Data Capture and Taxonomic Determination of Cycadales at the Royal Botanic Garden Edinburgh

This paper discusses a curatorial review of the Cycadales in the Living Collection at the Royal Botanic Garden Edinburgh (RBGE) following the methodology described by Frachon et al. (2009). It provides an understanding of the cycads in the Living Collection and the diversity of the group represented at RBGE. The paper also describes the determination process and any changes in identification during the course of the project. This project was carried out as part of the second year project of the HND in Horticulture with Plantsmanship at RBGE

Early Life History Stages of Gulf Sturgeon in the Suwannee River, Florida

Egg sampling confirmed that Suwannee River Gulf sturgeon Acipenser ozyrinchus desotoi, a subspecies of Atlantic sturgeon A. o. oxyrinchus use the same spawning site at river kilometer (rkm) 215 from the mouth of the river each year. Forty-nine eggs were recorded in 1995, and 368 were recorded in 1996. Spawning began 4-7 d after the March new moon in both years and lasted 10-11 d; in 1996, a second 10-d spawning round began on the April new moon. Developmental synchrony among eggs recovered suggested serval discrete spawning events in both years. Total eggs deposited for three 1996 sampling days was estimated as 405,600-711,000/d, approximating the fecundity range of a large female Gulf sturgeon. Eggs were found only in the southern half of the river, an area with surface currents of 0.5-1.5 m/s and numerous eddies producing reverse bottom currents of 0.1-0.5 m/s. Egg substrate consisted of bedrock limestone thinly overlain by fine sand and densely distributed elliptical gravel 2-10 cm in diameter. Eggs were found predominantly in depths of 2-4 m at water temperatures of 17-21oC, conductivities of 20-100 uS, and dissolved oxygen levels exceeding 5.0 mg/L. The Cody Scarp, 15 rkm above the spawning ground, may mark the upstream limit of spawning areas in the river. Three 2-4-month-old riverine juveniles (82-115 mm total length, TL) collected are the smallest yet captured from any river. Data for 18 riverine age-0 juveniles (to 350 mm TL) suggest that this stage lasts 6-10 months, terminating with migration of fish to the river mouth in January-February. Less than 2% of 461 juveniles captured at the estuarine river mouth (1990-1993) were under 350 mm TL. Riverine age-0 fish were collected over long shallow stretches (typically \u3c4 m deep) of relatively barren sand (rkm 12-238)

New approaches for the conservation genomics of the genus Cycas L. in Australia

Cycad species exist as small fragmented populations, therefore understanding their genetic variation is imperative for their conservation to ensure their long-term survival. Genetic data plays a fundamental role in identifying genotypes and detecting populations with the highest genetic diversity. This project uses next generation sequencing (NGS) and restriction associated DNA sequencing (RADseq) to identify thousands of genome-wide polymorphisms from populations of selected cycad species from the Northern Territory, Australia, namely: Cycas armstrongii, Cycas calcicola, Cycas maconochiei ssp. maconochiei and the interspecific hybrid C. armstrongii x maconochiei. RADseq was used to determine intra- and interspecific genetic variation in populations, verify the putative hybrid, recognize populations of conservation priority and determine if botanic garden collections currently represent the genetic diversity inherent in the wild. Cycas calcicola showed very low levels of genetic diversity and high inbreeding, and although there was significant geographic partitioning between populations in the Katherine and Litchfield National Park regions, which correlated with genetic differentiation. Additionally, the results showed that C. calcicola was not genetically, well represented in ex-situ collections. The genomic diversity of Cycas armstrongii, C. maconochiei ssp. maconochiei and C. armstrongii x maconochiei differs from that of C. calcicola and shows very low levels of genetic diversity yet generally with lower levels of inbreeding. The results show little genetic distance between Cycas armstrongii and C. maconochiei ssp. maconochiei, the most likely explanation is that they represent morphological extremes of a single species. The results from RADseq have far reaching significance for the conservation of cycads. In the case of C. calcicola, a far more structured acquisition of genetic material will be required if the full genetic diversity of this species is to be preserved in ex-situ collections

Pultenaea williamsii (Fabaceae: Mirbelieae), a new species endemic to the New England Tableland Bioregion of New South Wales

Pultenaea williamsii I.Telford, Clugston & R.L.Barrett (Fabaceae, Faboideae, Mirbelieae), endemic to the New England Bioregion, New South Wales, Australia, is described as new, segregated from the P. flexilis–P. juniperina–P. blakelyi species assemblage. Its distribution is mapped, and habitat and conservation status discussed

Conservation genomics of an Australian cycad, cycas calcicola and the absence of key genotypes in botanic gardens

