A technique to randomise consecutive codons in a sequence of DNA using MAX oligonucleotides

Randomisation of DNA using conventional methodology requires an excess of genes to be cloned, since with randomised codons NNN or NNG/T 64 genes or 32 genes must be cloned to encode 20 amino acids respectively. Thus, as the number of randomised codons increases, the number of genes required to encode a full set of proteins increases exponentially. Various methods have been developed that address the problems associated with excess of genes that occurs due to the degeneracy of the genetic code. These range from chemical methodologies to biological methods. These all involve the replacement, insertion or deletion of codon(s) rather than individual nucleotides. The biological methods are however limited to random insertion/deletion or replacement. Recent work by Hughes et al., (2003) has randomised three binding residues of a zinc finger gene. The drawback with this is the fact that consecutive codons cannot undergo saturation mutagenesis. This thesis describes the development of a method of saturation mutagenesis that can be used to randomise any number of consecutive codons in a DNA strand. The method makes use of “MAX” oligonucleotides coding for each of the 20 amino acids that are ligated to a conserved sequence of DNA using T4 DNA ligase. The “MAX” oligonucleotides were synthesised in such a way, with an MlyI restriction site, that restriction of the oligonucleotides occurred after the three nucleotides coding for the amino acids. This use of the MlyI site and the restrict, purify, ligate and amplify method allows the insertion of “MAX” codons at any position in the DNA. This methodology reduces the number of clones that are required to produce a representative library and has been demonstrated to be effective to 7 amino acid positions.

Optical packet transmission in 42.6 Gbit/s wavelength-division-multiplexed clockwork-routed networks

The use of amplitude-modulated phase-shift-keyed (AM-PSK) optical data transmission is investigated in a sequence of concatenated links in a wavelength-division-multiplexed clockwork-routed network. The narrower channel spacing made possible by using AM-PSK format allows the network to contain a greater number of network nodes. Full differential precoding at the packet source reduces the amount of high-speed electronics required in the network and also offers simplified header recognition and time-to-live mechanisms.

Direct sequence spread spectrum based PWM strategy for harmonic reduction and communication

Switched mode power supplies (SMPSs) are essential components in many applications, and electromagnetic interference is an important consideration in the SMPS design. Spread spectrum based PWM strategies have been used in SMPS designs to reduce the switching harmonics. This paper proposes a novel method to integrate a communication function into spread spectrum based PWM strategy without extra hardware costs. Direct sequence spread spectrum (DSSS) and phase shift keying (PSK) data modulation are employed to the PWM of the SMPS, so that it has reduced switching harmonics and the input and output power line voltage ripples contain data. A data demodulation algorithm has been developed for receivers, and code division multiple access (CDMA) concept is employed as communication method for a system with multiple SMPSs. The proposed method has been implemented in both Buck and Boost converters. The experimental results validated the proposed DSSS based PWM strategy for both harmonic reduction and communication.

Peak -to -average power ratio reduced parallel interference cancellation Multicarrier-Code Division Multiple Access system with anti -interference property

Orthogonal Frequency-Division Multiplexing (OFDM) has been proved to be a promising technology that enables the transmission of higher data rate. Multicarrier Code-Division Multiple Access (MC-CDMA) is a transmission technique which combines the advantages of both OFDM and Code-Division Multiplexing Access (CDMA), so as to allow high transmission rates over severe time-dispersive multi-path channels without the need of a complex receiver implementation. Also MC-CDMA exploits frequency diversity via the different subcarriers, and therefore allows the high code rates systems to achieve good Bit Error Rate (BER) performances. Furthermore, the spreading in the frequency domain makes the time synchronization requirement much lower than traditional direct sequence CDMA schemes. There are still some problems when we use MC-CDMA. One is the high Peak-to-Average Power Ratio (PAPR) of the transmit signal. High PAPR leads to nonlinear distortion of the amplifier and results in inter-carrier self-interference plus out-of-band radiation. On the other hand, suppressing the Multiple Access Interference (MAI) is another crucial problem in the MC-CDMA system. Imperfect cross-correlation characteristics of the spreading codes and the multipath fading destroy the orthogonality among the users, and then cause MAI, which produces serious BER degradation in the system. Moreover, in uplink system the received signals at a base station are always asynchronous. This also destroys the orthogonality among the users, and hence, generates MAI which degrades the system performance. Besides those two problems, the interference should always be considered seriously for any communication system. In this dissertation, we design a novel MC-CDMA system, which has low PAPR and mitigated MAI. The new Semi-blind channel estimation and multi-user data detection based on Parallel Interference Cancellation (PIC) have been applied in the system. The Low Density Parity Codes (LDPC) has also been introduced into the system to improve the performance. Different interference models are analyzed in multi-carrier communication systems and then the effective interference suppression for MC-CDMA systems is employed in this dissertation. The experimental results indicate that our system not only significantly reduces the PAPR and MAI but also effectively suppresses the outside interference with low complexity. Finally, we present a practical cognitive application of the proposed system over the software defined radio platform.

