Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane

Folding and insertion of β-barrel outer membrane proteins (OMPs) is essential for Gram-negative bacteria. This process is mediated by the multiprotein complex BAM, composed of the essential β-barrel OMP BamA and four lipoproteins (BamBCDE). The periplasmic domain of BamA is key for its function and contains five "polypeptide transport-associated" (POTRA) repeats. Here, we report the crystal structure of the POTRA4-5 tandem, containing the essential for BAM complex formation and cell viability POTRA5. The domain orientation observed in the crystal is validated by solution NMR and SAXS. Using previously determined structures of BamA POTRA1-4, we present a spliced model of the entire BamA periplasmic domain validated by SAXS. Solution scattering shows that conformational flexibility between POTRA2 and 3 gives rise to compact and extended conformations. The length of BamA in its extended conformation suggests that the protein may bridge the inner and outer membranes across the periplasmic space.     

Species choice for comparative genomics: being greedy works

Several projects investigating genetic function and evolution through sequencing and comparison of multiple genomes are now underway. These projects consume many resources, and appropriate planning should be devoted to choosing which species to sequence, potentially involving cooperation among different sequencing centres. A widely discussed criterion for species choice is the maximisation of evolutionary divergence. Our mathematical formalization of this problem surprisingly shows that the best long-term cooperative strategy coincides with the seemingly short-term “greedy” strategy of always choosing the next best single species. Other criteria influencing species choice, such as medical relevance or sequencing costs, can also be accommodated in our approach, suggesting our results' broad relevance in scientific policy decisions.     

High-field/ high-frequency EPR study on stable free radicals formed in sucrose by gamma-irradiation

The EPR spectrum of sucrose irradiated by high-energy radiation is complex due to the presence of more than one radical species. In order to decompose the spectrum and elucidate the radical magnetic parameters a high-field (HF(-)EPR) study on stable free radicals in gamma-irradiated polycrystalline sucrose (table sugar) was performed at three different high frequencies--94, 190 and 285 GHz as well as at the conventional X-band. We suggest a presence of three stable radicals R1, R2 and R3 as the main radical species. Due to the increase of g-factor resolution at high fields the g-tensors of these radicals could be extracted by accurate simulations. The moderate g-anisotropy suggests that all three radicals are carbon-centred. Results from an earlier ENDOR study on X-irradiated sucrose single crystals (Vanhaelewyn et al., Appl Radiat Isot, 52, 1221 (2000)) were used for analyzing of the spectra in more details. It was confirmed that the strongest hyperfine interaction has a relatively small anisotropy, which indicates either the absence of alpha-protons or a strongly distorted geometry of the radicals.     

NMR solution structure determination of RNAs

During the past several years, there have been significant advances in NMR solution structure determination of macromolecules. The ability to easily measure residual dipolar couplings, to directly detect NHellipsisN hydrogen bonding interactions and to study much larger macromolecules by the application of heteronuclear experiments that select narrow lines in 2D and 3D spectra of isotopically labeled molecules promises to dramatically improve solution structure determination of nucleic acids.     

L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies

L-Measure (LM) is a freely available software tool for the quantitative characterization of neuronal morphology. LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions. This report illustrates several LM protocols: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of approximately 20 neurons. The tool is available at http://krasnow.gmu.edu/cn3 for either online use on any Java-enabled browser and platform or download for local execution under Windows and Linux.     

The distribution and role of carnitine in the mammalian brain

A differential distribution of carnitine was found in twelve microdissected areas of the frozen canine brain. The cerebellar cortex showed the highest level of carnitine, while the lowest amounts were found in the hippocampus and pons sections of the brain. However, the inability to demonstrate changes in carnitine levels after $\text{in vivo}$ stimulation of the major afferent pathways in the caudate nucleus, and failure to demonstrate K+ stimulated release of carnitine in rat brain slices suggest that carnitine does not have a direct neurotransmitter role in the brain.     

Possible Brucellosis in an Early Hominin Skeleton from Sterkfontein,South Africa

We report on the paleopathological analysis of the partial skeleton of the late Pliocene hominin species Australopithecus africanus Stw 431 from Sterkfontein, South Africa. A previous study noted the presence of lesions on vertebral bodies diagnosed as spondylosis deformans due to trauma. Instead, we suggest that these lesions are pathological changes due to the initial phases of an infectious disease, brucellosis. The macroscopic, microscopic and radiological appearance of the lytic lesions of the lumbar vertebrae is consistent with brucellosis. The hypothesis of brucellosis (most often associated with the consumption of animal proteins) in a 2.4 to 2.8 million year old hominid has a host of important implications for human evolution. The consumption of meat has been regarded an important factor in supporting, directing or altering human evolution. Perhaps the earliest (up to 2.5 million years ago) paleontological evidence for meat eating consists of cut marks on animal remains and stone tools that could have made these marks. Now with the hypothesis of brucellosis in A. africanus, we may have evidence of occasional meat eating directly linked to a fossil hominin.