title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1134 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The association of EGF rs2237051 variant, serum EGF levels and generalized aggressive periodontitis: a preliminary study link: https://peerj.com/articles/9212 last-modified: 2020-05-19 description: BackgroundEpidermal growth factor (EGF) is a pro-inflammatory small peptide that stimulates cell growth, proliferation and differentiation through binding to its receptor. EGF rs2237051 and serum EGF levels have been demonstrated to be related with a variety of diseases, including several tumors and inflammatory diseases. Therefore, this study aims to investigate the association of the EGF rs2237051 variant and serum EGF levels in Chinese patients with generalized aggressive periodontitis (GAgP).Material and MethodsA case-control study was conducted among 216 patients with GAgP and 138 healthy controls. The clinical parameters of plaque index, probing depth, attachment loss and bleeding index were recorded. The EGF rs2237051 polymorphism was genotyped using time-of-flight mass spectrometry, and serum EGF levels were determined. Logistic and linear regression models were used to investigate the association between the genotypes of EGF rs2237051, serum EGF levels and GAgP risk.ResultsThe AA genotype of EGF rs2237051 showed higher risk for GAgP than the combined genotypes GG and AG (adjusted OR = 1.65, 95% CI [1.06–2.57]). Increased serum EGF levels were associated with GAgP (adjusted OR = 1.18, 95% CI [1.14–1.22]). Moreover, the serum EGF level for the AA genotype was significantly higher than that for the AG/GG genotypes in patients with GAgP (adjusted β = 4.70, 95% CI [2.09–7.31]).ConclusionWe demonstrated that EGF rs2237051 variant and the increased level of serum EGF were associated with the risk of GAgP, the serum EGF was up-regulated in patients with GAgP. It was indicated that serum EGF might be a biomarker of GAgP and EGF rs2237051 may be related to the genetic background of GAgP. creator: Xian’e Wang creator: Wenjing Li creator: Li Xu creator: Ruifang Lu creator: Huanxin Meng uri: https://doi.org/10.7717/peerj.9212 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: The case for extended lifespan in cooperatively breeding mammals: a re-appraisal link: https://peerj.com/articles/9214 last-modified: 2020-05-19 description: Recent comparative studies have suggested that cooperative breeding is associated with increases in maximum lifespan among mammals, replicating a pattern also seen in birds and insects. In this study, we re-examine the case for increased lifespan in mammalian cooperative breeders by analysing a large dataset of maximum longevity records. We did not find any consistent, strong evidence that cooperative breeders have longer lifespans than other mammals after having controlled for variation in body mass, mode of life and data quality. The only possible exception to this general trend is found in the African mole-rats (the Bathyergid family), where all members are relatively long-lived, but where the social, cooperatively breeding species appear to be much longer-lived than the solitary species. However, solitary mole-rat species have rarely been kept in captivity or followed longitudinally in the wild and so it seems likely that their maximum lifespan has been underestimated when compared to the highly researched social species. Although few subterranean mammals have received much attention in a captive or wild setting, current data instead supports a causal role of subterranean living on lifespan extension in mammals. creator: Jack Thorley uri: https://doi.org/10.7717/peerj.9214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Thorley title: Plasma antioxidants and oxidative stress status in obese women: correlation with cardiopulmonary response link: https://peerj.com/articles/9230 last-modified: 2020-05-19 description: IntroductionA high body fat coupled with low cardiopulmonary fitness and an increase in oxidative stress has been connoted as contributing factors in developing cardiovascular comorbidities. This study aimed to investigate the correlation between antioxidants and oxidative stress status with cardiopulmonary responses in women of different body mass index (BMI).Subjects and MethodsEighty female adults were recruited and divided into three groups; normal weight (n = 23), overweight (n = 28) and obese (n = 29), according to their BMI. Blood samples were obtained prior to cardiopulmonary exercise testing. Plasma samples were separated by centrifugation and analysed for enzymatic antioxidant activity including catalase, glutathione peroxidase and superoxide dismutase. Non-enzymatic antioxidant activities were assessed using 2, 2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging and ferric reducing ability of plasma (FRAP) assays. To evaluate the oxidative stress status of subjects, levels of reactive oxygen species and malondialdehyde, the