The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties.

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties.

Iowa Historic Property Study: Iowa-Illinois Memorial Bridge Carrying I-74 and U.S. 6 over Mississippi River between Bettendorf, Scott County, Iowa and Moline, Rock Island County, Illinois, 2012

The 1935 Iowa-Illinois Memorial Bridge is being documented at this time to fulfill the requirements of the Memorandum of Agreement regarding the removal of the Iowa-Illinois Memorial Bridge and the Iowana Farms Milk Company Building for the proposed improvements to Interstate 7 4 in Bettendorf, Iowa, and Moline, Illinois.1 The 1959 twin suspension bridge will be removed as well, but it was determined to be ineligible for the National Register of Historic Places. Discussion of the history of the 1959 twin span is included, however, in the current report as part of the overall history of the Iowa-Illinois Memorial Bridge. Fieldwork for the documentation occurred in November 2009 and October 2010 (Fig. 1). Limitations on photography included limited shoreline access on the Illinois side, making good views of the bridge from the south somewhat challenging. Also, photographs on the bridge deck were not possible because of interstate traffic and prohibitions on pedestrian traffic. Within the last few years, online primary sources have proliferated, along with historical materials regarding the Iowa-Illinois Memorial Bridge. Sources available online for this report included numerous historical photographs, as well as historical Davenport, Iowa, and U.S. newspapers that document the bridge planning and construction. Additional primary source material was found at the University of Iowa Libraries, the State Historical Society of Iowa in Iowa City, the Bettendorf Public Library, the Richardson-Sloane Special Collections Center at the Davenport Public Library, and the Iowa State University Special Collections in Ames.

Geohydrology of Muscatine Island, Muscatine County, Iowa, 1977

The availability of large quantities of high-quality ground water from the Muscatine Island aquifer has had a tremendous impact upon urban, industrial and agricultural development of this part of Iowa. Although the nonpumping level of water has been lowered significantly near major pumping centers through time, proper management of this water resource can assure a continued supply of water for all competing users. This report provides basic information for long range management. Fold out maps are included.

A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system.

BACKGROUND: The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs). RESULTS: On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two identical gly-tRNA genes in tandem are present at the proximal end of this genetic element. Several mobility genes encoding transposases and bacteriophage-related proteins are located within this chromosome region. Thus, this region largely fulfills the criteria of GIs. The G+C content analysis shows that several modules compose this GI. Surprisingly, one of them encodes all genes essential for F-like conjugative DNA transfer (traF, traG, traH, traN, traU, traW, and trbC), involved in sex pilus retraction and mating pair stabilization, strongly suggesting that, similarly to the other F-like operons, the parachlamydial tra unit is devoted to DNA transfer. A close relatedness of this tra unit to F-like tra operons involved in conjugative transfer is confirmed by phylogenetic analyses performed on concatenated genes and gene order conservation. These analyses and that of gly-tRNA distribution in 140 GIs suggest a proteobacterial origin of the parachlamydial tra unit. CONCLUSIONS: A GI of the UWE25 chromosome encodes a potentially functional F-like DNA conjugative system. This is the first hint of a putative conjugative system in chlamydiae. Conjugation most probably occurs within free-living amoebae, that may contain hundreds of Parachlamydia bacteria tightly packed in vacuoles. Such a conjugative system might be involved in DNA transfer between internalized bacteria. Since this system is absent from the sequenced genomes of Chlamydiaceae, we hypothesize that it was acquired after the divergence between Parachlamydiaceae and Chlamydiaceae, when the Parachlamydia-related symbiont was an intracellular bacteria. It suggests that this heterologous DNA was acquired from a phylogenetically-distant bacteria sharing an amoebal vacuole. Since Parachlamydiaceae are emerging agents of pneumonia, this GI might be involved in pathogenicity. In future, conjugative systems might be developed as genetic tools for Chlamydiales.

A Study of Fine Sand from Nine Mile Island at Dubuque, MLR-88-08, 1988

The specifications for concrete sand in Iowa have been used for many years with very good results. In several locations of the state, it is becoming more difficult to produce concrete sand consistently at a reasonable cost. Both ASTM and AASHTO have specifications for concrete sands that allow a finer, poorer graded sand than the Iowa specification. The ASTM and AASHTO specifications are based on the use of trial mix testing prior to construction. Iowa does not currently use the trial mix procedure.

M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island.

