Flood-Plain and Channel Aggradation at Selected Bridge Sites in the Iowa and Skunk River Basins, Iowa, HR-350, 1996

Flood-plain and channel-aggradation rates were estimated at selected bridge sites in central and eastern Iowa using four aggradation-measurement methods. Aggradation rates were quantified at 10 bridge sites on the Iowa River upstream of Coralville Lake and at two bridge sites in the central part of Skunk River Basin. Measurement periods used to estimate average aggradation rates ranged in length from 1 to 98 years and varied among methods and sites. A direct comparison cannot be made between aggradation rates calculated using each of the four measurement methods because of differences in time periods and aggradational processes that were measured by each method.

Which anatomical sites should be sampled for screening of methicillin-resistant Staphylococcus aureus carriage by culture or by rapid PCR test?

The nose is the anatomical site usually recommended for methicillin-resistant Staphylococcus aureus (MRSA) screening. Other sites are also recommended, but are more controversial. We showed that the sensitivities of MRSA detection from nasal swabs alone were 48% and 62% by culture or by rapid PCR test, respectively. These percentages increased to 79% and 92% with the addition of groin swabs, and to 96% and 99% with the addition of groin and throat swabs. In conclusion, neither by culture nor by rapid PCR test is nose sampling alone sufficient for MRSA detection. Additional anatomical sites should include at least the groin and throat.

High-magnification vascular imaging to reject false-positive sites in situ during Hexvix® fluorescence cystoscopy

Fluorescence imaging for detection of non-muscle-invasive bladder cancer is based on the selective production and accumulation of fluorescing porphyrins-mainly, protoporphyrin IX-in cancerous tissues after the instillation of Hexvix®. Although the sensitivity of this procedure is very good, its specificity is somewhat limited due to fluorescence false-positive sites. Consequently, magnification cystoscopy has been investigated in order to discriminate false from true fluorescence positive findings. Both white-light and fluorescence modes are possible with the magnification cystoscope, allowing observation of the bladder wall with magnification ranging between 30× for standard observation and 650×. The optical zooming setup allows adjusting the magnification continuously in situ. In the high-magnification (HM) regime, the smallest diameter of the field of view is 600 microns and the resolution is 2.5 microns when in contact with the bladder wall. With this cystoscope, we characterized the superficial vascularization of the fluorescing sites in order to discriminate cancerous from noncancerous tissues. This procedure allowed us to establish a classification based on observed vascular patterns. Seventy-two patients subject to Hexvix® fluorescence cystoscopy were included in the study. Comparison of HM cystoscopy classification with histopathology results confirmed 32/33 (97%) cancerous biopsies and rejected 17/20 (85%) noncancerous lesions.

Variation in soil nutrient concentrations and bulk density within peatland forest sites

Abstract

Missouri River Flood Coordination Task Force Report, September 25, 2011

The Missouri River floods of 2011 will go down in history as the longest duration flooding event this state has seen to date. The combination of above normal snowfall in the upper Missouri River basin followed by the equivalent of nearly one year’s worth of rainfall in May created an above normal runoff situation which filled the Missouri River and the six main reservoirs within the basin. Compounding this problem was colder than normal temperatures which kept much of the snow pack in the upper basin on the ground longer into the spring, setting the stage for this historic event.

Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors.

BACKGROUND: To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanisms of target gene regulation by human estrogen receptor alpha (hERalpha), we combine extensive location and expression datasets with genomic sequence analysis. In particular, we study the influence of patterns of DNA occupancy by hERalpha on expression phenotypes. RESULTS: We find that strong ChIP-chip sites co-localize with strong hERalpha consensus sites and detect nucleotide bias near hERalpha sites. The localization of ChIP-chip sites relative to annotated genes shows that weak sites are enriched near transcription start sites, while stronger sites show no positional bias. Assessing the relationship between binding configurations and expression phenotypes, we find binding sites downstream of the transcription start site (TSS) to be equally good or better predictors of hERalpha-mediated expression as upstream sites. The study of FOX and SP1 cofactor sites near hERalpha ChIP sites shows that induced genes frequently have FOX or SP1 sites. Finally we integrate these multiple datasets to define a high confidence set of primary hERalpha target genes. CONCLUSION: Our results support the model of long-range interactions of hERalpha with the promoter-bound cofactor SP1 residing at the promoter of hERalpha target genes. FOX motifs co-occur with hERalpha motifs along responsive genes. Importantly we show that the spatial arrangement of sites near the start sites and within the full transcript is important in determining response to estrogen signaling.

