Consequences of Shifts in Abundance and Distribution of American Chestnut for Restoration of a Foundation Forest Tree

Restoration of foundation species, such as the American chestnut (Castanea dentata) that was devastated by an introduced fungus, can restore ecosystem function. Understanding both the current distribution as well as biogeographic patterns is important for restoration planning. We used United States Department of Agriculture Forest Service Forest Inventory and Analysis data to quantify the current density and distribution of C. dentata. We then review the literature concerning biogeographic patterns in C. dentata. Currently, 431 +/- 30.2 million stems remain. The vast majority (360 +/- 22 million) are sprouts \u3c 2.5 cm dbh. Although this number is approximately 10% of the estimated pre-blight population, blight has caused a major shift in the size structure. The current-day population has a larger range, particularly west and north, likely due to human translocation. While climate change could facilitate northward expansion, limited seed reproduction makes this unlikely without assisted migration. Previous research demonstrates that the current, smaller population contains slightly higher genetic diversity than expected, although little information exists on biogeographic patterns in the genetics of adaptive traits. Our research provides a baseline characterization of the contemporary population of C. dentata, to enable monitoring stem densities and range limits to support restoration efforts

Analysis of environment-marker associations in American chestnut

American chestnut (Castanea dentata Borkh.) was a dominant tree species in its native range in eastern North America until the accidentally introduced fungus Cryphonectria parasitica (Murr.) Barr, that causes chestnut blight, led to a collapse of the species. Different approaches (e.g., genetic engineering or conventional breeding) are being used to fight against chestnut blight and to reintroduce the species with resistant planting stock. Because of large climatic differences within the distribution area of American chestnut, successful reintroduction of the species requires knowledge and consideration of local adaptation to the prevailing environmental conditions. Previous studies revealed clear patterns of genetic diversity along the northeast-southwest axis of the Appalachian Mountains, but less is known about the distribution of potentially adaptive genetic variation within the distribution area of this species. In this study, we investigated neutral and potentially adaptive genetic variation in nine American chestnut populations collected from sites with different environmental conditions. In total, 272 individuals were genotyped with 24 microsatellite (i.e., simple sequence repeat (SSR)) markers (seven genomic SSRs and 17 EST-SSRs). An FST-outlier analysis revealed five outlier loci. The same loci, as well as five additional ones, were significantly associated with environmental variables of the population sites in an environmental association analysis. Four of these loci are of particular interest, since they were significant in both methods, and they were associated with environmental variation, but not with geographic variation. Hence, these loci might be involved in (temperature-related) adaptive processes in American chestnut. This work aims to help understanding the genetic basis of adaptation in C. dentata, and therefore the selection of suitable provenances for further breeding efforts

A conceptual framework for restoration of threatened plants: the effective model of American chestnut (Castanea dentata) reintroduction

We propose a conceptual framework for restoration of threatened plant species that encourages integration of technological, ecological, and social spheres. A sphere encompasses ideas relevant to restoration and the people working within similar areas of influence or expertise. Increased capacity within a sphere and a higher degree of coalescing among spheres predict a greater probability of successful restoration. We illustrate this with Castanea dentata, a foundation forest tree in North America that was annihilated by an introduced pathogen; the species is a model that effectively merges biotechnology, reintroduction biology, and restoration ecology. Because of C. dentata\u27s ecological and social importance, scientists have aggressively pursued blight resistance through various approaches. We summarize recent advancements in tree breeding and biotechnology that have emerged from C. dentata research, and describe their potential to bring new tools to bear on socio-ecological restoration problems. Successful reintroduction of C. dentata will also depend upon an enhanced understanding of its ecology within contemporary forests. We identify a critical need for a deeper understanding of societal influences that may affect setting and achieving realistic restoration goals. Castanea dentata may serve as an important model to inform reintroduction of threatened plant species in general and foundation forest trees in particular

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)

BACKGROUND: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. RESULTS: The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r(2)) between pairs of SNPs linked within single scaffolds decaying to half maximum (r(2) = 0.22) within 55 bp, to r(2) = 0.1 within 192 bp, and to r(2) = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. CONCLUSIONS: The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users

TDP-43 Proteinopathy in Aging: Associations with Risk-Associated Gene Variants and with Brain Parenchymal Thyroid Hormone Levels

TDP-43 proteinopathy is very prevalent among the elderly (affecting at least 25% of individuals over 85 years of age) and is associated with substantial cognitive impairment. Risk factors implicated in age-related TDP-43 proteinopathy include commonly inherited gene variants, comorbid Alzheimer\u27s disease pathology, and thyroid hormone dysfunction. To test parameters that are associated with aging-related TDP-43 pathology, we performed exploratory analyses of pathologic, genetic, and biochemical data derived from research volunteers in the University of Kentucky Alzheimer\u27s Disease Center autopsy cohort (n = 136 subjects). Digital pathologic methods were used to discriminate and quantify both neuritic and intracytoplasmic TDP-43 pathology in the hippocampal formation. Overall, 46.4% of the cases were positive for TDP-43 intracellular inclusions, which is consistent with results in other prior community-based cohorts. The pathologies were correlated with hippocampal sclerosis of aging (HS-Aging) linked genotypes. We also assayed brain parenchymal thyroid hormone (triiodothyronine [T3] and thyroxine [T4]) levels. In cases with SLCO1A2/IAPP or ABCC9 risk associated genotypes, the T3/T4 ratio tended to be reduced (p = .051 using 2-tailed statistical test), and in cases with low T3/T4 ratios (bottom quintile), there was a higher likelihood of HS-Aging pathology (p = .025 using 2-tailed statistical test). This is intriguing because the SLCO1A2/IAPP and ABCC9 risk associated genotypes have been associated with altered expression of the astrocytic thyroid hormone receptor (protein product of the nearby gene SLCO1C1). These data indicate that dysregulation of thyroid hormone signaling may play a role in age-related TDP-43 proteinopathy

