•Temperate, C4 warm season grasses are being developed as bioenergy crops.•Switchgrass is among the best understood among these species.•These grasses undergo seasonal cycling through dormancy and ...regrowth.•Need data on mechanisms impacting dormancy and winter survival in switchgrass.•Common elements could control phenology of shoot development and rhizome dormancy.
Perennial, temperate, C4 grasses, such as switchgrass and miscanthus have been tabbed as sources of herbaceous biomass for the production of green fuels and chemicals based on a number of positive agronomic traits. Although there is important literature on the management of these species for biomass production on marginal lands, numerous aspects of their biology are as yet unexplored at the molecular level. Perenniality, a key agronomic trait, is a function of plant dormancy and winter survival of the below-ground parts of the plants. These include the crowns, rhizomes and meristems that will produce tillers. Maintaining meristem viability is critical for the continued survival of the plants. Plant tillers emerge from the dormant crown and rhizome meristems at the start of the growing period in the spring, progress through a phase of vegetative growth, followed by flowering and eventually undergo senescence. There is nutrient mobilization from the aerial portions of the plant to the crowns and rhizomes during tiller senescence. Signals arising from the shoots and from the environment can be expected to be integrated as the plants enter into dormancy. Plant senescence and dormancy have been well studied in several dicot species and offer a potential framework to understand these processes in temperate C4 perennial grasses. The availability of latitudinally adapted populations for switchgrass presents an opportunity to dissect molecular mechanisms that can impact senescence, dormancy and winter survival. Given the large increase in genomic and other resources for switchgrass, it is anticipated that projected molecular studies with switchgrass will have a broader impact on related species.
Germline mutation rates in humans have been estimated for a variety of mutation types, including single-nucleotide and large structural variants. Here, we directly measure the germline ...retrotransposition rate for the three active retrotransposon elements: L1,
, and SVA. We used three tools for calling mobile element insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. We identified 26 de novo MEIs in 437 births. The retrotransposition rate estimates for
elements, one in 40 births, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude similar to that observed for single-nucleotide variants. The L1 retrotransposition rate is one in 63 births and is within range of previous estimates (1:20-1:200 births). The SVA retrotransposition rate, one in 63 births, is much higher than the previous estimate of one in 900 births. Our large, three-generation pedigrees allowed us to assess parent-of-origin effects and the timing of insertion events in either gametogenesis or early embryonic development. We find a statistically significant paternal bias in
retrotransposition. Our study represents the first in-depth analysis of the rate and dynamics of human retrotransposition from WGS data in three-generation human pedigrees.
Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, ...Huntington disease, and fragile X syndrome. Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. These pedigrees contain both sets of grandparents, the parents, and an average of 9 grandchildren per family.
We use HipSTR to identify de novo STR mutations in the 2nd generation of these pedigrees and require transmission to the third generation for validation. Analyzing approximately 1.6 million STR loci, we estimate the empirical de novo STR mutation rate to be 5.24 × 10
mutations per locus per generation. Perfect repeats mutate about 2 × more often than imperfect repeats. De novo STRs are significantly enriched in Alu elements.
Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. Phasing these mutations to the parent of origin shows that parental transmission biases vary among families. We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants.
The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across ...families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.
ObjectivesThe aim of the study was to understand the experiences of living with multiple chronic conditions (MCC) from the perspective of community-living older adults with MCC.DesignA qualitative ...study using an interpretive description approach.SettingParticipants were recruited from southern Ontario, Canada.Participants21 community-living, older adults (≥65 years) with an average of 7.4 chronic conditions including one of diabetes, dementia or stroke.MethodsData were collected through digitally-recorded, in-depth, semi-structured in-person interviews. Interview transcripts were analysed and coded using Thorne’s interpretive description approach.ResultsFive themes were identified representing older adults' experiences of living with MCC: (a) trying to stay healthy while living with MCC, (b) depending on family caregivers for support with just about everything, (c) paying the high costs of living with MCC, (d) making healthcare decisions by proxy and (e) receiving healthcare services that do not address the complex needs of persons living with MCC.ConclusionsThe experience of living with MCC in the community was complex and multi-faceted. The need for a person-centred and family-centred approach to care in the community, which includes the coordination of health and social services that are tailored to the needs of older adults and their informal caregivers, was underscored. Such an approach would facilitate improved information-sharing and discussion of care management options between health professionals and their patients, enable older adults with MCC to actively engage in priority-setting and decision-making and may result in improved health and quality of life for older adults with MCC.
