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https://www.readbyqxmd.com/read/28729959/shot-gun-proteome-and-transcriptome-mapping-of-the-jujube-floral-organ-and-identification-of-a-pollen-specific-s-locus-f-box-gene
#1
Ruihong Chen, Guoliang Chen, Jian Huang
The flower is a plant reproductive organ that forms part of the fruit produced as the flowering season ends. While the number and identity of proteins expressed in a jujube (Ziziphus jujuba Mill.) flower is currently unknown, integrative proteomic and transcriptomic analyses provide a systematic strategy of characterizing the floral biology of plants. We conducted a shotgun proteomic analysis on jujube flowers by using a filter-aided sample preparation tryptic digestion, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
2017: PeerJ
https://www.readbyqxmd.com/read/28729958/mutational-analysis-of-driver-genes-with-tumor-suppressive-and-oncogenic-roles-in-gastric-cancer
#2
Tianfang Wang, Yining Liu, Min Zhao
Gastric cancer (GC) is a complex disease with heterogeneous genetic mechanisms. Genomic mutational profiling of gastric cancer not only expands our knowledge about cancer progression at a fundamental genetic level, but also could provide guidance on new treatment decisions, currently based on tumor histology. The fact that precise medicine-based treatment is successful in a subset of tumors indicates the need for better identification of clinically related molecular tumor phenotypes, especially with regard to those driver mutations on tumor suppressor genes (TSGs) and oncogenes (ONGs)...
2017: PeerJ
https://www.readbyqxmd.com/read/28729957/decline-of-heterozygosity-in-a-large-but-isolated-population-a-45-year-examination-of-moose-genetic-diversity-on-isle-royale
#3
Renae L Sattler, Janna R Willoughby, Bradley J Swanson
Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alces) population on Isle Royale (Lake Superior) from 1960-2005. We characterized samples, partitioned into five different 5-year periods, using nine microsatellite loci and a portion of the mtDNA control region...
2017: PeerJ
https://www.readbyqxmd.com/read/28729956/predicting-the-host-of-influenza-viruses-based-on-the-word-vector
#4
Beibei Xu, Zhiying Tan, Kenli Li, Taijiao Jiang, Yousong Peng
Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using the Support Vector Machine (SVM) classifier based on the word vector, a new representation and feature extraction method for biological sequences. The results show that the length of the word within the word vector, the sequence type (DNA or protein) and the species from which the sequences were derived for generating the word vector all influence the performance of models in predicting the host of influenza viruses...
2017: PeerJ
https://www.readbyqxmd.com/read/28729955/identification-of-four-prognostic-lncrnas-for-survival-prediction-of-patients-with-hepatocellular-carcinoma
#5
Zhonghao Wang, Qian Wu, Shu Feng, Yanhua Zhao, Chuanmin Tao
BACKGROUND: As the fifth most common cancer worldwide, Hepatocellular carcinoma (HCC) is also the third most common cause of cancer-related death in China. Several lncRNAs have been demonstrated to be associated with occurrence and prognosis of HCC. However, identification of prognostic lncRNA signature for HCC with expression profiling data has not been conducted yet. METHODS: With the reuse of public available TCGA data, expression profiles of lncRNA for 371 patients with HCC were obtained and analyzed to find the independent prognostic lncRNA...
2017: PeerJ
https://www.readbyqxmd.com/read/28729954/clinical-streptococcal-isolates-distinct-from-streptococcus-pneumoniae-but-containing-the-%C3%AE-glucosyltransferase-tts-gene-and-expressing-serotype-37-capsular-polysaccharide
#6
Carmen L Sheppard, Georgia Kapatai, Karen Broughton, Ulf Schaefer, Matthew Hannah, David J Litt, Norman K Fry
The major virulence factor of the pneumococcus, and target for conjugate vaccines, is the polysaccharide capsule, which is usually encoded by the highly variable cps locus. Serotype 37 is an unusual pneumococcal type in which the single β-glucosyltransferase gene responsible for serotype capsule production (tts) is located outside of the capsular operon region. Using a previously described automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT, we identified and investigated seven clinical isolates (three from blood cultures) of non-pneumococcal streptococci containing a highly homologous tts and included them in a study panel of 20 isolates which included a 11 further clinical isolates of S...
2017: PeerJ
https://www.readbyqxmd.com/read/28729953/demographic-inference-through-approximate-bayesian-computation-skyline-plots
#7
Miguel Navascués, Raphaël Leblois, Concetta Burgarella
The skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of the demographic trajectory. Because of this flexibility in shape, skyline plots can, in principle, provide realistic descriptions of the complex demographic scenarios that occur in natural populations. Currently, demographic estimates needed for skyline plots are estimated using coalescent samplers or a composite likelihood approach...
