Search for methylamine in high mass hot cores

We aim to detect methylamine, CH$_{3}$NH$_{2}$, in a variety of hot cores and use it as a test for the importance of photon-induced chemistry in ice mantles and mobility of radicals. Specifically, CH$_3$NH$_2$ cannot be formed from atom addition to CO whereas other NH$_2$-containing molecules such as formamide, NH$_2$CHO, can. Submillimeter spectra of several massive hot core regions were taken with the James Clerk Maxwell Telescope. Abundances are determined with the rotational diagram method where possible. Methylamine is not detected, giving upper limit column densities between 1.9 $-$ 6.4 $\times$ 10$^{16}$ cm$^{-2}$ for source sizes corresponding to the 100 K envelope radius. Combined with previously obtained JCMT data analyzed in the same way, abundance ratios of CH$_{3}$NH$_{2}$, NH$_{2}$CHO and CH$_{3}$CN with respect to each other and to CH$_{3}$OH are determined. These ratios are compared with Sagittarius B2 observations, where all species are detected, and to hot core models. The observed ratios suggest that both methylamine and formamide are overproduced by up to an order of magnitude in hot core models. Acetonitrile is however underproduced. The proposed chemical schemes leading to these molecules are discussed and reactions that need further laboratory studies are identified. The upper limits obtained in this paper can be used to guide future observations, especially with ALMA.Comment: 14 pages, 5 figures, accepted for publication in A&

Interstellar bromine abundance is consistent with cometary ices from Rosetta

Cometary ices are formed during star and planet formation, and their molecular and elemental makeup can be related to the early solar system via the study of inter- and protostellar material. The first cometary abundance of the halogen element bromine (Br) was recently made available by the Rosetta mission. Its abundance in protostellar gas is thus far unconstrained, however. We set out to place the first observational constraints on the interstellar gas-phase abundance of bromine (Br). We further aim to compare the protostellar Br abundance with that measured by Rosetta in the ices of comet 67P/Churyumov-Gerasimenko. Archival Herschel data of Orion KL, Sgr B2(N), and NGC 6334I are examined for the presence of HBr and HBr$^{+}$ emission or absorption lines. A chemical network for modelling HBr in protostellar molecular gas is compiled to aid in the interpretation. HBr and HBr$^{+}$ were not detected towards any of our targets. However, in the Orion KL Hot Core, our upper limit on HBr/H$_{2}$O is a factor of ten below the ratio measured in comet 67P. This result is consistent with the chemical network prediction that HBr is not a dominant gas-phase Br carrier. Cometary HBr is likely predominantly formed in icy grain mantles which lock up nearly all elemental Br.Comment: Accepted for publication in A&A. 9 pages, 6 figure

Interstellar bromine abundance is consistent with cometary ices from Rosetta

Cometary ices are formed during star and planet formation, and their molecular and elemental makeup can be related to the early solar system via the study of inter- and protostellar material. The first cometary abundance of the halogen element bromine (Br) was recently made available by the Rosetta mission. Its abundance in protostellar gas is thus far unconstrained, however. We set out to place the first observational constraints on the interstellar gas-phase abundance of bromine (Br). We further aim to compare the protostellar Br abundance with that measured by Rosetta in the ices of comet 67P/Churyumov-Gerasimenko. Archival Herschel data of Orion KL, Sgr B2(N), and NGC 6334I are examined for the presence of HBr and HBr$^{+}$ emission or absorption lines. A chemical network for modelling HBr in protostellar molecular gas is compiled to aid in the interpretation. HBr and HBr$^{+}$ were not detected towards any of our targets. However, in the Orion KL Hot Core, our upper limit on HBr/H$_{2}$O is a factor of ten below the ratio measured in comet 67P. This result is consistent with the chemical network prediction that HBr is not a dominant gas-phase Br carrier. Cometary HBr is likely predominantly formed in icy grain mantles which lock up nearly all elemental Br.Comment: Accepted for publication in A&A. 9 pages, 6 figure

Predicting binding energies of astrochemically relevant molecules via machine learning

The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with time-consuming experiments, computationally expensive quantum chemical calculations, or the inexpensive, but inaccurate, linear addition method. In this work we propose a new method based on machine learning for predicting binding energies that is accurate, yet computationally inexpensive. A machine learning model based on Gaussian Process Regression is created and trained on a database of binding energies of molecules collected from laboratory experiments presented in the literature. The molecules in the database are categorized by their features, such as mono- or multilayer coverage, binding surface, functional groups, valence electrons, and H-bond acceptors and donors. The performance of the model is assessed with five-fold and leave-one-molecule-out cross validation. Predictions are generally accurate, with differences between predicted and literature binding energies values of less than $\pm$20\%. The validated model is used to predict the binding energies of twenty one molecules that have recently been detected in the interstellar medium, but for which binding energy values are not known. A simplified model is used to visualize where the snowlines of these molecules would be located in a protoplanetary disk. This work demonstrates that machine learning can be employed to accurately and rapidly predict binding energies of molecules. Machine learning complements current laboratory experiments and quantum chemical computational studies. The predicted binding energies will find use in the modelling of astrochemical and planet-forming environments.Comment: Accepted in astronomy and astrophysic

