[Play the "combo fist" in the diagnosis and treatment of advanced gastric cancer]

The incidence of gastric cancer ranks fifth among malignant tumors worldwide, with the fourth highest mortality rate. A noteworthy characteristic of our country is the high prevalence of advanced-stage patients of approximately 40%. Advanced-stage gastric cancer carries an unfavorable prognosis with median survival of around one year. Diagnosis methods for advanced-stage gastric cancer (such as laparoscopic exploration, molecular profiling, and artificial intelligence) are still being continuously improved, while chemotherapy remains the primary treatment. With the rapid development of medical science, the role of surgical intervention in advanced-stage gastric cancer is becoming increasingly prominent. Therefore, as gastric tumor surgeons, we should consider how to use a combination of treatments, including surgery, chemotherapy, targeted therapy, immunotherapy, and interventional therapy, based on different pathological stages and the heterogeneity of tumors. With a multidisciplinary approach involving experts from various fields, we can collectively improve the survival rate and quality of life for advanced-stage patients. This article provides a brief overview of the current advances in the diagnosis and treatment of advanced-stage gastric cancer, and discusses therapeutic decision primarily from the perspective of surgeons.

MYH1G-AS is a chromatin-associated lncRNA that regulates skeletal muscle development in chicken

BACKGROUND

Skeletal muscle development is pivotal for animal growth and health. Recently, long noncoding RNAs (lncRNAs) were found to interact with chromatin through diverse roles. However, little is known about how lncRNAs act as chromatin-associated RNAs to regulate skeletal muscle development. Here, we aim to investigate the regulation of chromatin-associated RNA (MYH1G-AS) during skeletal muscle development.

METHODS

We provided comprehensive insight into the RNA profile and chromatin accessibility of different myofibers, combining RNA sequencing (RNA-seq) with an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). The dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay were used to analyze the transcriptional regulation mechanism of MYH1G-AS. ALKBH5-mediated MYH1G-AS N6-methyladenosine (m6A) demethylation was assessed by a single-base elongation and ligation-based qPCR amplification method (SELECT) assay. Functions of MYH1G-AS were investigated through a primary myoblast and lentivirus/cholesterol-modified antisense oligonucleotide (ASO)-mediated animal model. To validate the interaction of MYH1G-AS with fibroblast growth factor 18 (FGF18) protein, RNA pull down and an RNA immunoprecipitation (RIP) assay were performed. Specifically, the interaction between FGF18 and SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5) protein was analyzed by coimmunoprecipitation (Co-IP) and a yeast two-hybrid assay.

RESULTS

A total of 45 differentially expressed (DE) lncRNAs, with DE ATAC-seq peaks in their promoter region, were classified as open chromatin-associated lncRNAs. A skeletal muscle-specific lncRNA (MSTRG.15576.9; MYH1G-AS), which is one of the open chromatin-associated lncRNA, was identified. MYH1G-AS transcription is coordinately regulated by transcription factors (TF) SMAD3 and SP2. Moreover, SP2 represses ALKBH5 transcription to weaken ALKBH5-mediated m6A demethylation of MYH1G-AS, thus destroying MYH1G-AS RNA stability. MYH1G-AS accelerates myoblast proliferation but restrains myoblast differentiation. Moreover, MYH1G-AS drives a switch from slow-twitch to fast-twitch fibers and causes muscle atrophy. Mechanistically, MYH1G-AS inhibits FGF18 protein stabilization to reduce the interaction of FGF18 to SMARCA5, thus repressing chromatin accessibility of the SMAD4 promoter to activate the SMAD4-dependent pathway.

CONCLUSIONS

Our results reveal a new pattern of the regulation of lncRNA expression at diverse levels and help expound the regulation of m6A methylation on chromatin status.

[Epidemiological trend of early-onset gastric cancer and late-onset gastric cancer in China from 2000 to 2019]

Objective: In order to understand the changing trends of gastric cancer incidence and mortality in early-onset and late-onset in China from 2000 to 2019. Methods: The Global Burden of Disease research data was collected, and Excel and R 4.2.1 softwares were used to examine the incidence rate, mortality rate, and disability-adjusted life years (DALY) of Chinese people from 2000 to 2019, with a focus on gender, age, and year. Results: In 2019, the crude incidence rates were 7.06/100 000 (95%UI: 6.63/100 000-7.59/100 000) and 114.52/100 000 (95%UI: 108.79/100 000-121.63/100 000) for early- and late-onset gastric cancer, respectively. The crude mortality rate for early-onset gastric cancer was 3.29/100 000 (95%UI: 3.11/100 000- 3.50/100 000), while the crude mortality rate for late-onset gastric cancer was 81.88/100 000 (95%UI: 78.15/100 000-86.04/100 000). Additionally, the crude DALY rates for these two types of gastric cancer were 156.48/100 000 (95%UI: 148.82/100 000-165.84/100 000) and 1 750.13/100 000 (95%UI: 1 661.21/100 000-1 852.99/100 000). The standardized incidence of early-onset gastric cancer decreased from 5.49/100 000 in 2000 to 4.76/100 000 in 2019, and that of late-onset gastric cancer decreased from 143.45/100 000 in 2000 to 123.02/100 000 in 2019.The standardized mortality rate of early-onset gastric cancer decreased from 4.16/100 000 in 2000 to 2.18/100 000 in 2019, and that of late-onset gastric cancer decreased from 140.82/100 000 in 2000 to 91.49/100 000 in 2019. The standardized DALY rate for early-onset gastric cancer in 2019 was 105.87/100 000 (95%UI: 87.98/100 000 -125.60/100 000), lower than 198.84/100 000 (95%UI: 179.47/100 000- 219.83/100 000) in 2000. The standardized DALY rate for late onset gastric cancer in 2019 was 1 821.11/100 000 (95%UI: 1 509.42/100 000-2 158.53/100 000), lower than 2 932.52/100 000 (95%UI: 2 665.92/100 000-3 252.60/100 000) in 2000. Conclusions: The standardized mortality rate of early-onset gastric cancer in China showed a decreasing trend from 2000 to 2019. The standardized mortality rate of late onset gastric cancer showed a trend of first increasing and then decreasing. Notably, the incidence, mortality, and DALY of late-onset gastric cancer were significantly higher than those of early-onset gastric cancer during this period. Additionally, male incidence, mortality, and crude DALY rates were higher than female.

Shifts in the diversity of root endophytic microorganisms across the life cycle of the ratooning rice Jiafuzhan

The diversity of root endophytic microorganisms, which is closely related to plant life activities, is known to vary with the plant growth stage. This study on the ratooning rice Jiafuzhan explored the diversity of the root endophytic bacteria and fungi and their dynamics during the plant life cycle. By sequencing the 16S ribosomal ribonucleic acid (16S rRNA) and internal transcribed spacer (ITS) genes, 12,154 operational taxonomic units (OTUs) and 497 amplicon sequence variants (ASVs) were obtained, respectively. The root endophytic microorganisms of rice in the seedling, tillering, jointing, heading, and mature stages of the first crop and at 13, 25, and 60 days after regeneration (at the heading, full heading, and mature stages of the second crop, respectively) were analyzed using diversity and correlation analyses. There were significant differences in the α-diversity and β-diversity of root endophytic bacteria and fungi in the growth stage. Additionally, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed biomarker bacteria for each growth stage, but biomarker fungi did not exist in every stage. Moreover, the correlation analysis showed that the bacterial and fungal biomarkers interacted with each other. Furthermore, the nitrogen-fixing genus Bradyrhizobium existed in all growth stages. These findings indicate the pattern of root endophytic microorganisms of ratooning rice at different growth stages, and they provide new insights into the high yield of the second crop of ratooning rice (in light of the abundance of various bacteria and fungi).

