Biomedical subjects

Alexander Tikhonov

Publications and source records attributed to Alexander Tikhonov.

4 recordsLinked to original sources

PubMed2006

Origin of the bacterial SET domain genes: vertical or horizontal?

The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria-host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.

Amino Acid Sequence↗

PubMed2004

Diffraction in crystalline colloidal-array photonic crystals.

We characterized the diffraction and crystal structure of a crystalline colloidal array (CCA) photonic crystal composed of 270 nm diameter polystyrene spheres which have a nearest neighbor spacing of approximately 540 nm. This CCA diffracts light in first order at approximately 1200 nm and shows strong diffraction in the visible spectral region from higher order planes. We quantitatively examined the relative diffraction intensities of the putative fcc (111), (200), (220), and (311) planes. Comparing these intensities to those calculated theoretically we find that the crystal structure is fcc with significant stacking faults. Essentially, no light transmits at the Bragg angle for the fcc (111) planes even through thin approximately 40 microm thick CCA. However, much of this light is diffusely scattered about the Bragg angle due to crystal imperfections. Significant transmission occurs from thin samples oriented at the Bragg condition for the fcc (200), (220), and (311) planes. We also observe moderately intense two-dimensional diffraction from the first few layers at the crystal surfaces. We also examined the sample thickness dependence of diffraction from CCA photonic crystals prepared from approximately 120 nm polystyrene spheres whose fcc (111) planes diffract in the visible spectral region. These experimental observations, aided by calculations based upon a simple but flexible model of light scattering from an arbitrary collection of colloidal spheres, make clear that fabrication of three-dimensional photonic band gap crystals will be challenged by crystal imperfections.

Biophysics↗

PubMed2004

Nanogel nanosecond photonic crystal optical switching.

We developed a robust nanosecond photonic crystal switching material by using poly(N-isopropylacrylamide) (PNIPAM) nanogel colloidal particles that self-assemble into crystalline colloidal arrays (CCAs). The CCA was polymerized into a loose-knit hydrogel which permits the individual embedded nanogel PNIPAM particles to coherently and synchronously undergo their thermally induced volume phase transitions. A laser T-jump from 30 to 35 degrees C actuates the nanogel particle shrinkage; the resulting increased diffraction decreases light transmission within 900 ns. Additional transmission decreases occur with characteristic times of 19 and 130 ns. Individual NIPAM sphere volume switching occurs in the approximately 100 ns time regime. These nanogel nanosecond phenomena may be useful in the design of fast photonic crystal switches and optical limiting materials. Smaller nanogels will show even faster volume phase transitions.

Journal Article↗

PubMed2004

Neuromagnetic activity in medial parietooccipital cortex reflects the perception of visual motion during eye movements.

We usually perceive a stationary, stable world despite coherent visual motion induced by eye movements. This astonishing example of perceptual invariance results from a comparison of visual information with internal reference signals (nonretinal signals) predicting the visual consequences of an eye movement. The important consequence of this concept is that our subjective percept of visual motion reflects the outcome of this comparison rather than retinal image slip. To localize the cortical networks underlying this comparison, we compared magnetoencephalography (MEG) responses under two conditions of pursuit-induced retinal image motion, which were identical physically but--due to different calibrational states of the nonretinal signal prompted under our experimental conditions--gave rise to different percepts of visual motion. This approach allows us to demonstrate that our perception of self-induced visual motion resides in comparably "late" parts of the cortical hierarchy of motion processing sparing the early stages up to cortical area MT/V5 but including cortex in and around the medial aspect of the parietooccipital cortex as one of its core elements.

Attention↗