Sargassum blooms in the Caribbean alter the trophic structure of the sea urchin Diadema antillarum
The arrival of large masses of drifting Sargassum since 2011 has caused changes in the natural dynamics of Caribbean coastal ecosystems. In the summer of 2015, unprecedented and massive mats of S. fluitans and S. natans have been observed throughout the Mexican Caribbean including exceptional accumulations ashore. This study uses stable isotopes to assess the impact of Sargassum blooms on the trophic dynamics of the Diadema antillarum sea urchin, a keystone herbivore on many Caribbean reefs. Bayesian models were used to estimate the variations in the relative proportions of carbon and nitrogen of assimilated algal resources. At three lagoon reef sites, the niche breadth of D. antillarum was analysed and compared under massive influx of drifting Sargassum spp. vs. no influx of Sargassum blooms. The effects of the leachates generated by the decomposition of Sargassum led to hypoxic conditions on these reefs and reduced the taxonomic diversity of macroalgal food sources available to D. antillarum. Our trophic data support the hypothesis that processes of assimilation of carbon and nitrogen were modified under Sargassum effect. Isotopic signatures of macroalgae associated with the reef sites exhibited significantly lower values of δ15N altering the natural herbivory of D. antillarum. The Stable Isotopes Analysis in R (SIAR) indicated that, under the influence of Sargassum blooms, certain algal resources (Dictyota, Halimeda and Udotea) were more assimilated due to a reduction in available algal resources. Despite being an abundant available resource, pelagic Sargassum was a negligible contributor to sea urchin diet. The Stable Isotope Bayesian Ellipses in R (SIBER) analysis displayed differences between sites, and suggests a reduction in trophic niche breadth, particularly in a protected reef lagoon. Our findings reveal that Sargassum blooms caused changes in trophic characteristics of D. antillarum with a negative impact by hypoxic conditions. These dynamics, coupled with the increase in organic matter in an oligotrophic system could lead to reduce coral reef ecosystem function.
Cabanillas-Terán et al. (2019) Sargassum blooms in the Caribbean alter the trophic structure of the sea urchin Diadema antillarum. PeerJ 7:e7589 https://doi.org/10.7717/peerj.7589
The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene
Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.
Zhong et al. (2019) The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene. PeerJ 7:e7596 https://doi.org/10.7717/peerj.7596
Two salamander species respond differently to timber harvests in a managed New England forest
Background Managing forests for timber while protecting wildlife habitat is of increasing concern. Amphibians may be particularly sensitive to forest management practices due to their unique biology; however, it is not clear how different species respond to timber harvest practices—particularly over longer time scales. Methods Here we report on the differential responses of two salamander species—the eastern red-backed salamander (Plethodon cinereus Green) and the eastern newt (Notophthalmus viridescens Rafinesque)—to forest harvesting, by examining communities across a 25-year chronosequence of regenerating shelterwood harvests. Results Populations of both species were lowest immediately after harvest, but increased at substantially different rates. Red-backed salamander populations were highest in 20–25 year-old shelterwoods—significantly higher than in mature, unharvested, control (100–120 year old) stands. Eastern newt populations, however, were greatest in unharvested control stands and still had not recovered to population levels found in mature stands in the 25 years since harvest. Red-backed salamander abundances were strongly tied to stand age as well as abundance of decayed coarse woody debris, suggesting that timber harvests influence some wildlife species by affecting a suite of interacting habitat variables that change over time. In contrast, newt abundances were not directly related to stand age but were more related to downed wood and vegetation characteristics. Our results highlight markedly variable responses by two common salamander species to forest harvesting—species with markedly different life histories and reproductive patterns—and that time since harvest may be useful in predicting abundance.