Integrated analysis of methylation profiles and transcriptome of MDV-infected chicken spleens reveal hypomethylation of CD4 and HMGB1 genes might promote MD tumorigenesis

Marek's disease (MD) is a lymphoproliferative neoplastic disease caused by Marek's disease virus (MDV). Previous studies have showed that DNA methylation was involved in MD development, but systematic studies are still lacking. Herein, we performed whole genome bisulfite sequencing (WGBS) and RNA-seq in MDV-infected tumorous spleens (IN), noninfected spleens (NoIN), and survivor (SUR) spleens of chickens to identify the genes playing important roles in MD tumor transformation. We generated the first genome-wide DNA methylation profile of MDV-infected, noninfected, and survivor chickens. Combined the WGBS and RNA-Seq, we found that the expression of 25% differential expression genes (DEGs) were significantly correlated with methylation of CpG sites in their gene bodies or promoters. Further, we focused on the DEGs with differentially methylated regions (DMRs) on genes' body and promoter, and it showed the expression of 60% DEGs were significantly correlated with methylation of CpG sites in DMRs. Finally, we identified 8 genes, including CD4, CTLA4, DTL, HMGB1, LGMN, NUP210, RAD52, and ZAP70, and their expression was negatively correlated with methylation of DMRs in their promoters in both IN vs. NoIN and IN vs. SUR. These 8 genes showed specifically high expression in IN groups and clustered in module turquoise analyzed by WGCNA. Out of 8 genes, CD4 and HMGB1 were drop in QTLs associated with MD resistance. Thus, we overexpressed the 2 genes to simulate their high expression in the IN group and found they significantly promoted MDCC-MSB-1 cell proliferation, which revealed they might play promoting roles in MD tumorigenesis in IN due to their high expression induced by hypomethylation.

IPA1 improves drought tolerance by activating SNAC1 in rice

Drought is a major abiotic stress to rice (Oryza sativa) during growth. Ideal Plant Architecture (IPA1), the first cloned gene controlling the ideal plant type in rice, has been reported to function in both ideal rice plant architecture and biotic resistance. Here, we report that the IPA1/OsSPL14, encoding a transcriptional factor, positively regulates drought tolerance in rice. The IPA1 is constitutively expressed and regulated by H₂O₂, abscisic acid, NaCl and polyethylene glycol 6000 treatments in rice. Furthermore, the IPA1-knockout plants showed much greater accumulation of H₂O₂ as measured by 3,3'-diaminobenzidine staining in leaves compared with WT plants. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assays indicated that the IPA1 directly activates the promoter of SNAC1. Expression of SNAC1 is significantly down-regulated in IPA1 knockout plants. Further investigation indicated that the IPA1 plays a positive role in drought-stress tolerance by inducing reactive oxygen species scavenging in rice. Together, these findings indicated that the IPA1 played important roles in drought tolerance by regulating SNAC1, thus activating the antioxidant system in rice.

Short communication: diversity of endogenous avian leukosis virus subgroup E elements in 11 chicken breeds

Avian leukosis virus subgroup E (ALVE) as a kind of endogenous retroviruses extensively exists in chicken genome. The insertion of ALVE has some effects on chicken production traits and appearance. Most of the work on ALVEs has been done with commercial breeds. We present here an investigation of ALVE elements in seven Chinese domestic breeds and four standard breeds. Firstly, we established an ALVE insertion site dataset by using the obsERVer pipeline to identify ALVEs from whole-genome sequence data of eleven chicken breeds, seven Chinese domestic breeds, including Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Shouguang (SG), Silkie (SK), Tibetan (TB) and Wenchang (WC), four standard breeds, including White Leghorn (WL), White Plymouth Rock (WR), Cornish (CS), and Rhode Island Red (RIR). A total of 37 ALVE insertion sites were identified and 23 of them were novel. Most of these insertion sites were distributed in intergenic regions and introns. We then used locus-specific PCR to validate the insertion sites in an expanded population with 18~60 individuals in each breed. The results showed that all predicted integration sites in 11 breeds were verified by PCR. Some ALVE insertion sites were breeds specific, and 16 out of 23 novel ALVEs were found in only one Chinese domestic chicken breed. We randomly selected three ALVE insertions including ALVE_CAU005, ALVE_ros127, and ALVE_ros276, and obtained their insertion sequences by long-range PCR and Sanger sequencing. The insertion sequences were all 7525 bp, which were full-length ALVE insertion and all of them were highly homologous to ALVE1 with similarity of 99%. Our study identified the distribution of ALVE in 11 chicken breeds, which expands the current research on ALVE in Chinese domestic breeds.

[Modified mattress inversion suturing with double barbed sutures used for totally laparoscopic esophagojejunostomy overlap anastomosis after radical total gastrectomy]

Objective: To explore the advantages and safety of a modified mattress inversion suturing using double barbed sutures compared with the traditional overlap method in totally laparoscopic esophagojejunostomy overlap anastomosis. Methods: A retrospective cohort study was conducted. The inclusion criteria were as follows: (1) patients were aged 18 - 80 years old; (2) adenocarcinoma was preoperatively confirmed by pathological analysis; (3) patients had undergone a complete laparoscopic radical total gastrectomy; (4) patients had undergone esophagojejunostomy using the overlap method; (5) patients received a grade of I-III on the American Society of Anesthesiologists physical status classification system; (6) patients' complete follow-up data had been collected. Patients with a history of other malignant tumors, multi-origin tumors, emergency surgery, non-R0 radical resection or distant metastasis were excluded. The clinical data of 89 gastric cancer patients who underwent total laparoscopic radical total gastrectomy in the Department of Gastrointestinal Surgery in the Sixth Affiliated Hospital of Sun Yat-sen University from January 2019 to December 2020 were collected. These patients were grouped according to the esophagojejunostomy method used. Of 89 patients, 32 received modified mattress inversion suturing with double barbed sutures to close the common opening of esophagojejunostomy (the modified anastomosis group), while 57 received traditional overlap anastomosis in which the common opening was closed by barbed suture (the traditional anastomosis group). The operation conditions (incision length, conversion to laparotomy, duration of esophagojejunostomy) and postoperative recovery (time to commencement of a liquid diet, duration of postoperative hospital stay, anastomotic leakage, anastomotic stenosis, and anastomotic bleeding) were compared between the two groups. Results: There was no significant difference in the baseline data of the two groups for any parameter (all P>0.05). All patients received complete laparoscopic radical gastrectomy without conversion to laparotomy. There were no significant differences in the length of the median incision, the proportion of food intake on the first day after surgery, or in the incidence of anastomotic complications such as anastomotic leakage, anastomotic stenosis, and anastomotic bleeding between the two groups (P>0.05). Compared with the traditional anastomosis group, patients in the modified anastomosis group had shorter anastomosis time [26 (19-62) minutes vs. 36 (20-50) minutes, Z=-2.546, P=0.011] and postoperative hospital stay [7 (6-12) days vs. 9 (7-42) days, Z=-4.202, P<0.001]. The differences were statistically significant (all P<0.05). In a subgroup analysis of tumor TNM stage III, Siewert type II and neoadjuvant chemotherapy patients, there was no significant difference in the incidence of anastomotic complications between the modified group and the traditional group. However, the postoperative hospital stay duration in the modified anastomosis group was less than in the traditional anastomosis group. The duration of anastomosis in Siewert type II patients was also shorter in the modified anastomosis group than in the traditional anastomosis group [26 (19-62) minutes vs. 38 (21-50) minutes, Z=-2.105, P=0.035], and the difference was statistically significant (all P<0.05). Conclusion: Complete laparoscopic esophagojejunostomy using modified mattress inversion suturing with double barbed sutures is a safe and feasible anastomosis method to close the common opening of esophagojejunostomy, with shorter operation time, faster postoperative recovery and shorter hospital stay than the traditional method.

