Non-autonomy of AGAMOUS function in flower development: use of a Cre/loxP method for mosaic analysis in Arabidopsis

Angiosperms use a multi-layered meristem (typically L1, L2 and L3) to produce primordia that then develop into plant organs, A number of experiments show that communication between the cell layers is important for normal development. We examined whether the function of the flower developmental control gene AGAMOUS involves communication across these layers. We developed a mosaic strategy using the Cre/loxP site-specific recombinase system, and identified the sector structure for mosaics that produced mutant flowers. The major conclusions were that (1) AGAMOUS must be active in the L2 for staminoid and carpelloid tissues, (2) that AGAMOUS must be active in the L2 and the L3 for floral meristem determinacy, and (3) that epidermal cell identity can be communicated by the L2 to the L1 layer

Computational Studies of Chiral Hydroxyl Carboxylic Acids: The Allylboration of Aldehydes

The mechanism of the asymmetric BINOL-derived hydroxyl carboxylic acid catalyzed allylboration of benzaldehyde was investigated using density functional theory calculations. A new reaction model is proposed, and the roles of the two Brønsted acidic sites of the catalyst elucidated. Catalyst distortion was found to be a key factor in determining stereoselectivity. The flexibility of the hydroxyl carboxylic acid catalyst leads to significant differences in the mechanism and origins of selectivity compared to the equivalent phosphoric acid catalyzed reaction

Machine learning and semi-empirical calculations: a synergistic approach to rapid, accurate, and mechanism-based reaction barrier prediction

Modern QM modelling methods, such as DFT, have provided detailed mechanistic insights into countless reactions. However, their computational cost inhibits their ability to rapidly screen large numbers of substrates and catalysts in reaction discovery. For a C–C bond forming nitro-Michael addition, we introduce a synergistic semi-empirical quantum mechanical (SQM) and machine learning (ML) approach that allows the prediction of DFT-quality reaction barriers in minutes, even on a standard laptop using widely available modelling software. Mean absolute errors (MAEs) are obtained that are below the accepted chemical accuracy threshold of 1 kcal mol(−1) and substantially better than SQM methods without ML correction (5.71 kcal mol(−1)). Predictive power is shown to hold when the ML models are applied to an unseen set of compounds from the toxicology literature. Mechanistic insight is also achieved via the generation of full SQM transition state (TS) structures which are found to be very good approximations for the DFT-level geometries, revealing important steric interactions in some TSs. This combination of speed, accuracy, and mechanistic insight is unprecedented; current ML barrier models compromise on at least one of these important criteria

Machine learning and semi-empirical calculations: a synergistic approach to rapid, accurate, and mechanism-based reaction barrier prediction

Modern QM modelling methods, such as DFT, have provided detailed mechanistic insights into countless reactions. However, their computational cost inhibits their ability to rapidly screen large numbers of substrates and catalysts in reaction discovery. For a C–C bond forming nitro-Michael addition, we introduce a synergistic semi-empirical quantum mechanical (SQM) and machine learning (ML) approach that allows the prediction of DFT-quality reaction barriers in minutes, even on a standard laptop using widely available modelling software. Mean absolute errors (MAEs) are obtained that are below the accepted chemical accuracy threshold of 1 kcal mol−1 and substantially better than SQM methods without ML correction (5.71 kcal mol−1). Predictive power is shown to hold when the ML models are applied to an unseen set of compounds from the toxicology literature. Mechanistic insight is also achieved via the generation of full SQM transition state (TS) structures which are found to be very good approximations for the DFT-level geometries, revealing important steric interactions in some TSs. This combination of speed, accuracy, and mechanistic insight is unprecedented; current ML barrier models compromise on at least one of these important criteria

A genetic and molecular model for flower development in Arabidopsis thaliana

Cells in developing organisms do not only differentiate, they differentiate in defined patterns. A striking example is the differentiation of flowers, which in most plant families consist of four types of organs: sepals, petals, stamens and carpels, each composed of characteristic cell types. In the families of flowering plants in which these organs occur, they are patterned with the sepals in the outermost whorl or whorls of the flower, with the petals next closest to the center, the stamens even closer to the center, and the carpels central. In each species of flowering plant the disposition and number (or range of numbers) of these organs is also specified, and the floral 'formula' is repeated in each of the flowers on each individual plant of the species. We do not know how cells in developing plants determine their position, and in response to this determination differentiate to the cell types appropriate for that position. While there have been a number of speculative proposals for the mechanism of organ specification in flowers (Goethe, 1790; Goebel, 1900; Heslop-Harrison, 1964; Green, 1988), recent genetic evidence is inconsistent with all of them, at least in the forms in which they were originally presented (Bowman et al. 1989; Meyerowitz et al. 1989). We describe here a preliminary model, based on experiments with Arabidopsis thaliana. The model is by and large consistent with existing evidence, and has predicted the results of a number of genetic and molecular experiments that have been recently performed

