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Dive into the research topics where G. Tremberger is active.

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Featured researches published by G. Tremberger.


Proceedings of SPIE | 2007

ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes

T. Holden; R. Subramaniam; R. Sullivan; E. Cheung; C. Schneider; G. Tremberger; A. Flamholz; D. Lieberman; T. Cheung

The radiation resistance-repair genes in Deinococcus radiodurans (DR) and E-coli were analyzed in terms of the A, T, C, G nucleotide fluctuations. The studied genes were Rec-A, Rec-Q, and the unique DR PprA gene. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis. Fractal analysis using the Higuchi method gave a fractal dimension increase of the Deinococcus radiodurans genes as compared to E-coli, which is comparable to the enhancement observed in the human HAR1 region (HAR1F gene) over that of the chimpanzee. Near neighbor fluctuation was also studied via the Black-Scholes model where the increment sequence was treated as a random walk series. The Deinococcus radiodurans radiation gene standard deviations were consistently higher than that of the E-coli deviations, and agree with the fractal analysis results. The sequence stacking interaction was studied using the published nucleotide-pair melting free energy values and Deinococcus radiodurans radiation genes were shown to possess larger negative free energies. The high sensitivity of the fractal dimension as a biomarker was tested with correlation analysis of the gamma ray dose versus fractal dimension, and the R square values were found to be above 0.9 (N=5). When compared with other nucleotide sequences such as the rRNA sequences, HAR1 and its chimpanzee counterpart, the higher fluctuation (correlated randomness) and larger negative free energy of a DR radiation gene suggested that a radiation resistance-repair sequence exhibited higher complexity. As the HAR1 nucleotide sequence complexity and its transcription activity of co-expressing cortex protein reelin supported a positive selection event in humans, a similar inference of positive selection of coding genes could be drawn for Deinococcus radiodurans when compared to E-coli. The origin of such a positive selection would be consistent with that of a Martian environment.


Proceedings of SPIE | 2012

Fiber optic based heart-rate and pulse pressure shape monitor

D. Kokkinos; Sunil Dehipawala; T. Holden; E. Cheung; M. Musa; G. Tremberger; P. Schneider; D. Lieberman; T. Cheung

Macro-bending fiber optic based heart-rate and pulse pressure shape monitors have been fabricated and tested for non-invasive measurement. Study of fiber bending loss and its stability and variations are very important especially for sensor designs based on optical fiber bending. Wavelengths from 1300 nm to 1550 nm have been used with fabrication based on multimode fiber, single mode fiber, and photonic crystal fiber. The smallest studied curvature would demand the use of single mode standard fibers. The collected data series show high quality suitable for random series analysis. Fractal property of optically measured pulse pressure data has been observed to correlate with physical activity. Correlation to EKG signal suggests that the fabricated monitors are capable of measuring the differential time delays at wrist and leg locations. The difference in time delay could be used to formulate a velocity parameter for diagnostics. The pulse shape information collected by the fiber sensor provides additional parameters for the analysis of the fractal nature of the heart. The application to real time measurement of blood vessel stiffness with this optical non-invasive fiber sensor is discussed.


Proceedings of SPIE | 2012

Optical diffusion property of cerumen from ear canal and correlation to metal content measured by synchrotron x-ray absorption

T. Holden; Sumudu Dehipawala; E. Cheung; U. Golebiewska; P. Schneider; G. Tremberger; D. Kokkinos; D. Lieberman; Sunil Dehipawala; T. Cheung

Human (and other mammals) would secrete cerumen (ear wax) to protect the skin of the ear canal against pathogens and insects. The studies of biodiversity of pathogen in human include intestine microbe colony, belly button microbe colony, etc. Metals such as zinc and iron are essentials to bio-molecular pathways and would be related to the underlying pathogen vitality. This project studies the biodiversity of cerumen via its metal content and aims to develop an optical probe for metal content characterization. The optical diffusion mean free path and absorption of human cerumen samples dissolved in solvent have been measured in standard transmission measurements. EXFAS and XANES have been measured at Brookhaven Synchrotron Light Source for the determination of metal contents, presumably embedded within microbes/insects/skin cells. The results show that a calibration procedure can be used to correlate the optical diffusion parameters to the metal content, thus expanding the diagnostic of cerumen in the study of human pathogen biodiversity without the regular use of a synchrotron light source. Although biodiversity measurements would not be seriously affected by dead microbes and absorption based method would do well, the scattering mean free path method would have potential to further study the cell based scattering centers (dead or live) via the information embedded in the speckle pattern in the deep-Fresnel zone.


