title: An examination of novel archaeal stress response genes

authors: Dinger, Marcel Eduard

abstract: The regulation of gene expression is the fundamental system employed by cells and organisms to respond to changes in their surroundings. To further understand the origins and nature of the processes underlying gene regulatory systems, the stress response in the thermophilic archaeon, Thermococcus zilligii, was examined. Microorganisms respond to stress by triggering physiological and morphological changes, which are largely brought about by adaptive changes in gene expression. The use of a thermophilic archaeon in this research is significant, since this group of organisms is widely regarded to resemble ancient life more closely than other extant life on Earth. Moreover, since the informational processing systems in archaea are thought to be closely related to those of the eukaryal nucleus, the study of the archaeal stress-response may further the understanding of the evolutionary relationship between the Archaea and the Eucarya. The stress response of T. zilligii was examined by analysing the total cytoplasmic protein complements from cultures ranging from mid-log to late stationary phase. Using N-terminal sequencing and BLASTP searches, homologues of four low molecular weight proteins that varied in level were identified in the genome sequences of members of the closely related genus, Pyrococcus. The genes originated from four distinct families, which were named srb, src, srd and sre. 
The srb family represents an essentially undescribed group of genes (COGI433), that occurs primarily amongst members of the Euryarchaeota. Due to the sporadic distribution of srb genes amongst extant life, the srb genes are suggested to have undergone horizontal transfer across large phylogenetic distances on several occasions. A sequence homologous to srb family members was identified as part of a hypothetical ORF in Clostridium perfringens, which encodes a protein that consists of a fusion of a transcriptional regulator belonging to the ArsR family and an SRB homologue. Several srb genes were found to occur as part of putative operons, the majority of which included genes homologous to the MinD family of P-loop ATPases. 
The src family encodes the highly conserved SaclOb family of DNA-binding proteins (COG1581). src genes occur exclusively amongst archaeal genomes, but were absent in Halobacterium sp. NRC-1, Methanopyrus kandleri, Methanosarcina mazei and M. acetivorans. The consensus secondary structure of the SRC proteins consists of a relatively long α-helix flanked by two small β-strands, followed by a second α-helix, and then three further β-strands. 
The srd family encodes proteins that are homologous to the C-terminal half of members of the Lrp/AsnC family of transcriptional regulators (COG1522). It is suggested here that the SRD family forms a logical subgroup that is structurally, and presumably functionally, distinct to the other members of the Lrp/AsnC family. srd genes occur in all nonmethanogenic archaea and in some bacteria. It is suggested that the srd family originated in the archaeal lineage and was later transferred to members of the Bacteria. The srd genes often appear as part of operon-like arrangements, which seem to be unrelated to one another, and consequently it is suggested that the SRD proteins are involved in a relatively generic function, such as transcriptional regulation. 
The sre family represents an undescribed group of highly conserved genes (COG1698) that occur exclusively amongst archaeal genomes. One sre gene was found in every archaeal genome sequenced to date, except for Pyrobaculum aerophilum and Halobacterium sp. NRC-1. Comparison of the SRE and 16S rRNA distance trees suggests that the sre genes were not prone to horizontal transfer. The secondary structure predicted from the SRE sequences consists of four large helical regions separated by short coiled regions. 
Recombinant proteins encoded by the srbPab1, srbPab2, srdPab2 and srePab genes cloned from Pyrococcus abyssi were produced in Escherichia coli and purified. An examination of the predicted quaternary associations of the recombinant proteins revealed that each of the proteins, with the exception rSRBPab2, formed multimeric structures. rSRBPabl formed dimer-sized multimers that occurred at 80°C, but not at room temperature. rSRDPab2 formed dimer-sized molecules that occurred preferentially at 80°C and in the presence of DNA. rSREPab formed structures that were consistent in size with those predicted for dimers and tetramers. Neither rSRBPabl, rSRDPab2 or rSREPab bound to DNA in the conditions examined.

