Unidentified Features Research Articles

Quantitative Proteomics Identifies DNA Repair as a Novel Biological Function for Hepatocyte Nuclear Factor 4α in Colorectal Cancer Cells.

Hepatocyte nuclear factor 4α (HNF4α) is a transcription factor that acts as a master regulator of genes for several endoderm-derived tissues, including the intestine, in which it plays a central role during development and tumorigenesis. To better define the mechanisms by which HNF4α can influence these processes, we identified proteins interacting with HNF4α using stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomics with either immunoprecipitation of green fluorescent protein (GFP) or with proximity-dependent purification by the biotin ligase BirA (BioID), both fused to HNF4α. Surprisingly, these analyses identified a significant enrichment of proteins characterized with a role in DNA repair, a so far unidentified biological feature of this transcription factor. Several of these proteins including PARP1, RAD50, and DNA-PKcs were confirmed to interact with HNF4α in colorectal cancer cell lines. Following DNA damage, HNF4α was able to increase cell viability in colorectal cancer cells. Overall, these observations identify a potential role for this transcription factor during the DNA damage response.

An X-ray spectroscopic search for dark matter and unidentified line signatures in the Perseus cluster with Hitomi

Abstract The reported detection of a 3.5 keV emission signal in the Perseus cluster core by Bulbul et al. (2014, ApJ, 789, 13) was ruled out at high confidence in analysis conducted by Aharonian et al. (2017, ApJ, 837, L15) of X-ray spectra at 5 eV energy resolution obtained with the Hitomi observatory Soft X-ray Spectrometer (SXS). Using the same data, we search the full 2–12 keV SXS energy band for previously unidentified emission and absorption features. No significant unidentified line emission or absorption is found. Line flux upper limits (1σ per resolution element) vary with photon energy and assumed intrinsic width, decreasing from ∼100 at 2 keV to <10 photons cm−2 s−1 sr−1 over most of the 5–10 keV energy range for a Gaussian line with Doppler broadening of 640 km s−1. Limits for narrower and broader lines have a similar energy dependence and are systematically smaller and larger, respectively. These line flux limits are used to constrain the decay rate of hypothetical dark matter candidates. For the sterile neutrino decay rate, we place new constraints over the mass range of 4–24 keV with mass resolution better than any previous X-ray analysis. Additionally, the accuracy of relevant thermal spectral models and atomic data are evaluated. The Perseus cluster spectra may be described by a composite of multi-temperature thermal and active galactic nuclei (AGN) power-law continua. Superposed on these, a few line emission signals possibly originating from unmodeled atomic processes (including Si xiv and Fe xxv) are marginally detected and tabulated. Comparisons with previous X-ray upper limits and future prospects for dark matter searches using high-energy resolution spectroscopy are discussed.

Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites

BackgroundExposure to arsenic and cadmium is common. Epidemiological and animal studies have suggested that exposure to these two heavy metals can cause metabolic health problems, including type 2 diabetes (T2DM). It has been hypothesized that T2DM could be mediated through the gut microbiome and the metabolites it produces. Although many studies have investigated the association between the gut microbiome and T2DM, few have focused on the connection to arsenic and cadmium. ResultsWe applied 16S rRNA gene amplicon sequencing and untargeted LC-MS/MS metabolomics to examine the changes in the gut microbiome and metabolite profiles of exposed mice to relevant levels of cadmium and arsenic in the drinking water over two weeks. Cadmium chloride (Cd) exposure significantly changed the mice gut microbiome and resulted in a significantly lower microbial diversity whereas sodium arsenite (As) caused a non-significant decrease in microbial diversity. For Cd and As treatment respectively, we identified 5 and 2 phyla with significant changes and 42 and 24 genera. Bacterial genera that were observed to decline upon both treatments, included several butyrate-producers. Both As and Cd treatment perturbed the metabolome significantly, with 50 ppm Cd compound exposure having the greatest effect when compared to 50 ppm As compound exposure. Two unidentified features were differentially abundant in the As group, while 33 features changed in the Cd group. Differential abundance analysis of all bile acid associated molecular components showed differences under both treatments. Finally, integrative network analysis via bipartite correlation networks suggested that several genera, including the metabolically important Blautia, Eisenbergiella, Clostridium_XlVa, etc. declined in numbers of metabolite interactions. ConclusionsThese results demonstrated that As and Cd exposure caused significant changes to the gut microbiome and metabolome by affecting bile acids, amino acids and taxa associated with metabolic health.

