sp. Nov. and sp. Nov., Two Marine Bacteria Isolated from the Sediment Core near Hydrothermal Fields of Southern Okinawa Trough.

Two strains, 81s02 and 334s03, were isolated from the sediment core near the hydrothermal field of southern Okinawa Trough. The cells of both strains were observed to be rod-shaped, non-gliding, Gram-staining negative, yellow-pigmented, facultatively anaerobic, catalase and oxidase positive, and showing optimum growth at 30 °C and pH 7.5.

Thermal coupling of the Indo-Pacific warm pool and Southern Ocean over the past 30,000 years.

The role of the tropical Pacific Ocean and its linkages to the southern hemisphere during the last deglacial warming remain highly controversial. Here we explore the evolution of Pacific horizontal and vertical thermal gradients over the past 30 kyr by compiling 340 sea surface and 7 subsurface temperature records, as well as one new ocean heat content record. Our records reveal that La Niña-like conditions dominated during the deglaciation as a result of the more intense warming in the western Pacific warm pool.

The Mechanism of and the Contribution of Biomineralization to the Formation of Oceanic Ferromanganese Nodules.

Ferromanganese nodules are an important mineral resource in the seafloor; however, the genetic mechanism is still unknown. The biomineralization of microorganisms appears to promote ferromanganese nodule formation. To investigate the possible mechanism of microbial-ferromanganese nodule interaction, to test the possibility of marine microorganisms as deposition template for ferromanganese nodules minerals, the interactions between strain CW126-A03 and ferromanganese nodules were studied.

Structural evolution of in situ boron-doped SiGe ultrathin film analyzed by multi-optical methods.

In situ boron (B)-doped SiGe (BSG) layer is extensively used in the source (S)/(D) drain of metal-oxide-semiconductor field-effect transistors. An unexpected structural evolution occurs in BSG during metallization and activation annealing during actual fabrication, which involves a correlated interaction between B and SiGe. Herein, the complicated phenomena of the structural evolution of BSG were analyzed by 325 nm micro-Raman spectroscopy, x-ray photoelectron spectroscopy (XPS), reflective second harmonic generation (RSHG), and synchrotron x-ray diffraction (XRD).

Strong correlation between optical properties and mechanism in deficiency of normalized self-assembly ZnO nanorods.

Although, post annealing is an efficient way to annihilate/restructure deficiencies in self-assembly (SA) ZnO nanorods (ZNRs), the detailed investigation about the surface properties of annealed SA-ZNRs is a long standing issue and the major discrepancy is mainly due to single step annealing. We demonstrate the strategic two step annealing process to create reliable structural configuration in SA-ZNRs during the first round of annealing at 800 °C in vacuum (VA process), and create intrinsic defects in the second step of annealing in oxygen rich atmosphere (OA process) to correlate the formation of the defects related to green/orange-red emission. SA-ZNRs annealed in VA-OA processes reveal positive correlations between the oxygen flow rate and formation of oxygen interstitials (O) and zinc vacancies (V).

Migration Energy Barriers for the Surface and Bulk of Self-Assembly ZnO Nanorods.

Post-annealing treatment is a necessary process to create/eliminate/repair defects in self⁻assembly (SA) metal oxide by providing enough thermal energy to the O atoms to overcome the migration energy barrier in ZnO. The height of migration energy barrier is dependent on the depth from the surface, which is hard to be estimated by theoretical calculations, as well as the optical analyses. SA ZnO nanorods (ZNRs) have high surface-to-volume ratio to provide complete picture between the optical and surface properties obtained by photoluminescence (PL) and ultraviolet/X-ray photoemission spectroscopy (UPS/XPS), which is used to investigate the evolution of structure and chemical states of the surface layers to reveal mutual agreement on all observations in PL, XPS, and UPS.

Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in .

is a commensal human pathogen and a major cause of nosocomial infections. As gaseous signaling molecules, endogenous hydrogen sulfide (HS) and nitric oxide (NO·) protect from antibiotic stress synergistically, which we propose involves the intermediacy of nitroxyl (HNO). Here, we examine the effect of exogenous sulfide and HNO on the transcriptome and the formation of low-molecular-weight (LMW) thiol persulfides of bacillithiol, cysteine, and coenzyme A as representative of reactive sulfur species (RSS) in wild-type and Δ strains of .

Resolution of Stepwise Cooperativities of Copper Binding by the Homotetrameric Copper-Sensitive Operon Repressor (CsoR): Impact on Structure and Stability.

The cooperativity of ligand binding is central to biological regulation and new approaches are needed to quantify these allosteric relationships. Herein, we exploit a suite of mass spectrometry (MS) experiments to provide novel insights into homotropic Cu-binding cooperativity, gas-phase stabilities and conformational ensembles of the D2 -symmetric, homotetrameric copper-sensitive operon repressor (CsoR) as a function of Cu(I) ligation state. Cu(I) binding is overall positively cooperative, but is characterized by distinct ligation state-specific cooperativities.

