title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1661 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Relationship between hemoglobin glycation index and extent of coronary heart disease in individuals with type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/3875 last-modified: 2017-10-05 description: BackgroundIndividuals with type 2 diabetes (T2D) are at an increased risk of coronary heart disease (CHD). Diabetic complications have recently been associated with a measure of glucose metabolism known as the hemoglobin glycation index (HGI). Currently there is insufficient information regarding a potential link between HGI and cardiovascular disease. This study aimed to investigate the relationship between HGI and extent of CHD in individuals with T2D.MethodsThis cross-sectional study screened individuals visiting the endocrinology clinic between June 2012 and May 2016 for eligibility. Enrollment criteria included individuals above 21 years of age with T2D diagnosed in the preceding ten years. Candidates with hemoglobin disorders, pregnancy, and existing coronary artery disease were excluded. Fasting plasma glucose (FPG) and glycated hemoglobin A1c (HbA1c) were sampled three months prior to angiography. The regression equation of predicted HbA1c = 0.008 × FPG + 6.28 described the linear relationship between these variables. HGI was calculated as the difference between the measured HbA1c and predicted HbA1c. Participants were classified into two groups according to the presence of supranormal (≥0) or subnormal HGI (<0).ResultsAmong 423 participants, people with supranormal HGI harbored an increased prevalence of multiple vessel disease relative to those with subnormal HGI (Odds ratio (OR): 3.9, 95% CI [2.64–5.98], P < 0.001). Moreover, individuals with supranormal HGI more frequently demonstrated lesions involving the left anterior descending artery (OR: 3.0, 95% CI [1.97–4.66], P < 0.001). The intergroup difference in mean HbA1c was statistically nonsignificant (7.5 ± 1.0% versus 7.4 ± 1.1%, P = 0.80).DiscussionThis study demonstrated that HGI correlated with the extent of CHD in individuals with T2D. People with supranormal HGI harbored a higher prevalence of extensive cardiovascular disease compared to those with subnormal HGI. The relationship between HGI and extent of CHD enables cardiovascular risk stratification in at risk individuals. Overall, HGI provides useful information concerning cardiovascular risk in clinical practice. creator: Po Chung Cheng creator: Shang Ren Hsu creator: Yun Chung Cheng creator: Yu Hsiu Liu uri: https://doi.org/10.7717/peerj.3875 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cheng et al. title: Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean link: https://peerj.com/articles/3873 last-modified: 2017-10-05 description: Although the invasive azooxanthellate corals Tubastraea coccinea and T. tagusensis are spreading quickly and outcompeting native species in the Atlantic Ocean, there is little information regarding the genetic structure and path of introduction for these species. Here we present the first data on genetic diversity and clonal structure from these two species using a new set of microsatellite markers. High proportions of clones were observed, indicating that asexual reproduction has a major role in the local population dynamics and, therefore, represents one of the main reasons for the invasion success. Although no significant population structure was found, results suggest the occurrence of multiple invasions for T. coccinea and also that both species are being transported along the coast by vectors such as oil platforms and monobouys, spreading these invasive species. In addition to the description of novel microsatellite markers, this study sheds new light into the invasive process of Tubastraea. creator: Katia Cristina Cruz Capel creator: Robert J. Toonen creator: Caio T.C.C. Rachid creator: Joel C. Creed creator: Marcelo V. Kitahara creator: Zac Forsman creator: Carla Zilberberg uri: https://doi.org/10.7717/peerj.3873 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Capel et al. title: New whaitsioids (Therapsida: Therocephalia) from the Teekloof Formation of South Africa and therocephalian diversity during the end-Guadalupian extinction link: https://peerj.com/articles/3868 last-modified: 2017-10-05 description: Two new species of therocephalian therapsids are described from the upper Permian Teekloof Formation of the Karoo Basin, South Africa. They include two specimens of a whaitsiid, Microwhaitsia mendrezi gen. et sp. nov., and a single, small whaitsioid Ophidostoma tatarinovi gen. et sp. nov., which preserves a combination of primitive and apomorphic features. A phylogenetic analysis of 56 therapsid taxa and 136 craniodental and postcranial characters places the new taxa within the monophyletic sister group of