Organic Molecules in the Icy Bodies of Planetary Systems – Accepted Notions and New Ideas

Abstract Cometary bodies are acknowledged to contain some of the most pristine matter in the Solar System, including ices and minerals. Certain number of previously unidentified spectral emission features detected in comets can be explained as emission by hydrocarbon molecules enclosed in a Shpolskii matrix and forming frozen hydrocarbon particles. UV-induced photoluminescence spectra of several self-organized molecules exhibit emission lines coincident with unidentified cometary lines, and open the possibility of the presence of this complex organic as components of the pristine organic inventory of comets. Complex organic was detected also in three satellites of Saturn. We describe in this paper results of our investigation of complex organic of the small bodies and present new approaches and hypotheses.

Metabolome changes are induced in the arbuscular mycorrhizal fungus Gigaspora margarita by germination and by its bacterial endosymbiont.

Metabolomic profiling is becoming an increasingly important technique in the larger field of systems biology by allowing the simultaneous measurement of thousands of small molecules participating in and resulting from cellular reactions. In this way, metabolomics presents an opportunity to observe the physiological state of a system, which may provide the ability to monitor the whole of cellular metabolism as the technology progresses. The arbuscular mycorrhizal fungus Gigaspora margarita has not previously been explored with regard to metabolite composition. To develop a better understanding of G. margarita and the influences of its endosymbiont Candidatus Glomeribacter gigasporarum, a metabolomic analysis was applied to quiescent and germinated spores with and without endobacteria. Over 100 metabolites were identified and greater than 2600 unique unidentified spectral features were observed. Multivariate analysis of the metabolomes was performed, and a differentiation between all metabolic states of spores and spores hosting the endobacteria was observed. The known metabolites were recruited to many biochemical pathways, with many being involved in maintenance of the antioxidant potential, tyrosine metabolism, and melanin production. Each of the pathways had higher metabolite abundances in the presence of the endosymbiont. These metabolomics data also agree with previously reported transcriptomics results demonstrating the capability of this technique to confirm hypotheses and showing the feasibility of multi-omic approaches for the study of arbuscular mycorrhizal fungi and their endobacterial communities. Challenges still exist in metabolomic analysis, e.g., the identification of compounds is demanding due to incomplete libraries. A metabolomics technique to probe the effects of bacterial endosymbionts on fungal physiology is presented herein, and this method is useful for hypothesis generation as well as testing as noted above.

METHODOLOGICAL TRAINING SYSTEM OF FUTURE TEACHERS FOR SPECIALIZED TEACHING AND ITS STRUCTURE

At present, the system of teacher training for future teachers being formed does not take into account the true nature of the methodological assistance that arises in the process of solving various practical tasks of the teacher. Our research is dedicated to form a methodological preparation system of future teachers for specialized teaching in curricular and extracurricular teaching processes. In the current paper we list the opportunities for learning, teaching and learning, as well as the presence of a leading contradiction between the unidentified functional features of the components that form the methodological system for the training of future teachers in curricula and outside the learning process. Thus, scientifically formulated methodological training allows future teachers to adapt to various changes in their professional assistance, skillfully apply teaching methods and use them by changing, using traditional and innovative approaches flexibly within their pedagogical "laboratory" framework to combine methodological knowledge and skills.Purpose of the study: To develop a system of methodological training of future professional education teachers in the process of study and out-of-class learning and to describe their functional components.Research Methods: studying of the mechanism of conditions in the field of globalization, preservation of the originality, cultural values, customs, traditions, expressing the importance of self-determination.Practical value: According to the system of methodological training provided, the future teacher develops methodological knowledge, business and skill based on subject and metaphorically developed functional character.

A high-resolution HPLC-QqTOF platform using parallel reaction monitoring for in-depth lipid discovery and rapid profiling

Here, we developed a robust lipidomics workflow merging both targeted and untargeted approaches on a single liquid chromatography coupled to quadrupole-time of flight (LC-QqTOF) mass spectrometry platform with parallel reaction monitoring (PRM). PRM assays integrate both untargeted profiling from MS1 scans and targeted profiling obtained from MS/MS data. This workflow enabled the discovery of more than 2300 unidentified features and identification of more than 600 lipid species from 23 lipid classes at the level of fatty acid/long chain base/sterol composition in a barley root extracts. We detected the presence of 142 glycosyl inositol phosphorylceramides (GIPC) with HN(Ac)-HA as the core structure of the polar head, 12 cardiolipins and 17 glucuronosyl diacylglycerols (GlcADG) which have been rarely reported previously for cereal crops. Using a scheduled algorithm with up to 100 precursors multiplexed per duty cycle, the PRM assay was able to achieve a rapid profiling of 291 species based on MS/MS data by a single injection. We used this novel approach to demonstrate the applicability and efficiency of the workflow to study salt stress induced changes in the barley root lipidome. Results show that 221 targeted lipids and 888 unknown features were found to have changed significantly in response to salt stress. This combined targeted and untargeted single workflow approach provides novel applications of lipidomics addressing biological questions.