Like other complex multicellular organisms, plants are composed of different cell types with specialized shapes and functions. For example, most laminar leaves consist of multiple photosynthetic cell ...types. These cell types include the palisade mesophyll, which typically forms one or more cell layers on the adaxial side of the leaf. Despite their importance for photosynthesis, we know little about how palisade cells differ at the molecular level from other photosynthetic cell types. To this end, we have used a combination of cell-specific profiling using fluorescence-activated cell sorting and single-cell RNA-sequencing methods to generate a transcriptional blueprint of the palisade mesophyll in Arabidopsis thaliana leaves. We find that despite their unique morphology, palisade cells are otherwise transcriptionally similar to other photosynthetic cell types. Nevertheless, we show that some genes in the phenylpropanoid biosynthesis pathway have both palisade-enriched expression and are light-regulated. Phenylpropanoid gene activity in the palisade was required for production of the ultraviolet (UV)-B protectant sinapoylmalate, which may protect the palisade and/or other leaf cells against damaging UV light. These findings improve our understanding of how different photosynthetic cell types in the leaf can function uniquely to optimize leaf performance, despite their transcriptional similarities.
In response to touch, some carnivorous plants such as the Venus flytrap have evolved spectacular movements to capture animals for nutrient acquisition. However, the molecules that confer this ...sensitivity remain unknown. We used comparative transcriptomics to show that expression of three genes encoding homologs of the MscS-Like (MSL) and OSCA/TMEM63 family of mechanosensitive ion channels are localized to touch-sensitive trigger hairs of Venus flytrap. We focus here on the candidate with the most enriched expression in trigger hairs, the MSL homolog FLYCATCHER1 (FLYC1). We show that
transcripts are localized to mechanosensory cells within the trigger hair, transfecting
induces chloride-permeable stretch-activated currents in naïve cells, and transcripts coding for
homologs are expressed in touch-sensing cells of Cape sundew, a related carnivorous plant of the Droseraceae family. Our data suggest that the mechanism of prey recognition in carnivorous Droseraceae evolved by co-opting ancestral mechanosensitive ion channels to sense touch.
Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the ...level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects' DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European-American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.
Hydrogen peroxide (H₂O₂) as a source of reactive oxygen species (ROS) significantly stimulated germination of switchgrass (Panicum virgatum L.) seeds with an optimal concentration of 20 mM at both 25 ...and 35°C. For non-dormant switchgrass seeds exhibiting different levels of germination, treatment with H₂O₂ resulted in rapid germination (<3 days) of all germinable seeds as compared to seeds placed on water. Exposure to 20 mM H₂O₂ elicited simultaneous growth of the root and shoot system, resulting in more uniform seedling development. Seeds of big bluestem (Andropogon gerardii Vitman) and indiangrass Sorghastrum nutans (L.) Nash also responded positively to H₂O₂ treatment, indicating the universality of the effect of H₂O₂ on seed germination in warm-season prairie grasses. For switchgrass seeds, abscisic acid (ABA) and the NADPH-oxidase inhibitor, diphenyleneiodonium (DPI) at 20 μM retarded germination (radicle emergence), stunted root growth and partially inhibited NADPH-oxidase activity in seeds. H₂O₂ reversed the inhibitory effects of DPI and ABA on germination and coleoptile elongation, but did not overcome DPI inhibition of root elongation. Treatment with H₂O₂ appeared to enhance endogenous production of nitric oxide, and a scavenger of nitric oxide abolished the peroxide-responsive stimulation of switchgrass seed germination. The activities and levels of several proteins changed earlier in seeds imbibed on H₂O₂ as compared to seeds maintained on water or on ABA. These data demonstrate that seed germination of warm-season grasses is significantly responsive to oxidative conditions and highlights the complex interplay between seed redox status, ABA, ROS and NO in this system.
Osteoporosis is one of the most under-diagnosed and under-treated health conditions in Canada. This study questioned whether an invitation to self-refer for osteoporosis risk evaluation would improve ...the number of patients who were tested for bone mineral density (BMD) at a rural Primary Health Care Center (PHCC).
The purpose of this study is to improve osteoporosis care and decrease bone fracture risk in a population of patients 65 years of age and older.
A quasi-experimental research design was used to review screening rates of BMD testing and identified patients in this population who were at low, moderate, and high risk for developing osteoporosis. Screening rates at the PHCC were compared to screening rates at another rural PHCC in the province.
The self-referral program for BMD testing and a nurse-led intervention resulted in an increased number of people who were BMD tested at the study PHCC compared with the control PHCC, and identified more male patients 65 years of age and older who were at risk for osteoporosis and bone fractures. Recommendations suggest future research in other provincial PHCCs that may encourage self-referral programs for BMD testing and improved osteoporosis care for patients 65 years of age and older.
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