The Quest to Identify a New Virus Disease of Sunflower from Nebraska

Between 2010 and 2018, sunflower plants exhibiting virus-like symptoms, including stunting, mottling, and chlorotic ringspots on leaves, were observed from commercial fields and research plots from four sites within three distinct counties of western Nebraska (Box Butte, Kimball, and Scotts Bluff). Near identical symptoms from field samples were reproduced on seedlings mechanically in the greenhouse on multiple occasions, confirming the presence of a sap-transmissible virus from each site. Symptomatic greenhouse-inoculated plants from the 2010 and 2011 Box Butte samples tested negative for sunflower mosaic virus (SuMV), sunflower chlorotic mottle virus (SuCMoV), and all potyviruses in general by ELISA and RT-PCR. Similar viral-like symptoms were later observed on plants in a commercial sunflower field in Kimball County in 2014, and again from volunteers in research plots in Scotts Bluff County in 2018. Samples from both of these years were again successfully reproduced on seedlings in the greenhouse as before following mechanical transmissions. Symptom expression for all years began 12 to 14 days after inoculation as mild yellow spots followed by the formation of chlorotic ringspots from the mottled pattern. The culture from 2014 tested negatively for three groups of nepoviruses via RT-PCR, ruling this group out. However, transmission electron microscopy assays of greenhouse-infected plants from both 2014 and 2018 revealed the presence of distinct, polyhedral virus particles. With the use of high throughput sequencing and RT-PCR, it was confirmed that the infections from both years were caused by a new virus in the tombusvirus genus and was proposed to be called Sunflower ring spot mottle virus (SuRSMV). Although the major objective of this project was to identify the causal agent of the disease, it became evident that the diagnostic journey itself, with all the barriers encountered on the 10-year trek, was actually more important and impactful than identification.

Recent two-year advances in anti-dengue small-molecule inhibitors

Dengue is an acute tropical infectious disease transmitted by mosquitoes, which has posed a major challenge to global public health. Unfortunately, there is a lack of clinically proven dengue-specific drugs for its prevention and treatment. As the pathogenesis of dengue has not been fully elucidated, the development of specific drugs is seriously hindered. This article briefly describes the pathogenesis of dengue fever, the molecular characteristics, and epidemiology of dengue virus, and focuses on the potential small-molecule inhibitors of dengue virus, including on-target and multi-targeted inhibitors, which have been reported in the past two years.

Occurrence and transfer characteristics of blaCTX-M genes among Escherichia coli in anaerobic digestion systems treating swine waste

Livestock waste is a known reservoir of Escherichia coli (E. coli) carrying clinically important CTX-M-type extended-spectrum β-lactamase genes (bla_CTX-M), however, the occurrence and transfer characteristics of bla_CTX-M genes during anaerobic digestion (AD) remain unclear. Herein, four full-scale and two parallel lab-scale AD systems treating swine waste under ambient and mesophilic conditions were investigated by both molecular- and culture-based methods to reveal the occurrence and transfer behaviors of bla_CTX-M genes during AD. Real-time TaqMan polymerase chain reaction revealed 1.3 × 10⁴-6.8 × 10⁵ and 3.0 × 10⁴-7.0 × 10⁵ copies/mL of bla_CTX-M groups 1 and 9 in all feeding substrates. While AD reduced the absolute abundance of groups 1 and 9 by 0.63-2.24 and 0.08-1.30 log (P < 0.05), 5.0 × 10²-4.1 × 10³ and 1.1 × 10⁴-3.5 × 10⁴ copies/mL of groups 1 and 9 remained in the anaerobic effluent, respectively. In total, 141 bla_CTX-M-carrying E. coli isolates resistant to cefotaxime were obtained from the AD reactors. Whole-genome sequencing showed that bla_CTX-M-65 mainly carried by E. coli ST155 was the most frequently detected group 9 subtype in the feeding substrate; whereas bla_CTX-M-14 associated with the dominant clones E. coli ST6802 and ST155 became the major subtype in AD effluent. Furthermore, bla_CTX-M-14 was flanked by ΔIS26 upstream and ΔIS903B downstream. The ΔIS26-bla_CTX-M-14-ΔIS903B element was mainly located on the IncHI2 plasmid in E. coli ST48 and ST6802 and also the IncFIB plasmid in ST155 in anaerobic effluent. Conjugation assays showed that the plasmids harboring bla_CTX-M-14 could be successfully transferred at a frequency of 10^-3-10^-2 cells per recipient cell. This study revealed that bla_CTX-M genes remained in both the full-scale and lab-scale AD effluents of swine waste. Thus, additional efforts should be implemented to block the discharge and spread of antibiotic resistance genes to the environment.

