Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

Two Higgs Bi-doublet Left-Right Model With Spontaneous P and CP Violation

A left-right symmetric model with two Higgs bi-doublet is shown to be a consistent model for both spontaneous P and CP violation. The flavor changing neutral currents can be suppressed by the mechanism of approximate global U(1) family symmetry. We calculate the constraints from neural $K$ meson mass difference $\Delta m_K$ and demonstrate that a right-handed gauge boson $W_2$ contribution in box-diagrams with mass well below 1 TeV is allowed due to a cancellation caused by a light charged Higgs boson with a mass range $150 \sim 300$ GeV. The $W_2$ contribution to $\epsilon_K$ can be suppressed from appropriate choice of additional CP phases appearing in the right-handed Cabbibo-Kobayashi-Maskawa matrix. The model is also found to be fully consistent with $B^0$ mass difference $\Delta m_B$, and the mixing-induced CP violation quantity $\sin2\beta_{J/\psi}$, which is usually difficult for the model with only one Higgs bi-doublet. The new physics beyond the standard model can be directly searched at the colliders LHC and ILC.Comment: 25 pages, 6 figures, typos corrected, 1 figure added, published versio

Global Topology and Local Violation of Discrete Symmetries

Cosmological models that are locally consistent with general relativity and the standard model in which an object transported around the universe undergoes P, C and CP transformations, are constructed. This leads to generalization of the gauge fields that describe electro-weak and strong interactions by enlarging the gauge groups to include anti-unitary transformations. Gedanken experiments show that if all interactions obey Einstein causality then P, C and CP cannot be violated in these models. But another model, which would violate charge superselection rule even for an isolated system, is allowed. It is suggested that the fundamental physical laws must have these discrete symmetries which are broken spontaneously, or they must be non causal.Comment: 12 pages, 1 figure, latex, Revtex. Charge conjugation which is physically implemented in a cosmology with the appropriate topology is described in more detail. Some minor errors are corrected. Shortened to meet the page limit of Physical Review Letters to which this paper was submitte

A Population of Faint Non-Transient Low Mass Black Hole Binaries

We study the thermal and viscous stability of accretion flows in Low Mass Black Hole Binaries (LMBHBs). We consider a model in which an inner advection-dominated accretion flow (ADAF) is surrounded by a geometrically thin accretion disk, the transition between the two zones occurring at a radius R_tr. In all the known LMBHBs, R_tr appears to be such that the outer disks could suffer from a global thermal-viscous instability. This instability is likely to cause the transient behavior of these systems. However, in most cases, if R_tr were slightly larger than the estimated values, the systems would be globally stable. This suggests that a population of faint persistent LMBHBs with globally stable outer disks could be present in the Galaxy. Such LMBHBs would be hard to detect because they would lack large amplitude outbursts, and because their ADAF zones would have very low radiative efficiencies, making the systems very dim. We present model spectra of such systems covering the optical and X-ray bands.Comment: LateX, 37 pages, 11 figures; Accepted for publication in The Astrophysical Journa

Coated Steel Rebar for Enhanced Concrete-Steel Bond Strength and Corrosion Resistance

This report summarizes the findings and recommendations on the use of enamel coating in reinforced concrete structures both for bond strength and corrosion resistance of steel rebar. Extensive laboratory tests were conducted to characterize the properties of one- and two-layer enamel coatings. Pseudostatic tests were performed with pullout, beam and column specimens to characterize mechanical properties and develop design equations for the development length of steel rebar in lap splice and anchorage areas. The splice length equation was validated with the testing of large-scale columns under cyclic loading. For corrosion properties, ponding, salt spray, accelerated corrosion, potentiodynamic and electrochemical impedance spectroscopy (EIS) tests were conducted to evaluate the corrosion resistance and performance of enamel-coated steel and rebar. Experimental procedures and observations from various laboratory tests are documented in detail. The corrosion performances of enamel and epoxy coatings were compared. It is concluded that a one-layer enamel coating doped with 50% calcium silicate has improved bond strengths with steel and concrete but its corrosion resistance is low due to porosity in the coating, allowing chloride ions to pass through. Based on limited laboratory tests, a two-layer enamel coating with an inner layer of pure enamel and an outer layer of enamel and calcium silicate mixture has been shown to be practical and effective for both corrosion resistance and bond strength. A coating factor of 0.85 is recommended to use with the current development length equations as specified in ACI318-08. The large-scale column tests indicated that the column-footing lap splice with enamel-coated dowel bars had higher load and energy dissipation capacities compared to uncoated dowel bars. When damaged unintentionally, chemically reactive enamel coatings limit corrosion to a very small area whereas epoxy coatings allow corrosion expansion in a wide area underneath the coating

Ultrafast control of donor-bound electron spins with single detuned optical pulses

