Spontaneous and initiated succession on unvegetated slopes in the abandoned lignite‐mining area of Goitsche,Germany

Abstract. In this study, we examined the colonization of unvegetated, dry slopes in the lignite‐mining area of Goitsche, Germany. The plots, characterized by different habitat conditions, were studied from 1994–2000. The vegetation development on treated plots was compared to untreated plots showing spontaneous succession. For initial treatments we used fresh plant clippings from a species‐rich sandy grassland (Armerion elongatae) mowed at the end of July. Soil seed bank samples, taken at the beginning of the experiments and cultivated for 18 months, confirmed that the vegetation development on the slopes started with primary succession. Because seed rain is considered to be an important factor in primary succession, we also studied the diaspore input during the first year. The hospitable Quaternary substrate of Site I (pH = 4.1–4.7, 92 % sand) supports fast vegetation development on treated and untreated plots. On treated plots, we have identified plant assemblages similar to initial stages of the Armerion elongatae community. On control plots, Coryne‐phorion communities have established spontaneously. At Site II (mixed Quaternary and Tertiary substrate, pH = 3.0–3.5,40 % sand) the total cover and number of psammophytic species was low. Treated plots showed development towards ruderal sandy grassland, but the establishment of Calamagrostis epigejos would eventually lead to monodominant stands. Untreated control plots showed basically the same pattern, however the development was slower. At Site III (pH = 1.8–2.8, 34 % sand), the hostile Tertiary substrate impeded the succession on both treated and untreated plots because low pH and therefore high amounts of Al³⁺ produced elemental toxicity to plants. The application of plant clippings accelerated the vegetation development in sites with a pH exceeding 3. On plots with the initial treatment, vegetation cover and total number of species were higher than on untreated plots. The application of fresh plant clippings from areas with similar habitat conditions appears to be a viable alternative to traditional restoration methods.     

1,2,4-Triazoloazine derivatives as a new type of herpes simplex virus inhibitors

A new class of inhibitors of herpes simplex virus replication was found. The compounds under study are derived from condensed 1,2,4-triazolo[5,1-c][1,2,4]triazines and 1,2,4-triazolo[1,5-a]pyrimidines, structural analogues of natural nucleic bases. Antiherpetic activity and cytotoxicity of the compounds were studied. The corresponding triphosphates of several active compounds were prepared and tested as inhibitors of DNA synthesis catalyzed by herpes simplex virus polymerase. The potential mechanism of their action is blocking of DNA dependent DNA polymerase, a key enzyme of viral replication.     

Kinetic investigation of the polymerase and exonuclease activities of human DNA polymerase ε holoenzyme

In eukaryotic DNA replication, DNA polymerase ε (Polε) is responsible for leading strand synthesis, whereas DNA polymerases α and δ synthesize the lagging strand. The human Polε (hPolε) holoenzyme is comprised of the catalytic p261 subunit and the noncatalytic p59, p17, and p12 small subunits. So far, the contribution of the noncatalytic subunits to hPolε function is not well understood. Using pre-steady-state kinetic methods, we established a minimal kinetic mechanism for DNA polymerization and editing catalyzed by the hPolε holoenzyme. Compared with the 140-kDa N-terminal catalytic fragment of p261 (p261N), which we kinetically characterized in our earlier studies, the presence of the p261 C-terminal domain (p261C) and the three small subunits increased the DNA binding affinity and the base substitution fidelity. Although the small subunits enhanced correct nucleotide incorporation efficiency, there was a wide range of rate constants when incorporating a correct nucleotide over a single-base mismatch. Surprisingly, the 3′→5′ exonuclease activity of the hPolε holoenzyme was significantly slower than that of p261N when editing both matched and mismatched DNA substrates. This suggests that the presence of p261C and the three small subunits regulates the 3′→5′ exonuclease activity of the hPolε holoenzyme. Together, the 3′→5′ exonuclease activity and the variable mismatch extension activity modulate the overall fidelity of the hPolε holoenzyme by up to 3 orders of magnitude. Thus, the presence of p261C and the three noncatalytic subunits optimizes the dual enzymatic activities of the catalytic p261 subunit and makes the hPolε holoenzyme an efficient and faithful replicative DNA polymerase.     

Stereospecificity of High-and Low-Affinity Transport of Choline Analogues into Rat Cortical Synaptosomes

The present experiments used methylcholines to examine the stereoselectivity of choline transport into rat synaptosomes. R(+)-alpha-methylcholine and S(+)-beta-methylcholine were significantly better inhibitors of the high-affinity choline transport system than were their enantiomers. Although both enantiomers of alpha- and of beta-methylcholine inhibited [3H]choline transport, only R(+)-alpha-methylcholine and S(+)-beta-methylcholine could be transported by the high-affinity choline uptake mechanism. Therefore, we conclude that the chiral requirements for recognition of and for transport by the high-affinity transporter are clearly different. In addition to high-affinity choline transport, Na(+)-independent low-affinity transport was measured. This process transported R(+)-alpha-methylcholine, but not S(-)-alpha-methylcholine; however, it showed no stereoselectivity for the enantiomers of beta-methylcholine. Thus, high- and low-affinity choline transport mechanisms exhibit distinct differences in their substrate selectivities. We suggest that the stereoselective properties of choline transport might present a unique opportunity to study choline uptake and metabolism.     

