scholarly journals Study of the triplet periodicity phase shifts in genes

2010 ◽  
Vol 7 (3) ◽  
pp. 219-230 ◽  
Author(s):  
Eugene V. Korotkov ◽  
Maria A. Korotkova

Abstract The definition of a phase shift of triplet periodicity (TP) is introduced. The mathematical algorithm for detection of TP phase shift of nucleotide sequences has been developed. Gene sequences from Kegg-46 data bank were analyzed with a purpose of searching genes with a phase shift of TP. The presence of a phase shift of triplet periodicity has been shown for 318329 genes (~10% from the number of genes in Kegg-46). We suppose that shifts of the TP phase may indicate the shifts of reading frame (RF) in genes. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.

1999 ◽  
Vol 07 (02) ◽  
pp. 113-130 ◽  
Author(s):  
I. M. DE LA FUENTE ◽  
L. MARTINEZ ◽  
J. M. AGUIRREGABIRIA ◽  
J. VEGUILLAS ◽  
M. IRIARTE

In biochemical dynamical systems during each transition between periodical behaviors, all metabolic intermediaries of the system oscillate with the same frequency but with different phase-shifts. We have studied the behavior of phase-shift records obtained from random transitions between periodic solutions of a biochemical dynamical system. The phase-shift data were analyzed by means of Hurst's rescaled range method (introduced by Mandelbrot and Wallis). The results show the existence of persistent behavior: each value of the phase-shift depends not only on the recent transitions, but also on previous ones. In this paper, the different kind of periodic solutions were determined by different small values of the control parameter. It was assessed the significance of this results through extensive Monte Carlo simulations as well as quantifying the long-range correlations. We have also applied this type of analysis on cardiac rhythms, showing a clear persistent behavior. The relationship of the results with the cellular persistence phenomena conditioned by the past, widely evidenced in experimental observations, is discussed.


2016 ◽  
Vol 54 (3) ◽  
pp. 247-261 ◽  
Author(s):  
Pieter Coppens ◽  
Johan Van den Bossche ◽  
Mieke De Cock

In a series of interviews with second year electronics engineering students, several of them showed problems with signal properties. In a questionnaire administered to over 150 students in Belgium, these problems were further explored to verify how widespread they are. The questions asked about different aspects of signals. Students showed that they understand the concept of a phase shift, although they have problems with the direction. However, they generally have no idea what a signal with two frequencies looks like in the time domain. Bode plots also proved to be a problem for students, who are not able to construct one from a set of (dummy) measurements. Most of these issues persist after lab instruction.


1988 ◽  
Vol 8 (8) ◽  
pp. 3439-3447 ◽  
Author(s):  
W Bajwa ◽  
T E Torchia ◽  
J E Hopper

GAL3 gene expression is required for rapid GAL4-mediated galactose induction of the galactose-melibiose regulon genes in Saccharomyces cerevisiae. Here we show by Northern (RNA) blot analysis that GAL3 gene expression is itself galactose inducible. Like the GAL1, GAL7, GAL10, and MEL1 genes, the GAL3 gene is severely glucose repressed. Like the MEL1 gene, but in contrast to the GAL1, GAL7, and GAL10 genes, GAL3 is expressed at readily detectable basal levels in cells grown in noninducing, nonrepressing media. We determined the sequence of the S. cerevisiae GAL3 gene and its 5'-noncoding region. Within the 5'-noncoding region of the GAL3 gene, we found two sequences similar to the UASGal elements of the other galactose-melibiose regulon genes. Deletion analysis indicated that only the most ATG proximal of these sequences is required for GAL3 expression. The coding region of GAL3 consists of a 1,275-base-pair open reading frame in the direction of transcription. A comparison of the deduced 425-amino-acid sequence with the protein data bank revealed three regions of striking similarity between the GAL3 protein and the GAL1-specified galactokinase of Saccharomyces carlsbergensis. One of these regions also showed striking similarity to sequences within the galactokinase protein of Escherichia coli. On the basis of these protein sequence similarities, we propose that the GAL3 protein binds a molecule identical to or structurally related to one of the substrates or products of the galactokinase-catalyzed reaction.


Intervirology ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 359-363 ◽  
Author(s):  
Sung Wook Seo ◽  
Kazuhiro Hara ◽  
Atsutaka Kubosaki ◽  
Yukiko Nasu ◽  
Takuya Nishimura ◽  
...  

2003 ◽  
Vol 15 (02) ◽  
pp. 61-67 ◽  
Author(s):  
MENG-HSIANG YANG ◽  
K. N. HUANG ◽  
C. F. HUANG ◽  
S. S. HUANG ◽  
M. S. YOUNG

A highly accurate Binary Amplitude-Shift-Keyed (BASK) ultrasonic tremor measurement system for use in isothermal air is developed. In this paper, we present a simple but efficient algorithm based upon phase shifts generated by three ultrasonic waves of different frequencies. By the proposed method, we can conduct larger range measurement than the phase-shift method and also get higher accuracy compared with the time-of-flight (TOF) method. Our microcomputer-based system includes two important parts. One of which is BASK modulation signal generator. The other is a phase meter designed to record and compute the phase shifts of the three different frequencies and the result motion is then sent to either an LCD for display or a PC for calibration. Experiments are done in the laboratory using BASK modulation for the frequencies of 200 Hz and 1 kHz with a 40 kHz carrier. The measurement accuracy of this measurement system in the reported experiments is within +/- 0.98 mm. The main advantages of this ultrasonic tremor measurement system are high resolution, narrow bandwidth requirement, low cost, and easy to be implemented.


