title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=572 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Dictyota defense: Developing effective chemical protection against intense fish predation for outplanted massive corals link: https://peerj.com/articles/14995 last-modified: 2023-03-08 description: The incorporation of coral species with massive (e.g., boulder, brain) morphologies into reef restoration is critical to sustain biodiversity and increase coral cover on degraded reef ecosystems. However, fragments and colonies of massive corals outplanted in Miami-Dade County, Florida, US, can experience intense predation by fish within the first week of outplanting, resulting in >70% mortality. Here, we tested for the first time the potential benefit of feeding corals powdered Dictyota, a brown reef alga that is chemically defended against grazing, to determine if exposure to Dictyota can confer chemical protection to coral fragments and reduce the impacts of fish predation after outplanting. We found that feeding corals every 2 to 3 days for 2 months with dried and powdered Dictyota prior to outplanting significantly reduced predation levels on Orbicella faveolata and Montastraea cavernosa fragments (with less than 20% of the fragments experiencing predation up to 1-month post-outplanting). We also found that a single exposure to Dictyota at a high concentration 1 to 2 days prior to outplanting significantly reduced predation for six coral species within the first 24 h following outplanting. Thus, feeding corals dry Dictyota ex situ prior to outplanting appears to confer protection from fish predation during the critical first days to weeks after outplanting when predation impacts are commonly high. This simple and cheap method can be easily scaled up for corals kept ex situ prior to outplanting, resulting in an increase in restoration efficiency for massive corals in areas with high fish predation. creator: Cailin Harrell creator: Diego Lirman uri: https://doi.org/10.7717/peerj.14995 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Harrell and Lirman title: Small worms of Sthenelanellinae, Pholoinae and Pisioninae (Annelida, Sigalionidae) from the Tropical Northwestern Atlantic link: https://peerj.com/articles/15005 last-modified: 2023-03-08 description: The family Sigalionidae is characterized, among other features, by including scale worms with large bodies. However, among sigalionids, the subfamilies Sthenelanellinae, Pholoinae, and Pisioninae stand out by their small representatives with few segments and fragile bodies. In the Tropical Northwestern Atlantic, which includes part of the Gulf of Mexico and the Caribbean Sea, these subfamilies have been rarely studied, with few species recorded, and questionable records. This contribution aims to improve the knowledge of sthenelanellins, pholoins, and pisionins in the region through a faunistic study based on material from two Mexican scientific collections: the Reference Collection of Laboratorio de Biodiversidad y Cambio Climático (BIOMARCCA) and the Reference Collection of Benthos (ECOSUR) of El Colegio de la Frontera Sur. Pisione wolfi is confirmed from the Tropical Northwestern Atlantic, and three new species are described: Sthenelanella pechi sp. nov., S. sarae sp. nov. and Taylorpholoe anabelae sp. nov. A key to all Sthenelanella and Taylorpholoe species is also included. creator: Christopher Cruz-Gómez uri: https://doi.org/10.7717/peerj.15005 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cruz-Gómez title: Determinants of age-related decline in walking speed in older women link: https://peerj.com/articles/14728 last-modified: 2023-03-07 description: BackgroundWalking speed is reduced with aging. However, it is not certain whether the reduced walking speed is associated with physical and coordination fitness. This study explores the physical and coordination determinants of the walking speed decline in older women.MethodsOne-hundred-eighty-seven active older women (72.2 ± 6.8 years) were asked to perform a 10-m walk test (self-selected and maximal walking speed) and a battery of the Senior fitness test: lower body strength, lower body flexibility, agility/dynamic balance, and aerobic endurance. Two parameters characterized the walking performance: closeness to the modeled speed minimizing the energetic cost per unit distance (locomotor rehabilitation index, LRI), and the ratio of step length to step cadence (walk ratio, WR). For dependent variables (self-selected and maximal walking speeds), a recursive partitioning algorithm (classification and regression tree) was adopted, highlighting