Improved SARS-CoV-2 main protease high-throughput screening assay using a 5-carboxyfluorescein substrate

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a global threat to human health has highlighted the need for the development of novel therapies targeting current and emerging coronaviruses with pandemic potential. The coronavirus main protease (M^pro, also called 3CL^pro) is a validated drug target against coronaviruses and has been heavily studied since the emergence of SARS-CoV-2 in late 2019. Here, we report the biophysical and enzymatic characterization of native M^pro, then characterize the steady-state kinetics of several commonly used FRET substrates, fluorogenic substrates, and six of the 11 reported SARS-CoV-2 polyprotein cleavage sequences. We then assessed the suitability of these substrates for high-throughput screening. Guided by our assessment of these substrates, we developed an improved 5-carboxyfluorescein-based FRET substrate, which is better suited for high-throughput screening and is less susceptible to interference and false positives than existing substrates. This study provides a useful framework for the design of coronavirus M^pro enzyme assays to facilitate the discovery and development of therapies targeting M^pro.     

Multiple Sequence Signals Direct Recognition and Degradation of Protein Substrates by the AAA+ Protease HslUV

Proteolysis is important for protein quality control and for the proper regulation of many intracellular processes in prokaryotes and eukaryotes. Discerning substrates from other cellular proteins is a key aspect of proteolytic function. The Escherichia coli HslUV protease is a member of a major family of ATP-dependent AAA+ degradation machines. HslU hexamers recognize and unfold native protein substrates and then translocate the polypeptide into the degradation chamber of the HslV peptidase. Although a wealth of structural information is available for this system, relatively little is known about mechanisms of substrate recognition. Here, we demonstrate that mutations in the unstructured N-terminal and C-terminal sequences of two model substrates alter HslUV recognition and degradation kinetics, including changes in V_max. By introducing N- or C-terminal sequences that serve as recognition sites for specific peptide-binding proteins, we show that blocking either terminus of the substrate interferes with HslUV degradation, with synergistic effects when both termini are obstructed. These results support a model in which one terminus of the substrate is tethered to the protease and the other terminus is engaged by the translocation/unfolding machinery in the HslU pore. Thus, degradation appears to consist of discrete steps, which involve the interaction of different terminal sequence signals in the substrate with different receptor sites in the HslUV protease.     

In vitro propagation of Typhonium flagelliforme (Lodd) blume

Summary An in vitro culture system was developed for Typhonium flagelliforme using buds from the rhizomes. The mineral salts of four media were tested. These were Murashige and Skoog (MS), Nitsch and Nitsch (NN), Gamborg B5 (GB5) and White (W) of which MS medium was found to be the best medium for in vitro culture of T. flagelliforme. The addition of as low as 0.1 mg l⁻¹ (0.54 μM) α-naphthalene acetic acid (NAA) with the presence or absence of N⁶-benzyladenine (BA) in the MS medium caused abnormal shoot formation. The best medium for maximizing shoot number combined with normal complete plantlets from each bud was MS medium supplemented with 0.3 mg l⁻¹ (1.33 μM) BA and 0.5 mg l⁻¹ (2.46 μM) indole-3-butyric acid (IBA). The best acclimatization process was to transfer the normal plantlets, with all the leaves removed, into sand plus coconut husks substrate (1∶1) and placed in intermittent water mists house or shaded plant house with 50% light exclusion. Ninety two percent of the plantlets survived using this acclimatization method.     

A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays

We report here a novel, water-soluble, nonfluorescent dye that efficiently quenches fluorescence from a broad range of visible and near-infrared (NIR) fluorophores in Förster resonance energy transfer (FRET) systems. A model FRET-based caspase-3 assay system was used to test the performance of the quencher dye. Fluorogenic caspase-3 substrates were prepared by conjugating the quencher, IRDye^® QC-1, to a GDEVDGAK peptide in combination with fluorescein (emission maximum ∼540 nm), Cy3 (∼570 nm), Cy5 (∼670 nm), IRDye 680 (∼700 nm), IRDye 700DX (∼690 nm), or IRDye 800CW (∼790 nm). The Förster distance R₀ values are calculated as 41 to 65 Å for these dye/quencher pairs. The fluorescence quenching efficiencies of these peptides were determined by measuring the fluorescence change on complete cleavage by recombinant caspase-3 and ranged from 97.5% to 98.8%. The fold increase in fluorescence on caspase cleavage of the fluorogenic substrates ranged from 40 to 83 depending on the dye/quencher pair. Because IRDye QC-1 effectively quenches both the NIR fluorophores (e.g., IRDye 700DX, IRDye 680, IRDye 800CW) and the visible fluorophores (e.g., fluorescein, Cy3, Cy5), it should find broad applicability in FRET assays using a wide variety of fluorescent dyes.     

Isolation and characterization of amino acid-analogue-resistant mutants of Spirulina platensis

Amino acid-analogue-resistant mutants of the cyanobacterium Spirulina platensis were isolated using amino acid analogues -2-thienylalanine, p-fluorophenylalanine, ethionine and azetidine-2-carboxylic acid. The growth and other cellular contents in these mutants were less than in the parent. The internal free amino acid pool showed varying amounts. Maximal overproduction occurred of proline whereas overproduction of aspartic acid, alanine and lysine was much less.     

Cloning of an isozyme of proline 3-hydroxylase and its purification from recombinant Escherichia coli

An isozyme gene of proline 3-hydroxylase was cloned from Streptomyces sp. strain TH1 (Mori H, Shibasaki T, Yano K, Ozaki A, J. Bacteriol. 1997, 179: 5677–5683). The isozyme gene (870 bp) encodes a protein of molecular weight of 33,573. Both 3-hydroxylase genes are identical at 76.2% in amino acid sequence. His-motifs conserved in 2-oxoglutarate-dependent dioxygenases are conserved in both genes. Although characteristics of both recombinant 3-hydroxylases are similar, specific activities to l-proline and proline analogs are different.