Computational identification of rare codons of Escherichia coli based on codon pairs preference

<p>Abstract</p> <p>Background</p> <p>Codon bias is believed to play an important role in the control of gene expression. In <it>Escherichia coli</it>, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not been well established. Here we focus on the patterns of rarely-used synonymous codons. A novel method was introduced to identify the rare codons merely by codon pair bias in <it>Escherichia coli</it>.</p> <p>Results</p> <p>In <it>Escherichia coli</it>, we defined the "rare codon pairs" by calculating the frequency of occurrence of all codon pairs in coding sequences. Rare codons which are disliked in genes could make great contributions to forming rare codon pairs. Meanwhile our investigation showed that many of these rare codon pairs contain termination codons and the recognized sites of restriction enzymes. Furthermore, a new index (F_rare) was developed. Through comparison with the classical indices we found a significant negative correlation between F_rareand the indices which depend on reference datasets.</p> <p>Conclusions</p> <p>Our approach suggests that we can identify rare codons by studying the context in which a codon lies. Also, the frequency of rare codons (F_rare) could be a useful index of codon bias regardless of the lack of expression abundance information.</p

Heated Area and Well Performance Analysis of Injection N2 and CO2 in Cycle Steam Stimulation Process

Application of steam injection technology to heavy oil reservoirs is the most commercially successful EOR method. Cycle steam stimulation (CSS) is known as the most widely used and mature technology compared with various thermal methods. Because of various reasons, such as too high initial oil viscosity, excessive overburden heat loss and so on, in CSS, the radius of heated zone is small and the viscosity of heavy oil still cannot be lowered effectively, which leads to the low oil productivity and poor oil well performance. A variation on CSS process is to add N2 and CO2 in steam injection. Because of the influence of the N2 and CO2, the heated area and well performance of N2 and CO2 assisted CSS are different from that of steam stimulation. Therefore, this paper describes a detailed study of N2 and CO2 influence to cycle steam stimulation. In this paper, the physical simulation experiments of N2 and CO2 influence to the mixture of heavy oil are carried out at first. Through physical experiments, the enhancing oil mechanisms of N2 and CO2,the recovery mechanism of reducing oil viscosity by CO2 dissolving, reducing interfacial tension between gas and heavy oil, which are different from the steam, are described respectively. Based on this, a numerical simulation model with a single horizontal well is built to carry out the quantitative and comparative study of heated area of formation. Results show that the development effect of N2 and CO2 assisted CSS is better than that of conventional steam stimulation in porous media. Next, the different well performance of the N2 and CO2 assisted CSS and conventional CSS are compared by numerical results. Finally, on the basis of the field data of two different heavy oil field, two typical wells of CSS and N2 and CO2 assisted CSS are analyzed in detail. Consequently, the N2 and CO2 injection together with steam is helpful to improve development effect in CSS process

Characterization of deep sub-wavelength nanowells by imaging the photon state scattering spectra

Optical-matter interactions and photon scattering in a sub-wavelength space are of great interest in many applications, such as nanopore-based gene sequencing and molecule characterization. Previous studies show that spatial distribution features of the scattering photon states are highly sensitive to the dielectric and structural properties of the nanopore array and matter contained on or within them, as a result of the complex optical-matter interaction in a confined system. In this paper, we report a method for shape characterization of subwavelength nanowells using photon state spatial distribution spectra in the scattering near field. Far-field parametric images of the near-field optical scattering from sub-wavelength nanowell arrays on a SiN substrate were obtained experimentally. Finite-difference time-domain simulations were used to interpret the experimental results. The rich features of the parametric images originating from the interaction of the photons and the nanowells were analyzed to recover the size of the nanowells. Experiments on nanoholes modified with Shp2 proteins were also performed. Results show that the scattering distribution of modified nanoholes exhibits significant differences compared to empty nanoholes. This work highlights the potential of utilizing the photon status scattering of nanowells for molecular characterization or other virus detection applications

Photo scattering signal amplification in gold-viral particle ligation towards fast infection screening

The polarization states of scattered photons can be used to map or image the anisotropic features of a nanostructure. However, the scattering strength depends heavily on the refractivity contrast in the near field under measurement, which limits the imaging sensitivity for viral particles which have little refractivity contrast with their nano-ambientes. In this paper, we show the photon scattering signal strength can be magnified by introducing a more abrupt change of refractivity at the virus particle using antibody-conjugated gold nanoparticles (AuNPs), allowing the presence of such viruses to be detected. Using two different deep learning methods to minimize scattering noise, the photon states scattering signal of a AuNPs ligated virus is enhanced significantly compared to that of a bare virus particle. This is confirmed by Finite Difference Time Domain (FDTD) numerical simulations. The sensitivity of the polarization state scattering spectra from a virus-gold particle doublet is 5.4 times higher than that of a conventional microscope image

The driver design for N

In this paper, the driver circuit for N2O gas detection system based on tunable interband cascade laser (ICL) is developed. Considering the influence of power supply stability on the digital-analog hybrid drive circuit of tunable diode laser absorption spectroscopy (TDALS), the high-efficiency TPS5430 is used to design the positive and negative power supply circuit. The large electrolytic capacitor + post-stage LC filter combination filter is used to effectively filter out high and low frequency ripple and switching noise. The use of thick high current trace + via + multilayer printed circuit board (PCB) design makes the line temperature rise smaller, more stable and durable, and uses high frequency shielding inductance to effectively reduce radiation interference to ensure the stability of the drive. The STM32F407, a highperformance microcontroller based on the ARM Cortex-M4 core, is used as the master control chip and generates a sawtooth scanning signal. The direct digital synthesizer (DDS) chip ICL8038 is used to generate a sinusoidal modulated signal of a specific frequency. The two signals are superimposed by a reverse addition circuit, and the laser drive signal is generated by a developed positive feedback balanced voltagecurrent conversion circuit. Experimental results show that the driver circuit can well meet the drive development requirements of N2O gas detection systems based on tunable interband cascade laser

Real-time monitoring of insects based on laser remote sensing

Monitoring animal activities help assess the effects of environmental conditions and anthropogenic factors on various species. Entomology-related monitoring methods based on radar, machine vision, and other technologies have developed rapidly in recent years. This research focuses on real-time, laser-based monitoring methods that enable online monitoring of insect activity and study the response of insect populations to changes in environmental conditions such as weather. We summarise four specific applications of monitoring insects based on various laser remote sensing techniques, including setting the electronic trap, collecting backscattered light or fluorescence from target insects in open space, and indirectly monitoring insect population activity by drawing forest canopy characteristics. We discuss the application opportunities of these methods and the challenges faced in practical monitoring and emphasise the trends and requirements for future research

Research on method for high sensitive detection of harmful gases in livestock houses based on laser absorption spectrum

Harmful gases such as ammonia and hydrogen sulfide in livestock and poultry houses can seriously damage the health of livestock and poultry as well as animal keepers, so it is great significant to detect these harmful gases rapidly and accurately for the improvement of the welfare of animals and the health of animal keepers. Laser absorption spectroscopy is a gas detection method with the advantages of high sensitivity and selectivity, and is widely used in industrial gas detection. However, it needs further exploring to verify whether laser absorption spectroscopy is useful in detecting low concentration harmful gases in livestock and poultry houses. This paper researches on the method for high-sensitivity detection of harmful gases in livestock and poultry houses based on laser absorption spectroscopy by detecting the absorption signals of ammonia with a self-designed system including a tunable laser wavelength scanning system, a photoelectric detecting system and a long light path gas absorption well, and verifies that laser absorption spectroscopy can be used for detecting harmful gases in livestock and poultry houses