interactions across all the independent variables.ResultsParticipants were aged from 60 to 88 years, and their self-selected and maximal speeds declined by 22% and 26% (p < 0.05), respectively. Similarly, all physical fitness variables worsened with aging (muscle strength: 33%; flexibility: 0 to −8 cm; balance: 22%; aerobic endurance: 12%; all p < 0.050). The predictors of maximal walking speed were only WR and balance. No meaningful predictions could be made using LRI and WR as dependent variables.DiscussionThe results suggest that at self-selected speed, the decrease in speed itself is sufficient to compensate for the age-related decline in the motor functions tested; by contrast, lowering the WR is required at maximal speed, presumably to prevent imbalance. Therefore, any excessive lowering of LRI and WR indicates loss of homeostasis of walking mechanics and invites diagnostic investigation. creator: Valéria Feijó Martins creator: Luigi Tesio creator: Anna Simone creator: Andréa Kruger Gonçalves creator: Leonardo A. Peyré-Tartaruga uri: https://doi.org/10.7717/peerj.14728 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Martins et al. title: Quantitative trait loci associated with straighthead-resistance used for marker assisted selection in rice (Oryza sativa L.) RIL populations link: https://peerj.com/articles/14866 last-modified: 2023-03-07 description: Straighthead is a physiological disorder of rice (Oryza sativa L.) that causes dramatic yield loss in susceptible cultivars. This disorder is found worldwide and is reported to increasingly occur in the southern United States. Genetic resistance breeding has been considered as one of the most efficient methods for straighthead prevention because the traditional prevention method wastes water and costs labor. In this study, we analyzed the genetic effects of five straighthead quantitative trait loci (QTLs), namely, AP3858-1 (qSH-8), RM225 (qSH-6), RM2 (qSH-7), RM206 (qSH-11), and RM282 (qSH-3), on the recombinant inbred lines (RILs) developed from Jing185/Cocodrie and Zhe733/R312 populations using our five previously identified markers linked to these QTLs. As a result, recombinant inbred lines (RILs) with four resistant alleles at the four loci (AP3858-1, RM225, RM2, and RM206) exhibited the highest straighthead resistance. This result suggests that the four markers could be efficiently used to select the straighthead-resistant recombinant inbred lines (RILs). Furthermore, by using AP3858-1, we successfully obtained five straighthead-resistant recombinant inbred lines (RILs) with more than 50% genetic similarity to Cocodrie. These markers and recombinant inbred lines (RILs) can be used for future straighthead resistance breeding through marker-assisted selection. creator: Xuhao Pan creator: Yiting Li creator: Xiaobai Li uri: https://doi.org/10.7717/peerj.14866 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pan et al. title: RNA-seq reveals Nup62 as a potential regulator for cell division after traumatic brain injury in mice hippocampus link: https://peerj.com/articles/14913 last-modified: 2023-03-07 description: BackgroundHippocampus impairment is a common condition encountered in the clinical diagnosis and treatment of traumatic brain injury (TBI). Several studies have investigated this phenomenon. However, its molecular mechanism remains unclear.MethodsIn this study, Illumina RNA-seq technology was used to determine the gene expression profile in mice hippocampus after TBI. We then conducted bioinformatics analysis to identify the altered gene expression signatures and mechanisms related to TBI-induced pathology in the hippocampus. Real-time quantitative polymerase chain reaction and western blot were adopted to verify the sequencing results.ResultsThe controlled cortical impact was adopted as the TBI model. Hippocampal specimens were removed for sequencing. Bioinformatics analysis identified 27 upregulated and 17 downregulated differentially expressed genes (DEGs) in post-TBI mouse models. Potential biological functions of the genes were determined via Gene Set Enrichment Analysis (GSEA)-based Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, which suggested a series of functional changes in the nervous system. Specifically, the nucleoporin 62 (Nup62) DEG was discussed and verified. Gene ontology biological process enriched analysis suggests that the cell division was upregulated significantly. The present study may be helpful for the treatment of impaired hippocampus after TBI in the future. creator: Jianwei Zhao creator: Weihua Wang creator: Ke Yan creator: Haifeng Zhao