Quantitative comparison of the in situ microbial communities in different biomes

A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography

Cantor Spectrum for Schr\"odinger Operators with Potentials arising from Generalized Skew-shifts

We consider continuous $SL(2,\mathbb{R})$-cocycles over a strictly ergodic homeomorphism which fibers over an almost periodic dynamical system (generalized skew-shifts). We prove that any cocycle which is not uniformly hyperbolic can be approximated by one which is conjugate to an $SO(2,\mathbb{R})$-cocycle. Using this, we show that if a cocycle's homotopy class does not display a certain obstruction to uniform hyperbolicity, then it can be $C^0$-perturbed to become uniformly hyperbolic. For cocycles arising from Schr\"odinger operators, the obstruction vanishes and we conclude that uniform hyperbolicity is dense, which implies that for a generic continuous potential, the spectrum of the corresponding Schr\"odinger operator is a Cantor set.Comment: Final version. To appear in Duke Mathematical Journa

Single-cell bioluminescence and GFP in biofilm research

Using flow cells and a combination of microscopy techniques, we can unequivocally identify single bacterial cells that express bioluminescent and fluorescent bioreporters. We have shown that, for attached cells, bioluminescence output within a bacterial strain can vary greatly from cell to cell

Caudal–rostral progression of alpha motoneuron degeneration in the SOD1G93A mouse model of amyotrophic lateral sclerosis

Mice with transgenic expression of human SOD1G93A are a widely used model of ALS, with a caudal–rostral progression of motor impairment. Previous studies have quantified the progression of motoneuron (MN) degeneration based on size, even though alpha (α-) and gamma (γ-) MNs overlap in size. Therefore, using molecular markers and synaptic inputs, we quantified the survival of α-MNs and γ-MNs at the lumbar and cervical spinal segments of 3- and 4-month SOD1G93A mice, to investigate whether there is a caudal–rostral progression of MN death. By 3 months, in the cervical and lumbar spinal cord, there was α-MN degeneration with complete γ-MN sparing. At 3 months, the cervical spinal cord had more α-MNs per ventral horn than the lumbar spinal cord in SOD1G93A mice. A similar spatial trend of degeneration was observed in the corticospinal tract, which remained intact in the cervical spinal cord at 3- and 4- months of age. These findings agree with the corticofugal synaptopathy model that α-MNs and CST of the lumbar spinal cord are more susceptible to degeneration in SOD1G93A mice. Hence, there is a spatial and temporal caudal–rostral progression of α-MN and CST degeneration in SOD1G93A mice

Ruled Laguerre minimal surfaces

A Laguerre minimal surface is an immersed surface in the Euclidean space being an extremal of the functional \int (H^2/K - 1) dA. In the present paper, we prove that the only ruled Laguerre minimal surfaces are up to isometry the surfaces R(u,v) = (Au, Bu, Cu + D cos 2u) + v (sin u, cos u, 0), where A, B, C, D are fixed real numbers. To achieve invariance under Laguerre transformations, we also derive all Laguerre minimal surfaces that are enveloped by a family of cones. The methodology is based on the isotropic model of Laguerre geometry. In this model a Laguerre minimal surface enveloped by a family of cones corresponds to a graph of a biharmonic function carrying a family of isotropic circles. We classify such functions by showing that the top view of the family of circles is a pencil.Comment: 28 pages, 9 figures. Minor correction: missed assumption (*) added to Propositions 1-2 and Theorem 2, missed case (nested circles having nonempty envelope) added in the proof of Pencil Theorem 4, missed proof that the arcs cut off by the envelope are disjoint added in the proof of Lemma

Temperature and Photoperiod Effects on Sterility in a Cytoplasmic Male-Sterile Soybean

Manual cross-pollination to produce large quantities of hybrid soybean seed is difficult and time consuming. An environmentally stable sterility system is one of the necessary components to produce large quantities of hybrid seed. The objective of this study was to subject cytoplasmic male-sterile (CMS) BC5F1 plants, from a cross of a Chinese Glycine max wild-type soybean with a Chinese wild annual soybean G. soja (male parent) and controls, to a variety of different temperature and photoperiod treatments to test whether CMS is stable under various environmental conditions. Plants were grown in growth chambers under controlled temperature, photoperiod, and irradiance regimes until pod set, and then they were transferred to a glasshouse until they matured. Plants were evaluated for time of anthesis after photoperiod induction (13 h light/11 h dark) and fertility or sterility. Anther squash and pod set data showed that sterility of the CMS line was stable under all environmental conditions tested, whereas fertility-restored control plants remained fertile. Extreme environmental conditions led to delayed floral induction and/or stunted growth

Glassiness and constrained dynamics of a short-range non-disordered spin model

We study the low temperature dynamics of a two dimensional short-range spin system with uniform ferromagnetic interactions, which displays glassiness at low temperatures despite the absence of disorder or frustration. The model has a dual description in terms of free defects subject to dynamical constraints, and is an explicit realization of the ``hierarchically constrained dynamics'' scenario for glassy systems. We give a number of exact results for the statics of the model, and study in detail the dynamical behaviour of one-time and two-time quantities. We also consider the role played by the configurational entropy, which can be computed exactly, in the relation between fluctuations and response.Comment: 10 pages, 9 figures; minor changes, references adde

