Engineering of a Spider Peptide via Conserved Structure-Function Traits Optimizes Sodium Channel Inhibition In Vitro and Anti-Nociception In Vivo

Venom peptides are potent and selective modulators of voltage-gated ion channels that regulate neuronal function both in health and in disease. We previously identified the spider venom peptide Tap1a from the Venezuelan tarantula Theraphosa apophysis that targeted multiple voltage-gated sodium and calcium channels in visceral pain pathways and inhibited visceral mechano-sensing neurons contributing to irritable bowel syndrome. In this work, alanine scanning and domain activity analysis revealed Tap1a inhibited sodium channels by binding with nanomolar affinity to the voltage-sensor domain II utilising conserved structure-function features characteristic of spider peptides belonging to family NaSpTx1. In order to speed up the development of optimized Na_V-targeting peptides with greater inhibitory potency and enhanced in vivo activity, we tested the hypothesis that incorporating residues identified from other optimized NaSpTx1 peptides into Tap1a could also optimize its potency for Na_Vs. Applying this approach, we designed the peptides Tap1a-OPT1 and Tap1a-OPT2 exhibiting significant increased potency for Na_V1.1, Na_V1.2, Na_V1.3, Na_V1.6 and Na_V1.7 involved in several neurological disorders including acute and chronic pain, motor neuron disease and epilepsy. Tap1a-OPT1 showed increased potency for the off-target Na_V1.4, while this off-target activity was absent in Tap1a-OPT2. This enhanced potency arose through a slowed off-rate mechanism. Optimized inhibition of Na_V channels observed in vitro translated in vivo, with reversal of nocifensive behaviours in a murine model of Na_V-mediated pain also enhanced by Tap1a-OPT. Molecular docking studies suggested that improved interactions within loops 3 and 4, and C-terminal of Tap1a-OPT and the Na_V channel voltage-sensor domain II were the main drivers of potency optimization. Overall, the rationally designed peptide Tap1a-OPT displayed new and refined structure-function features which are likely the major contributors to its enhanced bioactive properties observed in vivo. This work contributes to the rapid engineering and optimization of potent spider peptides multi-targeting Na_V channels, and the research into novel drugs to treat neurological diseases.

[The comparison of prognosis and risk factors after radical resection for pancreatic ductal adenocarcinoma between China Pancreas Data Center and SEER]

Objectives: To compare the prognosis of patients underwent radical resection for pancreatic ductal adenocarcinoma(PDAC) in Surveillance, Epidemiology, and End Results(SEER) and China Pancreas Data Center(CPDC), and to compare the prognostic factors for PDAC in both databases. Methods: The data of patients underwent radical resection for PDAC in CPDC database from January 2016 to December 2017 and SEER database from January 2014 to December 2015 were retrospectively analyzed. The prognosis of patients in both databases was analyzed by the Kaplan-Meier method, Log-rank method, and propensity score matching, and the Cox proportional hazard regression was used to analyze the independent prognosis factors for PDAC. Results: There were 1 977 cases and 2 220 cases of pancreatic cancer that underwent radical resection from CPDC and SEER, respectively. There were more male patients(60.90%,1 204/1 977) than female patients(39.10%,773/1 977) in CPDC, while nearly 1∶1 ratio(male:1 112 cases,female:1108)was observed between male and female in SEER(χ²=48.977,P<0.01). The proportion of patients under 45 years old was the smallest in both databases, and the age group with the most significant proportion was 60 to 74 years old. The ratio of patients over 75 years old in the SEER(24.28%,539/2 220) was higher than that of CPDC(7.89%,156/1 977)(χ²=202.090,P<0.01), while the proportion of patients between 45 and 59 years old in CPDC(33.69%,666/1 977) was higher than that in SEER(19.77%,439/2 220)(χ²=103.640,P<0.01). There were more pancreatic head cancers than body and tail cancers in both databases, and no statistical difference was found in tumor size between the two databases (W=2 181 502,P=0.740). More positive and examined lymph nodes were found in SEER patients (W=3 265 131,W=2 954 363,all P<0.01); and the proportion of patients who had at least 15 lymph nodes dissected was higher in SEER(63.24%,1 404/2 220)(χ²=532.130,P<0.01). There were more patients without neoadjuvant or adjuvant therapy in CPDC(57.16%,1 130/1 977) than that in SEER(24.91%,553/2 220)(χ²=451.390,P<0.01). After propensity score matching, the overall survival for CPDC was better than that for SEER(Log-rank test:χ²=4.500,P=0.034), and the median overall survival was 24 months and 23 months respectively. Cox regressional analysis showed the common independent prognosis factors in both databases were ≥75 years old, pancreatic head cancer, poorly differentiated and undifferentiated tumors, T stage, N stage(All P<0.05). Neoadjuvant or adjuvant therapy was a protective factor in both databases(CPDC:Wald=27.082;SEER:Wald=212.285, all P<0.01) and 45 to 59 years old was protective factor in the SEER database(Wald=5.212,P=0.020). Conclusions: The data in both databases have a good consistency. However, in terms of data quality, examined lymph nodes count, and neoadjuvant/adjuvant therapy rate, the CPDC differs greatly from the SEER.

