title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1788 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparative functional characterization of novel non-syndromic GJB2 gene variant p.Gly45Arg and lethal syndromic variant p.Gly45Glu link: https://peerj.com/articles/2494 last-modified: 2016-10-11 description: We characterized a novel GJB2 missense variant, c.133G>A, p.Gly45Arg, and compared it with the only other variant at the same amino acid position of the connexin 26 protein (Cx26) reported to date: c.134G>A, p.Gly45Glu. Whereas both variants are associated with hearing loss and are dominantly inherited, p.Gly45Glu has been implicated in the rare fatal keratitis-ichthyosis-deafness (KID) syndrome, which results in cutaneous infections and septicemia with premature demise in the first year of life. In contrast, p.Gly45Arg appears to be non-syndromic. Subcellular localization experiments in transiently co-transfected HeLa cells demonstrated that Cx26-WT (wild-type) and p.Gly45Arg form gap junctions, whereas Cx26-WT with p.Gly45Glu protein does not. The substitution of a nonpolar amino acid glycine in wildtype Cx26 at position 45 with a negatively charged glutamic acid (acidic) has previously been shown to interfere with Ca2+ regulation of hemichannel gating and to inhibit the formation of gap junctions, resulting in cell death. The novel variant p.Gly45Arg, however, changes this glycine to a positively charged arginine (basic), resulting in the formation of dysfunctional gap junctions that selectively affect the permeation of negatively charged inositol 1,4,5-trisphosphate (IP3) and contribute to hearing loss. Cx26 p.Gly45Arg transfected cells, unlike cells transfected with p.Gly45Glu, thrived at physiologic Ca2+ concentrations, suggesting that Ca2+ regulation of hemichannel gating is unaffected in Cx26 p.Gly45Arg transfected cells. Thus, the two oppositely charged amino acids that replace the highly conserved uncharged glycine in p.Gly45Glu and p.Gly45Arg, respectively, produce strikingly different effects on the structure and function of the Cx26 protein. creator: Juan Rodriguez-Paris creator: Jörg Waldhaus creator: Jeenal A. Gordhandas creator: Lynn Pique creator: Iris Schrijver uri: https://doi.org/10.7717/peerj.2494 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rodriguez-Paris et al. title: Phylogenetic relationships and evolutionary history of the greater horseshoe bat, Rhinolophus ferrumequinum, in Northeast Asia link: https://peerj.com/articles/2472 last-modified: 2016-10-11 description: The greater horseshoe bat, Rhinolophus ferrumequinum, is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process. Our results indicate a highly supported monophyletic group of Northeast Asian greater horseshoe bats, in which Japanese populations formed a single clade and clustered into the mixed branches of Northeast Chinese and South Korean populations. We infer that R. ferrumequinum in Northeast Asia originated in Northeast China and South Korea during a cold glacial period, while some ancestors likely arrived in Japan by flying or land bridge and subsequently adapted to the local environment. Consequently, during the warm Eemian interglaciation, the Korea Strait, between Japan and South Korea, became a geographical barrier to Japanese and inland populations, while the Changbai Mountains, between China and North Korea, did not play a significant role as a barrier between Northeast China and South Korea populations. creator: Tong Liu creator: Keping Sun creator: Yung Chul Park creator: Jiang Feng uri: https://doi.org/10.7717/peerj.2472 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liu et al. title: Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses link: https://peerj.com/articles/2463 last-modified: 2016-10-11 description: Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians. creator: Mei Fang Lin creator: Wen Hwa Chou creator: Marcelo V. Kitahara creator: Chao Lun Allen Chen creator: David John Miller creator: Sylvain Forêt uri: https://doi.org/10.7717/peerj.2463 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lin et al. title: Ecomorphological analysis of the astragalo-calcaneal complex in rodents and inferences of locomotor behaviours in extinct rodent species link: https://peerj.com/articles/2393 last-modified: 2016-10-11 description: Studies linking postcranial morphology with locomotion in mammals are common. However, such studies are mostly restricted to caviomorphs in rodents. We present here data from various families, belonging to the three main groups of rodents (Sciuroidea, Myodonta, and Ctenohystrica). The aim of this study is to define morphological indicators for the astragalus and calcaneus, which allow for inferences to be made about the locomotor