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

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

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

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

Do environmental factors affect the taxonomic reliability of leaf cuticular micromorphological characters? : a case study in Podocarpaceae

Leaf cuticle micromorphology has been cited as an important set of taxonomic characters in gymnosperms, but previous studies have largely been based on small sample sizes. The premise of this study was to understand whether external factors affect cuticular micromorphology of Podocarpaceae. Two example species, Prumnopitys andina and Podocarpus salignus, were studied. Of 21 sampled characters, nine (c.43% of the total) were visually assessed as being moderately reliable or highly reliable for taxonomic discrimination for both species, with an additional six (c.29%) being moderately reliable or highly reliable for only one or other of the example species, and six characters (c.29%) unreliable for both. Seven of the most variable stomatal characters were selected for further analysis to establish whether environmental factors affect them. The relationship between these seven stomatal characters, the environment and climate was analysed using the R 'vegan' package and climate data gathered from WorldClim. Our results showed that both species had larger stomata in moist and shady conditions, and a higher density of (smaller) stomata in sunny and drier conditions. An additional novel finding was the presence of stomata on the adaxial leaf surface in 46% of samples of Prumnopitys andina: the first record of adaxial stomata in this species, highlighting the necessity of studying multiple samples of a given species. In conclusion, these results indicate that larger sample sizes than have hitherto been employed in cuticle micromorphological studies are necessary to fully document the amount of phenotypic variation that exists

Morphological and molecular evidence refute a broad circumscription for Pultenaea glabra (Fabaceae: Mirbelieae), with implications for taxonomy, biogeography, and conservation

Morphological and single-nucleotide polymorphism data support splitting Pultenaea glabra Benth. into eight species, including one in Victoria, and seven in eastern and northern New South Wales. Six species are newly described, five of which are, like P. glabra, narrow-range endemics within the Greater Blue Mountains World Heritage Area and adjacent sandstone landforms of the Great Dividing Range. The recognition of six new species from what was broadly P. glabra has implications for conservation management, including for P. glabra itself, which has a smaller distribution and more precise habitat requirements than previously thought. One of the new species, P. percussa, is known by a single 1971 gathering only. The occurrence of several narrow-range Blue Mountains endemic Pultenaea species may be explained by the combination of edaphic diversity and topographic complexity, which could act in concert to promote divergences among small, allopatric populations. Hybrids between P. glabra and P. flexilis Sm. are documented for the first time; however, limited evidence for introgression between the two species was observed. The following new taxa are described: Pultenaea aculeata M.A.M.Renner, P.H.Weston & S.Clarke, Pultenaea percussa M.A.M.Renner & P.H.Weston, Pultenaea furcata M.A.M.Renner & R.L.Barrett, Pultenaea mutabilis M.A.M.Renner & P.H.Weston, Pultenaea mutabilis var. angusta M.A.M.Renner, P.H.Weston, & S.Clarke, Pultenaea praecipua M.A.M.Renner & P.H.Weston, Pultenaea praecipua subsp. temperata M.A.M.Renner & R.L.Barrett, and Pultenaea tenebrosa M.A.M.Renner, P.H.Weston & S.Clarke. Lectotypes are designated for Pultenaea villosa var. glabrescens Benth. and Pultenaea weindorferi Reader

Species relationships and phylogenetic diversity of the African genus Encephalartos Lehm. (Zamiaceae)

The African endemic cycad genus Encephalartos consists of 68 extant taxa, that are of great conservation concern as 85% are threatened (CR, EN, or VU) and four, are extinct in the wild (EW). Due to there being no formally published monographs for the genus, there is lack of consensus on taxonomically significant characters. This lack of clarity regarding the species relationships and access to several taxa have made researching this group challenging. Nevertheless, numerous studies have proven that this genus has low levels of genetic variation over a wide distribution. The aim of this study was to produce the most robust phylogenetic reconstruction of Encephalartos to date. This was done by using markers from three different genomes – plastid (rbcL, matK-trnK, trnH-psbA, cab), mitochondrial (nad1) and nuclear (26S, AGAMOUS, NEEDLY, nrITS1) – for all currently accepted taxa. The results obtained show an increase in resolution for both the backbone and species level relationships compared to previous work. This genus can be separated into five new geographic groups – northern African, central African, eastern African, Mozambican-Zimbabwean, and southern African. There is also an indication that the evolution of the southern African group is driven by a form of reproductive isolation. Further studies on this group should be approached systematically based on the foundation provided by the linages that are shown in this study

A Normative Reference vs. Baseline Testing Compromise for ImPACT: The CARE Consortium Multiple Variable Prediction (CARE-MVP) Norms

Sports medicine clinicians routinely use computerized neurocognitive testing in sport-related concussion management programs. Debates continue regarding the appropriateness of normative reference comparisons versus obtaining individual baseline assessments, particularly for populations with greater likelihood of having below- or above-average cognitive abilities. Improving normative reference methods could offer alternatives to perceived logistical and financial burdens imposed by universal baseline testing. To develop and validate the Concussion Assessment, Research, and Education (CARE) Consortium Multiple Variable Prediction (MVP) norms for the Immediate Postconcussion Assessment and Cognitive Testing (ImPACT). We developed the CARE-MVP norms for ImPACT composite scores using regression-based equations. Predictor variables included sex, race (white/Caucasian, black/African American, Asian, or Multiple Races), medical history [attention-deficit/hyperactivity disorder (ADHD), learning disorder (LD), prior concussion(s), prior psychiatric diagnosis], and an estimate of premorbid intellect (Wechsler Test of Adult Reading). CARE-MVP norms were first validated in an independent sample of healthy collegiate athletes by comparing predicted and actual baseline test scores using independent-samples t-tests and Cohen's d effect sizes. We then evaluated base rates of low scores in athletes self-reporting ADHD/LD (vs. non-ADHD/LD) and black/African American race (vs. white/Caucasian) across multiple normative reference methods (Chi square, Cramer's V effect size). Lastly, we validated the CARE-MVP norms in a concussed sample (dependent samples t test, Cohen's d effect size). A total of 5233 collegiate athletes (18.8 ± 1.2 years, 70.5% white/Caucasian, 39.1% female) contributed to the CARE-MVP norms (development N = 2616; internal validation N = 2617). Race and WTAR score were the strongest and most consistent ImPACT score predictors. There were negligible mean differences between observed and predicted (CARE-MVP) baseline scores (Cohen's d < 0.1) for all ImPACT composite scores except Reaction Time (predicted ~ 20 ms faster than observed, d = - 0.28). Low score base rates were similar for athletes across subpopulations when using CARE-MVP norms (ADHD/LD, V = 0.017-0.028; black/African American, V = 0.043-0.053); while, other normative reference methods resulted in disproportionately higher rates of low scores (ADHD/LD, V = 0.062-0.101; black/African American race, V = 0.163-0.221). Acute (24-48 h) postconcussion ImPACT scores were significantly worse than CARE-MVP norms but notably varied as a function of concussion symptom severity. Results support CARE-MVP norm use in populations typically underrepresented or not adjusted for in traditional normative reference samples, such as those self-reporting ADHD/LD or black/African American race. CARE-MVP norms improve upon prior normative methods and may offer a practical, simple alternative for collegiate institutions concerned about logistical and financial burden associated with baseline testing. An automated scoring program is provided