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https://www.readbyqxmd.com/read/28533988/strainseeker-fast-identification-of-bacterial-strains-from-raw-sequencing-reads-using-user-provided-guide-trees
#1
Märt Roosaare, Mihkel Vaher, Lauris Kaplinski, Märt Möls, Reidar Andreson, Maarja Lepamets, Triinu Kõressaar, Paul Naaber, Siiri Kõljalg, Maido Remm
BACKGROUND: Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. RESULTS: A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min...
2017: PeerJ
https://www.readbyqxmd.com/read/28533987/exoskeleton-may-influence-the-internal-body-temperatures-of-neotropical-dung-beetles-col-scarabaeinae
#2
Valentina Amore, Malva I M Hernández, Luis M Carrascal, Jorge M Lobo
The insect exoskeleton is a multifunctional coat with a continuum of mechanical and structural properties constituting the barrier between electromagnetic waves and the internal body parts. This paper examines the ability of beetle exoskeleton to regulate internal body temperature considering its thermal permeability or isolation to simulated solar irradiance and infrared radiation. Seven Neotropical species of dung beetles (Coleoptera, Scarabaeinae) differing in colour, surface sculptures, size, sexual dimorphism, period of activity, guild category and altitudinal distribution were studied...
2017: PeerJ
https://www.readbyqxmd.com/read/28533986/atorvastatin-alters-the-expression-of-genes-related-to-bile-acid-metabolism-and-circadian-clock-in-livers-of-mice
#3
Wen-Kai Li, Huan Li, Yuan-Fu Lu, Ying-Ying Li, Zidong Donna Fu, Jie Liu
AIM: Atorvastatin is a HMG-CoA reductase inhibitor used for hyperlipidemia. Atorvastatin is generally safe but may induce cholestasis. The present study aimed to examine the effects of atorvastatin on hepatic gene expression related to bile acid metabolism and homeostasis, as well as the expression of circadian clock genes in livers of mice. METHODS: Adult male mice were given atorvastatin (10, 30, and 100 mg/kg, po) daily for 30 days, and blood biochemistry, histopathology, and gene expression were examined...
2017: PeerJ
https://www.readbyqxmd.com/read/28533985/metabarcoding-monitoring-analysis-the-pros-and-cons-of-using-co-extracted-environmental-dna-and-rna-data-to-assess-offshore-oil-production-impacts-on-benthic-communities
#4
Olivier Laroche, Susanna A Wood, Louis A Tremblay, Gavin Lear, Joanne I Ellis, Xavier Pochon
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes...
2017: PeerJ
https://www.readbyqxmd.com/read/28533984/predictive-ability-of-the-mini-nutritional-assessment-short-form-mna-sf-in-a-free-living-elderly-population-a-cross-sectional-study
#5
Raimunda Montejano Lozoya, Nieves Martínez-Alzamora, Gonzalo Clemente Marín, Silamani J A Guirao-Goris, Rosa María Ferrer-Diego
BACKGROUND: Various scales have been used to perform a quick and first level nutritional assessment, and the MNA is one of the most used and recommended by experts in the elderly in all areas. This scale has a short form, the MNA-SF, revised and validated in 2009, which has two versions: the BMI-MNA-SF contains the first six items of the full scale including Body Mass Index while the CC-MNA-SF includes Calf Circumference instead of BMI. OBJECTIVE: To evaluate the predictive ability for nutritional status of the two versions of the MNA-SF against the MNA in free-living elderly in the province of Valencia...
2017: PeerJ
https://www.readbyqxmd.com/read/28533983/comparative-transcriptome-analyses-of-a-late-maturing-mandarin-mutant-and-its-original-cultivar-reveals-gene-expression-profiling-associated-with-citrus-fruit-maturation
#6
Lu Wang, Qingzhu Hua, Yuewen Ma, Guibing Hu, Yonghua Qin
Characteristics of late maturity in fruit are good agronomic traits for extending the harvest period and marketing time. However, underlying molecular basis of the late-maturing mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-Seq) technology was used to identify differentially expressed genes (DEGs) related to late-maturing characteristics from a late-maturing mutant 'Huawan Wuzishatangju' (HWWZSTJ) (Citrus reticulata Blanco) and its original line 'Wuzishatangju' (WZSTJ). A total of approximately 17...