Mossman et al. (2019) Two salamander species respond differently to timber harvests in a managed New England forest. PeerJ 7:e7604 https://doi.org/10.7717/peerj.7604
Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh)
The hedgehog signaling pathway plays a vital role in human and animal patterning and cell proliferation during the developmental process. The hedgehog gene family of vertebrate species includes three genes, Shh, Dhh, and Ihh, which possess different functions and expression patterns. Despite the importance of hedgehog genes, genomic evidence of this gene family in reptiles is lacking. In this study, the available genomes of a number of representative reptile species were explored by utilizing adaptive evolutionary analysis methods to characterize the evolutionary patterns of the hedgehog gene family. Altogether, 33 sonic hedgehog (Shh), 25 desert hedgehog (Dhh), and 20 Indian hedgehog (Ihh) genes were obtained from reptiles, and six avian and five mammalian sequences were added to the analysis. The phylogenetic maximum likelihood (ML) tree of the Shh, Dhh, and Ihh genes revealed a similar topology, which is approximately consistent with the traditional taxonomic group. No shared positive selection site was identified by the PAML site model or the three methods in the Data Monkey Server. Branch model and Clade model C analyses revealed that the Dhh and Ihh genes experienced different evolutionary forces in reptiles and other vertebrates, while the Shh gene was not significantly different in terms of selection pressure. The different evolutionary rates of the Dhh and Ihh genes suggest that these genes may be potential contributors to the discrepant sperm and body development of different clades. The different adaptive evolutionary history of the Shh, Dhh, and Ihh genes among reptiles may be due to their different functions in regulating cellular events of development from the embryonic stages to adulthood. Overall, this study has provided meaningful information regarding the evolution of the hedgehog gene family in reptiles and a theoretical foundation for further analyses on the functional and molecular mechanisms that have shaped the reptilian hedgehog genes.
Xia et al. (2019) Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh). PeerJ 7:e7613 https://doi.org/10.7717/peerj.7613
Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR)
Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.
Environmental Contamination and Remediation
Gómez-Basurto et al. (2019) Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR). PeerJ 7:e7152 https://doi.org/10.7717/peerj.7152
Postural control in girls with adolescent idiopathic scoliosis while wearing a Chêneau brace or performing active self-correction: a pilot study
Background It is known that adolescent idiopathic scoliosis (AIS) is often accompanied by balance deficits. This reciprocal relationship must be taken into account when prescribing new therapeutic modalities because these may differently affect postural control, interacting with therapy and influencing its results. Objective The purpose was to compare postural control in girls with AIS while wearing the Chêneau brace (BRA) or performing active self-correction (ASC) with their postural control in a quiet comfortable stance. Methods Nine subjects were evaluated on a force plate in three series of two 20-s quiet standing trials with eyes open or closed; three blocks were randomly arranged: normal quiet stance (QST), quiet stance with BRA, and quiet stance with ASC. On the basis of centre-of-pressure (COP) recordings, the spatial and temporal COP parameters were computed. Results and Discussion Performing ASC was associated with a significant backward excursion of the COP mean position with eyes open and closed (ES = 0.56 and 0.65, respectively; p < 0.05). This excursion was accompanied by an increase in the COP fractal dimension (ES = 1.05 and 0.98; p < 0.05) and frequency (ES = 0.78; p = 0.10 and ES = 1.14; p < 0.05) in the mediolateral (ML) plane. Finally, both therapeutic modalities decreased COP sample entropy with eyes closed in the anteroposterior (AP) plane. Wearing BRA resulted in ES = 1.45 (p < 0.05) while performing ASC in ES = 0.76 (p = 0.13). Conclusion The observed changes in the fractal dimension (complexity) and frequency caused by ASC account for better adaptability of patients to environmental demands and for their adequate resources of available postural strategies in the ML plane. These changes in sway structure were accompanied by a significant (around 25 mm) backward excursion of the mean COP position. However, this improvement was achieved at the cost of lower automaticity, i.e. higher attentional involvement in postural control in the AP plane. Wearing BRA may have an undesirable effect on some aspects of body balance.
