Using Student-Generated UV-Induced \u3cem\u3eEscherichia coli\u3c/em\u3e Mutants in a Directed Inquiry Undergraduate Genetics Laboratory

We report a thematic sequence of directed inquiry-based labs taking students from bacterial mutagenesis and phenotypic identification of their own self-created mutant, through identification of mutated genes by biochemical testing, to verification of mutant alleles by complementation, and finally to mutant allele characterization by DNA sequence analysis. The lab utilizes UV mutagenesis with wild-type Escherichia coli and a UV-sensitive isogenic derivative optimized for undergraduate use. The labs take advantage of the simplicity of E. coli in a realistic genetic investigation using safe UV irradiation methods for creation and characterization of novel mutants. Assessment data collected over three offerings of the course suggest that the labs, which combine original investigation in a scientifically realistic intellectual environment with learned techniques and concepts, were instrumental in improving students’ learning in a number of areas. These include the development of critical thinking skills and understanding of concepts and methods. Student responses also suggest the labs were helpful in improving students’understanding of the scientific process as a rational series of experimental investigations and awareness of the interdisciplinary nature of scientific inquiry

Using Experimentally Calibrated Regularized Stokeslets to Assess Bacterial Flagellar Motility Near a Surface

The presence of a nearby boundary is likely to be important in the life cycle and evolution of motile flagellate bacteria. This has led many authors to employ numerical simulations to model near-surface bacterial motion and compute hydrodynamic boundary effects. A common choice has been the method of images for regularized Stokeslets (MIRS); however, the method requires discretization sizes and regularization parameters that are not specified by any theory. To determine appropriate regularization parameters for given discretization choices in MIRS, we conducted dynamically similar macroscopic experiments and fit the simulations to the data. In the experiments, we measured the torque on cylinders and helices of different wavelengths as they rotated in a viscous fluid at various distances to a boundary. We found that differences between experiments and optimized simulations were less than 5% when using surface discretizations for cylinders and centerline discretizations for helices. Having determined optimal regularization parameters, we used MIRS to simulate an idealized free-swimming bacterium constructed of a cylindrical cell body and a helical flagellum moving near a boundary. We assessed the swimming performance of many bacterial morphologies by computing swimming speed, motor rotation rate, Purcell’s propulsive efficiency, energy cost per swimming distance, and a new metabolic energy cost defined to be the energy cost per body mass per swimming distance. All five measures predicted that the optimal flagellar wavelength is eight times the helical radius independently of body size and surface proximity. Although the measures disagreed on the optimal body size, they all predicted that body size is an important factor in the energy cost of bacterial motility near and far from a surface

Spatial Structure of the Mormon Cricket Gut Microbiome and Its Predicted Contribution to Nutrition and Immune Function

The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the niches available for microbes to colonize. We present a high-resolution analysis of the structure of the gut microbiome in the Mormon cricket Anabrus simplex, an insect known for its periodic outbreaks in the western United States and nutrition-dependent mating system. The Mormon cricket microbiome was dominated by eleven taxa from the Lactobacillaceae, Enterobacteriaceae, and Streptococcaeae. While most of these were represented in all gut regions, there were marked differences in their relative abundance, with lactic-acid bacteria (Lactobacillaceae) more common in the foregut and midgut and enteric (Enterobacteriaceae) bacteria more common in the hindgut. Differences in community structure were driven by variation in the relative prevalence of three groups: a Lactobacillus in the foregut, Pediococcus lactic-acid bacteria in the midgut, and Pantoea agglomerans, an enteric bacterium, in the hindgut. These taxa have been shown to have beneficial effects on their hosts in insects and other animals by improving nutrition, increasing resistance to pathogens, and modulating social behavior. Using PICRUSt to predict gene content from our 16S rRNA sequences, we found enzymes that participate in carbohydrate metabolism and pathogen defense in other orthopterans. These were predominately represented in the hindgut and midgut, the most important sites for nutrition and pathogen defense. Phylogenetic analysis of 16S rRNA sequences from cultured isolates indicated low levels of divergence from sequences derived from plants and other insects, suggesting that these bacteria are likely to be exchanged between Mormon crickets and the environment. Our study shows strong spatial variation in microbiome community structure, which influences predicted gene content and thus the potential of the microbiome to influence host function

