Increasing the number of characters used in phylogenetic studies is the next crucial step towards generating robust and stable phylogenetic hypotheses—i.e., strongly supported and consistent across ...reconstruction method. Here we describe a genomic approach to finding new protein-coding genes for systematics in nonmodel taxa, which can be PCR amplified from standard, slightly degraded genomic DNA extracts. We test this approach on Lepidoptera, searching the draft genomic sequence of the silk moth Bombyx mori, for exons > 500 bp in length, removing annotated gene families, and compared remaining exons with butterfly EST databases to identify conserved regions for primer design. These primers were tested on a set of 65 taxa primarily in the butterfly family Nymphalidae. We were able to identify and amplify six previously unused gene regions (Arginine Kinase, GAPDH, IDH, MDH, RpS2, and RpS5) and two rarely used gene regions (CAD and DDC) that when added to the three traditional gene regions (COI, EF-1α and wingless) gave a data set of 8114 bp. Phylogenetic robustness and stability increased with increasing numbers of genes. Smaller taxanomic subsets were also robust when using the full gene data set. The full 11-gene data set was robust and stable across reconstruction methods, recovering the major lineages and strongly supporting relationships within them. Our methods and insights should be applicable to taxonomic groups having a single genomic reference species and several EST databases from taxa that diverged less than 100 million years ago.
Fossil palms provide qualitative evidence of (sub-) tropical conditions and frost-free winters in the geological past, including modern cold climate regions (e.g., boreal, or polar climates). The ...freeze intolerance of palms varies across different organs and life stages, with seedlings in particular less tolerant of sub-zero temperatures than adult plants, limiting successful establishment of populations while permitting adult palms to survive in cultivation outside their natural ranges. Quantitatively, palms indicate minimum cold month mean temperature (CMMT) at 2-8 °C in palaeoclimate reconstructions. These data have accentuated model-proxy mismatches for high latitudes during Paleogene hyperthermals when palms expanded poleward in both hemispheres. We constructed a manually filtered dataset of >20,000 georeferenced Arecaceae records, by eliminating cultivars. Statistically derived mean annual temperature, mean annual temperature range, and CMMT thresholds for the Arecaceae and lower rank subfamilies and tribes reveal large differences in temperature sensitivity depending on lower taxonomic classification. Cold tolerant tribes such as the Trachycarpeae produce thresholds as low as CMMT ≥ 2.2 °C. However, within the palm family, CMMT < 5 °C is anomalous. Moreover, palm expansion into temperate biomes is likely a post-Palaeogene event. We recognize a CMMT ≥ 5.2 °C threshold for the palm family, unless a lower taxonomic rank can be assigned.
Introduction
The assessment of left‐ and right‐sided cardiac function via closed‐chest pressure‐volume loops is important to understanding and diagnosing a wide range of cardiovascular pathologies. ...In the vast majority of pre‐clinical studies, either left‐ or right‐sided heart function is assessed in isolation, or, more recently, by sequentially right‐ and left‐sided catheterization1. Synchronous biventricular catheterization would offer a significant advancement for pre‐clinical research. To date, closed‐chest synchronous biventricular pressure‐volume loops have only been obtained in a few studies, limited to porcine models2. Here, we describe initial results from what we believe to be the first synchronous biventricular pressure‐volume loops obtained in the rodent using a closed‐chest approach.
Aim
To obtain biventricular pressure‐volume loops in the anesthetized rat using a closed‐chest approach
Methods
A total of 8 Wistar rats were anesthetized with urethane (1.5mg/kg), tracheotomised, ventilated, and subsequently had a solid state catheter placed in the femoral artery to measure blood pressure, and admittance pressure‐volume catheters placed in the right‐ and left‐ventricle to obtain synchronous biventricular pressure‐volume loops. Admittance probes were set to different frequencies to avoid cross‐talk. All catheters were left to stabilize for a minimum of 10 min after which we extracted and averaged 1 minute of basal pressure‐volume indices.
