Isolation, growth, and nitrogen fixation rates of the Hemiaulus-Richelia (diatom-cyanobacterium) symbiosis in culture
Nitrogen fixers (diazotrophs) are often an important nitrogen source to phytoplankton nutrient budgets in N-limited marine environments. Diazotrophic symbioses between cyanobacteria and diatoms can dominate nitrogen-fixation regionally, particularly in major river plumes and in open ocean mesoscale blooms. This study reports the successful isolation and growth in monocultures of multiple strains of a diatom-cyanobacteria symbiosis from the Gulf of Mexico using a modified artificial seawater medium. We document the influence of light and nutrients on nitrogen fixation and growth rates of the host diatom Hemiaulus hauckii Grunow together with its diazotrophic endosymbiont Richelia intracellularis Schmidt, as well as less complete results on the Hemiaulus membranaceus-R. intracellularis symbiosis. The symbioses rates reported here are for the joint diatom-cyanobacteria unit. Symbiont diazotrophy was sufficient to support both the host diatom and cyanobacteria symbionts, and the entire symbiosis replicated and grew without added nitrogen. Maximum growth rates of multiple strains of H. hauckii symbioses in N-free medium with N2 as the sole N source were 0.74–0.93 div d−1. Growth rates followed light saturation kinetics in H. hauckii symbioses with a growth compensation light intensity (EC) of 7–16 µmol m−2s−1and saturation light level (EK) of 84–110 µmol m−2s−1. Nitrogen fixation rates by the symbiont while within the host followed a diel pattern where rates increased from near-zero in the scotophase to a maximum 4–6 h into the photophase. At the onset of the scotophase, nitrogen-fixation rates declined over several hours to near-zero values. Nitrogen fixation also exhibited light saturation kinetics. Maximum N2 fixation rates (84 fmol N2 heterocyst−1h−1) in low light adapted cultures (50 µmol m−2s−1) were approximately 40–50% of rates (144–154 fmol N2 heterocyst−1h−1) in high light (150 and 200 µmol m−2s−1) adapted cultures. Maximum laboratory N2 fixation rates were ~6 to 8-fold higher than literature-derived field rates of the H. hauckii symbiosis. In contrast to published results on the Rhizosolenia-Richelia symbiosis, the H. hauckii symbiosis did not use nitrate when added, although ammonium was consumed by the H. hauckii symbiosis. Symbiont-free host cell cultures could not be established; however, a symbiont-free H. hauckii strain was isolated directly from the field and grown on a nitrate-based medium that would not support DDA growth. Our observations together with literature reports raise the possibility that the asymbiotic H. hauckii are lines distinct from an obligately symbiotic H. hauckii line. While brief descriptions of successful culture isolation have been published, this report provides the first detailed description of the approaches, handling, and methodologies used for successful culture of this marine symbiosis. These techniques should permit a more widespread laboratory availability of these important marine symbioses.
Pyle et al. (2020) Isolation, growth, and nitrogen fixation rates of the Hemiaulus-Richelia (diatom-cyanobacterium) symbiosis in culture. PeerJ 8:e10115 https://doi.org/10.7717/peerj.10115
Overgrazing-induced legacy effects may permit Leymus chinensis to cope with herbivory
There is growing evidence that herbivory-induced legacy effects permit plants to cope with herbivory. However, herbivory-induced defense strategies in plants against grazing mammals have received little attention. To further understand the grazing-induced legacy effects on plants, we conducted a greenhouse experiment with Leymus chinensis experiencing different grazing histories. We focused on grazing-induced legacy effects on above-ground spatial avoidance and below-ground biomass allocation. Our results showed that L. chinensis collected from the continuous overgrazing plot (OG) exhibited higher performance under simulated grazing in terms of growth, cloning and colonizing ability than those collected from the 35-year no-grazing plot (NG). The enhanced adaptability of OG was attributed to increased above-ground spatial avoidance, which was mediated by larger leaf angle and shorter height (reduced vertical height and increased leaf angle contributed to the above-ground spatial avoidance at a lower herbivory stubble height, while reduced tiller natural height contributed to above-ground spatial avoidance at a higher herbivory stubble height). Contrary to our prediction, OG pre-allocated less biomass to the rhizome, which does not benefit the herbivory tolerance and avoidance of L. chinensis; however, this also may reflect a tolerance strategy where reduced allocation to rhizomes is associated with increased production of ramets.