baurioids—Whaitsioidea—with Microwhaitsia as a basal whaitsiid and Ophidostoma as an aberrant whaitsioid just outside the hofmeyriid+whaitsiid subclade. The new records support that whaitsioids were diverse during the early-late Permian (Wuchiapingian) and that the dichotomy between whaitsiid-line and baurioid-line eutherocephalians was established early on. The oldest Gondwanan whaitsiid Microwhaitsia and additional records from the lower strata of the Teekloof Formation suggest that whaitsioids had diversified by the early Wuchiapingian and no later than Pristerognathus Assemblage Zone times. Prior extinction estimates based on species counts are reflected in an analysis of origination/extinction rates, which imply increasing faunal turnover from Guadalupian to Lopingian (late Permian) times. The new records support a growing body of evidence that some key Lopingian synapsid clades originated near or prior to the Guadalupian-Lopingian boundary ca. 260–259 million years ago, but only radiated following the end-Guadalupian extinction of dinocephalians and basal therocephalian predators (long-fuse model). Ongoing collecting in older portions of the Teekloof Formation (e.g., Pristerognathus Assemblage Zone) will shed further light on early eutherocephalians during this murky but critical time in their evolutionary diversification. creator: Adam K. Huttenlocker creator: Roger M.H. Smith uri: https://doi.org/10.7717/peerj.3868 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Huttenlocker and Smith title: The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants link: https://peerj.com/articles/3766 last-modified: 2017-10-05 description: BackgroundThe current first line drugs for treating uncomplicated malaria are artemisinin (ART) combination therapies. However, Plasmodium falciparum parasites resistant to ART and partner drugs are spreading, which threatens malaria control efforts. Rodent malaria species are useful models for understanding antimalarial resistance, in particular genetic variants responsible for cross resistance to different compounds.MethodsThe Plasmodium berghei RC strain (PbRC) is described as resistant to different antimalarials, including chloroquine (CQ) and ART. In an attempt to identify the genetic basis for the antimalarial resistance trait in PbRC, its genome was sequenced and compared with five other previously sequenced P. berghei strains.ResultsWe found that PbRC is eight-fold less sensitive to the ART derivative artesunate than the reference strain PbANKA. The genome of PbRC is markedly different from other strains, and 6,974 single nucleotide variants private to PbRC were identified. Among these PbRC private variants, non-synonymous changes were identified in genes known to modulate antimalarial sensitivity in rodent malaria species, including notably the ubiquitin carboxyl-terminal hydrolase 1 gene. However, no variants were found in some genes with strong evidence of association with ART resistance in P. falciparum such as K13 propeller protein.DiscussionThe variants identified in PbRC provide insight into P. berghei genome diversity and genetic factors that could modulate CQ and ART resistance in Plasmodium spp. creator: Warangkhana Songsungthong creator: Supasak Kulawonganunchai creator: Alisa Wilantho creator: Sissades Tongsima creator: Pongpisid Koonyosying creator: Chairat Uthaipibull creator: Sumalee Kamchonwongpaisan creator: Philip J. Shaw uri: https://doi.org/10.7717/peerj.3766 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Songsungthong et al. title: Assessing the living and dead proportions of cold-water coral colonies: implications for deep-water Marine Protected Area monitoring in a changing ocean link: https://peerj.com/articles/3705 last-modified: 2017-10-05 description: Coral growth patterns result from an interplay of coral biology and environmental conditions. In this study colony size and proportion of live and dead skeletons in the cold-water coral (CWC) Lophelia pertusa (Linnaeus, 1758) were measured using video footage from Remotely Operated Vehicle (ROV) transects conducted at the inshore Mingulay Reef Complex (MRC) and at the offshore PISCES site (Rockall Bank) in the NE Atlantic. The main goal of this paper was to explore the development of a simple method to quantify coral growth and its potential application as an assessment tool of the health of these remote habitats. Eighteen colonies were selected and whole colony and dead/living layer size were measured. Live to dead layer ratios for each colony were then determined and analysed. The age of each colony was estimated using previously published data. Our paper shows that: (1) two distinct morphotypes can be described: at the MRC, colonies displayed a ‘cauliflower-shaped’ morphotype whereas at the PISCES site, colonies presented a more flattened ‘bush-shaped’ morphotype; (2) living layer size was positively