DNA meets the SVD

This paper introduces an important area of computational cell biology where complex, publicly available genomic data is being examined by linear algebra methods, with the aim of revealing biological and medical insights

Coregulated Genes Link Sulfide:Quinone Oxidoreductase and Arsenic Metabolism in Synechocystis sp. Strain PCC6803

Although the biogeochemistry of the two environmentally hazardous compounds arsenic and sulfide has been extensively investigated, the biological interference of these two toxic but potentially energy-rich compounds has only been hypothesized and indirectly proven. Here we provide direct evidence for the first time that in the photosynthetic model organism Synechocystis sp. strain PCC6803 the two metabolic pathways are linked by coregulated genes that are involved in arsenic transport, sulfide oxidation, and probably in sulfide-based alternative photosynthesis. Although Synechocystis sp. strain PCC6803 is an obligate photoautotrophic cyanobacterium that grows via oxygenic photosynthesis, we discovered that specific genes are activated in the presence of sulfide or arsenite to exploit the energy potentials of these chemicals. These genes form an operon that we termed suoRSCT, located on a transposable element of type IS4 on the plasmid pSYSM of the cyanobacterium. suoS (sll5036) encodes a light-dependent, type I sulfide:quinone oxidoreductase. The suoR (sll5035) gene downstream of suoS encodes a regulatory protein that belongs to the ArsR-type repressors that are normally involved in arsenic resistance. We found that this repressor has dual specificity, resulting in 200-fold induction of the operon upon either arsenite or sulfide exposure. The suoT gene encodes a transmembrane protein similar to chromate transporters but in fact functioning as an arsenite importer at permissive concentrations. We propose that the proteins encoded by the suoRSCT operon might have played an important role under anaerobic, reducing conditions on primordial Earth and that the operon was acquired by the cyanobacterium via horizontal gene transfer

Frequency-dependent electron power absorption mode transitions in capacitively coupled argon-oxygen plasmas

Phase Resolved Optical Emission Spectroscopy (PROES) measurements combined with 1d3v Particle-in-Cell/Monte Carlo Collision (PIC/MCC) simulations are performed to investigate the excitation dynamics in low-pressure capacitively coupled plasmas (CCPs) in argon-oxygen mixtures. The system used for this study is a geometrically symmetric CCP reactor operated in a fixed mixture gas composition, at fixed pressure and voltage amplitude, with a wide range of driving RF frequencies (2$~$MHz$~\le f \le~15~$MHz). The measured and calculated spatio-temporal distributions of the electron impact excitation rates from the Ar ground state to the Ar$~\rm{2p_1}$ state (with a wavelength of 750.4~nm) show good qualitative agreement. The distributions show significant frequency dependence, which is generally considered to be predictive of transitions in the dominant discharge operating mode. Three frequency ranges can be distinguished, showing distinctly different excitation characteristics: (i) in the low frequency range ($f \le~3~$MHz), excitation is strong at the sheaths and weak in the bulk region; (ii) at intermediate frequencies (3.5$~$MHz$~\le f \le~5~$MHz), the excitation rate in the bulk region is enhanced and shows striation formation; (iii) above 6$~$MHz, excitation in the bulk gradually decreases with increasing frequency. Boltzmann term analysis was performed to quantify the frequency dependent contributions of the Ohmic and ambipolar terms to the electron power absorption.Comment: arXiv admin note: text overlap with arXiv:2205.0644

The Essential Role of ClpXP in Caulobacter crescentus Requires Species Constrained Substrate Specificity

The ClpXP protease is a highly conserved AAA+ degradation machine that is present throughout bacteria and in eukaryotic organelles. ClpXP is essential in some bacteria, such as Caulobacter crescentus, but dispensible in others, such as Escherichia coli. In Caulobacter, ClpXP normally degrades the SocB toxin and increased levels of SocB result in cell death. ClpX can be deleted in cells lacking this toxin, but these ΔclpX strains are still profoundly deficient in morphology and growth supporting the existence of additional important functions for ClpXP. In this work, we characterize aspects of ClpX crucial for its cellular function. Specifically, we show that although the E. coli ClpX functions with the Caulobacter ClpP in vitro, this variant cannot complement wildtype activity in vivo. Chimeric studies suggest that the N-terminal domain of ClpX plays a crucial, species-specific role in maintaining normal growth. We find that one defect of Caulobacter lacking the proper species of ClpX is the failure to properly proteolytically process the replication clamp loader subunit DnaX. Consistent with this, growth of ΔclpX cells is improved upon expression of a shortened form of DnaX in trans. This work reveals that a broadly conserved protease can acquire highly specific functions in different species and further reinforces the critical nature of the N-domain of ClpX in substrate choice

Modeling of variant copies of subunit D1 in the structure of photosystem II from Thermosynechococcus elongatus

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.In the cyanobacterium Thermosynechococcus elongatus BP-1, living in hot springs, the light environment directly regulates expression of genes that encode key components of the photosynthetic multi-subunit protein-pigment complex photosystem II (PSII). Light is not only essential as an energy source to power photosynthesis, but leads to formation of aggressive radicals which induce severe damage of protein subunits and organic cofactors. Photosynthetic organisms develop several protection mechanisms against this photo-damage, such as the differential expression of genes coding for the reaction center subunit D1 in PSII. Testing the expression of the three different genes (psbAI, psbAII, psbAIII) coding for D1 in T. elongatus under culture conditions used for preparing the material used in crystallization of PSII showed that under these conditions only subunit PsbA1 is present. However, exposure to high-light intensity induced partial replacement of PsbA1 with PsbA3. Modeling of the variant amino acids of the three different D1 copies in the 3.0 Å resolution crystal structure of PSII revealed that most of them are in the direct vicinity to redox-active cofactors of the electron transfer chain. Possible structural and mechanistic consequences for electron transfer are discussed.DFG, SFB 498, Protein-Kofaktor-Wechselwirkungen in biologischen ProzessenEC/FP6/516510/EU/Linking molecular genetics and bio-mimetic chemistry - a multidisciplinary approach to achieve renewable hydrogen production/SOLAR-

The future of the humanities in primary schools – reflections in troubled times

This article reflects on the implications for practitioners, researchers and policy makers of the future of the humanities in primary schools, in the light of the challenges facing future generations. There is wide divergence in the four jurisdictions of the UK. The humanities are perceived as important, in principle, though curriculum frameworks differ. However, the status of the humanities is often uncertain, in practice, given the current emphasis on outcomes in literacy and numeracy. There is a lack of robust research on how and by whom the humanities are taught. The more theoretical articles suggest that the humanities, broadly conceived, are an essential aspect of young children’s education, to enable a deeper understanding of human culture and identity and develop the qualities and values needed in a diverse world. Curricular breadth is needed and that a focus on propositional knowledge is limiting. While this has implications for the whole curriculum, History, Geography and Religious Education have key roles in meeting these aims and in engaging and motivating young children. A stronger policy steer to ensure that schools give more priority to humanities education, with greater investment in professional development in Initial Teacher Education and beyond

Why focus on the primary humanities now?

Editorial. No abstract. This is a special issue of the journal coordinated by the four authors named above