Horizontal gene transfer from Eukarya to Bacteria and domain shuffling: the α-amylase model

-Amylases are present in all kingdoms of the living world. Despite strong conservation of the tertiary structure, only a few amino acids are conserved in interkingdom comparisons. Animal -amylases are characterized by several typical motifs and biochemical properties. A few cases of such -amylases have been previously reported in some eubacterial species. We screened the bacterial genomes available in the sequence databases for new occurrences of animal-like -amylases. Three novel cases were found, which belong to unrelated bacterial phyla: Chloroflexus aurantiacus, Microbulbifer degradans, and Thermobifida fusca. All the animal-like -amylases in Bacteria probably result from repeated horizontal gene transfer from animals. The M. degradans genome also contains bacterial-type and plant-type -amylases in addition to the animal-type one. Thus, this species exhibits -amylases of animal, plant, and bacterial origins. Moreover, the similarities in the extra C-terminal domains (different from both the -amylase domain C and the starch-binding domain), when present, also suggest interkingdom as well as intragenomic shuffling.Received 17 October 2003; accepted 6 November 2003     

Mutations in a new member of the chromodomain gene family cause CHARGE syndrome

CHARGE syndrome is a common cause of congenital anomalies affecting several tissues in a nonrandom fashion. We report a 2.3-Mb de novo overlapping microdeletion on chromosome 8q12 identified by array comparative genomic hybridization in two individuals with CHARGE syndrome. Sequence analysis of genes located in this region detected mutations in the gene CHD7 in 10 of 17 individuals with CHARGE syndrome without microdeletions, accounting for the disease in most affected individuals.     

Active genes are tri-methylated at K4 of histone H3

Lysine methylation of histones in vivo occurs in three states: mono-, di- and tri-methyl. Histone H3 has been found to be di-methylated at lysine 4 (K4) in active euchromatic regions but not in silent heterochromatic sites. Here we show that the Saccharomyces cerevisiae Set1 protein can catalyse di- and tri-methylation of K4 and stimulate the activity of many genes. Using antibodies that discriminate between the di- and tri-methylated state of K4 we show that di-methylation occurs at both inactive and active euchromatic genes, whereas tri-methylation is present exclusively at active genes. It is therefore the presence of a tri-methylated K4 that defines an active state of gene expression. These findings establish the concept of methyl status as a determinant for gene activity and thus extend considerably the complexity of histone modifications.     

Crumbs, the Drosophila homologue of human CRB1/RP12, is essential for photoreceptor morphogenesis

The apical transmembrane protein Crumbs is a central regulator of epithelial apical-basal polarity in Drosophila. Loss-of-function mutations in the human homologue of Crumbs, CRB1 (RP12), cause recessive retinal dystrophies, including retinitis pigmentosa. Here we show that Crumbs and CRB1 localize to corresponding subdomains of the photoreceptor apical plasma membrane: the stalk of the Drosophila photoreceptor and the inner segment of mammalian photoreceptors. These subdomains support the morphogenesis and orientation of the photosensitive membrane organelles: rhabdomeres and outer segments, respectively. Drosophila Crumbs is required to maintain zonula adherens integrity during the rapid apical membrane expansion that builds the rhabdomere. Crumbs also regulates stalk development by stabilizing the membrane-associated spectrin cytoskeleton, a function mechanistically distinct from its role in epithelial apical-basal polarity. We propose that Crumbs is a central component of a molecular scaffold that controls zonula adherens assembly and defines the stalk as an apical membrane subdomain. Defects in such scaffolds may contribute to human CRB1-related retinal dystrophies.     

Exercise conditioning decreases downstream movement of pond-reared razorback suckers released into a stream environment

