title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1569 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas link: https://peerj.com/articles/4812 last-modified: 2018-05-16 description: The seed oil of Jatropha curcas is considered a potential bioenergy source that could replace fossil fuels. However, the seed yield of Jatropha is low and has yet to be improved. We previously reported that exogenous cytokinin treatment increased the seed yield of Jatropha. Cytokinin levels are directly regulated by isopentenyl transferase (IPT), cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A), and cytokinin oxidase/dehydrogenase (CKX). In this study, we cloned six IPT genes, one JcCYP735A gene, and seven JcCKX genes. The expression patterns of these 14 genes in various organs were determined using real-time quantitative PCR. JcIPT1 was primarily expressed in roots and seeds, JcIPT2 was expressed in roots, apical meristems, and mature leaves, JcIPT3 was expressed in stems and mature leaves, JcIPT5 was expressed in roots and mature leaves, JcIPT6 was expressed in seeds at 10 days after pollination, and JcIPT9 was expressed in mature leaves. JcCYP735A was mainly expressed in roots, flower buds, and seeds. The seven JcCKX genes also showed different expression patterns in different organs of Jatropha. In addition, CK levels were detected in flower buds and seeds at different stages of development. The concentration of N6-(Δ2-isopentenyl)-adenine (iP), iP-riboside, and trans-zeatin (tZ) increased with flower development, and the concentration of iP decreased with seed development, while that of tZ increased. We further analyzed the function of JcCYP735A using the CRISPR-Cas9 system, and found that the concentrations of tZ and tZ-riboside decreased significantly in the Jccyp735a mutants, which showed severely retarded growth. These findings will be helpful for further studies of the functions of cytokinin metabolic genes and understanding the roles of cytokinins in Jatropha growth and development. creator: Li Cai creator: Lu Zhang creator: Qiantang Fu creator: Zeng-Fu Xu uri: https://doi.org/10.7717/peerj.4812 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cai et al. title: Geographical variation in colour of female threespine stickleback (Gasterosteus aculeatus) link: https://peerj.com/articles/4807 last-modified: 2018-05-16 description: The ecological multifunctionality of colour often results in multiple selective pressures operating on a single trait. Most research on colour evolution focuses on males because they are the most conspicuous sex in most species. This bias can limit inferences about the ecological drivers of colour evolution. For example, little is known about population divergence in colour of female threespine stickleback (Gasterosteus aculeatus), which is among the most intensively-studied model vertebrates in evolution, ecology, and behaviour. In contrast, the evolution and ecology of colour in male stickleback has received considerable attention. One aspect of female colouration that is lacking previous research is non-ornamental body colour. Non-ornamental colour can play defensive and social roles, and indicate other aspects of female stickleback ecology. To remedy this knowledge gap, we measured the colour and brightness of one dorsal and one ventral lateral area on female stickleback from nine lake populations on Vancouver Island. We found that lake populations varied in overall colour brightness and dorso-ventral contrast. In addition, we found that female brightness increased with lake size, indicating potential ecological drivers of these colour differences. Our results demonstrate that there is substantial scope for future research on female colour diversification, which has been overlooked because past researchers focused on dramatic male nuptial colours. creator: Connor M. French creator: Travis Ingram creator: Daniel I. Bolnick uri: https://doi.org/10.7717/peerj.4807 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 French et al. title: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines link: https://peerj.com/articles/4781 last-modified: 2018-05-16 description: Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region. creator: Andrian P. Gajigan creator: Aletta T. Yñiguez creator: Cesar L. Villanoy creator: Maria Lourdes San Diego-McGlone creator: Gil S. Jacinto creator: Cecilia Conaco uri: https://doi.org/10.7717/peerj.4781 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gajigan et al. title: Genetic inactivation of alpha-synuclein affects embryonic development of dopaminergic neurons of the substantia nigra, but not the ventral tegmental area, in mouse brain link: https://peerj.com/articles/4779 last-modified: 2018-05-16 description: Lesion of the dopaminergic neurons of the nigrostriatal system is a key feature of Parkinson’s disease (PD). Alpha-synuclein is a protein that is a major component of Lewy bodies, histopathological hallmarks of PD, and is involved in regulation of dopamine (DA) neurotransmission. Previous studies of knockout mice have shown that inactivation of alpha-synuclein gene can lead to the reduction in number of DA neurons in the substantia