Is There Genetic Diversity in the ‘Leucaena Bug’ \u3cem\u3eSynergistes jonesii\u3c/em\u3e Which May Reflect Ability to Degrade Leucaena Toxins?

Leucaena leucocephala, a nutritionally rich forage tree legume, contains a non-protein amino acid, mimosine, which is degraded by ruminal bacteria to toxic metabolites 3,4-DHP and 2,3-DHP resulting in goitre-like symptoms in animals, severely restricting weight gain. Raymond Jones, in the early 1980s, discovered the ‘leucaena bug’ in the rumen of goats in Hawaii that degraded these toxic DHP metabolites into non-toxic compounds (Jones and Lowry 1984) which was named Synergistes jonesii (Allison et al. 1992) Subsequently, a rumen inoculum containing S. jonesii was used as an ‘oral drench’ for cattle, kept in continuous culture (Klieve et al. 2002) and supplied to farmers to dose cattle foraging on leucaena. Studies on Queensland herds that received this oral drench showed that up to 50% of 44 herds grazing on leucaena had apparent subclinical toxicity based on high 3,4- and 2,3-DHP excretion in urine (Dalzell et al., 2012). In another study by Graham et al. (2013), a 16S rDNA nested PCR showed that rumen digesta from 6 out of 8 properties tested had a variant DNA profile from S. jonesii ATCC 78.1 strain, which suggested a different strain of the bacterium. It was postulated that either the continually cultured oral inoculum may have undergone genetic modification and/or that animals could harbor other DHP degrading bacteria or S. jonesii strains with differential DHP degrading potential (McSweeney et al. unpublished). The present study looks at changes in the 16S rDNA gene at the molecular level that may suggest divergence from the type strain S. jonesii 78.1 (ATCC) in Queensland cattle as well as in cattle and other ruminants, internationally. These changes can appear as discrete mutations or ‘single nucleotide polymorphisms’ (SNPs) and may be correlated to their ability to degrade DHP, relative to the type strain

Drum vortons in high density QCD

Recently it was shown that high density QCD supports of number of topological defects. In particular, there are U(1)_Y strings that arise due to K^0 condensation that occurs when the strange quark mass is relatively large. The unique feature of these strings is that they possess a nonzero K^+ condensate that is trapped on the core. In the following we will show that these strings (with nontrivial core structure) can form closed loops with conserved charge and currents trapped on the string worldsheet. The presence of conserved charges allows these topological defects, called vortons, to carry angular momentum, which makes them classically stable objects. We also give arguments demonstrating that vortons carry angular momentum very efficiently (in terms of energy per unit angular momentum) such that they might be the important degrees of freedom in the cores of neutron stars.Comment: 11 pages, accepted for publication in Physical Review

A human embryonic kidney 293T cell line mutated at the Golgi -mannosidase II locus

Disruption of Golgi -mannosidase II activity can result in type II congenital dyserythropoietic anemia and can induce lupus-like autoimmunity in mice. Here, we isolate a mutant human embryonic kidney (HEK) 293T cell line, called Lec36, that displays sensitivity to ricin that lies between the parental HEK 293T cells, whose secreted and membrane-expressed proteins are dominated by complex-type glycosylation, and 293S Lec1 cells, which only produce oligomannose-type N-linked glycans. The stem cell marker, 19A, was transiently expressed in the HEK 293T Lec36 cells, and in parental HEK 293T cells with and without the potent Golgi -mannosidase II inhibitor, swainsonine. Negative-ion nano-electrospray ionization mass spectra of the 19A N-linked glycans from HEK 293T Lec36 and swainsonine-treated HEK 293T cells were qualitatively indistinguishable and, as shown by collision-induced dissociation spectra, dominated by hybrid-type glycosylation. Nucleotide sequencing revealed mutations in each allele of MAN2A1, the gene encoding Golgi -mannosidase II: a point mutation in one allele mapping to the active site and an in-frame deletion of twelve-nucleotides in the other. Expression of wild-type but not the mutant MAN2A1 alleles in Lec36 cells restored processing of the 19A reporter glycoprotein to complex-type glycosylation. The Lec36 cell line will be useful for expressing therapeutic glycoproteins with hybrid-type glycans and provides a sensitive host for detecting mutations in human MAN2A1 causing type II congenital dyserythropoietic anemia

