Systems Biology: The Next Frontier for Bioinformatics

Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii) the use of near-comprehensive data sets derived from ‘omics platform technologies, in particular “downstream” technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a) quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b) development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c) applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems

The thermo-oxidative degradation of poly(4-methylstyrene) and its relationship to flammability

Polystyrene and poly(4-methylstyrene) have very similar chemical structures with the only differences being the para methyl group of poly(4-methylstyrene). This methyl group is susceptible to oxidation at elevated temperatures. Here we demonstrate that it is possible to introduce oxidative cross-links to poly(4-methylstyrene), via the para methyl group, by thermal oxidative treatment at 230 °C, 250 °C and 270 °C in the absence of catalyst, leading to a material with markedly modified thermal degradation chemistry. Thermal gravimetric analysis and differential scanning calorimetry were used to characterise and compare untreated and post-oxidised materials and established that as the temperature of pre-treatment was increased, the subsequent thermal stability of the material increased. FTIR, NMR and microanalysis indicated that after the thermal oxidative pre-treatment ether cross-links are present alongside new oxygen containing functional groups such as aldehydes, carboxylic acids and hydroxyl groups. Finally, data obtained from pyrolysis combustion flow calorimetry confirmed that as the number of oxidative cross-links increase, a reduction in the polymer's flammability as assessed by heat release data is observed

DNA recognition by the Salmonella enterica serovar Typhimurium transcription factor SlyA

The Salmonella regulatory protein, SlyA is implicated in virulence, survival in macrophages and resistance to oxidative stress and anti-microbial peptides.  SlyA is a member of the MarR family of winged-helix transcription factors. Systematic mutational analysis of the SlyA operator sequence and of the predicted DNA-binding region of SlyA shows that no single base pair in the palindromic SlyA operator sequence is essential for DNA binding, and identifies amino acid residues required to allow SlyA to recognise DNA. Combining the structure-function studies described here and elsewhere with the structures of MarR family proteins suggests a possible model for regulation of SlyA binding to DNA

Temperature and velocity measurements of a rising thermal plume

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 16 (2015): 579–599, doi:10.1002/2014GC005576.The three-dimensional velocity and temperature fields surrounding an isolated thermal plume in a fluid with temperature-dependent viscosity are measured using Particle-Image Velocimetry and thermochromatic liquid crystals, respectively. The experimental conditions are relevant to a plume rising through the mantle. It is shown that while the velocity and the isotherm surrounding the plume can be used to visualize the plume, they do not reveal the finer details of its structure. However, by computing the Finite-Time Lyapunov Exponent fields from the velocity measurements, the material lines of the flow can be found, which clearly identify the shape of the plume head and characterize the behavior of the flow along the plume stem. It is shown that the vast majority of the material in the plume head has undergone significant stretching and originates from a wide region very low in the fluid domain, which is proposed as a contributing factor to the small-scale isotopic variability observed in ocean-island basalt regions. Lastly, the Finite-Time Lyapunov Exponent fields are used to calculate the steady state rise velocity of the thermal plume, which is found to scale linearly with the Rayleigh number, in contrast to some previous work. The possible cause and the significance of these conflicting results are discussed, and it is suggested that the scaling relationship may be affected by the temperature-dependence of the fluid viscosity in the current work.This work was funded by the National Science Foundation (grant EAR-055199) and the MAPS Dean's Office at UCL.2015-09-0

Constraining the source of mantle plumes

© The Author(s), 2016. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Earth and Planetary Science Letters 453 (2016): 55-63, doi:10.1016/j.epsl.2015.12.008.In order to link the geochemical signature of hot spot basalts to Earth’s deep interior, it is first necessary to understand how plumes sample different regions of the mantle. Here, we investigate the relative amounts of deep and shallow mantle material that are entrained by an ascending plume and constrain its source region. The plumes are generated in a viscous syrup using an isolated heater for a range of Rayleigh numbers. The velocity fields are measured using stereoscopic Particle-Image Velocimetry, and the concept of the ‘vortex ring bubble’ is used to provide an objective definition of the plume geometry. Using this plume geometry, the plume composition can be analysed in terms of the proportion of material that has been entrained from different depths. We show that the plume composition can be well described using a simple empirical relationship, which depends only on a single parameter, the sampling coefficient, Sc. High-Sc plumes are composed of material which originated from very deep in the fluid domain, while low-Sc plumes contain material entrained from a range of depths. The analysis is also used to show that the geometry of the plume can be described using a similarity solution, in agreement with previous studies. Finally, numerical simulations are used to vary both the Rayleigh number and viscosity contrast independently. The simulations allow us to predict the value of the sampling coefficient for mantle plumes; we find that as a plume reaches the lithosphere, 90% of its composition has been derived from the lowermost 260−750 km in the mantle, and negligible amounts are derived from the shallow half of the lower mantle. This result implies that isotope geochemistry cannot provide direct information about this un-sampled region, and that the various known geochemical reservoirs must lie in the deepest few hundred kilometres of the mantle.This work was funded by the National Science Foundation (grant EAR-055199), the MAPS Dean’s Office at UCL and the CIDER workshop (EAR-1135452).2016-12-2