Study on Catalytic Oxidation, Flocculation and Sedimentation of Acidizing and Fracturing Wastewater

The acidizing and fracturing waste fluid in a wellsite in northern Shaanxi was treated by catalytic oxidation and flocculation precipitation. It investigated the effect of different coagulants and their dosage and the wastewater pH on coagulation precipitation. As for chemical oxidation experiment, it investigated the effect of oxidant dosage and reaction time on its treatment effect. The results showed that when 30% hydrogen peroxide (volume percentage) was added at the dosage of 0.3% and oxidized for 50 min, the pH was adjusted to 7.5 and 350 mg/L polyaluminum chloride (PAC) and 4 mg/L polyacrylamide were added (PAM); after processing the waste liquid, total iron, chemical oxygen demand (COD), chromaticity, and average corrosion rate were reduced from 252.75 mg/L, 3427.50 mg/L, 624.15°, and 0.1226 mm/a to 0.12 mg/L, 275.18 mg/L, 125° and 0.0217 mm/a, respectively; effective removal of iron and color, reduced COD, and controlled corrosion was achieved.

[Mesenchymal Stem Cells Cultured in 3D System Inhibit Non-small Cell Lung Cancer Cells Through p38 MAPK and CXCR4/AKT Pathways by IL-24 Regulating]

Non-small cell lung cancer (NSCLC) is prevalent worldwide and has a high mortality rate. Even if mesenchymal stem cells (MSCs) are suggested as cancer treatment, the studies of their effects on NSCLC cells contradict each other, mainly due to utilization of two-dimensional (2D) culture system. Three-dimensional (3D) culture systems resemble tissue organization in vivo. Here we comprehensively explore the inhibitory effects of MSCs on NSCLC cells in a 3D culture system. We confirmed that the inhibitory effects of 3D-cultured MSCs (3D-MSCs) on the proliferation and migration of NSCLC cells are greater than that of the 2D-cultured MSCs. 3D-MSCs overexpress IL-24, which serve as the key factor enhancing antitumor effects of MSCs. In these cells, IL-24 affects p38 MAPK and CXCR4/AKT pathways. Overall, this study provides the support for use of MSCs in tumor.

Pollination promotes ABA synthesis but not sexual reproduction in the apomictic species Zanthoxylum bungeanum Maxim

