Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform

BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method) is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1), after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming) but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies

A new analytic approach for power system fault diagnosis employing the temporal information of alarm messages

Traditional analytic models for power system fault diagnosis are usually formulated as an unconstrained 0–1 integer programming problem. The key issue of the models is to seek the fault hypothesis that minimizes the discrepancy between the actual and the expected states of the concerned protective relays and circuit breakers. The temporal information of alarm messages has not been well utilized in these methods, and as a result, the diagnosis results may be not unique and hence indefinite, especially when complicated and multiple faults occur. In order to solve this problem, this paper presents a novel analytic model employing the temporal information of alarm messages along with the concept of related path. The temporal relationship among the actions of protective relays and circuit breakers, and the different protection configurations in a modern power system can be reasonably represented by the developed model, and therefore, the diagnosed results will be more definite under different circumstances of faults. Finally, an actual power system fault was served to verify the proposed method

Functional Analysis of the Ferric Uptake Regulator Gene fur in Xanthomonas vesicatoria.

Iron is essential for the growth and survival of many organisms. Intracellular iron homeostasis must be maintained for cell survival and protection against iron toxicity. The ferric uptake regulator protein (Fur) regulates the high-affinity ferric uptake system in many bacteria. To investigate the function of the fur gene in Xanthomonas vesicatoria (Xv), we generated a fur mutant strain, fur-m, by site-directed mutagenesis. Whereas siderophore production increased in the Xv fur mutant, extracellular polysaccharide production, biofilm formation, swimming ability and quorum sensing signals were all significantly decreased. The fur mutant also had significantly reduced virulence in tomato leaves. The above-mentioned phenotypes significantly recovered when the Xv fur mutation allele was complemented with a wild-type fur gene. Thus, Fur either negatively or positively regulates multiple important physiological functions in Xv

Construction of Ni(CN)₂ /NiSe₂ heterostructures by stepwise topochemical pathways for efficient electrocatalytic oxygen evolution

Exploiting effective electrocatalysts based on elaborate heterostructures for the oxygen evolution reaction (OER) has been considered as a promising strategy for boosting water splitting efficiency to produce the clean energy-hydrogen. However, constructing catalytically active heterostructures with novel composition and architecture remains poorly developed due to the synthetic challenge. In this work, it is demonstrated that unique Ni(CN)2 /NiSe2 heterostructures, composed of single-crystalline Ni(CN)2 nanoplates surrounded by crystallographically aligned NiSe2 nanosatellites, can be created from nickel-based Hofmann-type coordination polymers through stepwise topochemical pathways. When employed as the OER electrocatalyst, the Ni(CN)2 /NiSe2 heterostructures show enhanced performance, which could be attributed to optimized geometric and electronic structures of the catalytic sites endowed by the synergy between the two components. This work demonstrates a rational synthetic route for creating a novel Ni-based OER electrocatalyst that possesses nanoscale heterostructure, whose composition, spatial organization, and interface configuration can be finely manipulated.Ministry of Education (MOE)The authors acknowledge financial support by the funding of “Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang” (No. 2020R01002), the National Natural Science Foundation of China (Nos. 21902144, 11904317, and 51722210), and the Natural Science Foundation of Zhejiang Province (LD18E020003). The authors thank Beijing PARATERA Tech CO., Ltd. for providing HPC resources that have contributed to the research results reported within this paper. X.W.L. acknowledges the funding support from the Ministry of Education of Singapore via the Academic Research Fund (AcRF) Tier-1 grant (RG3/20)

Effect of <i>fur</i> on biofilm formation (A) and quorum sensing (QS) signals in <i>Xv</i> (B).

<p>Biofilm formation is indicated by the ring formed on the surface of glass test tubes. QS signal expression was indicated by blue halos 12–18 h after each strain was spotted and after incubation on ABM plates at 28°C. A QS assay was used to detect signaling molecules as a blue halo. <i>Xv</i>17: wild-type <i>Xv</i> strain; fur-m: <i>fur</i> mutation strain of <i>Xv</i>17; and fur-c: <i>fur</i> complementation strain of fur-m. Ecc3: <i>E</i>. <i>carotovora</i> subsp. <i>carotovora</i> strain 3 as a positive control for expression of QS signals.</p

Quantitative comparison of siderophore production in <i>Xv</i> strains.

<p>Black diamond: wild-type strain <i>Xv</i>17; black square: <i>fur</i> mutation strain fur-m; and black triangle: <i>fur</i> complementation strain fur-c. </p