Negative Cross-Communication among Wheat Rhizosphere Bacteria: Effect on Antibiotic Production by the Biological Control Bacterium Pseudomonas aureofaciens 30-84

Phenazine antibiotic production in the biological control bacterium Pseudomonas aureofaciens 30-84 is regulated in part via the PhzR/PhzI N-acyl homoserine lactone (AHL) system. Previous work showed that a subpopulation of the wheat rhizosphere community positively affected phenazine gene expression in strain 30-84 via AHL signals (E. A. Pierson, D. W. Wood, J. A. Cannon, F. M. Blachere, and L. S. Pierson III, Mol. Plant-Microbe Interact. 11:1078-1084, 1998). In the present work, a second subpopulation, one that negatively affected phenazine gene expression, was identified from this rhizosphere community. Strain 30-84 grown in conditioned medium (CM) from several strains produced lower levels of phenazines (1.5- to 9.3-fold) than control when grown in CM from the strain 30-84I₁/I₂. Growth of the phzB::lacZ reporter strain 30-84Z in this CM resulted in decreased lacZ expression (4.3- to 9.2-fold) compared to growth of the control strain in CM, indicating that inhibition of phzB occurred at the level of gene expression. Preliminary chemical and biological characterizations suggested that these signals, unlike other identified negative signals, were not extractable in ethyl acetate. Introduction of extra copies of phzR and phzI, but not phzI alone, in trans into strain 30-84Z reduced the negative effect on phzB::lacZ expression. The presence of negative-signal-producing strains in a mixture with strain 30-84 reduced strain 30-84's ability to inhibit the take-all disease pathogen in vitro. Together, the results from the previous work on the positive-signal subpopulation and the present work on the negative-signal subpopulation suggest that cross-communication among members of the rhizosphere community and strain 30-84 may control secondary metabolite production and pathogen inhibition.     

Molecular Characterization of Novel Red Green Nonsulfur Bacteria from Five Distinct Hot Spring Communities in Yellowstone National Park

We characterized and compared five geographically isolated hot springs with distinct red-layer communities in Yellowstone National Park. Individual red-layer communities were observed to thrive in temperatures ranging from 35 to 60°C and at pH 7 to 9. All communities were dominated by red filamentous bacteria and contained bacteriochlorophyll a (Bchl a), suggesting that they represented novel green nonsulfur (GNS) bacteria. The in vivo absorption spectra of individual sites were different, with two sites showing unusual Bchl a protein absorption bands beyond 900 nm. We prepared and analyzed 16S rRNA libraries from all of these sites by using a combination of general bacterial primers and new GNS-specific primers described here. These studies confirmed the presence of novel GNS-like bacteria in all five communities. All GNS-like clones were most similar to Roseiflexus castenholzii, a red filamentous bacterium from Japan that also contains only Bchl a. Phylogenies constructed by using GNS-like clones from Yellowstone red-layer communities suggest the presence of a moderately diverse new “red” cluster within the GNS lineage. Within this cluster, at least two well-supported subclusters emerged: YRL-A was most similar to Roseiflexus and YRL-B appeared to be novel, containing no known isolates. While these patterns showed some site specificity, they did not correlate with observed Bchl a spectrum differences or obvious features of the habitat.     

Growth and cellular organization of Arabidopsis pollen tubes in vitro

Tricellular pollen tubes of Arabidopsis thaliana were cultured in vitro on solid media and studied with respect to growth, cellular organization and ultrastructure, cytoskeletal organization, organelle movement, deposition and structure of the wall and the occurrence of coated pits, all elements assumed to be relevant for tip growth. For our ultrastructural studies we used freeze fixation and freeze substitution. Although Arabidopsis pollen tubes are broadly similar to those of bicellular species such as Nicotiana tabacum and Lilium spec. and in vivo grown pollen tubes of Arabidopsis, some differences occurred. The density of the equally distributed, relatively small (85 nm) secretory vesicles (SV) in the tip is low (five/µm ²). In between the SV of the tip, membranous material, possibly smooth endoplasmic reticulum, fragments of rough endoplasmic reticulum and loose ribosomes are present. The wall in the tip is not amorphous but layered and a secondary wall is formed already in the flanks of the tip. The general pattern of organelle motion is reverse fountain-like, but individual organelles move in distinct lanes at speeds of up to 2 µm/s, and about half of the organelle population shows a moderate velocity or Brownian movement. These properties are discussed in relation to the low growth rate (10 µm/h) of Arabidopsis pollen grown in vitro. The two similar sperm cells are closely attached and are always found near the vegetative nucleus. No surrounding wall and no cytoskeletal elements were obvious in the sperm cells. The preferential location of the mitochondria at the wall and the large (up to 400 nm) coated pits are unique for angiosperm pollen tubes. The size of the coated pits may allow not only membrane retrieval but also pinocytosis.     