behaviours in rodents. Several specimens were dissected and described to bridge the myology of the leg with the morphology of the bones of interest. Osteological characters were described, compared, mechanically interpreted, and correlated with a “functional sequence” comprising six categories linked to the lifestyle and locomotion (jumping, cursorial, generalist, fossorial, climber and semi-aquatic). Some character states are typical of some of these categories, especially arboreal climbers, fossorial and “cursorial-jumping” taxa. Such reliable characters might be used to infer locomotor behaviours in extinct species. Linear discriminant analyses (LDAs) were used on a wider sample of species and show that astragalar and calcaneal characters can be used to discriminate the categories among extant species whereas a posteriori inferences on extinct species should be examined with caution. creator: Samuel Ginot creator: Lionel Hautier creator: Laurent Marivaux creator: Monique Vianey-Liaud uri: https://doi.org/10.7717/peerj.2393 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ginot et al. title: Associations between different components of fitness and fatness with academic performance in Chilean youths link: https://peerj.com/articles/2560 last-modified: 2016-10-06 description: ObjectivesTo analyze the associations between different components of fitness and fatness with academic performance, adjusting the analysis by sex, age, socio-economic status, region and school type in a Chilean sample.MethodsData of fitness, fatness and academic performance was obtained from the Chilean System for the Assessment of Educational Quality test for eighth grade in 2011 and includes a sample of 18,746 subjects (49% females). Partial correlations adjusted by confounders were done to explore association between fitness and fatness components, and between the academic scores. Three unadjusted and adjusted linear regression models were done in order to analyze the associations of variables.ResultsFatness has a negative association with academic performance when Body Mass Index (BMI) and Waist to Height Ratio (WHR) are assessed independently. When BMI and WHR are assessed jointly and adjusted by cofounders, WHR is more associated with academic performance than BMI, and only the association of WHR is positive. For fitness components, strength was the variable most associated with the academic performance. Cardiorespiratory capacity was not associated with academic performance if fatness and other fitness components are included in the model.ConclusionsFitness and fatness are associated with academic performance. WHR and strength are more related with academic performance than BMI and cardiorespiratory capacity. creator: Pedro R. Olivares creator: Javier García-Rubio uri: https://doi.org/10.7717/peerj.2560 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Olivares and García-Rubio title: Histology and gametogenesis in Heleobia piscium (Cochliopidae) from the Multiple Use Reserve “Isla Martín García,” Buenos Aires, Argentina link: https://peerj.com/articles/2548 last-modified: 2016-10-06 description: Heleobia piscium (d’Orbigny, 1835), a member of the Cochliopidae family found only in South America, is distributed from Entre Ríos, Delta del Paraná, and the littoral of the Río de la Plata down as far as to Punta Indio (Buenos Aires), the southernmost limit of the snail’s geographical distribution. To date, little information is available regarding the reproductive cycle of species within this family either in Argentina or throughout South America. The present work analyzed the histology of the reproductive system of the gonochoric species H. piscium and determined the stages oogenesis and spermatogenesis under natural conditions. Specimens of H. piscium were collected in the Multiple-Use Natural Reserve Isla Martín García, located in the Upper Río de la Plata estuary to the south of the mouth of the Uruguay River. The gametogenic cycle in both sexes was found to consist of the following stages: early maturation, maturation, and evacuation. The maturation period was found to extend from January to October and evacuation of the gametes to start in November and end in February (summer in the Southern Hemisphere). The results indicated the H. piscium exhibit a reproductive cycle without a resting period. creator: Stella Maris Martin creator: Ana C. Díaz uri: https://doi.org/10.7717/peerj.2548 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Martin and Díaz title: Higher central fat and poor self-body image in short-stature overweight/obese women living in Brazilian shantytowns link: https://peerj.com/articles/2547 last-modified: 2016-10-06 description: BackgroundShort stature in adult life, a possible consequence of poor