Bifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding ...studies with exogenous bifidobacteria show they don't remain in the intestine, suggesting they may lose competitive fitness when grown outside the gut.
To further the understanding of genetic attenuation that may be occurring in bifidobacteria cultures, we obtained the complete genome sequence of an intestinal isolate, Bifidobacterium longum DJO10A that was minimally cultured in the laboratory, and compared it to that of a culture collection strain, B. longum NCC2705. This comparison revealed colinear genomes that exhibited high sequence identity, except for the presence of 17 unique DNA regions in strain DJO10A and six in strain NCC2705. While the majority of these unique regions encoded proteins of diverse function, eight from the DJO10A genome and one from NCC2705, encoded gene clusters predicted to be involved in diverse traits pertinent to the human intestinal environment, specifically oligosaccharide and polyol utilization, arsenic resistance and lantibiotic production. Seven of these unique regions were suggested by a base deviation index analysis to have been precisely deleted from strain NCC2705 and this is substantiated by a DNA remnant from within one of the regions still remaining in the genome of NCC2705 at the same locus. This targeted loss of genomic regions was experimentally validated when growth of the intestinal B. longum in the laboratory for 1,000 generations resulted in two large deletions, one in a lantibiotic encoding region, analogous to a predicted deletion event for NCC2705. A simulated fecal growth study showed a significant reduced competitive ability of this deletion strain against Clostridium difficile and E. coli. The deleted region was between two IS30 elements which were experimentally demonstrated to be hyperactive within the genome. The other deleted region bordered a novel class of mobile elements, termed mobile integrase cassettes (MIC) substantiating the likely role of these elements in genome deletion events.
Deletion of genomic regions, often facilitated by mobile elements, allows bifidobacteria to adapt to fermentation environments in a very rapid manner (2 genome deletions per 1,000 generations) and the concomitant loss of possible competitive abilities in the gut.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Monoatomic carbon chains and carbyne-rich composites are promising materials for many applications from protective coatings to nanoelectronic devices. Therefore, a thorough understanding of both the ...atomic and electronic structure of chained carbon is important. In this study, a combination of Raman scattering and electron photoemission techniques is used to study the bonding types, electron work functions and band gaps for carbyne-containing films on copper and silicon substrates. Raman mapping shows the nonuniform distribution of sp1 hybridization across the carbon-coated area on polycrystalline copper substrate due to adhesion differences. UV-excited electron emission dependence on thickness and ambient pressure confirms the difference between the silicon- and copper-based samples. Comparison with DFT calculations performed on surface slab models allows to draw conclusions about the chained composite structure.
Display omitted
Using the methods of optically stimulated electron emission (OSEE) and ambient pressure photoemission spectroscopy (APS), the energy characteristics of carbyne-containing films on copper and silicon ...substrates have been studied. The average contact potential difference and the work function were determined, and the positions of the Fermi level for carbyne-containing films of various thicknesses were calculated. It was found that the electrons work function and the position of the Fermi level of the studied film samples do not depend on the film thickness and the type of substrate. The information content of the OSEE and APS methods for evaluating the quality of carbon coatings on substrates is shown.
Display omitted
•Two different types of boron-doped graphene on copper have been studied.•Experiment and theory demonstrate stability of boron-doped graphene cover in the air.•The mechanism of the ...penetration of oxygen toward the copper substrate was proposed.•Possible application of boron-doped graphene/copper interface as catalyst was discussed.
Two different types of boron-doped graphene/copper interfaces synthesized using two different flow rates of Ar through the bubbler containing the boron source were studied. X-ray photoelectron spectra (XPS) and optically stimulated electron emission (OSEE) measurements have demonstrated that boron-doped graphene coating provides a high corrosion resistivity of Cu-substrate with the light traces of the oxidation of carbon cover. The density functional theory calculations suggest that for the case of substitutional (graphitic) boron-defect only the oxidation near boron impurity is energetically favorable and creation of the vacancies that can induce the oxidation of copper substrate is energetically unfavorable. In the case of non-graphitic boron defects oxidation of the area, a nearby impurity is metastable that not only prevent oxidation but makes boron-doped graphene. Modeling of oxygen reduction reaction demonstrates high catalytic performance of these materials.
The paper studies the electronic structure of proton-conducting oxides based on the lanthanum scandate La1-xSrxScO3-x/2 for advancing in understanding the mechanisms of hydrogen uptake from dry and ...humid atmospheres into the lattice of oxides with a perovskite structure. The process of protons incorporation from H2O containing atmospheres is considered to describe by the reaction H2O+OO×+VO••=2OHO•. However, there is no established concept of a mechanism for proton uptake from a dry H2 atmosphere. At such an uptake, a positively charged proton defect will be formed in the oxide lattice, and a negative charge must appear for compensation of the excess positive charge. Formally, the reaction of this process can be represented as 12H2+OO×=OHO•+e′. In this case an uncompensated electron appears, and the question arises as to where it is localized. In order to answer this question, it is necessary to study the electronic structure of perovskites.
