Green Fluorescent Protein in the sea urchin: new experimental approaches to transcriptional regulatory analysis in embryos and larvae

The use of Green Fluorescent Protein (GFP) as a reporter for expression transgenes opens the way to several new experimental strategies for the study of gene regulation in sea urchin development. A GFP coding sequence was associated with three different previously studied cis-regulatory systems, viz those of the SM50 gene, expressed in skeletogenic mesenchyme, the CyIIa gene, expressed in archenteron, skeletogenic and secondary mesenchyme, and the Endo16 gene, expressed in vegetal plate, archenteron and midgut. We demonstrate that the sensitivity with which expression can be detected is equal to or greater than that of whole-mount in situ hybridization applied to detection of CAT mRNA synthesized under the control of the same cis-regulatory systems. However, in addition to the important feature that it can be visualized nondestructively in living embryos, GFP has other advantages. First, it freely diffuses even within fine cytoplasmic cables, and thus reveals connections between cells, which in sea urchin embryos is particularly useful for observations on regulatory systems that operate in the syncytial skeletogenic mesenchyme. Second, GFP expression can be dramatically visualized in postembryonic larval tissues. This brings postembryonic larval developmental processes for the first time within the easy range of gene transfer analyses. Third, GFP permits identification and segregation of embryos in which the clonal incorporation of injected DNA has occurred in any particular desired region of the embryo. Thus, we show explicitly that, as expected, GFP transgenes are incorporated in the same nuclei together with other transgenes with which they are co-injected

Compensation effects in GaN:Mg probed by Raman spectroscopy and photoluminescence measurements

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Appl. Phys. 113, 103504 (2013) and may be found at https://doi.org/10.1063/1.4794094.Compensation effects in metal organic chemical vapour deposition grown GaN doped with magnesium are investigated with Raman spectroscopy and photoluminescence measurements. Examining the strain sensitive E2(high) mode, an increasing compressive strain is revealed for samples with Mg-concentrations lower than 7 × 1018 cm−3. For higher Mg-concentrations, this strain is monotonically reduced. This relaxation is accompanied by a sudden decrease in crystal quality. Luminescence measurements reveal a well defined near band edge luminescence with free, donor bound, and acceptor bound excitons as well as a characteristic donor acceptor pair (DAP) luminescence. Following recent results, three acceptor bound excitons and donor acceptor pairs are identified. Along with the change of the strain, a strong modification in the luminescence of the dominating acceptor bound exciton and DAP luminescence is observed. The results from Raman spectroscopy and luminescence measurements are interpreted as fingerprints of compensation effects in GaN:Mg leading to the conclusion that compensation due to defect incorporation triggered by Mg-doping already affects the crystal properties at doping levels of around 7 × 1018 cm−3. Thereby, the generation of nitrogen vacancies is introduced as the driving force for the change of the strain state and the near band edge luminescence.DFG, 43659573, SFB 787: Halbleiter - Nanophotonik: Materialien, Modelle, Bauelement

Temperature dependent photoluminescence of lateral polarity junctions of metal organic chemical vapor deposition grown GaN

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Journal of Applied Physics 110, 093503 (2011) and may be found at https://doi.org/10.1063/1.3656987.We report on fundamental structural and optical properties of lateral polarity junctions in GaN. GaN with Ga- to N-polar junctions was grown on sapphire using an AlN buffer layer. Results from scanning electron microscopy and Raman spectroscopy measurements indicate a superior quality of the Ga-polar GaN. An extremely strong luminescence signal is observed at the inversion domain boundary (IDB). Temperature dependent micro photoluminescence measurements are used to reveal the recombination processes underlying this strong emission. At 5 K the emission mainly arises from a stripe along the inversion domain boundary with a thickness of 4-5 μm. An increase of the temperature initially leads to a narrowing to below 2 μm emission area width followed by a broadening at temperatures above 70 K. The relatively broad emission area at low temperatures is explained by a diagonal IDB. It is shown that all further changes in the emission area width are related to thermalization effects of carriers and defects attracted to the IDB. The results are successfully used to confirm a theoretical model for GaN based lateral polarity junctions. Due to the strong and pronounced emission of IDBs even at elevated temperatures, it is demonstrated that lateral polarity junctions exhibit a strong potential for future high efficiency devices.DFG, 43659573, SFB 787: Halbleiter - Nanophotonik: Materialien, Modelle, Bauelement

Phonon pressure coefficients and deformation potentials of wurtzite AlN determined by uniaxial pressure-dependent Raman measurements

© 2014 American Physical Society. We studied bulk crystals of wurtzite AlN by means of uniaxial pressure-dependent Raman measurements. As a result, we derive the phonon pressure coefficients and deformation potentials for all zone center optical phonon modes. For the A1 and E1 modes, we further experimentally determined the uniaxial pressure dependence of their longitudinal optical-transverse optical (LO-TO) splittings. Our experimental approach delivers new insight into the large variance among previously reported phonon deformation potentials, which are predominantly based on heteroepitaxial growth of AlN and the ball-on-ring technique. Additionally, the measured phonon pressure coefficients are compared to their theoretical counterparts obtained by density functional theory implemented in the siesta package. Generally, we observe a good agreement between the calculated and measured phonon pressure coefficients but some particular Raman modes exhibit significant discrepancies similar to the case of wurtzite GaN and ZnO, clearly motivating the presented uniaxial pressure-dependent Raman measurements on bulk AlN crystals