[Effects of celastrol on autophagy and endoplasmic reticulum stress-mediated apoptosis in a mouse model of nonalcoholic fatty liver disease]

Objective: To investigate the effect of celastrol (CEL) on autophagy and endoplasmic reticulum stress-mediated apoptosis in a mouse model of nonalcoholic fatty liver disease (NAFLD). Methods: Eighteen male C57BL/6J mice were randomly divided into normal control (NC, n=6), high-fat diet (HFD, n=6) and celastrol group (HFD+CEL, n=6). The normal control group was fed with regular diet, and the high-fat diet and celastrol group were fed with high-fat diet for 12 weeks. After successful modeling, celastrol group were injected with 100 μg⋅kg^-1⋅d^-1 celastrol intraperitoneally for 4 weeks, and NC and HFD group were injected intraperitoneally with the same doses of normal saline. Serum concentrations of alanine aminotransferase (ALT), aspartate aminotransferase (AST), triglyceride (TG), total cholesterol (TC), high density lipoprotein cholesterol (HDL-C) and low density lipoprotein cholesterol (LDL-C) were measured in mouse after 4-weeks of intervention. HE and Oil Red O staining were used to observe the pathomorphological changes and lipid droplet deposition in mouse liver, and the findings were scored according to NAFLD activity score (NAS). Western blot was used to detect the expression levels of liver microtubule associated protein 1 light chain 3 (LC3), P62, glucose-regulated protein 78 (GRP78), protein kinase R-like endoplasmic reticulum kinase (PERK), phosphorylated PERK (p-PERK), activated transcription factor 4 (ATF4), C/EBP homologous protein (CHOP), cleaved Caspase-3(cleaved caspase-3), B-cell lymphoma-2 (Bcl-2) and Bcl-2 related X protein (Bax).TUNEL staining was used to observe the apoptosis of hepatocytes. One-way analysis of variance was used for the intergroup comparison. Results: Serum levels of ALT (68.71±8.57) U/L, AST (209.63±28.64) U/L, TG (0.97±0.14) mmol/L, TC (4.12±0.64) mmol/L, and LDL -C (0.40±0.06) mmol/L were lower in celastrol group mouse than HFD group [(110.19±10.79) U/L, (399.72±73.47) U/L, (1.44±0.13) mmol/L, (5.65±0.54) mmol /L, (0.61±0.07) mmol/L] (P<0.05); while the serum HDL-C level (1.29±0.17) mmol/L was higher in celastrol than HFD group (0.72±0.13) mmol/L (P<0.05). HE and Oil Red O staining showed that lipid deposition and intralobular inflammation were apparent in the liver tissue of HFD group mouse, and the NAS score was significantly increased, while the hepatocyte steatosis and intralobular inflammation were alleviated after celastrol intervention, and the NAS score was decreased significantly (P<0.05). Compared with HFD group, the ratio of LC3II/I was significantly increased in the liver of celastrol group mouse, and the P62 was significantly decreased (P<0.05). Meanwhile, the expression level of GRP78, p-PERK/PERK , ATF4, and CHOP was significantly lower in celastrol than HFD group (P<0.05). In addition, the expressions of cleaved caspase-3 and Bax were significantly lower in celastrol than HFD group, and the expression of Bcl-2 was significantly increased (P<0.05). At the same time, the apoptosis rate of hepatocytes was also significantly lower in celastrol than HFD group (P<0.05). Conclusion: Celastrol can effectively alleviate the lipid deposition, protect hepatocytes and delay the progression of non-alcoholic fatty liver disease in mouse liver with non-alcoholic fatty liver disease. In addition, its mechanism of action may be related to the induction of autophagy, inhibition of endoplasmic reticulum stress PERK/ATF4/CHOP pathway and its mediated apoptosis.

