Response patterns of lncRNAs of the Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae under 23 pesticide treatments.

The response of Spodoptera frugiperda genes toward insecticides is crucial for guiding insecticide use. The regulation of the S. frugiperda genes via long noncoding RNAs (lncRNAs) under insecticide treatment should be investigated. In this study, 452 differentially expressed lncRNAs were identified by analyzing RNA-sequencing data of S. frugiperda under 23 pesticide treatments. We found 59 and 43 differentially expressed lncRNAs that could regulate detoxification-related cytochrome P450 and UDP-glucuronosyltransferase genes, respectively. Furthermore, the target genes of differentially expressed lncRNAs were enriched in Pfam, including chitin bind 4 and gene ontology terms such as structural constituent of the cuticle, revealing their potential mechanism of action on the growth inhibition of S. frugiperda larvae. Insecticide-specific expression of lncRNAs highlights the properties and commonalities of different insecticide-induced lncRNA regulatory mechanisms. To conclude, the results of this study provide new insights and perspectives on the use of 23 insecticides via lncRNA regulation of mRNAs.

Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection.

The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.

Multiple variation patterns of terpene synthases in 26 maize genomes.

Terpenoids are important compounds associated with the pest and herbivore resistance mechanisms of plants; consequently, it is essential to identify and explore terpene synthase (TPS) genes in maize. In the present study, we identified 31 TPS genes based on a pan-genome of 26 high-quality maize genomes containing 20 core genes (present in all 26 lines), seven dispensable genes (present in 2 to 23 lines), three near-core genes (present in 24 to 25 lines), and one private gene (present in only 1 line). Evaluation of ka/ks values of TPS in 26 varieties revealed that TPS25 was subjected to positive selection in some varieties. Six ZmTPS had ka/ks values less than 1, indicating that they were subjected to purifying selection. In 26 genomes, significant differences were observed in ZmTPS25 expression between genes affected by structural variation (SV) and those not affected by SV. In some varieties, SV altered the conserved structural domains resulting in a considerable number of atypical genes. The analysis of RNA-seq data of maize Ostrinia furnacalis feeding revealed 10 differentially expressed ZmTPS, 9 of which were core genes. However, many atypical genes for these responsive genes were identified in several genomes. These findings provide a novel resource for functional studies of ZmTPS.

Terpene Synthases in Rice Pan-Genome and Their Responses to Chilo suppressalis Larvae Infesting.

Terpene synthase (TPS) catalyzes the synthesis of terpenes and plays an important role in plant defense. This study identified 45 OsTPS genes (32 core genes and 13 variable genes) based on the high-quality rice gene-based pan-genome. This indicates limitations in OsTPS gene studies based on a single reference genome. In the present study, through collinearity between multiple rice genomes, one OsTPS gene absent in the reference (Nipponbare) genome was found and two TPS genes in the reference genome were found to have atypical structures, which would have been ignored in single genome analysis. OsTPS genes were divided into five groups and TPS-b was lost according to the phylogenetic tree. OsTPSs in TPS-c and TPS-g were all core genes indicating these two groups were stable during domestication. In addition, through the analysis of transcriptome data, some structural variations were found to affect the expression of OsTPS genes. Through the Ka/Ks calculation of OsTPS genes, we found that different OsTPS genes were under different selection pressure during domestication; for example, OsTPS22 and OsTPS29 experienced stronger positive selection than the other OsTPS genes. After Chilo suppressalis larvae infesting, 25 differentially expressed OsTPS genes were identified, which are involved in the diterpene phytoalexins precursors biosynthesis and ent-kaurene biosynthesis pathways. Overall, the present study conducted a bioinformatics analysis of OsTPS genes using a high-quality rice pan-genome, which provided a basis for further study of OsTPS genes.

Pan-Genome Analysis Reveals the Abundant Gene Presence/Absence Variations Among Different Varieties of Melon and Their Influence on Traits.