Proceedings of SPIE | 2008

Nucleotide fluctuation of RecA repair gene in Siberian permafrost Psychrobacter cryohalolentis K5

G. Tremberger; T. Holden; E. Cheung; R. Subramaniam; R. Sullivan; P. Schneider; A. Flamholz; Paul J. Marchese; D. Lieberman; T. Cheung

A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the RecA repair gene of Psychrobacter cryohalolentis K5, Psychrobacter arcticus 273-4, and Psychrobacter sp. PRwf-1. The fractal dimension was found to correlate with the genes operating temperature with the highest fractal dimension associated with P. cryohalolentis K5 living at the low temperatures found in Siberian permafrost. The CpG dinucleotide content was found to be about 5% for the three species of Psychrobacters, which is substantially lower than that of Deinococcus radiodurans at about 12%. The average nucleotide pair-wise free energy was found to be lowest for Psychrobacter sp. PRwf-1, the species with the lowest fractal dimension of the three, consistent with the recent finding that Psychrobacter sp. PRw-f1 has a temperature growth maximum of 15-20°C higher than P. arcticus 273-4 and P. cryohaloentis K5. The results suggest that microbial vitality in extreme environments is associated with fractal dimension as well as high CpG dinucleotide content, while the average nucleotide pair-wise free energy is related to the operating environment. Evidence that extreme temperature operation would impose constraints measurable by Shannon entropy is also discussed. A quantitative estimate of an entropy-based measure having the characteristics of a mechanical pressure shows that the Psychrobacter RecA sequence experiences lower pressure than that of the human HAR1 sequence.


Proceedings of SPIE | 2012

Single mode and sub-cellular fiber probes for cell scattering and density variation measurements

D. Kokkinos; T. Holden; Sunil Dehipawala; L. Mora; W. Huazhco; N. Gadura; U. Golebiewska; P. Schneider; G. Tremberger; D. Lieberman; T. Cheung

Cell density is an important parameter in the question of bio-variation and the studying of cell scattering could be a viable tool. The development of spatially resolved optical fiber probe would enable the characterization of optical scattering from cells within a colony. Single mode fiber probe would be budget friendly as compared to a 50-nm sub-cellular fiber probe. This project develops a calibration procedure to correlate the optical scattering measured by a single mode fiber probe to that of a 50-nm sub-cellular fiber probe in the context of cell density variation. The Fourier transform of intensity angular transmission would give correlation information in the Efield in the spatial coordinate. Monte Carlo simulation could be used to constrain the input intensity function spatial content resembling microscopy. The use of a 50-nm sub-cellular fiber probe for detailed study of biological samples would give sub-micron scale length information.


international conference on bioinformatics and biomedical engineering | 2008

Fractal Analysis of Filamentous Actin Fluorescent Speckle Microscope Patterns in Cell Migration

Todd Holden; R. Sullivan; G. Tremberger; R. Subramaniam; E. Cheung; C. Schneider; A. Flamholz; Paul J. Marchese; H. Yao; D. Lieberman; T. Cheung

The fluorescent speckle microscope pattern of newt lung epithelial cell filamentous actin during migration was analyzed using the Higuchi fractal method. The public domain datasets of 2004 PNAS Vallotton et al. were studied. The time series data from time lapsed images exhibited similar fractal dimensions (about 1.68 to 1.82) for various cell regions. Computer simulation of random time series data suggested an average fractal dimension of about 2 with a standard deviation of about 0.027. Speckle trend removals revealed pulsation features which were further studied using a sinusoidal signal model commonly used in gene regulatory studies. Gaussian noise models mixed with sinusoidal signal were used to simulate the observed fractal dimensions. The extracted constraints could be interpreted as polymerization and control pathway related. The administration of contractility promotion drug calyculin-A resulted in an increase of the overall image fractal dimension, which is consistent with the loss of correlation due to random direction contractions. It appears that high fractal dimension could be interpreted as being due to further randomization. Two doses of 20 nM calyculin-A increased cell noise by about 45%. Extension of this proof-of-concept fractal analysis to clinical treatment was also discussed.


Proceedings of SPIE | 2008

DNA sequence-based comparative studies between non-extremophile and extremophile organisms with implications in exobiology

T. Holden; Paul J. Marchese; G. Tremberger; E. Cheung; R. Subramaniam; R. Sullivan; P. Schneider; A. Flamholz; D. Lieberman; T. Cheung

We have characterized function related DNA sequences of various organisms using informatics techniques, including fractal dimension calculation, nucleotide and multi-nucleotide statistics, and sequence fluctuation analysis. Our analysis shows trends which differentiate extremophile from non-extremophile organisms, which could be reproduced in extraterrestrial life. Among the systems studied are radiation repair genes, genes involved in thermal shocks, and genes involved in drug resistance. We also evaluate sequence level changes that have occurred during short term evolution (several thousand generations) under extreme conditions.


international conference on signal processing | 2016

Bioinformatics of CYP2E1 CpG intron methylation sites and application to HAR1-RELN sequence analysis

