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sigma(28) RNA polymerase is an alternative RNA polymerase that has been postulated to have a role in developmental gene regulation in Chlamydia. Although a consensus bacterial sigma(28) promoter sequence has been proposed, it is based on a relatively small number of defined promoters, and the promoter structure has not been systematically analyzed. To evaluate the sequence of the sigma(28)-dependent promoter, we performed a comprehensive mutational analysis of the Chlamydia trachomatis hctB promoter, testing the effect of point substitutions on promoter activity. We defined a -35 element recognized by chlamydial sigma(28) RNA polymerase that resembles the consensus -35 sequence. Within the -10 element, however, chlamydial sigma(28) RNA polymerase showed a striking preference for a CGA sequence at positions -12 to -10 rather than the longer consensus -10 sequence. We also observed a strong preference for this CGA sequence by Escherichia Coli sigma(28) RNA polymerase, suggesting that this previously unrecognized motif is the critical component of the -10 promoter element recognized by sigma(28) RNA polymerase. Although the consensus spacer length is 11 nucleotides (nt), we found that sigma(28) RNA polymerase from both Chlamydia and E. coli transcribed a promoter with either an 11- or 12-nt spacer equally well. Altogether, we found very similar results for a sigma(28) RNA polymerase from C trachomatis and E. coli, suggesting that promoter recognition by this alternative RNA polymerase is well conserved among bacteria. The preferred sigma(28) promoter that we defined in the context of the hctB promoter is TAAAGwwy-n(11/12)-ryCGAwrn, where w is A or T, r is a purine, y is a pyrimidine, n is any nucleotide, and n(11/12) is a spacer of 11 or 12 nt.

Laser-assisted atom probe tomography (APT) and high-resolution dark-field electron holography (HR-DFEH) were performed to investigate the composition of a polar [0001] GaN/AlxGa1 − xN/InyGa1 − yN light emitting diode. In particular, the III-site fraction of both AlxGa1 − xN and InyGa1 − yN alloys was studied adopting a comparative approach. HR-DFEH allows mapping the projected strain with a subnanometer spatial resolution which is used for the calculation of the two-dimensional alloy composition distribution. APT provides three-dimensional alloys composition distribution with a nanometer spatial resolution. However, here we reveal that important inaccuracies affect local composition measurements. A Ga-poor composition is obtained in high DC-electric field regions. Moreover, such inaccuracies may be locally enhanced where the [0001] pole intersects the surface of the analyzed specimen, leading to a lower fraction of Ga measured. III-site fractions closer to the nominal values were measured at low field conditions. Ga loss is thought to be due to preferential DC field induced evaporation of Ga ions between laser pulses. This is explained in terms of formation of a metallic layer on the tip surface during APT analysis, where weak Ga-Ga bonds are formed, promoting the loss of Ga at high field conditions. [ABSTRACT FROM AUTHOR]

The use of a tip-shaped sample for the atom probe tomography technique offers the unique opportunity to analyze the dynamics of molecular ions in strong DC fields. We investigate here the stability of AlN2+ and GaN2+ dications emitted from an Al0.25Ga0.75N sample in a joint theoretical and experimental study. Despite the strong chemical resemblance of these two molecules, we observe only stable AlN2+, while GaN2+ can only be observed as a transient species. We simulate the emission dynamics of these ions on field-perturbed potential energy surfaces obtained from quantum chemical calculations. We show that the dissociation is governed by two independent processes. For all bound states, a mechanical dissociation is induced by the distortion of the potential energy surface in the close vicinity of the emitting tip. In the specific case of GaN2+, the relatively small electric dipole of the dication in its ground 13Σ− and excited 11Δ states induces a weak coupling with the electric field so that the mechanical dissociation into Ga+ + N+ lasts for sufficient time to be observed. By contrast, the AlN2+ mechanical dissociation leads to Al2+ + N which cannot be observed as a correlated event. For some deeply bound singlet excited states, the spin-orbit coupling with lower energy triplet states gives another chance of dissociation by system inter-system crossing with specific patterns observed experimentally in a correlated time of flight map. [ABSTRACT FROM AUTHOR]