Exploring morphological correlations among H2CO, 12CO, MSX and continuum mappings

There are relatively few H2CO mappings of large-area giant molecular cloud (GMCs). H2CO absorption lines are good tracers for low-temperature molecular clouds towards star formation regions. Thus, the aim of the study was to identify H2CO distributions in ambient molecular clouds. We investigated morphologic relations among 6-cm continuum brightness temperature (CBT) data and H2CO (111-110; Nanshan 25-m radio telescope), 12CO (1--0; 1.2-m CfA telescope) and midcourse space experiment (MSX) data, and considered the impact of background components on foreground clouds. We report simultaneous 6-cm H2CO absorption lines and H110\alpha radio recombination line observations and give several large-area mappings at 4.8 GHz toward W49 (50'\times50'), W3 (70'\times90'), DR21/W75 (60'\times90') and NGC2024/NGC2023 (50'\times100') GMCs. By superimposing H2CO and 12CO contours onto the MSX color map, we can compare correlations. The resolution for H2CO, 12CO and MSX data was about 10', 8' and 18.3", respectively. Comparison of H2CO and 12CO contours, 8.28-\mu m MSX colorscale and CBT data revealed great morphological correlation in the large area, although there are some discrepancies between 12CO and H2CO peaks in small areas. The NGC2024/NGC2023 GMC is a large area of HII regions with a high CBT, but a H2CO cloud to the north is possible against the cosmic microwave background. A statistical diagram shows that 85.21% of H2CO absorption lines are distributed in the intensity range from -1.0 to 0 Jy and the \Delta V range from 1.206 to 5 km/s.Comment: 18 pages, 22 figures, 5 tables. Accepted to be published in Astrophysics and Space Scienc

Animal-side serologic assay for rapid detection of Mycobacterium bovis infection in multiple species of free-ranging wildlife

Numerous species of mammals are susceptible to Mycobacterium bovis, the causative agent of bovine tuberculosis (TB). Several wildlife hosts have emerged as reservoirs of M. bovis infection for domestic livestock in different countries. In the present study, blood samples were collected from Eurasian badgers (n=1532), white-tailed deer (n=463), brushtail possums (n=129), and wild boar (n=177) for evaluation of antibody responses to M. bovis infection by a lateral-flow rapid test (RT) and multiantigen print immunoassay (MAPIA). Magnitude of the antibody responses and antigen recognition patterns varied among the animals as determined by MAPIA; however, MPB83 was the most commonly recognized antigen for each host studied. Other seroreactive antigens included ESAT-6, CFP10, and MPB70. The agreement of the RT with culture results varied from 74% for possums to 81% for badgers to 90% for wild boar to 97% for white-tailed deer. Small numbers of wild boar and deer exposed to M. avium infection or paratuberculosis, respectively, did not cross-react in the RT, supporting the high specificity of the assay. In deer, whole blood samples reacted similarly to corresponding serum specimens (97% concordance), demonstrating the potential for field application. As previously demonstrated for badgers and deer, antibody responses to M. bovis infection in wild boar were positively associated with advanced disease. Together, these findings suggest that a rapid TB assay such as the RT may provide a useful screening tool for certain wildlife species that may be implicated in the maintenance and transmission of M. bovis infection to domestic livestock.The authors are grateful to Peter Andersen and Jim McNair for kindly providing certain antigens used in C this study. Badger samples were taken under projects funded by the Department for Environment, Food, and Rural Affairs (Defra), UK. The authors acknowledge the support of staff from CSL, VLA Starcross, Defra Wildlife Unit, and permission from the Independent Scientific Group for use of sera from the RBCT. Spanish wild boar samples were obtained with support from MEC Plan Nacional AGL2005-07401 and Santander - Fundacion M. Botin

A systematic review of the quality of evidence of ablative therapy for small renal masses

Purpose: We critically assessed the methodological and reporting quality of published studies of ablative techniques for small renal masses. Materials and Methods: We performed a systematic PubMed® and EMBASE® literature search from January 1966 to March 2010 to identify all full text, original research publications on ablative therapy for renal masses. Six reviewers working independently in 3 teams performed duplicate data abstraction using Strengthening the Reporting of Observational Studies in Epidemiology criteria, which were pilot tested in a separate sample. Results: A total of 117 original research publications published in a 15-year period (1995 to 2009) met eligibility criteria. No randomized, controlled trials were identified. All studies were observational and 88.9 had 1 arm with no comparison group. Median sample size was 18 patients (IQR 5.5, 40.0) and 53.8 of studies included 20 or fewer patients. Median followup was 14.0 months (IQR 8.0, 23.8) and only 19.7 of studies had an average followup of greater than 24 months. Of the studies 20.5 mentioned the number of operators involved and only 6.0 provided information on their experience level. Of the studies 66.7 addressed the recurrence rate. Disease specific and overall survival was reported in only 15.4 and 16.2 of studies, respectively. Conclusions: The published literature on the therapeutic efficacy of ablative therapy for renal masses is largely limited to uncontrolled, 1-arm observational studies. In the absence of higher quality evidence ablative therapy outside research studies should be limited to select patients who are not candidates for surgical intervention. © 2012 American Urological Association Education and Research, Inc