nigra (SN). DA neurons of the SN are known to be the most affected in PD patients whereas DA neurons of neighboring ventral tegmental area (VTA) are much less susceptible to degeneration. Here we have studied the dynamics of changes in TH-positive cell numbers in the SN and VTA during a critical period of their embryonic development in alpha-synuclein knockout mice. This precise study of DA neurons during development of the SN revealed that not only is the number of DA neurons reduced by the end of the period of ontogenic selection, but that the way these neurons are formed is altered in alpha-synuclein knockout mice. At the same time, DA neurons in the VTA are not affected. Alpha-synuclein exerts a modulating effect on the formation of DA neurons in the SN and has no effect on the formation of DA neurons in VTA, the structure that is much less susceptible to degeneration in a brain with PD, suggesting a potential role of alpha-synuclein in the development of the population of DA neurons in substantia nigra. creator: Tatiana V. Tarasova creator: Olga A. Lytkina creator: Valeria V. Goloborshcheva creator: Larisa N. Skuratovskaya creator: Alexandr I. Antohin creator: Ruslan K. Ovchinnikov creator: Michail S. Kukharsky uri: https://doi.org/10.7717/peerj.4779 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tarasova et al. title: Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil link: https://peerj.com/articles/4776 last-modified: 2018-05-16 description: Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil. creator: Amalia Soenens creator: Juan Imperial uri: https://doi.org/10.7717/peerj.4776 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Soenens and Imperial title: Pollution of the sediments of the coastal zone of the Sambia Peninsula and the Curonian Spit (Southeastern Baltic Sea) link: https://peerj.com/articles/4770 last-modified: 2018-05-16 description: The detailed environmental survey of the coastal zone of the Kaliningrad Region northern coast was carried out. The pollutants distribution in the silty clay fraction and calculation of ecological indexes allowed the evaluation of distribution of potentially harmful elements (PHEs). The sources of pollution in the most intensively used areas were identified, and transit and accumulation zones were allocated. A large area of anomalous content of PHEs was revealed on the underwater coastal slope of the Curonian Spit National Park, which is situated far from the sources of pollution. The alongshore bed load transport provides the contamination of the underwater slope whereas the beaches are less exposed to pollution. creator: Alexander Krek creator: Viktor Krechik creator: Aleksandr Danchenkov creator: Elena Krek uri: https://doi.org/10.7717/peerj.4770 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Krek et al. title: A new species of Pseudopaludicola (Anura, Leiuperinae) from Espírito Santo, Brazil link: https://peerj.com/articles/4766 last-modified: 2018-05-16 description: We describe a new anuran species of the genus Pseudopaludicola that inhabits sandy areas in resting as associated to the Atlantic Forest biome in the state of Espírito Santo, Brazil. The new species is characterized by: SVL 11.7–14.6 mm in males, 14.0–16.7 mm in females; body slender; fingertips knobbed, with a central groove; hindlimbs short; abdominal fold complete; arytenoid cartilages wide; prepollex with base and two segments; prehallux with base and one segment; frontoparietal fontanelle partially exposed; advertisement call with one note composed of two isolated pulses per call; call dominant frequency ranging 4,380–4,884 Hz; diploid chromosome number 22; and Ag-NORs on 8q subterminal. In addition, its 16S rDNA sequence shows high genetic distances when compared to sequences of related species, which provides strong evidence that the new species is an independent lineage. creator: Dario E. Cardozo creator: Diego Baldo creator: Nadya Pupin creator: João Luiz Gasparini creator: Célio F. Baptista Haddad uri: https://doi.org/10.7717/peerj.4766 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cardozo et al. title: Integrated bioinformatic changes and analysis of retina with time in diabetic rats link: https://peerj.com/articles/4762 last-modified: 2018-05-16 description: Diabetic retinopathy (DR) is the most common chronic complication of diabetes. It can cause impaired vision and even blindness. However, the pathological mechanism of DR is still unknown. In the present study, we use bioinformatic analysis to reveal the pathological changes of early DR in a streptozotocin (STZ) induced diabetes rat model. The dataset GSE28831 was downloaded from the Gene Expression Omnibus (GEO) database. To clarify the pathological mechanism of early DR, genes which were up-regulated (UP group) or down-regulated (DOWN group) over time were identified. One hundred eighty six genes in the UP group and 85 genes in the DOWN group were defined. There were in total 28 Gene ontology (GO) terms with a P value lower than 0.05 in UP group, including astrocyte development, neutrophil chemotaxis, neutrophil aggregation, mesenchymal cell proliferation and so on. In the DOWN group, there were