Bacteria communicate with one another using chemical signal molecules. As in higher organisms, the information supplied by these molecules is critical for synchronizing the activities of large groups of cells. In bacteria, chemical communication involves producing, releasing, detecting, and responding to small hormone-like molecules termed autoinducers. This process, termed quorum sensing, allows bacteria to monitor the environment for other bacteria and to alter behavior on a population-wide scale in response to changes in the number and/or species present in a community. Most quorum-sensing-controlled processes are unproductive when undertaken by an individual bacterium acting alone but become beneficial when carried out simultaneously by a large number of cells. Thus, quorum sensing confuses the distinction between prokaryotes and eukaryotes because it enables bacteria to act as multicellular organisms. This review focuses on the architectures of bacterial chemical communication networks; how c...

/pdf/quorum-sensing-cell-to-cell-communication-in-bacteria-15ypp5joz7.pdf

QUORUM SENSING: Cell-to-Cell Communication in Bacteria

Auxin: regulation, action, and interaction.

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we
report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000
protein-coding genes—more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer
than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology
including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism,
and important differences in Ca21 signalling as compared with plants and animals. Neurospora possesses the widest array of
genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced
point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the
creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related
genes.

/pdf/the-genome-sequence-of-the-filamentous-fungus-neurospora-2jw3s2832k.pdf

The genome sequence of the filamentous fungus Neurospora crassa

Structures in Other Domains The methodology of structural analysis discussed in this article has been applied beyond the narrow realm of natural language syntax that we have discussed in this article. Within the study of language, similar methods of analysis have been pervasively applied to the study of sounds (phonology), words (morphology), and meanings (semantics), yielding a range of of abstract structural representations whose properties bear considerable explanatory burden. There are a wealth of cases in each of these domains analogous to those discussed here, though space prevents us from going in these (see Akmajian, Demers, Farmer and Harnish 1995 for a traditional overview, and Jackendo 1994 for one more focused on connections with cognitive science). Additionally, these representations have shed substantial light on the processes of language acquisition and language change. It has been found that variation in the types of sentences that are used, whether during the course of children's acquisition of their native languages or in the centuries-long periods of linguistic change, are best characterized not as super cial and haphazard alterations, but rather in terms of parametric modi cations to the fundamental underlying grammatical rules and constraints. Moving outside the domain of language, one application of these same methods has been in the study of music cognition. Just as the representations of linguistic theory arise out of an attempt to model speakers' intuitions about well-formedness and possible meanings of the sentences of their

Structural analysis

Map-based cloning is an iterative approach that identifies the underlying genetic cause of a mutant phenotype. The major strength of this approach is the ability to tap into a nearly unlimited resource of natural and induced genetic variation without prior assumptions or knowledge of specific genes. One begins with an interesting mutant and allows plant biology to reveal what gene or genes are involved. Three major advances in the past 2 years have made map-based cloning in Arabidopsis fairly routine: sequencing of the Arabidopsis genome, the availability of more than 50,000 markers in the Cereon Arabidopsis Polymorphism Collection, and improvements in the methods used for detecting DNA polymorphisms. Here, we describe the Cereon Collection and show how it can be used in a generic approach to mutation mapping in Arabidopsis. We present the map-based cloning of the VTC2 gene as a specific example of this approach.

/pdf/arabidopsis-map-based-cloning-in-the-post-genome-era-30powz3zt9.pdf

Arabidopsis Map-Based Cloning in the Post-Genome Era

To understand pattern formation in an organism one needs to know what factors control the differentiation of each cell type and what elements are responsible for the spatial arrangement of these cell types. In the cellular slime mould Dictyostelium discoideum, the problem is relatively simple since the mature fruiting body consists of two basic cell types—stalk cells and spores. The stalk cells of the mature fruiting body are derived from the anterior cells of the multicellular masses formed by aggregation, whereas the spores are derived from the posterior cells1. Cells that are plated at a density too low for aggregation, or are allowed to aggregate under water do not normally differentiate into stalk or spore cells. In many of our experiments we have made use of the fact that cells plated on agar at any density fail to undergo development beyond the stage of aggregation if they are covered by a thin layer of Cellophane. In this paper we present observations on cell differentiation which derive from the original report of Bonner2 of stalk-cell induction by cyclic AMP in isolated cells. We have found that stalk-cell induction by cyclic AMP is markedly dependent on cell density, and present evidence for the involvement of a low molecular weight diffusible factor in this process. We also describe the isolation of a mutant which gives rise to spore cells under cellophane.

Cell differentiation without morphogenesis in Dictyostelium discoideum

Root induction by auxins is still not well understood at the molecular level. In this study a system has been devised which distinguishes between the two active auxins indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA). IBA, but not IAA, efficiently induced adventitious rooting in Arabidopsis stem segments at a concentration of 10 microM. In wild-type plants, roots formed exclusively out of calli at the basal end of the segments. Root formation was inhibited by 10 microM 3,4,5-triiodobenzoic acid (TIBA), an inhibitor of polar auxin transport. At intermediate IBA concentrations (3-10 microM), root induction was less efficient in trp1, a tryptophan auxotroph of Arabidopsis with a bushy phenotype but no demonstrable reduction in IAA levels. By contrast, two mutants of Arabidopsis with measurably higher levels of IAA (trp2, amt1) show root induction characteristics very similar to the wild type. Using differential display, transcripts specific to the rooting process were identified by devising a protocol that distinguished between callus production only and callus production followed by root initiation. One fragment was identical to the sequence of a putative regulatory subunit B of protein phosphatase 2A. It is suggested that adventitious rooting in Arabidopsis stem segments is due to an interaction between endogenous IAA and exogenous IBA. In stem explants, residual endogenous IAA is transported to the basal end of each segment, thereby inducing root formation. In stem segments in which the polar auxin transport is inhibited by TIBA, root formation does not occur.

/pdf/analysis-of-indole-3-butyric-acid-induced-adventitious-root-427uznd9xp.pdf

Analysis of indole-3-butyric acid-induced adventitious root formation on Arabidopsis stem segments.

Sequence and organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana.

We summarize studies on stalk and spore cell formation in D. discoideum cell monolayers, aimed at revealing factors involved in controlling the prestalk:prespore pattern in this organism. We propose that there are no cell interactions dependent on cell contact per se. Formation of mature stalk cells from isolated amoebae incubated in a buffered salts medium requires only cyclic AMP and a lipid-like factor (DIF) released by cells developing at high density. In addition, a variety of sporogenous mutants can form spores rapidly and efficiently when incubated at low density in tissue culture dishes containing a similar cyclic AMP and salts medium. In some cases spore formation is improved by the addition of one or other of a variety of protective agents such as bovine serum albumin. Wild-type amoebae at low density form prespore cells under the same conditions. We present some evidence that DIF is the activator of prestalk cell formation in a two-component patterning mechanism of the kind proposed by Wolpert et al. (Symp. Soc. exp. Biol. 25, 391-415 (1971)) and Gierer & Meinhardt (Kybernetik 12, 30-39 (1972)). We also provide data indicating that the role of inhibitor is played by ammonia, an idea first mooted by Sussman & Schindler (Differentiation 10, 1-5 (1978)).

Christopher D. Town

Papers

Cell differentiation without morphogenesis in Dictyostelium discoideum

Analysis of indole-3-butyric acid-induced adventitious root formation on Arabidopsis stem segments.

Sequence and organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana.

Cell Patterning in Dictyostelium

Developmental regulation of a stalk cell differentiation-inducing factor in Dictyostelium discoideum.