Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China.

OBJECTIVES: Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes mirabilis is the most widely distributed species and the only Nepenthes species that is naturally distributed within China. Herein, we reported the genome and transcriptome assemblies of N. mirabilis. The assemblies will be useful resources for comparative genomics, to understand the adaptation and conservation of carnivorous species. DATA DESCRIPTION: This work produced ~ 139.5 Gb N. mirabilis whole genome sequencing reads using leaf tissues, and ~ 21.7 Gb and ~ 27.9 Gb of raw RNA-seq reads for its leaves and flowers, respectively. Transcriptome assembly obtained 339,802 transcripts, in which 79,758 open reading frames (ORFs) were identified. Function analysis indicated that these ORFs were mainly associated with proteolysis and DNA integration. The assembled genome was 691,409,685 bp with 159,555 contigs/scaffolds and an N50 of 10,307 bp. The BUSCO assessment of the assembled genome and transcriptome indicated 91.1% and 93.7% completeness, respectively. A total of 42,961 genes were predicted in the genome identified, coding for 45,461 proteins. The predicted genes were annotated using multiple databases, facilitating future functional analyses of them. This is the first genome report on the Nepenthaceae family.

The complete chloroplast genome sequence of Begonia coptidifolia.

Begonia (Begoniaceae) is a large, pantropically distributed genus, comprising more than 1900 species. Due to poorly available genome resources, the phylogeny of this species-rich genus is still challenged. B. coptidifolia is a newly discovered species of restricted distribution in Southern China, and its genetic relationship with the other Begonia species has not been reported. Therefore, in this study, we report for the first time its chloroplast genome for future phylogenetic analysis. The circular chloroplast genome of B. coptidifolia is 169,412 bp in length, with a GC content of 35.57%. Its large single-copy region is 75,937 bp, a small single-copy region is 18,362 bp, and two inverted repeat regions are 37,556 bp and 37,557 bp, respectively. The genome encodes 82 protein-coding genes, 8 ribosomal RNA genes, and 40 transfer RNA genes. Phylogenetic analysis indicated that B. coptidifolia is genetically closest to B. pulchrifolia.

Preliminary analysis of the effect of vagus nerve stimulation in the treatment of children with intractable epilepsy.

BACKGROUND: Implant vagus nerve stimulation is an adjunctive treatment for intractable epilepsy when patients are not suitable for resective surgery. AIM: To identify the safety and efficacy of vagus nerve stimulation in children with intractable epilepsy and analyze the effects on different epilepsy syndromes. METHODS: Eligible children with intractable epilepsy were admitted to the study. We collected data from preoperative assessments as the baseline. During the follow-up time, we recorded the process of seizures (frequency, duration, and seizure type), the changes of drugs or parameters, the complications, etc. The mean reduction rate of seizures, response rate, and McHugh scale were chosen as the outcomes. RESULTS: A total of 213 patients were implanted with Tsinghua Pins vagus nerve stimulators, and the average age was 6.6 years. In the follow-up time of postoperative 3 mo, 6 mo, 12 mo, 18 mo, and 24 mo, the average reduction rate was 30.2%, 49.5%, 56.3%, 59.4%, and 63.2%, while the response rate was 21.8%, 62.5%, 57.1%, 69.2%, and 70.7%. In addition, implanted vagus nerve stimulation had different effects on epilepsy syndromes. The reduction rate of West syndrome increased from 36.4% (postoperative 6 m) to 74.3% (postoperative 24 m). The reduction rate of Lennox-Gastaut syndrome improved from 25.4% to 73.1% in 24 mo. The chi-square test of the five efficacy grades showed P < 0.05. The comparison between the 3-mo follow-up and the 6-mo follow-up showed P < 0.05, and the comparison between the 6-mo follow-up and the 24-mo follow-up showed P > 0.05. CONCLUSION: Vagus nerve stimulation is safe and effective in children with intractable epilepsy, and the seizure reduction occurred in a time-dependent manner. Moreover, patients with West syndrome may get the most benefits.

Clinical phenotypes, genotypes and treatment in Chinese dystonia patients with KMT2B variants.

