230 research outputs found

    Statistics of soil organic carbon density at three soil depth intervals (0–30 cm, 0–50 cm, and 0–100 cm).

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    <p><i>Notes:</i> SOCD, soil organic carbon density; N, number of samples; Std.D., standard Deviation.</p

    Internal transcribed spacer (ITS) sequence alignment of <i>Phytophthora</i> Γ—<i>stagnum</i>, <i>P. mississippiae</i> and <i>P.</i> taxon PgChlamydo.

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    <p>Position numbers are given based on the alignment. Yellow indicates sequences belong to <i>P.</i> taxon PgChlamydo authentic isolates. Blue indicates sequences belong to <i>P. mississippiae</i> type isolate 57J3. <sup>a</sup>Position 15 is in the poly(A) region of ITS 1, which may contain sequencing errors. Thus, it is excluded from the analysis of hybridization. However, the indel of position 15 among three types of <i>P.</i> Γ—<i>stagnum</i> clones explains continual polymorphism and unreadable sequences of the ITS 1 regions amplified with the forward primer ITS6F in the initial sequencing before cloning. <sup>b</sup>Type 1 and 2 occurred 21 and 10 times among 31 clones producing 816-bp sequences.</p

    Relationships between soil organic carbon density and biomass at different depth intervals.

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    <p><i>Notes</i>: AGB, above-ground biomass; BGB, below-ground biomass; TB, total biomass; SOCD, soil organic carbon density.</p

    Relationships between soil organic carbon density and environmental factors at different depth intervals.

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    <p><i>Notes</i>: SOCD, soil organic carbon density; MAT, mean annual temperature; AP, annual precipitation; SM, soil moisture.</p

    Post-translational Introduction of d‑Alanine into Ribosomally Synthesized Peptides by the Dehydroalanine Reductase NpnJ

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    Ribosomally synthesized peptides are generally limited to l-amino acid building blocks. Given the advantageous properties of peptides containing d-amino acids such as stabilization of certain turns and against proteolytic degradation, methods to introduce d-stereocenters are valuable. Here we report the first <i>in vitro</i> reconstitution and characterization of a dehydrogenase that carries out the asymmetric reduction of dehydroalanine. NpnJ<sub>A</sub> reduces dehydroalanine to d-Ala using NAPDH as cosubstrate. The enzyme displays high substrate tolerance allowing introduction of d-Ala into a range of non-native substrates. In addition to the <i>in vitro</i> reactions, we describe five examples of using Escherichia coli as biosynthetic host for d-alanine introduction into ribosomal peptides. A deuterium-label-based coupled-enzyme assay was used to rapidly determine the stereochemistry of the newly installed alanine

    Michael-Type Cyclizations in Lantibiotic Biosynthesis Are Reversible

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    Lanthipeptides are members of the ribosomally synthesized and post-translationally modified peptides (RiPPs). They are generated in two biosynthetic steps: dehydration of Ser and Thr residues to the corresponding dehydroamino acids and subsequent conjugate addition by the thiol of Cys residues to generate the characteristic lanthionine and methyllanthionine thioether-bridged structures. Typically, a lanthipeptide contains multiple thioether cross-links. Recent studies have proposed that the final ring topology may be under thermodynamic control. If so, then the Michael-type cyclization reaction would need to be reversible, but such reversibility has never been demonstrated. We show here for the class I lanthipeptide cyclase NisC and class II lanthipeptide synthetase HalM2 that, indeed, the conjugate addition reactions are reversible and that the enzymes can open up all thioether rings in their products. We also propose that a His residue that is conserved among the lanthipeptide cyclases acts as the acid or base that protonates or generates the enolate intermediate during thioether ring formation and opening, respectively

    Relationships between above-ground biomass, enhanced vegetation index, and soil organic carbon density at depth interval of 0–30 cm.

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    <p><i>Notes</i>: AGB, above-ground biomass; EVI, enhanced vegetation index; SOCD, soil organic carbon density.</p

    Average daily radial growth of <i>Phytophthora</i> Γ—<i>stagnum</i> representative isolates in carrot agar (CA) and 20% clarified V8 juice agar (CV8A) over an 8-days period.

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    <p>Average daily radial growth of <i>Phytophthora</i> Γ—<i>stagnum</i> representative isolates in carrot agar (CA) and 20% clarified V8 juice agar (CV8A) over an 8-days period.</p
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