title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1770 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Dendrobium alkaloids prevent Aβ25–35-induced neuronal and synaptic loss via promoting neurotrophic factors expression in mice link: https://peerj.com/articles/2739 last-modified: 2016-12-13 description: BackgroundNeuronal and synaptic loss is the most important risk factor for cognitive impairment. Inhibiting neuronal apoptosis and preventing synaptic loss are promising therapeutic approaches for Alzheimer’s disease (AD). In this study, we investigate the protective effects of Dendrobium alkaloids (DNLA), a Chinese medicinal herb extract, on β-amyloid peptide segment 25–35 (Aβ25-35)-induced neuron and synaptic loss in mice.MethodAβ25–35(10 µg) was injected into the bilateral ventricles of male mice followed by an oral administration of DNLA (40 mg/kg) for 19 days. The Morris water maze was used for evaluating the ability of spatial learning and memory function of mice. The morphological changes were examined via H&E staining and Nissl staining. TUNEL staining was used to check the neuronal apoptosis. The ultrastructure changes of neurons were observed under electron microscope. Western blot was used to evaluate the protein expression levels of ciliary neurotrophic factor (CNTF), glial cell line-derived neurotrophic factor (GDNF), and brain-derived neurotrophic factor (BDNF) in the hippocampus and cortex.ResultsDNLA significantly attenuated Aβ25–35-induced spatial learning and memory impairments in mice. DNLA prevented Aβ25–35-induced neuronal loss in the hippocampus and cortex, increased the number of Nissl bodies, improved the ultrastructural injury of neurons and increased the number of synapses in neurons. Furthermore, DNLA increased the protein expression of neurotrophic factors BDNF, CNTF and GDNF in the hippocampus and cortex.ConclusionsDNLA can prevent neuronal apoptosis and synaptic loss. This effect is mediated at least in part via increasing the expression of BDNF, GDNF and CNTF in the hippocampus and cortex; improving Aβ-induced spatial learning and memory impairment in mice. creator: Jing Nie creator: Yong Tian creator: Yu Zhang creator: Yan-Liu Lu creator: Li-Sheng Li creator: Jing-Shan Shi uri: https://doi.org/10.7717/peerj.2739 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nie et al. title: Regulation of S1P receptors and sphingosine kinases expression in acute pulmonary endothelial cell injury link: https://peerj.com/articles/2712 last-modified: 2016-12-13 description: BackgroundAcute lung injury and acute respiratory distress syndrome (ALI/ARDS) is a severe clinical syndrome with mortality rate as high as 30–40%. There is no treatment yet to improve pulmonary endothelial barrier function in patients with severe pulmonary edema. Developing therapies to protect endothelial barrier integrity and stabilizing gas exchange is getting more and more attention. Sphingosine-1-phosphate (S1P) is able to enhance the resistance of endothelial cell barrier. S1P at physiological concentrations plays an important role in maintaining endothelial barrier function. Proliferation, regeneration and anti-inflammatory activity that mesenchymal stem cells (MSCs) exhibit make it possible to regulate the homeostatic control of S1P.MethodsBy building a pulmonary endothelial cell model of acute injury, we investigated the regulation of S1P receptors and sphingosine kinases expression by MSCs during the treatment of acute lung injury using RT-PCR, and investigated the HPAECs Micro-electronics impedance using Real Time Cellular Analysis.ResultsIt was found that the down-regulation of TNF-α expression was more significant when MSC was used in combination with S1P. The combination effection mainly worked on S1PR2, S1PR3 and SphK2. The results show that when MSCs were used in combination with S1P, the selectivity of S1P receptors was increased and the homeostatic control of S1P concentration was improved through regulation of expression of S1P metabolic enzymes.DiscussionsThe study found that, as a potential treatment, MSCs could work on multiple S1P related genes simultaneously. When it was used in combination with S1P, the expression regulation result of related genes was not simply the superposition of each other, but more significant outcome was obtained. This study establishes the experimental basis for further exploring the efficacy of improving endothelial barrier function in acute lung injury, using MSCs in combination with S1P and their possible synergistic mechanism. creator: Huiying Liu creator: Zili Zhang creator: Puyuan Li creator: Xin Yuan creator: Jing Zheng creator: Jinwen Liu creator: Changqing Bai creator: Wenkai Niu uri: https://doi.org/10.7717/peerj.2712 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liu et al. title: Self-reported frequency, severity of, and awareness of hypoglycemia in type 2 diabetes patients in Turkey link: https://peerj.com/articles/2700 last-modified: 2016-12-13 description: ObjectivesHypoglycemia is a common side effect of insulin therapy in type 1 and type 2 diabetes. Limited data exist on the frequency of hypoglycemic events in type 2 diabetic patients in Turkey. Our study investigated self-reported