Diatoms as indicators of the effects of river impoundment at multiple spatial scales
River impoundment constitutes one of the most important anthropogenic impacts on the World’s rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n = 77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow targets.
Krajenbrink et al. (2019) Diatoms as indicators of the effects of river impoundment at multiple spatial scales. PeerJ 7:e8092 https://doi.org/10.7717/peerj.8092
Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants
Background Genomics diagnostic tests are done for a wide spectrum of complex genetics conditions such as autism and cancer. The growth of technology has not only aided in successfully decoding the genetic variants that causes or trigger these disorders. However, interpretation of these variants is not a trivial task even at a level of distinguish pathogenic vs benign variants. Methods We used the clinically significant variants from ClinVar database to evaluate the performance of 14 most popular in-silico predictors using supervised learning methods. We implemented a feature selection and random forest classification algorithm to identify the best combination of predictors to evaluate the pathogenicity of a variant. Finally, we have also utilized this combination of predictors to reclassify the variants of unknown significance in MeCP2 gene that are associated with the Rett syndrome. Results The results from analysis shows an optimized selection of prediction algorithm and developed a combinatory predictor method. Our combinatory approach of using both best performing independent and ensemble predictors reduces any algorithm biases in variant characterization. The reclassification of variants (such as VUS) in MECP2 gene associated with RETT syndrome suggest that the combinatory in-silico predictor approach had a higher success rate in categorizing their pathogenicity.
Ganakammal et al. (2019) Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants. PeerJ 7:e8106 https://doi.org/10.7717/peerj.8106
Arboreal twig-nesting ants form dominance hierarchies over nesting resources
Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a linear dominance hierarchy. We described the dominance relationships among 10 species of ants and measured the uncertainty and steepness of the inferred dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the randomized Elo-rating method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. Our results show that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked species winning contests against lower ranked species was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities organize into dominance hierarchies.
Yitbarek et al. (2019) Arboreal twig-nesting ants form dominance hierarchies over nesting resources. PeerJ 7:e8124 https://doi.org/10.7717/peerj.8124
Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship
Background This 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. Methods This 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. Results Significant 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. Discussion The 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. Conclusions Results 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.
Keogh et al. (2019) Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship. PeerJ 7:e8140 https://doi.org/10.7717/peerj.8140
Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue
Background Foam 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. Methods A 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. Results FR 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. Conclusions Both FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability.
de Benito et al. (2019) Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue. PeerJ 7:e8000 https://doi.org/10.7717/peerj.8000
A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean
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.
Alvarez-Filip et al. (2019) A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 7:e8069 https://doi.org/10.7717/peerj.8069
Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae
Background Coelidiinae, 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. Methods Specimens 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. Results The 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.
Wang et al. (2019) Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae. PeerJ 7:e8072 https://doi.org/10.7717/peerj.8072
Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology
Background There 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. Methods Indigenous 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. Results We 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.
Ma et al. (2019) Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology. PeerJ 7:e8079 https://doi.org/10.7717/peerj.8079
Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
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.
Zhang et al. (2019) Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma. PeerJ 7:e8096 https://doi.org/10.7717/peerj.8096
Oxidative stress and antioxidants in the trabecular meshwork
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.
Wang et al. (2019) Oxidative stress and antioxidants in the trabecular meshwork. PeerJ 7:e8121 https://doi.org/10.7717/peerj.8121