2017: PeerJ
https://www.readbyqxmd.com/read/28729952/nano-sized-zeolites-as-modulators-of-thiacloprid-toxicity-on-chironomus-riparius
#8
Carla S Lorenz, Anna-Jorina Wicht, Leyla Guluzada, Barbara Crone, Uwe Karst, Hwa Jun Lee, Rita Triebskorn, Stefan B Haderlein, Carolin Huhn, Heinz-R Köhler
This study investigated whether zeolites of different size (Y30 (nano-sized) and H-Beta(OH)-III (forming large aggregates/agglomerates composed of 50 nm small primary particles)) exerted acute toxicity on larvae of the non-biting midge, Chironomus riparius, and whether such zeolites are able to modulate the toxicity of a common insecticide, thiacloprid, by means of adsorption of a dissolved toxicant. We conducted acute toxicity tests with fourth instar larvae of C. riparius. In these tests, larvae were exposed to zeolites or thiacloprid solely, or to mixtures of both compounds...
2017: PeerJ
https://www.readbyqxmd.com/read/28729951/young-children-do-not-require-perceptual-motor-feedback-to-solve-aesop-s-fable-tasks
#9
Rachael Miller, Sarah A Jelbert, Elsa Loissel, Alex H Taylor, Nicola S Clayton
Aesop's Fable tasks-in which subjects drop objects into a water-filled tube to raise the water level and obtain out-of-reach floating rewards -have been used to test for causal understanding of water displacement in both young children and non-human animals. However, a number of alternative explanations for success on these tasks have yet to be ruled out. One hypothesis is that subjects may respond to perceptual-motor feedback: repeating those actions that bring the reward incrementally closer. Here, we devised a novel, forced-choice version of the Aesop's Fable task to assess whether subjects can solve water displacement tasks when this type of feedback is removed...
2017: PeerJ
https://www.readbyqxmd.com/read/28729950/alder-and-the-golden-fleece-high-diversity-of-frankia-and-ectomycorrhizal-fungi-revealed-from-alnus-glutinosa-subsp-barbata-roots-close-to-a-tertiary-and-glacial-refugium
#10
Melanie Roy, Adrien C Pozzi, Raphaëlle Gareil, Melissande Nagati, Sophie Manzi, Imen Nouioui, Nino Sharikadze, Patricia Jargeat, Hervé Gryta, Pierre-Arthur Moreau, Maria P Fernandez, Monique Gardes
BACKGROUND: Recent climatic history has strongly impacted plant populations, but little is known about its effect on microbes. Alders, which host few and specific symbionts, have high genetic diversity in glacial refugia. Here, we tested the prediction that communities of root symbionts survived in refugia with their host populations. We expected to detect endemic symbionts and a higher species richness in refugia as compared to recolonized areas. METHODS: We sampled ectomycorrhizal (EM) root tips and the nitrogen-fixing actinomycete Frankia communities in eight sites colonized by Alnus glutinosa subsp...
2017: PeerJ
https://www.readbyqxmd.com/read/28729949/modeling-the-effect-of-blunt-impact-on-mitochondrial-function-in-cartilage-implications-for-development-of-osteoarthritis
#11
Georgi I Kapitanov, Bruce P Ayati, James A Martin
OBJECTIVE: Osteoarthritis (OA) is a disease characterized by degeneration of joint cartilage. It is associated with pain and disability and is the result of either age and activity related joint wear or an injury. Non-invasive treatment options are scarce and prevention and early intervention methods are practically non-existent. The modeling effort presented in this article is constructed based on an emerging biological hypothesis-post-impact oxidative stress leads to cartilage cell apoptosis and hence the degeneration observed with the disease...
2017: PeerJ
https://www.readbyqxmd.com/read/28717600/implementation-of-the-xpert-mtb-rif-assay-for-tuberculosis-in-mongolia-a-qualitative-exploration-of-barriers-and-enablers
#12
Nicole L Rendell, Solongo Bekhbat, Gantungalag Ganbaatar, Munkhjargal Dorjravdan, Madhukar Pai, Claudia C Dobler
OBJECTIVE: The aim of our study was to identify barriers and enablers to implementation of the Xpert MTB/RIF test within Mongolia's National Tuberculosis Program. METHODS: Twenty-foursemi-structured interviews were conducted between June and September 2015 with laboratory staff and tuberculosis physicians in Mongolia's capital Ulaanbaatar and regional towns where Xpert MTB/RIF testing had been implemented. Interviews were recorded, transcribed, translated and analysed thematically using NVIVO qualitative analysis software...