Melon (Cucumismelo L.) is an important vegetable crop that has been subjected to domestication and improvement. Several varieties of melons with diverse phenotypes have been produced. In this study, we constructed a melon pan-genome based on 297 accessions comprising 168 Mb novel sequences and 4,325 novel genes. Based on the results, there were abundant genetic variations among different melon groups, including 364 unfavorable genes in the IMP_A vs. LDR_A group, 46 favorable genes, and 295 unfavorable genes in the IMP_M vs. LDR_M group. The distribution of 709 resistance gene analogs (RGAs) was also characterized across 297 melon lines, of which 603 were core genes. Further, 106 genes were found to be variable, 55 of which were absent in the reference melon genome. Using gene presence/absence variation (PAV)-based genome-wide association analysis (GWAS), 13 gene PAVs associated with fruit length, fruit shape, and fruit width were identified, four of which were located in pan-genome additional contigs.

The Key Glutathione S-Transferase Family Genes Involved in the Detoxification of Rice Gramine in Brown Planthopper Nilaparvata lugens.

Phytochemical toxins are considered a defense measure for herbivore invasion. To adapt this defensive strategy, herbivores use glutathione S-transferases (GSTs) as an important detoxification enzyme to cope with toxic compounds, but the underlying molecular basis for GST genes in this process remains unclear. Here, we investigated the basis of how GST genes in brown planthopper (BPH, Nilaparvata lugens (Stål)) participated in the detoxification of gramine by RNA interference. For BPH, the LC25 and LC50 concentrations of gramine were 7.11 and 14.99 µg/mL at 72 h after feeding, respectively. The transcriptions of seven of eight GST genes in BPH were induced by a low concentration of gramine, and GST activity was activated. Although interferences of seven genes reduced BPH tolerance to gramine, only the expression of NlGST1-1, NlGSTD2, and NlGSTE1 was positively correlated with GST activities, and silencing of these three genes inhibited GST activities in BPH. Our findings reveal that two new key genes, NlGSTD2 and NlGSTE1, play an essential role in the detoxification of gramine such as NlGST1-1 does in BPH, which not only provides the molecular evidence for the coevolution theory, but also provides new insight into the development of an environmentally friendly strategy for herbivore population management.

Partial (two-thirds) nephrectomy in pigs: A comparison of three surgical approaches.

Partial (2/3) nephrectomy can be performed via the laparoscopic, retroperitoneal, and transperitoneal approach. Outcomes of the three approaches were compared in this study. 2/3 nephrectomy were performed in 21 healthy Bama miniature pigs (mean bodyweight 20.59±2.78kg). Pigs were divided into three groups: those that underwent 2/3 nephrectomy via laparoscopy (LN group, n=7), the retroperitoneal approach (RN group, n=7), or the transperitoneal approach (TN group, n=7). We monitored pre- and postoperative physiologic parameters, blood cell count, and stress and renal function biomarkers. Differences among groups were analyzed. 2/3 nephrectomy was successfully performed in all pigs without any complications. Mean surgical time in the LN group (60.71±7.34min) and the TN group (58.57±4.72min) was significantly longer than that in the RN group (41.14±5.33min). Warm ischemia in the LN group (38±7.57min) was significantly longer than that in the TN group (28.86±4.53min), which was significantly longer than that in the RN group (17.86±2.34min). The postoperative serum concentration of C-reactive protein in the TN group was significantly higher than that in the LN group (p<0.05). So retroperitoneal approach was best choice in case of bilateral renal lesion resulted in shortest ischemia time, and laparoscopic partial nephrectomy should be the primary choice in majority situations resulted in less body stress, smaller surgical incisions and less blood loss.

High resolution global chromosomal aberrations from spontaneous miscarriages revealed by low coverage whole genome sequencing.

