Bacterial genome mapping by two-dimensional pulsed-field gel electrophoresis (2D-PFGE)

Macrorestriction mapping is often the first step toward a thorough physical and genetic characterization of a bacterial genome. The problem of deducing the order of partially or completely digested macrorestriction fragments to yield a physical genome map may readily be solved by applying twodimensional pulsed-field gel electrophoresis (2D-PFGE) techniques. These powerful methods are quick and technically easy to perform; specifically, they are independent of DNA probes and should therefore be applicable to any bacterial species irrespective of its prior genetic characterization. In this article, detailed step-by-step protocols are given to set up, run, and evaluate 2D pulsed-field gels. Two basic methods are described: partial/complete 2D gels of one restriction enzyme and complete/complete 2D gels of two different restriction enzymes. Other topics include preparation of bacterial genomic DNA, screening for suitable rare-cutting restriction enzymes and determination of optimal running conditions. Accompanied by many notes, these protocols are meant to offer the novice a sound and rapid access to these important methods.     

Konstruktionsprinzipien des Schnabelskeletts beim schlupfreifen Jungvogel

Zusammenfassung Unter Einsatz einer neuartigen, direkt vergrößernden Röntgentechnologie wurde die Konstruktion des Schnabelskeletts von schlupfreifen Jungvögeln untersucht. Wie die bei Verwendung sog. Mikrofokus-Röntgengeräte erzielten Röntgenaufnahmen erkennen lassen, weist das Schnabelskelett der Schlüpflinge — unabhängig vom Entwicklungsmodus — bei allen untersuchten Formen einen recht einheitlichen Bau auf. Sowohl der Ossifikationsgrad der Kiefer als auch die spezifische Osteoarchitektur der Knochenelemente des Schnabelapparates, insbesondere im Bereich der Substantia spongiosa des Os praemaxillare können als anatomische Anpassungen an die beim Sprengen der Eischale auftretenden mechanischen Belastungen des Kieferskeletts gewertet werden.

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Construction principles of the beak skeleton in the hatchling

Summary The structure of the beak skeleton of hatchlings was analysed using a new direct magnifying X-ray technique. The application of these microfocus X-ray systems reveals a quite uniform construction of the beak skeleton in the hatchlings, independent from the mode of development of the bird species groups studied (precocial, altricial etc.). The amount of ossification as well as the specific osteoarchitecture of the jaw bones of the beak apparatus — especially in the region of Substantia spongiosa of the Os praemaxillare — may be considered as an anatomical adaptation to mechanical stress of the jaw bones during picking of the eggshell.

     

Long-Term Production of Ergot Peptides by Immobilized Claviceps purpurea in Semicontinuous and Continuous Culture

The semicontinuous and continuous production of pharmaceutically useful ergot peptides with immobilized Claviceps purpurea could be demonstrated. A key aspect was the presence of high concentrations of CaCl₂ (96.9 mM) to give marked prolongation of the productive phase, and cultivation in a bubble column reactor became possible. Restriction of the phosphate supply avoided an otherwise problematic massive increase of outgrowing hyphae.     

Interleukin-8 activates microtubule-associated protein 2 kinase (ERK1) in human neutrophils

The signal transduction initiated by the human cytokine interleukin-8 (IL-8), the main chemotactic cytokine for neutrophils, was investigated and found to encompass the stimulation of protein kinases. More specifically, IL-8 caused a transient, dose and time dependent activation of a Ser/Thr kinase activity towards myelin basic protein (MBP) and the MBP-derived peptide APRTPGGRR patterned after the specific concensus sequence in MBP for ERK enzymes. The activated MBP kinase was furthermore identified as an extracellular signal regulated kinase (ERK1) based on several criteria such as substrate specificity, molecular weight, activation-dependent mobility shift, and recognition by anti-ERK antibodies. For comparison, the chemotactic response of neutrophils to a stimulus of bacterial origin (fMet-Leu-Phe or fMLP) was also examined and found to involve the activation of a similar ERK enzyme. The present data clearly indicate that in terminally differentiated, non-proliferating human cells, the MBP kinase/ERK activity can serve other purposes than mitogenic signaling, and that processes such as chemotaxis, induced by bacterial peptides as well as by human cytokines like IL-8, involve the regulation of ERK enzyme.Abbreviations IL-8 interleukin-8 - fMLP fMet-Leu-Phe - MBP myelin basic protein - ERK extracellular signal regulated kinase - MAP2 microtubule-associated protein 2 - PK-A cAMP dependent protein kinase - PKI protein kinase inhibitor - PMSF phenyl-methanesulfonyl fluoride - PVDF poly-vinylidene difluoride - HBSF Hank's buffered salt solution - DAB 3,3-diaminobenzidine tetrahydrochloride - PNPP p-nitrophenyl-phosphate - HSA human serum albumin - EGTA [ethylenebis (oxyethylenenitrilo)]tetraacetic acid - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis     

Trade-offs and synergies between ecosystem productivity and stability in temperate grasslands

Aim

It is crucial to monitor how the productivity of grasslands varies with its temporal stability for management of these ecosystems. However, identifying the direction of the productivity–stability relationship remains challenging because ecological stability has multiple components that can display neutral, positive or negative covariations. Furthermore, evidence suggests that the direction of the productivity–stability relationship depends on the biotic interactions and abiotic conditions that underlie ecosystem productivity and stability. We decipher the relationships between grassland productivity and two components of its stability in four habitat types with contrasting environments and flora.

Location

France.

Time period

2000–2020.

Major taxa

Grassland plant species.

