DamID as a versatile tool for understanding gene regulation

The interaction of proteins and RNA with chromatin underlies the regulation of gene expression. The ability to profile easily these interactions is fundamental for understanding chromatin biology in vivo. DNA adenine methyltransferase identification (DamID) profiles genome-wide protein-DNA interactions without antibodies, fixation or protein pull-downs. Recently, DamID has been adapted for applications beyond simple assaying of protein-DNA interactions, such as for studying RNA-chromatin interactions, chromatin accessibility and long-range chromosome interactions. Here, we provide an overview of DamID and introduce improvements to the technology, discuss their applications and compare alternative methodologies

Hydration of an apolar solute in a two-dimensional waterlike lattice fluid

In a previous work, we investigated a two-dimensional lattice-fluid model, displaying some waterlike thermodynamic anomalies. The model, defined on a triangular lattice, is now extended to aqueous solutions with apolar species. Water molecules are of the "Mercedes Benz" type, i.e., they possess a D3 (equilateral triangle) symmetry, with three equivalent bonding arms. Bond formation depends both on orientation and local density. The insertion of inert molecules displays typical signatures of hydrophobic hydration: large positive transfer free energy, large negative transfer entropy (at low temperature), strong temperature dependence of the transfer enthalpy and entropy, i.e., large (positive) transfer heat capacity. Model properties are derived by a generalized first order approximation on a triangle cluster.Comment: 9 pages, 5 figures, 1 table; submitted to Phys. Rev.

Derivation and analysis of a novel bi-directional non-isolated multi-level DC-DC (MLDC) converter

A novel non-isolated Multi-level DC/DC (MLDC) converter using vertical interleaving technique is reported in this paper. This MLDC offers a wide range of voltage transfer ratio by using reduced number of low voltage power electronic devices and reduced size of the DC inductor, making this converter a potential candidate solution for high power Medium to Low Voltage (MV to LV) DC/DC conversion such as energy storage connection to Medium Voltage (MV) systems or drives. The derivation of the generic topology and power electronic device voltage rating selection have been given. Design considerations and all possible arrangement of the vertical interleaving sequences used in this MLDC has been introduced with mathematical expressions

Characterisation of a pucBA deletion mutant from Rhodopseudomonas palustris lacking all but the pucBAd genes

Rhodopseudomonas palustris is a species of purple photosynthetic bacteria that has a multigene family of puc genes that encode the alpha and beta apoproteins, which form the LH2 complexes. A genetic dissection strategy has been adopted in order to try and understand which spectroscopic form of LH2 these different genes produce. This paper presents a characterisation of one of the deletion mutants generated in this program, the pucBAd only mutant. This mutant produces an unusual spectroscopic form of LH2 that only has a single large NIR absorption band at 800 nm. Spectroscopic and pigment analyses on this complex suggest that it has basically a similar overall structure as that of the wild-type HL LH2 complex. The mutant has the unique phenotype where the mutant LH2 complex is only produced when cells are grown at LL. At HL the mutant only produces the LH1-RC core complex

The crystal structure of mycobacterial epoxide hydrolase A

The human pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis resulting in over 1 million fatalities every year, despite decades of research into the development of new anti-TB compounds. Unlike most other organisms M. tuberculosis has six putative genes for epoxide hydrolases (EH) of the α/β-hydrolase family with little known about their individual substrates, suggesting functional significance for these genes to the organism. Due to their role in detoxification, M. tuberculosis EH’s have been identified as potential drug targets. Here, we demonstrate epoxide hydrolase activity of M. thermoresistibile epoxide hydrolase A (Mth-EphA) and report its crystal structure in complex with the inhibitor 1,3-diphenylurea at 2.0 Å resolution. Mth-EphA displays high sequence similarity to its orthologue from M. tuberculosis and generally high structural similarity to α/β-hydrolase EHs. The structure of the inhibitor bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor. Comparison to other EHs from mycobacteria allows insight into the active site plasticity with respect to substrate specificity. We speculate that mycobacterial EHs may have a narrow substrate specificity providing a potential explanation for the genetic repertoire of epoxide hydrolase genes in M. tuberculosis

An auxin-inducible, GAL4-compatible, gene expression system for Drosophila

The ability to control transgene expression, both spatially and temporally, is essential for studying model organisms. In Drosophila, spatial control is primarily provided by the GAL4/UAS system, whilst temporal control relies on a temperature-sensitive GAL80 (which inhibits GAL4) and drug-inducible systems. However, these are not ideal. Shifting temperature can impact on many physiological and behavioural traits, and the current drug-inducible systems are either leaky, toxic, incompatible with existing GAL4-driver lines, or do not generate effective levels of expression. Here, we describe the auxin-inducible gene expression system (AGES). AGES relies on the auxin-dependent degradation of a ubiquitously expressed GAL80, and therefore, is compatible with existing GAL4-driver lines. Water-soluble auxin is added to fly food at a low, non-lethal, concentration, which induces expression comparable to uninhibited GAL4 expression. The system works in both larvae and adults, providing a stringent, non-lethal, cost-effective, and convenient method for temporally controlling GAL4 activity in Drosophila

Managing human activity and marine mammals: A biologically based, relativistic risk assessment framework

Presented here is a broadly applicable, transparent, repeatable analytical framework for assessing relative risk of anthropogenic disturbances on marine vertebrates, with the emphasis on the sound generating aspects of the activity. The objectives are to provide managers and action-proponents tools with which to objectively evaluate drivers of potential biological risk, to identify data gaps that limit assessment, and to identify actionable measures to reduce risk. Current regulatory assessments of how human activities (particularly those that produce sound) influence the likelihood of marine mammal behavioral responses and potential injury, rely principally on generalized characterizations of exposure and effect using simple, threshold-based criteria. While this is relatively straightforward in regulatory applications, this approach fails to adequately address realistic site and seasonal scenarios, other potential stressors, and scalable outcome probabilities. The risk assessment presented here is primarily based on a common and broad understanding of the spatial-temporal-spectral intersections of animals and anthropogenic activities, and specific examples of its application to hypothetical offshore wind farms are given. The resulting species- and activity-specific framework parses risk into two discrete factors: a population’s innate ‘vulnerability’ (potential degree of susceptibility to disturbance) and an ‘exposure index’ (magnitude-duration severity resulting from exposure to an activity). The classic intersection of these factors and their multi-dimensional components provides a relativistic risk assessment process for realistic evaluation of specified activity contexts, sites, and schedules, convolved with species-specific seasonal presence, behavioral-ecological context, and natural history. This process is inherently scalable, allowing a relativistic means of assessing potential disturbance scenarios, tunable to animal distribution, region, context, and degrees of spatial-temporal-spectral resolution

Covid-19 and the Return of the State in Africa

Abstract: As African countries battled the Covid-19 crisis in 2020, one of the questions that were raised was whether the state was taking a central stage in the affairs of society, especially solutions to major problems. The question was triggered by the fact that there has been a decline in the capacity, role and prestige of the state in Africa for decades. Yet it seems that the responses to Covid-19, following the WHO guidelines, have placed the state at the centre, without dislocating other stakeholders like the private sector and the civil society. This paper uses the evidence from a select number of African countries of different sizes in various regions of the continent to provide an empirical perspective on the role of the state in Covid-19 responses in 2020 to answer the question of whether Covid-19 has occasioned a return of the state, thus reversing the neoliberal designs in favour of a lean and mean state in Africa