perinatal conditions, is associated with higher risk of mortality and social disabilities. We aimed to determine whether low-income, overweight/obese, short-stature (SS) women show alterations in body composition, self-body-image perception, and biochemical profile compared to their non-short (NS) counterparts.MethodsA cross-sectional study was conducted with women living in shantytowns and mother or relatives to undernourished children treated in a center for recuperation and nutritional education. Inclusion criteria were: (1) age, 19–45 years; (2) stature < 152.3 cm or > 158.7 cm; and (3) body mass index > 25 kg/m2. Socioeconomic, anthropometric, biochemical, and body image data were collected. We analyzed 56 SS and 57 NS women.ResultsThe SS group showed a higher waist-to-height ratio (WHtR) (mean: 0.63; standard deviation: 0.06 for SS and mean: 0.60; standard deviation: 0.07 for the NS group; p = 0.02), and, in the adjusted analysis, showed lower fat-free mass (Estimated Marginal Mean for the SS group: 45.7 kg 95% confidence intervals (CI) (45.2–46.2) and for the NS group: 46.9 kg 95% CI (46.4–47.4); p < 0.01) and higher fat mass (Estimated Marginal Mean for the SS group: 32.5 95% CI (31.9–33.0) and for the NS group: 31.4 kg 95% CI (30.9–31.9); p < 0.01). Body mass index was a better predictor of current self-body-image perception for NS women. The SS coefficient values were β = 0.141, SE = 0.059, and R2-Nagelkerke = 0.107, and the NS coefficients values were β = 0.307, SE = 0.058, and R2-Nagelkerke = 0.491 (Z = 2.006; p < 0.05). Considering the obese subgroup, six out of 32 (18.8%) SS women and 14 out of 33 (42.4%) NS women perceived themselves as obese (χ2 = 4.27; p = 0.03). This difference remained significant even after adjustment by age, schooling, and number of children (p = 0.04). Only the total thyroxin showed significant differences between groups, lower in SS women (p = 0.04).DiscussionOverweight/obese, low-income SS women have more central adiposity and impaired self-body image perception, and the body mass index is a weaker predictor of it, compared to NS women. Misperception about body size may be linked with an overestimation of health and underestimation of risk, which may lead to a lower utilization of the health care system and inadequate physician counseling. These features may account, at least partially, for the higher mortality risk seen in SS adults. creator: Nassib Bezerra Bueno creator: Telma Toledo Florêncio creator: Fabiana Albuquerque Cavalcante creator: Isabela Lopes Lins creator: Ana Grotti Clemente creator: Ana Lydia Sawaya uri: https://doi.org/10.7717/peerj.2547 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bueno et al. title: Occurrence of Blastocystis sp. in water catchments at Malay villages and Aboriginal settlement during wet and dry seasons in Peninsular Malaysia link: https://peerj.com/articles/2541 last-modified: 2016-10-06 description: In the tropics, there are too few studies on isolation of Blastocystis sp. subtypes from water sources; in addition, there is also an absence of reported studies on the occurrence of Blastocystis sp. subtypes in water during different seasons. Therefore, this study was aimed to determine the occurrence of Blastocystis sp. subtypes in river water and other water sources that drained aboriginal vicinity of highly endemic intestinal parasitic infections during wet and dry seasons. Water samples were collected from six sampling points of Sungai Krau (K1–K6) and a point at Sungai Lompat (K7) and other water sources around the aboriginal villages. The water samples were collected during both seasons, wet and dry seasons. Filtration of the water samples were carried out using a flatbed membrane filtration system. The extracted DNA from concentrated water sediment was subjected to single round polymerase chain reaction and positive PCR products were subjected to sequencing. All samples were also subjected to filtration and cultured on membrane lactose glucuronide agar for the detection of faecal coliforms. During wet season, Blastocystis sp. ST1, ST2 and ST3 were detected in river water samples. Blastocystis sp. ST3 occurrence was sustained in the river water samples during dry season. However Blastocystis sp. ST1 and ST2 were absent during dry season. Water samples collected from various water sources showed contaminations of Blastocystis sp. ST1, ST2, ST3 and ST4, during wet season and Blastocystis sp. ST1, ST3, ST8 and ST10 during dry season. Water collected from all river sampling points during both seasons showed growth of Escherichia coli and Enterobacter aerogenes, indicating faecal contamination. In this study, Blastocystis sp. ST3 is suggested as the most robust and resistant subtype able to survive in any adverse environmental