The structural, compositional, and optical properties of ZnO/MgxZn1-xO m-plane heterostructures are investigated using scanning transmission electron microscopy, laser-assisted atom probe tomography, and micro-photoluminescence. Coupled with electron tomography, atom probe tomography is currently the only technique providing a 3D reconstruction of the position of the atoms of a nanoscale specimen with their chemical nature. The multi-quantum well system investigated exhibits a V-groove grating profile along the a-axis accompanied by the formation of Zn- and Mg-enriched regions corresponding to the edges pointing towards the substrate and towards the upper surface, respectively. The optical signature of these heterostructures has been investigated by performing micro-photoluminescence on atom probe tip specimens. Effective mass calculations based on the 3D microscopy data indicate that the quantum well geometry and barrier composition yield a localization of hole states at the bottom of the V-groove. [ABSTRACT FROM AUTHOR]

The dissemination of specimen data in scientific collections is a crucial step in making them available to the scientific community. However, even today, especially in some countries, little or nothing is known about the contents of the naturalistic collections of some museums. This is regrettable, especially in cases where the collections include historic specimens and endangered species. The Museum of Comparative Anatomy "Giovanni Battista Grassi", situated in Rome, Italy, houses historical anatomical and didactic collections, with specimens gathered from 1600s and almost worldwide. The collection holds 444 specimens of medium and large-sized terrestrial mammals, comprising 25 fossils, 40 skins, 186 skulls, 70 skeletons and 123 anatomical pieces, representing 63% of recent mammal orders, mainly from localities of Africa and Europe. A list of this material, indexed by the orders and families, is provided, as well as comments on the conservation status of the species. Remarkable data are summarised, including new data on a hippopotamus specimen from an extinct population and the record of three rhinoceros species from 1600s. Besides comparative anatomical studies, the Museum of Comparative Anatomy of Sapienza University emerges as a source of important material for biodiversity genomics., Competing Interests: No conflict of interest to declare Disclaimer: This article is (co-)authored by any of the Editors-in-Chief, Managing Editors or their deputies in this journal., (Alexandra M. R. Bezerra, Edoardo Di Russo, Riccardo Castiglia.)

By collecting simultaneously optical and chemical/morphological data from nanoscale volumes, the Photonic Atom Probe (PAP) can be applied not only to the study of the relationship between optical and structural properties of quantum emitter but also to evaluate the influence of other factors, such as the presence of point defects, on the photoluminescence. Through the analysis of multiple layers of InGaN/GaN quantum dots (QDs), grown so that the density of structural defects is higher with increasing distance from the substrate, we establish that the light emission is higher in the regions exhibiting a higher presence of structural defects. While the presence of intrinsic point defects with non-radiative recombination properties remains elusive, our result is consistent with the fact that QD layers closer to the substrate behave as traps for non-radiative point defects. This result demonstrates the potential of the PAP as a technique for the study of the optical properties of defects in semiconductors., Competing Interests: Conflict of interest The authors declare that they have no competing interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Microscopy Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The measurement of the composition of ε-Ga2O3 and the quantification of Sn doping in ε-Ga2O3:Sn by laser-assisted atom probe tomography (APT) may be inaccurate depending on the experimental conditions. Both the role of the laser energy and surface electric field were investigated, and the results clearly indicate that deviations from stoichiometry are observed changing the electric field conditions during APT. The measured atomic fraction of Ga can change from 0.45 at low field to 0.38 at high field, to be compared with the expected 0.4. This was interpreted in terms of preferential evaporation of Ga at high field and deficit of O at low field, which was caused by the formation of neutrals. The quantification of Sn-doping is accurate at low-field conditions, with an overestimation of the detected Sn-metallic fraction at high field. This suggests that Sn has a higher evaporation field compared to Ga. Finally, multiple detection events were in-depth studied, revealing that three dissociation reactions occur during APT: GaO2+ → Ga+ + O+; Ga2O22+ → Ga+ + GaO2+; Ga3O22+ → Ga+ + Ga2O2+. Nevertheless, only 2% of the detected events are related to such dissociation reactions, too small a fraction to fully explain the observed deviation from the stoichiometric composition in ε-Ga2O3.

