The Discrete Wavelet Transform (DWT) is a popular tool in the field of image and video compression applications. Because of its multi-resolution representation capability, the DWT has been used effectively in applications such as transient signal analysis, computer vision, texture analysis, cell detection, and image compression. Daubechies wavelets are one of the popular transforms in the wavelet family. Daubechies filters provide excellent spatial and spectral locality-properties which make them useful in image compression.<p> In this thesis, we present an efficient implementation of a shared hardware core to compute two 8-point Daubechies wavelet transforms. The architecture is based on a new two-level folded mapping technique, an improved version of the Algebraic Integer Quantization (AIQ). The scheme is developed on the factorization and decomposition of the transform coefficients that exploits the symmetrical and wrapping structure of the matrices. The proposed architecture is parallel, pipelined, and multiplexed. Compared to existing designs, the proposed scheme reduces significantly the hardware cost, critical path delay and power consumption with a higher throughput rate.<p> Later, we have briefly presented a new mapping scheme to error-freely compute the Daubechies-8 tap wavelet transform, which is the next transform of Daubechies-6 in the Daubechies wavelet series. The multidimensional technique maps the irrational transformation basis coefficients with integers and results in considerable reduction in hardware and power consumption, and significant improvement in image reconstruction quality.

The Discrete Wavelet Transform (DWT) is a popular tool in the field of image and video compression applications. Because of its multi-resolution representation capability, the DWT has been used effectively in applications such as transient signal analysis, computer vision, texture analysis, cell detection, and image compression. Daubechies wavelets are one of the popular transforms in the wavelet family. Daubechies filters provide excellent spatial and spectral locality-properties which make them useful in image compression.<p> In this thesis, we present an efficient implementation of a shared hardware core to compute two 8-point Daubechies wavelet transforms. The architecture is based on a new two-level folded mapping technique, an improved version of the Algebraic Integer Quantization (AIQ). The scheme is developed on the factorization and decomposition of the transform coefficients that exploits the symmetrical and wrapping structure of the matrices. The proposed architecture is parallel, pipelined, and multiplexed. Compared to existing designs, the proposed scheme reduces significantly the hardware cost, critical path delay and power consumption with a higher throughput rate.<p> Later, we have briefly presented a new mapping scheme to error-freely compute the Daubechies-8 tap wavelet transform, which is the next transform of Daubechies-6 in the Daubechies wavelet series. The multidimensional technique maps the irrational transformation basis coefficients with integers and results in considerable reduction in hardware and power consumption, and significant improvement in image reconstruction quality.

Several traffic characterization studies have been performed on wireless LANs with the main objective of realizing good and accurate models of the errors in the wireless channel. These models have been extended to model the effect of errors on higher layer protocols, mainly at the data link layer. However, no prior work has been done to study the application level characteristics of MPEG-4 video traffic over 802.11b wireless networks. In this thesis a traffic characterization study of MPEG-4 video traffic over IEEE 802.11b wireless LANs with the main goal of building a tool for software testing is performed. Using two freely available tools to send and receive real-time streams and collect and analyze traces, MPEG-4 encoded video frames are sent over a 11 Mbps, 802.11b wireless LAN to characterize the errors in the channel and the effect of those errors on the quality of the movie. The results of this traffic characterization were modeled using ARTA (Auto Regressive-To-Anything) software. These modeled characteristics were then used to build a tool that generates synthetic traffic emulating real wireless network scenario. The tool emulates the error length and error free length characteristics of the wireless network for the MPEG-4 video traffic using the corresponding modeled characteristics generated by ARTA. The tool can be used by software developers to test their MPEG-4 streaming media applications without the need of the real infrastructure. The tool can also be trained and extended to support testing of any streaming media applications.