totally 14 GO terms with a P value lower than 0.05, including visual perception, lens development in camera-type eye, camera-type eye development, bicellular tight junction and so on. Signaling pathways were analyzed with all genes in the UP and DOWN groups, and leukocyte transendothelial migration and tight junction were selected. Protein–protein interaction (PPI) network was constructed and six hub genes Diras3, Actn1, Tssk6, Cnot6l, Tek and Fgf4 were selected with connection degree ≥5. S100a8, S100a9 and Tek may be potential targets for DR diagnosis and treatment. This study provides the basis for the diagnosis and treatment of DR in the future. creator: Zekai Cui creator: Qiaolang Zeng creator: Yonglong Guo creator: Shiwei Liu creator: Jiansu Chen uri: https://doi.org/10.7717/peerj.4762 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cui et al. title: Occurrence of termites (Isoptera) on living and standing dead trees in a tropical dry forest in Mexico link: https://peerj.com/articles/4731 last-modified: 2018-05-16 description: Termites play a key role as ecosystem engineers in numerous ecological processes though their role in the dynamics of wood degradation in tropical dry forests, particularly at the level of the crown canopy, has been little studied. In this study, we analysed the occurrence of termites in the forest canopy by evaluating the density and proportion of living and standing dead trees associated with termites in deciduous and riparian habitats of the tropical dry forest in Chamela, Mexico. The results indicated that 60–98% of standing dead trees and 23–59% of living trees in Chamela were associated with termites. In particular, we found that the density of standing dead trees was higher in deciduous forests (0.057–0.066 trees/m2) than in riparian forests (0.022 and 0.027 trees/m2), even though the proportion of trees was not significantly different among habitats. Additionally, we found a higher density of trees associated with termites in trees of smaller size classes (0.01–0.09 trees/m2) than in larger class sizes (0–0.02 trees/m2). Interestingly, 72% of variation in the density of trees associated with termites is explained by the density of standing dead trees. Overall, these results indicate that standing dead tree availability might be the main factor regulating termite populations in Chamela forest and suggest that termites could play a key role in the decomposition of above-ground dead wood, mediating the incorporation of suspended and standing dead wood into the soil. creator: Nancy Calderón-Cortés creator: Luis H. Escalera-Vázquez creator: Ken Oyama uri: https://doi.org/10.7717/peerj.4731 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Calderón-Cortés et al. title: Overwintering temperature and body condition shift emergence dates of spring-emerging solitary bees link: https://peerj.com/articles/4721 last-modified: 2018-05-16 description: Solitary bees in seasonal environments must align their life-cycles with favorable environmental conditions and resources; the timing of their emergence is highly fitness relevant. In several bee species, overwintering temperature influences both emergence date and body weight at emergence. High variability in emergence dates among specimens overwintering at the same temperatures suggests that the timing of emergence also depends on individual body conditions. However, possible causes for this variability, such as individual differences in body size or weight, have been rarely studied. In a climate chamber experiment using two spring-emerging mason bees (Osmia cornuta and O. bicornis), we investigated the relationship between temperature, emergence date, body weight, and body size, the last of which is not affected by overwintering temperature. Our study showed that body weight declined during hibernation more strongly in warm than in cold overwintering temperatures. Although bees emerged earlier in warm than in cold overwintering temperatures, at the time of emergence, bees in warm overwintering temperatures had lower body weights than bees in cold overwintering temperatures (exception of male O. cornuta). Among specimens that experienced the same overwintering temperatures, small and light bees emerged later than their larger and heavier conspecifics. Using a simple mechanistic model we demonstrated that spring-emerging solitary bees use a strategic approach and emerge at a date that is most promising for their individual fitness expectations. Our results suggest that warmer overwintering temperatures reduce bee fitness by causing a decrease in body weight at emergence. We showed furthermore that in order to adjust their emergence dates, bees use not only temperature but also their individual body condition as triggers. This may explain differing responses to climate warming within and among bee populations and may have consequences for bee-plant interactions as well as for the persistence of bee populations under climate change. creator: Mariela Schenk creator: Oliver Mitesser creator: Thomas Hovestadt creator: Andrea Holzschuh uri: https://doi.org/10.7717/peerj.4721 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Schenk et al.