Pyruvate Formate Lyase and Acetate Kinase are Essential for Anaerobic Growth of \u3cem\u3eEscherichia coli\u3c/em\u3e on Xylose

During anaerobic growth of bacteria, organic intermediates of metabolism, such as pyruvate or its derivatives, serve as electron acceptors to maintain the overall redox balance. Under these conditions, the ATP needed for cell growth is derived from substrate-level phosphorylation. In Escherichia coli, conversion of glucose to pyruvate yields 2 net ATPs, while metabolism of a pentose, such as xylose, to pyruvate only yields 0.67 net ATP per xylose due to the need for one (each) ATP for xylose transport and xylulose phosphorylation. During fermentative growth, E. coli produces equimolar amounts of acetate and ethanol from two pyruvates, and these reactions generate one additional ATP from two pyruvates (one hexose equivalent) while still maintaining the overall redox balance. Conversion of xylose to acetate and ethanol increases the net ATP yield from 0.67 to 1.5 per xylose. An E. coli pfl mutant lacking pyruvate formate lyase cannot convert pyruvate to acetyl coenzyme A, the required precursor for acetate and ethanol production, and could not produce this additional ATP. E. coli pfl mutants failed to grow under anaerobic conditions in xylose minimal medium without any negative effect on their survival or aerobic growth. An ackA mutant, lacking the ability to generate ATP from acetyl phosphate, also failed to grow in xylose minimal medium under anaerobic conditions, confirming the need for the ATP produced by acetate kinase for anaerobic growth on xylose. Since arabinose transport by AraE, the low-affinity, high-capacity, arabinose/H+ symport, conserves the ATP expended in pentose transport by the ABC transporter, both pfl and ackA mutants grew anaerobically with arabinose. AraE-based xylose transport, achieved after constitutively expressing araE, also supported the growth of the pfl mutant in xylose minimal medium. These results suggest that a net ATP yield of 0.67 per pentose is only enough to provide for maintenance energy but not enough to support growth of E. coli in minimal medium. Thus, pyruvate formate lyase and acetate kinase are essential for anaerobic growth of E. coli on xylose due to energetic constraints

Shearing of loose granular materials: A statistical mesoscopic model

A two-dimensional lattice model for the formation and evolution of shear bands in granular media is proposed. Each lattice site is assigned a random variable which reflects the local density. At every time step, the strain is localized along a single shear-band which is a spanning path on the lattice chosen through an extremum condition. The dynamics consists of randomly changing the `density' of the sites only along the shear band, and then repeating the procedure of locating the extremal path and changing it. Starting from an initially uncorrelated density field, it is found that this dynamics leads to a slow compaction along with a non-trivial patterning of the system, with high density regions forming which shelter long-lived low-density valleys. Further, as a result of these large density fluctuations, the shear band which was initially equally likely to be found anywhere on the lattice, gets progressively trapped for longer and longer periods of time. This state is however meta-stable, and the system continues to evolve slowly in a manner reminiscent of glassy dynamics. Several quantities have been studied numerically which support this picture and elucidate the unusual system-size effects at play.Comment: 11 pages, 15 figures revtex, submitted to PRE, See also: cond-mat/020921

Non-universal exponents in interface growth

We report on an extensive numerical investigation of the Kardar-Parisi-Zhang equation describing non-equilibrium interfaces. Attention is paid to the dependence of the growth exponents on the details of the distribution of the noise. All distributions considered are delta-correlated in space and time, and have finite cumulants. We find that the exponents become progressively more sensitive to details of the distribution with increasing dimensionality. We discuss the implications of these results for the universality hypothesis.Comment: 12 pages, 5 figures; to appear in Phys. Rev. Let

