Effects of Zinc Adaptation on Histological Morphology, Antioxidant Responses, and Expression of Immune-Related Genes of Grass Carp (Ctenopharyngodon idella)

The study was conducted to evaluate the effect of zinc adaptation on histological morphology and antioxidant and immune responses of grass carp(Ctenopharyngodon idella). A total of 180 young grass carp (20.0 ± 2.0 g) was equally distributed into 9 groups, and triplicate groups were subjected to 0 μg/L Zn²⁺ (control group), 200 μg/L Zn²⁺, and 300 μg/L Zn²⁺ solution for 42 days, respectively. The results indicated that the liver and gill have obvious pathological changes after long-term adaptation to zinc except the intestine; the zinc adaptation can positively influence intestinal morphology. The activities of GPX (glutathione peroxidase activity), SOD (superoxide dismutase), and CAT (Catalase) were significantly increased in zinc treatment groups (P < 0.05). The genes expression levels of CuZnSOD (copper zinc superoxide dismutase), CAT, Hsp70 (heat shock protein-70), IL-1b (interleukin-1-b), and TGF-β1 (transforming growth factor-β1) were upregulated in the gill and intestine of grass carp following waterborne adaptation to zinc solution for 42 days (P < 0.05). In conclusion, zinc adaptation has different effects on organs of grass carp and may reduce the inflammatory response of the body's gills and intestines by improving the body's antioxidant and anti-stress defense capabilities.

Effect of Spirulina and Ferrous Fumarate on Intestinal Morphology and the Diversity of Gut Microbiota of Yellow River Carp

The study aimed to investigate the effect of diets supplemented with Spirulina and the mixture of Spirulina and ferrous fumarate on intestinal morphology and the diversity of gut microbiota of Yellow River carp. The results showed that the Spirulina and the mixture of Spirulina and ferrous fumarate could promote the development of intestinal villi, increase the thickness of intestinal muscular layer. Additionally, high-throughput sequencing of 16S rRNA gene revealed that the Spirulina and the mixture of Spirulina and ferrous fumarate could alter the composition, diversity, and richness of intestinal microbial communities. The relative abundances of the predominant phyla Firmicutes and Verrucomicrobia showed significant changes at the phylum level after fed with Spirulina and ferrous fumarate. At the genus level, the predominant genera with marked differences in abundances were Flavobacterium, Aeromonas, and Brevinema. In conclusion, this study indicated the Spirulina and the ferrous fumarate could alter the intestinal microbiota structure and could also cause positive impacts on the health of Yellow River carp. This study provides the valuable information for elucidating the mechanisms of Spirulina and ferrous fumarate in aquatic animals in the future.

[Clinical characteristics and prognosis of patients with anti-glutamic acid decarboxylase antibody-related cerebellar ataxia]

The clinical data, diagnosis, treatment, and prognosis of 10 patients with anti-glutamic acid decarboxylase (GAD) antibody-related cerebellar ataxia in Department of Neurology, Peking Union Medical College Hospital, from May 2015 to November 2021 were retrospectively analyzed. There were 8 female patients with a median age of 55 years old. Patients mainly presented with gait ataxia (10/10), dizziness (8/10), diplopia (6/10), and dysarthria (5/10). Four of them were complicated with other autoimmune disease, including vitiligo (3/4), Hashimoto thyroiditis (1/4), thrombocytopenia (1/4), and small cell lung cancer (1/4). All patients received immunotherapy, 6 out of 10 exhibited a good response, and half of them had satisfied functional prognosis. Patients of anti-GAD antibody-related cerebellar ataxia may be complicated with other autoimmune diseases, but underlying tumor is rare. More than half of patients have a good response to immunotherapy and satisfied prognosis.

[Pediatric autoimmune encephalitis associated with anti-glutamic acid decarboxylase 65 antibody: two cases report and literature review]

Objective: To investigate the clinical features and prognosis of pediatric autoimmune encephalitis associated with anti-glutamic acid decarboxylase 65 (GAD65) antibody. Methods: Clinical data of 2 patients diagnosed as autoimmune encephalitis associated with anti-GAD65 antibody at Department of Neurology, Beijing Children's Hospital in 2019 were analyzed retrospectively. A literature search with "anti-GAD65 antibody""encephalitis""epilepsy" or "cerebellar ataxia" as key words was conducted at China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform and PubMed (up to January 2020). The clinical features and prognosis of pediatric cases with complete clinical data were retrieved and summarized. Results: Two patients with positive anti-GAD65 antibody of serum and cerebrospinal fluid were both females. The onset age of case 1 was 57 months and her main clinical manifestations were fever and unconsciousness. The cranial magnetic resonance imaging (MRI) showed diffuse T2 weighted imaging (T2WI) abnormal signals, and the electroencephalogram (EEG) showed slow waves. The onset age of case 2 was 80 months and her main clinical manifestations of were recurrent focal seizures, memory loss, and headache. The MRI showed high T2WI signal in bilateral hippocampus, and the EEG showed abnormal discharge involving the temporal area. Both cases were treated with methylprednisolone and intravenous immunoglobulin, the short-term symptoms of them were both improved. They were followed up for 6 months and 1 year respectively, the case 1 recovered completely, and the case 2 still had focal seizures. Six English reports which included 6 cases were retrieved. Together with these 2 cases, a total of 8 cases were analyzed. The clinical symptoms included seizures (6 cases), memory loss (4 cases), loss of consciousness (3 cases), behavioral abnormalities (3 cases), cognitive impairment (2 cases), headache (2 cases), autonomic symptoms (1 case), ataxia (1 case), dysphagia (1 case), and aphasia (1 case). There were 5 cases with cranial MRI abnormalities in the acute phase or sub-acute phase, of whom 3 cases had the limbic system involvement, and 2 cases were mainly had extra limbic area involvement. Three cases had hippocampal atrophy or sclerosis during follow-up. All 8 patients were treated with immunotherapy. After immunotherapy, all patients had short-term improvement. Follow-up for 6 months to 6 years showed that 3 cases with extra limbic encephalitis improved to baseline levels, and 5 limbic encephalitis cases had poor outcomes, including 1 death and 4 cases still had focal epilepsy. Conclusions: Pediatric anti-GAD65 antibody associated autoimmune encephalitis is a rare but treatable disease, including limbic encephalitis and extra limbic encephalitis. The most common clinical manifestations are seizures and memory impairment. Early diagnosis and immunotherapy can improve the symptoms in a short time. But patients with limbic encephalitis often had refractory epilepsy in the chronic phase, and have a poor long-term outcome.