Uncertainty and Denial: A Resource-Rational Model of the Value of Information

Classical decision theory predicts that people should be indifferent to information that is not useful for making decisions, but this model often fails to describe human behavior. Here we investigate one such scenario, where people desire information about whether an event (the gain/loss of money) will occur even though there is no obvious decision to be made on the basis of this information. We find a curious dual trend: if information is costless, as the probability of the event increases people want the information more; if information is not costless, people''s desire for the information peaks at an intermediate probability. People also want information more as the importance of the event increases, and less as the cost of the information increases. We propose a model that explains these results, based on the assumption that people have limited cognitive resources and obtain information about which events will occur so they can determine whether to expend effort planning for them.     

Reflections onChloroflexus

A personal historic account is presented of the discovery of the anoxygenic filamentous bacteria of hot springs:Heliothrix oregonensis andChloroflexus aurantiacus. The later discoveries of marine and hypersaline forms are also described.     

Gramicidin S Production by Bacillus brevis in Simulated Microgravity

In a continuing study of microbial secondary metabolism in simulated microgravity, we have examined gramicidin S (GS) production by Bacillus brevis strain Nagano in NASA High Aspect Rotating Vessels (HARVs), which are designed to simulate some aspects of microgravity. Growth and GS production were found to occur under simulated microgravity. When performance under simulated microgravity was compared with that under normal gravity conditions in the bioreactors, GS production was found to be unaffected by simulated microgravity. The repressive effect of glycerol in flask fermentations was not observed in the HARV. Thus the negative effect of glycerol on specific GS formation is dependent on shear and/or vessel geometry, not gravity. Received: 7 August 1996 / Accepted: 17 September 1996     

SIMLR: A Tool for Large‐Scale Genomic Analyses by Multi‐Kernel Learning

SIMLR (S ingle‐cell I nterpretation via M ulti‐kernel L eaR ning), an open‐source tool that implements a novel framework to learn a sample‐to‐sample similarity measure from expression data observed for heterogenous samples, is presented here. SIMLR can be effectively used to perform tasks such as dimension reduction, clustering, and visualization of heterogeneous populations of samples. SIMLR was benchmarked against state‐of‐the‐art methods for these three tasks on several public datasets, showing it to be scalable and capable of greatly improving clustering performance, as well as providing valuable insights by making the data more interpretable via better a visualization. SIMLR is available on https://github.com/BatzoglouLabSU/SIMLR GitHub in both R and MATLAB implementations. Furthermore, it is also available as an R package on http://bioconductor.org     

Ultrasonography of the developing reproductive tract in ram lambs: effects of a GnRH agonist

In spring-born ram lambs, the testes (from 2 wk), prostate and vesicular glands (from 4 wk) were examined by ultrasonography every 2 wk up to 26 wk of age. Image analysis was done (numerical pixel values). Ram lambs were treated with a long acting formulation of a GnRH superagonist (Leuprolide acetate; 1.5 mg/kg) at 3 and 7 wk of age. In blood samples taken every 15 min for 8 h, mean serum LH, LH pulse amplitude, and basal and mean serum FSH concentrations were lower at 5 wk of age, and LH pulse frequency was lower at 15 wk of age in animals given Leuprolide acetate compared with those of the controls. There were no differences (P>0.05) in testis, prostate or vesicular gland development between treated and control animals. Testicular diameter of the left and right testes in transverse and longitudinal planes increased slowly to 8 wk of age, more rapidly to 18 wk of age, then more slowly to 26 wk of age (P<0.05). Numerical pixel values of testicular images decreased from 2 to 8 wk of age, increased to 22 wk of age and then plateaued. Width of the prostate increased from 4 to 26 wk of age, but length and width of the vesicular glands increased slowly to 8 wk of age, more rapidly to 18 wk of age and then plateaued (P<0.05). Numerical pixel values for the prostate declined from 4 to 8 wk and for the vesicular glands, declined from 4 to 10 wk of age; numerical pixel values increased to 12 wk and then decreased to a nadir at 18 wk, followed by a steady increase to 26 wk of age (P<0.05). We concluded that developmental patterns of numerical pixel values of the testes, prostate and vesicular glands in ram lambs reflect stages of development, but treatment with a GnRH superagonist at 3 and 7 weeks of age did not affect growth of testes, vesicular or prostate glands.