Bostonia: The Boston University Alumni Magazine. Volume 11

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Decoherence produces coherent states: an explicit proof for harmonic chains

We study the behavior of infinite systems of coupled harmonic oscillators as t->infinity, and generalize the Central Limit Theorem (CLT) to show that their reduced Wigner distributions become Gaussian under quite general conditions. This shows that generalized coherent states tend to be produced naturally. A sufficient condition for this to happen is shown to be that the spectral function is analytic and nonlinear. For a rectangular lattice of coupled oscillators, the nonlinearity requirement means that waves must be dispersive, so that localized wave-packets become suppressed. Virtually all harmonic heat-bath models in the literature satisfy this constraint, and we have good reason to believe that coherent states and their generalizations are not merely a useful analytical tool, but that nature is indeed full of them. Standard proofs of the CLT rely heavily on the fact that probability densities are non-negative. Although the CLT generally fails if the probability densities are allowed to take negative values, we show that a CLT does indeed hold for a special class of such functions. We find that, intriguingly, nature has arranged things so that all Wigner functions belong to this class.Comment: Final published version. 17 pages, Plain TeX, no figures. Online at http://astro.berkeley.edu/~max/gaussians.html (faster from the US), from http://www.mpa-garching.mpg.de/~max/gaussians.html (faster from Europe) or from [email protected]

Cosmological Constraints from the Clustering of the Sloan Digital Sky Survey DR7 Luminous Red Galaxies

We present the power spectrum of the reconstructed halo density field derived from a sample of Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey Seventh Data Release (DR7). The halo power spectrum has a direct connection to the underlying dark matter power for k <= 0.2 h/Mpc, well into the quasi-linear regime. This enables us to use a factor of ~8 more modes in the cosmological analysis than an analysis with kmax = 0.1 h/Mpc, as was adopted in the SDSS team analysis of the DR4 LRG sample (Tegmark et al. 2006). The observed halo power spectrum for 0.02 < k < 0.2 h/Mpc is well-fit by our model: chi^2 = 39.6 for 40 degrees of freedom for the best fit LCDM model. We find \Omega_m h^2 * (n_s/0.96)^0.13 = 0.141^{+0.009}_{-0.012} for a power law primordial power spectrum with spectral index n_s and \Omega_b h^2 = 0.02265 fixed, consistent with CMB measurements. The halo power spectrum also constrains the ratio of the comoving sound horizon at the baryon-drag epoch to an effective distance to z=0.35: r_s/D_V(0.35) = 0.1097^{+0.0039}_{-0.0042}. Combining the halo power spectrum measurement with the WMAP 5 year results, for the flat LCDM model we find \Omega_m = 0.289 +/- 0.019 and H_0 = 69.4 +/- 1.6 km/s/Mpc. Allowing for massive neutrinos in LCDM, we find \sum m_{\nu} < 0.62 eV at the 95% confidence level. If we instead consider the effective number of relativistic species Neff as a free parameter, we find Neff = 4.8^{+1.8}_{-1.7}. Combining also with the Kowalski et al. (2008) supernova sample, we find \Omega_{tot} = 1.011 +/- 0.009 and w = -0.99 +/- 0.11 for an open cosmology with constant dark energy equation of state w.Comment: 26 pages, 19 figures, submitted to MNRAS. The power spectrum and a module to calculate the likelihoods is publicly available at http://lambda.gsfc.nasa.gov/toolbox/lrgdr/ . v2 fixes abstract formatting issu

