Mechanism of a Volatile Organic Compound (6-Methyl-2-Heptanone) Emitted From Bacillus subtilis ZD01 Against Alternaria solani in Potato

The antagonistic mechanisms of soluble non-volatile bioactive compounds, such as proteins and lipopeptides emitted from Bacillus have been widely studied. However, there are limited studies on the antifungal mechanisms of volatile organic compounds (VOCs) produced by Bacillus against plant fungal diseases. In this study, the antagonistic mechanisms of one specific VOC, 6-methyl-2-heptanone, against Alternaria solani were investigated. To optimize the extraction conditions of headspace solid-phase microextraction, a 50/30-μm divinylbenzene/carboxen/polydimethylsiloxane fiber at 50°C for 40 min was used. For gas chromatography-mass spectrometry using a free fatty acid phase capillary column, 6-methyl-2-heptanone accounted for the highest content, at 22.27%, of the total VOCs from Bacillus subtilis ZD01, which inhibited A. solani mycelial growth strongly in vitro. Therefore, 6-methyl-2-heptanone was selected as the main active chemical to elucidate the action mechanisms against A. solani. Scanning and transmission electron microscopy analyses revealed that after exposure to an EC50 dose of 6-methyl-2-heptanone, A. solani hyphal cells had a wide range of abnormalities. 6-Methyl-2-heptanone also caused the capture of cellular fluorescent green label and the release of adenosine triphosphate (ATP) from outer membranes A. solani cells, which may enhance 6-methyl-2-heptanone ability to reach the cytoplasmic membrane. In addition, 6-methyl-2-heptanone showed strong inhibitory effect on A. solani conidial germination. It also damaged conidial internal structures, with the treated group having collapsed shrunken small vesicles as observed by transmission electron microscopy. Because 6-methyl-2-heptanone showed strong effects on mycelial integrity and conidial structure, the expression levels of related pathogenic genes in A. solani treated with 6-methyl-2-heptanone were investigated. The qRT-PCR results showed that transcriptional expression levels of slt2 and wetA genes were strongly down-regulated after exposure to 6-methyl-2-heptanone. Finally, because identifying the functions of pathogenic genes will be important for the biological control of A. solani, the wetA gene was identified as a conidia-associated gene that plays roles in regulating sporulation yield and conidial maturation. These findings provide further insights into the mechanisms of VOCs secreted by Bacillus against A. solani.

Ocular phenotype and genetical analysis in patients with retinopathy of prematurity

Background Retinopathy of prematurity (ROP) is a multifactorial retinal disease, involving both environmental and genetic factors; The purpose of this study is to evaluate the clinical presentations and genetic variants in Chinese patients with ROP. Methods A total of 36 patients diagnosed with ROP were enrolled in this study, their medical and ophthalmic histories were obtained, and comprehensive clinical examinations were performed. Genomic DNA was isolated from peripheral blood of ROP patients, polymerase chain reaction and direct sequencing of the associated pathogenic genes (FZD4, TSPAN12, and NDP) were performed. Results All patients exhibited the clinical manifestations of ROP. No mutations were detected in the TSPAN12 and NDP genes in all patients; Interestingly, three novel missense mutations were identified in the FZD4 gene (p.A2P, p.L79M, and p.Y378C) in four patients, for a detection rate of 11.1% (4/36). Conclusions This study expands the genotypic spectrum of FZD4 gene in ROP patients, and our findings underscore the importance of obtaining molecular analyses and comprehensive health screening for this retinal disease.

Uncovering the Potential Mechanism of Xue Fu Zhu Yu Decoction in the Treatment of Intracerebral Hemorrhage

Background Chinese herbal medicine (CHM) is characterized by “multi- compounds, multi-targets and multi-pathway”, which has advanced benefits for the preventing and treating complex diseases, but still exists unsolved issues, mainly include unclear material basis and underling mechanism of prescription. Integrated pharmacology is a hot cross research area based on system biology, mathematic and poly-pharmacology. It can systematically and comprehensively investigate the therapeutic reaction of compounds or drugs on pathogenic genes network, and is especially suitable for the study of complex CHM systems. Intracerebral Hemorrhage (ICH) is one of the main causes of death among Chinese residents, which is characterized by high mortality and high disability rate. In recent years, the treatment of ICH by CHM has been deeply researched. Xue Fu Zhu Yu Decoction (XFZYD), one of the commonly used prescriptions in treating ICH at clinic level, has not been clear about its mechanism in treating ICH. Methods Here, we established a strategy, which based on compounds-targets, pathogenetic genes, network analysis and node importance calculation. Using this strategy, the core compounds group (CCG) of XFZYD was predicted and validated by in vitro experiments. The molecular mechanism of XFZYD in treating ICH was deduced based on CCG and their targets. Results The results show that the CCG with 43 compounds predicted by this model is highly consistent with the corresponding Compound-Target (C-T) network in terms of gene coverage, enriched pathway coverage and accumulated contribution of key nodes at 89.49%, 88.72% and 90.11%, respectively, which confirmed the reliability and accuracy of the effective compound group optimization and mechanism speculation strategy proposed by us. Conclusions Our strategy of optimizing the effective compound groups and inferring the mechanism provides a strategic reference for explaining the optimization and inferring the molecular mechanism of prescriptions in treating complex diseases of CHM.