by-product of lipid peroxidation, were measured. Cardiopulmonary responses were analysed using cardiopulmonary exercise testing (CPET) which involved 15 various parameters such as peak oxygen consumption, metabolic equivalents and respiratory exchange ratio.ResultsThe obese group had significantly lower ABTS radical scavenging and FRAP activities than the normal weight group. A higher catalase activity was observed in the obese group than the normal weight group. Spearman’s correlation showed an inverse relationship between catalase and peak oxygen consumption, while partial correlation analysis showed inverse correlations between superoxide dismutase and respiratory frequency, ABTS activity and oxygen pulse, and between ABTS activity and cardiac output.ConclusionOur results demonstrate a lower cardiovascular fitness and antioxidant capacity in obese women; the higher catalase activity may be a compensatory mechanism. The negative correlations found between these two parameters may indicate the potential effect of antioxidants on the cardiopulmonary system and deserve further analysis in a larger population. Nevertheless, this study provides the basis for future studies to further explore the relationships between redox status and cardiopulmonary responses. This can potentially be used to predict future risk of developing diseases associated with oxidative stress, especially pulmonary and cardiovascular diseases. creator: Dyg Mastura Adenan creator: Zulkarnain Jaafar creator: Jaime Jacqueline Jayapalan creator: Azlina Abdul Aziz uri: https://doi.org/10.7717/peerj.9230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Adenan et al. title: Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi link: https://peerj.com/articles/9061 last-modified: 2020-05-18 description: The glycopeptidase GCP and its homologue proteins are conserved and essential for survival of bacteria. The ygjD gene (Glycopeptidase homologue) was cloned from Vibrio harveyi strain SF-1. The gene consisted of 1,017 bp, which encodes a 338 amino acid polypeptide. The nucleotide sequence similarity of the ygjD gene with that of V. harveyi FDAARGOS 107 was 95%. The ygjD gene also showed similarities of 68%, 67% and 50% with those of Salmonella enterica, Escherichia coli and Bacillus cereus. The ygjD gene was expressed in E. coli BL21 (DE3) and the recombinant YgjD was purified by Ni2+ affinity chromatography column. The purified YgjD showed a specific 37 kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and exhibited protease activities of 59,000 units/mg, 53,700 units/mg and 8,100 units/mg, respectively, on N-Acetyl-L-tyrosine ethyl ester monohydrate (ATEE), N-Benzoyl-L-tyrosine ethyl ester (BTEE) and N-Benzoyl-DL-arginine-4-nitroanilide hydrochloride (BAPNA) substrates. When the conserved amino acids of His111, Glu113 and His115 in the YgjD were replaced with alanine, respectively, the protease activities of the mutants were partly decreased. The two conserved His111 and His115 of YgjD were mutated and the protein lost the protease activity, which implied that the two amino acid played very important roles in maintaining its protease activity. The addition of the purified YgjD to the culture medium of V. harveyi strain SF-1 can effectively promote the bacteria growth. These results indicated that the protease activities may be involved in the survival of bacteria. creator: Yayuan Zhang creator: Jixiang Chen creator: Yonggang Wang creator: Yanlin Li creator: Wenhong Rui creator: Jiyi Zhang creator: Dan Luo uri: https://doi.org/10.7717/peerj.9061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: The influence of surrounding land cover on wetland habitat conditions: a case study of inland wetlands in South Korea link: https://peerj.com/articles/9101 last-modified: 2020-05-18 description: Wetland ecosystems have been globally degraded and lost due to rapid urbanization and climate change. An assessment of national scale inventory, including wetland types and conditions, is urgently required to understand the big picture of endangered wetlands, such as where they are and how they look like. We analyzed the spatial patterns of each inland wetland type (brackish wetland was included) in South Korea and the relative importance of land cover categories on wetland conditions. The wetlands were grouped into four dominant types (riverine, lake, mountain, and human-made) according to their topography. Riverine wetlands constituted the largest area (71.3%). The relative ratio of wetlands in a well-conserved condition (i.e., “A” rank) was highest in riverine wetlands (23.8%), followed by mountain wetlands (22.1%). The higher proportion of grasslands was related to a better condition ranking, but the increasing bareland area had a negative impact on wetland conditions. We also found that wetlands located near wetland protected areas tend to be in a better condition compared to remote sites. Our results further support the importance of