Caldolysin, a highly active protease from an extremely Thermophilic Bacterium

Proteases comprise a significant proportion of those proteins which have been subject to detailed characterisation (amino acid sequence and high resolution crystallographic analysis). The extent of research interest in proteolytic enzymes reflects both their historical status, and the practical advantages of proteases as research subjects (available in quantity, extracellular etc.) widely occurring

A New Generating Function for Calculating the Igusa Local Zeta Function

A new method is devised for calculating the Igusa local zeta function $Z_f$ of a polynomial $f(x_1,\dots,x_n)$ over a $p$-adic field. This involves a new kind of generating function $G_f$ that is the projective limit of a family of generating functions, and contains more data than $Z_f$. This $G_f$ resides in an algebra whose structure is naturally compatible with operations on the underlying polynomials, facilitating calculation of local zeta functions. This new technique is used to expand significantly the set of quadratic polynomials whose local zeta functions have been calculated explicitly. Local zeta functions for arbitrary quadratic polynomials over $p$-adic fields with $p$ odd are presented, as well as for polynomials over unramified $2$-adic fields of the form $Q+L$ where $Q$ is a quadratic form and $L$ is a linear form where $Q$ and $L$ have disjoint variables. For a quadratic form over an arbitrary $p$-adic field with odd $p$, this new technique makes clear precisely which of the three candidate poles are actual poles.Comment: 54 page

The industrial potential of enzymes from extremely thermophilic bacteria

The thermal regions of the central North Island of New Zealand are some of the most extensive in the world. In addition, they are readily accessible and contain a diversity of ecological habitats, including a large number at 100°C. These areas are regarded as an important tourist attraction, and as a source of geothermal power, It is now clear that they also contain an important and unique genetic resource

Buried Bedrock Topography of the Cannon River System Around Northfield, Minnesota

A geophysical survey in the area of Northfield, Minnesota, involving electrical earth resistivity profiling and seismic refraction soundings, showed sizeable buried river channels in the bedrock in the Cannon River Valley which greatly increase in size downstream of Northfield. The channels upstream from the Northfield appear to be continuous and connect with the large buried channel between Northfield and Cannon Falls. The major buried valley deviates from the modern course of the Cannon River within the City of Northfield, but appears to follow elsewhere

Rigid body visual servoing using navigation functions

Visual servo controllers in the literature rarely achieve provably large domains of attraction, and seldom address two important sensor limitations: (i) susceptibility to self-occlusions and (ii) finite field of view (FOV). We tackle the problem of global, occlusion-free visual servoing of a fully actuated rigid body by recourse to navigation functions on a compact manifold which encode these restrictions as control obstacles. For occlusion free rigid body servoing, the manifold of interest is the visible set of rigid body configurations, that is, those for which the feature points are within the field of view and unoccluded by the body. For a set of coplanar feature points on one face of a convex polyhedron, we show that a slightly conservative subset of the visible set has a simple topology amenable to analytical construction of a navigation function. We construct the controller via a closed form coordinate transformation from our problem domain into the topological model space and conclude with simulation results

Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long‐term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome‐wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long‐term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional‐scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149326/1/mec15042_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149326/2/mec15042.pd

Utility of CRISPR/Cas9 systems in hematology research

Since the end of the 20th century, the development of novel approaches have emerged to manipulate experimental models of hematological disorders, so they would more accurately mirror what is observed in the clinic. Despite these technological advances, the characterization of crucial genes for benign or malignant hematological disorders remains challenging, mainly because of the dynamic nature of the hematopoietic system and the genetic heterogeneity of these disorders. To overcome this limitation, genome editing technologies have been developed to specifically manipulate the genome via deletion, insertion or modification of targeted loci. These technologies have swiftly progressed, allowing their common use to investigate genetic function in experimental hematology. Amongst them, homologous recombination (HR)-mediated targeting technologies have facilitated the manipulation of specific loci by generating knockout and knock-in models. Despite promoting significant advances in the understanding of the molecular mechanisms involved in hematology, these inefficient, time-consuming and labor-intensive approaches did not permit the development of cellular or animal models recapitulating the complexity of hematological disorders. In October 2016, Dr. Ben Ebert and Dr. Chad Cowan shared their knowledge and experiences with the utilization of CRISPR for models of myeloid malignancy, disease, and novel therapeutics. Here we provide an overview of the topics they covered including insights into the novel applications of the technique as well as its strengths and limitations

