Large, long range tensile forces drive convergence during

Indirect evidence suggests that blastopore closure during gastrulation of anamniotes, including amphibians such as Xenopus laevis, depends on circumblastoporal convergence forces generated by the marginal zone (MZ), but direct evidence is lacking. We show that explanted MZs generate tensile convergence forces up to 1.5 mN during gastrulation and over 4 mN thereafter. These forces are generated by convergent thickening (CT) until the midgastrula and increasingly by convergent extension (CE) thereafter. Explants from ventralized embryos, which lack tissues expressing CE but close their blastopores, produce up to 2 mN of tensile force, showing that CT alone generates forces sufficient to close the blastopore. Uniaxial tensile stress relaxation assays show stiffening of mesodermal and ectodermal tissues around the onset of neurulation, potentially enhancing long-range transmission of convergence forces. These results illuminate the mechanobiology of early vertebrate morphogenic mechanisms, aid interpretation of phenotypes, and give insight into the evolution of blastopore closure mechanisms. © Shook et al

SpMyb functions as an intramodular repressor to regulate spatial expression of CyIIIa in sea urchin embryos

The CyIIIa actin gene of Strongylocentrotus purpuratus is transcribed exclusively in the embryonic aboral ectoderm, under the control of 2.3 kb cis-regulatory domain that contains a proximal module that controls expression in early embryogenesis, and a middle module that controls expression in later embryogenesis. Previous studies demonstrated that the SpRunt-1 target site within the middle module is required for the sharp increase in CyIIIa transcription which accompanies differentiation of the aboral ectoderm, and that a negative regulatory region near the SpRunt-1 target site is required to prevent ectopic transcription in the oral ectoderm and skeletogenic mesenchyme. This negative regulatory region contains a consensus binding site for the myb family of transcription factors. In vitro DNA-binding experiments reveal that a protein in blastula-stage nuclei interacts specifically with the myb target site. Gene transfer experiments utilizing CyIIIa reporter constructs containing oligonucleotide substitutions indicate that this site is both necessary and sufficient to prevent ectopic expression of CyIIIa. Synthetic oligonucleotides containing the myb target site were used to purify a protein from sea urchin embryo nuclear extracts by affinity chromatography. This protein is immunoprecipitated by antibodies specific to the evolutionarily conserved myb domain, and amino acid sequences obtained from the purified protein were found to be identical to sequences within the myb domain. Sequence information was used to obtain cDNA clones of SpMyb, the S. purpuratus member of the myb family of transcription factors. Through interactions within the middle module, SpMyb functions to repress activation of CyIIIa in the oral ectoderm and skeletogenic mesenchyme

Studies on Nucleic Acid Reassociation Kinetics: Retarded Rate of Hybridization of RNA with Excess DNA

The rate of reaction of excess double-stranded bacteriophage phi X174 and plasmid RSF2124 DNA drivers with enzymatically synthesized asymmetric RNA tracers was measured. Other reactions were carried out with excess Escherichia coli DNA and E. coli RNA labeled in vivo. RNA and DNA fragment lengths were held approximately equal. For each case it was shown that in DNA excess the rate constant for RNA· DNA hybridization is 3- to 4.5-fold lower than that of the renaturation rate constant for the driver DNA. This retardation was also observed in pseudo-first-order hybridization reactions driven by excess strand-separated RSF2124 DNA. It was concluded that the rate constant for RNA· DNA hybridization depends partially on which species is in excess

Inventories and scenarios of nitrous oxide emissions

Effective mitigation for N₂O emissions, now the third most important anthropogenic greenhouse gas and the largest remaining anthropogenic source of stratospheric ozone depleting substances, requires understanding of the sources and how they may increase this century. Here we update estimates and their uncertainties for current anthropogenic and natural N₂O emissions and for emissions scenarios to 2050. Although major uncertainties remain, ‘bottom-up’ inventories and‘top-down’ atmospheric modeling yield estimates that are in broad agreement. Global natural N₂O emissions are most likely between 10 and 12 Tg N2O-N yr˄−1. Net anthropogenic N₂O emissions are now about 5.3 Tg N₂O-N yr˄−1. Gross anthropogenic emissions by sector are 66% from agriculture, 15% from energy and transport sectors, 11% from biomass burning, and 8% from other sources. A decrease in natural emissions from tropical soils due to deforestation reduces gross anthropogenic emissions by about 14%. Business-as-usual emission scenarios project almost a doubling of anthropogenic N₂O emissions by 2050. In contrast, concerted mitigation scenarios project an average decline of 22% relative to 2005, which would lead to a near stabilization of atmospheric concentration of N₂O at about 350 ppb. The impact of growing demand for biofuels on future projections of N₂O emissions is highly uncertain; N₂O emissions from second and third generation biofuels could remain trivial or could become the most significant source to date. It will not be possible to completely eliminate anthropogenic N₂O emissions from agriculture, but better matching of crop N needs and N supply offers significant opportunities for emission reductions