Genetic Variation in an Individual Human Exome

There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's ‘exome,’ which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the ∼12,500 variants that affect the protein coding portion of an individual's genome. We identified ∼10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ∼15–20% are rare in the human population. We predict ∼1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the ∼700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of ∼12,500 nonsilent coding variants by ∼8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation

Renal Dysfunction Criteria in Critically Ill Children: The PODIUM Consensus Conference

CONTEXT Renal dysfunction is associated with poor outcomes in critically ill children. OBJECTIVE To evaluate the current evidence for criteria defining renal dysfunction in critically ill children and association with adverse outcomes. To develop contemporary consensus criteria for renal dysfunction in critically ill children. DATA SOURCES PubMed and Embase were searched from January 1992 to January 2020. STUDY SELECTION Included studies evaluated critically ill children with renal dysfunction, performance characteristics of assessment tools for renal dysfunction, and outcomes related to mortality, functional status, or organ-specific or other patient-centered outcomes. Studies with adults or premature infants (≤36 weeks' gestational age), animal studies, reviews, case series, and studies not published in English with inability to determine eligibility criteria were excluded. DATA EXTRACTION Data were extracted from included studies into a standard data extraction form by task force members. RESULTS The systematic review supported the following criteria for renal dysfunction: (1) urine output <0.5 mL/kg per hour for ≥6 hours and serum creatinine increase of 1.5 to 1.9 times baseline or ≥0.3 mg/dL, or (2) urine output <0.5 mL/kg per hour for ≥12 hours, or (3) serum creatinine increase ≥2 times baseline, or (4) estimated glomerular filtration rate <35 mL/minute/1.73 m2, or (5) initiation of renal replacement therapy, or (6) fluid overload ≥20%. Data also support criteria for persistent renal dysfunction and for high risk of renal dysfunction. LIMITATIONS All included studies were observational and many were retrospective. CONCLUSIONS We present consensus criteria for renal dysfunction in critically ill children

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

BACKGROUND: Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. RESULTS: The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM((Kosambi)) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, H(e), among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. CONCLUSIONS: Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda

Detection of blast-related traumatic brain injury in U.S. military personnel

BACKGROUND: Blast-related traumatic brain injuries have been common in the Iraq and Afghanistan wars, but fundamental questions about the nature of these injuries remain unanswered. METHODS: We tested the hypothesis that blast-related traumatic brain injury causes traumatic axonal injury, using diffusion tensor imaging (DTI), an advanced form of magnetic resonance imaging that is sensitive to axonal injury. The subjects were 63 U.S. military personnel who had a clinical diagnosis of mild, uncomplicated traumatic brain injury. They were evacuated from the field to the Landstuhl Regional Medical Center in Landstuhl, Germany, where they underwent DTI scanning within 90 days after the injury. All the subjects had primary blast exposure plus another, blast-related mechanism of injury (e.g., being struck by a blunt object or injured in a fall or motor vehicle crash). Controls consisted of 21 military personnel who had blast exposure and other injuries but no clinical diagnosis of traumatic brain injury. RESULTS: Abnormalities revealed on DTI were consistent with traumatic axonal injury in many of the subjects with traumatic brain injury. None had detectible intracranial injury on computed tomography. As compared with DTI scans in controls, the scans in the subjects with traumatic brain injury showed marked abnormalities in the middle cerebellar peduncles (P<0.001), in cingulum bundles (P = 0.002), and in the right orbitofrontal white matter (P = 0.007). In 18 of the 63 subjects with traumatic brain injury, a significantly greater number of abnormalities were found on DTI than would be expected by chance (P<0.001). Follow-up DTI scans in 47 subjects with traumatic brain injury 6 to 12 months after enrollment showed persistent abnormalities that were consistent with evolving injuries. CONCLUSIONS: DTI findings in U.S. military personnel support the hypothesis that blast-related mild traumatic brain injury can involve axonal injury. However, the contribution of primary blast exposure as compared with that of other types of injury could not be determined directly, since none of the subjects with traumatic brain injury had isolated primary blast injury. Furthermore, many of these subjects did not have abnormalities on DTI. Thus, traumatic brain injury remains a clinical diagnosis. (Funded by the Congressionally Directed Medical Research Program and the National Institutes of Health; ClinicalTrials.gov number, NCT00785304.