Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy.

BACKGROUND: Children with cancer receiving chemotherapy commonly report a cluster of psychoneurological symptoms (PNS), including pain, fatigue, anxiety, depression, and cognitive dysfunction. The role of the gut microbiome and its functional metabolites in PNS is rarely studied among children with cancer. This study investigated the associations between the gut microbiome-metabolome pathways and PNS in children with cancer across chemotherapy as compared to healthy children. METHODS: A case-control study was conducted. Cancer cases were recruited from Children's Healthcare of Atlanta and healthy controls were recruited via flyers. Participants reported PNS using the Pediatric Patient-Reported Outcomes Measurement Information System. Data for cases were collected pre-cycle two chemotherapy (T0) and post-chemotherapy (T1), whereas data for healthy controls were collected once. Gut microbiome and its metabolites were measured using fecal specimens. Gut microbiome profiling was performed using 16S rRNA V4 sequencing, and metabolome was performed using an untargeted liquid chromatography-mass spectrometry approach. A multi-omics network integration program analyzed microbiome-metabolome pathways of PNS. RESULTS: Cases (n = 21) and controls (n = 14) had mean ages of 13.2 and 13.1 years. For cases at T0, PNS were significantly associated with microbial genera (e.g., Ruminococcus, Megasphaera, and Prevotella), which were linked with carnitine shuttle (p = 0.0003), fatty acid metabolism (p = 0.001) and activation (p = 0.001), and tryptophan metabolism (p = 0.008). Megasphaera, clustered with aspartate and asparagine metabolism (p = 0.034), carnitine shuttle (p = 0.002), and tryptophan (p = 0.019), was associated with PNS for cases at T1. Gut bacteria with potential probiotic functions, along with fatty acid metabolism, tryptophan, and carnitine shuttle, were more clustered in cancer cases than the control network and this linkage with PNS needs further studies. CONCLUSIONS: Using multi-omics approaches, this study indicated specific microbiome-metabolome pathways linked with PNS in children with cancer across chemotherapy. Due to limitations such as antibiotic use in cancer cases, these findings need to be further confirmed in a larger cohort.

Microbiome and Growth in Infants with Congenital Heart Disease.

OBJECTIVES: To profile the gut microbiome in infants with congenital heart disease undergoing cardiac surgery compared with matched infants and to investigate the association with growth (weight, length, and head circumference). STUDY DESIGN: A prospective study in the Cardiac Intensive Care Unit at Children's Healthcare of Atlanta and newborn nursery within the Emory Healthcare system. Characteristics including weight, length, head circumference, and surgical variables were collected. Fecal samples were collected pre-surgery (T1), post-surgery (T2), and before discharge (T3), and once for controls. 16S rRNA V4 gene was sequenced from fecal samples and classified into taxonomy using Silva v138. RESULTS: There were 34 children with congenital heart disease (cases) and 34 controls. Cases had higher alpha-diversity, and beta-diversity showed significant dissimilarities compared with controls. Gut microbiome was associated with lower weight and smaller head circumference (z-score <2). Lower weight was associated with less Acinetobacter, Clostridioides, Parabacteroides, and Escherichia-Shigella. Smaller head circumference with more Veillonella, less Acinetobacter, and less Parabacteroides. CONCLUSIONS: Significant differences in gut microbiome diversity and abundance were observed between infants with congenital heart disease and control infants. Lower weight and smaller head circumference were associated with distinct gut microbiome patterns. Further study is needed to understand the longitudinal effect of microbial dysbiosis on growth in children with congenital heart disease.

On-Demand Portable Paper-Based Electrospray Ionization Mass Spectrometry for High-Sensitivity Analysis of Complex Samples.