[Clinical observation on the overlapping syndrome of myelin oligodendrocyte glycoprotein antibody and anti-N-methyl-D aspartate receptor in children]

Objective: To investigate the clinical features, imaging findings and prognosis of children with overlapping syndrome of myelin oligodendrocyte glycoprotein (MOG) antibody disease and anti-N-methyl-D aspartate receptor (NMDAR) encephalitis (MNOS). Methods: The clinical manifestations, immunological antibodies in blood and cerebrospinal fluid, cranial image, treatment and follow-up of 11 patients diagnosed as MNOS in the Department of Neurology, Beijing Children's Hospital from January 2011 to April 2019 were analyzed retrospectively. Results: A total of 11 patients, including 4 males and 7 females were analyzed, the age of onset was (10.4±2.3) years. A total of 29 episodes occurred in 11 children. At the last follow-up, 8 cases showed relapsed remission course, the interval of recurrence was 3 to 60 months. The onset symptoms of 11 patients included convulsions (10 cases), lethargy (6 cases), psychosis (6 cases). Among 29 episodes, the common symptoms were convulsions (16 episodes), psychosis (13 episodes),and lethargy (10 episodes). According to the diagnostic criteria of anti-NMDAR encephalitis and MOG-antibody disease, 29 episodes were divided into three phenotypes, including anti-NMDAR encephalitis(4 episodes), MOG-antibody diseases (10 episodes) and overlapping types (15 episodes).Twenty-seven times of acute stage cranial magnetic resonance imaging (MRI) were available, common lesions included cortical focus (22 times), subcortical white matter (7 times), brainstem (9 times). All patients were sensitive to first-line immunotherapy. Eight patients had recurrence during glucocorticoid reduction, 6 of them were treated with additional second-line immunosuppressive therapy, including cyclophosphamide (1 case) and mycophenolate mofetil (5 cases). The follow-up time of patients were 5-99 months. At the last follow-up, all patients were in remission, the pediatric cerebral performance category (PCPC) score was 1 (10 cases) and 2 (1 cases). Conclusions: MNOS mainly affects older children. In the period of acute episodes, convulsions and psychosis are common. The cranial MRI showed extensive brain involvement and mainly in the cortex. The recurrence rates of MNOS are relatively high, patients are sensitive to first-line immunotherapy. No significant neurological dysfunction was left in the remission stage.

[Anti-myelin-associated glycoprotein antibody positive IgM monoclonal gammopathy related peripheral neuropathy: 11 cases and literature review]

目的

提高对罕见的抗髓鞘相关糖蛋白（MAG）抗体阳性的IgM相关性周围神经病（IgM-PN）的认识。

方法

总结2014年1月至2019年4月北京协和医院诊断的11例抗MAG抗体阳性的IgM-PN患者的临床特点、实验室检查、治疗方案和预后。

结果

11例患者中，男8例，女3例，中位发病年龄63（52~77）岁。其中9例患者以远端肢体麻木起病，6例伴肌力减退。神经传导速度检查示，均为周围神经脱髓鞘损害，以下肢感觉神经损害为主，6例伴慢性轴索损害。11例患者均存在血清IgM型单克隆免疫球蛋白，6例为IgM κ型，3例为IgM λ型，2例为IgM κ/IgG κ双克隆型。3例患者继发于巨球蛋白血症。11例患者的血清抗MAG抗体均为阳性。9例患者接受利妥昔单抗单药或联合化疗，治疗后7例患者的神经症状稳定或改善。

结论

抗MAG抗体阳性的IgM-PN是一种罕见的M蛋白相关性疾病。对于伴IgM型M蛋白的周围神经病患者，应常规筛查抗MAG抗体。基于利妥昔单抗的治疗可作为其一线治疗方案。

[Epidemiological investigation of burn patients with Klebsiella pneumoniae infection and the analysis of risk factors for sepsis in them]

