-DEGs, NP-DEGs, and WB-DEGs. Expression of the common DEGs was partially validated by quantitative real-time-polymerase chain reaction (QRT-PCR). Results: In total, 846 AF-DEGs, 902 NP-DEGs, and 862 WB-DEGs were identified, and 22 DEGs were common among the three groups. Functional analyses showed that the common DEGs were enriched in 33 biological processes, 16 cellular components, 4 molecular functions, and 9 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; 13 of the common DEGs were included in the protein-protein interaction (PPI) network and superoxide dismutase 2 (SOD2) was identified as a hub gene in the PPI network. The QRT-PCR results for the expression of the genes protein disulfide isomerase family A member 4, FKBP prolyl isomerase 11, ectonucleotide pyrophosphatase/phosphodiesterase 4, SOD2, and actin binding LIM protein 1, were consistent with the gene chip hybridization results. Conclusions: This study identified key genes for future investigations of the underlying molecular mechanisms of IDD. These genes may provide future targets for the clinical treatment and diagnosis of IDD.