1,614 research outputs found
Molecular studies on some soil-Streptomyces strains of western region, Kingdom of Saudi Arabia (KSA)
Random amplified polymorphic of DNA-polymerase chain reaction (RAPD-PCR) analysis of the DNA extracted from seven Streptomyces strains of western region, KSA was the aim of this study. Partial sequence of 16S rRNA gene of Streptomyces polychromogenes was also attempted. Results show that a total number of 240 amplified fragments were amplified using 10 RAPD-PCR primers (OPA11, OPB10, OPB15, OPC03, OPC07, OPC18, OPD05, OPE05, OPO14 and OPO17). A total number of 97, 73, 88, 79, 100, 108 and 82 fragments were amplified from the DNA extracts of S. polychromogenes, Streptomyces chattanoogensis, Streptomyces lucensis, Streptomyces antibioticus, Streptomyces violans, Streptomyces griseorubiginosus and Streptomyces violaceus, respectively. An obvious variation in the amplified fragments was recorded using the 10 RAPD-PCR primers (31, 27, 17, 19, 23, 29, 24, 26, 23 and 21 fragments for the primers, respectively). The highest similarity (66.7%) was found between S. lucensis and S. chattanoogensis; lowest similarity (35%) was recorded between the gray S. chattanoogensis and the red S. violaceus. The 16S rRNA gene was isolated via PCR from the DNA of S. polychromogenes (1) and sequenced. Fragments of 1003 and 837 nts were amplified using the forward and reverse primers, respectively. On matching, a final sequence of about 1452 nts (GenBank: JQ962978.1) was obtained and compared with five universal Streptomyces strains and four bacterial clones. The percent identities between the isolate of this study and the compared bacterial strains was lowest (79.1%) compared to HQ844464.1 and highest (98.3%) compared to EU520331.1. Based on the phenotypic and genotypic (16S rRNA gene) features, the strain could be classified as a new strain of S. polychromogenes.Keywords: Identification, Streptomyces, RAPD-PCR, 16S rRNA gene, KSAAfrican Journal of Biotechnology Vol. 12(19), pp. 2558-256
Molecular and genetic characterization of OSH6 (Oryza sativa Homeobox 6) using dissociation (Ds) insertion mutant rice
Genetic studies of dissociation (Ds) insertion mutant rice plants indicated that ectopic expression of truncated OSH6 (Oryza sativa Homeobox 6) mRNA may be responsible for the mutant phenotype of knotted leaf formation at the peduncle. Additionally, ectopic expression of truncated OSH6 mRNA in the OSH6-Ds mutant plant led to alteration of other homeobox genes including OSH15 in leaf tissues. The OSH6-Ds mutant plant exhibited altered expression of more than 118 genes on a 22K rice microarray in comparison with wild type plants. Of these genes, 20 were up- or down-regulated in both OSH6-Ds and OSH6-overexpressing (OSH6-35S) plants. Especially, OsDof3 was not expressed in floral organs, but was present in the panicles of both OSH6-Ds and OSH6-35S plants. It is assumed that truncated OSH6 transcript might be actively involved in the gene expression during organ development. The genetic relationship between OSH6-Ds and OSH15 suggested that the formation of the extra leaf is independent of OSH6-Ds or OSH15 expression. These results suggest that truncated OSH6 mRNA influences lateral organ growth and development by regulating the expression of specific gene groups.Key words: Oryza sativa Homeobox 6 (OSH6) genes, Ds insertion lines, OSH15 mutant
DNA end resection by Dna2–Sgs1–RPA and its stimulation by Top3–Rmi1 and Mre11–Rad50–Xrs2
The repair of DNA double-strand breaks (DSBs) by homologous recombination requires processing of broken ends. For repair to start, the DSB must first be resected to generate a 3′-single-stranded DNA (ssDNA) overhang, which becomes a substrate for the DNA strand exchange protein, Rad51 (ref. 1). Genetic studies have implicated a multitude of proteins in the process, including helicases, nucleases and topoisomerases. Here we biochemically reconstitute elements of the resection process and reveal that it requires the nuclease Dna2, the RecQ-family helicase Sgs1 and the ssDNA-binding protein replication protein-A (RPA). We establish that Dna2, Sgs1 and RPA constitute a minimal protein complex capable of DNA resection in vitro. Sgs1 