Results
Reliable ventricular pressure waveforms were obtained from both the left (i.e., left‐ventricular end‐systolic pressure = 106±12mmHg) and right (i.e., right‐ventricular end systolic pressure = 28±8mmHg) side in all eight animals, and we were able to obtain standard left‐sided pressure‐volume loops from all eight animals (i.e., stroke work = 22±5mmHg/ml). We were only able to obtain reliable right‐sided pressure‐volume loops in two of eight animals, due to poor volume signals in the remaining 6 animals. In the two animals we were able to obtain synchronous pressure‐volume loops there was clear evidence of ventricular dependence across the respiratory cycle (Fig.1).
Conclusions
Obtaining synchronous biventricular pressure‐volume loops using a closed‐chest approach in rats is possible but technically challenging. Further work is needed to better obtain right‐sided ventricular volumes.
References
Potus F. et al., J. Vis. Exp (160), e61088, doi:10.3791/61088 (2020).
Lyhne MD. et al., J. Vis. Exp.(171), e62661, doi:10.3791/62661 (2021).
Seeds and the Art of Genome Maintenance Waterworth, Wanda M; Bray, Clifford M; West, Christopher E
Frontiers in plant science,
05/2019, Volume:
10
Journal Article
Peer reviewed
Open access
Successful germination represents a crucial developmental transition in the plant lifecycle and is important both for crop yields and plant survival in natural ecosystems. However, germination ...potential decreases during storage and seed longevity is a key determinant of crop production. Decline in germination vigor is initially manifest as an increasing delay to radicle emergence and the completion of germination and eventually culminating in loss of seed viability. The molecular mechanisms that determine seed germination vigor and viability remain obscure, although deterioration in seed quality is associated with the accumulation of damage to cellular structures and macromolecules including lipids, protein, and nucleic acids. In desiccation tolerant seeds, desiccation/rehydration cycles and prolonged periods in the dry quiescent state are associated with remarkable levels of stress to the embryo genome which can result in mutagenesis of the genetic material, inhibition of transcription and replication and delayed growth and development. An increasing number of studies are revealing DNA damage accumulated in the embryo genome, and the repair capacity of the seed to reverse this damage, as major factors that determine seed vigor and viability. Recent findings are now establishing important roles for the DNA damage response in regulating germination, imposing a delay to germination in aged seed to minimize the deleterious consequences of DNA damage accumulated in the dry quiescent state. Understanding the mechanistic basis of seed longevity will underpin the directed improvement of crop varieties and support preservation of plant genetic resources in seed banks.
Mesenchymal stem/stromal cells (MSCs) can regenerate tissues by direct differentiation or indirectly by stimulating angiogenesis, limiting inflammation, and recruiting tissue-specific progenitor ...cells. MSCs emerge and multiply in long-term cultures of total cells from the bone marrow or multiple other organs. Such a derivation in vitro is simple and convenient, hence popular, but has long precluded understanding of the native identity, tissue distribution, frequency, and natural role of MSCs, which have been defined and validated exclusively in terms of surface marker expression and developmental potential in culture into bone, cartilage, and fat. Such simple, widely accepted criteria uniformly typify MSCs, even though some differences in potential exist, depending on tissue sources. Combined immunohistochemistry, flow cytometry, and cell culture have allowed tracking the artifactual cultured mesenchymal stem/stromal cells back to perivascular anatomical regions. Presently, both pericytes enveloping microvessels and adventitial cells surrounding larger arteries and veins have been described as possible MSC forerunners. While such a vascular association would explain why MSCs have been isolated from virtually all tissues tested, the origin of the MSCs grown from umbilical cord blood remains unknown. In fact, most aspects of the biology of perivascular MSCs are still obscure, from the emergence of these cells in the embryo to the molecular control of their activity in adult tissues. Such dark areas have not compromised intents to use these cells in clinical settings though, in which purified perivascular cells already exhibit decisive advantages over conventional MSCs, including purity, thorough characterization and, principally, total independence from in vitro culture. A growing body of experimental data is currently paving the way to the medical usage of autologous sorted perivascular cells for indications in which MSCs have been previously contemplated or actually used, such as bone regeneration and cardiovascular tissue repair.