DNA-damage tolerance (DDT) in yeast is composed of two parallel pathways and mediated by sequential ubiquitination of proliferating cell nuclear antigen (PCNA). While monoubiquitination of PCNA promotes translesion synthesis (TLS), which is dependent on low fidelity polymerase ζ (Pol ζ) composed of a catalytic subunit Rev3 and a regulatory subunit Rev7, polyubiquitination of PCNA by Mms2-Ubc13-Rad5 promotes error-free lesion bypass. Inactivation of these two pathways results in a synergistic effect on DNA-damage responses; however, this two-branch DDT model has not been reported in any multicellular organisms. In order to examine whether Arabidopsis thaliana possesses a two-branch DDT system, rad5a rev3 double mutant plants were created and compared with the corresponding single mutants. Arabidopsis rad5a and rev3 mutations are indeed synergistic with respect to growth inhibition induced by replication-blocking lesions, suggesting that AtRAD5a and AtREV3 are required for error-free and TLS branches of DDT, respectively. Unexpectedly this study reveals three modes of genetic interactions in response to different types of DNA damage, indicating that plant RAD5 and REV3are also involved in DNA damage responses independent of DDT. By comparing with yeast cells, it is apparent that plant TLS is a more frequently utilized means of lesion bypass than error-free DDT. In addition, it was also observed that treatments with the DNA damaging agent methylmethanesulfonate increased the nuclear ploidy level in the double mutant plants.

Title from PDF of title page. / Document formatted into pages; contains 65 pages. / Thesis (M.S.C.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Several traffic characterization studies have been performed on wireless LANs with the main objective of realizing good and accurate models of the errors in the wireless channel. These models have been extended to model the effect of errors on higher layer protocols, mainly at the data link layer. However, no prior work has been done to study the application level characteristics of MPEG-4 video traffic over 802.11b wireless networks. In this thesis a traffic characterization study of MPEG-4 video traffic over IEEE 802.11b wireless LANs with the main goal of building a tool for software testing is performed. Using two freely available tools to send and receive real-time streams and collect and analyze traces, MPEG-4 encoded video frames are sent over a 11 Mbps, 802.11b wireless LAN to characterize the errors in the channel and the effect of those errors on the quality of the movie. The results of this traffic characterization were modeled using ARTA (Auto Regressive-To-Anything) software. These modeled characteristics were then used to build a tool that generates synthetic traffic emulating real wireless network scenario. The tool emulates the error length and error free length characteristics of the wireless network for the MPEG-4 video traffic using the corresponding modeled characteristics generated by ARTA. The tool can be used by software developers to test their MPEG-4 streaming media applications without the need of the real infrastructure. The tool can also be trained and extended to support testing of any streaming media applications. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

In Saccharomyces cerevisiae DNA postreplication repair (PRR) functions to bypass replication-blocking lesions to prevent damage-induced cell death. PRR employs two different mechanisms to bypass damaged DNA. While translesion synthesis (TLS) has been well characterized, little is known about the molecular events involved in error-free bypass although it has been assumed that homologous recombination (HR) is required for such a mode of lesion bypass. We undertook a genome-wide, synthetic genetic array (SGA) screen for novel genes involved in PRR and observed evidence of genetic interactions between error-free PRR and HR. We were screening for synthetic lethality which occurs when the combination of two mutations leads to an inviable organism, however, either single mutation allows for cell viability. In addition, we screened for conditionally synthetic lethal interaction which occurs when the combination of two mutations is inviable only in the presence of a DNA-damaging agent. This screen identified and assigned four genes, CSM2, PSY3, SHU1 and SHU2, whose products form a stable Shu complex, to the error-free PRR pathway. Previous studies have indicated that the Shu complex is required for efficient HR and that inactivation of any one of these genes is able to suppress the severe phenotypes of top3 and sgs1. We confirmed and further extended some of the reported observations and demonstrated that error-free PRR mutations are also epistatic to sgs1. Based on the above analyses, we propose a model in which error-free PRR utilizes the Shu complex to recruit HR to facilitate template switching, followed by double-Holliday junction resolution by Sgs1-Top3. Null mutations of HR genes including rad51, 52, 54, 55 and 57 are known to confer characteristic synergistic interactions with TLS mutations. To our surprise, null mutations of genes encoding the Mre11-Rad50-Xrs2 (MRX) complex, which is also required for HR, are epistatic to TLS mutations. The MRX complex confers an endo/exonuclease activity required for the detection and processing of DNA double-strand breaks (DSBs). Our results suggest that the MRX complex functions in both TLS and error-free PRR and that this function requires the nuclease activity of Mre11. This is in sharp contrast to other known HR genes that only function downstream of error-free PRR. Furthermore, we found that inactivation of SGS1 significantly inhibits proliferating cell nuclear antigen (PCNA) monoubiquitination and is epistatic to mutations in TLS, suggesting that Sgs1 also functions at earlier steps in DNA lesion bypass. We also examined the roles of Sae2 and Exo1, two accessory nucleases involved in DSB resection, in PRR. We found that while Sae2 is primarily required for TLS, Exo1 is exclusively involved in error-free PRR. In light of the distinct and overlapping activities of the above nucleases in the resection of DSBs, we propose that the distinct single-strand nuclease activities of MRX, Sae2 and Exo1 dictate the preference between TLS and error-free PRR for lesion bypass. While both PRR pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes non-canonical Lys63-linked polyubiquitinated PCNA to signal lesion bypass. This mechanism is dependent on the Mms2-Ubc13 complex being in close proximity to PCNA, a process thought to be dependent on Rad5. Rad5 is a member of the SWI/SNF family of ATPases that contains a RING finger motif characteristic of an E3 Ub ligase. Previous in vitro experiments demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase/ATPase activity. We therefore created site-specific mutants defective in either Rad5 RING finger or helicase/ATPase activity, or both, in order to examine their genetic interactions with known TLS and error-free PRR genes. Our results indicate that both the Rad5 RING finger motif and the helicase/ATPase activity are exclusively involved in error-free PRR. To our surprise, like the Rad5 RING finger, lack of the helicase/ATPase activity also abolishes the Lys63-linked PCNA polyubiquitin chain formation, suggesting that either the Rad5 helicase/ATPase-promoted replication fork regression signals PCNA polyubiquitination or this domain has a yet unidentified activity. In summary, results obtained from this thesis dissertation have revealed novel mechanisms of yeast PRR in S. cerevisiae, a mechanism that appears to be evolutionarily conserved throughout eukaryotes, from yeast to humans.