OBJECTIVE: Chromosome aberrations are generally considered as one of the most substantial causative factors contributing to spontaneous miscarriages. Cytogenetic analyses like G-banded karyotype and chromosomal microarray analyses are often performed to further investigate the chromosome status of a miscarried fetus. STUDY DESIGN: Here, we describe a novel method, AnnoCNV, to detect DNA copy number variations (CNVs) using low coverage whole genome sequencing (WGS). We investigated the overall frequency of chromosomal abnormalities in 149 miscarriage specimens using AnnoCNV. RESULTS: Among 149 fetal miscarriage samples, more than two fifths of them (42.95%, 64) carried at least one chromosomal abnormality, and a subset (40) was identified as autosomal trisomy which account for 26.84% of all samples. We have also developed a robust algorithm in AnnoCNV, which is able to differentiate specifically karyotype 69,XXY from sex chromosomal aneuploidy 45,X, and to identify 45,X/46,XX mosaicism. Lastly, across the whole genome AnnoCNV identifies CNVs, which are associated with both reported symptoms and unknown clinical conditions. CONCLUSION: This cost-effective strategy reveals genome wide discovery of chromosome aberrations at higher resolution, which are consistent with parallel investigation conducted by SNP based assay.

The association between an endothelial nitric oxide synthase gene polymorphism and coronary heart disease in young people and the underlying mechanism.

With the development of molecular biological technology, the association between genes and diseases has drawn increasing attention of researchers; the endothelial nitric oxide synthase (eNOS) gene has been reported to be a candidate gene for cardiovascular disease (CHD). The present study aimed to investigate the association between a polymorphism of eNOS and the risk of CHD in young people (≤40 years old), in addition to the underlying mechanism. A total of 234 cases of CHD in young individuals were collected as the CHD group and 228 cases of healthy individuals as the control group. Peripheral blood was collected and the genotype of the eNOS G894T polymorphism was identified by polymerase chain reaction-restriction fragment length polymorphism, the gene frequency was calculated and the distributions of genotype and allele frequency between the two groups were compared. Bioinformatics tools were employed to analyze the differences in the local protein structures of the eNOS G894T polymorphism and the biological mechanism was preliminary discussed. The results demonstrated that there were significant differences in the distribution of genotype frequency and allele frequency of the eNOS G894T gene polymorphism between the CHD group and control group (P<0.05). The risk of CHD in GT and TT genotypes were higher compared with the GG genotype (P<0.05). The G894T polymorphism led to Glu298Asp mutation of encoded protein, which is within the active site of eNOS, and partial structures of the protein were converted from random coil to α­helix. In conclusion, the eNOS G894T gene polymorphism was associated with the occurrence and development of CHD in young people. The potential mechanism is that the G894T polymorphism leads to altered protein structure, which affects the function of eNOS in generating nitric oxide and cardiovascular diastole. The results of the present study suggested a potential target gene for the prevention and treatment of CHD in young people (≤40 years old).

Osteogenic Differentiation Gene Expression Profiling of hMSCs on Hydroxyapatite and Mineralized Collagen.

In this study, human mesenchymal stem cells (hMSCs) were cultured on the hydroxyapatite (HA) and mineralized collagen (MC), and their proliferation, adhesion, and differentiation, especially the molecular mechanisms on gene level, were investigated. Proliferation and morphological responses of hMSCs and their osteogenic differentiation were detected by quantitative detection of alkaline phosphatase. Gene expression profilings were examined by microarrays, and the gene expression data were studied through gene ontology terms and pathway analyses. The results showed that MC promoted cell proliferation and osteogenic differentiation of hMSCs. Microarray analysis showed that MC was conducive to express osteogenesis-related genes, such as BMP-2, COL1A1, and CTSK, and stimulate osteogenic differentiation, such as osteoblast differentiation pathway and skeletal system development pathway.

Mutation analysis and prenatal diagnosis in a Chinese family with succinic semialdehyde dehydrogenase and a systematic review of the literature of reported ALDH5A1 mutations.