correlated with whole colony size; (3) live to dead layer ratio was negatively correlated to whole colony size; (4) live to dead layer ratio never exceeded 0.27. These results suggest that as a colony develops and its growth rate slows down, the proportion of living polyps in the colony decreases. Furthermore, at least 73% of L. pertusa colonies are composed of exposed dead coral skeleton, vulnerable to ocean acidification and the associated shallowing of the aragonite saturation horizon, with significant implications for future deep-sea reef framework integrity. The clear visual contrast between white/pale living and grey/dark dead portions of the colonies also gives a new way by which they can be visually monitored over time. The increased use of marine autonomous survey vehicles offers an important new platform from which such a surveying technique could be applied to monitor deep-water marine protected areas in the future. creator: Johanne Vad creator: Covadonga Orejas creator: Juan Moreno-Navas creator: Helen S. Findlay creator: J. Murray Roberts uri: https://doi.org/10.7717/peerj.3705 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vad et al. title: Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis link: https://peerj.com/articles/3872 last-modified: 2017-10-04 description: Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis. creator: Amaël Borzée creator: Kyungmin Kim creator: Kyongman Heo creator: Piotr G. Jablonski creator: Yikweon Jang uri: https://doi.org/10.7717/peerj.3872 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Borzée et al. title: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs link: https://peerj.com/articles/3889 last-modified: 2017-10-04 description: Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable. creator: Robert C. Edgar uri: https://doi.org/10.7717/peerj.3889 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Edgar title: Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander link: https://peerj.com/articles/3861 last-modified: 2017-10-03 description: Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic. creator: Jérémy Tissier creator: Jean-Claude Rage creator: Michel Laurin uri: https://doi.org/10.7717/peerj.3861 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tissier et al. title: Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication link: https://peerj.com/articles/3886 last-modified: 2017-10-03 description: Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control. creator: Anais Castagnola creator: Jerreme Jackson creator: Omaththage P. Perera creator: Cris Oppert creator: Shigetoshi Eda creator: Juan Luis Jurat-Fuentes uri: https://doi.org/10.7717/peerj.3886 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Castagnola et al. title: Perch, Perca fluviatilis show a directional preference for, but do not increase attacks toward, prey in response to water-borne cortisol link: https://peerj.com/articles/3883 last-modified: 2017-10-03 description: In freshwater environments, chemosensory cues play an important role in predator-prey interactions. Prey use a variety of chemosensory cues to detect and avoid predators. However, whether predators use the chemical cues released by disturbed or stressed prey has received less attention. Here we tested the hypothesis that the disturbance cue cortisol, in conjunction with visual cues of prey, elevates predatory behavior. We presented predators (perch, Perca fluviatilis) with three chemosensory choice tests and recorded their location, orientation, and aggressive behavior. We compared the responses of predators when provided with (i) visual cues of prey only (two adjacent tanks containing sticklebacks); (ii) visual and natural chemical cues of prey vs. visual cues only; and (iii) visual cues of prey with cortisol vs. visual cues only. Perch spent a significantly higher proportion of time in proximity to prey, and orientated toward prey more, when presented with a cortisol stimulus plus visual cues, relative to presentations of visual and natural chemical cues of prey, or visual cues of prey only. There was a trend that perch directed a higher proportion of predatory behaviors (number of lunges) toward sticklebacks when presented with a cortisol stimulus plus visual cues, relative to the other chemosensory conditions. But they did not show a significant increase in total predatory behavior in response to cortisol. Therefore, it is not clear whether water-borne cortisol, in conjunction with visual cues of prey, affects predatory behavior. Our results provide evidence that cortisol could be a source of public information about prey state and/or disturbance, but further work is required to confirm this. creator: Lindsay J. Henderson creator: Mary R. Ryan creator: Hannah M. Rowland uri: https://doi.org/10.7717/peerj.3883 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Henderson et al.