GMOIT: a tool for effective screening of genetically modified crops.

BACKGROUND: Advancement in agricultural biotechnology has resulted in increasing numbers of commercial varieties of genetically modified (GM) crops worldwide. Though several databases on GM crops are available, these databases generally focus on collecting and providing information on transgenic crops rather than on screening strategies. To overcome this, we constructed a novel tool named, Genetically Modified Organisms Identification Tool (GMOIT), designed to integrate basic and genetic information on genetic modification events and detection methods. RESULTS: At present, data for each element from 118 independent genetic modification events in soybean, maize, canola, and rice were included in the database. Particularly, GMOIT allows users to customize assay ranges and thus obtain the corresponding optimized screening strategies using common elements or specific locations as the detection targets with high flexibility. Using the 118 genetic modification events currently included in GMOIT as the range and algorithm selection results, a "6 + 4" protocol (six exogenous elements and four endogenous reference genes as the detection targets) covering 108 events for the four crops was established. Plasmids pGMOIT-1 and pGMOIT-2 were constructed as positive controls or calibrators in qualitative and quantitative transgene detection. CONCLUSIONS: Our study provides a simple, practical tool for selecting, detecting, and screening strategies for a sustainable and efficient application of genetic modification.

The molecular mechanism of aging and the role in neurodegenerative diseases.

Aging is a complex and inevitable biological process affected by a combination of external environmental and genetic factors. Humans are currently living longer than ever before, accompanied with aging-related alterations such as diminished autophagy, decreased immunological function, mitochondrial malfunction, stem cell failure, accumulation of somatic and mitochondrial DNA mutations, loss of telomere, and altered nutrient metabolism. Aging leads to a decline in body functions and age-related diseases, for example, Alzheimer's disease, which adversely affects human health and longevity. The quality of life of the elderly is greatly diminished by the increase in their life expectancy rather than healthy life expectancy. With the rise in the age of the global population, aging and related diseases have become the focus of attention worldwide. In this review, we discuss several major mechanisms of aging, including DNA damage and repair, free radical oxidation, telomeres and telomerase, mitochondrial damage, inflammation, and their role in neurodegenerative diseases to provide a reference for the prevention of aging and its related diseases.

Mechanism of V-Shaped Pits on Promoting Hole Injection in the InGaN MQWs: First-Principles Investigation.

In the InGaN multiple quantum wells (MQWs), V-shaped pits play a crucial role in carrier transport, which directly affects emitting efficiency. First-principles calculations are applied to investigate the formation of the V-shaped pits, and the results indicate that they are inclined to form in the N-rich environment. Meanwhile, we calculate the interfacial electronic properties of the sidewalls of the V-shaped pits with varying indium (In) and magnesium (Mg) compositions. The calculated valence band offset (VBO) of the In0.3Ga0.7N/Ga0.94Mg0.06N (0001) is 0.498 eV, while that of the In0.07Ga0.93N/Ga0.94Mg0.06N (101̅1) is 0.340 eV. The band alignment results show that the valence band edges in the Ga1-yMgyN layer are in higher energy than in the InxGa1-xN layer. These are in good agreement with the values reported in the previous numerical simulation. Moreover, the calculation of the projected density of states (PDOS) of interfaces discloses that the strong hybridization between the N 2p orbital and the Mg 2p orbital exerts a vital influence on the upward shifts of the valence band edges in the superlattices (SLs). All these results reveal that holes are easier to inject into the quantum wells (QWs) via the sidewall of V-shaped pits rather than the c-plane QWs, providing a theoretical basis for the growth of InGaN MQWs samples containing V-shaped pits.

Narrative Review: Pathogenesis of the Inflammatory Response and Intestinal Flora in Depression.

Depression, as a common mental illness that is often accompanied by suicidal and homicidal behaviors, is one of the most important diseases in the medical field that requires urgent attention. The pathogenesis of depression is complex, and the current therapeutic drugs such as tricyclic antidepressants (TCAs), monoamine oxidase inhibitors, and secondary serotonin reuptake inhibitors have certain shortcomings. The inflammatory factor hypothesis, one of the pathogenesis of depression, suggests that inflammatory response is a key factor leading to the occurrence and development of depression, and that overactivation of inflammatory factors such as NLRP3, Toll-like receptor 4, and IDO leads to immune-system dysfunction and depression. The other pathogenic hypothesis, the gut flora hypothesis, has also been the focus of recent research. The gut flora may work together with inflammatory factors to cause depression. The approach to treating depression has been by altering the gut flora through drugs or probiotics. However, effective and clear treatment methods are lacking. In this study, by exploring the involvement of intestinal flora and inflammatory factors in the pathogenesis of depression, we found that improving the intestinal flora can affect inflammatory factors and, therefore, provide research ideas for the development of novel drugs to treat depression.