Ubiquitination is an important biochemical reaction found in all eukaryotic organisms and is involved in a wide range of cellular processes. Conventional ubiquitination requires the formation of polyubiquitin chains linked through Lys48 of the ubiquitin, which targets proteins for degradation, while the noncanonical Lys63-linked polyubiquitination of the proliferating cell nuclear antigen is required for error-free DNA damage tolerance (DDT or postreplication repair) in yeast. The ubiquitin-conjugating enzyme <i>Ubc13</i> and a cognate Ubc enzyme variant (Uev or Mms2) are involved in this process. Because there is less information available on either Lys63-linked ubiquitination or error-free DDT in plants, the goal of my research was to study the functions of <i>Ubc13</i> and Uev in plants using <i>Arabidopsis thaliana</i> as the model organism.<p> Four <i>UEV1</i> genes from <i>Arabidopsis thaliana</i> were isolated and characterized. All four <i>Uev1</i> proteins can form a stable complex with AtUbc13 and can promote <i>Ubc13</i> mediated Lys63 polyubiquitination. All four <i>UEV1</i> genes can replace yeast MMS2 in DDT function in vivo. Although these genes are ubiquitously expressed in most tissues, <i>UEV1D</i> appears to be expressed at a much higher level in germinating seeds and pollen. We obtained and characterized two <i>uev1d</i> null mutant T-DNA insertion lines. Compared with wild-type plants, seeds from uev1d null plants germinated poorly when treated with a DNA-damaging agent. Seeds that germinated grew slow and the majority ceased growth within 2 weeks. Pollen from uev1d plants also displayed a moderate but significant decrease in germination in the presence of DNA damage agent. These results indicate that <i>Ubc13-Uev</i> complex functions in DNA damage response in <i>Arabidopsis thaliana.</i> <i>Arabidopsis thaliana</i> contains two <i>UBC13</i> genes, AtUBC13A and AtUBC13B, that are highly conserved with respect to DNA sequence, protein sequence and genomic organization, suggesting that they are derived from a recent gene duplication event. Both <i>AtUbc13</i> proteins are able to physically interact with human and yeast Mms2, implying that plants also employ a Lys63-linked polyubiquitination reaction. Furthermore, Both <i>AtUBC13</i> genes were able to functionally complement the yeast ubc13 null mutants, suggesting the existence of an error-free DNA damage tolerance pathway in plants. The <i>AtUBC13</i> genes appear to be expressed ubiquitously and were not induced by various conditions tested.<p> The <i>ubc13a/b</i> double mutant lines were created and displayed strong phenotypic changes. The double mutant plants were delayed in seed germination as well as cotyledon and true leaf development. When seedlings were grown vertically on plates, the roots of the double mutant were shorter and grew in a zig-zag manner, compared to the straight growth of wild type roots. Root length and number of lateral roots on wild type and <i>ubc13a</i> and <i>ubc13b</i> single mutant plants were about 3 times longer than those of double mutant plants after 9 and 12 days of growth. When double mutant seeds were sown directly into soil, many did not germinate and those that germinated grew much slower than wild type. At 35 days, double mutant plants were smaller with thinner, flatter, and lighter coloured rosette leaves compared to wild type plants. These phenotypes indicate that <i>AtUbc13</i> not only plays a role in DDT to protect genome integrity but also is involved in plant development. Hence, this study set a cornerstone for future investigations into the roles of <i>Ubc13</i> and <i>Uev1</i> in plant development.

