De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus

The nematode Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. In this project the transcriptome of P. superbus was sequenced using the 454 (Roche) platform. To enrich for stress-related genes, nema- todes were exposed to one of the following stresses (desiccation, cold, heat or oxidation). Equal numbers of nematodes from each stress treatment were combined with unstressed control nematodes prior to RNA extraction. Nor- malised and unnormalised cDNA libraries were prepared from this mixed population. A de novo assembly of the transcriptome was generated using a variety of assembly programs and strategies. A Sanger sequenced expressed sequence dataset comprising 3,982 unigenes was fully annotated and inte- grated into the de novo transcriptome assembly. The de novo assembly has also been annotated and putative stress response genes were identified. The haploid karyotype of P. superbus was determined to be n=4. P. superbus genomic DNA was sequenced using 454 (Roche) methods along with 50 bp and 100 bp paired end Illumina reads. Eight different gDNA assemblies were prepared, generating predicted genome sizes ranging from 87.9 kilobases to 159.7 kilobases. The longest contigs were obtained from the 454 genomic DNA assembly and the assemblies of the Illumina reads generated shorter contigs. The gene order of the P. superbus mitochondrial DNA genome was obtained and a draft assembly of the mitochondrial genome is presented. The current transcriptome assembly is a resource suitable for use as a refer- ence for aligning high throughput RNA Seq reads. Both the transcriptome and genome assemblies can be used to generate a protein reference database for the mass spectrometry based identification of the proteome of control and desiccated P. superbus for future studies

Steady State RF Fingerprinting for Identity Verification: One Class Classifier Versus Customized Ensemble

Mobile phone proliferation and increasing broadband penetration presents the possibility of placing small cellular base stations within homes to act as local access points. This can potentially lead to a very large increase in authentication requests hitting the centralized authentication infrastructure unless access is mediated at a lower protocol level. A study was carried out to examine the effectiveness of using Support Vector Machines to accurately identify if a mobile phone should be allowed access to a local cellular base station using differences imbued upon the signal as it passes through the analogue stages of its radio transmitter. Whilst allowing prohibited transmitters to gain access at the local level is undesirable and costly, denying service to a permitted transmitter is simply unacceptable. Two different learning approaches were employed, the first using One Class Classifiers (OCCs) and the second using customized ensemble classifiers. OCCs were found to perform poorly, with a true positive (TP) rate of only 50% (where TP refers to correctly identifying a permitted transmitter) and a true negative (TN) rate of 98% (where TN refers to correctly identifying a prohibited transmitter). The customized ensemble classifier approach was found to considerably outperform the OCCs with a 97% TP rate and an 80% TN rate

Steady State RF Fingerprinting for Identity Verification: One Class Classifier Versus Customized Ensemble

Mobile phone proliferation and increasing broadband penetration presents the possibility of placing small cellular base stations within homes to act as local access points. This can potentially lead to a very large increase in authentication requests hitting the centralized authentication infrastructure unless access is mediated at a lower protocol level. A study was carried out to examine the effectiveness of using Support Vector Machines to accurately identify if a mobile phone should be allowed access to a local cellular base station using differences imbued upon the signal as it passes through the analogue stages of its radio transmitter. Whilst allowing prohibited transmitters to gain access at the local level is undesirable and costly, denying service to a permitted transmitter is simply unacceptable. Two different learning approaches were employed, the first using One Class Classifiers (OCCs) and the second using customized ensemble classifiers. OCCs were found to perform poorly, with a true positive (TP) rate of only 50% (where TP refers to correctly identifying a permitted transmitter) and a true negative (TN) rate of 98% (where TN refers to correctly identifying a prohibited transmitter). The customized ensemble classifier approach was found to considerably outperform the OCCs with a 97% TP rate and an 80% TN rate

A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags

<p>Abstract</p> <p>Background</p> <p>Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. <it>Panagrolaimus superbus </it>is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that <it>P. superbus </it>uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis.</p> <p>Results</p> <p>To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of <it>P. superbus</it>. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at <url>http://www.nematodes.org/nembase4/species_info.php?species=PSC</url>. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from <it>P. superbus</it>. Notable among those is a putative lineage expansion of the <it>lea </it>(late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific <it>sxp/ral-2 </it>family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-β-1,3-glucanase (GHF5 family), most similar to a sequence from <it>Phytophthora infestans</it>. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This <it>P. superbus </it>sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants <it>glutathione peroxidase, dj-1 </it>and <it>1-Cys peroxiredoxin</it>, an <it>shsp </it>sequence and an <it>lea </it>gene.</p> <p>Conclusions</p> <p><it>P. superbus </it>appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of <it>lea </it>genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of <it>P. superbus</it>.</p

De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus

The nematode Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. In this project the transcriptome of P. superbus was sequenced using the 454 (Roche) platform. To enrich for stress-related genes, nema- todes were exposed to one of the following stresses (desiccation, cold, heat or oxidation). Equal numbers of nematodes from each stress treatment were combined with unstressed control nematodes prior to RNA extraction. Nor- malised and unnormalised cDNA libraries were prepared from this mixed population. A de novo assembly of the transcriptome was generated using a variety of assembly programs and strategies. A Sanger sequenced expressed sequence dataset comprising 3,982 unigenes was fully annotated and inte- grated into the de novo transcriptome assembly. The de novo assembly has also been annotated and putative stress response genes were identified. The haploid karyotype of P. superbus was determined to be n=4. P. superbus genomic DNA was sequenced using 454 (Roche) methods along with 50 bp and 100 bp paired end Illumina reads. Eight different gDNA assemblies were prepared, generating predicted genome sizes ranging from 87.9 kilobases to 159.7 kilobases. The longest contigs were obtained from the 454 genomic DNA assembly and the assemblies of the Illumina reads generated shorter contigs. The gene order of the P. superbus mitochondrial DNA genome was obtained and a draft assembly of the mitochondrial genome is presented. The current transcriptome assembly is a resource suitable for use as a refer- ence for aligning high throughput RNA Seq reads. Both the transcriptome and genome assemblies can be used to generate a protein reference database for the mass spectrometry based identification of the proteome of control and desiccated P. superbus for future studies