A large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo

The primary mesenchyme cells (PMCs) of the sea urchin embryo have been an important model system for the analysis of cell behavior during gastrulation. To gain an improved understanding of the molecular basis of PMC behavior, a set of 8293 expressed sequenced tags (ESTs) was derived from an enriched population of mid-gastrula stage PMCs. These ESTs represented approximately 1200 distinct proteins, or about 15% of the mRNAs expressed by the gastrula stage embryo. 655 proteins were similar (P<10-7 by BLAST comparisons) to other proteins in GenBank, for which some information is available concerning expression and/or function. Another 116 were similar to ESTs identified in other organisms, but not further characterized. We conservatively estimate that sequences encoding at least 435 additional proteins were included in the pool of ESTs that did not yield matches by BLAST analysis. The collection of newly identified proteins includes many candidate regulators of primary mesenchyme morphogenesis, including PMC-specific extracellular matrix proteins, cell surface proteins, spicule matrix proteins and transcription factors. This work provides a basis for linking specific molecular changes to specific cell behaviors during gastrulation. Our analysis has also led to the cloning of several key components of signaling pathways that play crucial roles in early sea urchin development

Evidence for prelocalization of cytoplasmic factors affecting gene activation in early embryogenesis

Differentiation begins early in embryogenesis as different genes become active in different cells. Within the closed system of the early embryo, equal genomes thus direct the creation of diverse cell types. Though the nuclei of these cells contain complete copies of the same genome,(1,2) the nucleoplasmic and cytoplasmic environments of these genomes are not the same, as a result of the distribution of cleavage nuclei into diverse areas of egg cytoplasm early in the cleavage process. In some cases the fate of these nuclei, i.e., the type of differentiated cell to which they or their descendants give rise, has been seen to depend on the area of cytoplasm in which they come to lie

Effect of land use change on the carbon cycle in Amazon soils

The overall goal of this study was to provide a quantitative understanding of the cycling of carbon in the soils associated with deep-rooting Amazon forests. In particular, we wished to apply the understanding gained by answering two questions: (1) what changes will accompany the major land use change in this region, the conversion of forest to pasture? and (2) what is the role of carbon stored deeper than one meter in depth in these soils? To construct carbon budgets for pasture and forest soils we combined the following: measurements of carbon stocks in above-ground vegetation, root biomass, detritus, and soil organic matter; rates of carbon inputs to soil and detrital layers using litterfall collection and sequential coring to estimate fine root turnover; C-14 analyses of fractionated SOM and soil CO2 to estimate residence times; C-13 analyses to estimate C inputs to pasture soils from C-4 grasses; soil pCO2, volumetric water content, and radon gradients to estimate CO2 production as a function of soil depth; soil respiration to estimate total C outputs; and a model of soil C dynamics that defines SOM fractions cycling on annual, decadal, and millennial time scales

Kidney regeneration: common themes from the embryo to the adult

The vertebrate kidney has an inherent ability to regenerate following acute damage. Successful regeneration of the injured kidney requires the rapid replacement of damaged tubular epithelial cells and reconstitution of normal tubular function. Identifying the cells that participate in the regeneration process as well as the molecular mechanisms involved may reveal therapeutic targets for the treatment of kidney disease. Renal regeneration is associated with the expression of genetic pathways that are necessary for kidney organogenesis, suggesting that the regenerating tubular epithelium may be “reprogrammed” to a less-differentiated, progenitor state. This review will highlight data from various vertebrate models supporting the hypothesis that nephrogenic genes are reactivated as part of the process of kidney regeneration following acute kidney injury (AKI). Emphasis will be placed on the reactivation of developmental pathways and how our understanding of the resulting regeneration process may be enhanced by lessons learned in the embryonic kidney.Fil: Cirio, Maria Cecilia. University of Pittsburgh; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: de Groh, Eric D.. University of Pittsburgh; Estados UnidosFil: de Caestecker, Mark P.. Vanderbilt University; Estados UnidosFil: Davidson, Alan J.. The University of Auckland; Nueva ZelandaFil: Hukriede, Neil A.. University of Pittsburgh; Estados Unido