Understanding the genetic diversity of wild populations is fundamental to conserving species in-situ and ex-situ. To aid conservation plans and to inform ex-situ conservation, we examined the genetic diversity of the cycad Cycas calcicola (Cycadaceae). Samples were collected from wild populations in the Litchfield National Park and Katherine regions in the Northern Territory, Australia. Additional samples were obtained from botanic garden plants that were originally collected in the Katherine region, Daly River and Spirit Hills in the Northern Territory, Australia. Using RADseq we recovered 2271 informative genome-wide SNPs, revealing low to moderate levels of gene diversity (uHe = 0.037 to 0.135), very low levels of gene flow, and significant levels of inbreeding (mean FIS = 0.491). Population structure and multivariate analysis showed that populations fall into two genetic groups (Katherine vs Litchfield + Daly River + Spirit Hills). Genetic differentiation was twice as high between populations of the Katherine and Litchfield regions (FST ~ 0.1) compared to within these two regions (FST ~ 0.05). Increasing population fragmentation together with high levels of inbreeding and very little gene flow are concerning for the future adaptability of this species. The results indicated that the ex-situ collections (1) had significantly lower genetic diversity than the wild populations, and (2) only partly capture the genetic diversity present, particularly because the Litchfield National Park populations are not represented. We recommend that ex-situ collections be expanded to incorporate the genetic diversity found in Litchfield National Park and to increase the number of representatives from Daly River/Spirit Hills, and that in-situ populations from the Katherine and Greater Litchfield regions be conserved as separate management units

RADseq as a valuable tool for plants with large genomes-a case study in cycads

Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60 Gbp. Restriction site-associated DNA sequencing (RADseq) offers an approach to find genome-wide informative markers and has proven to be effective with both model and nonmodel organisms. We tested the application of RADseq using ezRAD across all 10 genera of the Cycadales including an example data set of Cycas calcicola representing 72 samples from natural populations. Using previously available plastid and mitochondrial genomes as references, reads were mapped recovering plastid and mitochondrial genome regions and nuclear markers for all of the genera. De novo assembly generated up to 138,407 high-depth clusters and up to 1,705 phylogenetically informative loci for the genera, and 4,421 loci for the example assembly of C. calcicola. The number of loci recovered by de novo assembly was lower than previous RADseq studies, yet still sufficient for downstream analysis. However, the number of markers could be increased by relaxing our assembly parameters, especially for the C. calcicola data set. Our results demonstrate the successful application of RADseq across the Cycadales to generate a large number of markers for all genomic compartments, despite the large number of plastids present in a typical plant cell. Our modified protocol was adapted to be applied to cycads and other organisms with large genomes to yield many informative genome-wide markers

Industrial Relations Climate and Union Commitment: An Evaluation of Workplace-Level Effects

This paper examines the relationship between industrial relations (IR) climate and union commitment. Using a multi-workplace sample from North East England, aggregation analysis provided support for treating IR climate as a workplace-level variable, and workplace IR climate was negatively associated with union commitment. However, IR climate moderated none of the relationships between individual-level antecedents and union commitment

Characterization of 4-HNE Modified L-FABP Reveals Alterations in Structural and Functional Dynamics

4-Hydroxynonenal (4-HNE) is a reactive α,β-unsaturated aldehyde produced during oxidative stress and subsequent lipid peroxidation of polyunsaturated fatty acids. The reactivity of 4-HNE towards DNA and nucleophilic amino acids has been well established. In this report, using proteomic approaches, liver fatty acid-binding protein (L-FABP) is identified as a target for modification by 4-HNE. This lipid binding protein mediates the uptake and trafficking of hydrophobic ligands throughout cellular compartments. Ethanol caused a significant decrease in L-FABP protein (P<0.001) and mRNA (P<0.05), as well as increased poly-ubiquitinated L-FABP (P<0.001). Sites of 4-HNE adduction on mouse recombinant L-FABP were mapped using MALDI-TOF/TOF mass spectrometry on apo (Lys57 and Cys69) and holo (Lys6, Lys31, His43, Lys46, Lys57 and Cys69) L-FABP. The impact of 4-HNE adduction was found to occur in a concentration-dependent manner; affinity for the fluorescent ligand, anilinonaphthalene-8-sulfonic acid, was reduced from 0.347 µM to Kd1 = 0.395 µM and Kd2 = 34.20 µM. Saturation analyses revealed that capacity for ligand is reduced by approximately 50% when adducted by 4-HNE. Thermal stability curves of apo L-FABP was also found to be significantly affected by 4-HNE adduction (ΔTm = 5.44°C, P<0.01). Computational-based molecular modeling simulations of adducted protein revealed minor conformational changes in global protein structure of apo and holo L-FABP while more apparent differences were observed within the internal binding pocket, revealing reduced area and structural integrity. New solvent accessible portals on the periphery of the protein were observed following 4-HNE modification in both the apo and holo state, suggesting an adaptive response to carbonylation. The results from this study detail the dynamic process associated with L-FABP modification by 4-HNE and provide insight as to how alterations in structural integrity and ligand binding may a contributing factor in the pathogenesis of ALD