Deciphering interplay between Salmonella invasion effectors

Bacterial pathogens have evolved a specialized type III secretion system (T3SS) to translocate virulence effector proteins directly into eukaryotic target cells. Salmonellae deploy effectors that trigger localized actin reorganization to force their own entry into non-phagocytic host cells. Six effectors (SipC, SipA, SopE/2, SopB, SptP) can individually manipulate actin dynamics at the plasma membrane, which acts as a ‘signaling hub’ during Salmonella invasion. The extent of crosstalk between these spatially coincident effectors remains unknown. Here we describe trans and cis binary entry effector interplay (BENEFIT) screens that systematically examine functional associations between effectors following their delivery into the host cell. The results reveal extensive ordered synergistic and antagonistic relationships and their relative potency, and illuminate an unexpectedly sophisticated signaling network evolved through longstanding pathogen–host interaction

Theory of the "honeycomb chain-channel" reconstruction of Si(111)3x1

First-principles electronic-structure methods are used to study a structural model for Ag/Si(111)3x1 recently proposed on the basis of transmission electron diffraction data. The fully relaxed geometry for this model is far more energetically favorable than any previously proposed, partly due to the unusual formation of a Si double bond in the surface layer. The calculated electronic properties of this model are in complete agreement with data from angle-resolved photoemission and scanning tunneling microscopy.Comment: 4 pages, 4 figures, submitted to Phys. Rev. Lett (the ugly postscript error on page 4 has now been repaired

Redesign of the Gossamer Albatross using a Boxwing

Historically, human powered aircraft (HPA) have been known to have very large wingspans. For example, the Gossamer Albatross has a wingspan of 96 ft. greater than that of a Boeing 717 which is a commercial airplane with the capability of carrying over 100 passengers. The main reason why HPA have such large wingspans is for aerodynamic performance. During low speeds, the predominant type of drag is the induced drag which is a by-product of large wing tip vortices generated at the wing tips during slow flight at higher coefficients of lift. In order to reduce this phenomenon, higher aspect ratio wings are used which is the reason behind the very large wingspans for HPA. Due to its high Oswald efficiency factor, the boxwing configuration is presented as a possible solution to decrease the wingspan while not affecting the aerodynamic performance of the airplane. The new configuration is analyzed through the use of VLAERO+, a commercial vortex lattice method analysis software, after proper calibration procedures are applied. The parasitic drag was estimated using empirical methods based on the friction drag of a flat plate. The structural weight changes in the boxwing design were estimated using “area weights” derived from the original Gossamer Albatross. The two aircraft were compared at a cruise velocity of 22 ft/s where the boxwing configuration showed a net drag reduction of approxiametly 0.36 lb, which can be deduced from a decrease of 0.81 lb of the induced drag plus an increase of the parasite drag of around 0.45 lb. Therefore, for an aircraft with approximately half the wingspan, easier to handle, and more practical, the drag is essentially reduced by 4.4%

Evaluation of the Applicability of the Vortex Lattice Method to the Analysis of Human Powered Aircraft

The applicability of the vortex lattice method to the design of human powered aircraft is investigated. Aerodynamic data such as coefficients of lift, drag, and moment are calculated for the Gossamer Albatross using VLAERO+ã, a vortex lattice method commercial computer program, and compared to flight test data . The differences are analyzed and explained. Although the computations display similar trends to the experimental data, there exist discrepancies that can be explained by the inherent limitations of the method, such as being linear and inviscid. However, the program allows for certain calibration, through additive and multiplication factors. The Gossamer model, once calibrated, can be used with confidence for the calculation of aerodynamic properties and stability analysis for the range of Mach numbers between 0.016 and 0.0248, and angles of attack between -2 to 10 degrees

Galaxy Rotation Curve Fitting Using Machine Learning Tools

Galaxy rotation curve (RC) fitting is an important technique which allows the placement of constraints on different kinds of dark matter (DM) halo models. In the case of non-phenomenological DM profiles with no analytic expressions, the art of finding RC best-fits including the full baryonic $+$ DM free parameters can be difficult and time-consuming. In the present work, we use a gradient descent method used in the backpropagation process of training a neural network, to fit the so-called Grand Rotation Curve of the Milky Way (MW) ranging from $\sim$1 pc all the way to $\sim$$10^5$ pc. We model the mass distribution of our Galaxy including a bulge (inner $+$ main), a disk, and a fermionic dark matter (DM) halo known as the Ruffini-Arg\"uelles-Rueda (RAR) model. This is a semi-analytical model built from first-principle physics such as (quantum) statistical mechanics and thermodynamics, whose more general density profile has a dense core -- diluted halo morphology with no analytic expression. As shown recently and further verified here, the dark and compact fermion-core can work as an alternative to the central black hole in SgrA* when including data at milliparsec scales from the S-cluster stars. Thus, we show the ability of this state-of-the-art machine learning tool in providing the best-fit parameters to the overall MW RC in the $10^{-2}$--$10^5$ pc range, in a few hours of CPU time.Comment: 10 pages, 5 figures, 1 Table. Published in Univers

In vivo conditional deletion of HDAC7 reveals its requirement to establish proper B lymphocyte identity and development

Class IIa histone deacetylase (HDAC) subfamily members are tissue-specific gene repressors with crucial roles in development and differentiation processes. A prominent example is HDAC7, a class IIa HDAC that shows a lymphoid-specific expression pattern within the hematopoietic system. In this study, we explored its potential role in B cell development by generating a conditional knockout mouse model. Our study demonstrates for the first time that HDAC7 deletion dramatically blocks early B cell development and gives rise to a severe lymphopenia in peripheral organs, while also leading to pro-B cell lineage promiscuity. We find that HDAC7 represses myeloid and T lymphocyte genes in B cell progenitors through interaction with myocyte enhancer factor 2C (MEFC2). In B cell progenitors, HDAC7 is recruited to promoters and enhancers of target genes, and its absence leads to increased enrichment of histone active marks. Our results prove that HDAC7 is a bona fide transcriptional repressor essential for B cell development