Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction

We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without the target sites). We introduce and motivate the concept of `programmability', i.e. the ability to set the threshold concentration for TF binding over a wide range merely by mutating the binding sequence of a target site. This functional demand, together with physical constraints arising from the thermodynamics and kinetics of TF-DNA interaction, leads us to a narrow range of ``optimal'' interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TF's. This indicates that TF-DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TF's.Comment: 9 pages, 4 figures; revised version as published in PNA

The performance of plant species in removing nutrients from stormwater in biofiltration systems in Cape Town

In 2009, the City of Cape Town (CoCT) adopted a stormwater policy which mandates that new and existing developments should reduce the concentration of phosphorus and suspended solids in stormwater runoff by 45% and 80%, respectively, but offered no explicit guidance about how these water quality targets might be achieved. This study aims to contribute to the limited knowledge that exists about the performance of local plant species to treat stormwater. A large nursery-based study was conducted to investigate the performance of 9 locally-occurring plant species to remove orthophosphate (PO4-3), ammonia (NH3) and nitrate (NO3-) found in urban stormwater. Synthetic stormwater was applied to each species as well as a control consisting only of soil (Malmesbury shale). The discharge was collected from a drainage pipe at the base of each of the 150 containers. The results show that all species (excluding Ficinia) reduced the average concentrations of PO4-3 by 81% and NH3 by 90%. By contrast, NO3- was reduced by an average of 69% (excluding by Elegia and Phragmites) with 8 of the 9 species removing significantly more than the control. The species that performed well for all three nutrients include Agapanthus and turf grasses, Stenotaphrum and Pennisetum. The results of the study highlight three important factors in the design of biofilters: that a substantial proportion of nutrients can be captured or absorbed by plants; that the soil medium is an important factor in the removal of PO4-3 and NH3; and that plant choice is essential in the removal of NO3-. Future research should test plant species in both the laboratory and field settings, and should include additional contaminants such as household detergents, heavy metals and bacteria

Evidence of Planetesimal infall on to the very young Herbig Be star LkHα_\alpha234

We report here the first evidence for planetesimal infall onto the very young Herbig Be star LkH$_\alpha$234. These results are based on observations acquired over 31 days using spectroscopy of the sodium D lines, the He I 5876\AA, and hydrogen H$_\alpha$ lines. We find Redshifted Absorption Components (RAC) with velocities up to 200 km/s and very mild Blueshifted Absorption Components (BEC) up to 100 km/s in the Na I lines. No correlation is observed between the appearance of the Na I RAC & BEC and the H$_\alpha$ and He I line variability, which suggests that these (Na I RAC & BEC) are formed in a process unrelated to the circumstellar gas accretion. We interpret the Na I RAC as evidence for an infalling evaporating body, greater than 100 km in diameter, which is able to survive at distances between 2.0 to 0.1 AU from the star. The dramatic appearance of the sodium RAC and mild BEC is readily explained by the dynamics of this infalling body making LkH$_\alpha$234 the youngest (age $\sim$ 0.1 Myr) system with evidence for the presence of planetesimals.Comment: Accepted for publications in ApJLetter

2-{(E)-N-[2-(1H-Inden-3-yl)eth­yl]imino­meth­yl}-1H-imidazole

The asymmetric unit of the title compound, C15H15N3, contains two crystallographically independent mol­ecules with very similar geometries. The imidazole and indenyl planes are approximately orthogonal, making dihedral angles of 88.21 (9) and 83.08 (9)%deg; in the two independent molecules. In the crystal, the imidazole units are linked by N—H⋯N hydrogen bonds into chains parallel to the 101) plane stretched in the diagonal direction [translation vector (,1,0); C(4) motif]. Within a chain, there are two types of symmetrically non-equivalent alternating H-bonds which slightly differ in their parameters

Metatarsophalangeal joint function during sprinting: A comparison of barefoot and sprint spike shod foot conditions

This is the authors' post print as accepted for publication in Journal of Applied Biomechanics. The published version is available at http://journals.humankinetics.com/jabThe metatarsophalangeal joint is an important contributor to lower limb energetics during sprint running. This study compared the kinematics, kinetics and energetics of the metatarsophalangeal joint during sprinting barefoot and wearing standardised sprint spikes. The aim of this investigation was to determine whether standard sprinting footwear alters the natural motion and function of the metatatarsophalangeal joint exhibited during barefoot sprint running. Eight trained sprinters performed maximal sprints along a runway, four sprints in each condition. Three dimensional high speed (1000 Hz) kinematic and kinetic data were collected at the 20 m point. Joint angle, angular velocity, moment, power and energy were calculated for the metatarsophalangeal joint. Sprint spikes significantly increase sprinting velocity (0.3 m/s average increase), yet limit the range of motion about the metatarsophalangeal joint (17.9 % average reduction) and reduce peak dorsiflexion velocity (25.5 % average reduction), thus exhibiting a controlling affect over the natural behaviour of the foot. However, sprint spikes improve metatarsophalangeal joint kinetics by significantly increasing the peak metatarsophalangeal joint moment (15 % average increase) and total energy generated during the important push-off phase (0.5 J to 1.4 J). The results demonstrate substantial changes in metatarsophalangeal function and potential improvements in performance-related parameters due to footwear

TssA from Aeromonas hydrophila: expression, purification and crystallographic studies

TssA is a core subunit of the type VI secretion system, which is a major player in interspecies competition in Gram-negative bacteria. Previous studies on enteroaggregative Escherichia coli TssA suggested that it is comprised of three putative domains: a conserved N-terminal domain, a middle domain and a ring-forming C-terminal domain. X-ray studies of the latter two domains have identified their respective structures. Here, the results of the expression and purification of full-length and domain constructs of TssA from Aeromonas hydrophila are reported, resulting in diffraction-quality crystals for the middle domain (Nt2) and a construct including the middle and C-terminal domains (Nt2-CTD)

'An interesting paper but not sufficiently theoretical’ : what does theorising in social research look like

This article explores the concept of theorising in social research: what is theorising; how does theorising look to those doing it and how can it be explained as a practice. The article draws on different sources, including accounts of theory and theorising in the literature as well as first-hand reporting by academics. A view is reached of theorising as a personal undertaking involving a commitment to comprehend the world. It is argued that theorising is driven by the identification of interesting problems (practical or theoretical or both) and a motivation to solve them. Theorising involves a shift of awareness from subsidiary to focal and such a shift allows a more abstract level of understanding. Theorising tends to be an individual undertaking which draws on personal knowledge, but it is only made possible by psychological tools which have been handed down from the past, ones which need to be accessed, understood and adapted. Theorising requires a disciplined creativity in which the imagination is channelled into finding solutions that are compatible with observed data