Piątek et al. (2019) Postural control in girls with adolescent idiopathic scoliosis while wearing a Chêneau brace or performing active self-correction: a pilot study. PeerJ 7:e7513 https://doi.org/10.7717/peerj.7513
Effects of shading on the growth and leaf photosynthetic characteristics of three forages in an apple orchard on the Loess Plateau of eastern Gansu, China
Background Inclusion of forage into the orchard is of great help in promoting the use efficiency of resources, while shading from trees restricts forage growth and production in the Loess Plateau of China. This study was aimed to investigate how tree shading affected leaf trait, photosynthetic gas exchange and chlorophyll feature of forages under the tree in the orchard-forage system. Methods The shading treatments were set as partially cutting branches (reduced shading), normal fruit tree shading (normal shading) and normal tree shading plus sun-shading net (enhanced shading) in an apple orchard. Leaf trait, photosynthesis, chlorophyll component and fluorescence related parameters were measured with lucerne (Medicago sativa), white clover (Trifolium repens) and cocksfoot (Dactylis glomerata) which were sown under apple trees. Results Shading imposed significant impacts on the growth and leaf photosynthetic characteristics, while there were differences among species. Enhanced shading decreased leaf thickness, leaf dry matter content (LDMC) and leaf mass per unit area (LMA). Biomass accumulation decreased with enhanced shading in cocksfoot, but did not change in white clover and lucerne which had much lower biomass accumulation than cocksfoot. Enhanced shading reduced net photosynthetic rate (Pn) of white clover and lucerne, but rarely affected cocksfoot, while it decreased instantaneous water use efficiency (WUEi) of cocksfoot but had few effects on the other forages. Enhanced shading reduced leaf dark respiration rate (Rd), light compensation point (LCP) and maximum assimilation rate. The Rd and LCP of cocksfoot were much lower than those of white clover and lucerne. Chlorophyll contents and chlorophyll a/b changed little with shading. Cocksfoot had the highest contents but lowest ratio. Maximum photochemical rate of photosystem II increased and non-photochemical quenching decreased with enhanced shading in cocksfoot, while did not change in the other forages. Discussion Leaf trait, photosynthetic gas exchange and chlorophyll feature were variously affected by species, shading and their interaction. Cocksfoot was more efficient than the other two forages in use of weakened light and more tolerant to tree shading. In the apple orchard, we recommend that reducing the density of apple tree or partially cutting branches together with selecting some shading-tolerant forages, i.e., cocksfoot, would be a practical option for the orchard-forage system in the Loess Plateau of China.
Yang et al. (2019) Effects of shading on the growth and leaf photosynthetic characteristics of three forages in an apple orchard on the Loess Plateau of eastern Gansu, China. PeerJ 7:e7594 https://doi.org/10.7717/peerj.7594
Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance
Heat stress inhibits rice panicle development and reduces the spikelet number per panicle. This study investigated the mechanism involved in heat-induced damage to panicle development and spikelet formation in rice cultivars that differ in heat tolerance. Transcriptome data from developing panicles grown at 40 °C or 32 °C were compared for two rice cultivars: heat-tolerant Huanghuazhan and heat-susceptible IR36. Of the differentially expressed genes (DEGs), 4,070 heat stress-responsive genes were identified, including 1,688 heat-resistant-cultivar-related genes (RHR), 707 heat-susceptible-cultivar-related genes (SHR), and 1,675 common heat stress-responsive genes (CHR). A Gene Ontology (GO) analysis showed that the DEGs in the RHR category were significantly enriched in 54 gene ontology terms, some of which improved heat tolerance, including those in the WRKY, HD-ZIP, ERF, and MADS transcription factor families. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs in the RHR and SHR categories were enriched in 15 and 11 significant metabolic pathways, respectively. Improved signal transduction capabilities of endogenous hormones under high temperature seemed to promote heat tolerance, while impaired starch and sucrose metabolism under high temperature might have inhibited young panicle development. Our transcriptome analysis provides insights into the different molecular mechanisms of heat stress tolerance in developing rice.
Wang et al. (2019) Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance. PeerJ 7:e7595 https://doi.org/10.7717/peerj.7595
Mapping research trends of retinal vein occlusion from 2009 to 2018: a bibliometric analysis
Objectives To map publication trends and explore research hotspots of retinal vein occlusion (RVO) study. Methods Based on Web of Science Core Collection (WoSCC), a bibliometric analysis was carried out. The knowledge map was constructed by VOSviewer v.1.6.10 to visualize the annual publication number, the distribution of countries, international collaborations, author productivity, source journals, cited reference and keywords in this field. Results A total of 2,135 peer-reviewed papers were retrieved on RVO from 2009 to 2018. The United States ranks highest among countries with the most publications and the most active institution was Kyoto University. Noma H contributed the most publications in this field. Retina—The Journal of Retinal and Vitreous Disease was the most prolific journal in RVO research. The top cited references mainly presented anti-VEGF medications on the management of RVO. The keywords formed six clusters: (1) Risk factors and pathogenesis of RVO; (2) Metabolismof RVO; (3) Therapeutic use of corticosteroids on RVO; (4) Diagnostic methodsof RVO; (5) Management of macular edema secondary to RVO (6) Anti-VEGFtreatment of RVO. Conclusions The six major research hotspots could provide an insight into RVO research and valuable information for researchers to identify potential collaborators and partner institutions.
Zhao et al. (2019) Mapping research trends of retinal vein occlusion from 2009 to 2018: a bibliometric analysis. PeerJ 7:e7603 https://doi.org/10.7717/peerj.7603
Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza
Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.
Li et al. (2019) Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza. PeerJ 7:e7605 https://doi.org/10.7717/peerj.7605