On the origins of morphological complexity in block copolymer surfactants

Amphiphilic compounds such as lipids and surfactants are fundamental building blocks of soft matter. We describe experiments with poly(1,2-butadiene-b-ethylene oxide) (PB-PEO) diblock copolymers, which form Y-junctions and three-dimensional networks in water at weight fractions of PEOintermediate to those associated with vesicle and wormlike micelle morphologies. Fragmentation of the network produces a nonergodic array of complex reticulated particles that have been imaged by cryogenic transmission electron microscopy. Data obtained with two sets of PB-PEOcompounds indicate that this type of self-assembly appears above a critical molecular weight. These block copolymers represent versatile amphiphiles, mimicking certain low molecular weight three-component (surfactant/water/oil) microemulsions, without addition of a separate hydrophobe.     

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.     

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. O?mycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known o?mycete avirulence genes.     

The origins of taxonomy

There are approximately 10 million kinds of olganisms in the world, of which we have described some 15 percent. The rapid growth of the human population will cause most of the remainder to disappear from the earth before they are seen by a taxonomist. These facts suggest a more rigorous application of priorities in systematic biology as well as a careful review of the principles upon which our taxonomic system is based. Folk taxonomies all over the world are shallow hierarchically and comprise a strictly limited number of generic taxa ranging from about 250 to 800 forms applied to plants and a similar number applied to animals. These numbers are consistent, regardless of the richness of the environment in which the particular people live. Very few specific and varietal taxa are recognized in folk taxonomic systems. Until the invention of movable type in the mid-l5th century, written taxonomies were simply records of the folk taxonomies of particular regions. Subsequently, with the possibility for the wide distribution of books, it began to seem worth while to attempt to describe and name all species of plants and animals in the world. By the year 1700, 698 genera of plants were recognized; and by the year 1778, some 1350 genera, including tens of thousands of species. In 1789 de Jussieu interpolated the family as a higher level taxonomic category in an attempt to reduce the number of important units in the system to a memorable number. The family is still the focal point in systems of angiosperm classification at present, several hundred families being recognized. Problems with the taxonomic system stem largely from the fact that it is not designed as an information retrieval device. In folk taxonomies, names are given to organisms and these are used to communicate about the organisms with others who already know the culturally significant properties of the organisms being discussed. In dealing with the vast numbers of organisms that exist, we tend to overemphasize the process of classification and the decisions it involves at the expense of the information about the organisms that we are supposedly accumulating. Frequent changes in names exacerbate the difficulties of the system and render it still less useful for information retrieval. With modern electronic data processing equipment, it has become possible to record information about organisms, to retain this information in a data bank, and to utilize it for various purposes, including the construction of various taxonomic systems. The invention of high-speed electronic data processing equipment is seen as analogous to but more important than the invention of movable type in the history of systematic biology. By using such equipment to its full potentialities, we should be able to achieve a qualitative improvement in our perception of the living world.     

Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons

A comparison of the proteins encoded in the recently (nearly) completed human genome to those from the fly and nematode genomes reveals a major increase in the complexity of the apoptotic molecular machinery in vertebrates, in terms of both the number of proteins involved and their domain architecture. Several components of the apoptotic system are shared by humans and flies, to the exclusion of nematodes, which seems to support the existence of a coelomate clade in animal evolution. A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis.     

The origins of genomic duplications in Arabidopsis

Large segmental duplications cover much of the Arabidopsis thaliana genome. Little is known about their origins. We show that they are primarily due to at least four different large-scale duplication events that occurred 100 to 200 million years ago, a formative period in the diversification of the angiosperms. A better understanding of the complex structural history of angiosperm genomes is necessary to make full use of Arabidopsis as a genetic model for other plant species.     

The origins of gene instability in yeast

Two unstable mutations at the his4 locus of yeast are due to the insertion of the transposable elements Ty912 and Ty917 into the his4 regulatory region. The two transposons are related, one being derived from the other by a substitution of 4000 base pairs of DNA. Element Ty912 includes identical terminal repeats, whereas the terminal repeats of Ty917 are not identical. Transposition of Ty912 or Ty917 generates 5-base-pair duplications of the target DNA at either end of the element. Expression and reversion of a his4 gene containing Ty912 or Ty917 is controlled by three unlinked regulatory genes. The properties of these regulatory genes are similar to those described for the controlling elements in maize.