Advances in Genetical Genomics of Plants

Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research

Comparison of quantum field perturbation theory for the light front with the theory in lorentz coordinates

The relationship between the perturbation theory in light-front coordinates and Lorentz-covariant perturbation theory is investigated. A method for finding the difference between separate terms of the corresponding series without their explicit evaluation is proposed. A procedure of constructing additional counter-terms to the canonical Hamiltonian that compensate this difference at any finite order is proposed. For the Yukawa model, the light-front Hamiltonian with all of these counter-terms is obtained in a closed form. Possible application of this approach to gauge theories is discussed.Comment: LaTex 2.09, 20 pages, 5 figure

Why pair production cures covariance in the light-front?

We show that the light-front vaccum is not trivial, and the Fock space for positive energy quanta solutions is not complete. As an example of this non triviality we have calculated the electromagnetic current for scalar bosons in the background field method were the covariance is restored through considering the complete Fock space of solutions. We also show thus that the method of "dislocating the integration pole" is nothing more than a particular case of this, so that such an "ad hoc" prescription can be dispensed altogether if we deal with the whole Fock space. In this work we construct the electromagnetic current operator for a system composed of two free bosons. The technique employed to deduce these operators is through the definition of global propagators in the light front when a background electromagnetic field acts on one of the particles.Comment: 11 pages, 2 figure

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds.

MAIN CONCLUSION: During re-establishment of desiccation tolerance (DT), early events promote initial protection and growth arrest, while late events promote stress adaptation and contribute to survival in the dry state. Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose desiccation tolerance (DT) while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). To gain temporal resolution and identify relevant genes in this process, data from a time series of microarrays were used to build a gene co-expression network. The network has two regions, namely early response (ER) and late response (LR). Genes in the ER region are related to biological processes, such as dormancy, acquisition of DT and drought, amplification of signals, growth arrest and induction of protection mechanisms (such as LEA proteins). Genes in the LR region lead to inhibition of photosynthesis and primary metabolism, promote adaptation to stress conditions and contribute to seed longevity. Phenotyping of 12 hubs in relation to re-establishment of DT with T-DNA insertion lines indicated a significant increase in the ability to re-establish DT compared with the wild-type in the lines cbsx4, at3g53040 and at4g25580, suggesting the operation of redundant and compensatory mechanisms. Moreover, we show that re-establishment of DT by polyethylene glycol and ABA occurs through partially overlapping mechanisms. Our data confirm that co-expression network analysis is a valid approach to examine data from time series of transcriptome analysis, as it provides promising insights into biologically relevant relations that help to generate new information about the roles of certain genes for DT

Global analysis of gene expression associated with chlorophyll retention in soybean seeds.

Edição Especial contendo os Anais do XVIII Congresso Brasileiro de Sementes, Florianópolis, set. 2013

The formation of CO2_2 through consumption of gas-phase CO on vacuum-UV irradiated water ice

[Abridged] Observations of protoplanetary disks suggest that they are depleted in gas-phase CO. It has been posed that gas-phase CO is chemically consumed and converted into less volatile species through gas-grain processes. Observations of interstellar ices reveal a CO$_2$ component within H$_2$O ice suggesting co-formation. The aim of this work is to experimentally verify the interaction of gas-phase CO with solid-state OH radicals above the sublimation temperature of CO. Amorphous solid water (ASW) is deposited at 15 K and followed by vacuum-UV (VUV) irradiation to dissociate H$_2$O and create OH radicals. Gas-phase CO is simultaneously admitted and only adsorbs with a short residence time on the ASW. Products in the solid state are studied with infrared spectroscopy and once released into the gas phase with mass spectrometry. Results show that gas-phase CO is converted into CO$_2$, with an efficiency of 7-27%, when interacting with VUV irradiated ASW. Between 40 and 90 K, CO$_2$ production is constant, above 90 K, O$_2$ production takes over. In the temperature range of 40-60 K, the CO$_2$ remains in the solid state, while at temperatures $\geq$ 70 K the formed CO$_2$ is released into the gas phase. We conclude that gas-phase CO reacts with solid-state OH radicals above its sublimation temperature. This gas-phase CO and solid-state OH radical interaction could explain the observed CO$_2$ embedded in water-rich ices. It may also contribute to the observed lack of gas-phase CO in planet-forming disks, as previously suggested. Our experiments indicate a lower water ice dissociation efficiency than originally adopted in model descriptions of planet-forming disks and molecular clouds. Incorporation of the reduced water ice dissociation and increased binding energy of CO on a water ice surfaces in these models would allow investigation of this gas-grain interaction to its full extend.Comment: Accepted for publication in Astronomy & Astrophysic