the condition of surrounding areas for wetland conservation. creator: Ran-Young Im creator: Taekyu Kim creator: Chung-Yeol Baek creator: Chang-Su Lee creator: Song-Hyun Kim creator: Jung-Hwan Lee creator: Ji Yoon Kim creator: Gea-Jae Joo uri: https://doi.org/10.7717/peerj.9101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Im et al. title: Mitochondrial DNA variation in the Italian Heavy Draught Horse link: https://peerj.com/articles/8996 last-modified: 2020-05-15 description: BackgroundIn the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook.MethodologyTo provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds.ResultsAmong the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices. creator: Hovirag Lancioni creator: Irene Cardinali creator: Andrea Giontella creator: Maria Teresa Antognoni creator: Arianna Miglio uri: https://doi.org/10.7717/peerj.8996 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lancioni et al. title: A new genus of sinogaleaspids (Galeaspida, stem-Gnathostomata) from the Silurian Period in Jiangxi, China link: https://peerj.com/articles/9008 last-modified: 2020-05-15 description: Galeaspids are an endemic clade of jawless stem-gnathostomes known as ostracoderms. Their existence illuminates how specific characteristics developed in jawed vertebrates. Sinogaleaspids are of particular interest among the galeaspids but their monophyly is controversial because little is known about Sinogaleaspis xikengensis. Newly discovered sinogaleaspids from the Lower Silurian of Jiangxi, China provide a wealth of data and diagnostic features used to establish the new genus, Rumporostralis gen. nov., for Sinogaleaspis xikengensis. A morphological study showed that the sensory canal system of sinogaleaspids had mosaic features similar to those of three known galeaspids. There are 3–8 pairs of transverse canals in the Sinogaleaspidae, which suggests that the sensory canal system of galeaspid probably had a grid distribution with transverse canals arranged throughout the cephalic division. Phylogenetic analysis of Galeaspida supports the monophyly of the Sinogaleaspidae, consisting of Sinogaleaspis, Rumporostralis, and Anjiaspis. However, Shuyu and Meishanaspis form another monophyletic group, Shuyuidae fam. nov., which is outside all other eugaleaspidiforms. We propose a cladistically-based classification of Galeaspida based on our analysis. creator: Xianren Shan creator: Min Zhu creator: Wenjin Zhao creator: Zhaohui Pan creator: Pingli Wang creator: Zhikun Gai uri: https://doi.org/10.7717/peerj.9008 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shan et al. title: The chemistry and histology of sexually dimorphic mental glands in the freshwater turtle, Mauremys leprosa link: https://peerj.com/articles/9047 last-modified: 2020-05-15 description: Despite evidence from anatomy, behavior and genomics indicating that the sense of smell in turtles is important, our understanding of chemical communication in this group is still rudimentary. Our aim was to describe the microanatomy of mental glands (MGs) in a freshwater turtle, Mauremys leprosa (Geoemydidae), and to assess the chemical composition of their secretions with respect to variation among individuals and between sexes. MGs are paired sac-like organs on the gular region of the neck and are dimorphic in this species with males having fully functional holocrine glands while those of females appear non-secretory and vestigial. In adult males, the glandular epithelium of the inner portion of the gland provides exocytotic products as well as cellular debris into the lumen of the gland. The contents of the lumen can be secreted through the narrow duct portion of the gland ending in an orifice on the surface of the skin. Females have invaginated structures similar in general outline to male glands, but lack a glandular epithelium. Using gas chromatography coupled to mass spectrometry, we identified a total of 61 compounds in mental gland secretions, the most numerous being carboxylic acids, carbohydrates, alkanes, steroids and alcohols. The number of compounds per individual varied widely (mean (median) ± SD = 14.54 (13) ± 8.44; min = 3; max = 40), but only cholesterol was found in all samples. We found that the relative abundances of only six chemicals were different between the sexes, although males tended to have larger amounts of particular compounds. Although the lipid fraction of mental gland secretions is rich in chemical compounds, most occur in both sexes suggesting that they are metabolic byproducts with no role in chemical signaling. However, the relative amounts of some compounds tended to be higher in males, with significantly larger amounts of two carboxylic acids and one steroid, suggesting their putative involvement in chemical communication. creator: Alejandro Ibáñez creator: Albert Martínez-Silvestre creator: Dagmara Podkowa creator: Aneta Woźniakiewicz creator: Michał Woźniakiewicz creator: Maciej