Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina

Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.Fil: Martínez, Fabiana Lilian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; Argentina. University of Maryland; Estados UnidosFil: Anton, B. P.. New England Biolabs; Estados UnidosFil: DasSarma, P.. University of Maryland; Estados UnidosFil: Rajal, Verónica Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; ArgentinaFil: Irazusta, Verónica Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; ArgentinaFil: Roberts, Roy. New England Biolabs; Estados UnidosFil: DasSarma, S.. University of Maryland; Estados Unido

Spin-isospin textured excitations in a double layer at filling factor ν=2\nu =2

We study the charged excitations of a double layer at filling factor 2 in the ferromagnetic regime. In a wide range of Zeeman and tunneling splittings we find that the low energy charged excitations are spin-isospin textures with the charge mostly located in one of the layers. As tunneling increases, the parent spin texture in one layer becomes larger and it induces, in the other layer, a shadow spin texture antiferromagnetically coupled to the parent texture. These new quasiparticles should be observable by measuring the strong dependence of its spin on tunneling and Zeeman couplings.Comment: 4 pages, 4 figure

Microbial Fuel Cells Applied to the Metabolically-Based Detection of Extraterrestrial Life

Since the 1970's, when the Viking spacecrafts carried out experiments aimed to the detection of microbial metabolism on the surface of Mars, the search for nonspecific methods to detect life in situ has been one of the goals of astrobiology. It is usually required that the methodology can detect life independently from its composition or form, and that the chosen biological signature points to a feature common to all living systems, as the presence of metabolism. In this paper we evaluate the use of Microbial Fuel Cells (MFCs) for the detection of microbial life in situ. MFCs are electrochemical devices originally developed as power electrical sources, and can be described as fuel cells in which the anode is submerged in a medium that contains microorganisms. These microorganisms, as part of their metabolic process, oxidize organic material releasing electrons that contribute to the electric current, which is therefore proportional to metabolic and other redox processes. We show that power and current density values measured in MFCs using microorganism cultures or soil samples in the anode are much larger than those obtained using a medium free of microorganisms or sterilized soil samples, respectively. In particular, we found that this is true for extremophiles, usually proposed to live in extraterrestrial environments. Therefore, our results show that MFCs have the potential to be used to detect microbial life in situ.Comment: To be published in Astrobiolog

Conductivity in quasi two-dimensional systems

The conductivity in quasi two-dimensional systems is calculated using the quantum kinetic equation. Linearizing the Lenard-Balescu collision integral with the extension to include external field dependences allows one to calculate the conductivity with diagrams beyond the GW approximation including maximally crossed lines. Consequently the weak localization correction as an interference effect appears here from the field dependence of the collision integral (the latter dependence sometimes called intra-collisional field effect). It is shown that this weak localization correction has the same origin as the Debye-Onsager relaxation effect in plasma physics. The approximation is applied to a system of quasi two-dimensional electrons in hetero-junctions which interact with charged and neutral impurities and the low temperature correction to the conductivity is calculated analytically. It turns out that the dynamical screening due to charged impurities leads to a linear temperature dependence, while the scattering from neutral impurities leads to the usual Fermi-liquid behavior. By considering an appropriate mass action law to determine the ratio of charged to neutral impurities we can describe the experimental metal-insulator transition at low temperatures as a Mott-Hubbard transition.Comment: 7 pages 7 pages appendix 11 figure

Temperature dependent resistivity of spin-split subbands in GaAs 2D hole system

We calculate the temperature dependent resistivity in spin-split subbands induced by the inversion asymmetry of the confining potential in GaAs 2D hole systems. By considering both temperature dependent multisubband screening of impurity disorder and hole-hole scattering we find that the strength of the metallic behavior depends on the symmetry of the confining potential (i.e., spin-splitting) over a large range of hole density. At low density above the metal-insulator transition we find that effective disorder reduces the enhancement of the metallic behavior induced by spin-splitting. Our theory is in good qualitative agreement with existing experiments

Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA

<p>Abstract</p> <p>Background</p> <p>Archaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in several Archaea, including <it>Halobacterium </it>sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters.</p> <p>Results</p> <p>We attempted to knock out all six TBP and seven TFB genes in <it>Halobacterium </it>sp. NRC-1 using the <it>ura</it>3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, <it>tbp</it>CDF and <it>tfb</it>ACG, indicating that they are not essential for cell viability under standard conditions. Screening of a population of 1,000 candidate mutants showed that genes which did not yield mutants contained less that 0.1% knockouts, strongly suggesting that they are essential. The transcriptomes of two mutants, Δ<it>tbp</it>D and Δ<it>tfb</it>A, were compared to the parental strain and showed coordinate down regulation of many genes. Over 500 out of 2,677 total genes were regulated in the Δ<it>tbp</it>D and Δ<it>tfb</it>A mutants with 363 regulated in both, indicating that over 10% of genes in both strains require the action of both TbpD and TfbA for normal transcription. Culturing studies on the Δ<it>tbp</it>D and Δ<it>tfb</it>A mutant strains showed them to grow more slowly than the wild-type at an elevated temperature, 49°C, and they showed reduced viability at 56°C, suggesting TbpD and TfbA are involved in the heat shock response. Alignment of TBP and TFB protein sequences suggested the expansion of the TBP gene family, especially in <it>Halobacterium </it>sp. NRC-1, and TFB gene family in representatives of five different genera of haloarchaea in which genome sequences are available.</p> <p>Conclusion</p> <p>Six of thirteen TBP and TFB genes of <it>Halobacterium </it>sp. NRC-1 are non-essential under standard growth conditions. TbpD and TfbA coordinate the expression of over 10% of the genes in the NRC-1 genome. The Δ<it>tbp</it>D and Δ<it>tfb</it>A mutant strains are temperature sensitive, possibly as a result of down regulation of heat shock genes. Sequence alignments suggest the existence of several families of TBP and TFB transcription factors in <it>Halobacterium </it>which may function in transcription of different classes of genes.</p

Low-pass sequencing for microbial comparative genomics

BACKGROUND: We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile Haloarcula marismortui; (2) the non-pigmented Natrialba asiatica; (3) the psychrophile Halorubrum lacusprofundi and (4) the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. RESULTS: As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI) for their predicted proteins. Multiple insertion sequence (IS) elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP) and transcription factor IIB (TFB) homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. CONCLUSION: Despite the diverse habitats of these species, all five halophiles share (1) high GC content and (2) low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the IS-element rich genome of H. sp. NRC-1. Identification of multiple TBP and TFB homologs in these four halophiles are consistent with the hypothesis that different types of complex transcriptional regulation may occur through multiple TBP-TFB combinations in response to rapidly changing environmental conditions. Low-pass shotgun sequence analyses of genomes permit extensive and diverse analyses, and should be generally useful for comparative microbial genomics

Imaging Coulomb Islands in a Quantum Hall Interferometer

In the Quantum Hall regime, near integer filling factors, electrons should only be transmitted through spatially-separated edge states. However, in mesoscopic systems, electronic transmission turns out to be more complex, giving rise to a large spectrum of magnetoresistance oscillations. To explain these observations, recent models put forward that, as edge states come close to each other, electrons can hop between counterpropagating edge channels, or tunnel through Coulomb islands. Here, we use scanning gate microscopy to demonstrate the presence of quantum Hall Coulomb islands, and reveal the spatial structure of transport inside a quantum Hall interferometer. Electron islands locations are found by modulating the tunneling between edge states and confined electron orbits. Tuning the magnetic field, we unveil a continuous evolution of active electron islands. This allows to decrypt the complexity of high magnetic field magnetoresistance oscillations, and opens the way to further local scale manipulations of quantum Hall localized states

Complex Effects of Cytochrome P450 Monooxygenase on Purple Membrane and Bacterioruberin Production in an Extremely Halophilic Archaeon: Genetic, Phenotypic, and Transcriptomic Analyses

Halophilic archaea are known to produce a diverse array of pigments for phototrophy and photoprotection. The aim of this paper was to determine the role of a Halobacterium gene encoding the predicted cytochrome P450 monooxygenase (CYP174A1) in pigment synthesis through a combined genetic, phenotypic, and transcriptomic approach. We report on the observed phenotype changes [increased bacterioruberin levels and the loss of purple membrane (PM)] between the Halobacterium salinarum R1 and its CYP174A1-deletion mutant. In addition, we report on the whole-genome DNA microarray analysis, which supports the phenotype of PM loss. This work expands our understanding of the bop-gene regulon, and its relation to carotenoid biosynthesis, and sheds light on our broader understanding of the role (s) of CYP174A1 in archaeal pigment synthesis. To date, this is the first study in which the physiological role of any cytochrome P450 monooxygenase (CYP450) in extremely halophilic archaea has been reported