Consumption of globally traded agricultural commodities like soy and palm oil is one of the primary causes of deforestation and biodiversity loss in some of the world’s most species-rich ecosystems. ...However, the complexity of global supply chains has confounded efforts to reduce impacts. Companies and governments with sustainability commitments struggle to understand their own sourcing patterns,while the activities of more unscrupulous actors are conveniently masked by the opacity of global trade. We combine state-of-the-art material flow, economic trade, and biodiversity impact models to produce an innovative approach for understanding the impacts of trade on biodiversity loss and the roles of remote markets and actors.We do this for the production of soy in the Brazilian Cerrado, home to more than 5% of the worlds species. Distinct sourcing patterns of consumer countries and trading companies result in substantially different impacts on endemic species. Connections between individual buyers and specific hot spots explain the disproportionate impacts of some actors on endemic species and individual threatened species, such as the particular impact of European Union consumers on the recent habitat losses for the iconic giant anteater (Myrmecophaga tridactyla). In making these linkages explicit, our approach enables commodity buyers and investors to target their efforts much more closely to improve the sustainability of their supply chains in their sourcing regions while also transforming our ability to monitor the impact of such commitments over time.
The desiccated, quiescent state of seeds confers extended survival of the embryonic plant. However, accumulation of striking levels of genome damage in quiescence impairs germination and threatens ...plant survival. The mechanisms by which seeds mitigate this damage remain unclear. Here, we reveal that imbibed
Arabidopsis
seeds display high resistance to DNA damage, which is lost as seeds advance to germination, coincident with increasing cell cycle activity. In contrast to seedlings, we show that seeds minimize the impact of DNA damage by reducing meristem disruption and delaying SOG1-dependent programmed cell death. This promotes root growth early postgermination. In response to naturally accumulated DNA damage in aging seeds, SOG1 activates cell death postgermination. SOG1 activities are also important for promoting successful seedling establishment. These distinct cellular responses of seeds and seedlings are reflected by different DNA damage transcriptional profiles. Comparative analysis of DNA repair mutants identifies roles of the major genome maintenance pathways in germination but that the repair of cytotoxic chromosomal breaks is the most important for seed longevity. Collectively, these results indicate that high levels of DNA damage incurred in seeds are countered by low cell cycle activity, cell cycle checkpoints, and DNA repair, promoting successful seedling establishment. Our findings reveal insight into both the physiological significance of plant DNA damage responses and the mechanisms which maintain seed longevity, important for survival of plant populations in the natural environment and sustainable crop production under changing climates.
Seeds are important to agriculture and conservation of plant biodiversity. In agriculture, seed germination performance is an important determinant of crop yield, in particular under adverse climatic ...conditions. Deterioration in seed quality is associated with the accumulation of cellular damage to macromolecules including lipids, protein, and DNA. Mechanisms that mitigate the deleterious cellular damage incurred in the quiescent state and in cycles of desiccation–hydration are crucial for the maintenance of seed viability and germination vigour. In early-imbibing seeds, damage to the embryo genome must be repaired prior to initiation of cell division to minimize growth inhibition and mutation of genetic information. Here we review recent advances that have established molecular links between genome integrity and seed quality. These studies identified that maintenance of genome integrity is particularly important to the seed stage of the plant lifecycle, revealing new insight into the physiological roles of plant DNA repair and recombination mechanisms. The high conservation of DNA repair and recombination factors across plant species underlines their potential as promising targets for the improvement of crop performance and development of molecular markers for prediction of seed vigour.
PDF