Objective: To analyze the prevalence trend of Klebsiella pneumoniae (KP) infection in the Department of Burns of the Second Affiliated Hospital of Zhejiang University School of Medicine (hereinafter referred to as the author's department) from 2015 to 2017, and to screen out the independent risk factors for sepsis in burn patients with KP infection. Methods: The clinical and bacteriological data of burn patients with KP infection from January 1, 2015 to December 31, 2017 were collected from the author's department. The variation trend in infection rates of KP and carbapenems-resistant KP (CRKP) during the three years were statistically analyzed, and the data were processed with chi-square test. Clinical data were processed with binary logistic regression analysis to screen out the independent risk factors for sepsis in burn patients with KP infection. Results: (1) From 2015 to 2017, 91 patients (50 males and 41 females, aged 15-90 years) with KP infection were diagnosed in the author's department, of which 65 cases were CRKP positive, and 26 cases were carbapenems-sensitive KP positive. The KP infection rates of patients in 2015, 2016, and 2017 were 5.79% (35/605), 4.08% (23/564), and 5.54% (33/596), respectively. The CRKP infection rates of patients in 2015, 2016, and 2017 were 3.31% (20/605), 3.37% (19/564), and 4.36% (26/596), respectively. There were no statistically significant differences in KP infection rate and CRKP infection rate of patients among the three years (χ(2)=2.007, 1.175, P>0.05). (2) Total burn area and CRKP infection were independent risk factors for sepsis in burn patients with KP infection (odds ratios=1.03, 5.88, 95% confidence intervals=1.01-1.05, 1.08-31.94, P<0.05). Conclusions: From 2015 to 2017, the infection rates of KP and CRKP in the author's department did not increase obviously, but the proportion of CRKP infection was high. CRKP infection is one of the independent risk factors for sepsis in burn patients with KP infection. Strengthening the prevention and treatment of CRKP infection may have certain value in decreasing the incidence of burn sepsis.

[Clinical experience and next-generation sequencing analysis of encephalitis caused by pseudorabies virus]

Objective: To detect potential pathogens including pseudorabies virus in patients with encephalitis of unknown etiology in China and describe novel encephalitic entities. Methods: Patients with clinically suspected infectious encephalitis were enrolled in a multicenter study to identify the pathogens in PUMCH Encephalitis Program.Next-generation sequencing(NGS) of cerebrospinal fluid (CSF) was used in patients with encephalitis of unknown etiology enrolled from 2016 to 2017.The patients diagnosed as PRV encephalitis were studied to describe this novel entity. Results: The four patients(3 male, 1 male, 38-54 years old) had occupational exposure to raw park when working in the production or marketing of pork and at least one got injured during pork-cutting.Two of them were confirmed with NGS of CSF, and anti-PRV antibodies were positive in 3 patients whose serum was available for serological analysis.They all presented with an acute onset of fever, convulsion, loss of consciousness and respiratory failure within 1 to 4 days and rapidly deteriorated even on extensive treatment.All the patients needed ICU admission and 3 needed mechanical ventilation.Two patients also had bilateral retinitis.Neuroimaging revealed symmetric gray matter lesions including limbic system, basal ganglia and midbrain without obvious hemorrhage.Lumbar puncture revealed elevated intracranial pressure and lymphocytic pleocytosis [(6-64)×10(6)/L] of CSF.The patients failed to response to the treatment of acyclovir combined with intravenous immunoglobulin and steroids.Modified Rankin Score was 3, 5, 5 and 6 (died) for the 4 patients respectively on last follow-up. Conclusions: PRV could be a cause of severe encephalitis.The patients with suspected pseudorabies encephalitis (PRE) need to be tested for PRV DNA timely.Severe encephalitis with bilateral involvement of limbic system, basal ganglion, thalamus and midbrain in patient with occupational exposure indicate this emerging infectious encephalitis.

Flexible modulation of electronic and magnetic properties of zigzag H-MoS2 nanoribbons by crack defects

The effects of crack defects on electronic and magnetic properties of zigzag MoS₂ nanoribbons are investigated systematically by first-principles calculations based on spin-polarized density functional theory. We find that not only the electronic and spin transport ability of zigzag MoS₂ nanoribbons can be enhanced significantly by the armchair crack defects, but also their magnetism could be modulated flexibly by crack defects. Our study suggests that the introduction of crack defect is a feasible way to modulate the electronic and magnetic properties of zigzag MoS₂ nanoribbons. We further propose that the crack defects may also provide a useful tool for improving the performance of devices.

Discovery and characterization of conserved and novel microRNAs from blunt snout bream (Megalobrama amblycephala) by deep sequencing

MicroRNAs (miRNAs) are short, single stranded RNA molecules with approximately 22 nts in length, which regulate the stability and translation of messenger RNAs in several organisms. To increase the repertoire of miRNAs characterized in M. amblycephala, we used the deep sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the 4 different tissues of M. amblycephala. A total of 309 conserved miRNAs that originated from 131 miRNA families were detected. 15 novel candidates miRNA were identified. Randomly selected 6 miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in 6 different tissues of M. amblycephala. Furthermore, the potential targets were predicted. GO analysis showed that most of the targets were involved in a broad range of physiological functions including fish growth, development, metabolism, stress responses and so on. Overall, our results significantly increased the number of novel miRNAs in M. amblycephala, which should be useful for further investigation into the role of miRNAs in regulating diverse biological processes.