Apomixis is a form of reproduction that does not involve the fertilization of female gametes by male gametes but instead involves the production of offspring directly from the female parent. The offspring of apomixis are genetically identical to the female parent and inherit its traits. Therefore, apomixis has great potential for application to agricultural genetic breeding. However, it remains unclear whether apomictic species require pollination, and the impacts of pollination on such species are poorly understood. We investigated the effects of pollination on the apomictic species Zanthoxylum bungeanum Maxim. by analyzing its fertilization process, assembling its transcriptome, and measuring hormone concentrations, fruit setting rate and gene expression levels. Transcriptome sequencing of pollinated and unpollinated fruits resulted in a total of 69,131 PacBio reads. Of these, 7102 genes were up-regulated and 6491 genes were down-regulated. Analysis of the differentially expressed genes (DEGs) and construction of a weighted gene co-expression network showed that many DEGs were involved in plant hormone signal transduction, suggesting that hormonal signaling during development differs between pollinated and unpollinated fruit. The germination rate of Z. bungeanum pollen in vitro was only 11%, and pollen could not germinate in the embryo sac to complete fertilization. Although pollination did not enable Z. bungeanum to complete the sexual reproduction process, it significantly increased abscisic acid (ABA) concentration and fruit setting rate. Spraying 100 μg l-1 ABA also significantly increased the fruit setting rate. Therefore, ABA appears to be a key factor in the regulation of fruit setting in apomictic Z. bungeanum. Based on these results, we suggest that some male plants be cultivated in Z. bungeanum plantations or exogenous ABA be sprayed to increase the likelihood of pollination and thereby increase the fruit setting rate.

[Association of sepM gene mutation with mutacin Ⅳ production by Streptococcus mutans]

OBJECTIVE

To investigate the types of sepM gene mutations and their distribution in clinical isolates of Streptococcus mutans (S. mutans) and explore the association of sepM gene mutation with the capacity of mutacin Ⅳ production by S. mutans.

OBJECTIVE

We assessed the capacity of mutacin Ⅳ production in 80 clinical isolates of S. mutans using an inhibition zone assay. The minimum spanning tree and phylogenetic tree of these isolates were constructed using core genome multilocus sequence typing and maximum likelihood method, respectively. GeneMarkS software was used to predict the coding genes of these isolates, and the predicted genes were blasted against the sepM gene sequence of the reference genome UA159 to determine sepM gene mutations and their distribution characteristics in the clinical isolates. The mutation types affecting mutacin Ⅳ production were identified by analyzing the differentially distributed mutations between mutacin Ⅳ-producing isolates and mutacin Ⅳ-free isolates and by comparing the inhibition zones between isolates with sepM gene mutations and those without mutations.

OBJECTIVE

Among the 80 clinical isolates of S. mutans, 25 isolates were capable of mutacin Ⅳ production and 55 did not produce mutacin Ⅳ. The minimum spanning tree showed that the allelic differences were less among the mutacin Ⅳproducing isolates than among the mutacin Ⅳ-free isolates, and the origins of the mutacin Ⅳ-producing isolates were similar. We identified a total of 34 single base mutations in the 80 clinical isolates, and among them, C31T (P=0.001), G533A (P < 0.001), C756T (P=0.025), and C1036T (P=0.003) showed significant differential distributions between the mutacin Ⅳ-producing and mutacin Ⅳ-free isolates. These differentially distributed mutations were positively correlated with the capacity of mutacin Ⅳ production of the bacteria.

OBJECTIVE

sepM gene mutations that affect the capacity of mutacin Ⅳ production are present in the clinical strains of S. mutans.

Nano-TiO2 particles inhibit the biological behavior and mineralization of bone marrow mesenchymal stem cells transfected with CXCR4

OBJECTIVE

Bone marrow mesenchymal stem cells (BMSC) are widely used as experimental cells with potential differentiation function. Nanomaterials are currently a research hotspot. We assessed nano-TiO2 particles' effect on the biological behavior and mineralization of CXCR4 transfected BMSCs.

PATIENTS AND METHODS

After transfection of BMSC with CXCR4, cells were divided into blank group (no transfection), control group (transfection with CXCR4) and observe group (transfection with CXCR4 containing nanoparticles). Then, cell proliferation and ALP staining were measured along with analysis of Runx2 and BGP level by Western blot or RT-PCR and mineralization detection.

RESULTS

With increased culture time, the observed fractionation on day 14 showed significantly reduced activity; 3 mn nano-TiO2 particles significantly inhibited cell proliferation and bone formation after CXCR4 transfection with an inhibitory effect on the osteogenic ability of CXCR4-transfected BMCS cells in a time-dependent manner. The longer the culture time, the more significantly inhibitory effect; 3 mn nano-TiO2 particles can inhibit the mineralization of BMSCs after transfection of CXCR4 to a certain extent.