Paper spray ionization has been demonstrated to be the most promising substrate-based source, but this technique suffers from the low desorption efficiency of target compounds and poor portability. In the current study, we describe a portable paper-based electrospray ionization (PPESI) in which a piece of triangle paper and adsorbent are packed sequentially into a modified disposable micropipette tip. This source not only captures the feature of paper spray and adsorbent for highly efficient suppression of sample matrixes for target compound analysis but also takes advantage of a micropipette tip to prevent spray solvent from rapid evaporation. The performance of developed PPESI depends on the type and amount of packed adsorbent, paper substrate, and spray solvent and applied voltage. Moreover, by contrast to other related sources, the analytical sensitivity and the spray duration of PPESI in tandem with MS have been improved by factors of 2.8-32.3 and 2.0-13.3, respectively. Based on its high accuracy (>96%) and precision (less than 3% relative standard deviation), the PPESI coupled to a mass spectrometer has been used to determine diverse therapeutic drugs and pesticides in complex biological (e.g., whole blood, serum, and urine) and food (e.g., milk and orange juice) matrixes, and the limits of detection and quantification were 2-4 pg mL-1 and 7-13 pg mL-1, respectively. Taking the portability, high sensitivity, and repeatability, the technique may be a promising alternative for complex sample analysis.

Performance evaluation of a deep learning-based cascaded HRNet model for automatic measurement of X-ray imaging parameters of lumbar sagittal curvature.

PURPOSE: To develop a deep learning-based cascaded HRNet model, in order to automatically measure X-ray imaging parameters of lumbar sagittal curvature and to evaluate its prediction performance. METHODS: A total of 3730 lumbar lateral digital radiography (DR) images were collected from picture archiving and communication system (PACS). Among them, 3150 images were randomly selected as the training dataset and validation dataset, and 580 images as the test dataset. The landmarks of the lumbar curve index (LCI), lumbar lordosis angle (LLA), sacral slope (SS), lumbar lordosis index (LLI), and the posterior edge tangent angle of the vertebral body (PTA) were identified and marked. The measured results of landmarks on the test dataset were compared with the mean values of manual measurement as the reference standard. Percentage of correct key-points (PCK), intra-class correlation coefficient (ICC), Pearson correlation coefficient (r), mean absolute error (MAE), mean square error (MSE), root-mean-square error (RMSE), and Bland-Altman plot were used to evaluate the performance of the cascade HRNet model. RESULTS: The PCK of the cascaded HRNet model was 97.9-100% in the 3 mm distance threshold. The mean differences between the reference standard and the predicted values for LCI, LLA, SS, LLI, and PTA were 0.43 mm, 0.99°, 1.11°, 0.01 mm, and 0.23°, respectively. There were strong correlation and consistency of the five parameters between the cascaded HRNet model and manual measurements (ICC = 0.989-0.999, R = 0.991-0.999, MAE = 0.63-1.65, MSE = 0.61-4.06, RMSE = 0.78-2.01). CONCLUSION: The cascaded HRNet model based on deep learning algorithm could accurately identify the sagittal curvature-related landmarks on lateral lumbar DR images and automatically measure the relevant parameters, which is of great significance in clinical application.

Gray matter reduction in bilateral insula mediating adverse psychiatric effects of body mass index in schizophrenia.

BACKGROUND: Both schizophrenia (SZ) and overweight/obesity (OWB) have shown some structural alterations in similar brain regions. As higher body mass index (BMI) often contributes to worse psychiatric outcomes in SZ, this study was designed to examine the effects of OWB on gray matter volume (GMV) in patients with SZ. METHODS: Two hundred fifty subjects were included and stratified into four groups (n = 69, SZ patients with OWB, SZ-OWB; n = 74, SZ patients with normal weight, SZ-NW; n = 54, healthy controls with OWB, HC-OWB; and n = 53, HC with NW, HC-NW). All participants were scanned using high-resolution T1-weighted sequence. The whole-brain voxel-based morphometry was applied to examine the GMV alterations, and a 2 × 2 full factorial analysis of variance was performed to identify the main effects of diagnosis (SZ vs HC), BMI (NW vs OWB) factors, and their interactions. Further, the post hoc analysis was conducted to compare the pairwise differences in GMV alterations. RESULTS: The main effects of diagnosis were located in right hippocampus, bilateral insula, rectus, median cingulate/paracingulate gyri and thalamus (SZ < HC); while the main effects of BMI were displayed in right amygdala, left hippocampus, bilateral insula, left lingual gyrus, and right superior temporal gyrus (OWB < NW). There were no significant diagnosis-by-BMI interaction effects in the present study, but the results showed that both SZ and OWB were additively associated with lower GMV in bilateral insula. Moreover, mediation analyses revealed the indirect effect of BMI on negative symptom via GMV reduction in bilateral insula. CONCLUSION: This study further supports that higher BMI is associated with lower GMV, which may increase the risk of unfavourable disease courses in SZ.