Genome and Phylogenetic Analysis of Cucumber Green Mottle Mosaic Virus Global Isolates and Validation of a Highly Sensitive RT-qPCR Assay

The last two decades have seen exponential growth in the international movement of seeds for annual food crops, from a gross U.S. import value of $349 million in 1999 to $1.05 billion in 2019. This has led to the proportionate growth of seedborne pathogens dispersed with seed stocks. One such viral pathogen is cucumber green mottle mosaic virus (CGMMV), a tobamovirus that infects cucurbit crops such as melon, watermelon, cucumber, pumpkin, and squash. The first CGMMV introduction to California occurred in 2013, with subsequent annual outbreaks or detections since then. Here, we describe the use of next-generation sequencing to characterize the full genomes of 25 CGMMV isolates collected between 2013 and 2020 in California, either from CGMMV field detections or seed lots identified as CGMMV positive. We sequenced an additional 31 CGMMV isolates collected in Europe, Israel, and southeast Asia that were provided by industry collaborators. We also performed an in silico nucleotide database search in GenBank for full genome CGMMV sequences to include in all in silico analyses. Based on conserved regions within the coat protein gene, we then developed a quantitative reverse-transcription PCR assay for the sensitive and specific detection of CGMMV in seed and plant samples. Finally, based on our sequence and phylogenetic analysis, our data support that CGMMV has been introduced multiple times into California.

[Dynamic changes of locus coeruleus damage in Parkinson's disease-like mice induced by paraquat]

Objective: To observe the dynamic changes of brainstem locus coeruleus (LC) damage in Parkinson' s disease (PD) -like mice by paraquat (PQ) . Methods: In October 2019, 36 male C57BL/6 mice were randomly divided into the exposure group and the control group, with 18 mice in each group. The mice in the exposure group were given intraperitoneal injection of 15 mg/kg PQ, and the mice in the control group were given intraperitoneal injection of 0.9% saline, twice a week for 8 weeks. Neurobehavioral changes (pole climbing test, swimming test, open field test, tail hanging test, high plus maze test and water maze test) were observed at 4 weeks, 6 weeks and 8 weeks, respectively, and the changes of motor ability, emotion and cognitive function were evaluated. The brain tissue of mice were taken and stained with Hematoxylin-Eosin (HE) to observe the pathological changes of LC. Nissl staining was used to detect the changes of neuronal Nissl bodies in LC. Immunohistochemistry (IHC) staining was used to detect the expression of neuron nuclear antigen (NeuN) , dopamine (DA) neurons and norepinephrine (NE) neuron markers tyrosine hydroxylase (TH) , α-synuclein (α-syn) in substantia nigra (SN) and LC. The expression levels of NeuN, TH and α-syn in the midbrain and brainstem were detected by Western blotting. TUNEL staining was used to detect neuronal apoptosis in LC. Results: Compared with the 4th week of PQ exposure group, the time of pole climbing and swimming immobility were gradually increased, the ratio of open arm residence time of high plus maze test and the number of times of the platform and the residence time of platform quadrant in water maze test were gradually decreased (P<0.05) in the exposure group with the progress of exposure time. The results of HE and Nissl staining showed that the neurons in LC gradually arranged loosely, the nucleus were deeply stained, the cytoplasm was pyknosis, and the number of Nissl bodies gradually decreased (P<0.05) in the exposure group with the progress of exposure time. IHC results showed that the number of NeuN and TH positive cells in SN and LC of mice were gradually decreased, and the positive expression of α-syn was gradually increased (P<0.05) in the exposure group with the progress of exposure time. Western blotting results showed that the expression levels of NeuN and TH in the midbrain and brainstem were gradually decreased, and the expression level of α-syn was gradually increased (P<0.05) in the exposure group with the progress of exposure time. TUNEL staining showed that the apoptosis rates of neurons in LC were gradually increased (P<0.05) in the exposure group with the progress of exposure time. Conclusion: PQ induces progressive damage in the LC area of PD-like mice, which may be caused by the abnormal accumulation of pathological α-syn in the LC area.

