Bacterial genospecies that are not ecologically coherent : population genomics of Rhizobium leguminosarum

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional 'polyphasic taxonomy' that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as 'biovars' within species that are defined by core gene phylogeny

Free Flap Selection and Outcomes of Soft Tissue Reconstruction Following Resection of Intra-oral Malignancy.

Introduction: Surgery to resect intra-oral malignancy is a well-established mode of primary treatment. The tissue requirement in this area is for a thin, pliable flap with minimal bulk and this has historically been provided by free tissue transfer with a radial forearm free flap (RFFF). More recently, a role for the anterolateral thigh free flap (ALTFF) has been described, although in populations with a westernized diet, body habitus may preclude use of an ALTFF due to flap thickness, relative to a radial forearm free flap. Methods: An analysis of data was performed retrospectively for 90 consecutive patients with intra-oral malignancy, requiring immediate soft tissue reconstruction by the senior author, at Addenbrooke's Hospital between July 2008 and April 2016. Cases requiring bony reconstruction were excluded. Data on patient age, sex, indication for surgery, tumor location and defect type, complications, success rates, and length of stay were recorded. Results: The majority of patients received an ALTFF (n = 56) with 38% receiving a RFFF (n = 34). Surgical resection took place in the floor of the mouth most frequently. These were closed with ALTFF and RFFF in 41 and 28 occasions, respectively. A success rate of 97% was observed in the RFFF group; 1 flap developed partial necrosis and required complete revision. In the ALTFF group, there was a 100% flap success rate. ALTFF usage resulted in a reduction in the number of intraoperative (p = 0.021) in addition a reduction in the number of days in ITU (p = 0.01) and post-operative clinic visits (p = 0.025). Conclusion: We present a series that used predominately the ALTFF to reconstruct intra-oral defects following resection of squamous cell carcinoma in a Western population. The results demonstrate that this treatment can produce at least as comparable results as to the use of a RFFF repair in this population, whilst avoiding the donor site morbidity and aesthetic compromise of a RFFF

From molecules to neural morphology: understanding neuroinflammation in autism spectrum condition.

Growing evidence points toward a critical role for early (prenatal) atypical neurodevelopmental processes in the aetiology of autism spectrum condition (ASC). One such process that could impact early neural development is inflammation. We review the evidence for atypical expression of molecular markers in the amniotic fluid, serum, cerebrospinal fluid (CSF), and the brain parenchyma that suggest a role for inflammation in the emergence of ASC. This is complemented with a number of neuroimaging and neuropathological studies describing microglial activation. Implications for treatment are discussed.Medical Research Council, Autism Research Trust, William Binks Autism Neuroscience FellowshipThis is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13229-016-0068-

Analytic Kramer kernels, Lagrange-type interpolation series and de Branges spaces

The classical Kramer sampling theorem provides a method for obtaining orthogonal sampling formulas. In particular, when the involved kernel is analytic in the sampling parameter it can be stated in an abstract setting of reproducing kernel Hilbert spaces of entire functions which includes as a particular case the classical Shannon sampling theory. This abstract setting allows us to obtain a sort of converse result and to characterize when the sampling formula associated with an analytic Kramer kernel can be expressed as a Lagrange-type interpolation series. On the other hand, the de Branges spaces of entire functions satisfy orthogonal sampling formulas which can be written as Lagrange-type interpolation series. In this work some links between all these ideas are established

Accelerating global left-ventricular function assessment in mice using reduced slice acquisition and three-dimensional guide-point modelling