Unidentified emission features in the R Coronae Borealis star V854 Centauri

During its 2012 decline, the R Coronae Borealis star (RCB) V854 Cen was spectroscopically monitored with X-shooter on the ESO Very Large Telescope. The obscured optical and near-infrared spectrum exhibits many narrow and several broad emission features, as previously observed. The envelope is spatially resolved along the slit and allows for a detailed study of the circumstellar material. In this Letter, we report on the properties of a number of unidentified visual emission features (UFs), including the detection of a new feature at 8692 Å. These UFs have been observed in the Red Rectangle (RR), but their chemical and physical nature is still a mystery. The previously known UFs behave similarly in the RR and in V854 Cen, but are not detected in six other observed RCBs. Some hydrogen might be required for the formation of their carrier(s). The λ8692 UF is present in all RCBs. Its carrier is likely of a carbonaceous molecular nature, presumably different from that of the other UFs.

Analysis of the Human Mucosal Response to Cholera Reveals Sustained Activation of Innate Immune Signaling Pathways.

To better understand the innate immune response to Vibrio cholerae infection, we tracked gene expression in the duodenal mucosa of 11 Bangladeshi adults with cholera, using biopsy specimens obtained immediately after rehydration and 30 and 180 days later. We identified differentially expressed genes and performed an analysis to predict differentially regulated pathways and upstream regulators. During acute cholera, there was a broad increase in the expression of genes associated with innate immunity, including activation of the NF-κB, mitogen-activated protein kinase (MAPK), and Toll-like receptor (TLR)-mediated signaling pathways, which, unexpectedly, persisted even 30 days after infection. Focusing on early differences in gene expression, we identified 37 genes that were differentially expressed on days 2 and 30 across the 11 participants. These genes included the endosomal Toll-like receptor gene TLR8, which was expressed in lamina propria cells. Underscoring a potential role for endosomal TLR-mediated signaling in vivo, our pathway analysis found that interferon regulatory factor 7 and beta 1 and alpha 2 interferons were among the top upstream regulators activated during cholera. Among the innate immune effectors, we found that the gene for DUOX2, an NADPH oxidase involved in the maintenance of intestinal homeostasis, was upregulated in intestinal epithelial cells during cholera. Notably, the observed increases in DUOX2 and TLR8 expression were also modeled in vitro when Caco-2 or THP-1 cells, respectively, were stimulated with live V. cholerae but not with heat-killed organisms or cholera toxin alone. These previously unidentified features of the innate immune response to V. cholerae extend our understanding of the mucosal immune signaling pathways and effectors activated in vivo following cholera.

Improving calibration and validation of cosmic-ray neutron sensors in the light of spatial sensitivity

Abstract. In the last few years the method of cosmic-ray neutron sensing (CRNS) has gained popularity among hydrologists, physicists, and land-surface modelers. The sensor provides continuous soil moisture data, averaged over several hectares and tens of decimeters in depth. However, the signal still may contain unidentified features of hydrological processes, and many calibration datasets are often required in order to find reliable relations between neutron intensity and water dynamics. Recent insights into environmental neutrons accurately described the spatial sensitivity of the sensor and thus allowed one to quantify the contribution of individual sample locations to the CRNS signal. Consequently, data points of calibration and validation datasets are suggested to be averaged using a more physically based weighting approach. In this work, a revised sensitivity function is used to calculate weighted averages of point data. The function is different from the simple exponential convention by the extraordinary sensitivity to the first few meters around the probe, and by dependencies on air pressure, air humidity, soil moisture, and vegetation. The approach is extensively tested at six distinct monitoring sites: two sites with multiple calibration datasets and four sites with continuous time series datasets. In all cases, the revised averaging method improved the performance of the CRNS products. The revised approach further helped to reveal hidden hydrological processes which otherwise remained unexplained in the data or were lost in the process of overcalibration. The presented weighting approach increases the overall accuracy of CRNS products and will have an impact on all their applications in agriculture, hydrology, and modeling.