Analysing the influencing factors on caregivers' burden among amyotrophic lateral sclerosis patients in China: a cross-sectional study based on data mining

OBJECTIVES

There is significant burden on caregivers of patients with amyotrophic lateral sclerosis (ALS). However, only a few studies have focused on caregivers, and traditional research methods have obvious shortcomings in dealing with multiple influencing factors. This study was designed to explore influencing factors on caregiver burden among ALS patients and their caregivers from a new perspective.

DESIGN

Cross-sectional study.

SETTING

The data were collected at an affiliated hospital in Guangzhou, Guangdong, China.

PARTICIPANTS

Fifty-seven pairs of patients with ALS and their caregivers were investigated by standardised questionnaires.

MAIN OUTCOME MEASURES

This study primarily assessed the influencing factor of caregiver burden including age, gender, education level, economic status, anxiety, depression, social support, fatigue, sleep quality and stage of disease through data mining. Statistical analysis was performed using SPSS 24.0, and least absolute shrinkage and selection operator (LASSO) regression model was established by Python 3.8.1 to minimise the effect of multicollinearity.

RESULTS

According to LASSO regression model, we found 10 variables had weights. Among them, Milano-Torinos (MITOS) stage (0-1) had the highest weight (-12.235), followed by younger age group (-3.198), lower-educated group (2.136), fatigue (1.687) and social support (-0.455). Variables including sleep quality, anxiety, depression and sex (male) had moderate weights in this model. Economic status (common), economic status (better), household (city), household (village), educational level (high), sex (female), age (older) and MITOS stage (2-4) had a weight of zero.

CONCLUSIONS

Our study demonstrates that the severity of ALS patients is the most influencing factor in caregiver burden. Caregivers of ALS patients may suffer less from caregiver burden when the patients are less severe, and the caregivers are younger. Low educational status could increase caregiver burden. Caregiver burden is positively correlated with the degree of fatigue and negatively correlated with social support. Hopefully, more attention should be paid to caregivers of ALS, and effective interventions can be developed to relieve this burden.

Role of gga-miR-29b-3p in suppressing the proliferation, invasion and migration of MSB1 Marek’s disease tumor cells by the targeting of the DNMT3B gene

Background

Methods

Results

Conclusions

Characterization and expression analysis of the glycosyltransferase 64 familyin rice (Oryza sativa)

The glycosyltransferase 64 (GT64) family is widely conserved in many species, including animals and plants. The functions of GT64 family genes in animals have been well characterized in the biosynthesis of extracellular heparan sulfate, whereas two GT64 members in Arabidopsis thaliana are involved in the glycosylation of plasma membrane glycosylinositol phosphorylceramides (GIPCs). GIPCs are the main components of plant sphingolipids and serve as important signal molecules in various developmental processes and stress responses. Rice (Oryza sativa), a model monocot plant, contains four GT64 members in its genome. Using phylogenetic analysis, 73 GT64s from 19 plant species were divided into three main groups. Each group can be represented by the three members in Arabidopsis and show a trend of monocot-eudicot divergences. A promoter and genomic variation analysis of GT64s in rice showed that various stress-related regulatory elements exist in their promoters, and many sequence variations were found between the two main rice subspecies, japonica and indica. Additionally, the transmembrane domain and subcellular localization analyses revealed that these genes all encode membrane-bound glycosyltransferases and localize to the Golgi apparatus. Finally, expression analysis of the four GT64 genes in rice, as assessed by real-time quantitative PCR, showed that they have distinct tissue-specific expression patterns and respond to different hormone treatments or abiotic stresses. Our results indicated that this family of genes may play a role in different stress responses and hormone signaling pathways in rice, and therefore provides fundamental information for the further investigation of their function in rice.

LncEDCH1 improves mitochondrial function to reduce muscle atrophy by interacting with SERCA2

Skeletal muscle is a regulator of the body's energy expenditure and metabolism. Abnormal regulation of skeletal muscle-specific genes leads to various muscle diseases. Long non-coding RNAs (lncRNAs) have been demonstrated to play important roles in muscle growth and muscle atrophy. To explore the potential function of muscle-associated lncRNA, we analyzed our previous RNA-sequencing data and selected the lncRNA (LncEDCH1) as the research object. In this study, we report that LncEDCH1 is specifically enriched in skeletal muscle, and its transcriptional activity is positively regulated by transcription factor SP1. LncEDCH1 regulates myoblast proliferation and differentiation in vitro. In vivo, LncEDCH1 reduces intramuscular fat deposition, activates slow-twitch muscle phenotype, and inhibits muscle atrophy. Mechanistically, LncEDCH1 binds to sarcoplasmic/ER calcium ATPase 2 (SERCA2) protein to enhance SERCA2 protein stability and increase SERCA2 activity. Meanwhile, LncEDCH1 improves mitochondrial efficiency possibly through a SERCA2-mediated activation of the AMPK pathway. Our findings provide a strategy for using LncEDCH1 as an effective regulator for the treatment of muscle atrophy and energy metabolism.

SDR7-6, a short-chain alcohol dehydrogenase/reductase family protein, regulates light-dependent cell death and defence responses in rice

Lesion mimic mutants resembling the hypersensitive response without pathogen attack are an ideal material to understand programmed cell death, the defence response, and the cross-talk between defence response and development in plants. In this study, mic, a lesion mimic mutant from cultivar Yunyin treated with ethyl methanesulphonate (EMS), was screened. By map-based cloning, a short-chain alcohol dehydrogenase/reductase with an atypical active site HxxxK was isolated and designated as SDR7-6. It functions as a homomultimer in rice and is localized at the endoplasmic reticulum. The lesion mimic phenotype of the mutant is light-dependent. The mutant displayed an increased resistance response to bacterial blight, but reduced resistance to rice blast disease. The mutant and knockout lines showed increased reactive oxygen species, jasmonic acid content, antioxidant enzyme activity, and expression of pathogenicity-related genes, while chlorophyll content was significantly reduced. The knockout lines showed significant reduction in grain size, seed setting rate, 1000-grain weight, grain weight per plant, panicle length, and plant height. SDR7-6 is a new lesion mimic gene that encodes a short-chain alcohol dehydrogenase with atypical catalytic site. Disruption of SDR7-6 led to cell death and had adverse effects on multiple agricultural characters. SDR7-6 may act at the interface of the two defence pathways of bacterial blight and rice blast disease in rice.

105 The Epigenetics and Plasticity of CD4+ T Cells in Poultry Health

Marek’s disease (MD) is one of the top priority diseases in chicken. The mechanisms through which immune cells react to virus infection and pathway signals represent the fundamental cell biological question to defeat MD. We hypothesized epigenetic status in immune organs and cells is directly associated with how the Marek’s disease virus (MDV) infection influences intrinsic transcriptional and regulatory networks in MD. To investigate the epigenetics in CD4+ T cells induced by MDV infection, we assembled a multifaceted approach with epigenetics, deep sequencing, and computational methods together to explore the roles of epigenetics in unique inbred lines of chickens. First, a genome-wide transcriptome analysis in the immune organs from resistant line 63 and susceptible line 72 chickens was performed to explore disease resistance mechanisms. MDV infection influences both cytokine-cytokine receptor interaction and cellular development in resistant and susceptible chickens. Second, we examined the epigenetic status of CD4+ T cells induced by MDV infection, including DNA methylations, histone modifications, chromatin accessibility, and 3D chromatin structures. Our results revealed more than 5,000 epigenetic modification changes (FDR&lt; 0.01) and methylation changes (&gt;15,000, FDR&lt; 0.01) caused by MDV infection. Only resistant line 63 chickens could initiate robust adaptive immune responses at the transcription level (&gt;200 genes, FDR&lt; 0.05). The increase in chromatin accessibility (P &lt; 0.001) and chromosome reorganization represented by A/B compartment flipping were related to up-regulated genes induced by MDV infection ten days post-infection in line 63 chickens. Our findings provided a deeper insight into the CD4+ T cell commitment and responses toward viral infection. In particular, the identifications of cis-acting and trans-acting regulations and lipid pathways will improve our understanding of the sequence, structural basis of RNA-protein, and RNA-DNA interactions and serve as the impetus for mechanistic studies to refine the genomic and epigenetic control of MD resistance in poultry.

Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper Nilaparvata lugens (Stål)

Simple Summary

The brown planthopper Nilaparvata lugens (Stål) (BPH) is one of the main rice pests in Asian areas. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. In this study, 123 rice germplasms were identified for resistance and durable resistance by using the rice planthopper resistance identification system. Forty-two of the 123 rice varieties were classified as resistant to brown planthopper, and among them, twelve rice varieties had a long, durable resistance period. One potential durable resistance to brown planthopper locus on chromosome 2 was found by a genome-wide association study (GWAS). There are 13 candidate genes at this locus, and several of them are related to disease and pest resistance. Our study found a potential durable resistance locus to BPH, which has guiding significance for subsequent resistance breeding.

Abstract

The brown planthopper (BPH) is one of the main pests endangering rice yields. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. To identify new BPH resistance-related genes, a total of 123 rice varieties were assessed for resistance and durable resistance. Three varieties were immune, and nine were highly resistant to BPH. After whole-genome resequencing of all 123 varieties, 1,897,845 single nucleotide polymorphisms (SNPs) were identified. Linkage disequilibrium (LD) decay analysis showed that the average LD of the SNPs at 20 kb was 0.30 (r²) and attenuated to half value (~0.30) at a distance of about 233 kb. A genome-wide association study (GWAS) of durable resistance to BPH was conducted using the Fast-MLM model. One quantitative trait locus, identified on chromosome 2, included 13 candidate genes. Two candidate genes contained a leucine-rich repeat and CC-NBS-LRR or NB-ARC domains, which might confer resistance to pests or diseases. Interestingly, LOC_Os02g27540 was highly expressed and was induced by BPH; GWAS identified potential rice genes coding for durable resistance to BPH. This study helps to elucidate the mechanism of durable resistance to BPH in rice and provides essential genetic information for breeding and functional verification of resistant varieties.

Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 6₃ and 7₂. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 6₃ and 7₂ have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.

PEPC of sugarcane regulated glutathione S-transferase and altered carbon-nitrogen metabolism under different N source concentrations in Oryza sativa

BACKGROUND

Phosphoenolpyruvate carboxylase (PEPC) plays an important role in the primary metabolism of higher plants. Several studies have revealed the critical importance of PEPC in the interaction of carbon and nitrogen metabolism. However, the function mechanism of PEPC in nitrogen metabolism is unclear and needs further investigation.

RESULTS

This study indicates that transgenic rice expressing the sugarcane C4-PEPC gene displayed shorter primary roots and fewer crown roots at the seedling stage. However, total nitrogen content was significantly higher in transgenic rice than in wild type (WT) plants. Proteomic analysis revealed that there were more differentially expressed proteins (DEPs) responding to nitrogen changes in transgenic rice. In particular, the most enriched pathway "glutathione (GSH) metabolism", which mainly contains GSH S-transferase (GST), was identified in transgenic rice. The expression of endogenous PEPC, GST and several genes involved in the TCA cycle, glycolysis and nitrogen assimilation changed in transgenic rice. Correspondingly, the activity of enzymes including GST, citrate synthase, 6-phosphofructokinase, pyruvate kinase and ferredoxin-dependent glutamate synthase significantly changed. In addition, the levels of organic acids in the TCA cycle and carbohydrates including sucrose, starch and soluble sugar altered in transgenic rice under different nitrogen source concentrations. GSH that the substrate of GST and its components including glutamic acid, cysteine and glycine accumulated in transgenic rice. Moreover, the levels of phytohormones including indoleacetic acid (IAA), zeatin (ZT) and isopentenyladenosine (2ip) were lower in the roots of transgenic rice under total nutrients. Taken together, the phenotype, physiological and biochemical characteristics of transgenic rice expressing C₄-PEPC were different from WT under different nitrogen levels.

CONCLUSIONS

Our results revealed the possibility that PEPC affects nitrogen metabolism through regulating GST, which provide a new direction and concepts for the further study of the PEPC functional mechanism in nitrogen metabolism.

Glycine-Histidine-Lysine (GHK) Alleviates Astrocytes Injury of Intracerebral Hemorrhage via the Akt/miR-146a-3p/AQP4 Pathway

Intracerebral hemorrhage (ICH) is a major type of cerebrovascular disease with poor prognosis. Recent studies have shown that Glycyl-l-histidyl-l-lysine (GHK) is a kind of natural human tripeptide which could inhibit inflammation and against neurodegenerative diseases, but neither its role nor the mechanisms in ICH have yet been explicit. Currently, we investigated the possible strategies of GHK on ICH injury. Neurological deficit scores, brain water content, Nissl staining, and aquaporin 4 (AQP4) immunohistochemistry were detected in different groups of rats. The expression of microRNAs (miRNAs) was examined by real-time PCR. Inflammatory factors were detected using enzyme-linked immunosorbent assay (ELISA). Cell viability and cell proliferation were detected by Cell Counting Kit-8 (CCK-8). Matrix metalloproteinase 2 (MMP2), MMP9, tissue inhibitors of metalloproteinase-1 (TIMP1), AQP4 expression were detected/assessed using western blot. We observed that 5 and 10 μg/g of GHK improved neurological recovery by significantly reducing brain water content, improving neurological deficits, and promoting neuron survival. Besides, GHK alleviated inflammatory reaction and downregulated AQP4 expression. Furthermore, the effects of GHK on astrocyte were associated with the upregulation of miRNA-146a-3p, which partially regulated the expression of AQP4. Our results demonstrated that the phosphatidylinositol 3-kinase (PI3K)/AKT pathway participated in the GHK-induced upregulation of miR-146a-3p and miR-146a-3p/AQP4 interaction plays a role in the injury following ICH. These findings suggested that GHK could provide a novel therapeutic strategy for ICH.

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Background

Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 6₃ (MD-resistant) and 7₂ (MD-susceptible), as well as their F₁ generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD.

Results

In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 6₃ and 7₂, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using quantitative real-time PCR (qPCR), all of which were successfully confirmed. Finally, qPCR was also used to validate two deletion events in line 7₂ that were definitely normal in line 6₃. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study.

Conclusions

Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.