Sunil Dehipawala; Reginia Sullivan; G. Tremberger; D. Lieberman; T. Cheung

The CYP2E1 CpG methylation sites in the first intron (site +626 to +742 from the starting ATG) as reported in a 2015 epigenetics psychiatry study were analyzed from a bioinformatics perspective. The studied sequences for human, monkey, dog and cow showed a high correlation (R-sq > 0.99) between CpG content and mononucleotide entropy. A comparably high correlation (R-sq > 0.95) was also found between the first exon sequences and mononucleotide entropy. These findings lend support to the hypothesis that CpG content is proportional to nucleotide availability when the latter quantity is computed as information entropy. To probe the nature of CpG sites in HAR1, a comparative study was conducted using the known promoter methylation regions in RELN and EGFR sequences. The observed high correlation (R-sq = 0.999) suggests that the eight CpG sites in HAR1 may function as human-specific gene expression controller sites since the equivalent chimp sequence has no CpG sites. A general scheme using randomly selected CpG methylation sites that precede the starting ATG codon is discussed with regard to fractal dimension modeling. Furthermore, an analysis of the studied RELN homolog CDS sequences for human, bovine, mouse and rat showed a high correlation of dinucleotide entropy with free energy (R > 0.9), consistent with the high correlation (R > 0.9) observed in a similar analysis of the studied pro-BDNF homolog CDS sequences for human, chimp, mouse and rat.


Proceedings of SPIE | 2015

Bioinformatics comparison of sulfate-reducing metabolism nucleotide sequences

G. Tremberger; Sunil Dehipawala; A. Nguyen; E. Cheung; R. Sullivan; T. Holden; D. Lieberman; T. Cheung

The sulfate-reducing bacteria can be traced back to 3.5 billion years ago. The thermodynamics details of the sulfur cycle have been well documented. A recent sulfate-reducing bacteria report (Robator, Jungbluth, et al , 2015 Jan, Front. Microbiol) with Genbank nucleotide data has been analyzed in terms of the sulfite reductase (dsrAB) via fractal dimension and entropy values. Comparison to oil field sulfate-reducing sequences was included. The AUCG translational mass fractal dimension versus ATCG transcriptional mass fractal dimension for the low temperature dsrB and dsrA sequences reported in Reference Thirteen shows correlation R-sq ~ 0.79 , with a probably of about 3% in simulation. A recent report of using Cystathionine gamma-lyase sequence to produce CdS quantum dot in a biological method, where the sulfur is reduced just like in the H2S production process, was included for comparison. The AUCG mass fractal dimension versus ATCG mass fractal dimension for the Cystathionine gamma-lyase sequences was found to have R-sq of 0.72, similar to the low temperature dissimilatory sulfite reductase dsr group with 3% probability, in contrary to the oil field group having R-sq ~ 0.94, a high probable outcome in the simulation. The other two simulation histograms, namely, fractal dimension versus entropy R-sq outcome values, and di-nucleotide entropy versus mono-nucleotide entropy R-sq outcome values are also discussed in the data analysis focusing on low probability outcomes.


Proceedings of SPIE | 2015

Complexity of genetic sequences modified by horizontal gene transfer and degraded-DNA uptake

G. Tremberger; Sunil Dehipawala; A. Nguyen; E. Cheung; R. Sullivan; T. Holden; D. Lieberman; T. Cheung

Horizontal gene transfer has been a major vehicle for efficient transfer of genetic materials among living species and could be one of the sources for noncoding DNA incorporation into a genome. Our previous study of lnc- RNA sequence complexity in terms of fractal dimension and information entropy shows a tight regulation among the studied genes in numerous diseases. The role of sequence complexity in horizontal transferred genes was investigated with Mealybug in symbiotic relation with a 139K genome microbe and Deinococcus radiodurans as examples. The fractal dimension and entropy showed correlation R-sq of 0.82 (N = 6) for the studied Deinococcus radiodurans sequences. For comparison the Deinococcus radiodurans oxidative stress tolerant catalase and superoxide dismutase genes under extracellular dGMP growth condition showed R-sq ~ 0.42 (N = 6); and the studied arsenate reductase horizontal transferred genes for toxicity survival in several microorganisms showed no correlation. Simulation results showed that R-sq < 0.4 would be improbable at less than one percent chance, suggestive of additional selection pressure when compared to the R-sq ~ 0.29 (N = 21) in the studied transferred genes in Mealybug. The mild correlation of R-sq ~ 0.5 for fractal dimension versus transcription level in the studied Deinococcus radiodurans sequences upon extracellular dGMP growth condition would suggest that lower fractal dimension with less electron density fluctuation favors higher transcription level.

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T. Cheung

Queensborough Community College

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D. Lieberman

Queensborough Community College

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T. Holden

Queensborough Community College

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E. Cheung

Queensborough Community College

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P. Schneider

Queensborough Community College

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Sunil Dehipawala

Queensborough Community College

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A. Flamholz

Queensborough Community College

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R. Sullivan

Queensborough Community College

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Paul J. Marchese

Queensborough Community College

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R. Subramaniam

Queensborough Community College

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