Effects of soil type and composition of rhizodeposits on rhizosphere priming phenomena

Inputs of fresh plant-derived C may stimulate microbially-mediated turnover of soil organic matter (SOM) in the rhizosphere. But studies of such ‘priming’ effects in artificial systems often produce conflicting results, depending on such variables as rates of substrate addition, substrate composition, whether pure compounds or mixtures of substrates are used, and whether the addition is pulsed or continuous. Studies in planted systems are less common, but also produce apparently conflicting results, and the mechanisms of these effects are poorly understood. To add to the evidence on these matters, we grew a C4 grass for 61 d in two contrasting soils – an acid sandy soil and a more fertile clay-loam – which had previously only supported C3 vegetation. We measured total soil respiration and its C isotope composition, and used the latter to partition the respiration between plant- and soil-C sources. We found SOM turnover was enhanced (i.e. positive priming) by plant growth in both soils. In treatments in which the grass was clipped, net growth was greatly diminished, and priming effects were correspondingly weak. In treatments without clipping, net plant growth, total soil respiration and SOM-derived respiration were all much greater. Further, SOM-derived respiration increased over time in parallel with increases in plant growth, but the increase was delayed in the less fertile soil. We conclude the observed priming effects were driven by microbial demand for N, fuelled by deposition of C substrate from roots and competition with roots for N. The extent of priming depended on soil type and plant growing conditions. In a further experiment, we simulated rhizodeposition of soluble microbial substrates in the same two soils with near-continuous additions for 19 d of either C4-labelled sucrose (i.e. a simple single substrate) or a maize root extract (i.e. a relatively diverse substrate), and we measured soil respiration and its C isotope signature. In the more fertile soil, sucrose induced increasingly positive priming effects over time, whereas the maize root extract produced declining priming effects over time. We suggest this was because N and other nutrients were provided from the mineralization of this more diverse substrate. In the less-fertile soil, microbial N demand was probably never satisfied by the combined mineralization from added substrate and soil organic matter. Therefore priming effects were approximately constant over time. We conclude that the chemical nature of putative priming compounds can greatly influence priming phenomena

Roads as nitrogen deposition hot spots

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 114 (2013): 149-163, doi:10.1007/s10533-013-9847-z.Mobile sources are the single largest source of nitrogen emissions to the atmosphere in the US. It is likely that a portion of mobile-source emissions are deposited adjacent to roads and thus not measured by traditional monitoring networks, which were designed to measure longterm and regional trends in deposition well away from emission sources. To estimate the magnitude of near-source nitrogen deposition, we measured concentrations of both dissolved inorganic nitrogen (DIN) and total (inorganic + organic) dissolved nitrogen (TDN) in throughfall (i.e., the nitrogen that comes through the forest canopy) along transects perpendicular to two moderately trafficked roads on Cape Cod in Falmouth MA, coupled with measurements of both DIN and TDN in bulk precipitation made in adjacent open fields at the same transect distances. We used the TDN throughfall data to estimate total nitrogen deposition, including dry gaseous nitrogen deposition in addition to wet deposition and dry particle deposition. There was no difference in TDN in the bulk collectors along the transects at either site; however TDN in the throughfall collectors was always higher closest to the road and decreased with distance. These patterns were driven primarily by differences in the inorganic N and not the organic N. Annual throughfall deposition was 8.7 (+0.4) and 6.8 (+0.5) TDN - kg N ha-1 yr-1 at sites 10 m and 150 m away from the road respectively. We also characterized throughfall away from a non-road edge (power line right-of-way) to test whether the increased deposition observed near road edges was due to deposition near emission sources or due to a physical, edge effect causing higher deposition. The increased deposition we observed near roads was due to increases in inorganic N especially NH4 +. This increased deposition was not the result of an edge effect; rather it is due to near source deposition of mobile source emissions. We scaled these results to the entire watershed and estimate that by not taking into account the effects of increased gaseous N deposition from mobile sources we are underestimating the amount of N deposition to the watershed by 13% - 25%.This research was supported by Woods Hole SeaGrant (grant NA06OAR4170021), NSF IGERT (grant DGE 0221658), an Edna Bailey Sussman Environmental Internship Award from Cornell University, and a Mellon Foundation award though Cornell University.2014-04-1