An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species

A hallmark of the Gram-positive bacteria, such as the soil-dwelling bacterium Bacillus subtilis, is their cell wall. Here, we report that d -leucine and flavomycin, biofilm inhibitors targeting the cell wall, activate the β-lactamase PenP. This β-lactamase contributes to ampicillin resistance in B. subtilis under all conditions tested. In contrast, both Spo0A, a master regulator of nutritional stress, and the general cell wall stress response, differentially contribute to β-lactam resistance under different conditions. To test whether β-lactam resistance and β-lactamase genes are widespread in other Bacilli, we isolated Bacillus species from undisturbed soils, and found that their genomes can encode up to five β-lactamases with differentiated activity spectra. Surprisingly, the activity of environmental β-lactamases and PenP, as well as the general stress response, resulted in a similarly reduced lag phase of the culture in the presence of β-lactam antibiotics, with little or no impact on the logarithmic growth rate. The length of the lag phase may determine the outcome of the competition between β-lactams and β-lactamases producers. Overall, our work suggests that antibiotic resistance genes in B. subtilis and related species are ancient and widespread, and could be selected by interspecies competition in undisturbed soils.     

Synthesis and active oxygen generation by new emodin derivatives and their gonadotropin-releasing hormone conjugates

In an attempt to develop efficient chemotherapeutic agents targeted at malignant cells that express receptors, we synthesized five new emodin derivatives and their gonadotropin-releasing hormone (GnRH) conjugates to be used as potential photoactive conjugates. Emodin was modified at its hydroxy groups and included different spacers for conjugation of the peptide. We used electron spin resonance (ESR) and spin trapping techniques to study the light-stimulated redox properties of the emodin derivatives and their GnRH conjugates. Upon irradiation, all new emodin derivatives and their conjugates stimulated the formation of singlet oxygen, that is, (1)O(2), and oxygen radicals, that is, O(2)(-)(*) and OH(*). However, substantial differences were found between the tested derivatives as to the efficacy of reactive oxygen species (ROS) production. Because of its superior ROS production properties, [d-Lys(6)(MeoEmo)]GnRH was selected as a leading conjugate. En-route to evaluate its targeting capacity, this potentially cytotoxic conjugate was tested in vitro to determine its hormonal activity and binding affinity to GnRH receptors.     

Variation in Endogenous Gibberellins,Abscisic Acid,and Carbohydrate Content During the Growth Cycle of Colored <Emphasis Type="Italic">Zantedeschia</Emphasis> spp., a Tuberous Geophyte

Phenologic changes and variation in the level of endogenous gibberellins (GAs), abscisic acid (ABA), carbohydrate content, and α-amylase activity were examined in colored Zantedeschia spp. cv. Cala Gold. These changes were examined in the primary bud tissues and in the attached tuber tissue during the growth cycle. Dormant tubers were dry-stored at 20°C for 3 months, planted in a phytotron, and grown under 22/16 ± 1°C. Plant development was monitored under continued irrigation until leaf senescence and tuber dormancy. GAs and ABA were extracted from the primary bud tissues, fractionated by HPLC, and analyzed using GC-SIM. Starch, glucose, soluble protein, and α-amylase activity were monitored in the tuber tissue attached to the primary bud. Endogenous changes in GAs and ABA in the primary bud were correlated with endogenous changes in carbohydrate content and α-amylase activity in the attached tuber tissue. These correlations were observed during the rest and the growth periods and were associated with developmental changes in the plant, that is, bud dormancy relaxation, bud growth, and inflorescence differentiation. ABA content decreased and a transient pulse of GA was measured in the primary bud concomitantly with the onset of shoot elongation in dry tubers during storage, before planting. The sharp increase of GAs in the bud preceded inflorescence differentiation as observed in dissected apices by about 15 days, as well as the increase in α-amylase activity in the attached tuber tissue. A steep decrease in starch level was measured in the tuber after planting, concomitantly with massive plant growth. These findings suggest a possible involvement of gibberellin in the initiation of α-amylase activity during dormancy relaxation in colored Zantedeschia and in the autonomous induction of flowering.     