With increasing in dopant concentration x the absorption band at 5.6 eV overlapping with the edge of fundamental absorption increases. Most probably it can be related with oxygen vacancies. When protons are incorporated from the H2 atmosphere into the La1-xSrxScO3-x/2 lattice, the absorption intensity in this band decreases, which can be due to the transition of the defects causing this band to another charge state. In addition, specific defects that absorb in the red and IR region at hν < 2.2 eV are formed. They are found to be located deep enough in the bang-gap and not to be an electronic traps. It is also shown that in La1-xSrxScO3-x/2 there are electron traps located at a depth of 2–4.5 eV in the band-gap relative to the bottom of the conduction band. On the basis of the obtained data, it can be assumed that these defects are somehow associated with oxygen vacancies, but their charge state is not obvious. It is important that these traps participate in the capture of uncompensated electrons during the proton uptake from the H2 atmosphere.
Thermal destruction processes of paramagnetic GeE'-centers in two different types of GeO2 glass have been studied. By investigating the temperature dependence of the electron emission typical of ...these processes, we found that the electron energy is sensitive to the structural disorder. The obtained results obtained were interpreted within the framework of modified Perel-Karpus model for the ionization of local centers in electric field. It was found that the electron-phonon coupling for GeE'-centers is a parameter that depends on the structure. We have shown that relatively weak electron-phonon coupling and low values of internal electric field are characteristic features of glassy GeO2 with high degree of continual disorder. Thus, the structural disorder, that at least depends on the synthesis conditions, can be considered as an effective tool governing the fundamental and functional properties of the glass.
•The thermal destruction process of GeE'-centers is accompanied by electron emission.•Emission parameters sensitive to degree of structural disordering were determined.•Disorder increasing in glassy GeO2 leads to reduction of electron-phonon coupling.
Thermostable DNA polymerases have a crucial role in current methods of DNA amplification and sequencing. Major improvements in these methods have been made in recent years, largely as a result of a ...marked increase in our understanding of how DNA polymerases function, particularly in DNA sequencing and the polymerase chain reaction. There is an untapped potential in genetically modified DNA polymerases, which could provide significant advantages over their natural counterparts that are used today. The development of such enzymes would have an immediate impact on the efficiency and accuracy of DNA amplification applications essential to the success of the Human Genome Initiative.
The effect of high-dose irradiation by electron beam with nanosecond duration and by gamma-rays on thermoluminescence (TL) yield of anion-defective dosimetric Al2O3:С crystals is studied. It is shown ...that in a wide dose range up to 10 kGy no significant changes in the TL curve shape and the temperature position of the main dosimetric peak (T = 460 K) are observed. The TL yield of this peak is in saturation in the high-dose range 5–80 kGy. Then anomalous increase in TL yield is registered at the dose growth up to 800 kGy. With that an intensive band appears in the green spectrum region in the photoluminescence spectrum. The role of aggregate defects forming F2-type centers with the increase of TL yield in Al2O3:С crystals under high-dose irradiation is discussed.
•In TLD-500 detectors the dosimetric glow curve does not change with dose increase.•Sublinear dose response of the main TL peak was found in the range 80–800 kGy.•In PL spectra of irradiated detectors there appears a band with λmax = 550 nm.•PL intensity in a new spectrum band depends on the dose.•F2-type centers are responsible for the change in PL spectra and TL yield.
The genomes of two closely related lytic Thermus thermophilus siphoviruses with exceptionally long (∼800 nm) tails, bacteriophages P23-45 and P74-26, were sequenced completely. The P23-45 genome ...consists of 84,201 bp with 117 putative open reading frames (ORFs), and the P74-26 genome has 83,319 bp and 116 putative ORFs. The two genomes are 92% identical with 113 ORFs shared. Only 25% of phage gene product functions can be predicted from similarities to proteins and protein domains with known functions. The structural genes of P23-45, most of which have no similarity to sequences from public databases, were identified by mass spectrometric analysis of virions. An unusual feature of the P23-45 and P74-26 genomes is the presence, in their largest intergenic regions, of long polypurine-polypyrimidine (R-Y) sequences with mirror repeat symmetry. Such sequences, abundant in eukaryotic genomes but rare in prokaryotes, are known to form stable triple helices that block replication and transcription and induce genetic instability. Comparative analysis of the two phage genomes shows that the area around the triplex-forming elements is enriched in mutational variations. In vitro, phage R-Y sequences form triplexes and block DNA synthesis by Taq DNA polymerase in orientation-dependent manner, suggesting that they may play a regulatory role during P23-45 and P74-26 development.
As an example of thin silica films, 30nm SiO2–Si heterostructures implanted with Ge+ ions (1016cm−2 fluence) and rapid thermally annealed (RTA) at 950°C are studied by means of optically stimulated ...electron emission (OSEE) in the spectral region of optical transparency for bulk silica. Quartz glass samples were used as references. Experimental data revealed a strong dependence between electron emission spectral features and RTA annealing time. The spectral contributions of both surface band tail states and interband transitions were clearly distinguished. The application of emission Urbach rule as well as Kane and Pässler equations allowed to analyze the OSEE spectra at different optical excitation energy ranges and to retrieve the important microstructural and energy parameters. The observed correlations between parameter values of Urbach- and Kane-related models suggest the implantation-induced conversion of both the vibrational subsystem and energy band of surface and interface electronic states.
•Peculiarities of electron emission from excited surface states of SiO2:Ge structures are studied.•Spectral contributions of surface band tails and interband transitions are distinguished.•Urbach and Kane models allow to examine photo-thermal emission mechanism.•Surface energy gap and structural disorder parameters are determined.
PDF
