Drivers of vegetative dormancy across herbaceous perennial plant species

Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.     

KIBRA (WWC1) Is a Metastasis Suppressor Gene Affected by Chromosome 5q Loss in Triple-Negative Breast Cancer

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Clinical utility of tumor genomic profiling in patients with high plasma circulating tumor DNA burden or metabolically active tumors

Background

This retrospective study was undertaken to determine if the plasma circulating tumor DNA (ctDNA) level and tumor biological features in patients with advanced solid tumors affected the detection of genomic alterations (GAs) by a plasma ctDNA assay.

Method

Cell-free DNA (cfDNA) extracted from frozen plasma (N?=?35) or fresh whole blood (N?=?90) samples were subjected to a 62-gene hybrid capture-based next-generation sequencing assay FoundationACT. Concordance was analyzed for 51 matched FoundationACT and FoundationOne (tissue) cases. The maximum somatic allele frequency (MSAF) was used to estimate the amount of tumor fraction of cfDNA in each sample. The detection of GAs was correlated with the amount of cfDNA, MSAF, total tumor anatomic burden (dimensional sum), and total tumor metabolic burden (SUVmax sum) of the largest ten tumor lesions on PET/CT scans.

Results

FoundationACT detected GAs in 69 of 81 (85%) cases with MSAF >?0. Forty-two of 51 (82%) cases had ≥?1 concordance GAs matched with FoundationOne, and 22 (52%) matched to the National Comprehensive Cancer Network (NCCN)-recommended molecular targets. FoundationACT also detected 8 unique molecular targets, which changed the therapy in 7 (88%) patients who did not have tumor rebiopsy or sufficient tumor DNA for genomic profiling assay. In all samples (N?=?81), GAs were detected in plasma cfDNA from cancer patients with high MSAF quantity (P?=?0.0006) or high tumor metabolic burden (P?=?0.0006) regardless of cfDNA quantity (P?=?0.2362).

Conclusion

This study supports the utility of using plasma-based genomic assays in cancer patients with high plasma MSAF level or high tumor metabolic burden.

     

Microbial ecoenzyme stoichiometry,nutrient limitation,and organic matter decomposition in wetlands of the conterminous United States

Microbial respiration (R_m) and ecoenzyme activities (EEA) related to microbial carbon, nitrogen, and phosphorus acquisition were measured in 792 freshwater and estuarine wetlands (representing a cumulative area of 217,480 km²) across the continental United States as part of the US EPA’s 2011 National Wetland Condition Assessment. EEA stoichiometry was used to construct models for and assess nutrient limitation, carbon use efficiency (CUE), and organic matter decomposition (? k). The wetlands were classified into ten groups based on aggregated ecoregion and wetland type. The wetlands were also assigned to least, intermediate, and most disturbed classes, based on the extent of human influences. Ecoenzyme activity related to C, N and P acquisition, R_m, CUE, and ? k differed among ecoregion–wetland types and, with the exception of C acquisition and ? k, among disturbance classes. R_m and EEA were positively correlated with soil C, N and P content (r = 0.15–0.64) and stoichiometry (r = 0.15–0.48), and negatively correlated with an index of carbon quality (r = ? 0.22 to ? 0.39). EEA stoichiometry revealed that wetlands were more often P- than N-limited, and that P-limitation increases with increasing disturbance. Our enzyme-based approach for modeling C, N, and P acquisition, and organic matter decomposition, all rooted in stoichiometric theory, provides a mechanism for modeling resource limitations of microbial metabolism and biogeochemical cycling in wetlands. Given the ease of collecting and analyzing soil EEA and their response to wetland disturbance gradients, enzyme stoichiometry models are a cost-effective tool for monitoring ecosystem responses to resource availability and the environmental drivers of microbial metabolism, including those related to global climate changes.     

Patterns of dental emergence in early anthropoid primates from the Fayum Depression,Egypt

Abstract

Paleontological field work in the Fayum Depression of Egypt has produced a remarkable diversity of fossil anthropoids, and this, combined with advances in genetic analyses of living anthropoids, has led to establishment of a temporal and phylogenetic framework for anthropoids that is achieving some degree of consensus. Less well understood are the evolutionary mechanisms and selective factors behind the origin and early diversification of anthropoids. One area that has remained under explored is investigation into the life history patterns of early anthropoids, a major omission given that understanding patterns of growth and development is essential for interpreting the paleobiology of fossil species. Here we detail dental emergence sequences for five species in four families of early anthropoid primates from the Fayum, and use these data to test Schultz’s Rule concerning the timing of emergence of molars versus premolars in mammals. Two important results are generated: (1) only one species had a dental eruption sequence identical to that observed among crown catarrhine primates; and (2) in all cases, the permanent canine was the last post-incisor dental element to fully erupt, a finding that may be significant for interpreting early anthropoid behavioral strategies.     