text: An examination of novel archaeal stress response genes The regulation of gene expression is the fundamental system employed by cells and organisms to respond to changes in their surroundings. To further understand the origins and nature of the processes underlying gene regulatory systems, the stress response in the thermophilic archaeon, Thermococcus zilligii, was examined. Microorganisms respond to stress by triggering physiological and morphological changes, which are largely brought about by adaptive changes in gene expression. The use of a thermophilic archaeon in this research is significant, since this group of organisms is widely regarded to resemble ancient life more closely than other extant life on Earth. Moreover, since the informational processing systems in archaea are thought to be closely related to those of the eukaryal nucleus, the study of the archaeal stress-response may further the understanding of the evolutionary relationship between the Archaea and the Eucarya. The stress response of T. zilligii was examined by analysing the total cytoplasmic protein complements from cultures ranging from mid-log to late stationary phase. Using N-terminal sequencing and BLASTP searches, homologues of four low molecular weight proteins that varied in level were identified in the genome sequences of members of the closely related genus, Pyrococcus. The genes originated from four distinct families, which were named srb, src, srd and sre. 
The srb family represents an essentially undescribed group of genes (COGI433), that occurs primarily amongst members of the Euryarchaeota. Due to the sporadic distribution of srb genes amongst extant life, the srb genes are suggested to have undergone horizontal transfer across large phylogenetic distances on several occasions. A sequence homologous to srb family members was identified as part of a hypothetical ORF in Clostridium perfringens, which encodes a protein that consists of a fusion of a transcriptional regulator belonging to the ArsR family and an SRB homologue. Several srb genes were found to occur as part of putative operons, the majority of which included genes homologous to the MinD family of P-loop ATPases. 
The src family encodes the highly conserved SaclOb family of DNA-binding proteins (COG1581). src genes occur exclusively amongst archaeal genomes, but were absent in Halobacterium sp. NRC-1, Methanopyrus kandleri, Methanosarcina mazei and M. acetivorans. The consensus secondary structure of the SRC proteins consists of a relatively long α-helix flanked by two small β-strands, followed by a second α-helix, and then three further β-strands. 
The srd family encodes proteins that are homologous to the C-terminal half of members of the Lrp/AsnC family of transcriptional regulators (COG1522). It is suggested here that the SRD family forms a logical subgroup that is structurally, and presumably functionally, distinct to the other members of the Lrp/AsnC family. srd genes occur in all nonmethanogenic archaea and in some bacteria. It is suggested that the srd family originated in the archaeal lineage and was later transferred to members of the Bacteria. The srd genes often appear as part of operon-like arrangements, which seem to be unrelated to one another, and consequently it is suggested that the SRD proteins are involved in a relatively generic function, such as transcriptional regulation. 
The sre family represents an undescribed group of highly conserved genes (COG1698) that occur exclusively amongst archaeal genomes. One sre gene was found in every archaeal genome sequenced to date, except for Pyrobaculum aerophilum and Halobacterium sp. NRC-1. Comparison of the SRE and 16S rRNA distance trees suggests that the sre genes were not prone to horizontal transfer. The secondary structure predicted from the SRE sequences consists of four large helical regions separated by short coiled regions. 
Recombinant proteins encoded by the srbPab1, srbPab2, srdPab2 and srePab genes cloned from Pyrococcus abyssi were produced in Escherichia coli and purified. An examination of the predicted quaternary associations of the recombinant proteins revealed that each of the proteins, with the exception rSRBPab2, formed multimeric structures. rSRBPabl formed dimer-sized multimers that occurred at 80°C, but not at room temperature. rSRDPab2 formed dimer-sized molecules that occurred preferentially at 80°C and in the presence of DNA. rSREPab formed structures that were consistent in size with those predicted for dimers and tetramers. Neither rSRBPabl, rSRDPab2 or rSREPab bound to DNA in the conditions examined.

year: 2003

title: Finite-time singularity formation at a magnetic neutral line in Hall magnetohydrodynamics

authors: Litvinenko, Yuri E.