Ubiquitination is an important biochemical reaction found in all eukaryotic organisms and is involved in a wide range of cellular processes. Conventional ubiquitination requires the formation of polyubiquitin chains linked through Lys48 of the ubiquitin, which targets proteins for degradation, while the noncanonical Lys63-linked polyubiquitination of the proliferating cell nuclear antigen is required for error-free DNA damage tolerance (DDT or postreplication repair) in yeast. The ubiquitin-conjugating enzyme <i>Ubc13</i> and a cognate Ubc enzyme variant (Uev or Mms2) are involved in this process. Because there is less information available on either Lys63-linked ubiquitination or error-free DDT in plants, the goal of my research was to study the functions of <i>Ubc13</i> and Uev in plants using <i>Arabidopsis thaliana</i> as the model organism.<p> Four <i>UEV1</i> genes from <i>Arabidopsis thaliana</i> were isolated and characterized. All four <i>Uev1</i> proteins can form a stable complex with AtUbc13 and can promote <i>Ubc13</i> mediated Lys63 polyubiquitination. All four <i>UEV1</i> genes can replace yeast MMS2 in DDT function in vivo. Although these genes are ubiquitously expressed in most tissues, <i>UEV1D</i> appears to be expressed at a much higher level in germinating seeds and pollen. We obtained and characterized two <i>uev1d</i> null mutant T-DNA insertion lines. Compared with wild-type plants, seeds from uev1d null plants germinated poorly when treated with a DNA-damaging agent. Seeds that germinated grew slow and the majority ceased growth within 2 weeks. Pollen from uev1d plants also displayed a moderate but significant decrease in germination in the presence of DNA damage agent. These results indicate that <i>Ubc13-Uev</i> complex functions in DNA damage response in <i>Arabidopsis thaliana.</i> <i>Arabidopsis thaliana</i> contains two <i>UBC13</i> genes, AtUBC13A and AtUBC13B, that are highly conserved with respect to DNA sequence, protein sequence and genomic organization, suggesting that they are derived from a recent gene duplication event. Both <i>AtUbc13</i> proteins are able to physically interact with human and yeast Mms2, implying that plants also employ a Lys63-linked polyubiquitination reaction. Furthermore, Both <i>AtUBC13</i> genes were able to functionally complement the yeast ubc13 null mutants, suggesting the existence of an error-free DNA damage tolerance pathway in plants. The <i>AtUBC13</i> genes appear to be expressed ubiquitously and were not induced by various conditions tested.<p> The <i>ubc13a/b</i> double mutant lines were created and displayed strong phenotypic changes. The double mutant plants were delayed in seed germination as well as cotyledon and true leaf development. When seedlings were grown vertically on plates, the roots of the double mutant were shorter and grew in a zig-zag manner, compared to the straight growth of wild type roots. Root length and number of lateral roots on wild type and <i>ubc13a</i> and <i>ubc13b</i> single mutant plants were about 3 times longer than those of double mutant plants after 9 and 12 days of growth. When double mutant seeds were sown directly into soil, many did not germinate and those that germinated grew much slower than wild type. At 35 days, double mutant plants were smaller with thinner, flatter, and lighter coloured rosette leaves compared to wild type plants. These phenotypes indicate that <i>AtUbc13</i> not only plays a role in DDT to protect genome integrity but also is involved in plant development. Hence, this study set a cornerstone for future investigations into the roles of <i>Ubc13</i> and <i>Uev1</i> in plant development.