BACKGROUND: The increasing number of completely sequenced bacterial genomes allows comparing their architecture and genetic makeup. Such new information highlights the crucial role of lateral genetic exchanges in bacterial evolution and speciation. RESULTS: Here we analyzed the twelve sequenced genomes of Streptococcus pyogenes by a naïve approach that examines the preferential nucleotide usage along the chromosome, namely the usage of G versus C (GC-skew) and T versus A (TA-skew). The cumulative GC-skew plot presented an inverted V-shape composed of two symmetrical linear segments, where the minimum and maximum corresponded to the origin and terminus of DNA replication. In contrast, the cumulative TA-skew presented a V-shape, which segments were interrupted by several steep slopes regions (SSRs), indicative of a different nucleotide composition bias. Each S. pyogenes genome contained up to nine individual SSRs, encompassing all described strain-specific prophages. In addition, each genome contained a similar unique non-phage SSR, the core of which consisted of 31 highly homologous genes. This core includes the M-protein, other mga-related factors and other virulence genes, totaling ten intrinsic virulence genes. In addition to a high content in virulence-related genes and to a peculiar nucleotide bias, this SSR, which is 47 kb-long in a M1GAS strain, harbors direct repeats and a tRNA gene, suggesting a mobile element. Moreover, its complete absence in a M-protein negative group A Streptococcus natural isolate demonstrates that it could be spontaneously lost, but in vitro deletion experiments indicates that its excision occurred at very low rate. The stability of this SSR, combined to its presence in all sequenced S. pyogenes sequenced genome, suggests that it results from an ancient acquisition. CONCLUSION: Thus, this non-phagic SSR is compatible with a pathogenicity island, acquired before S. pyogenes speciation. Its potential excision might bear relevance for vaccine development, because vaccines targeting M-protein might select for M-protein-negative variants that still carry other virulence determinants.

Models for vertical wood density of Scots pine, Norway spruce and birch stems, and their application to determine average wood density

Abstract

Natural development of stand structure in peatland Scots pine following drainage : results based on long-term monitoring of permanent sample plots

Abstract

Statistical properties of population differentiation estimators under stepwise mutation in a finite island model.

Microsatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is R(ST) which is independent of the mutation rate under a generalized stepwise mutation model. F(ST) and R(ST) are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual-based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining R(ST) over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While R(ST) better reflects population differentiation in populations characterized by very low gene-exchange, F(ST) gives better estimates in cases of high levels of gene flow. The number of loci sampled (12, 24, or 96) has only a minor effect on the relative performance of the estimators under study. For all estimators there is a striking effect of the number of samples, with the differentiation estimates showing very odd distributions for two samples.

Height distributions of Scots pine sapling stands affected by retained tree and edge stand competition

Abstract

Natural regeneration of Scots pine and Norway spruce close to the timberline in northern Finland

Abstract

Colonization by mites of glacier-free areas in King George Island, Antarctica

This work aimed to investigate the ratio of colonization by terrestrial mites on ice-free areas created by the ongoing climate-induced melting of Antarctic glaciers. Glacier retreat opens new ice-free areas for the colonization by vegetation and animals. The study was undertaken on the Antarctic Specially Protected Area no. 128 (West Coast of the Admiralty Bay, King George Island, South Shetlands Islands). Transects marked between the Ecology, Baranowski and Windy Glaciers, and a sea shore were used to collect soil samples. Oribatid mites were found only on near-shore areas, on patches of vegetation of more than 30 years of age. The colonization by mite communities is strongly determined by the presence of plants.

Community structures of soil animals and survival of land snails on an island of the Ogasawara Archipelago

On Chichijima, one of the Ogasawara (Bonin) Islands located in the Western Pacific Ocean, land snails have declined, the suggested cause being predation pressure by an invasive flatworm (Platydemus manokwari). Soil fauna were investigated in areas where the snail survives, and where it has become extinct. Much of the fauna, dominated by introduced earthworms and ants, was undiminished, however, one undescribed but endemic carabid (Badister sp.), which selectively feeds on land snails, was absent in snail-extinct areas. The invasive flatworm P. manokwari has been reported to feed also on the carcasses of earthworms, as well as on live snails, and is therefore expected to occur in most parts of Chichijima Island. Among other groups, the density of isopods (also dominated by exotic species) was very low, in comparison with the reported ones 30 years ago. Community structure is currently reflected by dominance of earthworms and ants, decline of endemic isopods, and a high frequency of introduced or alien species.