Artificial and natural duplicates in pyrosequencing reads of metagenomic data

<p>Abstract</p> <p>Background</p> <p>Artificial duplicates from pyrosequencing reads may lead to incorrect interpretation of the abundance of species and genes in metagenomic studies. Duplicated reads were filtered out in many metagenomic projects. However, since the duplicated reads observed in a pyrosequencing run also include natural (non-artificial) duplicates, simply removing all duplicates may also cause underestimation of abundance associated with natural duplicates.</p> <p>Results</p> <p>We implemented a method for identification of exact and nearly identical duplicates from pyrosequencing reads. This method performs an all-against-all sequence comparison and clusters the duplicates into groups using an algorithm modified from our previous sequence clustering method cd-hit. This method can process a typical dataset in ~10 minutes; it also provides a consensus sequence for each group of duplicates. We applied this method to the underlying raw reads of 39 genomic projects and 10 metagenomic projects that utilized pyrosequencing technique. We compared the occurrences of the duplicates identified by our method and the natural duplicates made by independent simulations. We observed that the duplicates, including both artificial and natural duplicates, make up 4-44% of reads. The number of natural duplicates highly correlates with the samples' read density (number of reads divided by genome size). For high-complexity metagenomic samples lacking dominant species, natural duplicates only make up <1% of all duplicates. But for some other samples like transcriptomic samples, majority of the observed duplicates might be natural duplicates.</p> <p>Conclusions</p> <p>Our method is available from <url>http://cd-hit.org</url> as a downloadable program and a web server. It is important not only to identify the duplicates from metagenomic datasets but also to distinguish whether they are artificial or natural duplicates. We provide a tool to estimate the number of natural duplicates according to user-defined sample types, so users can decide whether to retain or remove duplicates in their projects.</p

A germanium/single-walled carbon nanotube composite paper as a free-standing anode for lithium-ion batteries

Paper-like free-standing germanium (Ge) and single-walled carbon nanotube (SWCNT) composite anodes were synthesized by the vacuum filtration of Ge/SWCNT composites, which were prepared by a facile aqueous-based method. The samples were characterized by X-ray diffraction, field emission scanning electron microscopy, and transmission electron microscopy. Electrochemical measurements demonstrate that the Ge/SWCNT composite paper anode with the weight percentage of 32% Ge delivered a specific discharge capacity of 417 mA h g−1 after 40 cycles at a current density of 25 mA g−1, 117% higher than the pure SWCNT paper anode. The SWCNTs not only function as a flexible mechanical support for strain release, but also provide excellent electrically conducting channels, while the nanosized Ge particles contribute to improving the discharge capacity of the paper anode

Non-Fragile Observer-Based Adaptive Integral Sliding Mode Control for a Class of T-S Fuzzy Descriptor Systems With Unmeasurable Premise Variables

The issue of non-fragile observer-based adaptive integral sliding mode control for a class of Takagi–Sugeno (T-S) fuzzy descriptor systems with uncertainties and unmeasurable premise variables is investigated. General nonlinear systems are represented by nonlinear T-S fuzzy descriptor models, because premise variables depend on unmeasurable system states and fuzzy models have different derivative matrices. By introducing the system state derivative as an auxiliary state vector, original fuzzy descriptor systems are transformed into augmented systems for which system properties remain the same. First, a novel integral sliding surface, which includes estimated states of the sliding mode observer and controller gain matrices, is designed to obtain estimation error dynamics and sliding mode dynamics. Then, some sufficient linear matrix inequality (LMI) conditions for designing the observer and the controller gains are derived using the appropriate fuzzy Lyapunov functions and Lyapunov theory. This approach yields asymptotically stable sliding mode dynamics. Corresponding auxiliary variables are introduced, and the Finsler's lemma is employed to eliminate coupling of controller gain matrices, observer gain matrices, Lyapunov function matrices, and/or observer gain perturbations. An observer-based integral sliding mode control strategy is obtained to assure that reachability conditions are satisfied. Moreover, a non-fragile observer and a non-fragile adaptive controller are developed to compensate for system uncertainties and perturbations in both the observer and the controller. Finally, example results are presented to illustrate the effectiveness and merits of the proposed method

Lini0.5mn1.5o4 spinel cathode using room temperature ionic liquid as electrolyte

In this study, LiNi0.5Mn1.5O4 (LNMO) nanoparticles were prepared as a 5 V cathode material via a rheological phase method and annealed at different temperatures: 680 ◦C, 750 ◦C, and 820 ◦C. The sample annealed at 750 ◦C shows the best performance. A room temperature ionic liquid (RTIL) containing 1 M lithium bis(trifluoromethanesulfonyl) imide (LiNTf2) in N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl) imide (C4mpyrNTf2) was used as novel electrolyte in conjunction with the LNMO cathodes and their electrochemical properties have been investigated. The results show that the LNMO using RTIL as electrolyte has better coulombic efficiency and comparable discharge capacities to those of the cells assembled with standard liquid electrolyte (1 M LiPF6 in ethylene carbonate/diethyl carbonate). Electrochemical impedance spectroscopy shows that the RTIL is much more stable as the electrolyte for LiNi0.5Mn1.5O4 than the conventional electrolyte