DOK5 as a Prognostic Biomarker of Gastric Cancer Immunoinvasion: A Bioinformatics Analysis

Background. Docking protein 5 (DOK5) is a member of the docking protein group of membrane proteins and is an adapter protein involved in signal transduction. Nevertheless, the role of DOK5 expression in the prognosis of gastric cancer (GC) remains unclear. Methods. In this study, clinical prognostic parameters and survival data related to DOK5, in patients with GC, were analyzed using bioinformatics analysis comprising Oncomine and TIMER, UALCAN database, Kaplan-Meier plotter, GEPIA, GSEA, DAVID, and cBioPortal websites. Results. In our study, GC contained various DOK5 expressions, which forecasted poor survival outcomes. Moreover, our research showed that high DOK5 could predict high-level infiltration of several GC immune cells, as evidenced by M1, TAM, M2, B cell, and T cell failure. Hence, DOK5 might become a new gastric cancer biomarker and therapeutic target. In the following analysis, in order to explore the prognostic value of DOK5 in GC, more clinical trials are needed to validate our results. Conclusions. Through multiple database verifications, DOK5 was found to be part of the pathogenic genes for GC. Thus, it can change the formation and progression of tumors by acting on human immunity.

Risk assessment of gastric cancer in the presence of Helicobacter pylori cagA and hopQII genes

Helicobacter pylori bacterium is one of the most common bacterial infections globally and is the leading cause of indigestion, gastric and duodenal ulcers, and gastric cancer. This bacterium can escape the antibacterial effects of stomach acid by adapting to the inner layers of the stomach. It combines with the natural sugars in the gastric mucosa. The compound is so effective that it makes bacterium resistant. For genes related to the pathogenesis of H. pylori, using the existence of genes such as cagA, hopQI, and hopQII, PCR is performed on some of these genes to amplify fragments of different lengths. One of the less-studied cases is that two or more pathogenic genes are simultaneously associated with H. pylori. This study examined the frequency of diseases and healthy individuals infected with H. pylori and cagA and hopQII genotypes. To diagnose H. pylori infection in healthy and stomach cancer patients, the PCR products are electrophoresed on the agarose gel after glmM gene amplification by PCR. To this aim, stomach tissue biopsies were used for patients, and saliva was used for healthy individuals. For this purpose, 150 gastric biopsy samples from stomach cancer patients and 150 saliva samples from healthy people were collected. Data showed a significant relationship between the coexistence of two genes, cagA and hopQII, and stomach cancer. 34.2% of patients and 10.1% of healthy individuals showed two genotypes, while other healthy people (89.9%) infected with H. pylori did not have this genotype. Therefore, the simultaneous presence of these two bacterial genes in human societies can be an essential biomarker for the diagnosis and prognosis of gastric cancer.

Systemic lupus erythematosus after delivery and myasthenia gravis with COL6A1 gene mutation: A case report

The coexistence of systemic lupus erythematosus (SLE) and myasthenia gravis (MG) is rarely reported, especially the appearance of SLE before MG. In addition to the production of autoantibodies after thymectomy, gene mutation may be an important contributing factor to the overlap of SLE and MG. Here, we report a case of a female patient diagnosed with SLE before MG and found to carry the heterozygous variation COL6A1 c. 2608G>A. We propose that this gene variation weakens the function of COL6A1 and indirectly activates STAT1, resulting in the phenotype of these two autoimmune diseases. This report suggests that it is feasible to explore common pathogenic genes in SLE and MG through future large-scale research.

Anatomical Characteristics and Potential Gene Mutation Sites of a Familial Recurrent Patellar Dislocation

Background Recurrent patellar dislocation is the result of anatomical alignment and imbalance of restraint of bone and soft tissue. To investigate the anatomical characteristics of the knee joint in a family of patients with recurrent patella dislocation, and to screen the possible pathogenic genes in this family by whole exon sequencing in 4 patients and 4 healthy subjects, so as to provide theoretical basis for the pathogenesis of this disease. Methods The data related to patella dislocation were measured by imaging data. The peripheral blood DNA of related family members was extracted for full exon sequencing, and then the sequencing results were compared with the human database. By filtering out synonymous mutations and high-frequency mutations, and then integrating single nucleotide non-synonymous mutations of family members, disease-causing genes were found. Results All patients in this family have different degree of abnormal knee anatomy, which is closely related to patella dislocation. The sequencing results of patients and normal persons in this patella dislocation family were compared and analyzed, and the data were filtered through multiple biological databases. Find HOXB9(NM_024017.4:p.Glu135Gly/c.404A>G),COL1A1(NM_000088.3:p.Ala1256 Thr/c.3766G>A),GNPAT(NM_014236.3:p.Asp519Gly/c1556A>G),NANS(NM_018946.3:p.Glu68Asp/c.204G>C),SLC26A2(NM_000112.3:p.Thr689Ser/c.2065A>T) are not synonymous mutations (MISSENSE). Through Sanger sequencing, HOXB9 and SLC26A2 genes were found to be the pathogenic genes of this family with recurrent patella dislocation. Conclusions The anatomical structure of the knee joint of patients with recurrent patellar dislocation in this family is obviously abnormal. HOXB9 mutation may be the high frequency pathogenic gene of recurrent patella dislocation in this family, while COL1A1, GNPAT, NAans, SLC26A2 gene may be the sporadical pathogenic gene.