Metabolomics reveals distinct neurochemical profiles associated with stress resilience

Acute social defeat represents a naturalistic form of conditioned fear and is an excellent model in which to investigate the biological basis of stress resilience. While there is growing interest in identifying biomarkers of stress resilience, until recently, it has not been feasible to associate levels of large numbers of neurochemicals and metabolites to stress-related phenotypes. The objective of the present study was to use an untargeted metabolomics approach to identify known and unknown neurochemicals in select brain regions that distinguish susceptible and resistant individuals in two rodent models of acute social defeat. In the first experiment, male mice were first phenotyped as resistant or susceptible. Then, mice were subjected to acute social defeat, and tissues were immediately collected from the ventromedial prefrontal cortex (vmPFC), basolateral/central amygdala (BLA/CeA), nucleus accumbens (NAc), and dorsal hippocampus (dHPC). Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS) was used for the detection of water-soluble neurochemicals. In the second experiment, male Syrian hamsters were paired in daily agonistic encounters for 2 weeks, during which they formed stable dominant-subordinate relationships. Then, 24 h after the last dominance encounter, animals were exposed to acute social defeat stress. Immediately after social defeat, tissue was collected from the vmPFC, BLA/CeA, NAc, and dHPC for analysis using UPLC-HRMS. Although no single biomarker characterized stress-related phenotypes in both species, commonalities were found. For instance, in both model systems, animals resistant to social defeat stress also show increased concentration of molecules to protect against oxidative stress in the NAc and vmPFC. Additionally, in both mice and hamsters, unidentified spectral features were preliminarily annotated as potential targets for future experiments. Overall, these findings suggest that a metabolomics approach can identify functional groups of neurochemicals that may serve as novel targets for the diagnosis, treatment, or prevention of stress-related mental illness.

Laboratory measurements compellingly supports a charge-exchange mechanism for the “Dark matter” ∼ 3.5 keV X-ray line

SynopsisThe reported observations of an unidentified X-ray line feature at ∼ 3.5 keV from galaxy clusters have driven a lively discussion about its possible dark matter origin. Motivated by this, we have investigated the X-ray spectra of highly ionized bare sulfur ions following charge exchange with residual gas in the electron beam ion trap, as a source or a contributor to this X-ray line. The X-ray feature at about 3.5 keV shows up in the experiment, which could explain the the astrophysical observations and confirm the predictions of Gu et al.

LABORATORY MEASUREMENTS COMPELLINGLY SUPPORT A CHARGE-EXCHANGE MECHANISM FOR THE “DARK MATTER” ∼3.5 keV X-Ray LINE

ABSTRACT The reported observations of an unidentified X-ray line feature at ∼3.5 keV have driven a lively discussion about its possible dark matter origin. Motivated by this, we have measured the K-shell X-ray spectra of highly ionized bare sulfur ions following charge exchange with gaseous molecules in an electron beam ion trap, as a source of or a contributor to this X-ray line. We produced S16+ and S15+ ions and let them capture electrons in collision with those molecules with the electron beam turned off while recording X-ray spectra. We observed a charge-exchange-induced X-ray feature at the Lyman series limit (3.47 ± 0.06 keV). The inferred X-ray energy is in full agreement with the reported astrophysical observations and supports the novel scenario proposed by Gu et al.

TracMouse: A computer aided movement analysis script for the mouse inverted horizontal grid test.

In rodents, detection and quantification of motor impairments is difficult. The traction test (inverted grid with mice clinging to the underside) currently has no objective rating system. We here developed and validated the semi-automatic MATLAB script TracMouse for unbiased detection of video-recorded movement patterns. High precision videos were analyzed by: (i) principal identification of anatomical paw details frame-by-frame by an experimentally blinded rater; (ii) automatic retrieval of proxies by TracMouse for individual paws. The basic states of Hold and Step were discriminated as duration and frequency, and these principle parameters were converted into static and dynamic endpoints and their discriminating power assessed in a dopaminergic lesion model. Relative to hind paws, forepaws performed ~4 times more steps, they were ~20% longer, and Hold duration was ~5 times shorter in normal C57Bl/6 mice. Thus, forepaw steps were classified as exploratory, hind paw movement as locomotive. Multiple novel features pertaining to paw sequence, step lengths and exploratory touches were accessible through TracMouse and revealed subtle Parkinsonian phenotypes. Novel proxies using TracMouse revealed previously unidentified features of movement and may aid the understanding of (i) brain circuits related to motor planning and execution, and (ii) phenotype detection in experimental models of movement disorders.