Attaining low-resistivity Al x Ga 1- x N layers is one keystone to improve the efficiency of light-emitting devices in the ultraviolet spectral range. Here, we present a microstructural analysis of Al x Ga 1- x N/Ge samples with 0 ≤ x ≤ 1, and a nominal doping level in the range of 10 20 cm -3 , together with the measurement of Ge concentration and its spatial distribution down to the nanometer scale. Al x Ga 1- x N/Ge samples with x ≤ 0.2 do not present any sign of inhomogeneity. However, samples with x > 0.4 display μm-size Ge crystallites at the surface. Ge segregation is not restricted to the surface: Ge-rich regions with a size of tens of nanometers are observed inside the Al x Ga 1- x N/Ge layers, generally associated with Ga-rich regions around structural defects. With these local exceptions, the Al x Ga 1- x N/Ge matrix presents a homogeneous Ge composition which can be significantly lower than the nominal doping level. Precise measurements of Ge in the matrix provide a view of the solubility diagram of Ge in Al x Ga 1- x N as a function of the Al mole fraction. The solubility of Ge in AlN is extremely low. Between AlN and GaN, the solubility increases linearly with the Ga mole fraction in the ternary alloy, which suggests that the Ge incorporation takes place by substitution of Ga atoms only. The maximum percentage of Ga sites occupied by Ge saturates around 1%. The solubility issues and Ge segregation phenomena at different length scales likely play a role in the efficiency of Ge as an n-type AlGaN dopant, even at Al concentrations where Ge DX centers are not expected to manifest. Therefore, this information can have direct impact on the performance of Ge-doped AlGaN light-emitting diodes, particularly in the spectral range for disinfection (≈260 nm), which requires heavily doped alloys with a high Al mole fraction.

Atom Probe Tomography (APT) is a microscopy technique allowing for the 3D reconstruction of the chemical composition of a nanoscale needle-shaped sample with a precision close to the atomic scale. The photonic atom probe (PAP) is an evolution of APT featuring in situ and operando detection of the photoluminescence signal. The optical signatures of the light-emitting centers can be correlated with the structural and chemical information obtained by the analysis of the evaporated ions. It becomes thus possible to discriminate and interpret the spectral signatures of different light emitters as close as 20 nm, well beyond the resolution limit set by the exciting laser wavelength. This technique opens up new perspectives for the study of the physics of low dimensional systems, defects and optoelectronic devices.

Correlation between off-axis electron holography and atom probe tomography (APT) provides morphological, chemical and electrical information about Mg doping (p-type) in gallium nitride (GaN) layers that have been grown at different temperatures at a nanometric scale. APT allows access to the three-dimensional distribution of atoms and their chemical nature. In particular, this technique allows visualisation of the Mg-rich clusters observed in p-doped GaN layers grown by metal-organic chemical vapour deposition. As the layer growth temperature increases, the cluster density decreases but their size indicted by the number of atoms increases. Moreover, APT reveals that threading dislocations are decorated with Mg atoms. Off-axis electron holography provides complementary information about the electrical activity of the Mg doping. As only a small fraction of dopant atoms are ionised at room temperature, this fraction is increased by annealing the specimen to 400 °C in situ in a transmission electron microscope (TEM). A strong reduction of the dopant electrical activity is observed for increases in the layer growth temperature. The correlation of APT with TEM-based techniques was shown to be a unique approach in order to investigate how the growth temperature affects both the chemical distribution and electrical activity of Mg dopant atoms.

The use of a tip-shaped sample for the atom probe tomography technique offers the unique opportunity to analyze the dynamics of molecular ions in strong DC fields. We investigate here the stability of AlN 2+ and GaN 2+ dications emitted from an Al 0.25 Ga 0.75 N sample in a joint theoretical and experimental study. Despite the strong chemical resemblance of these two molecules, we observe only stable AlN 2+ , while GaN 2+ can only be observed as a transient species. We simulate the emission dynamics of these ions on field-perturbed potential energy surfaces obtained from quantum chemical calculations. We show that the dissociation is governed by two independent processes. For all bound states, a mechanical dissociation is induced by the distortion of the potential energy surface in the close vicinity of the emitting tip. In the specific case of GaN 2+ , the relatively small electric dipole of the dication in its ground 1 3 Σ - and excited 1 1 Δ states induces a weak coupling with the electric field so that the mechanical dissociation into Ga + + N + lasts for sufficient time to be observed. By contrast, the AlN 2+ mechanical dissociation leads to Al 2+ + N which cannot be observed as a correlated event. For some deeply bound singlet excited states, the spin-orbit coupling with lower energy triplet states gives another chance of dissociation by system inter-system crossing with specific patterns observed experimentally in a correlated time of flight map.

The composition of GaAs measured by laser-assisted atom probe tomography may be inaccurate depending on the experimental conditions. In this work, we assess the role of the DC field and the impinging laser energy on such compositional bias. The DC field is found to have a major influence, while the laser energy has a weaker one within the range of parameters explored. The atomic fraction of Ga may vary from 0.55 at low-field conditions to 0.35 at high field. These results have been interpreted in terms of preferential evaporation of Ga at high field. The deficit of As is most likely explained by the formation of neutral As complexes either by direct ejection from the tip surface or upon the dissociation of large clusters. The study of multiple detection events supports this interpretation.