2017: PeerJ
https://www.readbyqxmd.com/read/28717599/improving-the-trajectory-of-transpedicular-transdiscal-lumbar-screw-fixation-with-a-computer-assisted-3d-printed-custom-drill-guide
#13
Zhen-Xuan Shao, Jian-Shun Wang, Zhong-Ke Lin, Wen-Fei Ni, Xiang-Yang Wang, Ai-Min Wu
Transpedicular transdiscal screw fixation is an alternative technique used in lumbar spine fixation; however, it requires an accurate screw trajectory. The aim of this study is to design a novel 3D-printed custom drill guide and investigate its accuracy to guide the trajectory of transpedicular transdiscal (TPTD) lumbar screw fixation. Dicom images of thirty lumbar functional segment units (FSU, two segments) of L1-L4 were acquired from the PACS system in our hospital (patients who underwent a CT scan for other abdomen diseases and had normal spine anatomy) and imported into reverse design software for three-dimensional reconstructions...
2017: PeerJ
https://www.readbyqxmd.com/read/28717598/development-rate-rather-than-social-environment-influences-cognitive-performance-in-australian-black-field-crickets-teleogryllus-commodus
#14
Caitlin L Anderson, Michael M Kasumovic
Cognitive functioning is vital for enabling animals of all taxa to optimise their chances of survival and reproductive success. Learning and memory in particular are drivers of many evolutionary processes. In this study, we examine how developmental plasticity can affect cognitive ability by exploring the role the early social environment has on problem solving ability and learning of female black field crickets, Teleogryllus commodus. We used two learning paradigms, an analog of the Morris water maze and a novel linear maze, to examine cognitive differences between individuals reared in two acoustic treatments: silence or calling...
2017: PeerJ
https://www.readbyqxmd.com/read/28717597/cuticle-hydrocarbons-in-saline-aquatic-beetles
#15
María Botella-Cruz, Adrián Villastrigo, Susana Pallarés, Elena López-Gallego, Andrés Millán, Josefa Velasco
Hydrocarbons are the principal component of insect cuticle and play an important role in maintaining water balance. Cuticular impermeability could be an adaptative response to salinity and desiccation in aquatic insects; however, cuticular hydrocarbons have been poorly explored in this group and there are no previous data on saline species. We characterized cuticular hydrocarbons of adults and larvae of two saline aquatic beetles, namely Nebrioporus baeticus (Dytiscidae) and Enochrus jesusarribasi (Hydrophilidae), using a gas chromatograph coupled to a mass spectrometer...
2017: PeerJ
https://www.readbyqxmd.com/read/28717596/phenotypic-and-microrna-transcriptomic-profiling-of-the-mda-mb-231-spheroid-enriched-cscs-with-comparison-of-mcf-7-microrna-profiling-dataset
#16
Lily Boo, Wan Yong Ho, Norlaily Mohd Ali, Swee Keong Yeap, Huynh Ky, Kok Gan Chan, Wai Fong Yin, Dilan Amila Satharasinghe, Woan Charn Liew, Sheau Wei Tan, Soon Keng Cheong, Han Kiat Ong
Breast cancer spheroids have been widely used as in vitro models of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance...
2017: PeerJ
https://www.readbyqxmd.com/read/28717595/egg-clutch-dehydration-induces-early-hatching-in-red-eyed-treefrogs-agalychnis-callidryas
#17
María José Salica, James R Vonesh, Karen M Warkentin
Terrestrial eggs have evolved repeatedly in tropical anurans exposing embryos to the new threat of dehydration. Red-eyed treefrogs, Agalychnis callidryas, lay eggs on plants over water. Maternally provided water allows shaded eggs in humid sites to develop to hatching without rainfall, but unshaded eggs and those in less humid sites can die from dehydration. Hatching responses of amphibian eggs to dry conditions are known from two lineages with independent origins of terrestrial eggs. Here, we experimentally tested for dehydration-induced early hatching in another lineage (Agalychnis callidryas, Phyllomedusidae), representing a third independent origin of terrestrial eggs...
2017: PeerJ
https://www.readbyqxmd.com/read/28717594/effect-of-freshwater-mussels-on-the-vertical-distribution-of-anaerobic-ammonia-oxidizers-and-other-nitrogen-transforming-microorganisms-in-upper-mississippi-river-sediment
#18
Ellen M Black, Michael S Chimenti, Craig L Just
Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0...
2017: PeerJ
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#19
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28717592/epas1-variants-in-high-altitude-tibetan-wolves-were-selectively-introgressed-into-highland-dogs
#20
Bridgett vonHoldt, Zhenxin Fan, Diego Ortega-Del Vecchyo, Robert K Wayne
BACKGROUND: Admixture can facilitate adaptation. For example, black wolves have obtained the variant causing black coat color through past hybridization with domestic dogs and have higher fitness than gray colored wolves. Another recent example of the transfer of adaptive variation between the two species has been suggested by the similarity between high altitude Tibetan mastiffs and wolves at the EPAS1 gene, a transcription factor induced in low oxygen environments. METHODS: Here, we investigate the directionality of admixture in EPAS1 between 28 reference highland gray wolves, 15 reference domestic dogs, and 21 putatively admixed highland wolves...
2017: PeerJ
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