Guo et al. (2020) Overgrazing-induced legacy effects may permit Leymus chinensis to cope with herbivory. PeerJ 8:e10116 https://doi.org/10.7717/peerj.10116
Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis
Background Flower and fruit development are vital stages of the angiosperm lifecycle. We previously investigated the multi-silique trait in the rapeseed (Brassica napus) line zws-ms on a genomic and transcriptomic level, leading to the identification of two genomic regions and several candidate genes associated with this trait. However, some events on the transcriptome level, like alternative splicing, were poorly understood. Methods Plants from zws-ms and its near-isogenic line (NIL) zws-217 were both grown in Xindu with normal conditions and a colder area Ma’erkang. Buds from the two lines were sampled and RNA was isolated to perform the transcriptomic sequencing. The numbers and types of alternative splicing (AS) events from the two lines were counted and classified. Genes with AS events and expressed differentially between the two lines, as well as genes with AS events which occurred in only one line were emphasized. Their annotations were further studied. Results From the plants in Xindu District, an average of 205,496 AS events, which could be sorted into five AS types, were identified. zws-ms and zws-217 shared highly similar ratios of each AS type: The alternative 5′ and 3′ splice site types were the most common, while the exon skipping type was observed least often. Eleven differentially expressed AS genes were identified, of which four were upregulated and seven were downregulated in zws-ms. Their annotations implied that five of these genes were directly associated with the multi-silique trait. While samples from colder area Ma’erkang generated generally reduced number of each type of AS events except for Intron Retention; but the number of differentially expressed AS genes increased significantly. Further analysis found that among the 11 differentially expressed AS genes from Xindu, three of them maintained the same expression models, while the other eight genes did not show significant difference between the two lines in expression level. Additionally, the 205 line-specific expressed AS genes were analyzed, of which 187 could be annotated, and two were considered to be important. Discussion This study provides new insights into the molecular mechanism of the agronomically important multi-silique trait in rapeseed on the transcriptome level and screens out some environment-responding candidate genes.
Chai et al. (2020) Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis. PeerJ 8:e10135 https://doi.org/10.7717/peerj.10135
Adequacy of clinical information in X-ray referrals for traumatic ankle injury with reference to the Ottawa Ankle Rules—a retrospective clinical audit
Study Objective To assess the adequacy of clinical information with reference to the Ottawa Ankle Rules (OAR) in X-ray referrals for adults with traumatic ankle injury in the ED of a South Australian tertiary hospital and report upon referring trends between emergency department clinicians. Methods A retrospective clinical audit of adult ankle X-ray referrals in the emergency department was conducted. Eligible referrals were screened for their adherence to the OAR, patient details, clinical history and referrer. A logistic regression was used to determine the influence of these factors on the likelihood of being referred for X-rays despite not meeting the OAR criteria. Sensitivity, specificity, positive and negative likelihood ratios and their associated confidence intervals were calculated to assess the diagnostic accuracy of the OAR for those referred. Results Out of the 262 eligible referrals, 163 were deemed to have met the criteria for the OAR. Physiotherapists showed the highest OAR compliance of 77.3% and were the most accurate in their use of the rules, with a sensitivity of 0.86. Medical officers, registrars and interns were 2.5 times more likely to still refer a patient for X-ray if they did not meet the OAR criteria, compared to physiotherapists as the baseline. Patient age, duration of injury etc. were not significantly associated with likelihood of referral (even when they did not meet OAR criteria). The overall sensitivity, specificity, positive and negative likelihood ratios of the OAR were 0.59 (95% CI [0.47–0.71]), 0.37 (95% CI [0.30–0.44]), 0.93 (95% CI [0.76–1.16]) and 1.10 (95% CI [0.82–1.48]) respectively. Conclusion The results of this audit demonstrated poor sensitivity and moderate compliance by referrers with the rule. Reasonable evidence exists for the implementation of individual and/or institutional-based change strategies to improve clinician compliance and accuracy with use of the OAR.
Gomes et al. (2020) Adequacy of clinical information in X-ray referrals for traumatic ankle injury with reference to the Ottawa Ankle Rules—a retrospective clinical audit. PeerJ 8:e10152 https://doi.org/10.7717/peerj.10152
Coupled exuviae of the Ordovician Ovalocephalus (Pliomeridae, Trilobita) in South China and its behavioral implications
Ecdysis was a vital process during the lives of trilobites. In addition to preserving the morphological changes in trilobite ontogeny, the preservation of its action often captured interesting behavioral information. Abundant exuviae of Ovalocephalus tetrasulcatus are preserved in the Ordovician strata in central Hubei, China, and some of them are arranged with two or three together end to end or superimposed. The preserved patterns and burial conditions indicate that these specimens were caused by the active behavior of trilobites. It is speculated that these exuvial clusters were formed by two or three trilobites in line to molt; that is, after one trilobite finished molting, other trilobites molted in front of, behind, or overlying the previously molted shells. This ecdysis strategy is interpreted as related to the postulated herding behavior of some trilobites, representing a behavioral response of the trilobites to choose a nearby safe zone during some risky life activities.