BACKGROUND: KMT2B-related dystonia is a recently discovered hereditary dystonia that mostly occurs in childhood. This dystonia usually progresses to generalized dystonia with cervical, cranial, pharynx and larynx involvement. Our study summarizes genotype-phenotype features and deep brain stimulation (DBS) efficacy observed with KMT2B-related dystonia patients in China. METHODS: We identified 20 patients with KMT2B variations from dystonia samples with a gene panel and whole exome sequencing. Genetic, clinical and treatment analyses of these patients with KMT2B mutations were further conducted. RESULTS: We summarized the genotype and phenotypic characteristics of KMT2B-related patients in China, including 16 sporadic patients and 3 pedigrees (including 4 patients). Thirty-five percent (7/20) of patients had been published previously. The age of onset was between 1 month and 24 years (average 6.90 ± 5.72 years). Sixty-five percent (13/20) of patients had onset from lower limbs. Upper limbs or larynx accounted for 15% (3/20) and 20% (4/20) of patients, respectively. In the same family, male patients tended to have more severe symptoms than female patients. Carriers of KMT2B variants may present with nonmotor symptoms without dystonia. Abnormal endocrine metabolism could also be seen in our patients, including advanced bone age that had never been reported previously. Nine of our patients underwent DBS surgery. The mean follow-up time was 4.9 (range 1.3-16) months after DBS, and perceptible improvement of clinical symptoms were observed. CONCLUSIONS: The genotypic and phenotypic spectra of Chinese KMT2B-related dystonia patients were further expanded. DBS surgery might be the preferred option for severe KMT2B-related dystonia patients till now.

The Metabolic Activity of Caudate and Prefrontal Cortex Negatively Correlates with the Severity of Idiopathic Parkinson's Disease.

Positron emission tomography (PET) scan with tracer [18F]-fluorodeoxy-glucose (18F-FDG) is widely used to measure the glucose metabolism in neurodegenerative disease such as Idiopathic Parkinson's disease (IPD). Previous studies using 18F-FDG PET mainly focused on the motor or non-motor symptoms but not the severity of IPD. In this study, we aimed to determine the metabolic patterns of 18F-FDG in different stages of IPD defined by Hoehn and Yahr rating scale (H-Y rating scale) and to identify regions in the brain that play critical roles in disease progression. Fifty IPD patients were included in this study. They were 29 men and 21 women (mean±SD, age 57.7±11.1 years, disease duration 4.0±3.8 years, H-Y 2.2±1.1). Twenty healthy individuals were included as normal controls. Following 18F-FDG PET scan, image analysis was performed using Statistical Parametric Mapping (SPM) and Resting-State fMRI Data Analysis Toolkit (REST). The metabolic feature of IPD and regions-of-interests (ROIs) were determined. Correlation analysis between ROIs and H-Y stage was performed. SPM analysis demonstrated a significant hypometabolic activity in bilateral putamen, caudate and anterior cingulate as well as left parietal lobe, prefrontal cortex in IPD patients. In contrast, hypermetabolism was observed in the cerebellum and vermis. There was a negative correlation (p=0.007, r=-0.412) between H-Y stage and caudate metabolic activity. Moreover, the prefrontal area also showed a negative correlation with H-Y (P=0.033, r=-0.334). Thus, the uptake of FDG in caudate and prefrontal cortex can potentially be used as a surrogate marker to evaluate the severity of IPD.

Metabolic covariance networks combining graph theory measuring aberrant topological patterns in mesial temporal lobe epilepsy.

OBJECTIVE: We aimed to study the networks' mechanism of metabolic covariance networks in mesial temporal lobe epilepsy (mTLE), through examining the brain value of fluorine-18-fluorodeoxyglucose positron emission tomography (18 F-FDG-PET). METHODS: 18 F-FDG-PET images from 16 patients with mTLE were analyzed using local and global metabolic covariance network (MCN) approaches, including whole metabolic pattern analysis (WMPA), hippocampus-based (h-) MCN, whole brain (w-) MCN, and edge-based connectivity analysis (EBCA). RESULTS: WMPA showed a typical ipsilateral hypometabolism and contralateral hypermetabolism pattern to epileptic zones in mTLE. h-MCN revealed decreased hippocampus-based synchronization in contralateral regions. w-MCN exhibited a disrupted metabolic network with globally increased small-world properties and regionally decreased nodal metrics in the ipsilateral hemisphere. Hippocampus (h)-EBCA and whole brain EBCA (w-EBCA) both detected a reduced-connectivity dominated metabolic covariant network. Moreover, the reduced interhemisphere connectivity seemingly played a major role in the aberrant epileptic topological pattern. CONCLUSION: From a metabolic point of view, we demonstrated the damaging effects with reduced contralateral intranetwork metrics properties and the compensatory effects in contralateral intranetworks with increased network properties. However, the import role of significant reduced interhemisphere connection has rarely been reported in other mTLE studies. Taken together, 18 F-FDG-PET MCN analysis provides new evidence that the mTLE is a system neurological disorder with disrupted networks.