2017: PeerJ
https://www.readbyqxmd.com/read/28533982/lid-opening-and-conformational-stability-of-t1-lipase-is-mediated-by-increasing-chain-length-polar-solvents
#7
Jonathan Maiangwa, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Raja Noor Zaliha Raja Abd Rahman, Yahaya M Normi, Fairolniza Mohd Shariff, Thean Chor Leow
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%...
2017: PeerJ
https://www.readbyqxmd.com/read/28533981/effects-of-knee-sleeves-on-coordination-of-lower-limb-segments-in-healthy-adults-during-level-walking-and-one-leg-hopping
#8
Chang-Yong Ko, Yunhee Chang, Bora Jeong, Sungjae Kang, Jeicheong Ryu, Gyoosuk Kim
The evaluation of multisegment coordination is important in gaining a better understanding of the gait and physical activities in humans. Therefore, this study aims to verify whether the use of knee sleeves affects the coordination of lower-limb segments during level walking and one-leg hopping. Eleven healthy male adults participated in this study. They were asked to walk 10 m on a level ground and perform one-leg hops with and without a knee sleeve. The segment angles and the response velocities of the thigh, shank, and foot were measured and calculated by using a motion analysis system...
2017: PeerJ
https://www.readbyqxmd.com/read/28533980/mitochondrial-complex-i-deficiency-leads-to-the-retardation-of-early-embryonic-development-in-ndufs4-knockout-mice
#9
Mei Wang, Ya-Ping Huang, Han Wu, Ke Song, Cong Wan, A-Ni Chi, Ya-Mei Xiao, Xiao-Yang Zhao
BACKGROUND: The NDUFS4 gene encodes an 18-kD subunit of mitochondria complex I, and mutations in this gene lead to the development of a severe neurodegenerative disease called Leigh syndrome (LS) in humans. To investigate the disease phenotypes and molecular mechanisms of Leigh syndrome, the Ndufs4 knockout (KO) mouse has been widely used as a novel animal model. Because the homozygotes cannot survive beyond child-bearing age, whether Ndufs4 and mitochondrial complex I influence early embryonic development remains unknown...
2017: PeerJ
https://www.readbyqxmd.com/read/28533979/a-genome-wide-assessment-of-stages-of-elevational-parapatry-in-bornean-passerine-birds-reveals-no-introgression-implications-for-processes-and-patterns-of-speciation
#10
Robert G Moyle, Joseph D Manthey, Peter A Hosner, Mustafa Rahman, Maklarin Lakim, Frederick H Sheldon
Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo...
2017: PeerJ
https://www.readbyqxmd.com/read/28533978/conserved-queen-pheromones-in-bumblebees-a-reply-to-amsalem-et-al
#11
Luke Holman, Jelle S van Zweden, Ricardo C Oliveira, Annette van Oystaeyen, Tom Wenseleers
In a recent study, Amsalem, Orlova & Grozinger (2015) performed experiments with Bombus impatiens bumblebees to test the hypothesis that saturated cuticular hydrocarbons are evolutionarily conserved signals used to regulate reproductive division of labor in many Hymenopteran social insects. They concluded that the cuticular hydrocarbon pentacosane (C25), previously identified as a queen pheromone in a congeneric bumblebee, does not affect worker reproduction in B. impatiens. Here we discuss some shortcomings of Amsalem et al...
2017: PeerJ
https://www.readbyqxmd.com/read/28533977/serotonergic-activation-during-courtship-and-aggression-in-the-brown-anole-anolis-sagrei
#12
Jacob T Hartline, Alexandra N Smith, David Kabelik
The role of serotonin (5-hydroxytryptamine, 5-HT) in social behavior regulation is not fully understood. While 5-HT release in nuclei of the social behavior network has generally been associated with inhibition of aggressive behavior across multiple classes of vertebrates, less is known about its effects on sexual, especially non-copulatory courtship display behaviors. Furthermore, most research has examined effects at 5-HT release sites, while studies examining the behavioral relevance of source cell populations have generated contradictory findings...
2017: PeerJ
https://www.readbyqxmd.com/read/28533976/phylogenetic-climatic-niche-conservatism-and-evolution-of-climatic-suitability-in-neotropical-angraecinae-vandeae-orchidaceae-and-their-closest-african-relatives
#13
Marta Kolanowska, Elżbieta Grochocka, Kamil Konowalik
In the present study we investigate the concept of phylogenetic niche conservatism (PNC) within the American species of angraecoid orchids (Campylocentrum and Dendrophylax) and their closest relatives in the Old World (Angraecum) using ecological niche modelling (ENM). The predicted niche occupancy profiles were matched with the outcomes of previous phylogenetic studies to reconstruct the evolution of climatic suitability within the orchid group studied and evaluate the role of niche differentiation in the speciation of Angraecinae...