[Molluscicidal effect of 25% wettable powder of pyriclobenzuron sulphate in hilly schistosomiasis-endemic regions]

OBJECTIVE

To evaluate the molluscicidal effect of 25% wettable powder of pyriclobenzuron sulphate (WPPS) against Oncomelania snails in hilly schistosomiasis-endemic regions and test its toxicity to fish.

METHODS

In October 2020, a snail-infested setting which had been cleared was selected in Nanjian County, Yunnan Province and divided into several blocks, and the natural snail mortality was estimated. 25% WPPS was prepared into solutions at concentrations of 1 and 2 g/L, and 25% wettable powder of niclosamide ethanolamine salt (WPNES) was prepared into solutions at a concentration of 2 g/L. The different concentrations of drugs were sprayed evenly, and the same amount of water was used as blank control. Snails were surveyed using the systematic sampling method 1, 3 and 7 days post-treatment, and snail survival was observed. A fish pond was selected in Nanjian County, and 2 kg 25% WPPS was evenly sprayed on the water surface to allow the effective concentration of 20 g/L. Fish mortality was estimated 8, 24, 48 and 72 h post-treatment.

RESULTS

One-day treatment with 1 and 2 g/L WPPS and 2 g/L WPNES resulted in 97.99%, 97.99% and 94.11% adjusted snail mortality rates (χ² = 3.509 and 3.509, both P values > 0.05), and the adjusted snail mortality was all 100% 3 d post-treatment with 1 and 2 g/L WPPS and 2 g/L WPNES, while 7-day treatment with 1 and 2 g/L WPPS and 2 g/L WPNES resulted in 91.75%, 86.57% and 57.76% adjusted snail mortality rates (χ² = 14.893 and 42.284, both P values < 0.05). Treatment with 2 g/L WPPS for 72 h resulted in a 0.67% cumulative mortality rate of fish.

CONCLUSIONS

25% WPPS is effective for snail control and highly safe for fish, which is feasible for use in hilly schistosomiasis-endemic regions.

[Tracing investigation and analysis of a Clostridium botulinum food poisoning incident in Bayingolin Mongolian Autonomous Prefecture, Xinjiang]

To analyze a suspected case of Clostridium botulinum food poisoning in Bayingolin Mongolian Autonomous Prefecture, Xinjiang and to help validating the diagnosis and providing technical support for clinical treatment. The basic information and clinical manifestations of food poisoning cases were investigated by using the epidemiological method of food safety accidents. The botulinum toxin genes in the samples were detected by real-time PCR and inoculation of KM mouse. The enriched bacteria were further purified and validated. PFGE and cluster analysis were performed on five isolates. Clostridium botulinum type A was detected in two homemade fermented bean samples and stool lavage fluid samples of three patients from enriched samples by toxin test and real-time PCR, and were further validated after isolation of Clostridium botulinum. PFGE showed 100% homology among five isolates. Five isolates of bacteria isolated from the stool lavage fluid of three patients and two homemade fermented bean curd were identified as the same source through PFGE. The cause of this food poisoning cases is food pollution of Clostridium botulinum type A.

[Magnetic resonance imaging analysis on the effect of marathon on the dynamic changes of morphological characteristics of patellar tendon in amateur marathon runners after half marathon]