Peak-to-Average Power Ratio Reduced Parallel Interference Cancellation Multicarrier-Code Division Multiple Access System with Anti-Interference Property

Orthogonal Frequency-Division Multiplexing (OFDM) has been proved to be a promising technology that enables the transmission of higher data rate. Multicarrier Code-Division Multiple Access (MC-CDMA) is a transmission technique which combines the advantages of both OFDM and Code-Division Multiplexing Access (CDMA), so as to allow high transmission rates over severe time-dispersive multi-path channels without the need of a complex receiver implementation. Also MC-CDMA exploits frequency diversity via the different subcarriers, and therefore allows the high code rates systems to achieve good Bit Error Rate (BER) performances. Furthermore, the spreading in the frequency domain makes the time synchronization requirement much lower than traditional direct sequence CDMA schemes. There are still some problems when we use MC-CDMA. One is the high Peak-to-Average Power Ratio (PAPR) of the transmit signal. High PAPR leads to nonlinear distortion of the amplifier and results in inter-carrier self-interference plus out-of-band radiation. On the other hand, suppressing the Multiple Access Interference (MAI) is another crucial problem in the MC-CDMA system. Imperfect cross-correlation characteristics of the spreading codes and the multipath fading destroy the orthogonality among the users, and then cause MAI, which produces serious BER degradation in the system. Moreover, in uplink system the received signals at a base station are always asynchronous. This also destroys the orthogonality among the users, and hence, generates MAI which degrades the system performance. Besides those two problems, the interference should always be considered seriously for any communication system. In this dissertation, we design a novel MC-CDMA system, which has low PAPR and mitigated MAI. The new Semi-blind channel estimation and multi-user data detection based on Parallel Interference Cancellation (PIC) have been applied in the system. The Low Density Parity Codes (LDPC) has also been introduced into the system to improve the performance. Different interference models are analyzed in multi-carrier communication systems and then the effective interference suppression for MC-CDMA systems is employed in this dissertation. The experimental results indicate that our system not only significantly reduces the PAPR and MAI but also effectively suppresses the outside interference with low complexity. Finally, we present a practical cognitive application of the proposed system over the software defined radio platform.

Dna Extraction From Filter-paper Spots Of Vaginal Samples Collected After Sexual Violence.

To detect the presence of male DNA in vaginal samples collected from survivors of sexual violence and stored on filter paper. A pilot study was conducted to evaluate 10 vaginal samples spotted on sterile filter paper: 6 collected at random in April 2009 and 4 in October 2010. Time between sexual assault and sample collection was 4-48hours. After drying at room temperature, the samples were placed in a sterile envelope and stored for 2-3years until processing. DNA extraction was confirmed by polymerase chain reaction for human β-globin, and the presence of prostate-specific antigen (PSA) was quantified. The presence of the Y chromosome was detected using primers for sequences in the TSPY (Y7/Y8 and DYS14) and SRY genes. β-Globin was detected in all 10 samples, while 2 samples were positive for PSA. Half of the samples amplified the Y7/Y8 and DYS14 sequences of the TSPY gene and 30% amplified the SRY gene sequence of the Y chromosome. Four male samples and 1 female sample served as controls. Filter-paper spots stored for periods of up to 3years proved adequate for preserving genetic material from vaginal samples collected following sexual violence.

Transmission Of Intra-cellular Genetic Information: A System Proposal.

One of the great challenges of the scientific community on theories of genetic information, genetic communication and genetic coding is to determine a mathematical structure related to DNA sequences. In this paper we propose a model of an intra-cellular transmission system of genetic information similar to a model of a power and bandwidth efficient digital communication system in order to identify a mathematical structure in DNA sequences where such sequences are biologically relevant. The model of a transmission system of genetic information is concerned with the identification, reproduction and mathematical classification of the nucleotide sequence of single stranded DNA by the genetic encoder. Hence, a genetic encoder is devised where labelings and cyclic codes are established. The establishment of the algebraic structure of the corresponding codes alphabets, mappings, labelings, primitive polynomials (p(x)) and code generator polynomials (g(x)) are quite important in characterizing error-correcting codes subclasses of G-linear codes. These latter codes are useful for the identification, reproduction and mathematical classification of DNA sequences. The characterization of this model may contribute to the development of a methodology that can be applied in mutational analysis and polymorphisms, production of new drugs and genetic improvement, among other things, resulting in the reduction of time and laboratory costs.