Direction finding by hornets in a vertically rotating centrifuge

In a vertically rotating centrifuge, the direction of the resultant gravitational and centrifugal forces is constantly changing. Hornets placed in such a centrifuge will build their combs in the direction of the resultant only if the centrifuge is stopped every day and left in the same position for at least half an hour, because during the cessation of motion, they presumably “learn” some geometrical cues which enable them to determine the preferred angle of building. Hornets can detect and respond to a centrifugal force as small as 0·18% of the earth's gravitational force. At a rotational rate of 1/8 of a revolution per minute there was no comb construction whatsoever and hornet mortality rate was 100% within three days.     

Cell wall structure and composition in the comb built by hornets and wasps (Vespinae,hymenoptera)

Morphological, mineralogical, and chemical investigations were undertaken to determine the structure and composition of the cell walls of the comb in the nest of Vespa orientalis, Paravespula germanica, and Vespacrabro. Nests of V. orientalis were from three sites having different soil types, namely, Khamra soil, Gramosol soil, and organically rich soil from the city dump in Tel Aviv. Nests of P. germanica were from areas rich in organic matter, and those of V. crabro, shipped from Austria, were similarly comprised of organic matter. Structure and composition of cell walls in the three species differed; furthermore, grain size in the combs differed from that of particles in the surrounding soil.     

The involvement of ethylene in liatris corm dormancy

Corms of liatris (L. spicata, cv. Callilepsis) show a seasonal dormancy, being most active in the November harvest and least active in June. Storage of dormant corms at 3 °C for about 9 weeks resulted in a complete break of dormancy. This was accompanied by a sharp temporal increase in their rate of ethylene production, which was more pronounced in the buds than in the parenchyma tissue. Application of ethylene to the corms in the form of ethrel solution increased both ethylene production rate and sprouting. The ethylene-forming activity from ACC, measured both in vivo and in vitro, was higher in corms producing more ethylene. However, the content of 1-aminocyclopropane-1-carboxylic acid (ACC) of the corms was inversely related to their ethylene production rate. Ethylene thus seems to be involved in the dormancy control of liatris corms, and its production is apparently regulated mainly by the activity of the membranous ethylene-forming system.     

Spatial determinants of specificity in insulin action

Insulin is a potent stimulator of intermediary metabolism, however the basis for the remarkable specificity of insulin's stimulation of these pathways remains largely unknown. This review focuses on the role compartmentalization plays in insulin action, both in signal initiation and in signal reception. Two examples are discussed: (1) a novel signalling pathway leading to the phosphorylation of the caveolar coat protein caveolin, and (2) a recently identified scaffolding protein, PTG, involved directly in the regulation of enzymes controlling glycogen metabolism.     

Conformation of parathyroid hormone antagonists by CD,nmr, and molecular dynamics simulations

The conformation of two highly potent parathyroid hormone (PTH) antagonists was investigated in water/2, 2, 2-trifluoroethanol mixtures. The two peptides are derived from the sequence (7-34) of PTH and of PTH-related protein (PTHrP) and have a D -Trp replacing Gly in position 12. In the analogue derived from PTHrP, Lys¹¹ was replaced by Leu to remove the residual agonist activity. The study was conducted by CD and two-dimensional proton magnetic resonance spectroscopy, and the nuclear Overhauser effects found were utilized in restrained distance geometry and molecular dynamics simulations. Both peptides adopt a helical C-terminal conformation, which seems more stable in the case of the PTHrP analogue. A type II′ β-turn centered around D -Trp¹² and Lys¹³ is present inboth structures. © 1995 John Wiley & Sons, Inc.     

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a “reverse mapping” approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper’s utility for recovering depth of coverage, and accurate genotyping of SNP sites across the human genome. We show that genotyping unmapped reads can correctly inform a sample’s population, sex, and relatedness in a family setting. Detection of pathogen sequences within RNA-seq data was sensitive and accurate, performing comparably to existing methods, but with increased flexibility. We present two examples of ways in which this flexibility allows the analysis of genome features not well-represented in a linear reference. First, we analyze contigs from African genome sequencing studies, showing how they distribute across families from three distinct populations. Second, we show how gene-marking k-mers for the killer immune receptor locus allow allele detection in a region that is challenging for standard read mapping pipelines. The future adoption of the reverse mapping approach represented by FlexTyper will be enabled by more efficient methods for FM-index generation and biology-informed collections of reference queries. In the long-term, selection of population-specific references or weighting of edges in pan-population reference genome graphs will be possible using the FlexTyper approach. FlexTyper is available at https://github.com/wassermanlab/OpenFlexTyper.