MiR-139-5p/ENAH Affects Progression of Hepatocellular Carcinoma Cells.

This study aims to investigate the specific mechanism of miR-139-5p regulating hepatocellular carcinoma (HCC). Bioinformatic approaches was utilized to observe miR-139-5p level in HCC and unearth its target mRNA. Next, miR-139-5p and enabled homolog (ENAH) levels in HCC cell lines and normal liver cell line were evaluated with qRT-PCR. ENAH protein level was assessed by Western blot. The cell viability, migratory and invasive capacities of HepG2 cells was observed by cell functional assays. The binding of these two genes was proved through dual-luciferase method. Xenograft nude mouse model was prepared to identify the role of miR-139-5p in vivo. Poorly expressed miR-139-5p in HCC hindered the phenotypes of cancer cells. ENAH was at high level in HCC and it is a downstream target of miR-139-5p. Additionally, ENAH could reverse the suppressive impacts of miR-139-5p on HCC cell behaviors. Likewise, miR-139-5p was determined to perform tumor-suppressing function in vivo. MiR-139-5p hampered HCC cell processes by mediating ENAH, and miR-139-5p/ENAH is hopefully to be the possible target for HCC patients.

A label-free electrochemical impedimetric DNA biosensor for genetically modified soybean detection based on gold carbon dots.

A label-free electrochemical impedimetric biosensor was constructed based on gold carbon dots (GCDs) modified screen-printed carbon electrode for the detection of genetic modified (GM) soybean. The structure and property of GCDs were investigated. The GCDs can directly bind to single-stranded DNA probes through Au-thiol interaction and boost electric conductivity for the DNA sensor construction. The quantification of target DNA was monitored by the change of electron-transfer resistance (Ret) upon the DNA hybridization on sensor surface. Under the optimal conditions, the Ret response (vs. Ag reference electrode) increased with the logarithm of target DNA concentrations in a wide linear range of 1.0 × 10-7 - 1.0 × 10-13 M with a detection limit of 3.1 × 10-14 M (S/N = 3). It was also demonstrated that the proposed DNA sensor possessed high specificity for discriminating target DNA from mismatched sequences. Moreover, the developed biosensor was applied to detect SHZD32-1 in actual samples, and the results showed a good consistency with those obtained from the gel electrophoresis method. Compared with the previous reports for DNA detection, the label-free biosensor showed a comparatively simple platform due to elimination of complicated DNA labeling. Therefore, the proposed method showed great potential to be an alternative device for simple, sensitive, specific, and portable DNA sensor.

Qualitative and Quantitative Real-Time PCR Methods for Assessing False-Positive Rates in Genetically Modified Organisms Based on the Microbial-Infection-Linked HPT Gene.

The hygromycin phosphotransferase (HPT) gene as a selective marker is normally used in screening tests as a first step in detecting and quantifying genetically modified organisms (GMOs) in seeds, food, and feed materials. Nevertheless, if researchers only focus on the HPT gene, it is difficult to distinguish genetically modified (GM) crops from microbial infection, leading to miscalculation of the rate of GM materials in a given sample set. Here, we cloned the 7259 bp sequence carrying the HPT gene from soybean sprouts using the genome walking strategy. BLAST analysis revealed that this sequence was derived from plasmids naturally occurring in microorganisms, such as Escherichia coli, Klebsiella pneumoniae or Salmonella sp. Using the reconstructed plasmid pFP-hpt, qualitative PCR and quantitative real-time PCR (qPCR) methods were established, and 261 bp and 156 bp products were produced. The specificity of these assays was assessed against related pFP-hpt plasmids, plant species with important agronomic traits, and GM crops containing the HPT gene. No unexpected results were observed between samples using these qualitative PCR and qPCR methods. The sensitivity of this qualitative PCR assay was determined at 20 copies, while the limit of detection (LOD) and limit of quantification (LOQ) of qPCR were both 5 copies per reaction. Our in-house validation indicated that the amplification efficiency, linearity, and repeatability of this qPCR assay were in line with performance requirements. Furthermore, a qualitative and quantitative duplex PCR showed high reliability for the simultaneous detection of the HPT gene in a plant sample and environmental micro-organisms harboring the HPT gene in one PCR reaction. These qualitative PCR and qPCR assays were able to differentiate between plants infected with E. coli harboring the HPT gene from GM plants, indicating that these two methods are broadly applicable for routine GMO testing.