Objective: To explore the dynamic changes of morphological characteristics of patellar tendon (PT) in amateur athletes after a half-marathon using magnetic resonance imaging. Methods: A total of 19 male amateur marathon runners with 38 knee joints,aged from 26 to 53(41.5±7.9) years, running for 3 to 18 years, with a weekly running volume of 30-90 km and a monthly running volume of 100-300 km were enrolled and underwent 1.5T MRI scan before the half-marathon, within 3 hours after running and 3 days after running. Ten healthy male volunteers with 20 knee joints, who had never participated in marathon and exercised (including but not limited to running) per week for less than 150 minutes were recruited as the control group, aged from 26 to 54 (39.4±9.1) years. Firstly, the PT signal was qualitatively assessed on fat-suppressed proton density-weighted imaging (fs-PDWI) sequence to observe the presence of patellar tendinitis. Then, the length, proximal, middle and distal cross-sectional area (CSA), and volume of PT were measured using the post-processing tool ITK-SNAP, and the data were standardized. The independent sample t-test was used for comparing. One-way repeated measures analysis of variance was used to analyze the morphological changes of PT before and after half-marathon running. Results: The incidence of asymptomatic patellar tendinitis in amateur marathon runners was 26.3% (5/19). No significant MR signal changes of PT were observed in all runners after running. The proximal CSA in runners group was larger than that in controls [(4.20±0.62) mm²/kg^3/4 vs (3.63±0.57) mm²/kg^3/4, P<0.05], and there was no significant difference in length, medium and distal CSA and volume(all P>0.05). The length, proximal and distal CSA and volume of PT in runners group increased at 3 h after running [(47.35±3.22) mm vs (46.83±3.35) mm; (102.52±13.03) mm² vs (98.98±13.14) mm²; (108.67±15.72) mm² vs (100.27±14.37) mm²; (4 020.36±514.38) mm³ vs (3 826.57±499.23) mm³, all P<0.05]. There was no significant difference between before running and 3 days after running(all P>0.05). The middle CSA were not significantly different among different periods(all P>0.05). Conclusion: Marathon has effect on the normal PT morphology in male amateur marathon runners, showing an increase in proximal CSA. A half-marathon will cause reversible changes in PT length, regional CSA and volume.

Current and potential trends in the bioactive properties and health benefits of Prunus mume Sieb. Et Zucc: a comprehensive review for value maximization

Prunus mume Sieb. Et Zucc (P. mume) is an acidic fruit native to China (named Chinese Mei or greengage plum). It is currently cultivated in several Asian countries, including Japan ("Ume"), Korea (Maesil), and Vietnam (Mai or Mo). Due to its myriad nutritional and functional properties, it is accepted in different countries, and its characteristics account for its commercialization. In this review, we summarize the information on the bioactive compounds from the fruit of P. mume and their structure-activity relationships (SAR); the pulp has the highest enrichment of bioactive chemicals. The nutritional properties of P. mume and the numerous uses of its by-products make it a potential functional food. P. mume extracts exhibit antioxidant, anticancer, antimicrobial, and anti-hyperuricaemic properties, cardiovascular protective effects, and hormone regulatory properties in various in vitro and in vivo assays. SAR shows that the water solubility, molecular weight, and chemical conformation of P. mume extracts are closely related to their biological activity. However, further studies are needed to evaluate the fruit's potential nutritional and functional therapeutic mechanisms. The industrial process of large-scale production of P. mume and its extracts as functional foods or nutraceuticals needs to be further optimized.

[Differential expression profile of miRNAs in amniotic fluid exosomes from fetuses with Down syndrome]

OBJECTIVE

To investigate the role of miRNAs in amniotic fluid exosomes in growth and development of fetuses with Down syndrome (DS).

METHODS

Amniotic fluid were collected from 20 fetuses with DS and 20 normal fetuses (control) to extract amniotic exosome miRNA. MicroRNA sequencing technique was used to identify the differentially expressed miRNAs between the two groups, for which gene ontology (GO) and pathway analysis was performed. Three differentially expressed miRNAs with the strongest correlation with DS phenotype were selected for qPCR verification. Dual luciferase reporter assay was used to verify the activity of let-7d-5p for targeted regulation of BACH1.

