53 research outputs found
Living without Oxygen: Anoxia-Responsive Gene Expression and Regulation
Many species of marine mollusks demonstrate exceptional capacities for long term survival without oxygen. Analysis of gene expression under anoxic conditions, including the subsequent translational responses, allows examination of the functional mechanisms that support and regulate natural anaerobiosis and permit noninjurious transitions between aerobic and anoxic states. Identification of stress-specific gene expression can provide important insights into the metabolic adaptations that are needed for anoxia tolerance, with potential applications to anoxia-intolerant systems. Various methods are available to do this, including high throughput microarray screening and construction and screening of cDNA libraries. Anoxia-responsive genes have been identified in mollusks; some have known functions in other organisms but were not previously linked with anoxia survival. In other cases, completely novel anoxia-responsive genes have been discovered, some that show known motifs or domains that hint at function. Selected genes are expressed at different times over an anoxia-recovery time course with their transcription and translation being actively regulated to ensure protein expression at the optimal time. An examination of transcript status over the course of anoxia exposure and subsequent aerobic recovery identifies genes, and the proteins that they encode, that enhance cell survival under oxygen-limited conditions. Analysis of data generated from non-mainstream model systems allows for insight into the response by cells to anoxia stress
Current rectification by simple molecular quantum dots: an ab-initio study
We calculate a current rectification by molecules containing a conjugated
molecular group sandwiched between two saturated (insulating) molecular groups
of different length (molecular quantum dot) using an ab-initio non-equilibrium
Green's function method. In particular, we study S-(CH2)m-C10H6-(CH2)n-S
dithiol with Naphthalene as a conjugated central group. The rectification
current ratio ~35 has been observed at m = 2 and n = 10, due to resonant
tunneling through the molecular orbital (MO) closest to the electrode Fermi
level (lowest unoccupied MO in the present case). The rectification is limited
by interference of other conducting orbitals, but can be improved by e.g.
adding an electron withdrawing group to the naphthalene.Comment: 8 pages, 9 figure
First-principles investigation of spin polarized conductance in atomic carbon wire
We analyze spin-dependent energetics and conductance for one dimensional (1D)
atomic carbon wires consisting of terminal magnetic (Co) and interior
nonmagnetic (C) atoms sandwiched between gold electrodes, obtained employing
first-principles gradient corrected density functional theory and Landauer's
formalism for conductance. Wires containing an even number of interior carbon
atoms are found to be acetylenic with sigma-pi bonding patterns, while cumulene
structures are seen in wires containing odd number of interior carbon atoms, as
a result of strong pi-conjugation. Ground states of carbon wires containing up
to 13 C atoms are found to have anti-parallel spin configurations of the two
terminal Co atoms, while the 14 C wire has a parallel Co spin configuration in
the ground state. The stability of the anti-ferromagnetic state in the wires is
ascribed to a super-exchange effect. For the cumulenic wires this effect is
constant for all wire lengths. For the acetylenic wires, the super-exchange
effect diminishes as the wire length increases, going to zero for the atomic
wire containing 14 carbon atoms. Conductance calculations at the zero bias
limit show spin-valve behavior, with the parallel Co spin configuration state
giving higher conductance than the corresponding anti-parallel state, and a
non-monotonic variation of conductance with the length of the wires for both
spin configurations.Comment: revtex, 6 pages, 5 figure
Effect of impurities on transport through organic molecular films from first principles
We calculate electron transport through molecular monolayers of saturated
alkanes with point defects from first principles. Single defects (incorporated
Au ions, kinks, dangling bonds) produce deep localized levels in the gap
between occupied and unoccupied molecular levels. Single defects produce steps
on the I-V curve, whereas pairs of (unlike and like) defects give negative
differential resistance peaks. The results are discussed in relation to the
observed unusual transport behavior of organic monolayers and compared with
transport through conjugated polythiophenes.Comment: 5 pages, 2 figures. Small typos corrected and text slightly
shortened. To appear in Phys. Rev.
Density functional method for nonequilibrium electron transport
We describe an ab initio method for calculating the electronic structure,
electronic transport, and forces acting on the atoms, for atomic scale systems
connected to semi-infinite electrodes and with an applied voltage bias. Our
method is based on the density functional theory (DFT) as implemented in the
well tested Siesta approach (which uses non-local norm-conserving
pseudopotentials to describe the effect of the core electrons, and linear
combination of finite-range numerical atomic orbitals to describe the valence
states). We fully deal with the atomistic structure of the whole system,
treating both the contact and the electrodes on the same footing. The effect of
the finite bias (including selfconsistency and the solution of the
electrostatic problem) is taken into account using nonequilibrium Green's
functions. We relate the nonequilibrium Green's function expressions to the
more transparent scheme involving the scattering states. As an illustration,
the method is applied to three systems where we are able to compare our results
to earlier ab initio DFT calculations or experiments, and we point out
differences between this method and existing schemes. The systems considered
are: (1) single atom carbon wires connected to aluminum electrodes with
extended or finite cross section, (2) single atom gold wires, and finally (3)
large carbon nanotube systems with point defects.Comment: 18 pages, 23 figure
Molecular Cloning and Copy Number Variation of a Ferritin Subunit (Fth1) and Its Association with Growth in Freshwater Pearl Mussel Hyriopsis cumingii
Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cumingii) was isolated and characterized. The complete cDNA contained 822 bp, with an open reading frame (ORF) of 525 bp, a 153 bp 5′ untranslated region (UTR) and a 144 bp 3′ UTR. The complete genomic DNA was 4125 bp, containing four exons and three introns. The ORF encoded a protein of 174 amino acids without a signal sequence. The deduced ferritin contained a highly conserved motif for the ferroxidase center comprising seven residues of a typical vertebrate heavy-chain ferritin. It contained one conserved iron associated residue (Try27) and iron-binding region signature 1 residues. The mRNA contained a 27 bp iron-responsive element with a typical stem-loop structure in the 5′-UTR position. Copy number variants (CNVs) of Fth1 in two populations (PY and JH) were detected using quantitative real-time PCR. Associations between CNVs and growth were also analyzed. The results showed that the copy number of the ferritin gene of in the diploid genome ranged from two to 12 in PY, and from two to six in JH. The copy number variation in PY was higher than that in JH. In terms of shell length, mussels with four copies of the ferritin gene grew faster than those with three copies (P<0.05), suggesting that CNVs in the ferritin gene are associated with growth in shell length and might be a useful molecular marker in selective breeding of H. cumingii
Analysis of signal transduction pathways during anoxia exposure in a marine snail: A role for p38 MAP kinase and downstream signaling cascades
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