Classification of Gunshot Residue Using Laser Electrospray Mass Spectrometry and Offline Multivariate Statistical Analysis.

Nonresonant laser vaporization combined with high-resolution electrospray time-of-flight mass spectrometry enables analysis of a casing after discharge of a firearm revealing organic signature molecules including methyl centralite (MC), diphenylamine (DPA), N-nitrosodiphenylamine (N-NO-DPA), 4-nitrodiphenylamine (4-NDPA), a DPA adduct, and multiple unidentified features not observed in previous mass spectral measurements. Collision-induced dissociation measurements of unknown GSR signature ions reveals inorganic barium and derivatives BaOH, BaOHCH3, BaCH3COO remaining from the primer. Both hydrophilic and hydrophobic signatures are detected using water-methanol electrospray solution. Offline principal component analysis and discrimination of the laser electrospray mass spectral (LEMS) measurements resulted in perfect classification of the gun shot residue with respect to the manufacturer. Principal component analysis of recycled and reloaded casings resulted in classification of the penultimate manufacturer with an accuracy of 89%.

Nonthermal effects of acceleration in the resonance interaction between two uniformly accelerated atoms

We study the resonance interaction between two uniformly accelerated identical atoms, one excited and the other in the ground state, prepared in a correlated (symmetric or antisymmetric) state and interacting with the scalar field or the electromagnetic field in the vacuum state. In this case (resonance interaction), the interatomic interaction is a second-order effect in the atom-field coupling. We separate the contributions of vacuum fluctuations and radiation reaction to the resonance energy shift of the system, and show that only radiation reaction contributes, while Unruh thermal fluctuations do not affect the resonance interaction. We also find that beyond a characteristic length scale related to the atomic acceleration, non-thermal effects in the radiation reaction contribution change the distance-dependence of the resonance interaction. Finally, we find that previously unidentified features appear, compared with the scalar field case, when the interaction with the electromagnetic field is considered, as a consequence of the peculiar nature of the vacuum quantum noise of the electromagnetic field in a relativistically accelerated background.

Large-scale dynamo action precedes turbulence in shearing box simulations of the magnetorotational instability

We study the dynamo generation (exponential growth) of large scale (planar averaged) fields in unstratified shearing box simulations of the magnetorotational instability (MRI). In contrast to previous studies restricted to horizontal ($x$-$y$) averaging, we demonstrate the presence of large scale fields when either horizontal or vertical ($y$-$z$) averaging is employed. By computing planar averaged fields and power spectra, we find large scale dynamo action in the early MRI growth phase---a previously unidentified feature. Fast growing horizontal low modes and fiducial vertical modes over a narrow range of wave numbers amplify these planar averaged fields in the MRI growth phase, before turbulence sets in. The large scale field growth requires linear fluctuations but not nonlinear turbulence (as defined by mode-mode coupling) and grows as a direct global mode of the MRI. Only by vertical averaging, can it be shown that the growth of horizontal low wavenumber MRI modes directly feed-back to the initial vertical field providing a clue as to why the large scale vertical field sustains against turbulent diffusion in the saturation regime. We compute the terms in the planar averaged mean field equations to identify the individual contributions to large scale field growth for both vertical and horizontal averaging. The large scale fields obtained from such vertical averaging are found to compare well with global cylindrical simulations and quasilinear analytical analysis from a previous study by Ebrahimi \& Blackman. We discuss the potential implications of these new results for understanding large scale MRI dynamo saturation and turbulence.

ON THE RELATION BETWEEN THE MYSTERIOUS 21 μm EMISSION FEATURE OF POST-ASYMPTOTIC GIANT BRANCH STARS AND THEIR MASS-LOSS RATES

