Analysis of Haplotype Sequences

In this era of whole-genome, next-generation sequencing, it is important to have a clear understanding of the concept of “haplotype”. We show here that most of the important regions of the genome can be described in terms of polymorphic frozen blocks (PFB). At each PFB, there are numerous, even hundreds, of alternative ancestral haplotypes. Haplotypes, not genes, can be regarded as the principal unit of inheritance. We illustrate how sequence data can be analysed to reveal and define these ancestral haplotypes

Interspecies Translation: Bovine Marbling to Human Muscular Dystrophy

There are interesting similarities and differences when comparing the histopathology of bovine marbling and human muscular dystrophy. At the simplest level, both conditions are characterized by genetically controlled and more or less inexorable replacement of muscle fibers with fat cells. At issue is whether an improved understanding of these two processes can lead to better outcomes for patients. There are many forms of dystrophy that differ in their genetics and their histopathology. There are also many forms of “marbling” ranging from the coarse to fine, epimysial, perimysial to endomysial and even to total replacement or steatosis. A detailed examination of marbling will provide a framework for further investigation of human dystrophy. Ultimately, the many genetic factors involved can be addressed through a better understanding of the metabolic pathways involved in marbling

Valley-spin blockade and spin resonance in carbon nanotubes

Manipulation and readout of spin qubits in quantum dots made in III-V materials successfully rely on Pauli blockade that forbids transitions between spin-triplet and spin-singlet states. Quantum dots in group IV materials have the advantage of avoiding decoherence from the hyperfine interaction by purifying them with only zero-spin nuclei. Complications of group IV materials arise from the valley degeneracies in the electronic bandstructure. These lead to complicated multiplet states even for two-electron quantum dots thereby significantly weakening the selection rules for Pauli blockade. Only recently have spin qubits been realized in silicon devices where the valley degeneracy is lifted by strain and spatial confinement. In carbon nanotubes Pauli blockade can be observed by lifting valley degeneracy through disorder. In clean nanotubes, quantum dots have to be made ultra-small to obtain a large energy difference between the relevant multiplet states. Here we report on low-disorder nanotubes and demonstrate Pauli blockade based on both valley and spin selection rules. We exploit the bandgap of the nanotube to obtain a large level spacing and thereby a robust blockade. Single-electron spin resonance is detected using the blockade.Comment: 31 pages including supplementary informatio

A physics-enabled flow restoration algorithm for sparse PIV and PTV measurements

The gaps and noise present in particle image velocimetry (PIV) and particle tracking velocimetry (PTV) measurements affect the accuracy of the data collected. Existing algorithms developed for the restoration of such data are only applicable to experimental measurements collected under well-prepared laboratory conditions (i.e. where the pattern of the velocity flow field is known), and the distribution, size and type of gaps and noise may be controlled by the laboratory set-up. However, in many cases, such as PIV and PTV measurements of arbitrarily turbid coastal waters, the arrangement of such conditions is not possible. When the size of gaps or the level of noise in these experimental measurements become too large, their successful restoration with existing algorithms becomes questionable. Here, we outline a new physics-enabled flow restoration algorithm (PEFRA), specially designed for the restoration of such velocity data. Implemented as a 'black box' algorithm, where no user-background in fluid dynamics is necessary, the physical structure of the flow in gappy or noisy data is able to be restored in accordance with its hydrodynamical basis. The use of this is not dependent on types of flow, types of gaps or noise in measurements. The algorithm will operate on any data time-series containing a sequence of velocity flow fields recorded by PIV or PTV. Tests with numerical flow fields established that this method is able to successfully restore corrupted PIV and PTV measurements with different levels of sparsity and noise. This assessment of the algorithm performance is extended with an example application to in situ submersible 3D-PTV measurements collected in the bottom boundary layer of the coastal ocean, where the naturally-occurring plankton and suspended sediments used as tracers causes an increase in the noise level that, without such denoising, will contaminate the measurements