helicase unwinds the DNA to produce an intermediate that is digested by Dna2, and RPA stimulates DNA unwinding by Sgs1 in a species-specific manner. Interestingly, RPA is also required both to direct Dna2 nucleolytic activity to the 5′-terminated strand of the DNA break and to inhibit 3′ to 5′ degradation by Dna2, actions that generate and protect the 3′-ssDNA overhang, respectively. In addition to this core machinery, we establish that both the topoisomerase 3 (Top3) and Rmi1 complex and the Mre11–Rad50–Xrs2 complex (MRX) have important roles as stimulatory components. Stimulation of end resection by the Top3–Rmi1 heterodimer and the MRX proteins is by complex formation with Sgs1 (refs 5, 6), which unexpectedly stimulates DNA unwinding. We suggest that Top3–Rmi1 and MRX are important for recruitment of the Sgs1–Dna2 complex to DSBs. Our experiments provide a mechanistic framework for understanding the initial steps of recombinational DNA repair in eukaryotes
Atomic-scale observation of localized phonons at FeSe/SrTiO3 interface
In single unit-cell FeSe grown on SrTiO3, the superconductivity transition
temperature features a significant enhancement. Local phonon modes at the
interface associated with electron-phonon coupling may play an important role
in the interface-induced enhancement. However, such phonon modes have eluded
direct experimental observations. Indeed, the complicated atomic structure of
the interface brings challenges to obtain the accurate structure-phonon
relation knowledge from either experiment or theory, thus hindering our
understanding of the enhancement mechanism. Here, we achieve direct
characterizations of atomic structure and phonon modes at the FeSe/SrTiO3
interface with atomically resolved imaging and electron energy loss
spectroscopy in a scanning transmission electron microscope. We find several
phonon modes highly localized (~1.3 nm) at the unique double layer Ti-O
termination at the interface, one of which (~ 83 meV) engages in strong
interactions with the electrons in FeSe based on ab initio calculations. The
electron-phonon coupling strength for such a localized interface phonon with
short-range interactions is comparable to that of Fuchs-Kliewer (FK) phonon
mode with long-rang interactions. Thus, our atomic-scale study provides new
insights into understanding the origin of superconductivity enhancement at the
FeSe/SrTiO3 interface
Spin chirality on a two-dimensional frustrated lattice
The collective behavior of interacting magnetic moments can be strongly
influenced by the topology of the underlying lattice. In geometrically
frustrated spin systems, interesting chiral correlations may develop that are
related to the spin arrangement on triangular plaquettes. We report a study of
the spin chirality on a two-dimensional geometrically frustrated lattice. Our
new chemical synthesis methods allow us to produce large single crystal samples
of KFe3(OH)6(SO4)2, an ideal Kagome lattice antiferromagnet. Combined
thermodynamic and neutron scattering measurements reveal that the phase
transition to the ordered ground-state is unusual. At low temperatures,
application of a magnetic field induces a transition between states with
different non-trivial spin-textures.Comment: 7 pages, 4 figure
Recent Developments in the Casimir Effect
In this talk I review various developments in the past year concerning
quantum vacuum energy, the Casimir effect. In particular, there has been
continuing controversy surrounding the temperature correction to the Lifshitz
formula for the Casimir force between real materials, be they metals or
semiconductors. Consensus has emerged as to how Casimir energy accelerates in a
weak gravitational field; quantum vacuum energy, including the divergent parts
which renormalize the masses of the Casimir plates, accelerates indeed
according to the equivalence principle. Significant development has been
forthcoming in applying the multiple scattering formalism to describe the
interaction between nontrivial objects. In weak coupling, closed-form
expressions for the Casimir force between the bodies, which for example reveal
significant discrepancies from the naive proximity force approximation, can be