Age and growth assessment of western North Atlantic spiny butterfly ray <Emphasis Type="Italic">Gymnura altavela</Emphasis> (L. 1758) using computed tomography of vertebral centra

Life history strategies of batoid fishes have evolved within dynamic marine ecosystems. Adaptations in reproductive and developmental biology are paramount to the survival of species, and therefore knowledge of growth rates to maturity is fundamental for identifying constraints on the conservation of populations. The butterfly rays (Myliobatiformes: Gymnuridae) are highly derived batoids with generally low reproductive potentials for which age and growth information remains unknown. In this study we applied high-resolution X-ray computed tomography (HRXCT) to vertebral centra from a stingray for the first time to estimate age, and used a multimodel approach to investigate growth of spiny butterfly ray, Gymnura altavela. Estimated ages of the oldest male and female were 11 and 18 yrs. at disk widths (WD) 1355 mm and 2150 mm, respectively. Disk width-at-age data were analyzed using three growth models (von Bertalanffy, logistic, Gompertz), and the most parsimonious and empirically supported model was the logistic function with sex treated as a fixed effect on asymptotic disk width (WD _∞ ) and k parameters. Model parameter estimates were (males) WD _∞  = 1285.46 ± 67.27 mm, k = 0.60 ± 0.10, and (females) WD _∞  = 2173.51 ± 129.78 mm, k = 0.27 ± 0.04. Results indicated sexually dimorphic growth patterns, with males growing faster and reaching asymptotic size at earlier ages than females. These age and growth results are the first reported for the genus, and suggest that G. altavela grows at a similar rate as some teleosts and batoids, and relatively fast among chondrichthyans.     

The specificity of alcohol dehydrogenase with cis-retinoids. Activity with 11-cis-retinol and localization in retina.

Studies in knockout mice support the involvement of alcohol dehydrogenases ADH1 and ADH4 in retinoid metabolism, although kinetics with retinoids are not known for the mouse enzymes. Moreover, a role of alcohol dehydrogenase (ADH) in the eye retinoid interconversions cannot be ascertained due to the lack of information on the kinetics with 11-cis-retinoids. We report here the kinetics of human ADH1B1, ADH1B2, ADH4, and mouse ADH1 and ADH4 with all-trans-, 7-cis-, 9-cis-, 11-cis- and 13-cis-isomers of retinol and retinal. These retinoids are substrates for all enzymes tested, except the 13-cis isomers which are not used by ADH1. In general, human and mouse ADH4 exhibit similar activity, higher than that of ADH1, while mouse ADH1 is more efficient than the homologous human enzymes. All tested ADHs use 11-cis-retinoids efficiently. ADH4 shows much higher k(cat)/K(m) values for 11-cis-retinol oxidation than for 11-cis-retinal reduction, a unique property among mammalian ADHs for any alcohol/aldehyde substrate pair. Docking simulations and the kinetic properties of the human ADH4 M141L mutant demonstrated that residue 141, in the middle region of the active site, is essential for such ADH4 specificity. The distinct kinetics of ADH4 with 11-cis-retinol, its wide specificity with retinol isomers and its immunolocalization in several retinal cell layers, including pigment epithelium, support a role of this enzyme in the various retinol oxidations that occur in the retina. Cytosolic ADH4 activity may complement the isomer-specific microsomal enzymes involved in photopigment regeneration and retinoic acid synthesis.     

Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization.

The identification of differential gene expressionbetween cells is a frequent goal in modern biological research. Here we demonstrate the coupling of representational difference analysis (RDA) of cDNA with microarray analysis of the output for high throughput screening. Two primary Ewing's sarcoma tissue samples with different biological behavior in vivo were compared by RDA: one which was metastatic and progressed rapidly; the other localized and successfully treated. A modified RDA protocol that minimizes the necessary starting material was employed. After a reduced number of subtractive rounds, the output of RDA was shotgun cloned into a plasmid vector. Inserts from individual colonies from the subtracted library were amplified with vector-specific primers and arrayed at high density on glass slides. The arrays were then hybridized with differentially fluorescently labeled starting amplicons from the two tissues and fluorescent signals were measured at each DNA spot. We show that the relative amounts of fluorescent signal correlate well with the abundance of fragments in the RDA amplicon and in the starting mRNA. In our system, we analyzed 192 products and 173 (90%) were appropriately detected as being >2-fold differentially expressed. Fifty unique, differentially expressed clones were identified. Therefore, the use of RDA essentially provides an enriched library of differentially expressed genes, while analysis of this library with microarrays allows rapid and reproducible screening of thousands of DNA molecules simultaneously. The coupling of these two techniques in this system resulted in a large pool of differentially expressed genes.