[Effects of endostatin pretreatment on fibrosis of human skin fibroblasts and the mechanisms]

Objective: To explore the effects of endostatin pretreatment on fibrosis of human skin fibroblasts and the mechanisms. Methods: Human skin fibroblasts were routinely cultured in vitro, and then the cells of passage 3 to 5 were used in the following experiments. The cells were divided into blank control, endostatin, platelet-derived growth factor-BB (PDGF-BB), endostatin+ PDGF-BB, transforming growth factor-β(1) (TGF-β(1)), and endostatin+ TGF-β(1) groups according to the random number table, with 3 wells in each group. Cells in blank control group were cultured with DMEM medium for 24 h. Cells in endostatin group were cultured with DMEM medium containing 5 μg/mL endostatin for 24 h. Cells in PDGF-BB group and TGF-β(1) group were cultured with DMEM medium containing 200 ng/mL PDGF-BB and 10 ng/mL TGF-β(1) for 24 h, respectively. Cells in endostatin+ PDGF-BB group were pretreated with DMEM medium containing 5 μg/mL endostatin for 48 h and then cultured with DMEM medium containing 200 ng/mL PDGF-BB for 24 h. Cells in endostatin+ TGF-β(1) group were pretreated with DMEM medium containing 5 μg/mL endostatin for 48 h and then cultured with DMEM medium containing 10 ng/mL TGF-β(1) for 24 h. The content of type Ⅰ collagen in the cell culture supernatant of three wells in each group was determined by enzyme-linked immunosorbent assay. The protein expression levels of α-smooth muscle actin (α-SMA), PDGF receptor β (PDGFRβ), phosphorylated PDGFRβ (p-PDGFRβ), and phosphorylated extracellular signal-regulated protein kinases 1/2 (p-ERK1/2) of three wells in each group were detected by Western blotting. Data were processed with one-way analysis of variance and SNK test. Results: (1) Compared with (5.05±0.29) pg/mL in blank control group, content of type Ⅰ collagen in the cell culture supernatant of endostatin group [(4.72±0.37) pg/mL] was close to it (P>0.05), content of type Ⅰ collagen in the cell culture supernatant of PDGF-BB group and TGF-β(1) group [(8.60±0.57) and (9.20±0.64) pg/mL, respectively] was higher (with P values below 0.05). Content of type Ⅰ collagen in the cell culture supernatant of endostatin+ PDGF-BB group [(5.32±0.17) pg/mL] was lower than that of PDGF-BB group (P<0.05), and content of type Ⅰ collagen in the cell culture supernatant of endostatin+ TGF-β(1) group [(5.41±0.20) pg/mL] was lower than that of TGF-β(1) group (P<0.05). (2) Compared with those in blank control group, protein expression levels of α-SMA, PDGFRβ, p-PDGFRβ, and p-ERK1/2 of cells in endostatin group showed no obvious differences (with P values above 0.05), while those in PDGF-BB and TGF-β(1) group were significantly higher (with P values below 0.01). Protein expression levels of α-SMA, PDGFRβ, p-PDGFRβ, and p-ERK1/2 of cells in endostatin+ PDGF-BB group and endostatin+ TGF-β(1) group were significantly lower than those in PDGF-BB group and TGF-β(1) group, respectively (with P values below 0.05). Conclusions: Pretreatment of endostatin can inhibit the fibrosis of human skin fibroblast and its transformation into myofibroblast, which may be related to the down-regulation of protein expression of p-PDGFRβ, PDGFRβ, and p-ERK.

[Clinical analysis of paraneoplastic neurological syndrome associated with thymoma]

Objectives: To investigate the clinical features, diagnosis and treatment of antibody mediated paraneoplastic neurological syndrome associated with thymoma. Methods: From 2012 to 2017, the paraneoplastic antibody and neuron antibody were tested from both blood and cerebrospinal fluid (CSF) in consecutive patients clinically suspected with neurological paraneoplastic syndromes/unknown encephalitis in Peking Union Medical College Hospital.The clinical data, lab results, electrophysiological examinations, imaging features, treatment and clinical prognosis were collected.In this study, the patients who met the diagnostic criteria of both thymoma and neurological paraneoplastic syndrome were retrospectively analyzed.The functional severity was assessed by modified Rankin score(mRS). Results: Six patients (4 female and 2 male) were included for the analysis.Of them, 4 patients presented with limbic encephalitis, 1 with peripheral neuropathy accompanying with myasthenia gravis and 1 with spinal and cerebella degeneration.Three patients were in severe condition (mRS=5). Positive α-amino-3-hydroxy-5-methyl-4-iso xazolepropionic acid receptor, antibody (AMPAR) was identified in 3 patients(2 in blood and CSF, 1 in blood), CV2 plus acetylcholine receptor antibody (ACH-Ab) positive in blood was seen in 1 patient and positive N-methyl-D-aspartate receptor (NMDAR) in blood and CSF in 1 patient. Brain MRI showed abnormalities in 2 patients.The CT scan revealed thymoma in all 6 patients.All patients received intravenous immunogloblin (IVIG) and/or glucocorticoid immediately after diagnosis.Furthermore, thymectomy was performed in 5 patients. All the patients were remarkably improved with mRS 0-1 at discharge.Five patients were clinical stable within follow-up of 1-2.5 years.However, one patient who refused thymectomy experienced several clinical recurrencs. Conclusions: Antibodies mediated paraneoplastic neurological syndrome/autoimmune encephalitis can occur in patients with thymoma with typical characteristics. The correlated antibody test and chest CT might be important in patients clinically suspected with neurological paraneoplastic syndrome or encephalitis with unknown reason. Surgical thymectomy combining with active immunological treatment may play a role in the favorable prognosis, even in those clinical severe patients.