Spitzer Mid-Infrared Observations of Seven Bipolar Planetary Nebulae

We have investigated the mid-infrared (MIR) and visual structures of seven bipolar planetary nebulae (BPNe), using imaging and spectroscopy acquired using the Spitzer Space Telescope (SST), and the Observatorio Astronomico Nacional in Mexico. The results show that the sources are more extended towards longer MIR wavelengths, as well as having higher levels of surface brightness in the 5.8 and 8.0 microns bands. It is also noted that the 5.8/4.5 and 8.0/4.5 microns flux ratios increase with increasing distance from the nuclei of the sources. All of these latter trends may be attributable to emission by polycyclic aromatic hydrocarbons (PAHs) and/or warm dust continua within circum-nebular photo-dissociation regions (PDRs). A corresponding decrease in the flux ratios 8.0/5.8 microns may, by contrast, arise due to changes in the properties of the PAH emitting grains. We note evidence for possible 8.0 microns ring-like structures in the envelope of NGC 2346, located in a region beyond the minor axis limits of the ionized envelope. An analysis of the inner two rings shows that whilst they have higher surface brightnesses at longer MIR wavelengths, they are relatively stronger (compared to underlying emission) at 3.6 and 4.5 microns. There is also evidence for point reflection symmetry along the major axis of the outflow.Comment: 27 pages, 22 figures, Accepted for publication in MNRAS. 69 pages in arXi

Testing gravitational-wave searches with numerical relativity waveforms: Results from the first Numerical INJection Analysis (NINJA) project

The Numerical INJection Analysis (NINJA) project is a collaborative effort between members of the numerical relativity and gravitational-wave data analysis communities. The purpose of NINJA is to study the sensitivity of existing gravitational-wave search algorithms using numerically generated waveforms and to foster closer collaboration between the numerical relativity and data analysis communities. We describe the results of the first NINJA analysis which focused on gravitational waveforms from binary black hole coalescence. Ten numerical relativity groups contributed numerical data which were used to generate a set of gravitational-wave signals. These signals were injected into a simulated data set, designed to mimic the response of the Initial LIGO and Virgo gravitational-wave detectors. Nine groups analysed this data using search and parameter-estimation pipelines. Matched filter algorithms, un-modelled-burst searches and Bayesian parameter-estimation and model-selection algorithms were applied to the data. We report the efficiency of these search methods in detecting the numerical waveforms and measuring their parameters. We describe preliminary comparisons between the different search methods and suggest improvements for future NINJA analyses.Comment: 56 pages, 25 figures; various clarifications; accepted to CQ

Where do firms manage earnings?

Despite decades of research on how, why, and when companies manage earnings, there is a paucity of evidence about the geographic location of earnings management within multinational firms. In this study, we examine where companies manage earnings using a sample of 2,067 U.S. multinational firms from 1994 to 2009. We predict and find that firms with extensive foreign operations in weak rule of law countries have more foreign earnings management than companies with subsidiaries in locations where the rule of law is strong. We also find some evidence that profitable firms with extensive tax haven subsidiaries manage earnings more than other firms and that the earnings management is concentrated in foreign income. Apart from these results, we find that most earnings management takes place in domestic income, not foreign income.Arthur Andersen (Firm) (Arthur Andersen Faculty Fund

Real-Time Self-Regulation of Emotion Networks in Patients with Depression

Many patients show no or incomplete responses to current pharmacological or psychological therapies for depression. Here we explored the feasibility of a new brain self-regulation technique that integrates psychological and neurobiological approaches through neurofeedback with functional magnetic resonance imaging (fMRI). In a proof-of-concept study, eight patients with depression learned to upregulate brain areas involved in the generation of positive emotions (such as the ventrolateral prefrontal cortex (VLPFC) and insula) during four neurofeedback sessions. Their clinical symptoms, as assessed with the 17-item Hamilton Rating Scale for Depression (HDRS), improved significantly. A control group that underwent a training procedure with the same cognitive strategies but without neurofeedback did not improve clinically. Randomised blinded clinical trials are now needed to exclude possible placebo effects and to determine whether fMRI-based neurofeedback might become a useful adjunct to current therapies for depression