Scat DNA as a non-invasive method for estimating the abundance of the vulnerable mala (Lagorchestes hirsutus)

Context: Population-monitoring programs often use direct (e.g. live capture or spotlighting) or indirect (e.g. scats sightings) observations to estimate population abundance. Such methods, however, are often inadequate for rare, elusive, or cryptic species due to the difficulty in achieving sufficient encounters or detection rates. The mala (Lagorchestes hirsutus), a small native Australian macropod, listed as Vulnerable by the IUCN, is difficult to capture, susceptible to capture myopathy, and not easily sighted in their dense habitat; consequently, the population size cannot always be estimated. The use of molecular markers to identify individual genotypes from non-invasively collected samples is increasingly being used in wildlife conservation and may be an alternative approach for mala. Aim: The aim of this study was to evaluate the efficacy of non-invasive scat DNA sampling to estimate the population abundance of mala. Methods: A panel of microsatellite markers was developed for the identification of individual mala via profiling of their scats. Scats were systematically collected from a wild mala population located in an 1100-ha fenced reserve in Western Australia. Individual genotypes were determined using the microsatellite markers, and the abundance of mala was estimated using the genotypes with spatially explicit capture–recapture (SECR) and mark–resight analyses. Key results: The genetic markers proved variable and with sufficient exclusionary power to confidently identify unique individuals (mean locus genotyping error rate: 3.1%). Individual genetic identification from scat sampling, when used with traditional mark–recapture/resight analytical models, provides feasible estimates of population abundance. This is the first reliable abundance estimate of this mala population, suggesting a \u3e70% increase in population size since the initial reintroduction of 64 individuals in 2011–13. Conclusions: Given the inherent difficulties in surveying mala, this approach would be valuable to ensure effective monitoring of the few remaining fenced and island mala populations to prevent further decline of this vulnerable species. Implications: This is the first study to identify species-specific microsatellite markers for mala and use genetic-capture sampling with scat DNA to estimate the abundance of a mala population. The study provides an evaluation of a valuable species monitoring technique that can be applied to other rare, elusive, or cryptic threatened species

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFb signaling, p53 and beta-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy

Profiling the word reading abilities of school-age children with neurofibromatosis type 1

Objective: Reading difficulties are one of the most significant challenges for children with neurofibromatosis type 1 (NF1). The aims of this study were to identify and categorize the types of reading impairments experienced by children with NF1 and to establish predictors of poor reading in this population. Method: Children aged 7–12 years with NF1 (n = 60) were compared with typically developing children (n = 36). Poor word readers with NF1 were classified according to impairment type (i.e., phonological, surface, mixed), and their reading subskills were compared. A hierarchical multiple regression was conducted to identify predictors of word reading. Results: Compared to controls, children with NF1 demonstrated significantly poorer literacy abilities. Of the 49 children with NF1 classified as poor readers, 20 (41%) were classified with phonological dyslexia, 24 (49%) with mixed dyslexia, and 5 (10%) fell outside classification categories. Children with mixed dyslexia displayed the most severe reading impairments. Stronger working memory, better receptive language, and fewer inattentive behaviors predicted better word reading skills. Conclusions: The majority of children with NF1 experience deficits in key reading skills which are essential for them to become successful readers. Weaknesses in working memory, receptive language, and attention are associated with reading difficulties in children with NF1

Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia

Phylogeographic patterns of trees in topographically subdued, unglaciated landscapes are under-reported, and might reflect population persistence and the influences of environment and distance over historical (~2.6Mya-present) and contemporary (recent generations) time-scales. We examined this hypothesis using genetic analyses of four slowly evolving non-coding chloroplast sequences and 16 nuclear microsatellites in the tree Corymbia calophylla from south-western Australia that has been unglaciated since the Permian (.300-250Mya). We found strong population differentiation for chloroplast DNA and low differentiation for nuclear loci, consistent with higher gene flow by pollen than seed. We identified three divergent chloroplast lineages distributed in central, north and south geographic regions, and diversifying from the early (.3.028Mya), mid- (.0.793Mya) and late- (.0.426Mya) Pleistocene, respectively. Moderate-high nucleotide diversity with population-specific haplotypes supported long-term persistence but diversification of lineages provided evidence of unexpected episodic range expansion. We suggest this pattern reflects environmental influences of climatic oscillations during progressive drying of south-western Australia from the early Pleistocene. Significant tests for isolation by environment for nuclear loci also supported an influence of contemporary environmental (aridity) conditions on genetic structure, but isolation by distance (IBD) was greater. Significant chloroplast and nuclear IBD suggested distance was a major influence on gene flow at both time-scales

Ccal_genotypes_2017

Tab delimited text file of nuclear microsatellite genotypes at 16 loci of 24 individual adult trees from each of 27 populations of Corymbia calophylla (Lindl.) K.D. Hill & L.A.S. Johnson (Myrtaceae) from Western Australia. Coordinate reference system is GDA94. Missing = 0

Phonics training improves reading in children with neurofibromatosis type 1 : a prospective intervention trial

Objective: To examine the efficacy of a phonics-training program in children with neurofibromatosis type 1 (NF1) and reading difficulties. Study design: Thirty children (7-12 years of age) with NF1 completed a double-baseline, 24-week intervention trial. Literacy outcome measures were assessed at 4 time points: (1) at baseline; (2) after an 8-week no-treatment period; (3) immediately post-treatment; and (4) at follow-up 8 weeks post-treatment. Repeated-measures ANOVA were conducted to examine change over time for all outcome measures, and significant main effects were explored with planned comparisons. Predictors of treatment effects were examined by linear regressions. Results: Ninety percent of participants completed the intervention. Intervention-specific improvements were observed across a range of literacy outcomes, including reading accuracy (nonword reading, Cohen d = 1.10; regular-word reading, Cohen d = 0.32), letter-sound knowledge (Cohen d = 0.80), blending (Cohen d = 0.88), repetition of nonsense words (Cohen d = 0.94), phonemic decoding fluency (Cohen d = 0.55), and reading comprehension (Cohen d = 0.31). Improvements were maintained 8 weeks post-treatment. Age (P = .03) and working memory (P = .02) significantly influenced efficacy, with greatest improvements observed in older children with stronger verbal working memory capacity. Conclusions: Home-based, computerized reading intervention was effective in improving the reading and reading-related abilities of children with NF1 and reading difficulty. Trial registration: Australian and New Zealand Clinical Trials Registry: ACTRN12611000779976.8 page(s

A.ancistrocarpa sequence data

Chloroplast sequence data for A. ancistrocarpa in Nexus forma