Genome Sequence Of Streptomyces Wadayamensis Strain A23, An Endophytic Actinobacterium From Citrus Reticulata.

The actinobacterium Streptomyces wadayamensis A23 is an endophyte of Citrus reticulata that produces the antimycin and mannopeptimycin antibiotics, among others. The strain has the capability to inhibit Xylella fastidiosa growth. The draft genome of S. wadayamensis A23 has ~7.0 Mb and 6,006 protein-coding sequences, with a 73.5% G+C content.

Genome Sequence Of Bacillus Safensis Cfa06, Isolated From Biodegraded Petroleum In Brazil.

Bacillus safensis is a microorganism recognized for its biotechnological and industrial potential due to its interesting enzymatic portfolio. Here, as a means of gathering information about the importance of this species in oil biodegradation, we report a draft genome sequence of a strain isolated from petroleum.

Overlapped Sequence Types (sts) And Serogroups Of Avian Pathogenic (apec) And Human Extra-intestinal Pathogenic (expec) Escherichia Coli Isolated In Brazil.

Avian pathogenic Escherichia coli (APEC) strains belong to a category that is associated with colibacillosis, a serious illness in the poultry industry worldwide. Additionally, some APEC groups have recently been described as potential zoonotic agents. In this work, we compared APEC strains with extraintestinal pathogenic E. coli (ExPEC) strains isolated from clinical cases of humans with extra-intestinal diseases such as urinary tract infections (UTI) and bacteremia. PCR results showed that genes usually found in the ColV plasmid (tsh, iucA, iss, and hlyF) were associated with APEC strains while fyuA, irp-2, fepC sitDchrom, fimH, crl, csgA, afa, iha, sat, hlyA, hra, cnf1, kpsMTII, clpVSakai and malX were associated with human ExPEC. Both categories shared nine serogroups (O2, O6, O7, O8, O11, O19, O25, O73 and O153) and seven sequence types (ST10, ST88, ST93, ST117, ST131, ST155, ST359, ST648 and ST1011). Interestingly, ST95, which is associated with the zoonotic potential of APEC and is spread in avian E. coli of North America and Europe, was not detected among 76 APEC strains. When the strains were clustered based on the presence of virulence genes, most ExPEC strains (71.7%) were contained in one cluster while most APEC strains (63.2%) segregated to another. In general, the strains showed distinct genetic and fingerprint patterns, but avian and human strains of ST359, or ST23 clonal complex (CC), presented more than 70% of similarity by PFGE. The results demonstrate that some zoonotic-related STs (ST117, ST131, ST10CC, ST23CC) are present in Brazil. Also, the presence of moderate fingerprint similarities between ST359 E. coli of avian and human origin indicates that strains of this ST are candidates for having zoonotic potential.

Draft Genome Sequence Of Ft9, A Novel Bacillus Cereus Strain Isolated From A Brazilian Thermal Spring.

A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had its entire genome sequenced.

Phtx-ii A Basic Myotoxic Phospholipase A2 From Porthidium Hyoprora Snake Venom, Pharmacological Characterization And Amino Acid Sequence By Mass Spectrometry.

A monomeric basic PLA2 (PhTX-II) of 14149.08 Da molecular weight was purified to homogeneity from Porthidium hyoprora venom. Amino acid sequence by in tandem mass spectrometry revealed that PhTX-II belongs to Asp49 PLA2 enzyme class and displays conserved domains as the catalytic network, Ca2+-binding loop and the hydrophobic channel of access to the catalytic site, reflected in the high catalytic activity displayed by the enzyme. Moreover, PhTX-II PLA2 showed an allosteric behavior and its enzymatic activity was dependent on Ca2+. Examination of PhTX-II PLA2 by CD spectroscopy indicated a high content of alpha-helical structures, similar to the known structure of secreted phospholipase IIA group suggesting a similar folding. PhTX-II PLA2 causes neuromuscular blockade in avian neuromuscular preparations with a significant direct action on skeletal muscle function, as well as, induced local edema and myotoxicity, in mice. The treatment of PhTX-II by BPB resulted in complete loss of their catalytic activity that was accompanied by loss of their edematogenic effect. On the other hand, enzymatic activity of PhTX-II contributes to this neuromuscular blockade and local myotoxicity is dependent not only on enzymatic activity. These results show that PhTX-II is a myotoxic Asp49 PLA2 that contributes with toxic actions caused by P. hyoprora venom.