hypoglycemic events and awareness of hypoglycemia in Turkish patients with type 2 diabetes.MethodsPeople with type 2 diabetes older than 18 years of age were recruited from the two university hospital diabetes clinics. The frequency and severity of hypoglycemia and awareness of hypoglycemia during the preceding year were determinated using questionnaires by the face-to-face interview method.ResultsIn this study of 187 patients with type 2 diabetes, 83.4% had impaired awareness of their hypoglycemia, and 62% reported that they had missed some of the symptoms of hypoglycemia. Of the patients reporting hypoglycemic symptoms and severity level, 84.1% experienced mild hypoglycemia, 60% moderate, and 15.5% severe hypoglycemia in the past year. No significant association was made between hypoglycemia awareness and age, body-mass index (BMI), years of diabetes, dose of insulin, duration of insulin use, number of meals, or amount of snacking. A significant correlation was found between A1c levels and hypoglycemia awareness and severity of hypoglycemia. A significant correlation was found between dose of insulin, amount of snacking, and severity of hypoglycemia. No significant association was made between severity of hypoglycemia and age, BMI, years of diabetes, duration of insulin use, or the number of meals. However, the group with severe hypoglycemia had diabetes longer, and the average daily dose of insulin use was higher than in other groups.ConclusionsAccording to the study results, the percentage of patients with impaired awareness of hypoglycemia is high, and 62% of patients reported that they had missed some of the symptoms of hypoglycemia in type 2 diabetes. In addition, the percentage of severe hypoglycemic events is not low. Impaired awareness of hypoglycemia is a major risk factor for severe hypoglycemic events. Patients should be educated about the danger of hypoglycemia. Education should be improved, and a determined attempt should be made to eradicate the problem. creator: Dilek Büyükkaya Besen creator: Hamdiye Arda Sürücü creator: Cansu Koşar uri: https://doi.org/10.7717/peerj.2700 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Büyükkaya Besen et al. title: Malagasy Conostigmus (Hymenoptera: Ceraphronoidea) and the secret of scutes link: https://peerj.com/articles/2682 last-modified: 2016-12-13 description: We revise the genus Conostigmus Dahlbom 1858 occurring in Madagascar, based on data from more specimens than were examined for the latest world revision of the genus. Our results yield new information about intraspecific variability and the nature of the atypical latitudinal diversity gradient (LDG) observed in Ceraphronoidea. We also investigate cellular processes that underlie body size polyphenism, by utilizing the correspondence between epidermal cells and scutes, polygonal units of leather-like microsculpture. Our results reveal that body size polyphenism in Megaspilidae is most likely related to cell number and not cell size variation, and that cell size differs between epithelial fields of the head and that of the mesosoma. Three species, Conostigmus ballescoracasDessart, 1997, C. babaiax Dessart, 1996 and C. longulusDessart, 1997, are redescribed. Females of C. longulus are described for the first time, as are nine new species: C. bucephalus Mikó and Trietsch sp. nov., C. clavatus Mikó and Trietsch sp. nov., C. fianarantsoaensis Mikó and Trietsch sp. nov., C. lucidus Mikó and Trietsch sp. nov., C. macrocupula, Mikó and Trietsch sp. nov., C. madagascariensis Mikó and Trietsch sp. nov., C. missyhazenae Mikó and Trietsch sp. nov., C. pseudobabaiax Mikó and Trietsch sp. nov., and C. toliaraensis Mikó and Trietsch sp. nov. A fully illustrated identification key for Malagasy Conostigmus species and a Web Ontology Language (OWL) representation of the taxonomic treatment, including specimen data, nomenclature, and phenotype descriptions, in both natural and formal languages, are provided. creator: István Mikó creator: Carolyn Trietsch creator: Emily L. Sandall creator: Matthew Jon Yoder creator: Heather Hines creator: Andrew Robert Deans uri: https://doi.org/10.7717/peerj.2682 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mikó et al. title: Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs link: https://peerj.com/articles/2428 last-modified: 2016-12-13 description: The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases. creator: Guanglin Niu creator: Yalan Yang creator: YuanYuan Zhang creator: Chaoju Hua creator: Zishuai Wang creator: Zhonglin Tang creator: Kui Li uri: https://doi.org/10.7717/peerj.2428 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Niu et al. title: The relationship between cannabis use and measures of anxiety and depression in a sample of college campus cannabis users and non-users post state legalization in Colorado link: https://peerj.com/articles/2782 last-modified: 2016-12-08 description: As part of an ongoing research program into the relationship between cannabis use and emotion processing, participants were assessed on their level of cannabis exposure using the Recreational Cannabis Use Examination, a measure developed specifically to assess cannabis use in Colorado post state legalization. Three groups