Linolenic acid-metronidazole inhibits the growth of Helicobacter pylori through oxidation.

BACKGROUND: Resistance to antibiotics is one the main factors constraining the treatment and control of Helicobacter pylori (H. pylori) infections. Therefore, there is an urgent need to develop new antimicrobial agents to replace antibiotics. Our previous study found that linolenic acid-metronidazole (Lla-Met) has a good antibacterial effect against H. pylori, both antibiotic-resistant and sensitive H. pylori. Also, H. pylori does not develop resistance to Lla-Met. Therefore, it could be used for preparing broad-spectrum antibacterial agents. However, since the antibacterial mechanism of Lla-Met is not well understood, we explored this phenomenon in the present study. AIM: To understand the antimicrobial effect of Lla-Met and how this could be applied in treating corresponding infections. METHODS: H. pylori cells were treated with the Lla-Met compound, and the effect of the compound on the cell morphology, cell membrane permeability, and oxidation of the bacteria cell was assessed. Meanwhile, the differently expressed genes in H. pylori in response to Lla-Met treatment were identified. RESULTS: Lla-Met treatment induced several changes in H. pylori cells, including roughening and swelling. In vivo experiments revealed that Lla-Met induced oxidation, DNA fragmentation, and phosphatidylserine ectropionation in H. pylori cells. Inhibiting Lla-Met with L-cysteine abrogated the above phenomena. Transcriptome analysis revealed that Lla-Met treatment up-regulated the expression of superoxide dismutase SodB and MdaB genes, both anti-oxidation-related genes. CONCLUSION: Lla-Met kills H. pylori mainly by inducing oxidative stress, DNA damage, phosphatidylserine ectropionation, and changes on cell morphology.

N-region of Cry1Ia: A novel fusion tag for Escherichia coli and Pichia pastoris.

Secretory signal peptides (SPs) can increase enhanced green fluorescent protein (eGFP) expression in cytosol. In this study, SPs Iasp (Cry1Ia), Vasp (Vip3A), and their local sequences were used as fusion tags to compare their effects on eGFP expression in Escherichia coli MC4100 and Pichia pastoris GS115. In E coli, the solubility was almost opposite between the proteins encoded by Vegfp and Iegfp. This may be because the overall hydrophobicity of the SPs differed. When the hydrophobic H-region and C-region were removed, the negative effects on eGFP solubility of the N-regions of both SPs (IaN and VN) were significantly reduced without compromise on the expression level. IaN promotes eGFP protein yield 7.1-fold more than Iasp, and using this peptide in tandem (Ia3N) further enhanced fluorescent fusion protein solubility with an efficacy similar to that of a polycationic tag. Furthermore, the GS-IaNeGFP strain produced the highest fluorescent signal intensity when these fusion proteins were expressed in P. pastoris, and the expression was higher than in other strains, including eGFP. In conclusion, we revealed the potential of the N-region of Iasp as a fusion tag in both prokaryotic and eukaryotic cells and further demonstrated the value of the N-regions of abundant SPs.

Coexpressing the Signal Peptide of Vip3A and the Trigger Factor of Bacillus thuringiensis Enhances the Production Yield and Solubility of eGFP in Escherichia coli.

Many fusion tags have been developed to improve the expression of recombinant proteins. Besides the translocation of cargo proteins, the signal peptides (SPs) of some secretory proteins, such as the ssTorA and Iasp, have been used as an inclusion body tag (IB-tag) or the recombinant expression enhancer in the cytosol of E. coli. In this study, the approach to utilize the SP of Vip3A (Vasp) from Bacillus thuringiensis (Bt) as a fusion tag was investigated. The results showed that either the Vasp or its predicted N- (VN), H- (VH), and C-regions (VC), as well as their combinations (VNH, VNC, and VHC), were able to significantly enhance the production yield of eGFP. However, the hydrophobic region of the Vasp (VH and/or VC) made more than half of the eGFP molecules aggregated (VeGFP, VHeGFP, VCeGFP, VNHeGFP, VNCeGFP, and VHCeGFP). Interestingly, the addition of the Bt trigger factor (BtTF) led to the neutralization of the negative impact and solubilization of the fusion proteins. Therefore, the coexpression of Vasp or its derivates with the chaperone BtTF could be a novel dual-enhancement system for the production yield and solubility of recombinant proteins. Notably, EcTF was unable to impact the solubility of Vasp or its derivates guided proteins, suggesting its different specificities on the recognition or interaction. Additionally, this study also suggested that the translocation of Vip3 in the host cell would be regulated by the BtTF-involved model.