Development and assessment of a duplex droplet digital PCR method for quantification of GM rice Kemingdao.

The implementation of genetically modified organism (GMO) labeling policies requires accurate quantitative methods to measure the GMO content in test samples. A Kemingdao/phospholipase D (KMD/PLD) duplex ddPCR method was established with rice genomic DNA (gDNA) of homozygous KMD as template by optimizing the annealing temperature and cycle number. Duplex ddPCR showed a linear response over the dynamic range from 68 to 175,000 copies, covering four orders of magnitude. The limit of detection (LOD) and limit of quantification (LOQ) for duplex ddPCR were determined to be 9 copies and 34 copies of the rice haploid genome, respectively. A very high dilution factor would result in unacceptable bias and coefficients of variation for determining copy number of the gDNA solution, and more than 1000 copies of the DNA template in one reaction is preferred to obtain accurate quantitative results by duplex PCR. Five blinded DNA samples with copy number ratio of 10%, 5%, 1%, 0.1%, and 0.05%, and three blinded real-life matrix samples with mass fraction of 5%, 1%, and 0.5% were quantified by duplex ddPCR, simplex ddPCR, and qPCR. These three methods all gave comparable GMO content and copy numbers within the required precision, but the duplex ddPCR showed the narrowest uncertainty interval and provided the highest precision in comparison to simplex ddPCR and qPCR. The ddPCR is a more appealing and reliable technology for the accurate quantification of GMO content than simplex ddPCR and qPCR considering the uncertainty and precision of quantitative results, the time consumption of generating droplets, and the cost of ddPCR reagents.

Recent developments in mesoporous polydopamine-derived nanoplatforms for cancer theranostics.

Polydopamine (PDA), which is derived from marine mussels, has excellent potential in early diagnosis of diseases and targeted drug delivery owing to its good biocompatibility, biodegradability, and photothermal conversion. However, when used as a solid nanoparticle, the application of traditional PDA is restricted because of the low drug-loading and encapsulation efficiencies of hydrophobic drugs. Nevertheless, the emergence of mesoporous materials broaden our horizon. Mesoporous polydopamine (MPDA) has the characteristics of a porous structure, simple preparation process, low cost, high specific surface area, high light-to-heat conversion efficiency, and excellent biocompatibility, and therefore has gained considerable interest. This review provides an overview of the preparation methods and the latest applications of MPDA-based nanodrug delivery systems (chemotherapy combined with radiotherapy, photothermal therapy combined with chemotherapy, photothermal therapy combined with immunotherapy, photothermal therapy combined with photodynamic/chemodynamic therapy, and cancer theranostics). This review is expected to shed light on the multi-strategy antitumor therapy applications of MPDA-based nanodrug delivery systems.

Development of a certified genomic DNA reference material for detection and quantification of genetically modified rice KMD.