CONCLUSIONS

TiO2 nanoparticles have an inhibitory effect on the biological behavior and mineralization of BMSC cells transfected with CXCR4. The longer the culture time, the greater the inhibitory effect on osteogenic differentiation of BMSC cells transfected with CXCR4.

Similarities and Differences in Interoceptive Bodily Awareness Between US-American and Japanese Cultures: A Focus-Group Study in Bicultural Japanese-Americans

Interoceptive awareness is the conscious perception of sensations that create a sense of the physiological condition of the body. A validation study for the Japanese translation of the Multidimensional Assessment of Interoceptive Awareness (MAIA) surprised with a factor structure different from the original English-language version by eliminating two of eight scales. This prompted an exploration of the similarities and differences in interoceptive bodily awareness between Japanese and European Americans. Bicultural Japanese-Americans discussed concepts and experiences in the two cultures. We conducted focus groups and qualitative thematic analyses of transcribed recordings. 16 participants illustrated cross-cultural differences in interoceptive bodily awareness: switching between languages changes embodied experience; external versus internal attention focus; social expectations and body sensations; emphasis on form versus self-awareness; personal space; and mind-body relationship; context dependency of bodily awareness and self-construal. The participants explained key concepts that present challenges for a Japanese cultural adaptation of the MAIA, specifically the concept of self-regulation lost in the factor analysis. In Japanese culture, self-regulation serves the purpose of conforming to social expectations, rather than achieving an individual self-comforting sense of homeostasis. Our findings will inform the next phase of improving the MAIA's cross-cultural adaptation.

Yak milk-derived exosomes alleviate lipopolysaccharide-induced intestinal inflammation by inhibiting PI3K/AKT/C3 pathway activation

Intestinal epithelial cells (IEC) are important parts of the mucosal barrier, whose function can be impaired upon various injury factors such as lipopolysaccharide. Although food-derived exosomes are preventable against intestinal barrier injuries, there have been few studies on the effect of yak milk-derived exosomes and the underlying mechanism that remains poorly understood. This study aimed to characterize the effect of exosomal proteins derived from yak and cow milk on the barrier function of IEC-6 treated with lipopolysaccharide and the relevant mechanism involved. Proteomics study revealed 392 differentially expressed proteins, with 58 higher expressed and 334 lower expressed in yak milk-derived exosomes than those in cow exosomes. Additionally, the top 20 proteins with a relatively consistent higher expression in yak milk exosomes than cow milk exosomes were identified. Protein CD46 was found to be a regulator for alleviating inflammatory injury of IEC-6. In vitro assay of the role of yak milk exosomes on survival of IEC-6 in inflammation by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide assay confirmed the effectiveness of yak milk exosomes to increase IEC-6 survival up to 18% for 12 h compared with cow milk exosomes (up to 12%), indicating a therapeutic effect of yak milk exosomes in the prevention of intestinal inflammation. Furthermore, yak and cow milk exosomes were shown to activate the PI3K/AKT/C3 signaling pathway, thus promoting IEC-6 survival. Our findings demonstrated an important relationship between yak and cow milk exosomes and intestinal inflammation, facilitating further understanding of the mechanisms of inflammation-driven epithelial homeostasis. Interestingly, compared with cow milk exosomes, yak milk exosomes activated the PI3K/AKT/C3 signaling pathway more to lower the incidence and severity of intestine inflammation, which might represent a potential innovative therapeutic option for intestinal inflammation.

Chemical composition and protective effect of guava (Psidium guajava L.) leaf extract on piglet intestines

BACKGROUND

Dietary intervention is an important approach to improve intestinal function of weaned piglets. Phytogenic and herbal products have received increasing attention as in-feed antibiotic alternatives. This study investigated the chemical composition of guava leaf extract (GE) by ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Meanwhile, we investigated the effects of dietary supplementation with GE on diarrhea in relation to immune responses and intestinal health in weaned piglets challenged by enterotoxigenic Escherichia coli (ETEC).