RESULTS

We identified 15 differentially expressed miRNAs in DS as compared with the control group, among which 7 miRNAs were up-regulated and 8 were down-regulated. Target gene prediction results showed that the differentially expressed miRNAs targeted 17 DS-related genes. GO analysis revealed that the main functions of the target genes involved protein binding, protein transport, ATP binding, transferase activity and synapses. Pathway analysis revealed that the functional pathways were closely related with the development of the nervous system. qPCR results showed that the expression levels of miR-140-3p and let-7d-5p were significantly lower in DS group than in the control group (P < 0.05), as was consistent with miRNA sequencing results; the expression level of miR-4512 was significantly higher in DS group than in control group (P < 0.05), which was contrary to miRNA sequencing results. The results of double luciferase reporter gene assay confirmed that let-7d-5p was capable of targeted regulation of BACH1 expression.

CONCLUSION

Let-7d-5p in amniotic fluid exosomes may promote oxidative stress events in the brain of fetuses with DS by regulating BACH1 expression.

Therapeutic Potential of Exosomes Derived From circRNA_0002113 Lacking Mesenchymal Stem Cells in Myocardial Infarction

Exosomes are participated in the pathogenesis of cardiovascular diseases and can be secreted by mesenchymal stem cells (MSCs). However, the effects of circRNA, delivered by exosomes derived from MSCs, on myocardial injury remain unclear. Hence, this study aims to explore the therapeutic potential of exosomes derived from circRNA_0002113 lacking MSCs in the treatment of myocardial injury in vitro and in vivo. Our results reveal that exosomes derived from circRNA_0002113 lacking MSCs decreased cell apoptosis in anoxia-reoxygenation (A/R) model cells, and reduced myocardial injury by inhibiting nuclear translocation of RUNX1 in vitro and in vivo. Moreover, miR-188-3p, which targets RUNX1 in cardiomyocytes was also found to interact with circRNA_0002113. In conclusion, exosomes derived from circRNA_0002113 lacking MSCs could suppress myocardial infarction by sponging miR-188-3p to regulate RUNX1 nuclear translocation. The circRNA_0002113/miR-188-3p/RUNX1 axis mediated alleviation of apoptosis serves as a novel strategy to treat myocardial I/R injury.

Postmastectomy Radiotherapy Improves Survival Benefits in De Novo Stage IV Breast Cancer: A Propensity-Score Matched Analysis

Purpose The role of postmastectomy radiotherapy (PMRT) in patients with de novo stage IV breast cancer is unclear. This study aimed to evaluate the value of PMRT for metastatic breast cancer who underwent a modified radical mastectomy. Methods: Data on de novo stage IV breast cancer patients who received modified radical mastectomy between 2010 and 2015 were retrieved from the Surveillance, Epidemiology, and End Results (SEER) database. Propensity score matching (PSM) analysis based on age, T stage, N stage, breast subtype, and chemotherapy was conducted to balance baseline clinical characteristics. The prognostic roles of PMRT on cancer-specific survival (CSS) and overall survival (OS) were analyzed using the Kaplan-Meier method and Cox proportional hazard models. Results: A total of 1944 patients were enrolled before PSM. After PSM, 1458 patients were included. PMRT improved the prognosis of CSS and OS. Multivariate Cox analysis showed that PMRT was independently prognostic for CSS (HR 0.739, 95% CI. 0.619-0.884, P = 0.001) and OS (HR 0.744, 95%CI 0.628-0.8810, P = 0.001). Further subgroup analyses found that survival superiority was observed in T3-4 or N + subgroup (both P < 0.001 for CSS and OS), and Her2-/HR + breast subtype (HR 0.703, 95%CI 0.558-0.888 for CSS, and HR 0.712, 95%CI 0.573-0.885 for OS), especially in patients with bone metastasis but without brain metastasis. Conclusion: PMRT improved survival in de novo stage IV breast cancer patients in selected T3-4 or N + subgroup and Her2-/HR + breast subtype. However, these findings need to be validated by further studies before being incorporated into clinical practice.