Coordination between zinc and phosphate homeostasis involves the transcription factor PHR1, the phosphate exporter PHO1, and its homologue PHO1;H3 in Arabidopsis.

Interactions between zinc (Zn) and phosphate (Pi) nutrition in plants have long been recognized, but little information is available on their molecular bases and biological significance. This work aimed at examining the effects of Zn deficiency on Pi accumulation in Arabidopsis thaliana and uncovering genes involved in the Zn-Pi synergy. Wild-type plants as well as mutants affected in Pi signalling and transport genes, namely the transcription factor PHR1, the E2-conjugase PHO2, and the Pi exporter PHO1, were examined. Zn deficiency caused an increase in shoot Pi content in the wild type as well as in the pho2 mutant, but not in the phr1 or pho1 mutants. This indicated that PHR1 and PHO1 participate in the coregulation of Zn and Pi homeostasis. Zn deprivation had a very limited effect on transcript levels of Pi-starvation-responsive genes such as AT4, IPS1, and microRNA399, or on of members of the high-affinity Pi transporter family PHT1. Interestingly, one of the PHO1 homologues, PHO1;H3, was upregulated in response to Zn deficiency. The expression pattern of PHO1 and PHO1;H3 were similar, both being expressed in cells of the root vascular cylinder and both localized to the Golgi when expressed transiently in tobacco cells. When grown in Zn-free medium, pho1;h3 mutant plants displayed higher Pi contents in the shoots than wild-type plants. This was, however, not observed in a pho1 pho1;h3 double mutant, suggesting that PHO1;H3 restricts root-to-shoot Pi transfer requiring PHO1 function for Pi homeostasis in response to Zn deficiency.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Adsorption of glyphosate in chilean soils and its relationship with unoccupied phosphate binding sites

The objective of this work was to investigate glyphosate adsorption by soils and its relationship with unoccupied binding sites for phosphate adsorption. Soil samples of three Chilean soils series - Valdivia (Andisol), Clarillo (Inceptisol) and Chicureo (Vertisol) - were incubated with different herbicide concentrations. Glyphosate remaining in solution was determined by adjusting a HPLC method with a UV detector. Experimental maximum adsorption capacity were 15,000, 14,300 and 4,700 mg g¹ for Valdivia, Clarillo, and Chicureo soils, respectively. Linear, Freundlich, and Langmuir models were used to describe glyphosate adsorption. Isotherms describing glyphosate adsorption differed among soils. Maximum adjusted adsorption capacity with the Langmuir model was 231,884, 17,874 and 5,670 mg g-1 for Valdivia, Clarillo, and Chicureo soils, respectively. Glyphosate adsorption on the Valdivia soil showed a linear behavior at the range of concentrations used and none of the adjusted models became asymptotic. The high glyphosate adsorption capacity of the Valdivia soil was probably a result of its high exchangeable Al, extractable Fe, and alophan and imogolite clay type. Adsorption was very much related to phosphate dynamics in the Valdivia soil, which showed the larger unoccupied phosphate binding sites. However relationship between unoccupied phosphate binding sites and glyphosate adsorption in the other two soils (Clarillo and Chicureo) was not clear.

2014 Transportation Coordination in Iowa

The 2012 Iowa Code section 324A.4, subsection 2, states the Iowa Department of Transportation (DOT) “shall biennially prepare a report to be submitted to the general assembly and the governor prior to December 15 of even-numbered years. The report shall recommend methods to increase transportation coordination and improve the efficiency of federal, state, and local government programs used to finance public transit services and may address other topics as appropriate.” Iowa has long been a leader in transportation coordination, from designated public transit agencies covering all 99 counties with little duplication, to requiring any agency receiving public dollars for the provision of transportation to first coordinate with the local public transit agency before providing the transportation on their own, to the creation of the Iowa Transportation Coordination Council. Coordination allows Iowa to provide much needed transportation services to the citizens of Iowa with the most efficient use of public funds. Coordination has been an important topic in Iowa for many years, but during these times of economic constraint and restraint and Iowa’s changing demographics, coordination of transportation services becomes even more critical.

Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), beta-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.

Multi-Purpose ESS/ITS Data Collection Sites, SPR72-00-0003-042, 2014

This document presents the results of a state-of-practice survey of transportation agencies that are installing intelligent transportation sensors (ITS) and other devices along with their environmental sensing stations (ESS) also referred to as roadway weather information system (RWIS) assets.