Genome-wide analysis of circular RNAs involved in Marek's disease tumourigenesis in chickens

Marek's disease (MD), induced by Marek's disease virus (MDV), is a lymphotropic neoplastic disease and causes huge economic losses to the poultry industry. Non-coding RNAs (ncRNAs) play important regulatory roles in disease pathogenesis. To investigate host circular RNA (circRNA) and microRNA (miRNA) expression profile, RNA sequencing was performed in tumourous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). A total of 2,169 circRNAs were identified and more than 80% of circRNAs were derived from exon. The flanking introns of 1,744 exonic circRNAs possessed 579 reverse complementary matches (RCMs), which mainly overlapped with chicken repeat 1 family (CR1F). It suggested that CR1F mediated the cyclization of exons by intron pairing. Out of 2,169 circRNAs, 113 were differentially expressed circRNAs (DECs). The Q-PCR and Rnase R digestion experiments showed circRNA possessed high stability compared with their linear RNAs. Integrated with previous transcriptome data, we profiled regulatory networks of circRNA/long non-coding RNA (lncRNA)-miRNA-mRNA. Extensive competing endogenous RNA (ceRNA) networks were predicted to be involved in MD tumourigenesis. Interestingly, circZMYM3, an intronic circRNA, interacted with seven miRNAs which targeted some immune genes, such as SWAP70 and CCL4. Gga-miR-155 not only interacted with circGTDC1 and circMYO1B, but also targeted immune-related genes, such as GATA4, which indicated the roles of non-coding RNAs played to mediate immune responsive genes. Collectively, this is the first study that integrated RNA expression profiles in MD model. Our results provided comprehensive interactions of ncRNAs and mRNA in MD tumourigenesis.

Brassinosteroid signaling may regulate the germination of axillary buds in ratoon rice

BACKGROUND

Rice ratooning has traditionally been an important component of the rice cropping system in China. However, compared with the rice of the first harvest, few studies on factors effecting ratoon rice yield have been conducted. Because ratoon rice is a one-season rice cultivated using axillary buds that germinate on rice stakes and generate panicles after the first crop's harvest, its production is mainly affected by the growth of axillary buds. The objectives of this study were to evaluate the sprouting mechanism of axillary buds to improve the ratoon rice yield.

RESULTS

First, we observed the differentiation and growth dynamics of axillary buds at different nodes of Shanyou 63, and found that they differentiated from bottom to top before the heading of the mother stem, and that they developed very slowly. After heading they differentiated from top to bottom, and the ones on the top, especially the top 2nd node, developed much faster than those at the other nodes. The average length and dry weight of the axillary buds were significantly greater than those at other nodes by the yellow ripe stage, and they differentiated into pistils and stamens by 6 d after the yellow ripe stage. The morphology of vegetative organs from regenerated tillers of Shanyou 63 also suggested the superior growth of the upper buds, which was regulated by hormones, in ratoon rice. Furthermore, a comprehensive proteome map of the rice axillary buds at the top 2nd node before and after the yellow ripe stage was established, and some proteins involved in steroid biosynthesis were significantly increased. Of these, four took part in brassinosteroid (BR) biosynthesis. Thus, BR signaling may play a role in the germination of axillary buds of ratoon rice.

CONCLUSIONS

The data provide insights into the molecular mechanisms underlying BR signaling, and may allow researchers to explore further the biological functions of endogenous BRs in the germination of axillary buds of ratoon rice.

Integrated analysis of lncRNA and mRNA repertoires in Marek's disease infected spleens identifies genes relevant to resistance

BACKGROUND

Marek's disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without lesions after MDV infection, and five spleens from noninfected chickens (NS), to explore the underlying mechanism of host resistance in Marek's disease (MD).

RESULTS

By using a precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed (DE) mRNAs, putative lncRNAs, and known lncRNAs were profiled among three groups. We found that several specific intergroup differentially expressed genes were involved in important biological processes and pathways, including B cell activation and the Wnt signaling pathway; some of these genes were also found to be the hub genes in the co-expression network analyzed by WGCNA. Network analysis depicted both intergenic correlation and correlation between genes and MD traits. Five DE lncRNAs including MSTRG.360.1, MSTRG.6725.1, MSTRG.6754.1, MSTRG.15539.1, and MSTRG.7747.5 strongly correlated with MD-resistant candidate genes, such as IGF-I, CTLA4, HDAC9, SWAP70, CD72, JCHAIN, CXCL12, and CD8B, suggesting that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their target genes.

CONCLUSIONS

Our results provide both transcriptomic and epigenetic insights on MD resistance and its pathological mechanism. The comprehensive lncRNA and mRNA transcriptomes in MDV-infected chicken spleens were profiled. Co-expression analysis identified integrated lncRNA-mRNA and gene-gene interaction networks, implying that hub genes or lncRNAs exert critical influence on MD resistance and tumorigenesis.

Interferon-γ acts as a regulator in the trade-off between phagocytosis and production performance in dwarf chickens

Background

Interferon-γ (IFN-γ) is critical for innate and adaptive immunity against viral and bacterial infections. IFN-γ reportedly affects the phagocytic ability of monocytes and macrophages as well as regulates pituitary function in humans and mice. The present study analyzed the impact of IFN-γ on monocyte and macrophage phagocytosis, production performance, and pituitary function in vivo and in vitro (in dwarf chickens). IFN-γ was injected into dwarf chickens through a vein, and then, the laying rate, average egg weight, and levels of follicle-stimulating hormone (FSH) and IFN-γ were measured in treatment and control groups. For the in vitro experiment, the pituitary tissues were supplemented with IFN-γ, and the mRNA expression levels of follicle-stimulating hormone beta subunit (FSH-β), interferon gamma receptor 1 (IFNGR1), and interferon gamma receptor 2 (IFNGR2) in the pituitary were assessed.

Results

Monocyte and macrophage phagocytosis product (PP) was decreased by IFN-γ treatment in a dose-dependent manner in vitro. In the in vivo experiment, the level of IFN-γ in the treatment group was higher than that in the control group at 7 d (P < 0.05), 14 d (P < 0.01), and 21 d (P < 0.01) post-injection. Compared with the control group, monocyte and macrophage PP was lower in the treatment group after injection (P < 0.01). The laying rate was higher in the treatment group than in the control group at 2 and 3 wk post-injection (P < 0.05). There was a significant difference between the treatment and control groups in the levels of FSH at 1, 3, 7, and 14 d post-injection (P < 0.01). In the in vitro experiment, increased mRNA expression levels of FSH-β, IFNGR1, and IFNGR2 were observed in the treatment group after stimulation with 100 U/mL IFN-γ for 24 h compared to those in the control group (P < 0.05).

Conclusions

IFN-γ inhibited the phagocytosis of monocytes and macrophages; up-regulated the mRNA expression levels of the FSH-β, IFNGR1, and IFNGR2; enhanced the secretion of FSH; and improved the laying rate. IFN-γ might be an important regulator in the trade-off between the immune effect and production performance in dwarf chickens.

Dwarf chickens with low monocytes/macrophages phagocytic activity show low antibody titers but greater performance

Monocytes/macrophages phagocytosis has key roles in inflammatory responses. However, systematic research on the effects of monocytes/macrophages phagocytosis on production and reproductive performance in dwarf chickens is lacking. In this study, we developed the HCT-8-MTT method to detect monocytes/macrophages phagocytosis product (PP) which was accuracy, flexible, and saving time. Based on PP in 990 dwarf chickens (890 hens and 100 cocks), chickens were divided into high phagocytosis product group (HPPG) and low phagocytosis product group (LPPG). In production performance, chickens in LPPG have higher laying rate at 24 wk and 71 wk and higher average egg weight at 23 wk and 24 wk than in HPPG (P < 0.05). The levels of follicle-stimulating hormone and luteinizing hormone were higher in LPPG than in HPPG at 58 wk (P < 0.01). In the reproductive performance, the fertilization rate in LPPG was higher than that in HPPG at 45 wk, 49 wk, and 53 wk (P < 0.05). Chickens in LPPG have higher hatchability than HPPG at 45 wk and 49 wk (P < 0.05). In LPPG, the mRNA expression levels of follicle-stimulating hormone receptor and CD9 in the follicle were higher than HPPG (P < 0.05). In the immune response, chickens with higher PP levels showed higher antibody titers for the avian influenza virus H9 inactivated vaccine (P < 0.01). Therefore, monocytes/macrophages PP was positively associated with antibody titers and negatively related to production and reproductive performance, and these findings have practical applications for the optimization of production in the poultry industry.

Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken

The Creeper trait, a classical monogenic phenotype of chicken, is controlled by a dominant semi-lethal gene. This trait has been widely cited in the genetics and molecular biology textbooks for illustrating autosomal dominant semi-lethal inheritance over decades. However, the genetic basis of the Creeper trait remains unknown. Here we have utilized ultra-deep sequencing and extensive analysis for targeting causative mutation controlling the Creeper trait. Our results indicated that the deletion of Indian hedgehog (IHH) gene was only found in the whole-genome sequencing data of lethal embryos and Creeper chickens. Large scale segregation analysis demonstrated that the deletion of IHH was fully linked with early embryonic death and the Creeper trait. Expression analysis showed a much lower expression of IHH in Creeper than wild-type chickens. We therefore suggest the deletion of IHH to be the causative mutation for the Creeper trait in chicken. Our findings unravel the genetic basis of the longstanding Creeper phenotype mystery in chicken as the same gene also underlies bone dysplasia in human and mouse, and thus highlight the significance of IHH in animal development and human haploinsufficiency disorders.

Efficient production of pronuclear embryos in breeding and nonbreeding season for generating transgenic sheep overexpressing TLR4

BACKGROUND

Brucella is a zoonotic Gram-negative pathogen that causes abortion and infertility in ruminants and humans. TLR4 is the receptor for LPS which can recognize Brucella and initiate antigen-presenting cell activities that affect both innate and adaptive immunity. Consequently, transgenic sheep over-expressing TLR4 are an suitable model to investigate the effects of TLR4 on preventing Brucellosis. In this study, we generated transgenic sheep overexpressing TLR4 and aimed to evaluate the effects of different seasons (breeding and non-breeding season) on superovulation and the imported exogenous gene on growth.

RESULTS

In total of 43 donor ewes and 166 recipient ewes in breeding season, 37 donor ewes and 144 recipient ewes in non-breeding season were selected for super-ovulation and injected embryo transfer to generate transgenic sheep. Our results indicated the no. of embryos recovered of donors and the rate of pronuclear embryos did not show any significant difference between breeding and non-breeding seasons (P > 0.05). The positive rate of exogenous TLR4 tested were 21.21 % and 22.58 % in breeding and non-breeding season by Southern blot. The expression level of TLR4 in the transgenic sheep was 1.5 times higher than in the non-transgenic group (P < 0.05). The lambs overexpressing TLR4 had similar growth performance with non-transgenic lambs, and the blood physiological parameters of transgenic and non-transgenic were both in the normal range and did not show any difference.

CONCLUSIONS

Here we establish an efficient platform for the production of transgenic sheep by the microinjection of pronuclear embryos during the whole year. The over-expression of TLR4 had no adverse effect on the growth of the sheep.

Chicken gga-miR-130a targets HOXA3 and MDFIC and inhibits Marek's disease lymphoma cell proliferation and migration

Marek's disease (MD) is an infectious disease of chickens caused by MD virus (MDV), which is a herpesvirus that initiates tumor formation. Studies have indicated that microRNAs (miRNAs) are linked with the development of cancers or tumors. Previously, gga-miR-130a was discovered downregulated in MDV-infected tissues. Here, we aimed to explore the further function of gga-miR-130a in MD. The expression of gga-miR-130a in MDV-infected and uninfected spleens was detected by quantitative real-time PCR (qRT-PCR). Subsequently, proliferation and migration assays of MDV-transformed lymphoid cells (MSB1) were carried out by transfecting gga-miR-130a. The target genes of gga-miR-130a were predicted using TargetScan and miRDB and clustered through Gene Ontology analysis. The target genes were validated by western blot, qRT-PCR, and a dual luciferase reporter assay. Our results show that the expression of gga-miR-130a was reduced in MDV-infected spleens. Gga-miR-130a showed an inhibitory effect on MSB1 cell proliferation and migration. Two target genes, homeobox A3 (HOXA3) and MyoD family inhibitor domain containing (MDFIC), were predicted and clustered to cell proliferation. Results indicate that gga-miR-130a regulates HOXA3 and MDFIC at the protein level but not at the mRNA level. Moreover, the gga-miR-130a binding sites of two target genes have been confirmed. We conclude that gga-miR-130a can arrest MSB1 cell proliferation and migration, and target HOXA3 and MDFIC, which are both involved in the regulation of cell proliferation. Collectively, gga-miR-130a plays a critical role in the tumorigenesis associated with chicken MD.

Chicken gga-miR-181a targets MYBL1 and shows an inhibitory effect on proliferation of Marek's disease virus-transformed lymphoid cell line

Marek's disease (MD), caused by Marek's disease virus (MDV), is a lymphoproliferative neoplastic disease of chickens and is characterized by MD lymphoma in multiple visceral organs of chicken. It causes great damage to poultry health. Recently, miRNA has been reported to be involved in Marek's disease lymphomagenesis. Our previous study showed that gga-miR-181a was downregulated in MDV-induced lymphoma, and its target gene, v-myb myeloblastosis viral oncogene homolog-like 1 (MYBL1), was predicted. In this study, the interaction between gga-miR-181a and MYBL1 was further verified by detecting protein expression levels of MYBL1 after transfecting miR-181a mimic into MD lymphoma cell line, MSB1. The result showed that protein level of MYBL1 was lower in gga-miR-181a mimic transfecting group than that in the negative control group at 96 h post transfection, which indicated that MYBL1 was a target gene of gga-miR-181a. Additionally, we found that the expression of MYBL1 was higher in MDV-infected samples than that in non-infected controls, which agreed with the proposition that miRNA showed a negatively correlated expression pattern with its target gene. We observed the inhibitory effect of gga-miR-181a on MSB1 cell proliferation. Collectively, the aberrant expression of gga-miR-181a and MYBL1 in MD lymphoma suggested that they might be involved in MD tumor transformation and played important roles.

Association between high visceral fat area and postoperative complications in patients with Crohn's disease following primary surgery

AIM

The aim of this study was to determine the association between visceral fat area (VFA) on CT and postoperative complications after primary surgery in patients with Crohn's disease (CD).

METHOD

Inclusion criteria were patients with a confirmed diagnosis of CD who had preoperative abdominal CT scan. The areas of total fat, subcutaneous fat and visceral fat were measured using an established image-analysis method at the lumbar 3 (L3) level on CT cross-sectional images. Visceral obesity was defined as a visceral fat area (VFA) of ≥ 130 cm(2) . Clinical variables, intra-operative outcomes and postoperative courses within 30 days were analysed.

RESULTS

A total of 164 patients met the inclusion criteria. Sixty-three (38.4%) patients had postoperative complications. The mean age of the patients with complications (the study group) was 40.4 ± 15.4 years and of those without complications (the control group) was 35.8 ± 12.9 years (P = 0.049). There were no differences in disease location and behaviour between patients with or without complications (P > 0.05). In multivariable analysis, VFA [odds ratio (OR) = 2.69; 95% confidence interval (CI): 1.09-6.62; P = 0.032] and corticosteroid use (OR = 2.86; 95% CI: 1.32-6.21; P = 0.008) were found to be associated with postoperative complications. Patients with visceral obesity had a significantly longer operative time (P = 0.012), more blood loss (P = 0.019), longer bowel resection length (P = 0.003), postoperative ileus (P = 0.039) and a greater number of complications overall (P < 0.001).