Industrial application of antimicrobial peptides based on their biological activity and structure-activity relationship

Last several years, a rapid increase in drug resistance to traditional antibiotics has driven the emergence and development of antimicrobial peptides (AMPs). AMPs have also gained considerable attention from scientists due to their high potency in combatting infectious pathogens. A subset of analogues and their derivatives with specific targets have been successfully designed based on natural peptide patterns. In this review, scientific knowledge on the mechanisms of action related to biological activity and structure-activity relationship (SAR) of AMPs are summarized, and the biological applications in several important fields are critically discussed. SAR shows that the positive charge, secondary structure, special amino acid residues, hydrophobicity, and helicity of AMPs are closely related to their biological activities. The combination of nanotechnology, bioinformatics, and genetic engineering can accelerate to achieve the application of AMPs as effective, safe, economical, and nonresistant antimicrobial agents in medicine, the food and feed industries, and agriculture in coming years. Given the intense interest in AMPs, further investigations are needed in the future to evaluate the specific structure and function that make their use favorable in several industries. This review may provide a comprehensive reference for future studies on chemical modifications, mechanistic exploration, and applications of AMPs.

Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes

Organ development is dictated by the regulation of genes preferentially expressed in tissues or cell types. Gene expression profiling and identification of specific genes in organs can provide insights into organogenesis. Therefore, genome-wide analysis is a powerful tool for clarifying the mechanisms of development during organogenesis as well as tooth development. Single-cell RNA sequencing (scRNA-seq) is a suitable tool for unraveling the gene expression profile of dental cells. Using scRNA-seq, we can obtain a large pool of information on gene expression; however, identification of functional genes, which are key molecules for tooth development, via this approach remains challenging. In the present study, we performed cap analysis of gene expression sequence (CAGE-seq) using mouse tooth germ to identify the genes preferentially expressed in teeth. The CAGE-seq counts short reads at the 5'-end of transcripts; therefore, this method can quantify the amount of transcripts without bias related to the transcript length. We hypothesized that this CAGE data set would be of great help for further understanding a gene expression profile through scRNA-seq. We aimed to identify the important genes involved in tooth development via bioinformatics analyses, using a combination of scRNA-seq and CAGE-seq. We obtained the scRNA-seq data set of 12,212 cells from postnatal day 1 mouse molars and the CAGE-seq data set from postnatal day 1 molars. scRNA-seq analysis revealed the spatiotemporal expression of cell type-specific genes, and CAGE-seq helped determine whether these genes are preferentially expressed in tooth or ubiquitously. Furthermore, we identified candidate genes as novel tooth-enriched and dental cell type-specific markers. Our results show that the integration of scRNA-seq and CAGE-seq highlights the genes important for tooth development among numerous gene expression profiles. These findings should contribute to resolving the mechanism of tooth development and establishing the basis for tooth regeneration in the future.

[Association between a novel regulatory genetic variants and lung cancer risk in Chinese: a two-stage case-control study]

Objective: Regulatory quantitative trait loci (regQTL) theory can help to evaluate the regulation function of single nucleotide polymorphisms (SNPs) on crucial biological signals from a three-dimensional perspective. The aim of this study was to investigate the effect of these regQTL-SNPs on the susceptibility of lung cancer. Methods: Based on the regQTL theory, using the database of identified lung cancer regQTL-SNPs, we screened the SNPs that may function as regQTL in the reported susceptible regions of lung cancer by genome-wide association study(GWAS), and a two-stage case-control study was conducted (screening stage: 2 331 lung cancer cases and 3 077 healthy controls; validation stage: 626 lung cancer cases and 667 healthy controls) to definite the association of related regQTL-SNPs with the susceptibility of lung cancer. Results: A total of 8 regQTL-SNPs were screened in the reported susceptible regions of lung cancer by GWAS. Among which, 3 SNPs were significantly associated with the risk of lung cancer (P<0.05) in the screening stage. Further validation results indicated that the variant T allele of rs6998591 in ADRA1A was significantly associated with increased risk of lung cancer (additive model: OR=1.33, 95%CI:1.01-1.74, P=0.040). In addition, the variant G allele of rs11202916 in ACTA2 was significantly associated with decreased risk of lung cancer (recessive model: OR=0.71, 95%CI:0.52-0.96, P=0.026). Stratified analysis indicated that the variant T allele of rs6998591 significantly increased lung squamous cell carcinoma risk (additive model: OR=1.53, 95%CI: 1.01-2.32, P=0.043), while the variant G allele of rs11202916 significantly decreased lung adenocarcinoma risk (additive model: OR=0.83, 95%CI: 0.69-0.98, P=0.031). Gene-environment interaction analysis indicated that the risk of developing lung cancer increased by 235% in smoking individuals carrying rs6998591 variant T allele compared with those non-smoking individuals carrying no rs6998591 variant T allele(OR=3.35,95%CI:2.10-5.34,P<0.001). Conclusion: There are two regQTL-SNPs that could significantly affect the susceptibility of lung cancer in the GWAS reported susceptible regions of lung cancer.

