title: Simulations of 3D Magnetic Merging: Resistive Scalings for Null Point and QSL Reconnection

authors: Effenberger, Frederic

subjects: Science & Technology

abstract: Starting from an exact, steady-state, force-free solution of the magnetohydrodynamic (MHD) equations, we investigate how resistive current layers are induced by perturbing line-tied three-dimensional magnetic equilibria. This is achieved by the superposition of a weak perturbation field in the domain, in contrast to studies where the boundary is driven by slow motions, like those present in photospheric active regions. Our aim is to quantify how the current structures are altered by the contribution of so-called quasi-separatrix layers (QSLs) as the null point is shifted outside the computational domain. Previous studies based on magneto-frictional relaxation have indicated that despite the severe field line gradients of the QSL, the presence of a null is vital in maintaining fast reconnection. Here, we explore this notion using highly resolved simulations of the full MHD evolution. We show that for the null-point configuration, the resistive scaling of the peak current density is close to  J∼η−¹, while the scaling is much weaker, i.e.  J∼η⁻⁰.⁴, when only the QSL connectivity gradients provide a site for the current accumulation.

text: Simulations of 3D Magnetic Merging: Resistive Scalings for Null Point and QSL Reconnection Starting from an exact, steady-state, force-free solution of the magnetohydrodynamic (MHD) equations, we investigate how resistive current layers are induced by perturbing line-tied three-dimensional magnetic equilibria. This is achieved by the superposition of a weak perturbation field in the domain, in contrast to studies where the boundary is driven by slow motions, like those present in photospheric active regions. Our aim is to quantify how the current structures are altered by the contribution of so-called quasi-separatrix layers (QSLs) as the null point is shifted outside the computational domain. Previous studies based on magneto-frictional relaxation have indicated that despite the severe field line gradients of the QSL, the presence of a null is vital in maintaining fast reconnection. Here, we explore this notion using highly resolved simulations of the full MHD evolution. We show that for the null-point configuration, the resistive scaling of the peak current density is close to  J∼η−¹, while the scaling is much weaker, i.e.  J∼η⁻⁰.⁴, when only the QSL connectivity gradients provide a site for the current accumulation.

year: 2016

title: The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis

authors: Summers, Emma Louise

subjects: DNA binding protein

abstract: Lsr2 is a small, basic DNA binding protein that is highly conserved in mycobacteria and related actinomycetes. Lsr2 is essential for growth in Mycobacterium tuberculosis and previous studies have shown that Lsr2 is involved in down-regulating a wide range of genes involved in cell wall synthesis and metabolic functions. This regulatory function is likely to influence bacterial growth and survival.

This research investigated the biochemistry and 3D structure of Lsr2 from M. tuberculosis. Transmission electron microscopy (TEM) analysis of Lsr2 in complex with DNA revealed a regular fibril-like arrangement of protein coating double-stranded DNA. In addition, it was shown that Lsr2 physically protected DNA from DNase activity. The structure of the C-terminal DNA binding domain of Lsr2, determined by others part way through this research, prompted site directed mutagenesis of residues proposed to interact with DNA. Modification of arginine residues significantly reduced the binding of Lsr2 to DNA and fibril-like structures were not observed using TEM, for arginine mutants.

The first crystal structure of the N-terminal domain of Lsr2 is reported here. Two high resolution structures in monoclinic and hexagonal space groups were solved using X-ray crystallography and ab initio phasing. Proteolytic processing of the N-terminus of Lsr2 was revealed by the structure in P2₁ and this process was recreated using the protease trypsin which resulted in crystal formation in a P3₁21 space group. Both structures show linear chains of dimeric N-terminal Lsr2, as shown by crystallographic symmetry, linked by overlapping anti-parallel β-sheets, revealing a mechanism of protein oligomerisation. Oligomerisation only occurs after the removal of the first three residues M1, A2 and K3. In solution, protein oligomerisation was recreated with trypsin, resulting in the formation of large protein complexes. A change in DNA topology after the addition of trypsin to full-length Lsr2/DNA complexes was observed using TEM. This mechanism is likely to be important to M. tuberculosis under “stress” conditions where proteases are known to be upregulated and where cross-linking and condensation of DNA is critical.

text: The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis Lsr2 is a small, basic DNA binding protein that is highly conserved in mycobacteria and related actinomycetes. Lsr2 is essential for growth in Mycobacterium tuberculosis and previous studies have shown that Lsr2 is involved in down-regulating a wide range of genes involved in cell wall synthesis and metabolic functions. This regulatory function is likely to influence bacterial growth and survival.