Qualitative and quantitative detection of genetically modified products is inseparable from the application of reference materials (RMs). In this study, a batch of genomic DNA (gDNA) certified reference materials (CRMs) was developed using genetically modified rice Kemingdao (KMD) homozygotes as the raw material. The gDNA CRMs in this batch showed good homogeneity; the minimum sample intake was determined to be 2 µL. The stability study showed that transportation by cold chain is preferable, no significant degradation trend was observed during a 12-month period when storing the gDNA CRMs at 4 °C and - 20 °C, and the number of freeze-thaw cycles cannot exceed 10. The property values of the copy number ratio of transgene and endogenous gene and the copy number concentration for gDNA CRMs were determined by a collaborative characterization of eight laboratories using the duplex KMD/PLD droplet digital PCR (ddPCR) assays. The uncertainty components of characterization, potential between-unit heterogeneity, and potential degradation during long-term storage were combined to estimate the expanded uncertainty of the certified value with a coverage factor k of 2.0. The certified value of copy number ratio for KMD gDNA CRM is 0.99 ± 0.05, and that of copy number concentration is (1.76 ± 0.10) × 105 copies/µL. Compared to the gDNA CRMs in availability, this batch of KMD gDNA CRMs is assigned accurate property values and can be directly used for qualitative and quantitative detection of GMOs as well as evaluation of the parameters of analytical methods with no need of further DNA concentration measurement. Graphical abstract.

Development and strategy of reference materials for the DNA-based detection of genetically modified organisms.

The enforcement of GMO labeling regulations requires validated analytical methods and certified reference materials (CRMs). The early labeling regulations stipulated that the GMO content should be expressed as percentage, but did not specify what unit this percentage referred to. Two reference systems, using mass fraction and copy number ratio as measurement units, individually, are established for GMO analysis using different metrological traceability chains. Three types of CRMs, powder CRMs certified for mass fractions, genomic DNA CRMs, and plasmid DNA CRMs certified for copy number ratios, were developed for calibration and quality control. The type, certification, and measurement unit commutability of current GMO CRMs are presented and discussed in this paper. Both existing reference systems are facing a metrological challenge, although later EU regulations specified that the measurement unit of GMO content must be expressed in mass fraction and recommended to convert one unit into another by introducing a conversion factor, further efforts are required to explore which reference system is more metrologically sound. The determination of conversion factor per CRM batch is recommended to be based on the pure CRMs produced from pure GM materials, which is expected to be the best choice for calibration of PCR measurement results.

Aloperine suppresses human pulmonary vascular smooth muscle cell proliferation via inhibiting inflammatory response.

Abnormal pulmonary arterial vascular smooth muscle cells (PASMCs) proliferation is critical pathological feature of pulmonary vascular remodeling that acts as driving force in the initiation and development of pulmonary arterial hypertension (PAH), ultimately leading to pulmonary hypertension. Aloperine is a main active alkaloid extracted from the traditional Chinese herbal Sophora alopecuroides and possesses outstanding antioxidation and anti-inflammatory effects. Our group found Aloperine has protective effects on monocroline-induced pulmonary hypertension in rats by inhibiting oxidative stress in previous researches. However, the anti-inflammation effects of Aloperine on PAH remain unclear. Therefore, to further explore whether the beneficial role of Aloperine on PAH was connected with its anti-inflammatory effects, we performed experiments in vitro. Aloperine significantly inhibited the proliferation and DNA synthesis of human pulmonary artery smooth muscle cells (HPASMCs) induced by platelet-derived growth factor-BB, blocked progression through G0/G1to S phase of the cell cycle and promoted total ratio of apoptosis. In summary, these results suggested that Aloperine negatively regulated nuclear factor-κB signaling pathway activity to exert protective effects on PAH and suppressed HPASMCs proliferation therefore has a potential value in the treatment of pulmonary hypertension by negatively modulating pulmonary vascular remodeling.

Discussion on the Application of Multi-modal Magnetic Resonance Imaging Fusion in Schizophrenia.

In order to study the application of multi-modal magnetic resonance imaging (MRI) fusion technology in schizophrenia, a 4-way multi-modal fusion method based on mCCA+jICA is used to fuse the local consistency and functional network connection of resting-state functional MRI, gray matter volume of structural MRI, and partial anisotropy of diffusion MRI four characteristics of large sample of schizophrenic patients in multi-site China, trying to find out the common characteristics of function and structure of significant differences between schizophrenia and healthy controls. It is found that compared with normal people, schizophrenic patients show higher local consistency, lower gray matter volume, lower functional network connectivity and decreased white matter integrity in the anterior thalamic radiation, upper bundle and other bundles in brain areas such as basal ganglia network, hippocampus and prominence network. There is a significant correlation between a thalamocortical perceptual loop and auditory hallucination in schizophrenia, and there is a high degree of spatial consistency and commonality among the three MRI features. The higher the volume of gray matter in the dorsolateral and medial prefrontal cortex is, the higher the integrity of white matter fibers such as corticospinal tract, superior longitudinal tract and anterior thalamic radiation is, the higher the digital backward score is, and the better the working memory ability of the subjects is.