RESULTS

In total, 323 characterized compounds, which including 91 phenolic compounds and 232 other compounds were identified. Animal experiment results showed that the supplementation of 50-200 mg kg^-1 of GE in the diet could reduce diarrhea incidence, increase activities of superoxide dismutase, glutathione peroxidase and total anti-oxidant capacity in the serum (P < 0.05), decrease the levels of interleukin 1β, interleukin 6 and tumor necrosis factor α in the serum or jejunum mucosa (P < 0.05), and increase villus height and villus height to crypt depth ratio (P < 0.05) in the jejuna of piglets challenged by oral ETEC compared with negative control group (NC). Meanwhile, diet supplementation with 50-200 mg kg^-1 GE reduced the levels of D-lactate, endothelin-1 and diamine oxidase in the serum, and increased the expression of zonula occludens-1, Claudin-1, Occludin and Na⁺ /H⁺ exchanger 3 (P < 0.05) in the jejuna mucosa of piglets challenged by ETEC compared with the NC.

CONCLUSIONS

These results suggested that GE could attenuate diarrhea and improve intestinal barrier function of piglets challenged by ETEC. © 2020 Society of Chemical Industry.

[Chaihu Guizhi decoction produces antidepressant-like effects via sirt1-p53 signaling pathway]

OBJECTIVE

To investigate the mechanism of the antidepressant-like effects of Chaihu Guizhi decoction (CGD).

OBJECTIVE

Chaihu Guizhi decoction at the daily dose of 17 g/kg and solvent vehicle were administered by gavage in 12 and 14 male C57BL/6J mice for 7 consecutive days, respectively. Forced swimming test (FST), elevated plus maze (EPM) test, open field test (OFT) and novelty-suppressed feeding test (NSF) were performed to assess the depression- and anxiety-like behaviors and motor ability of the mice. We further used chronic social defeat stress (CSDS) and social interaction test to evaluate the antidepressant-like effects of CGD in comparison with the solvent vehicle. Western blotting and RT-qPCR were performed to detect the expressions of sirt1, p53, acetylated p53, and the neuron plasticity-related genes including synapsin I (Syn1), Rab4B, SNAP25 and tubulin beta4b in the hippocampus of the mice.

OBJECTIVE

In FST, the immobility time of CGDtreated mice was decreased significantly (P < 0.05); no significant differences were found in the performances in EPM, NSF and OFT tests between the two groups. In social interaction test, the mouse models of CSDS treated with CGD showed significantly increased time in the interaction zone (P < 0.05). Compared with those in the vehicle group, the CGD-treated mouse models exhibited significantly increased protein level of SIRT1 and decreased p53 acetylation (P < 0.05) with up-regulated synapsin I mRNA expression in the hippocampus (P < 0.05); no significant difference were found in Rab (P=0.813), SNAP (P=0.820), or Tubb mRNA expressions (P=0.864) between the two groups.

OBJECTIVE

CGD produces antidepressant-like effects in mice possibly through the sirt1-p53 signaling pathway and synaptic plasticity.

Small RNA sequencing provides candidate miRNA-target pairs for revealing the mechanism of apomixis in Zanthoxylum bungeanum

BACKGROUND

Apomixis is a form of asexual reproduction that produces offspring without the need for combining male and female gametes, and the offspring have the same genetic makeup as the mother. Therefore, apomixis technology has great application potential in plant breeding. To identify the apomixis types and critical period, embryonic development at different flower development stages of Zanthoxylum bungeanum was observed by cytology.

RESULTS

The results show that the S3 stage is the critical period of apomixis, during which the nucellar cells develop into an adventitious primordial embryo. Cytological observations showed that the type of apomixis in Z. bungeanum is sporophytic apomixis. Furthermore, miRNA sequencing, miRNA-target gene interaction, dual luciferase reporter assay, and RT-qPCR verification were used to reveal the dynamic regulation of miRNA-target pairs in Z. bungeanum apomixis. The miRNA sequencing identified 96 mature miRNAs, of which 40 were known and 56 were novel. Additionally, 29 differentially expressed miRNAs were screened according to the miRNAs expression levels at the different developmental stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that the target genes of the differentially expressed miRNAs were mainly enriched in plant hormone signal transduction, RNA biosynthetic process, and response to hormone pathways.