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH_(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5–270 nM), cobalt (0.5–6 nM), molybdenum (10–5600 nM) and tungsten (0.3–8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B_(12) biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments

Endophyte Microbiome Diversity in Micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities

Search for New Hadronic Decays of hch_c and Observation of hc→K+K−π+π−π0h_c\rightarrow K^{+}K^{-}\pi^{+}\pi^{-}\pi^{0}

Ten hadronic final states of the $h_c$ decays are investigated via the process $\psi(3686)\rightarrow \pi^0 h_c$, using a data sample of $(448.1 \pm 2.9) \times 10^6$ $\psi(3686)$ events collected with the BESIII detector. The decay channel $h_c\rightarrow K^{+}K^{-}\pi^{+}\pi^{-}\pi^{0}$ is observed for the first time with a significance of $6.0 \sigma$. The corresponding branching fraction is determined to be $\mathcal{B}(h_c\rightarrow K^{+}K^{-}\pi^{+}\pi^{-}\pi^{0}) =(3.3 \pm 0.6 \pm 0.6)\times 10^{-3}$ (the first uncertainty is statistical and the second systematical). Evidence for the decays $h_c\rightarrow \pi^{+} \pi^{-} \pi^{0} \eta$ and $h_c\rightarrow K^{0}_{S}K^{\pm}\pi^{\mp}\pi^{+}\pi^{-}$ is found with a significance of $3.6 \sigma$ and $3.8 \sigma$, respectively. The corresponding branching fractions (and upper limits) are obtained to be $\mathcal{B}(h_c\rightarrow \pi^{+} \pi^{-} \pi^{0} \eta ) =(7.2 \pm 1.8 \pm 1.3)\times 10^{-3}$ $(< 1.8 \times 10^{-2})$ and $\mathcal{B}(h_c\rightarrow K^{0}_{S}K^{\pm}\pi^{\mp}\pi^{+}\pi^{-}) =(2.8 \pm 0.9 \pm 0.5)\times 10^{-3}$ $(<4.7\times 10^{-3})$. Upper limits on the branching fractions for the final states $h_c \rightarrow K^{+}K^{-}\pi^{0}$, $K^{+}K^{-}\eta$, $K^{+}K^{-}\pi^{+}\pi^{-}\eta$, $2(K^{+}K^{-})\pi^{0}$, $K^{+}K^{-}\pi^{0}\eta$, $K^{0}_{S}K^{\pm}\pi^{\mp}$, and $p\bar{p}\pi^{0}\pi^{0}$ are determined at a confidence level of 90\%.Comment: 10 pages, 2 figure

Amplitude analysis of Ds+→π+π−π+D_s^{+} \rightarrow \pi^{+} \pi^{-} \pi^{+}

Utilizing the data set corresponding to an integrated luminosity of $3.19$ fb$^{-1}$ collected by the BESIII detector at a center-of-mass energy of 4.178 GeV, we perform an amplitude analysis of the $D_s^+\to\pi^+\pi^-\pi^+$ decay. The sample contains 13,797 candidates with a signal purity of $\sim$80%. The amplitude and phase of the contributing $\pi\pi$ ${\cal S}$ wave are measured based on a quasi-model-independent approach, along with the amplitudes and phases of the ${\cal P}$ and ${\cal D}$ waves parametrized by Breit-Wigner models. The fit fractions of different intermediate decay channels are also reported.Comment: 14 pages, 6 figure

Measurement of the Born cross sections for e+e- →η′π+π- at center-of-mass energies between 2.00 and 3.08 GeV

The Born cross sections for the process e+e-→η′π+π- at different center-of-mass energies between 2.00 and 3.08 GeV are reported with improved precision from an analysis of data samples collected with the BESIII detector operating at the BEPCII storage ring. An obvious structure is observed in the Born cross section line shape. Fit as a Breit-Wigner resonance, it has a statistical significance of 6.3σ and a mass and width of M=(2111±43±25) MeV/c2 and Γ=(135±34±30) MeV, where the uncertainties are statistical and systematic, respectively. These measured resonance parameters agree with the measurements of BABAR in e+e-→η′π+π- and BESIII in e+e-→ωπ0 within two standard deviations