Characterization of conserved and novel miRNAs using deep sequencing and prediction of miRNA targets in Crucian carp (Carassius auratus)

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs of -22 nucleotides that can base pair with their target mRNAs, which represses their translation or induces their degradation in various biological processes. However, little is known about identification of miRNAs and their target genes in C. auratus. In the present study, a small RNA library from pooled tissue of C. auratus was constructed and sequenced using the deep sequencing. A total of 320 conserved miRNAs (belonging to 105 families) as well as 11 potentially novel miRNAs were identified. Stem-loop qRT-PCR analysis confirmed that both conserved and novel miRNAs were expressed in C. auratus, and some of them were preferentially expressed in certain tissues. Subsequently, a total of 1668 potential target genes were predicted for these identified miRNAs and GO analysis showed that most of the targets were involved in lots of physiological actions. This study represents a first large-scale identification and characterization of C. auratus miRNAs and their potential target genes. Taken together, our results add new information to existing data on C. auratus miRNAs and should be useful for investigating the biological functions of miRNAs in fishes and other aquatic species.

[Analysis of prodromal phase and prodromal events in anti-N-methyl-D-aspartate receptor encephalitis]

Objective: To analyze prodromal phase and prodromal events of anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis. Methods: Clinical data of 179 patients hospitalized and diagnosed during 2010-2016 including adults and children in Peking Union Medical College Hospital and Beijing Children's Hospital were collected.Patients with prodromal phase or prodromal events were selected.A retrospective analysis of clinical characteristics including prodromal phase or prodromal events, course of disease, brain imaging, laboratory results and therapeutic effect was performed. Results: Prodromal phase was presented in 31.8% (57/179) of patients.Most common symptoms included fever (73.7%) and headache (68.4%). Prodromal phase was prolonged in 6 patients, the longest being 64 days.Among those 6 patients (10.5%), headache and fever were the only symptoms throughout disease courses in 3 cases.Prodromal events were reported in 6.1% (11/179) of patients, including 5 patients after HSV1 encephalitis, 1 after Japanese encephalitis, and 2 after resection of melanocytic nevi. Conclusions: Anti-NMDAR encephalitis can be preceded with prolonged prodromal phase.In some patients prodromal symptoms are the only clinical presentation.Clinical features of those atypical cases suggest that infection may be the precipitating factor.Viral encephalitis including HSV1 encephalitis and Japanese encephalitis may be prodromal events in some cases.

Identification and characterization of known and novel microRNAs in three tissues of Chinese giant salamander base on deep sequencing approach

MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although animal miRNAs have been extensively studied in model systems, less is known in other animal with limited genome sequence data, including Chinese giant salamander (Andrias davidianus). The identification of the full repertoire of miRNAs expressed in the liver, spleen and muscle of A. davidianus would significantly increase our understanding for physiological function of A. davidianus, in this ancient and endangered urodele amphibian. In this study, three independent small RNA libraries were constructed from the liver, spleen and muscle of A. davidianus. The libraries were subjected to high-throughput sequencing by using the Illumina deep sequencing. As a result, a total of 12,831,239, 13,592,195 and 9,887,531 raw reads representing 2,240,771, 1,363,266 and 1,964,252 clean reads per library were obtained separately. Through bioinformatics analysis, we identified total of 553 known miRNAs and 44 putative novel miRNAs in our small RNA dataset from liver, spleen and muscle tissues. Five known miRNAs (gga-miR-10a-5p, pma-miR-29d-5p, aca-miR-338-3p, hsa-miR-455-3p and ssa-miR-2184-5p_R-1) and three novel miRNAs (PC-5p-891_1763, PC-5p-32538_50 and PC-3p-33645_48) showed different expression in eight different tissues as revealed by stem-loop qPCR analysis. This study characterized the miRNA of A. davidianus for the first time, which provides an opportunity for further understanding of miRNA regulation function in A. davidianus ranked as living fossils.

Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus)

Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690 bp and N50 of 1263 bp. Unigenes were annotated through number of databases. These transcriptomic data of A. davidianus should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. The raw data in this study can be available in NCBI SRA database with accession number of SRP099564.

Identification and characterization of microRNAs and their target genes from Nile tilapia (Oreochromis niloticus)

MicroRNAs (miRNAs) are a class of small single-stranded, endogenous 21–22 nt non-coding RNAs that regulate their target mRNA levels by causing either inactivation or degradation of the mRNAs. In recent years, miRNA genes have been identified from mammals, insects, worms, plants, and viruses. In this research, bioinformatics approaches were used to predict potential miRNAs and their targets in Nile tilapia from the expressed sequence tag (EST) and genomic survey sequence (GSS) database, respectively, based on the conservation of miRNAs in many animal species. A total of 19 potential miRNAs were detected following a range of strict filtering criteria. To test the validity of the bioinformatics method, seven predicted Nile tilapia miRNA genes were selected for further biological validation, and their mature miRNA transcripts were successfully detected by stem–loop RT-PCR experiments. Using these potential miRNAs, we found 56 potential targets in this species. Most of the target mRNAs appear to be involved in development, metabolism, signal transduction, transcription regulation and stress responses. Overall, our findings will provide an important foundation for further research on miRNAs function in the Nile tilapia.