De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus

The nematode Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. In this project the transcriptome of P. superbus was sequenced using the 454 (Roche) platform. To enrich for stress-related genes, nema- todes were exposed to one of the following stresses (desiccation, cold, heat or oxidation). Equal numbers of nematodes from each stress treatment were combined with unstressed control nematodes prior to RNA extraction. Nor- malised and unnormalised cDNA libraries were prepared from this mixed population. A de novo assembly of the transcriptome was generated using a variety of assembly programs and strategies. A Sanger sequenced expressed sequence dataset comprising 3,982 unigenes was fully annotated and inte- grated into the de novo transcriptome assembly. The de novo assembly has also been annotated and putative stress response genes were identified. The haploid karyotype of P. superbus was determined to be n=4. P. superbus genomic DNA was sequenced using 454 (Roche) methods along with 50 bp and 100 bp paired end Illumina reads. Eight different gDNA assemblies were prepared, generating predicted genome sizes ranging from 87.9 kilobases to 159.7 kilobases. The longest contigs were obtained from the 454 genomic DNA assembly and the assemblies of the Illumina reads generated shorter contigs. The gene order of the P. superbus mitochondrial DNA genome was obtained and a draft assembly of the mitochondrial genome is presented. The current transcriptome assembly is a resource suitable for use as a refer- ence for aligning high throughput RNA Seq reads. Both the transcriptome and genome assemblies can be used to generate a protein reference database for the mass spectrometry based identification of the proteome of control and desiccated P. superbus for future studies

De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus

The nematode Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. In this project the transcriptome of P. superbus was sequenced using the 454 (Roche) platform. To enrich for stress-related genes, nema- todes were exposed to one of the following stresses (desiccation, cold, heat or oxidation). Equal numbers of nematodes from each stress treatment were combined with unstressed control nematodes prior to RNA extraction. Nor- malised and unnormalised cDNA libraries were prepared from this mixed population. A de novo assembly of the transcriptome was generated using a variety of assembly programs and strategies. A Sanger sequenced expressed sequence dataset comprising 3,982 unigenes was fully annotated and inte- grated into the de novo transcriptome assembly. The de novo assembly has also been annotated and putative stress response genes were identified. The haploid karyotype of P. superbus was determined to be n=4. P. superbus genomic DNA was sequenced using 454 (Roche) methods along with 50 bp and 100 bp paired end Illumina reads. Eight different gDNA assemblies were prepared, generating predicted genome sizes ranging from 87.9 kilobases to 159.7 kilobases. The longest contigs were obtained from the 454 genomic DNA assembly and the assemblies of the Illumina reads generated shorter contigs. The gene order of the P. superbus mitochondrial DNA genome was obtained and a draft assembly of the mitochondrial genome is presented. The current transcriptome assembly is a resource suitable for use as a refer- ence for aligning high throughput RNA Seq reads. Both the transcriptome and genome assemblies can be used to generate a protein reference database for the mass spectrometry based identification of the proteome of control and desiccated P. superbus for future studies

Steady State RF Fingerprinting for Identity Verification: One Class Classifier Versus Customized Ensemble

Mobile phone proliferation and increasing broadband penetration presents the possibility of placing small cellular base stations within homes to act as local access points. This can potentially lead to a very large increase in authentication requests hitting the centralized authentication infrastructure unless access is mediated at a lower protocol level. A study was carried out to examine the effectiveness of using Support Vector Machines to accurately identify if a mobile phone should be allowed access to a local cellular base station using differences imbued upon the signal as it passes through the analogue stages of its radio transmitter. Whilst allowing prohibited transmitters to gain access at the local level is undesirable and costly, denying service to a permitted transmitter is simply unacceptable. Two different learning approaches were employed, the first using One Class Classifiers (OCCs) and the second using customized ensemble classifiers. OCCs were found to perform poorly, with a true positive (TP) rate of only 50% (where TP refers to correctly identifying a permitted transmitter) and a true negative (TN) rate of 98% (where TN refers to correctly identifying a prohibited transmitter). The customized ensemble classifier approach was found to considerably outperform the OCCs with a 97% TP rate and an 80% TN rate

Steady State RF Fingerprinting for Identity Verification: One Class Classifier Versus Customized Ensemble

Mobile phone proliferation and increasing broadband penetration presents the possibility of placing small cellular base stations within homes to act as local access points. This can potentially lead to a very large increase in authentication requests hitting the centralized authentication infrastructure unless access is mediated at a lower protocol level. A study was carried out to examine the effectiveness of using Support Vector Machines to accurately identify if a mobile phone should be allowed access to a local cellular base station using differences imbued upon the signal as it passes through the analogue stages of its radio transmitter. Whilst allowing prohibited transmitters to gain access at the local level is undesirable and costly, denying service to a permitted transmitter is simply unacceptable. Two different learning approaches were employed, the first using One Class Classifiers (OCCs) and the second using customized ensemble classifiers. OCCs were found to perform poorly, with a true positive (TP) rate of only 50% (where TP refers to correctly identifying a permitted transmitter) and a true negative (TN) rate of 98% (where TN refers to correctly identifying a prohibited transmitter). The customized ensemble classifier approach was found to considerably outperform the OCCs with a 97% TP rate and an 80% TN rate