The ability to control spins in semiconductors is important in a variety of fields including spintronics and quantum information processing. Due to the potentially fast dephasing times of spins in the solid state [1-3], spin control operating on the picosecond or faster timescale may be necessary. Such speeds, which are not possible to attain with standard electron spin resonance (ESR) techniques based on microwave sources, can be attained with broadband optical pulses. One promising ultrafast technique utilizes single broadband pulses detuned from resonance in a three-level Lambda system [4]. This attractive technique is robust against optical pulse imperfections and does not require a fixed optical reference phase. Here we demonstrate the principle of coherent manipulation of spins theoretically and experimentally. Using this technique, donor-bound electron spin rotations with single-pulse areas exceeding pi/4 and two-pulses areas exceeding pi/2 are demonstrated. We believe the maximum pulse areas attained do not reflect a fundamental limit of the technique and larger pulse areas could be achieved in other material systems. This technique has applications from basic solid-state ESR spectroscopy to arbitrary single-qubit rotations [4, 5] and bang-bang control[6] for quantum computation.Comment: 15 pages, 4 figures, submitted 12/2008. Since the submission of this work we have become aware of related work: J. Berezovsky, M. H. Mikkelsen, N. G. Stoltz, L. A. Coldren, and D. D. Awschalom, Science 320: 349-352 (2008

A novel retinoblastoma therapy from genomic and epigenetic analyses.

Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the retinoblastoma genome is stable, but that multiple cancer pathways can be epigenetically deregulated. To identify the mutations that cooperate with RB1 loss, we performed whole-genome sequencing of retinoblastomas. The overall mutational rate was very low; RB1 was the only known cancer gene mutated. We then evaluated the role of RB1 in genome stability and considered non-genetic mechanisms of cancer pathway deregulation. For example, the proto-oncogene SYK is upregulated in retinoblastoma and is required for tumour cell survival. Targeting SYK with a small-molecule inhibitor induced retinoblastoma tumour cell death in vitro and in vivo. Thus, retinoblastomas may develop quickly as a result of the epigenetic deregulation of key cancer pathways as a direct or indirect result of RB1 loss

Effect of Deep Brain Stimulation on Parkinson's Nonmotor Symptoms following Unilateral DBS: A Pilot Study

Parkinson's disease (PD) management has traditionally focused largely on motor symptoms. Deep brain stimulation (DBS) of the subthalamic nucleus (STN) and globus pallidus internus (GPi) are effective treatments for motor symptoms. Nonmotor symptoms (NMSs) may also profoundly affect the quality of life. The purpose of this pilot study was to evaluate NMS changes pre- and post-DBS utilizing two recently developed questionnaires. Methods. NMS-Q (questionnaire) and NMS-S (scale) were administered to PD patients before/after unilateral DBS (STN/GPi targets). Results. Ten PD patients (9 STN implants, 1 GPi implant) were included. The three most frequent NMS symptoms identified utilizing NMS-Q in pre-surgical patients were gastrointestinal (100%), sleep (100%), and urinary (90%). NMS sleep subscore significantly decreased (−1.6 points ± 1.8, P = 0.03). The three most frequent NMS symptoms identified in pre-surgical patients using NMS-S were gastrointestinal (90%), mood (80%), and cardiovascular (80%). The largest mean decrease of NMS scores was seen in miscellaneous symptoms (pain, anosmia, weight change, and sweating) (−7 points ± 8.7), and cardiovascular/falls (−1.9, P = 0.02). Conclusion. Non-motor symptoms improved on two separate questionnaires following unilateral DBS for PD. Future studies are needed to confirm these findings and determine their clinical significance as well as to examine the strengths/weaknesses of each questionnaire/scale

The enrichment of an alkaliphilic biofilm consortia capable of the anaerobic degradation of isosaccharinic acid from cellulosic materials incubated within an anthropogenic, hyperalkaline environment.

Anthropogenic hyper-alkaline sites provide an environment that is analogous to proposed cementitious geological disposal facilities (GDF) for radioactive waste. Under anoxic, alkaline conditions cellulosic wastes will hydrolyse to a range of cellulose degradation products (CDP) dominated by isosaccharinic acids (ISA). In order to investigate the potential for microbial activity in a cementitious GDF, cellulose samples were incubated in the alkaline (∼pH 12), anaerobic zone of a lime kiln waste site. Following retrieval, these samples had undergone partial alkaline hydrolysis and were colonised by a Clostridia dominated biofilm community, where hydrogenotrophic, alkaliphilic methanogens were also present. When these samples were used to establish an alkaline CDP fed microcosm, the community shifted away from Clostridia, methanogens became undetectable and a flocculate community dominated by Alishewanella sp. established. These flocs were composed of bacteria embedded in polysaccharides and protein stabilised by extracellular DNA. This community was able to degrade all forms of ISA with >60% of the carbon flow being channelled into extracellular polymeric substance (EPS) production. This study demonstrated that alkaliphilic microbial communities can degrade the CDP associated with some radioactive waste disposal concepts at pH 11. These communities divert significant amounts of degradable carbon to EPS formation, suggesting that EPS has a central role in the protection of these communities from hyper-alkaline conditions