Application of CRISPR/Cas9 in Alzheimer’s Disease

Alzheimer’s disease (AD) is a progressive and irreversible neurodegenerative disorder clinically characterized by cognitive impairment, abnormal behavior, and social deficits, which is intimately linked with excessive β-amyloid (Aβ) protein deposition along with many other misfolded proteins, neurofibrillary tangles formed by hyperphosphorylated tau protein aggregates, and mitochondrial damage in neurons, leading to neuron loss. Currently, research on the pathological mechanism of AD has been elucidated for decades, still no effective treatment for this complex disease was developed, and the existing therapeutic strategies are extremely erratic, thereby leading to irreversible and progressive cognitive decline in AD patients. Due to gradually mental dyscapacitating of AD patients, AD not only brings serious physical and psychological suffering to patients themselves, but also imposes huge economic burdens on family and society. Accordingly, it is very imperative to recapitulate the progress of gene editing-based precision medicine in the emerging fields. In this review, we will mainly focus on the application of CRISPR/Cas9 technique in the fields of AD research and gene therapy, and summarize the application of CRISPR/Cas9 in the aspects of AD model construction, screening of pathogenic genes, and target therapy. Finally, the development of delivery systems, which is a major challenge that hinders the clinical application of CRISPR/Cas9 technology will also be discussed.

Molecular Analysis of Pathogenic Genes (lasB and exoA) in Pseudomonas aeruginosa Strains Isolated from Animal and Human Samples and Determination of Their Resistance Pattern

: Pseudomonas aeruginosa (P. aeruginosa) has a wide range of virulence factors. These factors have the potential to increase bacterial pathogenicity and serious infection. The purpose of this study was to evaluate the virulence profiles and antibiotic susceptibility of isolates of P. aeruginosa originated from animal and human samples. The samples were cultured on selective media before being extracted for DNA and subjected to a PCR technique to detect virulence genes. There was a significant difference in the isolation of P. areuginosa isolated from human and animal sources. Where, in humans, the percentage of P. areuginosa was 52 (68.42%) while in animals the percentage of P.aeruginosa was 24 (31.57%). In humans, the percentage of P. aeruginosa in blood was 26.92% (14 isolates), in urine it was 25% (13 isolates), in wound it was 40.38%21 isolates), and in sputum it was 7.69% (4 isolates). We used a PCR technique that produced highly specific and accurate results for detecting virulence factor genes in P. aeruginosa isolates that cause disease in humans and animals. The percentage of exoA genes was (83.33%) and (81.66%) in the animal and human, and that of lasB was (58.33%) and (92.30%) in animal and human samples respectively. Furthermore, both the exoA and lasB genes are found in 26.31% of animal strains and 17.10% of human strains. The disc diffusion method was used to determine antimicrobial susceptibility. In both animal and human isolates, P. aeruginosa showed the highest resistance to amikacin and the lowest resistance to ciprofloxacin. These findings could aid in the understanding of pathogenicity processes, treatment direction, and the development of strategies to control the spread of epidemic P. aeruginosa strains.

Comprehensive Analysis of Differential Expression Profiles of Long Non-coding RNAs with Associated Co-expression and Competing Endogenous RNA Networks in the Hippocampus of Patients with Alzheimer's Disease

Background: Alzheimer's disease (AD) is still one of the major threats to human health. Although a satisfactory treatment for AD has not yet been discovered, it is necessary to continue to search for novel approaches to deal with this insidious and debilitating disease. Although numerous studies have shown that long non-coding RNA (lncRNA) occupy a significant role in a variety of diseases, their roles in AD remain unclear. Objectives: Using data analysis to explore the role of lncRNA in the course of AD, to further our understanding of AD, and to look forward to finding a new breakthrough for the treatment of AD. Methods: We downloaded and screened expression data of the hippocampal regions of patients with AD from the Gene Expression Omnibus database. We generated lncRNA-miRNA-mRNA networks based on the competing endogenous RNA (ceRNA) hypothesis, and according to gene expression level, we constructed a coding-noncoding co-expression (CNC) network and then executed cis- and trans-regulation analyses. Results: Through comprehensive and systematic analyses, we found that lncRNAs MALAT1, OIP5-AS1, LINC00657, and lnc-NUMB-1 regulated the expression of the key AD pathogenic genes APP, PSEN1, BACE1; and that these lncRNAs may promote the distribution of β-amyloid (Aβ protein) in the brain through exosomes. In addition, lncRNAs were found to adjust viral transcriptional expression, thereby further supporting viral pathogenesis for AD. Conclusions: The lncRNAs MALAT1, OIP5-AS1, LINC00657, and lnc-NUMB-1 that are present in the hippocampus of AD patients exert an important influence on the development of this disease.