Methods

We used c. 20,000 vegetation plots spread across French permanent grasslands and remotely sensed vegetation indices to quantify grassland productivity and temporal stability. We decomposed stability into constancy (i.e., temporal invariability) and resistance (i.e., maximum deviation from average) and deciphered the direct and indirect effects of abiotic (namely growing season length and nitrogen input) and biotic (namely plant taxonomic diversity, trait diversity and community-weighted mean traits) factors on productivity–stability relationships using structural equation models.

Results

We found a positive relationship between productivity and constancy and a negative relationship between productivity and resistance in all habitats. Abiotic factors had stronger effects on productivity and stability compared with biotic factors. A longer growing season enhanced grassland productivity and constancy. Nitrogen input had positive and negative effects on grassland productivity and resistance, respectively. Trait values affected the constancy and resistance of grassland more than taxonomic and trait diversity, with effects varying from one habitat to another. Productivity was not related to any biotic factor.

Main conclusions

Our findings reveal how vital it is to consider both the multiple components of stability and the interaction between environment and biodiversity to gain an understanding of the relationships between productivity and stability in real-world ecosystems, which is a crucial step for sustainable grassland management.     

A physical and genetic map of Neisseria meningitidis B1940

A physical map of the chromosome of Neisseria meningitidis B1940 has been constructed by one- and two-dimensional pulsed-field gel electrophoresis techniques. Complete macrorestriction maps for the enzymes Nhe I (16 sites), Sgf I (13 sites), Sfi I (11 sites) and I-Ceu I (4 sites), as well as a partial restriction map for the restriction enzyme Spe I (15 of c. 28 sites) could be established. Altogether, 59 restriction sites were mapped on a single circular chromosome of 2.3 Mbp. By restriction endonuclease digestion and Southern hybridization of cloned genetic markers, 39 genetic loci were assigned to this map. Comparison with the metabolic maps of Neisseria gonorrhoeae MS11-N198 and FA1090 revealed a high degree of conservation in the arrangement of gene loci among these two species, although four out of 24 genetic loci are located at different chromosomal positions, indicating several genomic rearrangements.     

Carbon source utilization of soil extracted microorganisms as a tool to detect the effects of soil supplemented with genetically engineered and non-engineered Corynebacterium glutamicum and a recombinant peptide at the community level

Abstract: Substrate utilization of microbial cells extracted from soil with a 0.85% aqueous sodium chloride solution, was determined to estimate effects on soil microorganisms at the community level with microtiter plates (Biolog GN®) containing 95 different sources of organic carbon. A consistent pattern of utilized substrates was obtained after 24 h of microtiter plate incubation at 28°C. The absorbance values (OD₅₉₀) obtained from a microtiter plate reader after background correction were transformed by using the average absorbance values of oxidized substrates as a threshold to distinguish between well utilized and poorly or non-utilized substrates and thereby reduce variances between replicates. Doubling times of the extracted soil microorganisms in the microtiter plates were tested with 12 substrates and ranged from 1.96 h to 3.23 h, depending on the carbon source. The carbon source utilization assay was used to assess the effects of soil inoculation with Corynebacterium glutamicum with and without a genetically engineered plasmid (pUN1; 6.3 kb), which encoded for the synthesis of the mammalian protease inhibiting peptide, aprotinin. Additionally, aprotinin itself was added at two concentrations to soil samples. An identical decrease in the number of carbon sources utilized, especially carbohydrates, occurred upon soil inoculation with both C. glutamicum strains after inoculation with 10⁶ cells g⁻¹ soil. This effect was only detectable during the first three weeks of incubation, as long as cell numbers of C. glutamicum (pUN1) were above 10⁵ cfu g⁻¹. Soil amendment with aprotinin resulted in utilization of additional substrates, most of them carbohydrates. With 0.1 mg aprotinin g⁻¹ soil this stimulation lasted 2 days and with 10 mg g⁻¹ it lasted for 7 days.     

Cyanopeptolin S, a sulfate-containing depsipeptide from a water bloom of Microcystis sp.

Abstract A new sulfated, cyclic depsipeptide, called cyanopeptolin S, from Microcystis sp. was isolated from a water bloom in the Auensee/Leipzig (Germany). The depsipeptide had a relative molecular mass of 925 and contained l-arginine, l-threonine, l-isoleucine, N-methyl-l-phenylalanine, a l-glutamic acid-δ-aldehyde ring system and a sulfated d-configurated glyceric acid as a side chain. The structure was elucidated by means of two-dimensional ¹H and ¹³C nuclear magnetic resonance spectroscopy, fast atom bombardment mass spectroscopy, Fourier transformed infrared spectroscopy and combined gas-liquid chromatography/mass spectrometry. Cyanopeptolin S inhibited trypsin with an IC₅₀≤ 0.2 μg ml⁻¹.     

Conversion of a racemate into a single enantiomer in one step by chiral liquid chromatography: Studies with rac-2,2′-diiodobiphenyl

The enantiomers of rac-2,2′-diiodobiphenyl were separated by liquid chromatography on microcrystalline triacetylcellulose. The conformational lability, a large separation factor α, and a suitable capacity factor k′(+) of this biphenyl allowed us to convert the racemate into 90% of enantiomerically pure (-)-2,2′-diiodobiphenyl and 10% of pure (+)-2,2′-diiodobiphenyl, respectively, by a series of in situ racemization-elution cycles. The much better retained (+)-enantiomer was racemized on the chromatographic column at 50°C after the less retained (-)-enantiomer has already been eluted at 8°C. © 1995 Wiley-Liss, Inc.