Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya

Background Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells. Results In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene. Conclusions Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.Ope

A two-step target binding and selectivity support vector machines approach for virtual screening of dopamine receptor subtype-selective ligands

10.1371/journal.pone.0039076PLoS ONE76

A multi-task analysis and modelling paradigm using LSTM for multi-source monitoring data of inland vessels

The vessel monitoring data provide important information for people to understand the vessel dynamic status in real time and make appropriate decisions in vessel management and operations. However, some of the essential data may be incomplete or unavailable. In order to recover or predict the missing information and best exploit the vessels monitoring data, this paper combines statistical analysis, data mining and neural network methods to propose a multi-task analysis and modelling framework for multi-source monitoring data of inland vessels. Specifically, an advanced neural network, Long Short-Term Memory (LSTM) was tailored and employed to tackle three important tasks, including vessel trajectory repair, engine speed modelling and fuel consumption prediction. The developed models have been validated using the real-life vessel monitoring data and shown to outperform some other widely used modelling methods. In addition, statistics and data technologies were employed for data extraction, classification and cleaning, and an algorithm was designed for identification of the vessel navigational state

Delay-Range-Dependent Robust Constrained Model Predictive Control for Industrial Processes with Uncertainties and Unknown Disturbances

A delay-range-dependent robust constrained model predictive control is proposed for discrete-time system with uncertainties and unknown disturbances. The dynamic characteristic of the discrete-time system is established as a new extended state space model in which state variables and output tracking error are integrated and regulated independently. It is used as the design of control law of system, which cannot only guarantee the convergence and tracking performance but also offer more degrees of freedom for designed controller. Unlike the traditional robust model predictive control (RMPC), the novel, less conservative, and more simplified delay-range-dependent stable conditions are derived by linear matrix inequality (LMI) theory and some relaxed technologies, which make use of the information of the upper and lower bounds of the time-varying delay. Meanwhile, the H∞ performance index is introduced in the RMPC controller design, which can reject any unknown bounded disturbances. As a result, the design controller has better abilities of both tracking and disturbance rejection. The control results on the liquid level of tank system show that the proposed control method is effective and feasible

Nanopolymers Delivery of the Bone Morphogenetic Protein-4 Plasmid to Mesenchymal Stem Cells Promotes Articular Cartilage Repair In Vitro and In Vivo

The clinical application of viral vectors for gene therapy is limited for biosafety consideration. In this study, to promote articular cartilage repair, poly (lactic-co glycolic acid) (PLGA) nanopolymers were used as non-viral vectors to transfect rabbit mesenchymal stem cells (MSCs) with the pDC316-BMP4-EGFP plasmid. The cytotoxicity and transfection efficiency in vitro were acceptable measuring by CCK-8 and flow cytometry. After transfection, Chondrogenic markers (mRNA of Col2a1, Sox9, Bmp4, and Agg) of experimental cells (MSCs being transfected with BMP-4 plasmid by PLGA nanopolymers) were increased more than those of control cells (MSCs being transfected with naked BMP-4 plasmid alone). In vivo study, twelve rabbits (24 knees) with large full thickness articular cartilage defects were randomly divided into the experimental group (MSCs being transfected with BMP-4 plasmid by PLGA nanopolymers) and the control group (MSCs being transfected with naked BMP-4 plasmid). The experimental group showed better regeneration than the control group 6 and 12 weeks postoperatively. Hyaline-like cartilage formed at week 12 in the experimental group, indicating the local delivery of BMP-4 plasmid to MSCs by PLGA nanopolymers improved articular cartilage repair significantly. PLGA nanopolymers could be a promising and effective non-viral vector for gene therapy in cartilage repair

MicroRNA Expression Profile Analysis of <i>Chlamydomonas reinhardtii</i> during Lipid Accumulation Process under Nitrogen Deprivation Stresses

Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production

Prevalence of and Risk Factors for Cognitive Impairment Among Elderly Without Cardio- and Cerebrovascular Diseases: A Population-Based Study in Rural China

This study aimed to evaluate the prevalence of cognitive impairment and the distribution of its risk factors among residents aged ≥60 years without cardiovascular and cerebrovascular diseases in rural areas of northern China screened with the Chinese version of the Mini-Mental State Examination (MMSE). Between 2012 and 2013, a questionnaire survey was conducted to collect basic information from participants. Cognitive function was assessed using the MMSE. In the univariate analysis, risk factors for cognitive disorders were female sex, low education and central obesity, while drinking was found to be a protective factor. In the multivariate analysis, risk factors were old age (odds ratio [OR], 1.888; 95% confidence interval [CI]: 1.256–2.838; P = 0.002 for the 70-year-old group compared with the 60-year-old group; OR, 3.593; 95% CI, 2.468–5.230; P &lt; 0.001 for the ≥75-year-old group compared with the 60-year-old group), low education (OR, 3.779; 95% CI: 2.218–6.440; P &lt; 0.001 for the illiterate group compared with the group with ≥9 years of education; OR, 1.667; 95% CI, 1.001–2.775; P = 0.05 for the group with less than primary school compared with the group with ≥9 years of education), and higher blood pressure (BP; OR, 1.655; 95% CI: 1.076–2.544; P = 0.002 for individuals with stage III hypertension compared with those with normal BP). These findings suggest that it is crucial to manage and control level of BP, and improve educational attainment in order to reduce the prevalence and burden of cognitive impairment among low-income residents in rural China

Acupuncture for patients with mild to moderate Alzheimer’s disease: a randomized controlled trial

Abstract Background Alzheimer’s disease (AD) is the most common cause of dementia. However, none of medical treatment can stop or reverse the underlying neurodegenerative of AD at present. Acupuncture has attracted more and more attention in recent years due to its efficacy and very few side effects. Lately, a systematic review has thought that the evidence on the effectiveness of acupuncture in improving the cognitive function of AD patients was not powerful enough. Therefore, the aim of this study is to explore the efficacy and safety of acupuncture in patients with mild to moderate AD. Methods This was a randomized, controlled, parallel-group, exploratory study with 4-week baseline (T0), 12-week treatment phase (T1) and 12-week follow-up period (T2). Patients with mild to moderate AD meeting the included criteria were randomly allocated into either acupuncture or donepezil hydrochloride groups. The acupuncture group(AG) was given acupuncture treatment three times per week and the donepezil hydrochloride group(DG) group was administered donepezil hydrochloride once daily (5 mg/day for the first 4 weeks and 10 mg/day thereafter). Primary efficacy was measured using Alzheimer’s disease Assessment Scale-Cognitive (ADAS-cog) and Clinician’s Interview-Based Impression of Change-Plus (CIBIC-Plus). The second outcomes were measured with 23-Item Alzheimer’s disease Cooperative Study Activities of Daily Living Scales (ADAS-ADL23) and Neuropsychiatric Index (NPI). Results Of 87 participants enrolled in the study, 79 patients finished their treatment and follow-up processes. The ADAS-cog scores for AG group showed obvious decreases at T2 and ∆(T2-T0)when compared with DG group, and significant between-group differences were detected (all p < 0.05). The mean CIBIC-Plus values for the AG group at T1 and T2 were much lower than that for the DG group, and there were significant differences between the two groups (푃<0.05). There were no significant between-group differences in the scores of ADAS-ADL23 and NPI during the study period. Treatment discontinuations due to adverse events were 0 (0%) and 4 (9.09%) for the AG and DG groups, respectively. Conclusions Acupuncture is safe, well tolerated and effective in improving the cognitive function, global clinical status of AD. Trial Registration ChiCTR-IOR-17010465 (Retroactively registered on 18 JAN 2017)