Zong (2020) Coupled exuviae of the Ordovician Ovalocephalus (Pliomeridae, Trilobita) in South China and its behavioral implications. PeerJ 8:e10166 https://doi.org/10.7717/peerj.10166
A taxonomic review of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) from Japanese coastal waters
Japanese species of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) are reviewed. Astrocladus coniferus recently has two junior synonyms, A. dofleini Döderlein and A. pardalis Döderlein, however, status of these species has long been questioned. These species concepts have not been reviewed in recent years and no molecular phylogenetic analyses have been performed. Observations of the lectotype of A. coniferus, as well as the lectotype and four paralectotypes of A. dofleini and the holotype of A. pardalis have revealed that A. coniferus and A. pardalis are conspecific and morphologically distinguishable from A. dofleini. Astrocladus coniferus and A. dofleini are supported as distinct species by our molecular data. Additionally, we re-describe A. exiguus and A. annulatus, based on recently collected specimens and the holotype. We conclude that four species, A. annulatus, A. coniferus, A. dofleini, and A. exiguus are present in Japanese waters.
Okanishi et al. (2020) A taxonomic review of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) from Japanese coastal waters. PeerJ 8:e9836 https://doi.org/10.7717/peerj.9836
Lifestyle choices of Brazilian college students
Background Lifestyle choices reflect the beliefs that individuals attribute to aspects of life. This construct can be assessed with the Individual Lifestyle Profile (PEVI) questionnaire, which measures elements of Nutrition, Physical Activity, Preventive Behaviors, Social Relationships and Stress Management. Objective The objective of this study was to estimate the psychometric properties of the PEVI applied to a sample of Brazilian university students, identifying the prevalence of each lifestyle component according to participants’ age, sex, weight status, course area/field and economic stratum and to estimate the contribution of these characteristics on physical and psychological lifestyle. Methods The PEVI data was analyzed by confirmatory factor analysis, using the indexes chi-square per degrees of freedom ratio (χ2/df), Comparative Fit Index (CFI), Tucker-Lewis Index (TLI) and Root Mean Square Error of Approximation (RMSEA). First-order and second-order models (physical and psychological lifestyle) were tested. Prevalences of lifestyle components were calculated and compared by participants’ age, sex, weight status, course area/field and economic stratum. A hypothetical causal structural model was elaborated to investigate the impact of sample characteristics on physical and psychological lifestyles. This model was evaluated considering the global fit to the data (χ2/df, CFI, TLI and RMSEA) and the hypothetical causal trajectories (β) (α = 5%). Results A sample of 1,303 students was used. The mean age was 20.9 (standard deviation = 2.8) years, 66.8% of participants were females, 63.4% had weights in the normal range and 73.7% were students of the social and exact sciences. The PEVI data showed an adequate fit for both the first- (χ2/df = 2.03, CFI = 0.98; TLI = 0.97; RMSEA = 0.04) and second-order (χ2/df = 2.25; CFI = 0.97; TLI = 0.97; RMSEA = 0.04) models. There was a higher prevalence of unfavorable physical and psychological lifestyle choices among females, among underweight and obese individuals, in older students and in those with lower economic strata. Moreover, negative behaviors in physical lifestyle were more prevalent in students from human/social/exact sciences and worse psychological lifestyle was observed among health sciences students. These results were confirmed by a structural model. Conclusion The PEVI data presented validity and reliability. Negative lifestyle choices had high prevalence among students. Moreover, individual characteristics had different impact on physical and psychological lifestyle choices.
Martins et al. (2020) Lifestyle choices of Brazilian college students. PeerJ 8:e9830 https://doi.org/10.7717/peerj.9830
Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.
Kammerer et al. (2020) Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia). PeerJ 8:e9925 https://doi.org/10.7717/peerj.9925
Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages
Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen receptor-mediated signalling pathway, positive regulation of lymphocyte proliferation) that may play key roles in the immune functions of the goat submandibular glands at different developmental stages were identified. Moreover, we found that eight antibacterial peptide-encoding genes were downregulated in the tuberculosis and salivary secretion pathways, while all immunoglobulins were upregulated in 10 immune system pathways. These findings indicate that the submandibular glands may be important immunological organs during the growth process of goats and that the immune function of these glands gradually weakens with age up to 12 months but remains relatively stable after 12 months of age. Overall, this study will improve our understanding of transcriptional regulation related to goat submandibular gland immune function.
Wang et al. (2020) Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages. PeerJ 8:e9947 https://doi.org/10.7717/peerj.9947
SlMYB102 expression enhances low-temperature stress resistance in tomato plants
Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
Wang et al. (2020) SlMYB102 expression enhances low-temperature stress resistance in tomato plants. PeerJ 8:e10059 https://doi.org/10.7717/peerj.10059