<p>Abstract</p> <p>Background</p> <p>To investigate the utility of three-dimensional guide-point modeling (GPM) to reduce the time required for CMR evaluation of global cardiac function in mice, by reducing the number of image slices required for accurate quantification of left-ventricular (LV) mass and volumes.</p> <p>Methods</p> <p>Five female C57Bl/6 mice 8 weeks post myocardial infarction induced by permanent occlusion of the left coronary artery, and six male control (un-operated) C57Bl/6 mice, were subject to CMR examination under isoflurane anaesthesia. Contiguous short axis (SAX) slices (1 mm thick 7-9 slices) were obtained together with two long axis (LAX) slices in two chamber and four chamber orientations. Using a mathematical model of the heart to interpolate information between the available slices, GPM LV mass and volumes were determined using full slice (all SAX and two LAX), six slice (four SAX and two LAX) and four slice (two SAX and two LAX) analysis protocols. All results were compared with standard manual volumetric analysis using all SAX slices.</p> <p>Results</p> <p>Infarct size was 39.1 ± 5.1% of LV myocardium. No significant differences were found in left ventricular mass and volumes between the standard and GPM full and six slice protocols in infarcted mice (113 ± 10, 116 ± 11, and 117 ± 11 mg respectively for mass), or between the standard and GPM full, six and four slice protocols in control mice, (105 ± 14, 106 ± 10, 104 ± 12, and 105 ± 7 mg respectively for mass). Significant differences were found in LV mass (135 ± 18 mg) and EF using the GPM four slice protocol in infarcted mice (p < 0.05).</p> <p>Conclusion</p> <p>GPM enables accurate analysis of LV function in mice with relatively large infarcts using a reduced six slice acquisition protocol, and in mice with normal/symmetrical left-ventricular topology using a four slice protocol.</p

Molecular hydrogen beyond the optical edge of an isolated spiral galaxy

We know little about the outermost portions of galaxies because there is little light coming from them. We do know that in many cases atomic hydrogen (HI) extends well beyond the optical radius \cite{Casertano91}. In the centers of galaxies, however, molecular hydrogen (H2) usually dominates by a large factor, raising the question of whether H2 is abundant also in the outer regions but hitherto unseen.Here we report the detection of emission from carbon monoxide (CO), the most abundant tracer of H2, beyond the optical radius of the nearby galaxy NGC 4414. The molecular clouds probably formed in the regions of relatively high HI column density and in the absence of spiral density waves. The relative strength of the lines from the two lowest rotational levels indicates that both the temperature and density of the H2 are quite low compared to conditions closer to the center. The inferred surface density of the molecular material continues the monotonic decrease from the inner regions. We conclude that while molecular clouds can form in the outer region of this galaxy, there is little mass associated with them.Comment: 3 Nature page

Modelling outcomes after paediatric brain injury with admission laboratory values: a machine-learning approach.

BACKGROUND: Severe traumatic brain injury (TBI) is a leading cause of mortality in children, but the accurate prediction of outcomes at the point of admission remains very challenging. Admission laboratory results are a promising potential source of prognostic data, but have not been widely explored in paediatric cohorts. Herein, we use machine-learning methods to analyse 14 different serum parameters together and develop a prognostic model to predict 6-month outcomes in children with severe TBI. METHODS: A retrospective review of patients admitted to Cambridge University Hospital's Paediatric Intensive Care Unit between 2009 and 2013 with a TBI. The data for 14 admission serum parameters were recorded. Logistic regression and a support vector machine (SVM) were trained with these data against dichotimised outcomes from the recorded 6-month Glasgow Outcome Scale. RESULTS: Ninety-four patients were identified. Admission levels of lactate, H+, and glucose were identified as being the most informative of 6-month outcomes. Four different models were produced. The SVM using just the three most informative parameters was the best able to predict favourable outcomes at 6 months (sensitivity = 80%, specificity = 99%). CONCLUSIONS: Our results demonstrate the potential for highly accurate outcome prediction after severe paediatric TBI using admission laboratory data

In Vivo Time- Resolved Microtomography Reveals the Mechanics of the Blowfly Flight Motor