A Review of the Pathogenesis and Chinese Medicine Intervention of Alzheimer's Disease.

Alzheimer's disease (AD) is an age-related neurodegenerative disease that is primary characterized as a cognitive disorder. Its pathology is characterized by the formation of senile plaques in the brain from amyloid-beta (Aß) aggregation, neuronal fibrillary tangles from hyperphosphorylated tau protein aggregation, prolonged inflammatory responses, and neuronal death. The pathogenesis and clinical manifestations of AD are complex, but aging is generally accepted as one of the most important contributing factors. In addition, there are several hypotheses, including the Aß hypothesis based on amyloid plaques, the tau hypothesis based on neuronal fiber entanglement, the inflammation hypothesis based on long-term inflammatory responses causing brain damage, and the neuroprotection hypothesis based on synaptic dysfunction and neuronal death. Although the pathogenesis of AD has been broadly classified into four major hypotheses, there are multiple forms of interactions, which is one of the reasons for its complex pathogenesis. Numerous epidemiological studies have shown the important role of genes in AD, followed by brain damage, hyperlipidemia, diabetes, hypertension, and obesity as risk factors for the disease. Despite years of research, several mysteries in AD remain unsolved. Drugs based on various pathogenetic hypotheses are being investigated in large numbers, but the effects are unsatisfactory. In recent years, traditional Chinese medicine (TCM) has made excellent progress and is expected to provide a new possibility for AD treatment. In this review, we focus on the latest developments in studies on the risk factors-Aß aggregates and related factors such as apolipoprotein E, synaptic loss, and fatty acids, and then present the progress in the research of TCM based on the above pathogenesis, intended to provide a research reference and treatment for AD.

The signal peptide of Cry1Ia can improve the expression of eGFP or mCherry in Escherichia coli and Bacillus thuringiensis and enhance the host's fluorescent intensity.

BACKGROUND: The signal peptides (SPs) of secretory proteins are frequently used or modified to guide recombinant proteins outside the cytoplasm of prokaryotic cells. In the periplasmic space and extracellular environment, recombinant proteins are kept away from the intracellular proteases and often they can fold correctly and efficiently. Consequently, expression levels of the recombinant protein can be enhanced by the presence of a SP. However, little attention has been paid to the use of SPs with low translocation efficiency for recombinant protein production. In this paper, the function of the signal peptide of Bacillus thuringiensis (Bt) Cry1Ia toxin (Iasp), which is speculated to be a weak translocation signal, on regulation of protein expression was investigated using fluorescent proteins as reporters. RESULTS: When fused to the N-terminal of eGFP or mCherry, the Iasp can improve the expression of the fluorescent proteins and as a consequence enhance the fluorescent intensity of both Escherichia coli and Bt host cells. Real-time quantitative PCR analysis revealed the higher transcript levels of Iegfp over those of egfp gene in E. coli TG1 cells. By immunoblot analysis and confocal microscope observation, lower translocation efficiency of IeGFP was demonstrated. The novel fluorescent fusion protein IeGFP was then used to compare the relative strengths of cry1Ia (Pi) and cry1Ac (Pac) gene promoters in Bt strain, the latter promoter proving the stronger. The eGFP reporter, by contrast, cannot indicate unambiguously the regulation pattern of Pi at the same level of sensitivity. The fluorescent signals of E. coli and Bt cells expressing the Iasp fused mCherry (ImCherry) were also enhanced. Importantly, the Iasp can also enhanced the expression of two difficult-to-express proteins, matrix metalloprotease-13 (MMP13) and myostatin (growth differentiating factor-8, GDF8) in E. coli BL21-star (DE3) strain. CONCLUSIONS: We identified the positive effects of a weak signal peptide, Iasp, on the expression of fluorescent proteins and other recombinant proteins in bacteria. The produced IeGFP and ImCherry can be used as novel fluorescent protein variants in prokaryotic cells. The results suggested the potential application of Iasp as a novel fusion tag for improving the recombinant protein expression.