were created based on self-reported use: a control group who have never used, a casual user group and a chronic user group. Each participant also completed two measures of mood assessment, the Center for Epidemiologic Studies Depression Scale and the State-Trait Anxiety Inventory. Relationships between cannabis use groups and scores on these measures were then analyzed using both correlations and multivariate analysis of variance. Results indicate a relationship between casual cannabis use and scoring highly for depressive symptomatology on the Center for Epidemiologic Studies Depression Scale. There were no significant relationships between cannabis use and scores on the State-Trait Anxiety Inventory. creator: Lucy J. Troup creator: Jeremy A. Andrzejewski creator: Jacob T. Braunwalder creator: Robert D. Torrence uri: https://doi.org/10.7717/peerj.2782 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Troup et al. title: Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data link: https://peerj.com/articles/2781 last-modified: 2016-12-08 description: BackgroundNames used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed.MethodsWe analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes.ResultsBased on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. creator: Thomas Horn creator: Annette Häser uri: https://doi.org/10.7717/peerj.2781 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Horn and Häser title: Towards quantitative viromics for both double-stranded and single-stranded DNA viruses link: https://peerj.com/articles/2777 last-modified: 2016-12-08 description: BackgroundViruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).MethodsHere we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses.ResultsMock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample.DiscussionTogether these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems. creator: Simon Roux creator: Natalie E. Solonenko creator: Vinh T. Dang creator: Bonnie T. Poulos creator: Sarah M. Schwenck creator: Dawn B. Goldsmith creator: Maureen L. Coleman creator: Mya Breitbart creator: Matthew B. Sullivan uri: https://doi.org/10.7717/peerj.2777 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Roux et al. title: Shallow water sea slugs (Gastropoda: Heterobranchia) from the northwestern coast of the Sea of Japan, north of Peter the Great Bay, Russia link: https://peerj.com/articles/2774 last-modified: 2016-12-08 description: The coast of northern Primorye region, north of Peter the Great Bay has been sparsely studied in regards to its molluscan fauna, with just a few works reviewing the distribution of local mollusks. This work presents a survey of the shallow water heterobranch sea slugs currently occurring around Kievka Bay to Oprichnik Bay, Russia. Thirty-nine species of sea slugs were found in this study and the new species Cadlina olgae sp. nov., described herein. Most (24) of the species occurring in the area have widespread ranges in the northern Pacific Ocean. The eight species are endemic for the Sea of Japan and adjacent part of the Sea of Okhotsk. Seven other occur also in northern Atlantic and Arctic waters. Thirteen found species are not known from Peter the Great Bay but known from adjacent northern Pacific waters. The finding of a previously undescribed species emphasizes the need of further surveys, particularly in subtidal and deeper waters, in order to improve the knowledge on this neglected fauna in Primorye. creator: Anton Chichvarkhin uri: https://doi.org/10.7717/peerj.2774 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chichvarkhin title: Validation of internal reference genes for relative quantitation studies of gene expression in human laryngeal cancer link: https://peerj.com/articles/2763 last-modified: 2016-12-08 description: BackgroundThe aim of this study was to determine the expression stabilities of 12 common internal reference genes for the relative quantitation analysis of target gene expression performed by reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) in human laryngeal cancer.MethodsHep-2 cells and 14 laryngeal cancer tissue samples were investigated. The expression characteristics of 12 internal reference gene candidates (18S rRNA, GAPDH, ACTB, HPRT1, RPL29, HMBS, PPIA, ALAS1, TBP, PUM1, GUSB, and B2M) were assessed by RT-qPCR. The data were analyzed by three commonly used software programs: geNorm, NormFinder, and BestKeeper.ResultsThe use of the combination of four internal reference genes was more appropriate than the use of a single internal reference gene. The optimal combination was PPIA + GUSB + RPL29 + HPRT1 for both the cell line and tissues; while the most appropriate combination was GUSB + RPL29 + HPRT1 + HMBS for the tissues.ConclusionsOur recommended internal reference genes may improve the accuracy of relative quantitation analysis of target gene expression performed by the RT-qPCR method in further gene expression research on laryngeal tumors. creator: Xiaofeng Wang creator: Jinting He creator: Wei Wang creator: Ming Ren creator: Sujie Gao creator: Guanjie Zhao creator: Jincheng Wang creator: Qiwei Yang uri: https://doi.org/10.7717/peerj.2763 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al.