ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches

There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith–Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith–Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

Spatial processing in the auditory cortex of the macaque monkey

The patterns of cortico-cortical and cortico-thalamic connections of auditory cortical areas in the rhesus monkey have led to the hypothesis that acoustic information is processed in series and in parallel in the primate auditory cortex. Recent physiological experiments in the behaving monkey indicate that the response properties of neurons in different cortical areas are both functionally distinct from each other, which is indicative of parallel processing, and functionally similar to each other, which is indicative of serial processing. Thus, auditory cortical processing may be similar to the serial and parallel “what” and “where” processing by the primate visual cortex. If “where” information is serially processed in the primate auditory cortex, neurons in cortical areas along this pathway should have progressively better spatial tuning properties. This prediction is supported by recent experiments that have shown that neurons in the caudomedial field have better spatial tuning properties than neurons in the primary auditory cortex. Neurons in the caudomedial field are also better than primary auditory cortex neurons at predicting the sound localization ability across different stimulus frequencies and bandwidths in both azimuth and elevation. These data support the hypothesis that the primate auditory cortex processes acoustic information in a serial and parallel manner and suggest that this may be a general cortical mechanism for sensory perception.

The evolution of emergent computation.

A simple evolutionary process can discover sophisticated methods for emergent information processing in decentralized spatially extended systems. The mechanisms underlying the resulting emergent computation are explicated by a technique for analyzing particle-based logic embedded in pattern-forming systems. Understanding how globally coordinated computation can emerge in evolution is relevant both for the scientific understanding of natural information processing and for engineering new forms of parallel computing systems.

The universal ancestor

A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when “genetic temperatures” were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell “crystallized,” i.e., became refractory to lateral gene transfer, at different stages of “cooling,” with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

An alternative pathway for rod signals in the rodent retina: Rod photoreceptors, cone bipolar cells, and the localization of glutamate receptors

In the mammalian retina, extensive processing of spatiotemporal and chromatic information occurs. One key principle in signal transfer through the retina is parallel processing. Two of these parallel pathways are the ON- and OFF-channels transmitting light and dark signals. This dual system is created in the outer plexiform layer, the first relay station in retinal signal transfer. Photoreceptors release glutamate onto ON- and OFF-type bipolar cells, which are functionally distinguished by their postsynaptic expression of different types of glutamate receptors, namely ionotropic and metabotropic glutamate receptors. In the current concept, rod photoreceptors connect only to rod bipolar cells (ON-type) and cone photoreceptors connect only to cone bipolar cells (ON- and OFF-type). We have studied the distribution of (RS)-α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptor subunits at the synapses in the outer plexiform layer of the rodent retina by immunoelectron microscopy and serial section reconstruction. We report a non-classical synaptic contact and an alternative pathway for rod signals in the retina. Rod photoreceptors made synaptic contact with putative OFF-cone bipolar cells that expressed the AMPA glutamate receptor subunits GluR1 and GluR2 on their dendrites. Thus, in the retina of mouse and rat, an alternative pathway for rod signals exists, where rod photoreceptors bypass the rod bipolar cell and directly excite OFF-cone bipolar cells through an ionotropic sign-conserving AMPA glutamate receptor.

Microevolutionary responses in experimental populations of plants to CO2-enriched environments: parallel results from two model systems.

Despite the critical role that terrestrial vegetation plays in the Earth's carbon cycle, very little is known about the potential evolutionary responses of plants to anthropogenically induced increases in concentrations of atmospheric CO2. We present experimental evidence that rising CO2 concentration may have a direct impact on the genetic composition and diversity of plant populations but is unlikely to result in selection favoring genotypes that exhibit increased productivity in a CO2-enriched atmosphere. Experimental populations of an annual plant (Abutilon theophrasti, velvetleaf) and a temperate forest tree (Betula alleghaniensis, yellow birch) displayed responses to increased CO2 that were both strongly density-dependent and genotype-specific. In competitive stands, a higher concentration of CO2 resulted in pronounced shifts in genetic composition, even though overall CO2-induced productivity enhancements were small. For the annual species, quantitative estimates of response to selection under competition were 3 times higher at the elevated CO2 level. However, genotypes that displayed the highest growth responses to CO2 when grown in the absence of competition did not have the highest fitness in competitive stands. We suggest that increased CO2 intensified interplant competition and that selection favored genotypes with a greater ability to compete for resources other than CO2. Thus, while increased CO2 may enhance rates of selection in populations of competing plants, it is unlikely to result in the evolution of increased CO2 responsiveness or to operate as an important feedback in the global carbon cycle. However, the increased intensity of selection and drift driven by rising CO2 levels may have an impact on the genetic diversity in plant populations.