CONCLUSIONS

During the critical period of apomictic embryonic development, miR172c significantly reduces the expression levels of TOE3 and APETALA 2 (AP2) genes, thereby upregulating the expression of the AGAMOUS gene. A molecular regulation model of miRNA-target pairs was constructed based on their interactions and expression patterns to further understand the role of miRNA-target pairs in apomixis. Our data suggest that miR172c may regulates AGAMOUS expression by inhibiting TOE3 in the critical period of apomixis.

[Application of fecal DNA methylation biomarkers detection in gastric cancer screening]

Objective: Explore the feasibility of fecal gene methylation for screening gastric cancer and its relationship with clinical characteristics of gastric cancer patients. Methods: One hundred and fifty-six stool samples of patients in general surgery or digestive department of the First Affiliated Hospital of Soochow University from August 2018 to December 2019 were collected, detailed clinical information of gastric cancer patients were recorded. All patients and normal controls were divided into two sets including train sets (n=52)and test sets (n=104). Stool DNA was extracted for detection of methylation (SDC2, SFRP2, RASSF2 and TERT). Meanwhile, hemoglobin in stool samples were detected by immunoassays. A logistic regression model was built to analyze the sensitivity and specificity of single fecal DNA biomarker in detecting gastric cancer by Ct values of each stool-based DNA biomarker; Based on Akaike information criterion (AIC), the gastric cancer early screening model was constructed with each biomarker and the combinations, and evaluate the performance of the model in the test sets. Results: The accuracy of each stool biomarkers and their ranks were showed as SDC2(71.2%)>TERT(67.3%)=RASSF2(67.3%)>Hb(63.5%)>SFRP2(61.5%). By stepwise regression analysis, a combination composed of the methylation of SDC2 and TERT, fecal occult blood testing was well-behaved in the screening of gastric cancer.This combination showed a sensitivity of 66.7% for gastric cancer in train sets and test sets at the specificity of 78.9%. In different stages and parts of gastric cancer samples, the combination of this marker has the highest sensitivity in stage I gastric cancer(78.6%) and gastric body cancer(75.0%). Conclusion: The methylation of SDC2, SFRP2, TERT, RASSF2 has higher accuracy rate in the screening of gastric cancer, which is a potential fecal biomarker of gastric cancer.

Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Simple Summary

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. However, the roles of long non-coding RNAs (lncRNAs) in the interaction between plants and viruses is unclear, particularly for the Chinese wheat mosaic virus (CWMV) interaction. In this study, we used a deep RNA sequencing strategy to profile lncRNAs involved in the response to CWMV infection in Nicotiana benthamiana and analyzed differentially expressed lncRNAs that responded to CWMV infection, using a bioinformatics method. We identified 1175 new lncRNAs in N. benthamiana infected with CWMV, with 65 lncRNAs showing differential expression. These lncRNAs were mainly enriched in plant hormone signal transduction and other pathways according to GO and KEGG pathway enrichment analyses. In addition, differential expression of XLOC_006393 after CWMV infection may be the precursor of NbmiR168c, which can respond to CWMV infection by modulating the expression of its target gene NbAGO1. We believe that our study makes a significant contribution to the literature because these results provide a valuable resource for studying lncRNAs involved in CWMV infection and improving the understanding of the molecular mechanism of CWMV infection.

Abstract

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

Gene mapping reveals the association between tyrosine protein kinase Abl1 and the silk yield of Bombyx mori

The Z chromosome of the silkworm contains a major gene that influences silk yield. This major locus on chromosome Z accounts for 35.10% of the phenotypic variance. The location and identification of the gene have been a focus of silkworm genetics research. Unfortunately, identification of this gene has been difficult. We used extreme phenotype subpopulations and selected from a backcross population, BC₁ M, which was obtained using the high-yield strain 872B and the low-yield strain IS-Dazao as parents, for mapping the gene on the chromosome Z. The candidate region was narrowed down to 134 kb at the tip of the chromosome. BmAbl1 in this region correlated with silk gland development by spatiotemporal expression analysis. This gene was differentially expressed in the posterior silk glands of the high- and low-yield strains. In BmAbl1, an insertion-deletion (indel) within the 10th exonic region and an SNP within the 6th intronic region were detected and shown to be associated with cocoon shell weight in 84 Bombyx mori strains with different yields. Nucleotide diversity analysis of BmAbl1 and its 50 kb flanking regions indicated that BmAbl1 has experienced strong artificial selection during silkworm domestication. This study is the first to identify the genes controlling silk yield in the major QTL of the Z chromosome using forward genetics.