Cosmic biology in perspective

Abstract: A series of astronomical observations obtained over the period 1986 to 2018 supports the idea that life is a cosmic rather than a purely terrestrial or planetary phenomenon. These include (1) the detection of biologically relevant molecules in interstellar clouds and in comets, (2) mid-infrared spectra of interstellar grains and the dust from comets, (3) a diverse set of data from comets including the Rosetta mission showing consistency with biology and (4) the frequency of Earth-like or habitable planets in the Galaxy. We argue that the conjunction of all the available data suggests the operation of cometary biology and interstellar panspermia rather than the much weaker hypothesis of comets being only the source of the chemical building blocks of life. We conclude with specific predictions on the properties expected of extra-terrestrial life if it is discovered on Enceladus, Europa or beyond. A radically different biochemistry elsewhere can be considered as a falsification of the theory of interstellar panspermia

Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA

Abstract Background Francisella tularensis is a Gram-negative bacterium that infects hundreds of species including humans, and has evolved to grow efficiently within a plethora of cell types. RipA is a conserved membrane protein of F. tularensis, which is required for growth inside host cells. As a means to determine RipA function we isolated and mapped independent extragenic suppressor mutants in ∆ripA that restored growth in host cells. Each suppressor mutation mapped to one of two essential genes, lpxA or glmU, which are involved in lipid A synthesis. We repaired the suppressor mutation in lpxA (S102, LpxA T36N) and the mutation in glmU (S103, GlmU E57D), and demonstrated that each mutation was responsible for the suppressor phenotype in their respective strains. We hypothesize that the mutation in S102 altered the stability of LpxA, which can provide a clue to RipA function. LpxA is an UDP-N-acetylglucosamine acyltransferase that catalyzes the transfer of an acyl chain from acyl carrier protein (ACP) to UDP-N-acetylglucosamine (UDP-GlcNAc) to begin lipid A synthesis. Results LpxA was more abundant in the presence of RipA. Induced expression of lpxA in the ΔripA strain stopped bacterial division. The LpxA T36N S102 protein was less stable and therefore less abundant than wild type LpxA protein. Conclusion These data suggest RipA functions to modulate lipid A synthesis in F. tularensis as a way to adapt to the host cell environment by interacting with LpxA.http://deepblue.lib.umich.edu/bitstream/2027.42/110509/1/12866_2014_Article_336.pd

The Lantern Vol. 5, No. 3, May 1937

• Dedication • Dr. McClure: An Ursinus Man • Roar, O Wind! • To the Ladies! • The Futility of Dying • The Symbolism of the British Crown • Oh! • It Might Have Been • Treat Yourself? • Three Writers • Hawaii in June • On Being a Twin • Black Magic • Triangle • Who Longs? • A Son Passes • Sing an Old-Fashioned Song • Questioning • An Argument About a Fish • That Morning Eye-Opener • Scoop for the Sun • The Dead Do Not Die Once • Give Us Timehttps://digitalcommons.ursinus.edu/lantern/1010/thumbnail.jp

Galaxy and Mass Assembly (GAMA): active galactic nuclei in pairs of galaxies

There exist conflicting observations on whether or not the environment of broad- and narrowline active galatic nuclei (AGN) differ and this consequently questions the validity of the AGN unification model. The high spectroscopic completeness of the Galaxy and Mass Assembly (GAMA) survey makes it ideal for a comprehensive analysis of the close environment of galaxies. To exploit this, and conduct a comparative analysis of the environment of broad- and narrow-line AGN within GAMA, we use a double-Gaussian emission line fitting method to model the more complex line profiles associated with broad-line AGN. We select 209 type 1 (i.e. unobscured), 464 type 1.5–1.9 (partially obscured), and 281 type 2 (obscured) AGN within the GAMA II data base. Comparing the fractions of these with neighbouring galaxies out to a pair separation of 350 kpc h−1 and Δz < 0.012 shows no difference between AGN of different type, except at separations less than 20 kpc h−1 where our observations suggest an excess of type 2 AGN in close pairs. We analyse the properties of the galaxies neighbouring our AGN and find no significant differences in colour or the star formation activity of these galaxies. Further to this, we find that Σ5 is also consistent between broad- and narrow-line AGN. We conclude that the observations presented here are consistent with AGN unification