subjects: Finite-time singularities

abstract: The formation of a current sheet in a weakly collisional plasma can be modelled as a finite-time singularity solution of magnetohydrodynamic equations. We use an exact self-similar solution to confirm and generalise a previous finding that, in sharp contrast to two-dimensional solutions in standard MHD, a finite-time collapse to a current sheet can occur in Hall MHD. We derive a criterion for the finite-time singularity in terms of initial conditions, and we use an intermediate asymptotic solution for the evolution of an axial magnetic field to obtain a general expression for the singularity formation time. We illustrate the analytical results by numerical solutions.

text: Finite-time singularity formation at a magnetic neutral line in Hall magnetohydrodynamics The formation of a current sheet in a weakly collisional plasma can be modelled as a finite-time singularity solution of magnetohydrodynamic equations. We use an exact self-similar solution to confirm and generalise a previous finding that, in sharp contrast to two-dimensional solutions in standard MHD, a finite-time collapse to a current sheet can occur in Hall MHD. We derive a criterion for the finite-time singularity in terms of initial conditions, and we use an intermediate asymptotic solution for the evolution of an axial magnetic field to obtain a general expression for the singularity formation time. We illustrate the analytical results by numerical solutions.

year: 2015

title: Wāhine Māori engagement with literacies

authors: Masters-Awatere, Bridgette

subjects: Literacy

abstract: Wāhine Māori engagement with literacies (2023) is a case study report in collaboration with Te Whakaruruhau. It has been undertaken as part of a larger project, The expression, experience and transcendence of low skills in Aotearoa New Zealand (2019–2024), the aim of which is to provide policy recommendations to improve life-course trajectories and socio-economic outcomes for adults with low literacy and numeracy skills in Aotearoa New Zealand. Broadly speaking, Wāhine Māori engagement with literacy examines the framing and application of literacy measures in contemporary New Zealand culture. More specifically, it is about the lives and learning of wāhine (women) Māori (the indigenous peoples of Aotearoa New Zealand) within that culture and their attitudes towards, and complex relationships with, literacy as it is defined in their own lives and in the current setting. The study aims for a holistic understanding of lived literacies in driving the development of educational policies by public institutions and private groups. Reframing literacy as literacies is posited as a means to empower marginalised groups and to challenge the dominance of the Eurocentric education paradigm. Formal learning in English-language schools cannot be the extent of national literacy standards as it disregards Māori epistemological and ontological realities and can discount wāhine, many of whom may prioritise other modes of literacy. Centring their perspectives will bring about a more culturally inclusive future, one that makes space for the development of emotional and cultural literacies—as well as other forms such as digital, media, visual, financial, and health literacies—alongside the conventional version of literacy that has a monopoly in the present system.

text: Wāhine Māori engagement with literacies Wāhine Māori engagement with literacies (2023) is a case study report in collaboration with Te Whakaruruhau. It has been undertaken as part of a larger project, The expression, experience and transcendence of low skills in Aotearoa New Zealand (2019–2024), the aim of which is to provide policy recommendations to improve life-course trajectories and socio-economic outcomes for adults with low literacy and numeracy skills in Aotearoa New Zealand. Broadly speaking, Wāhine Māori engagement with literacy examines the framing and application of literacy measures in contemporary New Zealand culture. More specifically, it is about the lives and learning of wāhine (women) Māori (the indigenous peoples of Aotearoa New Zealand) within that culture and their attitudes towards, and complex relationships with, literacy as it is defined in their own lives and in the current setting. The study aims for a holistic understanding of lived literacies in driving the development of educational policies by public institutions and private groups. Reframing literacy as literacies is posited as a means to empower marginalised groups and to challenge the dominance of the Eurocentric education paradigm. Formal learning in English-language schools cannot be the extent of national literacy standards as it disregards Māori epistemological and ontological realities and can discount wāhine, many of whom may prioritise other modes of literacy. Centring their perspectives will bring about a more culturally inclusive future, one that makes space for the development of emotional and cultural literacies—as well as other forms such as digital, media, visual, financial, and health literacies—alongside the conventional version of literacy that has a monopoly in the present system.

year: 2023-09-28