Transcriptome and Metabolome Dynamics Explain Aroma Differences between Green and Red Prickly Ash Fruit

Green prickly ash (Zanthoxylum armatum) and red prickly ash (Zanthoxylum bungeanum) fruit have unique flavor and aroma characteristics that affect consumers' purchasing preferences. However, differences in aroma components and relevant biosynthesis genes have not been systematically investigated in green and red prickly ash. Here, through the analysis of differentially expressed genes (DEGs), differentially abundant metabolites, and terpenoid biosynthetic pathways, we characterize the different aroma components of green and red prickly ash fruits and identify key genes in the terpenoid biosynthetic pathway. Gas chromatography-mass spectrometry (GC-MS) was used to identify 41 terpenoids from green prickly ash and 61 terpenoids from red prickly ash. Piperitone was the most abundant terpenoid in green prickly ash fruit, whereas limonene was most abundant in red prickly ash. Intergroup correlation analysis and redundancy analysis showed that HDS2, MVK2, and MVD are key genes for terpenoid synthesis in green prickly ash, whereas FDPS2 and FDPS3 play an important role in the terpenoid synthesis of red prickly ash. In summary, differences in the composition and content of terpenoids are the main factors that cause differences in the aromas of green and red prickly ash, and these differences reflect contrasting expression patterns of terpenoid synthesis genes.

A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing

AIMS

Metagenomic next-generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture-free and hypothesis-free nucleic acid test for diagnosing all pathogens with known genomic sequences, including bacteria, fungi, viruses and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second-line choice due to lengthy procedures and microbial contaminations introduced from wet-lab processes. As a result, we aimed to reduce the hands-on time and exogenous contaminations in mNGS.

METHODS AND RESULTS

We developed a device (NGSmaster) that automates the wet-lab workflow, including nucleic acid extraction, PCR-free library preparation and purification. It shortens the sample-to-results time to 16 and 18·5 h for DNA and RNA sequencing respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR-free with PCR-based library prep and discovered no differences in microbial reads. Moreover we analysed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture.

CONCLUSION

NGSmaster can fulfil the microbiological diagnostic needs in a variety of sample types.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study opens up an opportunity of performing in-house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third-party laboratory.

ZbAGL11, a class D MADS-box transcription factor of Zanthoxylum bungeanum, is involved in sporophytic apomixis

Apomixis is a reproductive model that bypasses sexual reproduction, so it does not require the combination of paternal and maternal gametes but instead results in the production of offspring directly from maternal tissues. This reproductive mode results in the same genetic material in the mother and the offspring and has significant applications in agricultural breeding. Molecular and cytological methods were used to identify the reproductive type of Zanthoxylum bungeanum (ZB). Fluorescence detection of the amplified products of 12 pairs of polymorphic SSR primers showed consistent fluorescence signals for mother and offspring, indicating that no trait separation occurred during reproduction. In addition, the cytological observation results showed differentiation of ZB embryos (2n) from nucellar cells (2n) to form indefinite embryonic primordia and then form adventitious embryos (2n), indicating that the apomictic type of ZB is sporophytic apomixis. The MADS-box transcription factor ZbAGL11 was highly expressed during the critical period of nucellar embryo development in ZB. Unpollinated ZbAGL11-OE Arabidopsis produced fertile offspring and exhibited an apomictic phenotype. The overexpression of ZbAGL11 increased the callus induction rate of ZB tissue. In addition, the results of the yeast two-hybrid experiment showed that ZbAGL11 could interact with the ZbCYP450 and ZbCAD11 proteins. Our results demonstrate that ZbAGL11 can cause developmental disorders of Arabidopsis flower organs and result in apomixis-like phenotypes.