AIMS: Succinic semialdehyde dehydrogenase (SSADH) deficiency is a neurometabolic disease in which the degradation of γ-aminobutyric acid (GABA) is impaired. The purpose of this study was to report two novel ALDH5A1 mutations responsible for SSADH deficiency in a Chinese family and the prenatal diagnosis of an at-risk fetus with DNA sequencing. RESULTS: Genetic analysis of ALDH5A1, in a child with SSADH deficiency, parents, and 10 weeks' gestation at-risk fetus and 100 healthy unrelated volunteers, was performed. The coding sequence and the intron/exon junctions of ALDH5A1 were analyzed by bidirectional DNA sequencing. The proband was identified to have a compound heterozygous mutations with c.496T>C (p.W166R) and c.589G>A (p.V197M). Each of his parents carried a deleterious mutation. DNA sequencing of chorionic villus revealed the fetus was a carrier, but not affected, and this was confirmed after birth by genetic analysis of umbilical cord blood and urine organic acid analysis. A study in 2003 described 35 mutations of ALDH5A1 in 54 unrelated families, and the current study and systematic literature review identified nine additional novel mutations in eight unrelated families bringing the total number of unique mutations of ALDH5A1 resulting in SSADH deficiency to 44, and the 44 mutations occur from exon 1 to exon 10. No mutational hotspots or prevalent mutations were observed, and all mutations appeared vital for the function of SSADH. CONCLUSIONS: Two novel ALDH5A1 mutations likely responsible for SSADH deficiency were identified, and DNA sequencing provided an accurate diagnosis for an at-risk fetus whose sibling had SSADH deficiency.

Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes.

BACKGROUND: Brassica napus is an important oilseed crop. Dissection of the genetic architecture underlying oil-related biological processes will greatly facilitates the genetic improvement of rapeseed. The differential gene expression during pod development offers a snapshot on the genes responsible for oil accumulation in. To identify candidate genes in the linkage peaks reported previously, we used RNA sequencing (RNA-Seq) technology to analyze the pod transcriptomes of German cultivar Sollux and Chinese inbred line Gaoyou. METHODS: The RNA samples were collected for RNA-Seq at 5-7, 15-17 and 25-27 days after flowering (DAF). Bioinformatics analysis was performed to investigate differentially expressed genes (DEGs). Gene annotation analysis was integrated with QTL mapping and Brassica napus pod transcriptome profiling to detect potential candidate genes in oilseed. RESULTS: Four hundred sixty five and two thousand, one hundred fourteen candidate DEGs were identified, respectively, between two varieties at the same stages and across different periods of each variety. Then, 33 DEGs between Sollux and Gaoyou were identified as the candidate genes affecting seed oil content by combining those DEGs with the quantitative trait locus (QTL) mapping results, of which, one was found to be homologous to Arabidopsis thaliana lipid-related genes. DISCUSSION: Intervarietal DEGs of lipid pathways in QTL regions represent important candidate genes for oil-related traits. Integrated analysis of transcriptome profiling, QTL mapping and comparative genomics with other relative species leads to efficient identification of most plausible functional genes underlying oil-content related characters, offering valuable resources for bettering breeding program of Brassica napus. CONCLUSIONS: This study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.

Nerve growth factor for the treatment of spinocerebellar ataxia type 3: an open-label study.

BACKGROUND: Spinocerebellar ataxia type 3 (SCA3) is the most common subtype of SCA worldwide, and runs a slowly progressive and unremitting disease course. There is currently no curable treatment available. Growing evidence has suggested that nerve growth factor (NGF) may have therapeutic effects in neurodegenerative diseases, and possibly also in SCA3. The objective of this study was to test the efficacy of NGF in SCA3 patients. METHODS: We performed an open-label prospective study in genetically confirmed adult (>18 years old) SCA3 patients. NGF was administered by intramuscular injection (18 µg once daily) for 28 days consecutively. All the patients were evaluated at baseline and 2 and 4 weeks after treatment using the Chinese version of the scale for assessment and rating of ataxia (SARA). RESULTS: Twenty-one SCA3 patients (10 men and 11 women, mean age 39.14 ± 7.81 years, mean disease duration 4.14 ± 1.90 years, mean CAG repeats number 77.57 ± 2.27) were enrolled. After 28 days of NGF treatment, the mean total SARA score decreased significantly from a baseline of 8.48 ± 2.40 to 6.30 ± 1.87 (P < 0.001). Subsections SARA scores also showed significant improvements in stance (P = 0.003), speech (P = 0.023), finger chase (P = 0.015), fast alternating hand movements (P = 0.009), and heel-shin slide (P = 0.001). CONCLUSIONS: Our preliminary data suggest that NGF may be effective in treating patients with SCA3.