ABSTRACT Over two decades ago, a prominent, mysterious emission band peaking at ∼20.1 μm was serendipitously detected in four preplanetary nebulae (PPNe; also known as “protoplanetary nebulae”). To date, this spectral feature, designated as the “21 μm” feature, has been seen in 27 carbon-rich PPNe in the Milky Way and the Magellanic Clouds. The nature of its carriers remains unknown although many candidate materials have been proposed. The 21 μm sources also exhibit an equally mysterious, unidentified emission feature peaking at 30 μm. While the 21 μm feature is exclusively seen in PPNe, a short-lived evolutionary stage between the end of the asymptotic giant branch (AGB) and planetary nebula (PN) phases, the 30 μm feature is more commonly observed in all stages of stellar evolution from the AGB through PPN to PN phases. We derive the stellar mass-loss rates ( ) of these sources from their infrared (IR) emission, using the “2-DUST” radiative transfer code for axisymmetric dusty systems which allows one to distinguish the mass-loss rates of the AGB phase ( ) from that of the superwind ( ) phase. We examine the correlation between or and the fluxes emitted from the 21 and 30 μm features. We find that both features tend to correlate with , suggesting that their carriers are probably formed in the AGB phase. The nondetection of the 21 μm feature in AGB stars suggests that, unlike the 30 μm feature, the excitation of the carriers of the 21 μm feature may require ultraviolet photons which are available in PPNe but not in AGB stars.

Untargeted Metabolomics Reveal State‐Dependent Neurochemical Changes in Frontal Association (FrA) and Motor Cortex (M1) of C57BL/6J (B6) Mouse

Neurochemical monitoring using targeted and untargeted metabolomic approaches can provide unique insights into changes in brain chemistry that occur normally, in response to pathology, and after therapeutic intervention. This study used an established untargeted metabolomics method (Anal. Chem., 82:3212, 2010) to identify known and unknown brain metabolites by means of ultra‐performance liquid chromatography coupled with high‐resolution mass spectrometry (UPLC‐HRMS) on an Exactive Plus Orbitrap Instrument (Thermo Fisher Scientific). To date, analyses have been performed on microdialysis samples (n=408) obtained from FrA and M1 of intact, behaving B6 mice (n=5). Microdialysis samples were collected in conformance with the FASEB Statement of Principles for the use of animals in research during electroencephalographically confirmed intervals of extended wakefulness, recovery sleep, and subsequent extended wakefulness. Partial least squares discriminant analyses showed reliable and statistically significant state‐dependent clustering of metabolites. In addition to identifying approximately 20 known molecules, analyses revealed consistent associations with the first wakefulness period (acetoacetate and lactate), sleep (valine and leucine/isoleucine), and the second wakefulness period (pyruvate and tyrosine). The results also provided a list of unidentified spectral features in FrA (n=33) and M1 (n=43) that are being subjected to additional analyses using the metabolite databases (https://metlin.scripps.edu/index.php and http://www.hmdb.ca). These spectral features may ultimately lead to the discovery of novel molecules not previously known to be associated with states of sleep and wakefulness. By integrating the dynamic sampling tool of microdialysis with the unparalleled capabilities of UPLC‐HRMS, these studies are identifying and quantifying state‐dependent and region‐specific changes in mouse brain metabolome.Support or Funding InformationNIH grants HL65252 (RL and HAB); MH099231 and 1P01NS083514 (CC and GT); and support from the UT Joint Institute for Biological Sciences.

Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan

Xanthomonas campestris pv. campestris (Xcc) is the major producer of the exopolysaccharide xanthan, the commercially most important natural polysaccharide of microbial origin. The current work provides deeper insights into the yet uncharacterized transcriptomic features of the xanthan producing strain Xcc-B100. Towards this goal, RNA sequencing of a library based on the selective enrichment of the 5′ ends of native transcripts was performed. This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions. Among them, 1545 mapped upstream of an actively transcribed CDS and 1363 were classified as novel TSSs representing antisense, internal, and TSSs belonging to previously unidentified genomic features. Analyzing the transcriptional strength of primary and antisense TSSs revealed that in some instances antisense transcription seemed to be initiated at a higher level than its sense counterpart. Mapping the exact positions of TSSs aided in the identification of promoter consensus motifs, ribosomal binding sites, and enhanced the genome annotation of 159 in silico predicted translational start (TLS) sites. The global view on length distribution of the 5′ untranslated regions (5′-UTRs) deduced from the data pointed to the occurrence of leaderless transcripts and transcripts with unusually long 5′-UTRs, in addition to identifying seven putative riboswitch elements for Xcc-B100. Concerning the biosynthesis of xanthan, we focused on the transcriptional organization of the gum gene cluster. Under the conditions tested, we present evidence for a complex transcription pattern of the gum genes with multiple TSSs and an obvious considerable role of antisense transcription. The gene gumB, encoding an outer membrane xanthan exporter, is presented here as an example for genes that possessed a strong antisense TSS. Keywords: Xanthomonads, plant pathogens, RNA sequencing, 5′ enriched ends, transcription start sites, xanthan biosynthesis