Protein secretion and outer membrane assembly in Alphaproteobacteria

The assembly of β-barrel proteins into membranes is a fundamental process that is essential in Gram-negative bacteria, mitochondria and plastids. Our understanding of the mechanism of β-barrel assembly is progressing from studies carried out in Escherichia coli and Neisseria meningitidis. Comparative sequence analysis suggests that while many components mediating β-barrel protein assembly are conserved in all groups of bacteria with outer membranes, some components are notably absent. The Alphaproteobacteria in particular seem prone to gene loss and show the presence or absence of specific components mediating the assembly of β-barrels: some components of the pathway appear to be missing from whole groups of bacteria (e.g. Skp, YfgL and NlpB), other proteins are conserved but are missing characteristic domains (e.g. SurA). This comparative analysis is also revealing important structural signatures that are vague unless multiple members from a protein family are considered as a group (e.g. tetratricopeptide repeat (TPR) motifs in YfiO, β-propeller signatures in YfgL). Given that the process of the β-barrel assembly is conserved, analysis of outer membrane biogenesis in Alphaproteobacteria, the bacterial group that gave rise to mitochondria, also promises insight into the assembly of β-barrel proteins in eukaryotes

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

Klebsiella pneumoniae shows increasing emergence of multidrug-resistant lineages, including strains resistant to all available antimicrobial drugs. We conducted whole-genome sequencing of 178 highly drug-resistant isolates from a tertiary hospital in Lahore, Pakistan. Phylogenetic analyses to place these isolates into global context demonstrate the expansion of multiple independent lineages, including K. quasipneumoniae.This work was supported by National Health and Medical Research Council program grants (0606788 to R.A.S. and T. L.; 1092262 to R.A.S., G.D., and T.L.); the Wellcome Trust (206194); and the Higher Education Commission of Pakistan and The Children’s Hospital & The Institute of Child Health, Lahore, Pakistan. H.E. was supported by a scholarship from Higher Education Commission Pakistan under the International Research Support Initiative Program

Plume generation in natural thermal convection at high Rayleigh and Prandtl numbers

We study natural thermal convection of a fluid (corn syrup) with a large Prandtl number (10(3)-10(7)) and temperature-dependent viscosity. The experimental tank (1 x 1 x 0.3 m) is heated from below with insulating top and side boundaries, so that the fluid experiences secular heating as experiments proceed. This setup allows a focused study of thermal plumes from the bottom boundary layer over a range of Rayleigh numbers relevant to convective plumes in the deep interior of the Earth's mantle. The effective value of Ra, based on the viscosity of the fluid at the interior temperature, varies from 10(5) at the beginning to almost 10(8) toward the end of the experiments. Thermals (plumes) from the lower boundary layer are trailed by continuous conduits with long residence times. Plumes dominate flow in the tank, although there is a weaker large-scale circulation induced by material cooling at the imperfectly insulating top and sidewalls. At large Ra convection is extremely time-dependent and exhibits episodic bursts of plumes, separated by periods of quiescence. This bursting behaviour probably results from the inability of the structure of the thermal boundary layer and its instabilities to keep pace with the rate of secular change in the value of Ra. The frequency of plumes increases and their size decreases with increasing Ra, and we characterize these changes via in situ thermocouple measurements, shadowgraph videos, and videos of liquid crystal films recorded during several experiments. A scaling analysis predicts observed changes in plume head and tail radii with increasing Ra. Since inertial effects are largely absent no transition to 'hard' thermal turbulence is observed, in contrast to a previous conclusion from numerical calculations at similar Rayleigh numbers. We suggest that bursting behaviour similar to that observed may occur in the Earth's mantle as it undergoes secular cooling on the billion-year time scale

Assembly of the type II secretion system such as found in Vibrio cholerae depends on the novel Pilotin AspS

The Type II Secretion System (T2SS) is a molecular machine that drives the secretion of fully-folded protein substrates across the bacterial outer membrane. A key element in the machinery is the secretin: an integral, multimeric outer membrane protein that forms the secretion pore. We show that three distinct forms of T2SSs can be distinguished based on the sequence characteristics of their secretin pores. Detailed comparative analysis of two of these, the Klebsiella-type and Vibrio-type, showed them to be further distinguished by the pilotin that mediates their transport and assembly into the outer membrane. We have determined the crystal structure of the novel pilotin AspS from Vibrio cholerae, demonstrating convergent evolution wherein AspS is functionally equivalent and yet structurally unrelated to the pilotins found in Klebsiella and other bacteria. AspS binds to a specific targeting sequence in the Vibrio-type secretins, enhances the kinetics of secretin assembly, and homologs of AspS are found in all species of Vibrio as well those few strains of Escherichia and Shigella that have acquired a Vibrio-type T2SS