Discussion on Patients with Bipolar Disorder and Depressive Episode by Ratio Low Frequency Amplitude Combined with Grey Matter Volume Analysis.

In order to explore the brain functional and structural imaging results of patients with bipolar disorder and depressive episode without taking medicine, and to further explore the disease mechanism of bipolar disorder by combining with clinical symptoms and cognitive function (neuropsychological test), DPABI (Data Processing and Analysis (Resting-State) For Brain Image) software is used to pre-process fMRI (functional magnetic resonance imaging) data and calculate fALFF (ratio low frequency fluctuation amplitude) index. In addition, SPM8 is applied for grey matter volume analysis based on voxel morphology. Pearson correlation model is used to analyze the relationship between functional and morphological changes and clinical symptoms and cognitive tests. DPABI software and SPSS 22.0 software are used to analyze the data. The results show that corresponding abnormal brain areas are found in both functional and structural aspects of patients with bipolar disorder and depression, involving LCSPT emotional circuits. More importantly, the superior frontal gyrus shows significant abnormalities in both functional and structural analysis.

Vasodilatory Effects of Aloperine in Rat Aorta and Its Possible Mechanisms.

The aim of this study was to investigate the vasodilatory effects of aloperine, one of main alkaloid was extracted from Sophora alopecuroides, on rat isolated thoracic aortic rings and its possible mechanisms. The isolated aortic arteries from normotensive Sprague Dawley rats were precontracted with phenylephrine (1 × 10⁻6 M) or KCl (60 mM). Then, aloperine (3.44 × 10⁻³ ­ 17.21 × 10⁻³ M) was added cumulatively and the tension curves was observed and recorded. The changes in tension in both endothelium-intact and endothelium-denuded aortic rings were also recorded. Afterwards, the interaction between aloperine with NG-nitro-L-arginine methylester (0.1 mM), indomethacin (1 × 10⁻³ mM), tetraethylammonium (10 mM), 4-aminopyridine (5 mM), BaCl2 (1 mM) and glibenclamide (0.01 mM) was evaluated. In this study, aloperine caused concentration-dependent relaxations in aortic rings precontracted with phenylephrine, but this effect was not observed in KCl-pretreated rings. Removal of endothelium showed no influence on vasodilatory effects of aloperine. In addition, preincubation with NG-nitro-L-arginine methylester and indomethacin did not inhibit the vasodilatory effects of aloperine, suggesting that the vasodilative action is endothelium-independent. Relaxant responses to aloperine were inhibited by tetraethylammonium and 4-aminopyridine. However, the vasorelaxant effect of aloperine was also not influenced by the preincubation with BaCl2 and glibenclamide. These findings suggest that aloperine-induced vasorelaxation effects are mainly due to the operations of voltage-operated potassium channels and ATP-sensitive potassium channels.

Intranasal immunization with novel EspA-Tir-M fusion protein induces protective immunity against enterohemorrhagic Escherichia coli O157:H7 challenge in mice.