Macro-to-Micro Interface for the Control of Cellular Organization

The spatial organization of cellular communities plays a fundamental role in determining intercellular communication and emergent behavior. Few tools, however, exist to modulate tissue organization at the scale of individual cells, particularly in the case of dynamic manipulation. Micromechanical reconfigurable culture achieves dynamic control of tissue organization by culturing adherent cells on microfabricated plates that can be shifted to reorganize the arrangement of the cells. Although biological studies using this approach have been previously reported, this paper focuses on the engineering of the device, including the mechanism for translating manual manipulation to precise microscale position control, fault-tolerant design for manufacture, and the synthetic-to-living interface.National Science Foundation (U.S.) (Faculty Early Career Development Program)National Institute of Diabetes and Digestive and Kidney Diseases (U.S.)David & Lucile Packard FoundationNational Institutes of Health (U.S.). Ruth L. Kirschstein National Research Service Awar

Microenvironmental regulation of the sinusoidal endothelial cell phenotype in vitro

Author Manuscript: 2010 June 23.Liver sinusoidal endothelial cells (LSECs) differ, both structurally and functionally, from endothelial cells (ECs) lining blood vessels of other tissues. For example, in contrast to other ECs, LSECs possess fenestrations, have low detectable levels of platelet endothelial cell adhesion molecule 1 expression, and in rat tissue, they distinctively express a cell surface marker recognized by the SE-1 antibody. These unique phenotypic characteristics seen in hepatic tissue are lost over time upon culture in vitro; therefore, this study sought to systematically examine the effects of microenvironmental stimuli—namely, extracellular matrix and neighboring cells, on the LSEC phenotype in vitro. In probing the role of the underlying extracellular matrix, we identified collagen I and collagen III as well as mixtures of collagen I/collagen IV/fibronectin as having a positive effect on LSEC survival. Furthermore, using a stable hepatocellular model (hepatocyte–fibroblast) we were able to prolong the expression of both SE-1 and phenotypic functions of LSEC such as factor VIII activity and AcLOL uptake in cocultured LSECs through the production of short-range paracrine signals. In the course of these experiments, we identified the antigen recognized by SE-1 as CD32b. Conclusion: Collectively, this study has identified several microenvironmental regulators of liver sinusoidal endothelial cells that prolong their phenotypic functions for up to 2 weeks in culture, enabling the development of better in vitro models of liver physiology and disease

Enantioselective S‐H Insertion Reactions of α‐Carbonyl Sulfoxonium Ylides

The first example of enantioselective S‐H insertion reactions of sulfoxonium ylides is reported. Under the influence of thiourea catalysis, excellent levels of enantiocontrol (up to 95% ee) and yields (up to 97%) are achieved for 31 examples in S‐H insertion reactions of aryl thiols and α‐carbonyl sulfoxonium ylides

Radio Continuum and Recombination Line Study of UC HII Regions with Extended Envelopes

We have carried out 21 cm radio continuum observations of 16 UC HII regions using the VLA (D-array) in search of associated extended emission. We have also observed H76$_\alpha$ recombination line towards all the sources and He76$_\alpha$ line at the positions with strong H76$_\alpha$ line emission. The UC HII regions have simple morphologies and large (>10) ratios of single-dish to VLA fluxes. Extended emission was detected towards all the sources. The extended emission consists of one to several compact components and a diffuse extended envelope. All the UC HII regions but two are located in the compact components, where the UC HII regions always correspond to their peaks. The compact components with UC HII regions are usually smaller and denser than those without UC HII regions. Our recombination line observations indicate that the ultracompact, compact, and extended components are physically associated. The UC HII regions and their associated compact components are likely to be ionized by the same sources on the basis of the morphological relations mentioned above. This suggests that almost all of the observed UC HII regions are not `real' UC HII regions and that their actual ages are much greater than their dynamical age (<10000 yr). We find that most of simple UC HII regions previously known have large ratios of single-dish to VLA fluxes, similar to our sources. Therefore, the `age problem' of UC HII regions does not seem to be as serious as earlier studies argued. We present a simple model that explains extended emission around UC HII regions. Some individual sources are discussed.Comment: 29 pages, 28 postscript figures, Accepted for publication in Ap

Population genetics of Glossina morsitans submorsitans (Diptera: Glossinidae)

Breeding structure of Glossina morsitans submorsitans Newstead was evaluated by using genetic markers in mitochondrial DNA where diversity was scored at two loci in five natural populations from The Gambia and two populations in Ethiopia (form ugandensis Vanderplank), countries separated by c. 5450 km. Twenty six haplotype combinations were found, of which 17 were shared among two or more populations. Nine haplotypes were found in The Gambia and 23 haplotypes in Ethiopia. There were 12 unique haplotypes. Only six haplotypes were shared between the two countries. Populations in The Gambia (he = 0.26 ± 0.04) showed less than a third of the diversity of populations in Ethiopia (he= 0.84 ± 0.03). This suggests recovery from an earlier reduction in population. In a nested analysis of molecular variance of haplotype frequencies, 65%of the variance was due to differences within populations, 34% to differences between populations grouped by country, and only 1% was due to differences among populations within countries. In terms of gene flow, the fixation index FST= 0.35, which leads to an estimate by Wright’s island model of less than one reproducing migrant per generation exchanged between the eastern and western submorsitanspopulations. Nei’s genetic similarity measure showed a deep division between Gambian and Ethiopian populations