Feedback Control as a Framework for Understanding Tradeoffs in Biology

Control theory arose from a need to control synthetic systems. From regulating steam engines to tuning radios to devices capable of autonomous movement, it provided a formal mathematical basis for understanding the role of feedback in the stability (or change) of dynamical systems. It provides a framework for understanding any system with feedback regulation, including biological ones such as regulatory gene networks, cellular metabolic systems, sensorimotor dynamics of moving animals, and even ecological or evolutionary dynamics of organisms and populations. Here we focus on four case studies of the sensorimotor dynamics of animals, each of which involves the application of principles from control theory to probe stability and feedback in an organism's response to perturbations. We use examples from aquatic (electric fish station keeping and jamming avoidance), terrestrial (cockroach wall following) and aerial environments (flight control in moths) to highlight how one can use control theory to understand how feedback mechanisms interact with the physical dynamics of animals to determine their stability and response to sensory inputs and perturbations. Each case study is cast as a control problem with sensory input, neural processing, and motor dynamics, the output of which feeds back to the sensory inputs. Collectively, the interaction of these systems in a closed loop determines the behavior of the entire system.Comment: Submitted to Integr Comp Bio

Cloud Atlas: Rotational Spectral Modulations and potential Sulfide Clouds in the Planetary-mass, Late T-type Companion Ross 458C

Measurements of photometric variability at different wavelengths provide insights into the vertical cloud structure of brown dwarfs and planetary-mass objects. In seven Hubble Space Telescope consecutive orbits, spanning $\sim$10 h of observing time}, we obtained time-resolved spectroscopy of the planetary-mass T8-dwarf Ross 458C using the near-infrared Wide Field Camera 3. We found spectrophotometric variability with a peak-to-peak signal of 2.62$\pm$0.02 % (in the 1.10-1.60~$\mu$m white light curve). Using three different methods, we estimated a rotational period of 6.75$\pm$1.58~h for the white light curve, and similar periods for narrow $J$- and $H$- band light curves. Sine wave fits to the narrow $J$- and $H$-band light curves suggest a tentative phase shift between the light curves with wavelength when we allow different periods between both light curves. If confirmed, this phase shift may be similar to the phase shift detected earlier for the T6.5 spectral type 2MASS J22282889-310262. We find that, in contrast with 2M2228, the variability of Ross~458C shows evidence for a {color trend} within the narrow $J$-band, but gray variations in the narrow $H$-band. The spectral time-resolved variability of Ross 458C might be potentially due to heterogeneous sulfide clouds in the atmosphere of the object. Our discovery extends the study of spectral modulations of condensate clouds to the coolest T dwarfs, planetary-mass companions.Comment: Accepted in ApJ

Cloud Atlas: Discovery of Rotational Spectral Modulations in a Low-mass, L-type Brown Dwarf Companion to a Star

Observations of rotational modulations of brown dwarfs and giant exoplanets allow the characterization of condensate cloud properties. As of now rotational spectral modulations have only been seen in three L-type brown dwarfs. We report here the discovery of rotational spectral modulations in LP261-75B, an L6-type intermediate surface gravity companion to an M4.5 star. As a part of the Cloud Atlas Treasury program we acquired time-resolved Wide Field Camera 3 grism spectroscopy (1.1--1.69~$\mu$m) of LP261-75B. We find gray spectral variations with the relative amplitude displaying only a weak wavelength dependence and no evidence for lower-amplitude modulations in the 1.4~$\mu$m water band than in the adjacent continuum. The likely rotational modulation period is 4.78$\pm$0.95 h, although the rotational phase is not well sampled. The minimum relative amplitude in the white light curve measured over the whole wavelength range is 2.41$\pm$0.14\%. We report an unusual light curve with seemingly three peaks approximately evenly distributed in rotational phase. The spectral modulations suggests that the upper atmosphere cloud properties in {LP261-75B} are similar to two other mid-L dwarfs of typical infrared colors, but differ from that of the extremely red L-dwarf WISE0047