2020 ◽  
Author(s):  
Eric D. Hoffer ◽  
Samuel Hong ◽  
S. Sunita ◽  
Tatsuya Maehigashi ◽  
Ruben L. Gonzalez ◽  
...  

ABSTRACTModifications in the tRNA anticodon, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguaonosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop, immediately adjacent to the anticodon nucleotides 34-36. The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon-anticodon contexts and m1G37 destabilize interactions of tRNAPro with the peptidyl site, causing large conformational changes typically only seen during EF-G mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAPro with the ribosome and the influence of slippery codons on the mRNA reading frame.IMPACT STATEMENTChemical modifications near the tRNA anticodon and specific mRNA-tRNA pairs combine to control the ribosomal three-nucleotide mRNA reading frame, essential for the sequential addition of amino acids into polypeptide chains.Data depositionCrystallography, atomic coordinates, and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB codes 6NTA, 6NSH, 6NUO, 6NWY, 6O3M, 6OSI)


2018 ◽  
Vol 0 (0) ◽  
Author(s):  
Hilal Ahmad Sheikh ◽  
Anurag Sharma

AbstractThis research work provides an insight on a radio over fiber (RoF) based passive optical network (RoF-PON) utilizing two diverse electrical phase shifts with optical single sideband modulation (OSSB) by exploiting Mach Zender modulator. The influence of chromatic dispersion (CD) in PONs employing single mode fiber (SMF) is a noteworthy issue and should be limited. The two techniques of OSSB modulation, in view of the two distinct angles of the hybrid coupler are employed for the design and implementation of RoF-PON. The RF signal is partitioned into two ways equally before applying it to the dual drive Mach Zender modulator input, utilizing an electrical hybrid coupler that imparts two discrete phase shifts of 90° and 120° to generate two OSSB signals individually. By utilizing traditional OSSB technique having 90° phase shift, either of the first-order sideband (lower or upper first order) suppression occurs yet second-order harmonics are still existent in the system. As opposed to this, the OSSB technique using 120° phase shift causes the suppression of either lower first order and higher second order sideband or vice versa. When contrasted to the PON based on traditional technique (90° phase shift technique), the suppression of second order sideband in PON using 120° technique lessens the system CD. Hence the PON based on 120° phase shift technique has enhanced functionality in terms of system BER, received power and power losses as compared to that with traditional OSSB technique.


2021 ◽  
Author(s):  
Konstantinos Chasapis ◽  
Eugeny Buldakov ◽  
Helen Czerski

<p>The bubbles generated by breaking waves in the open ocean are an important feature of the ocean surface. They affect optical and acoustical properties of the top few meters of the ocean, influence surfactant scavenging, aerosol production and air-sea gas transfer. Short-lived larger bubbles which re-surface and burst dominate the transfer of less soluble gases such as carbon dioxide. A single wave crest approaching breaking deforms rapidly and in a storm sea the most common breaker is the spilling type. Detailed observations in space and time connecting the shape of the spilling breaker to subsequent bubble populations are limited, and the effect on the bubble penetration depth and residence time underwater is particularly important. In this study, we carried out a series of experiments to track the formation and evolution of large bubbles for different local crest geometries.</p><p>A breaking wave in a wave flume was generated with dispersive focusing of a wave group. The group has a pre-defined amplitude spectrum. Running experiments with different phase shifts of the same amplitude spectrum showed that when a peak-focussed wave (zero phase shift) breaks, then wave groups with other added phase shifts break as well. To investigate possible differences in the deformation of those breakers a laser imaging technique was used. An algorithm identified the 2D shape of the breaker in successive images. It also separated the crests from bulges based on geometric criteria. We showed that, despite wave groups having same spectra, the extracted bulges differed locally in shape, volume and velocity for each phase shift at the location of breaking. Therefore, breakers ranging from the more traditional spilling type, which has a bulge that collapses on the front face of the wave, to the micro-plunging type, which has a pronounced overturning tip, were observed depending on the phase shift. </p><p>The evolution of bubbles for each phase shifted bulge was captured by a high speed camera and measured by a feature extraction algorithm. We generally found that spilling bulges created fewer bubbles in total than micro-plungers. They also created fewer larger bubbles, i.e. with radius r>1 mm, at all measured flume areas. In contrast, micro-plungers that trap air within a small cavity as they break had less steep size distributions for r>1 mm. The maximum volume of air per radius showed a gradual shift from r>1 mm to r=1 mm moving away from the breaking location for all breakers. It is interesting, finally, that the maximum volume per radius did not shift to smaller radii as time passes. This is an indication that the largest bubbles, i.e. r>4 mm, rise to the surface and burst instead of splitting into smaller ones, irrespectively of the local breaker properties. </p>


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