Improvements of PKU PMECRIS for continuous hundred hours CW proton beam operation

In order to improve the source stability, a long term continuous wave (CW) proton beam experiment has been carried out with Peking University compact permanent magnet 2.45 GHz ECR ion source (PKU PMECRIS). Before such an experiment a lot of improvements and modifications were completed on the source body, the Faraday cup and the PKU ion source test bench. At the beginning of 2015, a continuous operation of PKU PMECRIS for 306 h with more than 50 mA CW beam was carried out after success of many short term tests. No plasma generator failure or high voltage breakdown was observed during that running period and the proton source reliability is near 100%. Total beam availability, which is defined as 35-keV beam-on time divided by elapsed time, was higher than 99% [S. X. Peng et al., Chin. Phys. B 24(7), 075203 (2015)]. A re-inspection was performed after another additional 100 h operation (counting time) and no obvious sign of component failure was observed. Counting the previous source testing time together, this PMECRs longevity is now demonstrated to be greater than 460 h. This paper is mainly concentrated on the improvements for this long term experiment.

Duty factor variation possibility from 1% to 100% with PKU microwave driven Cs-free volume H⁻ sources

Microwave driven cesium-free volume H(-) sources, that have the ability to deliver tens of mA H(-) at 35 keV both in CW and 10% duty factor (100 Hz/1 ms), were developed at Peking University (PKU) [S. X. Peng et al., in Proceeding of IPAC 2015, WEPWA027, Richmond, Virginia, USA, 3-8 May 2015]. Recently, special efforts were paid on the investigation of duty factor variation possibility from 1% to 100% with them. Most of the experiments were carried out with a pulsed length (τ) of 1 ms and different intervals of 99 ms, 49 ms, 39 ms, 29 ms, 19 ms, 9 ms, 4 ms, 2 ms, 1 ms, 0.5 ms, and 0 ms, respectively. Other experiments were focused on CW operation and fixed duty factor of 1%. Experimental results prove that PKU H(-) sources can deliver tens of mA H(-) at duty factor from 1% to 100%. The RF power efficiency increases steadily with the increasing of duty factor from 1% to CW at a fixed pulsed length. Under a given duty factor and pulsed length, RF power efficiency keeps constant and the H(-) current increases with RF power linearly. Details will be presented in the paper.

Study on space charge compensation in negative hydrogen ion beam

Negative hydrogen ion beam can be compensated by the trapping of ions into the beam potential. When the beam propagates through a neutral gas, these ions arise due to gas ionization by the beam ions. However, the high neutral gas pressure may cause serious negative hydrogen ion beam loss, while low neutral gas pressure may lead to ion-ion instability and decompensation. To better understand the space charge compensation processes within a negative hydrogen beam, experimental study and numerical simulation were carried out at Peking University (PKU). The simulation code for negative hydrogen ion beam is improved from a 2D particle-in-cell-Monte Carlo collision code which has been successfully applied to H(+) beam compensated with Ar gas. Impacts among ions, electrons, and neutral gases in negative hydrogen beam compensation processes are carefully treated. The results of the beam simulations were compared with current and emittance measurements of an H(-) beam from a 2.45 GHz microwave driven H(-) ion source in PKU. Compensation gas was injected directly into the beam transport region to modify the space charge compensation degree. The experimental results were in good agreement with the simulation results.

IDENTIFCATION AND VALIDATION OF NOVEL microRNA MOLECULE FROM THE PELODISCUS SINENSIS BY BIOINFORMATICS APPROACHES

MicroRNAs (miRNAs) are a group of endogenous, short non-coding RNAs with the length of about 22 nt, which mediate gene expression at the post-transcriptional level through mRNA degradation or translational repression. Among them, some are highly evolutionally conserved in the animal kingdom; this provides a powerful strategy for identifying miRNAs in new species. The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important freshwater aquaculture reptilian species in China, but related miRNAs have not been identified up to now. In the present study, a total of 10 Pelodiscus sinensis miRNAs were identified according to Pelodiscus sinensis ESTs and GSSs information in NCBI database by bioinformatics approaches. The RT-PCR-based assays were performed and found that 10 Pelodiscus sinensis miRNAs were expressed. Using these miRNAs, 22 target genes were identified. These genes encode 22 proteins involved in metabolism, signal transduction, transcriptional regulation, and development. These miRNAs and their targets will serve as useful resources for their, functional analyses in miRNA-regulated processes in Pelodiscus sinensis breeding and genetic research.