creator: Zhen Zhang creator: Yu Wang creator: Wenyu Zhu creator: Shiwen Chen uri: https://doi.org/10.7717/peerj.14913 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Functional verification of the JmLFY gene associated with the flowering of Juglans mandshurica Maxim. link: https://peerj.com/articles/14938 last-modified: 2023-03-07 description: In this study, a pBI121-JmLFY plant expression vector was constructed on the basis of obtaining the full-length sequence of the JmLFY gene from Juglans mandshurica, which was then used for genetic transformation via Agrobacterium inflorescence infection using wild-type Arabidopsis thaliana and lfy mutants as transgenic receptors. Seeds of positive A. thaliana plants with high expression of JmLFY were collected and sowed till the homozygous T3 regeneration plants were obtained. Then the expression of flowering-related genes (AtAP1, AtSOC1, AtFT and AtPI) in T3 generation plants were analyzed and the results showed that JmLFY gene overexpression promoted the expression of flowering-related genes and resulted in earlier flowering in A. thaliana. The A. thaliana plants of JmLFY-transformed and JmLFY-transformed lfy mutants appeared shorter leaves, longer fruit pods, and fewer cauline leaves than those of wild-type and the lfy mutants plants, respectively. In addition, some secondary branches in the transgenic plants converted into inflorescences, which indicated that the overexpression of JmLFY promoted the transition from vegetative growth to reproductive growth, and compensate the phenotypic defects of lfy mutant partially. The results provides a scientific reference for formulating reasonable genetic improvement strategies such as shortening childhood, improving yield and quality, and breeding desirable varieties, which have important guiding significance in production. creator: Jiayou Cai creator: Ruoxue Jia creator: Ying Jiang creator: Jingqi Fu creator: Tianyi Dong creator: Jifeng Deng creator: Lijie Zhang uri: https://doi.org/10.7717/peerj.14938 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cai et al. title: Apocynum venetum, a medicinal, economical and ecological plant: a review update link: https://peerj.com/articles/14966 last-modified: 2023-03-07 description: Apocynum venetum L. is an important medicinal perennial rhizome plant with good ecological and economic value. Its leaves have many pharmacological effects such as anti-inflammatory, anti-depression, anti-anxiolytic, etc., while its fibers have the title of “king of wild fibers”. Furthermore, it was suitable for the restoration of degraded saline soil in arid areas. An increasing studies have been published in the past years. A scientometric analysis was used to analyze the publications of Apocynum venetum L. to clearly review the pharmacology, fiber application of Apocynum venetum L. and the potential value with its similar species (Apocynum pictum Schrenk) to the environment. creator: Tian Xiang creator: Longjiang Wu creator: Murtala Bindawa Isah creator: Chen Chen creator: Xiaoying Zhang uri: https://doi.org/10.7717/peerj.14966 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xiang et al. title: Uncertainties regarding the natural mortality of fish can increase due global climate change link: https://peerj.com/articles/14989 last-modified: 2023-03-07 description: The increase in temperature resulting from global climate change can directly affect the survival of fish and therefore population parameters such as natural mortality (M). The estimation of this parameter and the understanding of the uncertainties in its estimates are enormous challenges for studies that evaluate fish stocks. In addition, the effects of increases in temperature may be associated with life strategies. Therefore, the fuzzy set theory was used to evaluate the effects of temperature increase on the natural mortality of fish, considering different life strategies. The model showed that the increase in temperature increased the uncertainties in M estimates for all species, regardless of the life strategy. However, opportunistic species present greater uncertainties in estimates of M compared to equilibrium species. The patterns found in uncertainties of M associated with species groupings by life strategies can be used in holistic approaches for the assessment and management of recently exploited fisheries resources or for those with limited biological data. creator: Caroline Pereira Campos creator: Sandro Dimy Barbosa Bitar creator: Carlos Freitas uri: https://doi.org/10.7717/peerj.14989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pereira Campos et al. title: Comparative ultrastructure of the antennae and sensory hairs in six species of crayfish link: https://peerj.com/articles/15006 last-modified: 2023-03-07 description: BackgroundAntennae in crayfish are essential for gaining information about the local topography and localising food, chemicals, conspecifics or predator. There are still gaps in the research on the morphology of antennae in decapods compared to other arthropods.MethodologyBiometrical and ultrastructural methods were applied using light and cryo-scanning electron microscopies to study the morphology of antennae in six different crayfish species, including marbled crayfish Procambarus virginalis, Mexican dwarf crayfish Cambarellus patzcuarensis, red swamp crayfish Procambarus clarkii, signal crayfish Pacifastacus leniusculus, common yabby Cherax destructor, and spiny-cheek crayfish Faxonius limosus to find their potential morphological differences.ResultsSignificant differences in the antenna length, length and width of each segment to carapace length ratios, and the number of segments were found in the six crayfish species. The ultrastructure revealed differences in the distribution of sensory hairs on the antenna and the morphology of the antennal surface.ConclusionsThe different morphology of antennae might reflect adaptation to the conditions of their specific habitats. In addition, results showed that a combination of differences in the morphological features and biometrical measurements of antennae could be used for the distinguishment of different studied crayfish species. creator: Golara Kor creator: Kifayatullah Mengal creator: Miloš Buřič creator: Pavel Kozák creator: Hamid Niksirat uri: https://doi.org/10.7717/peerj.15006 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kor et al. title: The study of the characteristics of the secondary flowering of Cerasus subhirtella ‘Autumnalis’ link: https://peerj.com/articles/14655 last-modified: 2023-03-06 description: The short flowering period of ornamental cherry trees is the main factor limiting their use in gardens. Determining the secondary flowering characteristics of ornamental cherry trees is required to prolong their flowering period. In this experiment, Cerasus subhirtella ‘Autumnalis’ was used as the experimental material. The phenological differences in their annual growth cycle were observed using the BBCH coding system. The cooling requirements of the flower buds were evaluated by the chilling hours model (temperature between 0 and 7.2 °C) and the Utah model. The expression of the core gene involved in bud dormancy regulation DAM (dormancy-associated MADS-box) from the completion of flower bud differentiation in one year until the following year was measured by performing real-time fluorescence-based quantitative PCR. The results showed that the flowering duration of C. subhirtella ‘Autumnalis’ from November to December was longer than that of C. yedoensis ‘Somei Yoshino’, which was from March to April. The progress from seed bud-break to flower bud opening took about 10 days for C. subhirtella ‘Autumnalis’, while the same stage for C. yedoensis ‘Somei Yoshino’ took around 20 days. Additionally, the flower buds of C. subhirtella ‘Autumnalis’ needed only the chilling temperature unit of 54.08 to satisfy the chilling requirement, while C. yedoensis ‘Somei Yoshino’ required a chilling temperature unit of 596.75. After the completion of flower bud differentiation, during low-temperature storage, the expression of DAM4 and DAM5 genes first increased and then decreased, whereas, the expression of the DAM6 gene continued to decrease, and the expression of DAM4, DAM5, and DAM6 in C. yedoensis ‘Somei Yoshino’ increased rapidly and was maintained at a high level. This showed that the upregulation of the expression of the DAM4, DAM5, and DAM6 genes can inhibit the flower bud germination of Cherry Blossom. The relative expression of the DAM gene of C. subhirtella ‘Autumnalis’ was significantly lower than that of the DAM gene of C. yedoensis ‘Somei Yoshino’ from the end of October to the beginning of December, leading to its secondary flowering in autumn. These results might elucidate why the flower buds of C. subhirtella ‘Autumnalis’ can break their internal dormancy and bloom in the autumn and then again in the following year. Our findings might provide a reference for conducting further studies on the mechanisms of secondary flowering and bud dormancy in cherries. creator: Yanxia Xu creator: Liyan Du creator: Xuebin Song creator: Chunling Zhou uri: https://doi.org/10.7717/peerj.14655 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al.