Villages and Urbanization

In this article comments by politician Boris Johnson and economist Edward Glaeser exemplify narratives of global urbanization that portray rural villages as redundant and perpetuate outdated notions of urban–rural division. Simultaneously, traditional urban–rural dialectics are distorted by divisive new urban projects like gated communities styled as villages. This paper argues for development models that acknowledge the vital environmental and economic roles played by rural villages, and opposes artificially created “villages” in cities. In so doing, alternative readings of rurality and villages by Rem Koolhaas, Brazilian land reformers, Mahatma Gandhi, and critics of contemporary Indian literature and urbanism are considered

Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination

Phage λ propagation in Escherichia coli host cells requires transcription antitermination on the λ chromosome mediated by λN protein and four host Nus factors, NusA, B, E (ribosomal S10) and G. Interaction of E. coli NusB:NusE heterodimer with the single stranded BoxA motif of λnutL or λnutR RNA is crucial for this reaction. Similarly, binding of NusB:NusE to a BoxA motif is essential to suppress transcription termination in the ribosomal RNA (rrn) operons. We used fluorescence anisotropy to measure the binding properties of NusB and of NusB:NusE heterodimer to BoxA-containing RNAs differing in length and sequence. Our results demonstrate that BoxA is necessary and sufficient for binding. We also studied the gain-of-function D118N NusB mutant that allows λ growth in nusA1 or nusE71 mutants. In vivo λ burst-size determinations, CD thermal unfolding measurements and X-ray crystallography of this as well as various other NusB D118 mutants showed the importance of size and polarity of amino acid 118 for RNA binding and other interactions. Our work suggests that the affinity of the NusB:NusE complex to BoxA RNA is precisely tuned to maximize control of transcription termination

Motor ability in children treated for idiopathic clubfoot. A controlled pilot study

<p>Abstract</p> <p>Background</p> <p>To study motor ability at seven years of age in children treated for idiopathic clubfoot and its relation to clubfoot laterality, foot status and the amount of surgery performed.</p> <p>Methods</p> <p>Twenty children (mean age 7.5 years, SD 3.2 months) from a consecutive birth cohort from our hospital catchments area (300.000 inhabitants from southern Sweden) were assessed with the Movement Assessment Battery for Children (MABC) and the Clubfoot Assessment Protocol (CAP).</p> <p>Results</p> <p>Compared to typically developing children an increased prevalence of motor impairment was found regarding both the total score for MABC (p < 0.05) and the subtest ABC-Ball skills (p < 0.05). No relationship was found between the child's actual foot status, laterality or the extent of foot surgery with the motor ability as measured with MABC. Only the CAP item "one-leg stand" correlated significantly with the MABC (rs = -0.53, p = 0.02).</p> <p>Conclusions</p> <p>Children with idiopathic clubfoot appear to have an increased risk of motor activity limitations and it is possible that other factors, independent of the clinical status, might be involved. The ability to keep balance on one leg may be a sufficient tool for determining which children in the orthopedic setting should be more thoroughly evaluated regarding their neuromotor functioning.</p

The Mathematical Universe

I explore physics implications of the External Reality Hypothesis (ERH) that there exists an external physical reality completely independent of us humans. I argue that with a sufficiently broad definition of mathematics, it implies the Mathematical Universe Hypothesis (MUH) that our physical world is an abstract mathematical structure. I discuss various implications of the ERH and MUH, ranging from standard physics topics like symmetries, irreducible representations, units, free parameters, randomness and initial conditions to broader issues like consciousness, parallel universes and Godel incompleteness. I hypothesize that only computable and decidable (in Godel's sense) structures exist, which alleviates the cosmological measure problem and help explain why our physical laws appear so simple. I also comment on the intimate relation between mathematical structures, computations, simulations and physical systems.Comment: Replaced to match accepted Found. Phys. version, 31 pages, 5 figs; more details at http://space.mit.edu/home/tegmark/toe.htm