Prediction and characterization of microRNAs from eleven fish species by computational methods

MicroRNAs (miRNAs) are a family of single-stranded RNA molecules about 22 nt in length, which can regulate protein-coding gene expression in various organisms by post-transcriptional repression of messenger. In this research, the potential miRNAs and their target genes were analyzed and predicted by computational methods from the EST and GSS databases of eleven fish species, 43 potential miRNAs were identified, they belong to 38 miRNA families, some miRNAs are highly conserved in animal kingdom, the predicted target genes are involved in development, signal transduction, response to environmental stress and pathogen invasion. Taken together, our data suggest that there are a plentiful of miRNAs in these eleven fish species, these miRNAs may play some important roles by regulating their target genes, and the data provide important information for further functional studies.

PiRNAs biogenesis and its functions

piRNAs (piwi-interacting RNA) are a novel class of non-coding small single-stranded RNAs with the length of 26-33 nt. The piRNAs play important biological role through the specific interaction with the piwi proteins of the Argonaute family. piRNA function in embryonic development, maintenance of germline DNA integrity, silencing of transposon transcription, suppressionof translation, formation of heterochromatin, and epigenetic regulation of sex determination. This review summarizes recent research and progress on biogenesis and function of piRNA in eukaryotic species.

Handling radiation generated during an ion source commissioning

Radiation is an important issue, which should be carefully treated during the design and commissioning of an ion source. Measurements show that X-rays are generated around the ceramics column of an extraction system when the source is powered up to 30 kV. The X-ray dose increases greatly when a beam is extracted. Inserting the ceramic column into a metal vacuum box is a good way to block X-ray emission for those cases. Moreover, this makes the online test of an intense H(+) ion beam with energy up to 100 keV possible. However, for deuteron ion source commissioning, neutron and gamma-ray radiation become a serious topic. In this paper, we will describe the design of the extraction system and the radiation doses of neutrons and gamma-rays measured at different D(+) beam energy during our 2.45 GHz deuteron electron cyclotron resonance ion source commissioning for PKUNIFTY (PeKing University Neutron Imaging FaciliTY) project at Peking University.

Commissioning and operation of the deuteron injector for PKUNIFTY project

PKUNIFTY (PeKing University Neutron Imaging FaciliTY), a thermal neutron imaging facility based on a 2 MeV RFQ accelerator, has been constructed at Peking University. Its deuteron injector, which consists of a 2.45 GHz permanent magnet electron cyclotron resonance (PMECR) deuteron ion source and a two-solenoid low energy beam transport (LEBT), aims at producing and delivering 50 mA, 50 keV deuteron beam with a duty factor of 10% (1 ms, 100 Hz). In the preliminary tests of RFQ accelerator, the ECR ion source and LEBT are required to operate at various duty factors (from 1% to 10%). The deuteron ion source has been tested with different pulse widths for this reason. In order to optimize the transmission parameters, the beam current at the exit of RFQ as a function of solenoids tuning and steering magnets tuning are carefully studied. The beam emittance at the entrance of RFQ has been measured with space charge compensation by different argon gas (RG) pressure from 1.6 × 10(-4) Pa to 4.7 × 10(-3) Pa. The measuring results show the best compensating pressure is 3.5 × 10(-3) Pa with a minimal normalized rms emittance of 0.12 pi mm mrad. During the commissioning, we found the purity of deuteron gas is an important factor which severely affects ECR discharge and plasma intensity inside the ion source chamber. The detailed experimental results obtained during the commissioning are discussed in this paper.

Plasma studies of the permanent magnet electron cyclotron resonance ion source at Peking University

At Peking University (PKU) we have developed several 2.45 GHz Permanent Magnet Electron Cyclotron Resonance ion sources for PKUNIFTY, SFRFQ, Coupled RFQ&SFRFQ, and Dielectric-Wall Accelerator (DWA) projects (respectively, 50 mA of D(+), 10 mA of O(+), 10 mA of He(+), and 50 mA of H(+)). In order to improve performance of these ion sources, it is necessary to better understand the principal factors that influence the plasma density and the atomic ion fraction. Theoretical analysis about microwave transmission and cut-off inside the discharge chamber were carried out to study the influence of the discharge chamber diameters. As a consequence, experimental studies on plasma density and ion fraction with different discharge chamber sizes have been carried out. Due to the difficulties in measuring plasma density inside the discharge chamber, the output beam current was measured to reflect the plasma density. Experimental results show that the plasma density increases to the maximum and then decreases significantly as the diameter changed from 64 mm to 30 mm, and the atomic ion fraction has the same tendency. The maximum beam intensity was obtained with the diameter of 35 mm, but the maximum atomic ion fraction with a diameter of 40 mm. The experimental results are basically accordant with the theoretical calculation. Details are presented in this paper.