This research investigated the biochemistry and 3D structure of Lsr2 from M. tuberculosis. Transmission electron microscopy (TEM) analysis of Lsr2 in complex with DNA revealed a regular fibril-like arrangement of protein coating double-stranded DNA. In addition, it was shown that Lsr2 physically protected DNA from DNase activity. The structure of the C-terminal DNA binding domain of Lsr2, determined by others part way through this research, prompted site directed mutagenesis of residues proposed to interact with DNA. Modification of arginine residues significantly reduced the binding of Lsr2 to DNA and fibril-like structures were not observed using TEM, for arginine mutants.

The first crystal structure of the N-terminal domain of Lsr2 is reported here. Two high resolution structures in monoclinic and hexagonal space groups were solved using X-ray crystallography and ab initio phasing. Proteolytic processing of the N-terminus of Lsr2 was revealed by the structure in P2₁ and this process was recreated using the protease trypsin which resulted in crystal formation in a P3₁21 space group. Both structures show linear chains of dimeric N-terminal Lsr2, as shown by crystallographic symmetry, linked by overlapping anti-parallel β-sheets, revealing a mechanism of protein oligomerisation. Oligomerisation only occurs after the removal of the first three residues M1, A2 and K3. In solution, protein oligomerisation was recreated with trypsin, resulting in the formation of large protein complexes. A change in DNA topology after the addition of trypsin to full-length Lsr2/DNA complexes was observed using TEM. This mechanism is likely to be important to M. tuberculosis under “stress” conditions where proteases are known to be upregulated and where cross-linking and condensation of DNA is critical.

year: 2012

title: Intersecting knowledge worlds: Describing the cultural interfaces within a socioscientific issue

authors: Wagner, Brent

subjects: cultural interface

abstract: Increasing numbers of science teachers in Aotearoa New Zealand are exploring ways to incorporate indigenous mātauranga Māori (Māori knowledge and ways of knowing) into their science programmes. This article presents findings from a study that examined how senior biology students in two English-medium secondary schools incorporated mātauranga Māori alongside biological science knowledge in their discussions about the use of 1080 poison to control mammalian predators. From a social constructivist ontology and interpretivist mode of inquiry using qualitative methodology, a triadic epistemic agency conceptual framework was developed inductively and used to analyse students’ written scripts for their national school leaving qualification (NCEA), and transcriptions of individual interviews. The study took place prior to the introduction of equal status to mātauranga Māori within the New Zealand Curriculum. Deductive analysis using the Triadic identified a group of ten students who drew from both knowledge systems, with varying degrees of knowledge integration. In addition to detailed representations of the theoretical space of the locale of the learner, the findings also identified three distinctive cultural interfaces occupied by the students: conflicted, parallel, and, connected. The findings underscore the importance of enabling diverse knowledge systems in biology classes to converge. Specifically, the incorporation of mātauranga Māori alongside biological science knowledge encourages a critical stance towards knowledge claims, supports pluralist knowledge use among culturally and linguistically diverse learners and promotes critical engagement with socioscientific issues (SSI) in senior secondary school biology.

text: Intersecting knowledge worlds: Describing the cultural interfaces within a socioscientific issue Increasing numbers of science teachers in Aotearoa New Zealand are exploring ways to incorporate indigenous mātauranga Māori (Māori knowledge and ways of knowing) into their science programmes. This article presents findings from a study that examined how senior biology students in two English-medium secondary schools incorporated mātauranga Māori alongside biological science knowledge in their discussions about the use of 1080 poison to control mammalian predators. From a social constructivist ontology and interpretivist mode of inquiry using qualitative methodology, a triadic epistemic agency conceptual framework was developed inductively and used to analyse students’ written scripts for their national school leaving qualification (NCEA), and transcriptions of individual interviews. The study took place prior to the introduction of equal status to mātauranga Māori within the New Zealand Curriculum. Deductive analysis using the Triadic identified a group of ten students who drew from both knowledge systems, with varying degrees of knowledge integration. In addition to detailed representations of the theoretical space of the locale of the learner, the findings also identified three distinctive cultural interfaces occupied by the students: conflicted, parallel, and, connected. The findings underscore the importance of enabling diverse knowledge systems in biology classes to converge. Specifically, the incorporation of mātauranga Māori alongside biological science knowledge encourages a critical stance towards knowledge claims, supports pluralist knowledge use among culturally and linguistically diverse learners and promotes critical engagement with socioscientific issues (SSI) in senior secondary school biology.

year: 2026