Despite augmentation stocking efforts, wild populations of razorback suckers ( Xyrauchen texanus ) continue to decline. Endangered razorback suckers are commonly raised in off-channel ponds until maturity (approximately 300 mm TL) and then stocked into the Colorado River or its tributaries. After fish are stocked, they commonly move large distances downstream. We conducted an experiment to determine if downstream dispersal could be reduced through exercise conditioning. Two groups of razorback suckers, exercised and nonexercised, were released into Fossil Creek, Arizona. Prior to release, a subsample from each treatment group was tested in a laboratory flow chamber. Razorback suckers that had been exercise conditioned were able to maintain a position in the flow chamber 2 times longer and at velocities 25 cm · s –1 higher than nonexercised fish. Although the intended method of field data collection via passive-integrated-transponder (PIT) antennas and a remote communication station failed because river otters ( Lontra canadensis ) preyed upon the released razorback suckers, implanted PIT tags were retained in otter scat. Recovered PIT tags enabled distributional analysis, which indicated that exercised razorback suckers did not move as far downstream from the point of release as nonexercised razorbacks. Exercise conditioning may increase overall fitness of pond-reared razorback suckers, and, consequently, increase the effectiveness of augmentation stocking. A pesar de los esfuerzos de repoblación, las poblaciones silvestres del matalote jorobado ( Xyrauchen texanus ) siguen en declive. Los matalotes jorobados, que están en peligro de extinción, se crían en estanques fuera del cauce hasta la etapa adulta (~300 mm) y después son liberados en el Río Colorado o uno de sus afluentes. Los peces suelen desplazarse largas distancias río abajo después de su introducción al río. Llevamos a cabo un experimento para determinar si la dispersión río abajo se podía reducir mediante el acondicionamiento por ejercicio. Dos grupos de matalotes fueron liberados en Fossil Creek, Arizona, uno que había sido acondicionado y otro que no. Antes de liberarlos, examinamos una submuestra de cada grupo en una cámara de flujo en el laboratorio. Los matalotes que habían sido acondicionados por ejercicio pudieron mantener sus posición en la cámara de flujo dos veces más tiempo y a velocidades de 25 cm · s –1 más altas que los peces no acondicionados. Aunque falló el método de colecta de datos mediante antenas de sistema PIT (passive integrated transponder) y una estación remota de comunicación, los matalotes liberados fueron depredados por nutrias de río ( Lontra canadensis ) y las marcas PIT implantadas se quedaron en las heces de las nutrias. La recuperación de estas etiquetas PIT permitió un análisis de distribución que indicó que los matalotes acondicionados no se desplazaron río abajo tan lejos del punto de liberación como los matalotes no acondicionados. El acondicionamiento por ejercicio podría mejorar la condición física de los matalotes jorobados criados en cautiverio y así aumentar la eficacia de la reintroducción.     

Controlling performance of bluebunch wheatgrass and spotted knapweed using nitrogen and sucrose amendments

Range- and wildlands are being invaded by nonindigenous plants, resulting in an unprecedented, rapid change in plant community composition across the United States. Successional management predicts that species performance may be modified by resource availability. The objective of this study was to determine whether species performance could be altered by modifying soil nitrate (NO 3 – ) and ammonium (NH 4 + ) concentrations within an Idaho fescue ( Festuca idahoensis )/bluebunch wheatgrass ( Pseudoroegneria spicata ) plant association. We planted bluebunch wheatgrass and spotted knapweed ( Centaurea maculosa ) in an addition series at 2 sites in southwestern Montana. Each plot in the addition series matrix was divided into thirds, and we applied nitrogen (N) to a subplot and sucrose to a 2nd subplot. The remaining subplot was not amended and considered a control. Nitrogen amendment tended to enhance the performance of spotted knapweed, while sucrose amendment had no effect. Bluebunch wheatgrass performance was not affected by either amendment. Sucrose treatments only decreased soil NO 3 – at the more productive site. Regression models for predicting bluebunch wheatgrass and spotted knapweed biomass accounted for only about 30% of the variation, suggesting other processes in addition to interference were responsible for explaining relative plant perfor - mance. We recommend that land managers prevent activities that increase soil N concentration while the effectiveness of carbon amendments as a means to decrease soil N concentrations and shift interference relationships is further investigated.     

Action Research: Its Role in the University/Business Relationship

The Action Research (AR) PhD program at Monash University had its genesis in Systems Thinking and Organizational Learning. This paper discusses the role of the university in AR projects in business and the central role that AR projects can have in a Faculty's strategic positioning. The issues that have emerged in the project to date are discussed.     

The Jurassic-Cretaceous transition of Southern Sweden—palynological and sedimentological interpretation

Palynological studies on the Vitab?ck Clay help resolve the position of the Jurassic-Cretaceous boundary in southern Sweden. Well-preserved assemblages of terrestrial pollen and spores, together with abundant algae (Botryococcus), and for the first time, dinoflagellates have been identified in the Vitab?ck Clay. A Berriasian age is corroborated for the Vitab?ck Clay based on the palynological data; the Jurassic-Cretaceous boundary being placed around the contact of this unit with the underlying “Nytorp Sand”. The terrestrial vegetation was dominated by coniferous forest with an understorey of ferns in a warm, temperate climate. The palynoflora shows compositional similarities to the Northern Chinese Floral Province and especially the Jehol Group. The majority of the Vitab?ck Clay represents a moderate-to low-energy paralic succession. However, the basal part of the unit incorporates anomalously coarse material of mixed terrestrial and marine origin. This sedimentary package is herein interpreted to represent tsunami deposits and is similar to coeval tsunami-related deposits in France.