Electrostatic occlusion and quaternary structural ion pairing are key determinants of Cu(I)-mediated allostery in the copper-sensing operon repressor (CsoR).

The copper-sensing operon repressor (CsoR) is an all-α-helical disc-shaped D2-symmetric homotetramer that forms a 2:1 tetramer/DNA operator complex and represses the expression of copper-resistance genes in a number of bacteria. A previous bioinformatics analysis of CsoR-family repressors distributes Cu(I)-sensing CsoRs in four of seven distinct clades on the basis of global sequence similarity. In this work, we define energetically important determinants of DNA binding in the apo-state (ΔΔGbind), and for allosteric negative coupling of Cu(I) binding to DNA binding (ΔΔGc) in a model clade IV CsoR from Geobacillus thermodenitrificans (Gt) of known structure, by selectively targeting for mutagenesis those charged residues uniquely conserved in clade IV CsoRs.

Conformational analysis and chemical reactivity of the multidomain sulfurtransferase, Staphylococcus aureus CstA.

The cst operon of the major human pathogen Staphylococcus aureus (S. aureus) is under the transcriptional control of CsoR-like sulfurtransferase repressor (CstR). Expression of this operon is induced by hydrogen sulfide, and two components of the cst operon, cstA and cstB, protect S.

Copper transport and trafficking at the host-bacterial pathogen interface.

CONSPECTUS: The human innate immune system has evolved the means to reduce the bioavailability of first-row late d-block transition metal ions to invading microbial pathogens in a process termed "nutritional immunity". Transition metals from Mn(II) to Zn(II) function as metalloenzyme cofactors in all living cells, and the successful pathogen is capable of mounting an adaptive response to mitigate the effects of host control of transition metal bioavailability. Emerging evidence suggests that Mn, Fe, and Zn are withheld from the pathogen in classically defined nutritional immunity, while Cu is used to kill invading microorganisms.

Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR).

The copper-sensing operon repressor (CsoR) is representative of a major Cu(I)-sensing family of bacterial metalloregulatory proteins that has evolved to prevent cytoplasmic copper toxicity. It is unknown how Cu(I) binding to tetrameric CsoRs mediates transcriptional derepression of copper resistance genes. A phylogenetic analysis of 227 DUF156 protein members, including biochemically or structurally characterized CsoR/RcnR repressors, reveals that Geobacillus thermodenitrificans (Gt) CsoR characterized here is representative of CsoRs from pathogenic bacilli Listeria monocytogenes and Bacillus anthracis.

Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery.

Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH(2)-Gly2-His3-Gly4 sequence.

Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation.

Selective chemical modification of protein side chains coupled with mass spectrometry is often most informative when used to compare residue-specific reactivities in a number of functional states or macromolecular complexes. Herein, we develop ratiometric pulse-chase amidination mass spectrometry (rPAm-MS) as a site-specific probe of lysine reactivities at equilibrium using the Cu(I)-sensing repressor CsoR from Bacillus subtilis as a model system. CsoR in various allosteric states was reacted with S-methyl thioacetimidate (SMTA) for pulse time, t, and chased with excess of S-methyl thiopropionimidate (SMTP) (Δ = 14 amu), quenched and digested with chymotrypsin or Glu-C protease, and peptides were quantified by high-resolution matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and/or liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS).

Anomalous contact angle hysteresis of a captive bubble: advancing contact line pinning.

Contact angle hysteresis of a sessile drop on a substrate consists of continuous invasion of liquid phase with the advancing angle (θ(a)) and contact line pinning of liquid phase retreat until the receding angle (θ(r)) is reached. Receding pinning is generally attributed to localized defects that are more wettable than the rest of the surface. However, the defect model cannot explain advancing pinning of liquid phase invasion driven by a deflating bubble and continuous retreat of liquid phase driven by the inflating bubble.

Communications: Wall free capillarity and pendant drop removal.

When a sessile drop encounters a pendant drop through a hole, it is generally anticipated that they will coalesce and flow downward due to gravity. However, like "wall-free" capillarity, we show that the pendant drop may be sucked up by a sliding drop instantaneously if the radius of the curvature of the former is smaller than that of the later. This phenomenon can be explained by Laplace-Young equation and convective Ostwald ripening.

Transdifferentiation of bone marrow stem cells into acinar cells using a double chamber system.

Background/purpose: Hypofunction of the salivary glands can substantially affect quality of life. Current treatments for salivary hypofunction are of limited effectiveness. Although the implantation of functional salivary gland tissue from autologous glandular cells represents a possible physiologic solution to this problem, tissue engineering of salivary glands would require the generation of a great number of acinar cells (ACs).