In Saccharomyces cerevisiae DNA postreplication repair (PRR) functions to bypass replication-blocking lesions to prevent damage-induced cell death. PRR employs two different mechanisms to bypass damaged DNA. While translesion synthesis (TLS) has been well characterized, little is known about the molecular events involved in error-free bypass although it has been assumed that homologous recombination (HR) is required for such a mode of lesion bypass. We undertook a genome-wide, synthetic genetic array (SGA) screen for novel genes involved in PRR and observed evidence of genetic interactions between error-free PRR and HR. We were screening for synthetic lethality which occurs when the combination of two mutations leads to an inviable organism, however, either single mutation allows for cell viability. In addition, we screened for conditionally synthetic lethal interaction which occurs when the combination of two mutations is inviable only in the presence of a DNA-damaging agent. This screen identified and assigned four genes, CSM2, PSY3, SHU1 and SHU2, whose products form a stable Shu complex, to the error-free PRR pathway. Previous studies have indicated that the Shu complex is required for efficient HR and that inactivation of any one of these genes is able to suppress the severe phenotypes of top3 and sgs1. We confirmed and further extended some of the reported observations and demonstrated that error-free PRR mutations are also epistatic to sgs1. Based on the above analyses, we propose a model in which error-free PRR utilizes the Shu complex to recruit HR to facilitate template switching, followed by double-Holliday junction resolution by Sgs1-Top3. Null mutations of HR genes including rad51, 52, 54, 55 and 57 are known to confer characteristic synergistic interactions with TLS mutations. To our surprise, null mutations of genes encoding the Mre11-Rad50-Xrs2 (MRX) complex, which is also required for HR, are epistatic to TLS mutations. The MRX complex confers an endo/exonuclease activity required for the detection and processing of DNA double-strand breaks (DSBs). Our results suggest that the MRX complex functions in both TLS and error-free PRR and that this function requires the nuclease activity of Mre11. This is in sharp contrast to other known HR genes that only function downstream of error-free PRR. Furthermore, we found that inactivation of SGS1 significantly inhibits proliferating cell nuclear antigen (PCNA) monoubiquitination and is epistatic to mutations in TLS, suggesting that Sgs1 also functions at earlier steps in DNA lesion bypass. We also examined the roles of Sae2 and Exo1, two accessory nucleases involved in DSB resection, in PRR. We found that while Sae2 is primarily required for TLS, Exo1 is exclusively involved in error-free PRR. In light of the distinct and overlapping activities of the above nucleases in the resection of DSBs, we propose that the distinct single-strand nuclease activities of MRX, Sae2 and Exo1 dictate the preference between TLS and error-free PRR for lesion bypass. While both PRR pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes non-canonical Lys63-linked polyubiquitinated PCNA to signal lesion bypass. This mechanism is dependent on the Mms2-Ubc13 complex being in close proximity to PCNA, a process thought to be dependent on Rad5. Rad5 is a member of the SWI/SNF family of ATPases that contains a RING finger motif characteristic of an E3 Ub ligase. Previous in vitro experiments demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase/ATPase activity. We therefore created site-specific mutants defective in either Rad5 RING finger or helicase/ATPase activity, or both, in order to examine their genetic interactions with known TLS and error-free PRR genes. Our results indicate that both the Rad5 RING finger motif and the helicase/ATPase activity are exclusively involved in error-free PRR. To our surprise, like the Rad5 RING finger, lack of the helicase/ATPase activity also abolishes the Lys63-linked PCNA polyubiquitin chain formation, suggesting that either the Rad5 helicase/ATPase-promoted replication fork regression signals PCNA polyubiquitination or this domain has a yet unidentified activity. In summary, results obtained from this thesis dissertation have revealed novel mechanisms of yeast PRR in S. cerevisiae, a mechanism that appears to be evolutionarily conserved throughout eukaryotes, from yeast to humans.

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