condition. Restriction and control of human and animal faecal contaminations to the river and other water sources shall prevent the transmission of Blastocystis sp. to humans and animals in this aboriginal community. creator: Samseh Abdullah Noradilah creator: Ii Li Lee creator: Tengku Shahrul Anuar creator: Fatmah Md Salleh creator: Siti Nor Azreen Abdul Manap creator: Noor Shazleen Husnie Mohd Mohtar creator: Syed Muhamad Azrul creator: Wan Omar Abdullah creator: Norhayati Moktar uri: https://doi.org/10.7717/peerj.2541 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Noradilah et al. title: Expediting evidence synthesis for healthcare decision-making: exploring attitudes and perceptions towards rapid reviews using Q methodology link: https://peerj.com/articles/2522 last-modified: 2016-10-06 description: BackgroundRapid reviews expedite the knowledge synthesis process with the goal of providing timely information to healthcare decision-makers who want to use evidence-informed policy and practice approaches. A range of opinions and viewpoints on rapid reviews is thought to exist; however, no research to date has formally captured these views. This paper aims to explore evidence producer and knowledge user attitudes and perceptions towards rapid reviews.MethodsA Q methodology study was conducted to identify central viewpoints about rapid reviews based on a broad topic discourse. Participants rank-ordered 50 text statements and explained their Q-sort in free-text comments. Individual Q-sorts were analysed using Q-Assessor (statistical method: factor analysis with varimax rotation). Factors, or salient viewpoints on rapid reviews, were identified, interpreted and described.ResultsAnalysis of the 11 individual Q sorts identified three prominent viewpoints: Factor A cautions against the use of study design labels to make judgements. Factor B maintains that rapid reviews should be the exception and not the rule. Factor C focuses on the practical needs of the end-user over the review process.ConclusionResults show that there are opposing viewpoints on rapid reviews, yet some unity exists. The three factors described offer insight into how and why various stakeholders act as they do and what issues may need to be resolved before increase uptake of the evidence from rapid reviews can be realized in healthcare decision-making environments. creator: Shannon E. Kelly creator: David Moher creator: Tammy J. Clifford uri: https://doi.org/10.7717/peerj.2522 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kelly et al. title: Positive effect of dietary lutein and cholesterol on the undirected song activity of an opportunistic breeder link: https://peerj.com/articles/2512 last-modified: 2016-10-06 description: Song is a sexually selected trait that is thought to be an honest signal of the health condition of an individual in many bird species. For species that breed opportunistically, the quantity of food may be a determinant of singing activity. However, it is not yet known whether the quality of food plays an important role in this respect. The aim of the present study was to experimentally investigate the role of two calorie-free nutrients (lutein and cholesterol) in determining the expression of a sexually selected behavior (song rate) and other behaviors (locomotor activity, self-maintenance activity, eating and resting) in male zebra finches (Taeniopygia guttata). We predicted that males supplemented with lutein and cholesterol would sing at higher rates than controls because both lutein and cholesterol have important health-related physiological functions in birds and birdsong mirrors individual condition. To control for testosterone secretion that may upregulate birdsong, birds were exposed to a decreasing photoperiod. Our results showed that control males down-regulated testosterone in response to a decreasing photoperiod, while birds treated with lutein or cholesterol maintained a constant singing activity. Both lutein- and cholesterol-supplemented groups sang more than control groups by the end of the experiment, indicating that the quality of food can affect undirected song irrespective of circulating testosterone concentrations. None of the other measured behaviors were affected by the treatment, suggesting that, when individuals have full availability of food, sexually selected song traits are more sensitive to the effect of food quality than other behavioral traits. Overall the results support our prediction that undirected song produced by male zebra finches signals access to high-quality food. creator: Stefania Casagrande creator: Rianne Pinxten creator: Erika Zaid creator: Marcel Eens uri: https://doi.org/10.7717/peerj.2512 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Casagrande et al.