title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1243 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship link: https://peerj.com/articles/8140 last-modified: 2019-11-27 description: BackgroundThis study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia.MethodsThis manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively.ResultsSignificant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r =  − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r =  − 0.30 to 0.33; p < 0.001 and relative risk ratio = 0.40–2.24; p < 0.05, respectively). MCA analysis of the change score data indicated that the first two dimensions explained 32.2% of the cumulative variance, with these dimensions representing whether a change occurred and the direction of change, respectively.DiscussionThe results advance our comprehension of the psychometric properties on the SARC-F, particularly its potential use in assessing changes in muscle function. Older adults’ perception of their baseline and training-related changes in their function, as self-reported by the SARC-F, closely matched objectively measured muscle function tests. This is important as there may be a lack of concordance between self-reported and clinician-measured assessments of older adults’ muscle function. However, the SARC-F has a relative lack of sensitivity to detecting training-related changes, even over a period of 24 weeks.ConclusionsResults of this study may provide clinicians and researchers a greater understanding of how they may use the SARC-F and its potential limitations. Future studies may wish to further examine the SARC-F’s sensitivity of change, perhaps by adding a few additional items or an additional category of performance to each item. creator: Justin W.L. Keogh creator: Tim Henwood creator: Paul A. Gardiner creator: Anthony G. Tuckett creator: Sharon Hetherington creator: Kevin Rouse creator: Paul Swinton uri: https://doi.org/10.7717/peerj.8140 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Keogh et al. title: Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue link: https://peerj.com/articles/8000 last-modified: 2019-11-26 description: BackgroundFoam roller and vibration techniques are currently used to assist in recovery after fatigue. The main purpose of this study was to determine the effects of the use of a foam roller with and without vibration on dynamic balance, ankle dorsiflexion, hamstring and lumbar spine flexibility and perceived knee and ankle stability after an induced fatigue protocol.MethodsA total of 24 healthy recreationally active participants (17 males and seven females) were recruited to a randomized cross over trial consisting of; no treatment (NT), foam roller treatment (FR) and vibration foam roller treatment (VFR). The assessments included; the Sit & Reach test, Y balance test and post-treatment perceived knee and ankle stability. Measurements were taken after a standardized warm up (baseline) and repeated following an exercise-induced muscle fatigue protocol consisting of repeated lunges until volitional fatigue. The three treatment conditions were assessed on three separate days in a randomized order. A 3 × 3 repeated measures ANOVA was used to investigate differences between the three treatments over the three time points and a one factor repeated measures ANOVA was used to determine any differences between treatments using the Global Rate of Change scale when considering perceived stability.ResultsFR and VFR conditions both showed a greater ankle dorsiflexion range of motion (ROM) (p < 0.001), greater posteromedial and posterolateral reach distances (p < 0.001) and a better knee and ankle perceived stability (p < 0.001) when compared to the NT condition. A trend toward significance was observed in the hamstring and lumbar spine flexibility (p = 0.074) in both treatment conditions when compared to the NT condition. However, no differences were seen between the FR and VFR conditions.ConclusionsBoth FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability. creator: Ana María de Benito creator: Raúl Valldecabres creator: Diego Ceca creator: Jim Richards creator: Joaquín Barrachina Igual creator: Ana Pablos uri: https://doi.org/10.7717/peerj.8000 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 de Benito et al. title: A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean link: https://peerj.com/articles/8069 last-modified: 2019-11-26 description: Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future. creator: Lorenzo Alvarez-Filip creator: Nuria Estrada-Saldívar creator: Esmeralda Pérez-Cervantes creator: Ana Molina-Hernández creator: Francisco J. González-Barrios uri: https://doi.org/10.7717/peerj.8069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Alvarez-Filip et al. title: Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae link: https://peerj.com/articles/8072 last-modified: 2019-11-26 description: BackgroundCoelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana.MethodsSpecimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.ResultsThe mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is consistent with the current morphological classification. creator: Xian-Yi Wang creator: Jia-Jia Wang creator: Zhi-Hua Fan creator: Ren-Huai Dai uri: https://doi.org/10.7717/peerj.8072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology link: https://peerj.com/articles/8079 last-modified: 2019-11-26 description: BackgroundThere are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep.MethodsIndigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis.ResultsWe identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (GenBank ID: 443299, g. 75320741G>A site), GUCY1A1 (GenBank ID: 101110000, g. 43266624C>T site), and COIL (GenBank ID: 101123134, g. 7321466C>G site) were found to be significantly or extremely significantly associated with litter size. These three loci are expected to be used as molecular markers to determine differences in litter size in sheep. creator: Haiyu Ma creator: Chao Fang creator: Lingling Liu creator: Qiong Wang creator: Jueken Aniwashi creator: Yiming Sulaiman creator: Kezierkailedi Abudilaheman creator: Wujun Liu uri: https://doi.org/10.7717/peerj.8079 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma link: https://peerj.com/articles/8096 last-modified: 2019-11-26 description: Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us understand the molecular mechanisms underlying the carcinogenesis and progression of ccRCC, and provide potential diagnostic, therapeutic and prognostic biomarkers. creator: Haiping Zhang creator: Jian Zou creator: Ying Yin creator: Bo Zhang creator: Yaling Hu creator: Jingjing Wang creator: Huijun Mu uri: https://doi.org/10.7717/peerj.8096 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Oxidative stress and antioxidants in the trabecular meshwork link: https://peerj.com/articles/8121 last-modified: 2019-11-26 description: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention. creator: Mingxuan Wang creator: Yajuan Zheng uri: https://doi.org/10.7717/peerj.8121 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang and Zheng title: Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia link: https://peerj.com/articles/8144 last-modified: 2019-11-26 description: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress. creator: Kyle K. Biggar creator: Jing Zhang creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.8144 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Biggar et al. title: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) link: https://peerj.com/articles/7929 last-modified: 2019-11-25 description: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species. creator: Xin Hu creator: Lili Zhu creator: Yi Zhang creator: Li Xu creator: Na Li creator: Xingguo Zhang creator: Yu Pan uri: https://doi.org/10.7717/peerj.7929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hu et al. title: Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications link: https://peerj.com/articles/8033 last-modified: 2019-11-25 description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong. creator: Siuli Mitra creator: Vaishnavi Kunteepuram creator: Klaus-Peter Koepfli creator: Neha Mehra creator: Wajeeda Tabasum creator: Ara Sreenivas creator: Ajay Gaur uri: https://doi.org/10.7717/peerj.8033 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mitra et al.