CONCLUSION

High VFA was found to be associated with an increased risk for 30-day postoperative complications in patients with CD undergoing primary surgery.

Tongue Epithelium Cells from shRNA Mediated Transgenic Goat Show High Resistance to Foot and Mouth Disease Virus

Foot and mouth disease induced by foot and mouth disease virus (FMDV) is severe threat to cloven-hoofed domestic animals. The gene 3Dpol in FMDV genome encodes the viral RNA polymerase, a vital element for FMDV replication. In this study, a conserved 3D-7414shRNA targeting FMDV-3Dpol gene was designed and injected into pronuclear embryos to produce the transgenic goats. Sixty-one goats were produced, of which, seven goats positively integrated 3D-7414shRNA. Loss of function assay demonstrated that siRNA effectively knockdown 3Dpol gene in skin epithelium cells of transgenic goats. Subsequently, the tongue epithelium cells from transgenic and non-transgenic goats were infected with FMDV O/YS/CHA/05 strain. A significant decrease of virus titres and virus copy number was observed in cells of transgenic goats compared with that of non-transgenic goats, which indicated that 3D-7414siRNA inhibited FMDV replication by interfering FMDV-3Dpol gene. Furthermore, we found that expression of TLR7, RIG-I and TRAF6 was lower in FMDV infected cells from transgenic goats compared to that from non-transgenic goats, which might result from lower virus copy number in transgenic goats’ cells. In conclusion, we successfully produced transgenic goats highly expressing 3D-7414siRNA targeting 3Dpol gene, and the tongue epithelium cells from the transgenic goats showed effective resistance to FMDV.

Avian sarcoma and leukosis virus gag gene in the Anser anser domesticus genome

Endogenous retroviruses are regarded as ideal genetic markers for evolutionary analyses. Birds were some of the initial vertebrates found to contain endogenous retroviruses. However, few studies have investigated the presence and distribution of endogenous retroviruses in goose. In this study, we detected the avian sarcoma and leukosis virus gag gene in the genomic DNA of 8 Chinese native breeds using polymerase chain reaction method. The results indicated that a 1.2-kb avian sarcoma and leukosis virus gag sequence was integrated into all 8 goose breeds. The mean genetic pairwise distance was 0.918% among the investigated geese. To the best of our knowledge, this is the first report demonstrating the presence of the endogenous retroviruses in the domestic goose genome. The genetic structure should be further examined in the domestic goose.

The inhibitory effects of gga-miR-199-3p, gga-miR-140-3p, and gga-miR-221-5p in Marek's disease tumorigenesis

Marek's disease (MD) is lymphoproliferative neoplastic disease in chickens, which is caused by Marek's disease virus (MDV). Our previous study profiled microRNA (miRNA) transcriptome in MD lymphoma, and found that gga-miR-199-3p, gga-miR-140-3p, and gga-miR-221-5p were down-regulated in MD lymphoma. In this study, we further investigated their differential expression between MDV-infected spleens and noninfected spleens at 4, 7, 14, 21, and 28 d postinfection (dpi) to elucidate whether deregulation of them was specific to late tumor transformation phase or not. The results showed that gga-miR-199-3p was down-regulated at 14 and 28 dpi, and the expression of gga-miR-140-3p was decreased at 14 dpi, which indicated that deregulation of these miRNAs appeared since early stage of MD tumor transformation. Additionally, the inhibitory effects of gga-miR-199-3p, gga-miR-140-3p, and gga-miR-221-5p on MDV-transformed lymphoid cell line (MSB1) cells proliferation were observed, which suggested that these miRNAs acted as MD tumor suppressors. Their aberrant expression at early tumor transformation phase and suppressive role in cell proliferation indicated that they were involved in MD lymphoma transformation, and might play crucial roles in MD tumorigenesis.

Antisense suppression of LOX3 gene expression in rice endosperm enhances seed longevity

Lipid peroxidation plays a major role in seed longevity and viability. In rice grains, lipid peroxidation is catalyzed by the enzyme lipoxygenase 3 (LOX3). Previous reports showed that grain from the rice variety DawDam in which the LOX3 gene was deleted had less stale flavour after grain storage than normal rice. The molecular mechanism by which LOX3 expression is regulated during endosperm development remains unclear. In this study, we expressed a LOX3 antisense construct in transgenic rice (Oryza sativa L.) plants to down-regulate LOX3 expression in rice endosperm. The transgenic plants exhibited a marked decrease in LOX mRNA levels, normal phenotypes and a normal life cycle. We showed that LOX3 activity and its ability to produce 9-hydroperoxyoctadecadienoic acid (9-HPOD) from linoleic acid were significantly lower in transgenic seeds than in wild-type seeds by measuring the ultraviolet absorption of 9-HPOD at 234 nm and by high-performance liquid chromatography. The suppression of LOX3 expression in rice endosperm increased grain storability. The germination rate of TS-91 (antisense LOX3 transgenic line) was much higher than the WT (29% higher after artificial ageing for 21 days, and 40% higher after natural ageing for 12 months). To our knowledge, this is the first report to demonstrate that decreased LOX3 expression can preserve rice grain quality during storage with no impact on grain yield, suggesting potential applications in agricultural production.

Antisense suppression of LOX3 gene expression in rice endosperm enhances seed longevity

Lipid peroxidation plays a major role in seed longevity and viability. In rice grains, lipid peroxidation is catalyzed by the enzyme lipoxygenase 3 (LOX3). Previous reports showed that grain from the rice variety DawDam in which the LOX3 gene was deleted had less stale flavour after grain storage than normal rice. The molecular mechanism by which LOX3 expression is regulated during endosperm development remains unclear. In this study, we expressed a LOX3 antisense construct in transgenic rice (Oryza sativa L.) plants to down-regulate LOX3 expression in rice endosperm. The transgenic plants exhibited a marked decrease in LOX mRNA levels, normal phenotypes and a normal life cycle. We showed that LOX3 activity and its ability to produce 9-hydroperoxyoctadecadienoic acid (9-HPOD) from linoleic acid were significantly lower in transgenic seeds than in wild-type seeds by measuring the ultraviolet absorption of 9-HPOD at 234 nm and by high-performance liquid chromatography. The suppression of LOX3 expression in rice endosperm increased grain storability. The germination rate of TS-91 (antisense LOX3 transgenic line) was much higher than the WT (29% higher after artificial ageing for 21 days, and 40% higher after natural ageing for 12 months). To our knowledge, this is the first report to demonstrate that decreased LOX3 expression can preserve rice grain quality during storage with no impact on grain yield, suggesting potential applications in agricultural production.

A 90-day toxicology study of meat from genetically modified sheep overexpressing TLR4 in Sprague-Dawley rats

Genetic modification offers alternative strategies to traditional animal breeding. However, the food safety of genetically modified (GM) animals has attracted increasing levels of concern. In this study, we produced GM sheep overexpressing TLR4, and the transgene-positive offsprings (F1) were confirmed using the polymerase chain reaction (PCR) and Southern blot. The expression of TLR4 was 2.5-fold compared with that of the wild-type (WT) sheep samples. During the 90-day safety study, Sprague-Dawley rats were fed with three different dietary concentrations (3.75%, 7.5%, and 15% wt/wt) of GM sheep meat, WT sheep meat or a commercial diet (CD). Blood samples from the rats were collected and analyzed for hematological and biochemical parameters, and then compared with hematological and biochemical reference ranges. Despite a few significant differences among the three groups in some parameters, all other values remained within the normal reference intervals and thus were not considered to be affected by the treatment. No adverse diet-related differences in body weights or relative organ weights were observed. Furthermore, no differences were observed in the gross necropsy findings or microscopic pathology of the rats whose diets contained the GM sheep meat compared with rats whose diets contained the WT sheep meat. Therefore, the present 90-day rat feeding study suggested that the meat of GM sheep overexpressing TLR4 had no adverse effect on Sprague-Dawley rats in comparison with WT sheep meat. These results provide valuable information regarding the safety assessment of meat derived from GM animals.