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 causes hemorrhagic colitis and hemolytic uremic syndrome in humans. Due to the risks associated with antibiotic treatment against EHEC O157:H7 infection, vaccines represent a promising method for prevention of EHEC O157:H7 infection. Therefore, we constructed the novel bivalent antigen EspA-Tir-M as a candidate EHEC O157:H7 subunit vaccine. We then evaluated the immunogenicity of this novel EHEC O157:H7 subunit vaccine. Immune responses to the fusion protein administered by intranasal and subcutaneous routes were compared in mice. Results showed higher levels of specific mucosal and systemic antibody responses induced by intranasal as compared to subcutaneous immunization. Intranasal immunization enhanced the concentration of interleukin-4, interleukin-10, and interferon-γ, while subcutaneous immunization enhanced only the latter two. In addition, intranasal immunization protected against EHEC O157:H7 colonization and infection in mice at a rate of 90%.Histopathological analysis revealed that vaccination reduced colon damage, especially when administered intranasally. In contrast, subcutaneous immunization elicited a weak immune response and exhibited a low protection rate. These findings demonstrate that intranasal immunization with the fusion protein induces both humoral and cellular immune (Th1/Th2) responses in mice. The novel EspA-Tir-M novel fusion protein therefore represents a promising subunit vaccine against EHEC O157:H7 infection.

Successful detection of foreign inserts in transgenic rice TT51-1 (BT63) by RNA-sequencing combined with PCR.

BACKGROUND: As event-specific sequence information for most unauthorised genetically modified organisms (GMOs) is currently still unavailable, detecting unauthorised GMOs remains challenging. Here, we used insect-resistant rice TT51-1 as an example to develop a novel approach via detecting GMOs by RNA-seq (sequencing) and PCR. RNA-seq of TT51-1 generated 4.8 million (M) 21-nt cDNA tags. Alignment to the Oryza sativa subsp. japonica reference genome revealed 24 098 unmapped tags. Foreign tags from the nopaline synthetic enzyme gene (NOS) terminator and insect-resistant genes were then identified by searching against the NCBI VecScreen and NT databases. RESULTS: To further isolate foreign DNA sequences, putative NOS terminator and insect-resistant gene tags were combined and used directly as primer pairs for long-range PCR, producing a 5016-bp fragment. The inserted DNA sequence of TT51-1 has been submitted to a database, and thus, similarity analysis using the database could identify a test sample. CONCLUSION: The novel approach has a great potential for application to the detection and identification of unauthorised GMOs in food and feed products. © 2016 Society of Chemical Industry.

Development and application of a general plasmid reference material for GMO screening.

The use of analytical controls is essential when performing GMO detection through screening tests. Additionally, the presence of taxon-specific sequences is analyzed mostly for quality control during GMO detection. In this study, 11 commonly used genetic elements involving three promoters (P-35S, P-FMV35S and P-NOS), four marker genes (Bar, NPTII, HPT and Pmi), and four terminators (T-NOS, T-35S, T-g7 and T-e9), together with the reference gene fragments from six major crops of maize, soybean, rapeseed, rice, cotton and wheat, were co-integrated into the same single plasmid to construct a general reference plasmid pBI121-Screening. The suitability test of pBI121-Screening plasmid as reference material indicated that the non-target sequence on the pBI121-Screening plasmid did not affect the PCR amplification efficiencies of screening methods and taxon-specific methods. The sensitivity of screening and taxon-specific assays ranged from 5 to 10 copies of pBI121-Screening plasmid, meeting the sensitivity requirement of GMO detection. The construction of pBI121-Screening solves the lack of a general positive control for screening tests, thereby reducing the workload and cost of preparing a plurality of the positive control.

A self-probing primer PCR method for detection of very short DNA fragments.

A novel self-probing primer method that based on the fluorescence resonance energy transfer principle is designed to detect DNA fragments of approximately 40 bp. Four self-probing primer reaction systems were developed to target a maize endogenous reference gene (HMG), a soybean endogenous reference gene (Lectin), a rapeseed endogenous reference gene (CruA) and an exogenous gene 5-enolpyruvylshikimate-3-phosphate synthase (ctp2-cp4epsps). These four primer systems were confirmed to have a high level of inter-species specificity and good intra-species stability. The limit of detection was estimated to be 10 copies of haploid genomes for all four assays. The validation results demonstrated that the self-probing primer methods are able to quantify the DNA amount in the different samples with good sensitivity and precision. When highly processed food products were assayed, the self-probing primer method produced better results than the TaqMan probe method. Overall, the self-probing primer method is suitable for qualitative and quantitative detection of very short DNA targets in samples of different sources.