Pabijan uri: https://doi.org/10.7717/peerj.9047 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ibáñez et al. title: Spirometric traits show quantile-dependent heritability, which may contribute to their gene-environment interactions with smoking and pollution link: https://peerj.com/articles/9145 last-modified: 2020-05-15 description: Background“Quantile-dependent expressivity” refers to a genetic effect that is dependent upon whether the phenotype (e.g., spirometric data) is high or low relative to its population distribution. Forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and the FEV1/FVC ratio are moderately heritable spirometric traits. The aim of the analyses is to test whether their heritability (h2) is constant over all quantiles of their distribution.MethodsQuantile regression was applied to the mean age, sex, height and smoking-adjusted spirometric data over multiple visits in 9,993 offspring-parent pairs and 1,930 sibships from the Framingham Heart Study to obtain robust estimates of offspring-parent (βOP), offspring-midparent (βOM), and full-sib regression slopes (βFS). Nonparametric significance levels were obtained from 1,000 bootstrap samples. βOPs were used as simple indicators of quantile-specific heritability (i.e., h2 = 2βOP/(1+rspouse), where rspouse was the correlation between spouses).ResultsβOP ± standard error (SE) decreased by 0.0009 ± 0.0003 (P = 0.003) with every one-percent increment in the population distribution of FEV1/FVC, i.e., βOP ± SE were: 0.182 ± 0.031, 0.152 ± 0.015; 0.136 ± 0.011; 0.121 ± 0.013; and 0.099 ± 0.013 at the 10th, 25th, 50th, 75th, and 90th percentiles of the FEV1/FVC distribution, respectively. These correspond to h2 ± SEs of 0.350 ± 0.060 at the 10th, 0.292 ± 0.029 at the 25th, 0.262 ± 0.020 at the 50th, 0.234 ± 0.025 at the 75th, and 0.191 ± 0.025 at the 90th percentiles of the FEV1/FVC ratio. Maximum mid-expiratory flow (MMEF) h2 ± SEs increased 0.0025 ± 0.0007 (P = 0.0004) with every one-percent increment in its distribution, i.e.: 0.467 ± 0.046, 0.467 ± 0.033, 0.554 ± 0.038, 0.615 ± 0.042, and 0.675 ± 0.060 at the 10th, 25th, 50th, 75th, and 90th percentiles of its distribution. This was due to forced expiratory flow at 75% of FVC (FEF75%), whose quantile-specific h2 increased an average of 0.0042 ± 0.0008 for every one-percent increment in its distribution. It is speculated that previously reported gene-environment interactions may be partially attributable to quantile-specific h2, i.e., greater heritability in individuals with lower FEV1/FVC due to smoking or airborne particles exposure vs. nonsmoking, unexposed individuals.ConclusionHeritabilities of FEV1/FVC, MMEF, and FEF75% from quantile-regression of offspring-parent and sibling spirometric data suggest their quantile-dependent expressivity. creator: Paul T. Williams uri: https://doi.org/10.7717/peerj.9145 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Depigmenting potential of lichen extracts evaluated by in vitro and in vivo tests link: https://peerj.com/articles/9150 last-modified: 2020-05-15 description: Melanin is the main pigment of human skin, playing the primary role of protection from ultraviolet radiation. Alteration of the melanin production may lead to hyperpigmentation diseases, with both aesthetic and health consequences. Thus, suppressors of melanogenesis are considered useful tools for medical and cosmetic treatments. A great interest is focused on natural sources, aimed at finding safe and quantitatively available depigmenting substances. Lichens are thought to be possible sources of this kind of compounds, as the occurrence of many phenolic molecules suggests possible effects on phenolase enzymes involved in melanin synthesis, like tyrosinase. In this work, we used four lichen species, Cetraria islandica Ach., Flavoparmelia caperata Hale, Letharia vulpina (L.) Hue, and Parmotrema perlatum (Hudson) M. Choisy, to obtain extracts in solvents of increasing polarity, viz. chloroform, chloroform-methanol, methanol, and water. Cell-free, tyrosinase inhibition experiments showed highest inhibition for L. vulpina methanol extract, followed by C. islandica chloroform-methanol one. Comparable results for depigmenting activities were observed by means of in vitro and in vivo systems, such as MeWo melanoma cells and zebrafish larvae. Our study provides first evidence of depigmenting effects of lichen extracts, from tyrosinase inhibition to cell and in vivo models, suggesting that L. vulpina and C. islandica extracts deserve to be further studied for developing skin-whitening products. creator: Paola Malaspina creator: Erica Catellani creator: Bruno Burlando creator: Daniele Brignole creator: Laura Cornara creator: Miriam Bazzicalupo creator: Simona Candiani creator: Valentina Obino creator: Vincenzo De Feo creator: Lucia Caputo creator: Paolo Giordani uri: https://doi.org/10.7717/peerj.9150 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Malaspina et al.