achieved in many cases.Comment: 29 pages, 14 figures, uses jpconf.cls style. Invited opening talk at
"60 Years of the Casimir Effect," Brasilia, June 21-29, 200
Note on New KLT relations
In this short note, we present two results about KLT relations discussed in
recent several papers. Our first result is the re-derivation of Mason-Skinner
MHV amplitude by applying the S_{n-3} permutation symmetric KLT relations
directly to MHV amplitude. Our second result is the equivalence proof of the
newly discovered S_{n-2} permutation symmetric KLT relations and the well-known
S_{n-3} permutation symmetric KLT relations. Although both formulas have been
shown to be correct by BCFW recursion relations, our result is the first direct
check using the regularized definition of the new formula.Comment: 15 Pages; v2: minor correction
Impact of foot-and-mouth disease on mastitis and culling on a large-scale dairy farm in Kenya
Foot and mouth disease (FMD) is a highly transmissible viral infection of cloven hooved animals associated with severe economic losses when introduced into FMD-free countries. Information on the impact of the disease in FMDV-endemic countries is poorly characterised yet essential for the prioritisation of scarce resources for disease control programmes. A FMD (virus serotype SAT2) outbreak on a large-scale dairy farm in Nakuru County, Kenya provided an opportunity to evaluate the impact of FMD on clinical mastitis and culling rate. A cohort approach followed animals over a 12-month period after the commencement of the outbreak. For culling, all animals were included; for mastitis, those over 18 months of age. FMD was recorded in 400/644 cattle over a 29-day period. During the follow-up period 76 animals were culled or died whilst in the over 18 month old cohort 63 developed clinical mastitis. Hazard ratios (HR) were generated using Cox regression accounting for non-proportional hazards by inclusion of time-varying effects. Univariable analysis showed FMD cases were culled sooner but there was no effect on clinical mastitis. After adjusting for possible confounders and inclusion of time-varying effects there was weak evidence to support an effect of FMD on culling (HR = 1.7, 95% confidence intervals [CI] 0.88-3.1, P = 0.12). For mastitis, there was stronger evidence of an increased rate in the first month after the onset of the outbreak (HR = 2.9, 95%CI 0.97-8.9, P = 0.057)
Dynamics, correlations and phases of the micromaser
The micromaser possesses a variety of dynamical phase transitions
parametrized by the flux of atoms and the time-of-flight of the atom within the
cavity. We discuss how these phases may be revealed to an observer outside the
cavity using the long-time correlation length in the atomic beam. Some of the
phase transitions are not reflected in the average excitation level of the
outgoing atom, which is the commonly used observable. The correlation length is
directly related to the leading eigenvalue of the time evolution operator,
which we study in order to elucidate the phase structure. We find that as a
function of the time-of-flight the transition from the thermal to the maser
phase is characterized by a sharp peak in the correlation length. For longer
times-of-flight there is a transition to a phase where the correlation length
grows exponentially with the flux. We present a detailed numerical and
analytical treatment of the different phases and discuss the physics behind
them.Comment: 60 pages, 18 figure files, Latex + \special{} for the figures, (some
redundant figures are eliminated and others are changed
Briefing: The role of human values in behavioural safety
Whilst behavioural based safety (BBS) is not new and is even becoming increasingly common, especially among large construction organisations; research on BBS and hence its implementation has paid limited attention to the role of innate drivers of behaviour, particularly human values (e.g. individual worker values). It is argued in this article that there is a need for empirical studies in this area towards the generation of fresh insight that could be valuable for designing more robust interventions for strengthening BBS programmes
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