Intense beams from gases generated by a permanent magnet ECR ion source at PKU

An electron cyclotron resonance (ECR) ion source is designed for the production of high-current ion beams of various gaseous elements. At the Peking University (PKU), the primary study is focused on developing suitable permanent magnet ECR ion sources (PMECRs) for separated function radio frequency quadrupole (SFRFQ) accelerator and for Peking University Neutron Imaging Facility. Recently, other kinds of high-intensity ion beams are required for new acceleration structure demonstration, simulation of fusion reactor material irradiation, aviation bearing modification, and other applications. So we expanded the ion beam category from O(+), H(+), and D(+) to N(+), Ar(+), and He(+). Up to now, about 120 mA of H(+), 83 mA of D(+), 50 mA of O(+), 63 mA of N(+), 70 mA of Ar(+), and 65 mA of He(+) extracted at 50 kV through a φ 6 mm aperture were produced by the PMECRs at PKU. Their rms emittances are less than 0.2 π mm mrad. Tungsten samples were irradiated by H(+) or He(+) beam extracted from this ion source and H∕He holes and bubbles have been observed on the samples. A method to produce a high intensity H∕He mixed beam to study synergistic effect is developed for nuclear material irradiation. To design a He(+) beam injector for coupled radio frequency quadruple and SFRFQ cavity, He(+) beam transmission experiments were carried out on PKU low energy beam transport test bench and the transmission was less than 50%. It indicated that some electrode modifications must be done to decrease the divergence of He(+) beam.

Deuteron injector for Peking University Neutron Imaging Facility project

The deuteron injector developed for the PKUNIFTY (Peking University Neutron Imaging Facility) has been installed and commissioned at Peking University (PKU). The injector system must transfer 50 keV 50 mA of D(+) ion beam to the entrance of the 2 MeV radio frequency quadrupole (RFQ) with 10% duty factor (1 ms, 100 Hz). A compact 2.45 GHz permanent magnet electron cyclotron resonance (PMECR) ion source and a 1.36 m long low energy beam transport (LEBT) line using two solenoids was developed as the deuteron injector. A φ5 mm four-quadrant diaphragm was used to simulate the entrance of RFQ electrodes. The beam parameters are measured after this core with an emittance measurement unit (EMU) and a bending magnet for ion fraction analysis at the end of injector. During the commissioning, 77 mA of total deuteron beam was extracted from PMECR and 56 mA of pure D(+) beam that passed through the φ5 mm four-quadrant diaphragm was obtained at the position of RFQ entrance with the measured normalized rms emittance 0.12-0.16π mm mrad. Ion species analysis results show that the deuteron fraction is as high as 99.5%. All of the parameters satisfy PKUNIFTY's requirements. In this paper, we will describe the deuteron injector design and report the commissioning results as well as the initial operation.

The deuteron injector progress of the Peking University Neutron Imaging Facility project

A deuteron radio frequency quadrupoles injector h has been developed at Peking University. A permanent magnetic electron cyclotron resonance (ECR) ion source is used in the injector system. A 50 keV 100 mA proton beam has been extracted from the ECR ion source and the measured normalized rms emittance is 0.11-0.14pi mm mrad. A deuteron beam has also been extracted at 50 kV with 83 mA total current and its emittance is less than 0.18pi mm mrad. The proton beam transmission has been investigated on a low energy beam transport test bench, and up to 93% transmission can be reached. The new injector with two solenoids has been designed and is being constructed. All the development results will be presented in this paper.

Preliminary studies on space charge compensation by analyzing residual argon gas ion signals

An experimental method is related to research the space charge compensation (SCC) effect in low energy intense proton beams by analyzing residual gas (RG) ion signals. The signal curves were measured with an energy spectrometer under the RG pressure from 1.2x10(-3) to 1.6x10(-2) Pa. Most of the data showed a similar trend with our theoretical predicts. From the RG ion energy spectra the potential distribution in the beam was calculated both with and without the SCC effect. Moreover, as a preliminary result, a best compensating point is achieved for the low energy beam transport transmission of 40 KeV, 60 mA H(+) beam in Peking University.

Upgrade of the extraction system of permanent magnet electron cyclotron resonance ion source

A set of new ion extraction electrodes have been designed for the permanent magnetic electron cyclotron resonance ion source at Peking University to improve beam quality and transmission. PBGUNS has been used to optimize the extraction electrodes and simulate the beam behavior at the extraction region. The experiments showed that with the new system, the beam half divergence angle can be less than 40 mrad and the normalized rms emittance is about 0.13pi mm mrad when the extracted current is 100 mA at 50 keV in pulse mode. The voltage of the suppression electrode has great effect on beam divergence. The effect of the microwave power and gas flow is also studied.

Macrokinetic model for methylotrophic Pichia pastoris based on stoichiometric balance

A macrokinetic model for Pichia pastoris expressing recombinant human serum albumin is proposed. The model describes the balances of some key metabolites, ATP and NADH, during glycerol and methanol metabolism. In the glycerol growth phase, the metabolic pathways mainly include phosphorylation, glycolysis, tricarboxylic acid cycle, and respiratory chain. In the methanol growth phase, methanol is oxidized to formaldehyde at first. Then, while a part of formaldehyde is oxidized to formate, the rest is condensed with xylulose-5-monophosphate to form glyceraldehyde-3-phosphate, and further assimilated to form cell constituents. The metabolic pathways following glyceraldehyde-3-phosphate were assumed to be similar to those in the glycerol growth phase. Based on the model, the macrokinetic bioreaction rates such as the specific substrate consumption rate, the specific growth rate, the specific acetyl-CoA formation rate as well as the specific oxygen uptake rate are obtained. The specific substrate consumption rate and the specific growth rate are then coupled into a bioreactor model such that the relationship between substrate feeding rates and the main state variables, i.e., the medium volume, the concentrations of the biomass, the substrate, and the product, is set up. Experimental results demonstrate that the model can describe the cell growth and the protein production with reasonable accuracy.