Relationship Between the King-Devick Test and Commonly Used Concussion Tests at Baseline

Context: Comprehensive assessments are recommended to evaluate sport-related concussion (SRC). The degree to which the King-Devick (KD) test adds novel information to an SRC evaluation is unknown. Objective: To describe relationships at baseline among the KD and other SRC assessments and explore whether the KD provides unique information to a multimodal baseline concussion assessment. Design: Cross-sectional study. Setting: Five National Collegiate Athletic Association institutions participating in the Concussion Assessment, Research and Education (CARE) Consortium. Patients or other participants: National Collegiate Athletic Association student-athletes (N = 2258, age = 20 ± 1.5 years, 53.0% male, 68.9% white) in 11 men's and 13 women's sports. Main outcome measure(s): Participants completed baseline assessments on the KD and (1) the Symptom Inventory of the Sport Concussion Assessment Tool-3rd edition, (2) the Brief Symptom Inventory-18, (3) the Balance Error Scoring System, (4) the Standardized Assessment of Concussion (SAC), (5) the Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) test battery, and (6) the Vestibular/Ocular Motor Screening tool during their first year in CARE. Correlation coefficients between the KD and the 6 other concussion assessments in isolation were determined. Assessments with ρ magnitude >0.1 were included in a multivariate linear regression analysis to evaluate their relative association with the KD. Results: Scores for SAC concentration, ImPACT visual motor speed, and ImPACT reaction time were correlated with the KD (ρ = -0.216, -0.276, and 0.164, respectively) and were thus included in the regression model, which explained 16.8% of the variance in baseline KD time (P < .001, Cohen f2 = 0.20). Better SAC concentration score (β = -.174, P < .001), ImPACT visual motor speed (β = -.205, P < .001), and ImPACT reaction time (β = .056, P = .020) were associated with faster baseline KD performance, but the effect sizes were small. Conclusions: Better performance on cognitive measures involving concentration, visual motor speed, and reaction time was weakly associated with better baseline KD performance. Symptoms, psychological distress, balance, and vestibular-oculomotor provocation were unrelated to KD performance at baseline. The findings indicate limited overlap at baseline among the CARE SRC assessments and the KD

Bifactor Model of the Sport Concussion Assessment Tool Symptom Checklist: Replication and Invariance Across Time in the CARE Consortium Sample

Background: Identifying separate dimensions of concussion symptoms may inform a precision medicine approach to treatment. It was previously reported that a bifactor model identified distinct acute postconcussion symptom dimensions. Purpose: To replicate previous findings of a bifactor structure of concussion symptoms in the Concussion Assessment Research and Education (CARE) Consortium sample, examine measurement invariance from pre- to postinjury, and evaluate whether factors are associated with other clinical and biomarker measures. Study design: Cohort study (Diagnosis); Level of evidence, 2. Methods: Collegiate athletes were prospectively evaluated using the Sport Concussion Assessment Tool-3 (SCAT-3) during preseason (N = 31,557); 2789 were followed at <6 hours and 24 to 48 hours after concussion. Item-level SCAT-3 ratings were analyzed using exploratory and confirmatory factor analyses. Bifactor and higher-order models were compared for their fit and interpretability. Measurement invariance tested the stability of the identified factor structure across time. The association between factors and criterion measures (clinical and blood-based markers of concussion severity, symptom duration) was evaluated. Results: The optimal structure for each time point was a 7-factor bifactor model: a General factor, on which all items loaded, and 6 specific factors-Vestibulo-ocular, Headache, Sensory, Fatigue, Cognitive, and Emotional. The model manifested strict invariance across the 2 postinjury time points but only configural invariance from baseline to postinjury. From <6 to 24-48 hours, some dimensions increased in severity (Sensory, Fatigue, Emotional), while others decreased (General, Headache, Vestibulo-ocular). The factors correlated with differing clinical and biomarker criterion measures and showed differing patterns of association with symptom duration at different time points. Conclusion: Bifactor modeling supported the predominant unidimensionality of concussion symptoms while revealing multidimensional properties, including a large dominant General factor and 6 independent factors: Headache, Vestibulo-ocular, Sensory, Cognitive, Fatigue, and Emotional. Unlike the widely used SCAT-3 symptom severity score, which declines gradually after injury, the bifactor model revealed separable symptom dimensions that have distinct trajectories in the acute postinjury period and different patterns of association with other markers of injury severity and outcome. Clinical relevance: The SCAT-3 total score remains a valuable, robust index of overall concussion symptom severity, and the specific factors identified may inform management strategies. Because some symptom dimensions continue to worsen in the first 24 to 48 hours after injury (ie, Sensory, Fatigue, Emotional), routine follow-up in this time frame may be valuable to ensure that symptoms are managed effectively