Dipteran flies are amongst the smallest and most agile of flying animals. Their wings are driven indirectly by large power muscles, which cause cyclical deformations of the thorax that are amplified through the intricate wing hinge. Asymmetric flight manoeuvres are controlled by 13 pairs of steering muscles acting directly on the wing articulations. Collectively the steering muscles account for <3% of total flight muscle mass, raising the question of how they can modulate the vastly greater output of the power muscles during manoeuvres. Here we present the results of a synchrotron-based study performing micrometre-resolution, time-resolved microtomography on the 145 Hz wingbeat of blowflies. These data represent the first four-dimensional visualizations of an organism's internal movements on sub-millisecond and micrometre scales. This technique allows us to visualize and measure the three-dimensional movements of five of the largest steering muscles, and to place these in the context of the deforming thoracic mechanism that the muscles actuate. Our visualizations show that the steering muscles operate through a diverse range of nonlinear mechanisms, revealing several unexpected features that could not have been identified using any other technique. The tendons of some steering muscles buckle on every wingbeat to accommodate high amplitude movements of the wing hinge. Other steering muscles absorb kinetic energy from an oscillating control linkage, which rotates at low wingbeat amplitude but translates at high wingbeat amplitude. Kinetic energy is distributed differently in these two modes of oscillation, which may play a role in asymmetric power management during flight control. Structural flexibility is known to be important to the aerodynamic efficiency of insect wings, and to the function of their indirect power muscles. We show that it is integral also to the operation of the steering muscles, and so to the functional flexibility of the insect flight motor

Enhanced flight performance by genetic manipulation of wing shape in Drosophila

Insect wing shapes are remarkably diverse and the combination of shape and kinematics determines both aerial capabilities and power requirements. However, the contribution of any specific morphological feature to performance is not known. Using targeted RNA interference to modify wing shape far beyond the natural variation found within the population of a single species, we show a direct effect on flight performance that can be explained by physical modelling of the novel wing geometry. Our data show that altering the expression of a single gene can significantly enhance aerial agility and that the Drosophila wing shape is not, therefore, optimized for certain flight performance characteristics that are known to be important. Our technique points in a new direction for experiments on the evolution of performance specialities in animals

Temperature Treatment of Highly Porous Zirconium-Containing Metal-Organic Frameworks Extends Drug Delivery Release.

Utilizing metal-organic frameworks (MOFs) as a biological carrier can lower the amount of the active pharmaceutical ingredient (API) required in cancer treatments to provide a more efficacious therapy. In this work, we have developed a temperature treatment process for delaying the release of a model drug compound from the pores of NU-1000 and NU-901, while taking care to utilize these MOFs' large pore volume and size to achieve exceptional model drug loading percentages over 35 wt %. Video-rate super-resolution microscopy reveals movement of MOF particles when located outside of the cell boundary, and their subsequent immobilization when taken up by the cell. Through the use of optical sectioning structured illumination microscopy (SIM), we have captured high-resolution 3D images showing MOF uptake by HeLa cells over a 24 h period. We found that addition of a model drug compound into the MOF and the subsequent temperature treatment process does not affect the rate of MOF uptake by the cell. Endocytosis analysis revealed that MOFs are internalized by active transport and that inhibiting the caveolae-mediated pathway significantly reduced cellular uptake of MOFs. Encapsulation of an anticancer therapeutic, alpha-cyano-4-hydroxycinnamic acid (α-CHC), and subsequent temperature treatment produced loadings of up to 81 wt % and demonstrated efficacy at killing cells beyond the burst release effect.M.H.T. thanks the Gates Cambridge Trust for funding, S. Haddad, D. Vulpe and Dr. C. Hockings for helpful discussions, and Dr. J. McMillan at the Cambridge Advanced Imaging Centre (CAIC), University of Cambridge. D.F.-J. thanks the Royal Society for funding through a University Research Fellowship. O.K.F. and J.T.H. gratefully acknowledge DTRA for financial support (grant HDTRA-1-14-1-0014). C.F.K. acknowledges funding from the UK Engineering and Physical Sciences Research Council, EPSRC (grants EP/L015889/1 and EP/H018301/1), the Wellcome Trust (grants 3-3249/Z/16/Z and 089703/Z/09/Z) and the UK Medical Research Council, MRC (grants MR/K015850/1 and MR/K02292X/1), and Infinitus (China) Ltd. Computational work was supported by the Cambridge High Performance Computing Cluster, Darwin