Effect of temperature on the persistence of fecal bacteria in ambient anaerobic digestion systems treating swine manure

This study aimed to explore the effect of temperature on the persistence of fecal bacteria by multiple approaches in ambient anaerobic digestion systems treating swine manure. Both lab-scale (15 °C, 20 °C, and 25 °C) and field (26 °C on average) studies were conducted by high-throughput sequencing and culture-based methods. A community-wide Bayesian SourceTracker method was used to identify and estimate the fecal bacterial proportion in anaerobic effluent. High proportional contributions of fecal bacteria were observed in effluent at 15 °C (73%) and 20 °C (75%), while less was found at 25 °C (19%). This was further verified by a field study (23%) and an anaerobic reactor study at 37 °C (0.01%). To explore the potential reasons for differences in fecal bacterial proportions, bacterial taxa were divided into "lost" and "survivor" taxa in manure waste by LEfSe. The "survivor" taxa abundance was positively correlated with SourceTracker proportion (r = 0.913, P = 0.001), but negatively correlated with temperature (r = -0.826, P = 0.006). In addition, biomarkers in effluent were divided into "enriched" and "de novo" taxa. "Enriched" taxa, including acidogenic and acetogenic bacteria, were found at all temperatures, whereas taxa related to organic degradation were multiplied "de novo" at 25 °C. Variation partition analysis showed that temperature could explain 30% of variations in effluent bacterial community. Moreover, coliforms isolated from the manure and effluents at 15 °C and 20 °C were also phylogenetically related. This study provided comprehensive insight into the impact of temperature on the persistence of fecal bacteria in anaerobic effluent, with temperatures over 25 °C recommended to reduce fecal pollution.

The Significance of MET Expression and Strategies of Targeting MET Treatment in Advanced Gastric Cancer

Background

Accurate assessment of predictive biomarker expression is critical in patient selection in clinical trials or clinical practice. However, changes in biomarker expression may occur after treatment. The aim of the present study was to evaluate the effects of chemotherapy on MET expression in gastric cancer (GC).

Methods

MET expression was examined immunohistochemically before and after treatment in 122 patients with unresectable or recurrent GC, and was evaluated according to H-score or the scoring criteria used in the MetMAb trial. MET gene amplification was assessed by chromogenic in situ hybridization (CISH). The antitumor effect of MET targeted therapy was investigated in human gastric cancer cells in vitro and in vivo, and the underlying molecular mechanisms were analyzed by western blot.

Results

MET expression was associated with Lauren classification as well as tumor differentiation by either scoring system. MET amplification was not associated with clinical characteristics. Of the 71 patients who had paired pre- and post-treatment tumor tissues, 28 patients (39%) were initially positive for MET expression, and 43 (61%) were negative. Twenty-five patients (35%) showed significant changes in MET expression after treatment (P=0.007). Additionally, there was a concomitant overexpression of MET and HER2 in a subset of GC patients. MET inhibitor volitinib could significantly inhibit cell proliferation and xenograft growth in vitro and in vivo in MKN45 cells with MET and phosphorylated MET (pMET) high expressions via suppressing downstream PI3K/Akt and MAPK signaling pathways. Furthermore, combination therapy targeting both MET and HER2 demonstrated a synergistic antitumor activity.

Conclusions

MET expression is altered post chemotherapy and MET status should be evaluated in real-time. Both MET and pMET expressions might need to be considered for patients suitable for volitinib treatment.