2017: PeerJ
https://www.readbyqxmd.com/read/28533975/an-exhaustive-survey-of-regular-peptide-conformations-using-a-new-metric-for-backbone-handedness-h
#14
Ranjan V Mannige
The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide's conformation simply from knowing the φ and ψ values of a peptide (e...
2017: PeerJ
https://www.readbyqxmd.com/read/28533974/foraging-behaviour-of-an-egg-parasitoid-exploiting-plant-volatiles-induced-by-pentatomids-the-role-of-adaxial-and-abaxial-leaf-surfaces
#15
Francesca Frati, Antonino Cusumano, Eric Conti, Stefano Colazza, Ezio Peri, Salvatore Guarino, Letizia Martorana, Roberto Romani, Gianandrea Salerno
Several phases of herbivorous insect attack including feeding and oviposition are known to induce plant defenses. Plants emit volatiles induced by herbivores to recruit insect parasitoids as an indirect defense strategy. So far, volatiles induced by herbivore walking and their putative role in the foraging behavior of egg parasitoids have not been investigated. In this paper we studied the response of the egg parasitoid Trissolcus basalis toward volatiles emitted by Vicia faba plants as consequence of the walking activity of the host Nezara viridula...
2017: PeerJ
https://www.readbyqxmd.com/read/28533973/plastomes-of-the-green-algae-hydrodictyon-reticulatum-and-pediastrum-duplex-sphaeropleales-chlorophyceae
#16
Hilary A McManus, Daniel J Sanchez, Kenneth G Karol
BACKGROUND: Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex...
2017: PeerJ
https://www.readbyqxmd.com/read/28533972/characterisation-of-false-positive-observations-in-botanical-surveys
#17
Quentin J Groom, Sarah J Whild
Errors in botanical surveying are a common problem. The presence of a species is easily overlooked, leading to false-absences; while misidentifications and other mistakes lead to false-positive observations. While it is common knowledge that these errors occur, there are few data that can be used to quantify and describe these errors. Here we characterise false-positive errors for a controlled set of surveys conducted as part of a field identification test of botanical skill. Surveys were conducted at sites with a verified list of vascular plant species...
2017: PeerJ
https://www.readbyqxmd.com/read/28533971/regression-assumptions-in-clinical-psychology-research-practice-a-systematic-review-of-common-misconceptions
#18
Anja F Ernst, Casper J Albers
Misconceptions about the assumptions behind the standard linear regression model are widespread and dangerous. These lead to using linear regression when inappropriate, and to employing alternative procedures with less statistical power when unnecessary. Our systematic literature review investigated employment and reporting of assumption checks in twelve clinical psychology journals. Findings indicate that normality of the variables themselves, rather than of the errors, was wrongfully held for a necessary assumption in 4% of papers that use regression...
2017: PeerJ
https://www.readbyqxmd.com/read/28533970/a-comparison-of-freezing-damage-during-isochoric-and-isobaric-freezing-of-the-potato
#19
Chenang Lyu, Gabriel Nastase, Gideon Ukpai, Alexandru Serban, Boris Rubinsky
BACKGROUND: Freezing is commonly used for food preservation. It is usually done under constant atmospheric pressure (isobaric). While extending the life of the produce, isobaric freezing has detrimental effects. It causes loss of food weight and changes in food quality. Using thermodynamic analysis, we have developed a theoretical model of the process of freezing in a constant volume system (isochoric). The mathematical model suggests that the detrimental effects associated with isobaric freezing may be reduced in an isochoric freezing system...
2017: PeerJ
https://www.readbyqxmd.com/read/28533969/ranking-of-critical-species-to-preserve-the-functionality-of-mutualistic-networks-using-the-k-core-decomposition
#20
Javier García-Algarra, Juan Manuel Pastor, José María Iriondo, Javier Galeano
BACKGROUND: Network analysis has become a relevant approach to analyze cascading species extinctions resulting from perturbations on mutualistic interactions as a result of environmental change. In this context, it is essential to be able to point out key species, whose stability would prevent cascading extinctions, and the consequent loss of ecosystem function. In this study, we aim to explain how the k-core decomposition sheds light on the understanding the robustness of bipartite mutualistic networks...
2017: PeerJ
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