Temporal expression and DNA hypomethylation profile of CD30 in Marek's disease virus-infected chicken spleens

Marek's disease (MD) is a viral neoplastic disease of chickens caused by Marek's disease virus (MDV), which is serious threat to worldwide poultry industry. Our previous studies showed that the CD30 gene was hypomethylated in MD lymphoma. In this study, we further analyzed differential expression patterns and methylation levels of the CD30 gene between MDV-infected and noninfected spleens at 4, 7, 14, 21, and 28 d postinfection (dpi). The results showed that the expression of CD30 in MDV-infected spleens was significantly lower than that in noninfected spleens at 4 dpi. The expression of CD30 did not present significant difference between MDV-infected and noninfected spleens at 7 and 14 dpi. However, an increased expression of CD30 was presented in MDV-infected spleens at both 21 and 28 dpi. Simultaneously, CD30 showed a lower DNA methylation level in MDV-infected spleens at 14, 21, and 28 dpi. The results indicated that CD30 gene was involved in the whole process of MD tumorigenesis and upregulated expression of CD30 in MDV-infected spleens might be attributed to the hypomethylation of promoter of CD30 gene.

gga-miR-26a targets NEK6 and suppresses Marek's disease lymphoma cell proliferation

MicroRNA (miRNA) are a class of highly conserved, small noncoding RNA that emerge as key posttranscriptional regulators in various neoplastic transformations. Our previous study profiling the miRNA transcriptome in Marek's disease virus (MDV)-induced lymphoma revealed many novel and differentially expressed miRNA, including gga-miR-26a, which was downregulated in MDV-infected spleens of chickens. In this study, differential expression of gga-miR-26a between MDV-infected and noninfected spleens at 4, 7, 14, 21, and 28 d postinfection was analyzed by real-time PCR. The results showed gga-miR-26a were downregulated in MDV-infected spleens at cytolytic infection, latency, and tumor transformation phases. Subsequent cell proliferation assay revealed cell viability was lower in gga-miR-26a mimic transfection group than that in negative controls. Target genes of gga-miR-26a were identified by luciferase reporter gene assay. The results showed significant interaction between gga-miR-26a and Never In Mitosis Gene A (NIMA)-related kinase 6 (NEK6) gene. Subsequent gain of function experiment and Western blot assay showed that mRNA and protein levels of NEK6 were downregulated after gga-miR-26 mimic was transfected into MDV-transformed lymphoid cell line (MSB-1), indicating that NEK6 was modulated by gga-miR-26a. The expression of NEK6 showed a higher trend in MDV-infected samples including tumorous spleen and MD lymphoma from liver than that in noninfected controls. The results suggested that gga-miR-26a inhibited MSB-1 cell proliferation. Gga-miR-26a and its direct target, NEK6, might play important roles in MDV infection.

Physiological and photosynthetic characteristics of indica Hang2 expressing the sugarcane PEPC gene

Phosphoenolpyruvate carboxylase (PEPC) is known to play a key role in the initial fixation of CO₂ in C4 photosynthesis. The PEPC gene from sugarcane (a C4 plant) was introduced into indica rice (Hang2), a process mediated by Agrobacterium tumefaciens. Integration patterns and copy numbers of the gene was confirmed by DNA blot analysis. RT-PCR and western blotting results showed that the PEPC gene was expressed at both the mRNA and protein levels in the transgenic lines. Real-time PCR results indicated that expression of the sugarcane PEPC gene occurred mostly in green tissues and changed under high temperature and drought stress. All transgenic lines showed higher PEPC enzyme activities compared to the untransformed controls, with the highest activity (11.1 times higher than the controls) being observed in the transgenic line, T34. The transgenic lines also exhibited higher photosynthetic rates. The highest photosynthetic rate was observed in the transgenic line, T54 (22.3 μmol m⁻² s⁻¹; 24.6 % higher than that in non-transgenic plants) under high-temperature conditions. Furthermore, the filled grain and total grain numbers for transgenic lines were higher than those for non-transgenic plants, but the grain filling (%) and 1,000-grain weights of all transgenic lines remained unchanged. We concluded that over-expression of the PEPC gene from sugarcane in indica rice (Hang2) resulted in higher PEPC enzyme activities and higher photosynthesis rates under high-temperature conditions.

Abundant polymorphisms at the microsatellite locus LEI0258 in indigenous chickens

The chicken major histocompatibility complex (MHC) has abundant SNP and indels, and is closely related with host genetic resistance or susceptibility to disease. The LEI0258 locus is the most variable in the MHC region, and is a useful marker in reflecting the variability of MHC. In this study, we applied the LEI0258 microsatellite marker to investigate polymorphism of MHC in Chinese indigenous chickens. The size of LEI0258 fragments in 1,617 individuals from 33 Chinese chicken breeds was detected by capillary electrophoresis, and 213 samples with different fragment sizes were further sequenced. A total of 69 alleles ranging from 193 to 489 bp were found, including 21 novel alleles and 28 private alleles that existed in only one breed. Three alleles, 249 bp (7.04%), 489 bp (6.57%), and 309 bp (6.10%), were the most frequent in the indigenous chickens. A 489-bp novel allele was unique in Chinese local chicken breeds. Three indels and 4 SNP of upstream/downstream of 2 repeat regions (R13/R12) were found. Abundant variations indicate high genetic diversity at the MHC region in indigenous chickens. Rare alleles are vulnerable to genetic drift in small populations, and can be used as molecular markers for monitoring the dynamic conservation of many indigenous breeds.

Quail FMO3 gene cloning, tissue expression profiling, polymorphism detection and association analysis with fishy taint in eggs

Quail eggs comprise a significant and favourable part of table eggs in certain countries. Some quail eggs, however, present fishy off-flavor which directly influences their quality. It is reported that flavin-containing monooxygenase 3 (FMO3) is associated with fish-odour trait in human and animal products. FMO3 is responsible for the degradation of trimethylamine (TMA) in vivo. Loss-of-function mutations in FMO3 gene can result in defective TMA N-oxygenation, giving rise to disorder known as “fish-odour syndrome” in human, as well as the fishy off-flavor in cow milk and chicken eggs. In order to reveal the genetic factor of fishy taint in quail eggs, we cloned the cDNA sequence of quail FMO3 gene, investigated FMO3 mRNA expression level in various tissues, detected SNPs in the coding region of the gene and conducted association analysis between a mutation and the TMA content in quail egg yolks. The 1888 bp cDNA sequence of quail FMO3 gene encoding 532 amino acids was obtained and characterized. The phylogenetic analysis revealed quail FMO3 had a closer relationship with chicken FMO3. The FMO3 mRNA was highly expressed in liver and kidney of quail. Nine SNPs were detected in the coding sequence of quail FMO3 gene, including a nonsense mutation (Q319X) which was significantly associated with the elevated TMA content in quail egg yolks. Genotype TT at Q319X mutation loci was sensitive to choline. With addition of choline in the feed, the quails with homozygote TT at the Q319X mutation loci laid fish-odour eggs, indicating an interaction between genotype and diet. The results indicated that Q319X mutation was associated with the fishy off-flavor in quail eggs. Identification of the unfavorable allele T of quail FMO3 gene can be applied in future quail breeding to eliminate fishy off-flavor trait in quail eggs.