The Global Genome Biodiversity Network (GGBN) Data Standard specification

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Methanobactin and the Link Between Copper and Bacterial Methane Oxidation

Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu2+ to Cu1+. In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs

13[C]-Urea Breath Test as a Novel Point-of-Care Biomarker for Tuberculosis Treatment and Diagnosis

BACKGROUND: Pathogen-specific metabolic pathways may be detected by breath tests based on introduction of stable isotopically-labeled substrates and detection of labeled products in exhaled breath using portable infrared spectrometers. METHODOLOGY/PRINCIPAL FINDINGS: We tested whether mycobacterial urease activity could be utilized in such a breath test format as the basis of a novel biomarker and diagnostic for pulmonary TB. Sensitized New-Zealand White Rabbits underwent bronchoscopic infection with either Mycobacterium bovis or Mycobacterium tuberculosis. Rabbits were treated with 25 mg/kg of isoniazid (INH) approximately 2 months after infection when significant cavitary lung pathology was present. [(13)C] urea was instilled directly into the lungs of intubated rabbits at selected time points, exhaled air samples analyzed, and the kinetics of delta(13)CO(2) formation were determined. Samples obtained prior to inoculation served as control samples for background (13)CO(2) conversion in the rabbit model. (13)CO(2), from metabolic conversion of [(13)C]-urea by mycobacterial urease activity, was readily detectable in the exhaled breath of infected rabbits within 15 minutes of administration. Analyses showed a rapid increase in the rate of (13)CO(2) formation both early in disease and prior to treatment with INH. Following INH treatment, all evaluable rabbits showed a decrease in the rate of (13)CO(2) formation. CONCLUSIONS/SIGNIFICANCE: Urea breath testing may provide a useful diagnostic and biomarker assay for tuberculosis and for treatment response. Future work will test specificity for M. tuberculosis using lung-targeted dry powder inhalation formulations, combined with co-administering oral urease inhibitors together with a saturating oral dose of unlabeled urea, which would prevent the delta(13)CO(2) signal from urease-positive gastrointestinal organisms

Measurement of Λ4H\rm ^4_{\Lambda}H and Λ4He\rm ^4_{\Lambda}He binding energy in Au+Au collisions at sNN\sqrt{s_\mathrm{NN}} = 3 GeV

Measurements of mass and $\Lambda$ binding energy of $\rm ^4_{\Lambda}H$ and $\rm ^4_{\Lambda}He$ in Au+Au collisions at $\sqrt{s_{_{\rm NN}}}=3$ GeV are presented, with an aim to address the charge symmetry breaking (CSB) problem in hypernuclei systems with atomic number A = 4. The $\Lambda$ binding energies are measured to be $\rm 2.22\pm0.06(stat.) \pm0.14(syst.)$ MeV and $\rm 2.38\pm0.13(stat.) \pm0.12(syst.)$ MeV for $\rm ^4_{\Lambda}H$ and $\rm ^4_{\Lambda}He$, respectively. The measured $\Lambda$ binding-energy difference is $\rm 0.16\pm0.14(stat.)\pm0.10(syst.)$ MeV for ground states. Combined with the $\gamma$-ray transition energies, the binding-energy difference for excited states is $\rm -0.16\pm0.14(stat.)\pm0.10(syst.)$ MeV, which is negative and comparable to the value of the ground states within uncertainties. These new measurements on the $\Lambda$ binding-energy difference in A = 4 hypernuclei systems are consistent with the theoretical calculations that result in $\rm \Delta B_{\Lambda}^4(1_{exc}^{+})\approx -\Delta B_{\Lambda}^4(0_{g.s.}^{+})<0$ and present a new method for the study of CSB effect using relativistic heavy-ion collisions.Comment: 8 pages, 5 figure

Tomography of Ultra-relativistic Nuclei with Polarized Photon-gluon Collisions

A linearly polarized photon can be quantized from the Lorentz-boosted electromagnetic field of a nucleus traveling at ultra-relativistic speed. When two relativistic heavy nuclei pass one another at a distance of a few nuclear radii, the photon from one nucleus may interact through a virtual quark-antiquark pair with gluons from the other nucleus forming a short-lived vector meson (e.g. ${\rho^0}$). In this experiment, the polarization was utilized in diffractive photoproduction to observe a unique spin interference pattern in the angular distribution of ${\rho^0\rightarrow\pi^+\pi^-}$ decays. The observed interference is a result of an overlap of two wave functions at a distance an order of magnitude larger than the ${\rho^0}$ travel distance within its lifetime. The strong-interaction nuclear radii were extracted from these diffractive interactions, and found to be $6.53\pm 0.06$ fm ($^{197} {\rm Au }$) and $7.29\pm 0.08$ fm ($^{238} {\rm U}$), larger than the nuclear charge radii. The observable is demonstrated to be sensitive to the nuclear geometry and quantum interference of non-identical particles

Observation of Global Spin Alignment of ϕ\phi and K∗0K^{*0} Vector Mesons in Nuclear Collisions

The strong force, as one of the four fundamental forces at work in the universe, governs interactions of quarks and gluons, and binds together the atomic nucleus. Notwithstanding decades of progress since Yukawa first developed a description of the force between nucleons in terms of meson exchange, a full understanding of the strong interaction remains a major challenge in modern science. One remaining difficulty arises from the non-perturbative nature of the strong force, which leads to the phenomenon of quark confinement at distance scales on the order of the size of the proton. Here we show that in relativistic heavy-ion collisions, where quarks and gluons are set free over an extended volume, two species of produced vector (spin-1) mesons, namely $\phi$ and $K^{*0}$, emerge with a surprising pattern of global spin alignment. In particular, the global spin alignment for $\phi$ is unexpectedly large, while that for $K^{*0}$ is consistent with zero. The observed spin-alignment pattern and magnitude for the $\phi$ cannot be explained by conventional mechanisms, while a model with strong force fields accommodates the current data. This is the first time that the strong force field is experimentally supported as a key mechanism that leads to global spin alignment. We extract a quantity proportional to the intensity of the field of the strong force. Within the framework of the Standard Model, where the strong force is typically described in the quark and gluon language of Quantum Chromodynamics, the field being considered here is an effective proxy description. This is a qualitatively new class of measurement, which opens a new avenue for studying the behaviour of strong force fields via their imprint on spin alignment

Search for the chiral magnetic effect via charge-dependent azimuthal correlations relative to spectator and participant planes in Au+Au collisions at sNN\sqrt{s_{NN}} = 200 GeV

The chiral magnetic effect (CME) refers to charge separation along a strong magnetic field due to imbalanced chirality of quarks in local parity and charge-parity violating domains in quantum chromodynamics. The experimental measurement of the charge separation is made difficult by the presence of a major background from elliptic azimuthal anisotropy. This background and the CME signal have different sensitivities to the spectator and participant planes, and could thus be determined by measurements with respect to these planes. We report such measurements in Au+Au collisions at a nucleon-nucleon center-of-mass energy of 200 GeV at the Relativistic Heavy-Ion Collider. It is found that the charge separation, with the flow background removed, is consistent with zero in peripheral (large impact parameter) collisions. Some indication of finite CME signals is seen with a significance of 1--3 standard deviations in mid-central (intermediate impact parameter) collisions. Significant residual background effects may, however, still be present.Comment: 8 pages, 3 figure