Interactions and self-organization in the soil-microbe complex

Soil is the most complicated biomaterial on the planet. As with any material, the physical habitat is of prime importance in determining and regulating biological activity. However, until recently the opaque nature of soil has meant that any interrogation of its interior architecture has been relatively rudimentary, restricted to simple qualitative expressions of the physical heterogeneity that fail to relate to any specific function. However, new techniques and insights into the biophysical and biochemical processes of this inner space are leading to the developments of theoretical frameworks and experimental approaches that will allow us to sustainably manage Earth's most important resource. We introduce the concept that the soil-microbe system is self-organized and suggest new priorities for research based on an integrative approach that combines biochemistry and biophysics.     

Bayesian inference towards the resolution of molecular evolution:application to the "Trichoderma harzianum sensu lato" clade

The Hypocrea lixii/Trichoderma harzianum species aggregate contains a group of taxa (H. lixii /T. harzianum, T. aggressivum, T. tomentosum, T. cerinum, T. velutinum, H. tawa) of which some (e.g. T. harzianum) are important for biocontrol of plant pathogenic fungi in agriculture, whereas others are aggressive pathogens of Agaricus spp. and Pleurotus spp. in mushroom farms (T. aggressivum), or opportunistic pathogens of immunocompromised mammals including humans (T. harzianum). We ch…     

Origin of the mesoamerican 260-day calendar

The sacred 260-day Mesoamerican calendar probably originated near a latitude of 15 degrees N, where there is a 260-day interval between transits of the zenithal sun. Archeological and faunal evidence favors an origin in the Pacific lowlands rather than in the highlands near Copán, Honduras, although Copán, which is located at the 15th parallel of latitude, later became the principal Mayan astronomical center.     

Developmental neuroethology: changes in escape and defensive behavior during growth of the lobster

The changes in relative efficacy of two incompatible behaviors was investigated during growth of the lobster, Homarus americanus. In larval and early juvenile stages, physiological and morphological factors favor use of the escape response over defensive behavior. In large animals, defensive behavior is preferred almost exclusively to escape behavior unless the claws are lost. The interaction of escape and defensive behavior is modified by neural and morphological factors, which are dependent on the stage in the life cycle of the organism.     

Ellipsosomes: organelles containing a cytochrome-like pigment in the retinal cones of certain fishes

Ellipsosomes are dense spherical bodies containing a very large concentration of a heme pigment spectroscopically resembling pure cytochrome c. They are located at the outer ends of the inner segments of the cones of certain fishes. Although, superficially, they resemble the similarly located oil droplets in the cones of birds and reptiles, their ultrastructure and staining properties resemble those of the neighboring mitochondria. However, like the oil droplets, they may serve as intracellular color filters.     

Autumn bloom of antarctic pack-ice algae

An autumn bloom of sea-ice algae was observed from February to June of 1992 within the upper 0.4 meter of multiyear ice in the Western Weddell Sea, Antarctica. The bloom was reliant on the freezing of porous areas within the ice that initiated a vertical exchange of nutrient-depleted brine with nutrient-rich seawater. This replenishment of nutrients to the algal community allowed the net production of 1760 milligrams of carbon and 200 milligrams of nitrogen per square meter of ice. The location of this autumn bloom is unlike that of spring blooms previously observed in both polar regions.     

Mutant Trp repressors with new DNA-binding specificities

Oligonucleotide-directed mutagenesis of the codons for glutamine-68 (Gln68), lysine-72 (Lys72), isoleucine-79 (Ile79), alanine-80 (Ala80), and threonine-81 (Thr81) of the Escherichia coli trpR (tryptophan aporepressor) gene was used to make mutant repressors with each of 36 different amino acid changes. Mutant repressors were tested for binding to each member of a set of 28 different operators closely related to the consensus trp operator. Of the 36 mutant repressors, 11 bind a subset of the 28 operators; 5 of these have new binding specificities. These new specificities indicate that the hydroxyl group of Thr81 makes a specific contact with one of the four critical base pairs in a trp operator half-site, and the methyl group of Thr81 determines specificity at a second, critical base pair. The Trp repressor does not use the first two amino acids of its "recognition alpha-helix," Ile79 and Ala80, to make sequence-specific DNA contacts, and interacts with its operator in vivo in a way fundamentally different from the way that phage lambda repressor, lambda Cro protein, and coliphage 434 repressor contact their respective binding sites.     

A high-resolution radiation hybrid map of the human genome draft sequence

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.     

Effects of size and temperature on metabolic rate

We derive a general model, based on principles of biochemical kinetics and allometry, that characterizes the effects of temperature and body mass on metabolic rate. The model fits metabolic rates of microbes, ectotherms, endotherms (including those in hibernation), and plants in temperatures ranging from 0 degrees to 40 degrees C. Mass- and temperature-compensated resting metabolic rates of all organisms are similar: The lowest (for unicellular organisms and plants) is separated from the highest (for endothermic vertebrates) by a factor of about 20. Temperature and body size are primary determinants of biological time and ecological roles.     

Role of adenine nucleotide translocator 1 in mtDNA maintenance

Autosomal dominant progressive external ophthalmoplegia is a rare human disease that shows a Mendelian inheritance pattern, but is characterized by large-scale mitochondrial DNA (mtDNA) deletions. We have identified two heterozygous missense mutations in the nuclear gene encoding the heart/skeletal muscle isoform of the adenine nucleotide translocator (ANT1) in five families and one sporadic patient. The familial mutation substitutes a proline for a highly conserved alanine at position 114 in the ANT1 protein. The analogous mutation in yeast caused a respiratory defect. These results indicate that ANT has a role in mtDNA maintenance and that a mitochondrial disease can be caused by a dominant mechanism.