Method for Estimating the Magnitude and Frequency of Floods at Ungaged Sites on Unregulated Rural Streams in Iowa, HR-268, 1987

This report provides techniques and procedures for estimating the probable magnitude and frequency of floods at ungaged sites on Iowa streams. Physiographic characteristics were used to define the boundaries of five hydrologic regions. Regional regression equations that relate the size of the drainage area to flood magnitude are defined for estimating peak discharges having specified recurrence intervals of 2, 5, 10, 25, 50, and 100 years. Regional regression equations are applicable to sites on streams that have drainage areas ranging from 0.04 to 5,150 square miles provided that the streams are not affected significantly by regulation upstream from the sites and that the drainage areas upstream from the sites are not mostly urban areas. Flood-frequency characteristics for the mainstems of selected rivers are presented in graphs as a function of drainage area.

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.

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.

Opportunity for sexual selection and effective population size in the lek-breeding European treefrog (Hyla arborea).

Sexual selection in lek-breeding species might drastically lower male effective population size, with potentially important consequences for evolutionary and conservation biology. Using field-monitoring and parental-assignment methods, we analyzed sex-specific variances in breeding success in a population of European treefrogs, to (1) help understanding the dynamics of genetic variance at sex-specific loci, and (2) better quantify the risk posed by genetic drift in this species locally endangered by habitat fragmentation. The variance in male mating success turned out to be markedly lower than values obtained from other amphibian species with polygamous mating systems. The ratio of effective breeding size to census breeding size was only slightly lower in males (0.44) than in females (0.57), in line with the patterns of genetic diversity previously reported from H. arborea sex chromosomes. Combining our results with data on age at maturity and adult survival, we show that the negative effect of the mating system is furthermore compensated by the effect of delayed maturity, so that the estimated instantaneous effective size broadly corresponded to census breeding size. We conclude that the lek-breeding system of treefrogs impacts only weakly the patterns of genetic diversity on sex-linked genes and the ability of natural populations to resist genetic drift.

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.

Provenance and family variation of Pinus caribaea var. hondurensis from Guatemala and Honduras, grown in Brazil, Colombia and Venezuela

Pinus caribaea var. hondurensis (Sénécl) Barr. & Golf. is a tropical pine that naturally occurs in lowland areas of Belize, El Salvador, Guatemala, Honduras, Nicaragua, and eastern Mexico. It has been one of the most studied tropical pines and the one with the most commercial importance in Brazil. The objective of this work was to select the best provenances for plantations and best trees in families for the establishment of seed orchards. For that a trial with five provenances and 47 open-pollinated families was planted near Planaltina, Federal District, in the Cerrado Region of Brazil. The provenances tested were Poptun (Guatemala), Gualjoco, Los Limones, El Porvenir and Santa Cruz de Yojoa (Honduras) and assessed at 12 years of age. Poptun and Gualjoco had larger volume, and Los Limones and El Porvenir the lowest incidence of forks and foxtails. Individual tree heritabilities for volume, stem form and branch diameter were 0.34, 0.06, and 0.26 respectively. More than 90% of the trees had defects, common in unimproved P. caribaea. Selection criteria for quality traits need to be relaxed in the first generation of breeding to allow for larger genetic gains in productivity. Results from this test compared with P. caribaea var. hondurensis trials in other Brazilian, Colombian and Venezuelan sites suggest that provenance x site and family x site interactions are not as strong as in other pine species.

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

Abstract

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.

Barn Owl (Tyto alba) breeding biology in relation to breeding season climate

Winter weather has a strong influence on Barn Owl (Tyto alba) breeding biology. Here, we analyzed the impacts of weather conditions on reproductive performance during the breeding season using data collected over 22 years in a Swiss Barn Owl population. Variations in rain and temperature during the breeding season played an important role in within-year variation in Barn Owl reproduction. An increase in rainfall during the period from 4 to 2 weeks preceding egg laying had a positive effect on clutch size. In contrast, fledgling body mass was negatively influenced by rainfall during the 24 h preceding the measurements. Finally, ambient temperature during the rearing period was positively associated with brood size at fledging. In conclusion, weather conditions during the breeding season place constraints on Barn Owl reproduction.

Resistance spectra of six elite breeding lines of upland rice to Pyricularia grisea

The objective of this work was to evaluate the resistance spectra of six elite breeding lines of rice, developed for improved yield and grain quality, in inoculation tests in the greenhouse and in the field. Forty-six isolates of Pyricularia grisea collected from the cultivar Primavera, 31 from the cultivar Maravilha and 19 from six elite breeding lines, totaling 96 were utilized for inoculations. Out of 11 international and 15 Brazilian pathotypes, IC-1, IB-9, and BD-16, respectively, were identified as most frequent isolates collected from the cultivar Primavera. The isolates retrieved from Maravilha belong to four international and 11 Brazilian pathotypes, the predominant ones being IB-9 and IB-49 and BB-1 and BB-21, respectively. Lines CNAs 8711 and CNAs 8983 showed resistant reaction to all test isolates from Maravilha, while CNAs 8983 was susceptible to three isolates of Primavera pertaining to the pathotype IC-1. A majority of isolates exhibiting compatible reaction to Primavera were incompatible to Maravilha and vice-versa.Field assessment of rice blast utilizing the area under disease progress curve as a criterion for measuring disease severity showed significant differences among the six breeding lines. The isolates of P. grisea exhibiting differential reaction on breeding lines can be utilized in pyramiding resistance genes in new upland rice cultivars.

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.