Screening of human chromosome 21 genes in the dorsolateral prefrontal cortex of individuals with Down syndrome.

The aim of the current study was to identify the genes on human chromosome 21 (HC21) that may serve important functions in the pathogenesis of Down syndrome (DS). The microarray data GSE5390 were obtained from the Gene Expression Omnibus database, which contained 7 DS and 8 healthy normal samples. The data were then normalized and the differentially expressed genes (DEGs) were identified using the LIMMA package and Bonferroni correction. Furthermore, the DEGs underwent clustering and gene ontology analysis. Additionally, the locations of the DEGs on HC21 were confirmed using human genome 19 in the University of California, Santa Cruz Interaction Browser. A total of 25 upregulated and 275 downregulated genes were screened between DS and healthy samples with a false discovery rate of <0.05 and |logFC|>1. The expression levels of these genes in the two samples were different. In addition, the up­ and downregulated genes were markedly enriched in organic substance biological processes (P=4.48x10­10) and cell­cell signaling (P=0.000227). Furthermore, 17 overexpressed genes were identified on the 21q21­22 area, including COL6A2, TTC3 and ABCG1. Together, these observations suggest that 17 upregulated genes on HC21 may be involved in the development of DS and provide the basis for understanding this disability.

Tyrosinase gene mutations in the Chinese Han population with OCA1.

Oculocutaneous albinism (OCA) is a heterogeneous autosomal recessive genetic disorder that affects melanin synthesis. OCA results in reduced or absent pigmentation in the hair, skin and eyes. Type 1 OCA (OCA1) is the result of tyrosinase (TYR) gene mutations and is a severe disease type. This study investigated TYR mutations in a Chinese cohort with OCA1. This study included two parts: patient genetic study and prenatal genetic diagnosis. A total of 30 OCA1 patients were subjected to TYR gene mutation analysis. Ten pedigrees were included for prenatal genetic diagnosis. A total of 100 unrelated healthy Chinese individuals were genotyped for controls. The coding sequence and the intron/exon junctions of TYR were analysed by bidirectional DNA sequencing. In this study, 20 mutations were identified, four of which were novel. Of these 30 OCA1 patients, 25 patients were TYR compound heterozygous; two patients carried homozygous TYR mutations; and three were heterozygous. Among the ten prenatally genotyped fetuses, three fetuses carried compound heterozygous mutations and seven carried no mutation or only one mutant allele of TYR and appeared normal at birth. In conclusion, we identified four novel TYR mutations and showed that molecular-based prenatal screening to detect TYR mutations in a fetus at risk for OCA1 provided essential information for genetic counselling of couples at risk.

[Mutation analysis and first-trimester prenatal diagnosis for a Chinese family with hidrotic ectodermal dysplasia].

OBJECTIVE: To analyze GJB6 gene mutations in a Chinese family with hidrotic ectodermal dysplasia and to provide first-trimester prenatal diagnosis for a fetus. METHODS: Mutation scanning was carried out with PCR and bilateral direct sequencing in 2 affected and 6 unaffected individuals from the family. After the mutation was confirmed, prenatal diagnosis was performed on chorionic villi samples obtained at 11th gestational week. RESULTS: A heterozygous missense mutation c.31G>A of the GJB6 gene was discovered in all of the patients, which has led to substitution of glycine by arginine at codon 11 (p.G11R) at the N-terminal of the GJB6 protein. Prenatal diagnosis indicated that the fetus had also carried the same p.G11R mutation. Following termination of the pregnancy, analysis of the aborted tissues was consistent with prenatal diagnosis. CONCLUSION: The missense mutation c.31G>A(p.G11R) of the GJB6 gene probably underlies the disease in this family. Prenatal diagnosis with DNA sequencing can facilitate genetic counseling of this family.