Targeted identification of genomic regions using TAGdb

Background

The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes.

Results

We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.

Conclusions

The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.     

Efficacy of Hyperimmunized Plasma in the Treatment of Horses with Acute Colitis

Colitis in the adult horse is a life-threatening clinical condition that can be caused by any of several enteric pathogens. This study was conducted to determine whether treating horses with plasma obtained from donors that were hyperimmunized against the common equine diarrheal pathogens Clostridium difficile, Clostridium perfringens, and Salmonella sp shortens the duration of diarrhea in acute colitis. To evaluate the efficacy of plasma treatment, 42 horses with acute onset of diarrhea were studied. Horses were enrolled if they were of age >1 year, duration of diarrhea at presentation was <72 hours, and they had not received equine plasma within the last 3 months. In addition, the serum cortisol concentrations of horses with acute diarrhea were studied.Horses were randomized to receive hyperimmunized plasma, control plasma (collected from nonimmunized horses), or no plasma therapy. Clinical parameters and fecal consistency were observed until resolution, discharge, or death, and complete blood counts (CBCs) and biochemical profiles were collected throughout the study. A total of 38 horses completed the study. The mean duration of diarrhea was 40.7 ± 9.8 (mean ± SEM) hours, 119.2 ± 56.1 hours, and 72.0 ± 24.5 hours for the hyperimmunized plasma, normal plasma (NP), and control groups, respectively. Using survival analysis techniques, this difference did not achieve statistical significance (P = .374). Serum cortisol was found to be increased in all horses at presentation and to decrease with time in all treatment groups. There was no difference in cortisol concentrations between the three treatment groups studied (P = .237).     

Biofortification of tomato (Solanum lycopersicum) fruit with the anticancer compound methylselenocysteine using a selenocysteine methyltransferase from a selenium hyperaccumulator

Methylselenocysteine (MeSeCys) is an amino acid derivative that possesses potent anticancer activity in animals. Plants that can tolerate growth on soils with high Se content, known as Se hyperaccumulators, do so by converting inorganic Se to MeSeCys by the enzyme selenocysteine methyltransferase (SMT). A cDNA encoding the SMT from a Se hyperaccumulator was overexpressed in tomato (Solanum lycopersicum). Transgenic plants were provided with selenite or selenate to the roots during fruit development, and liquid chromatography-mass spectrometry was used to show that MeSeCys accumulated in the fruit but not in the leaves. Depending on the transgenic line and Se treatment, up to 16% of the total Se in the fruit was present as MeSeCys. MeSeCys was produced more effectively from selenite on a percentage conversion basis, but greater accumulation of MeSeCys could be achieved from selenate due to its better translocation from the roots. MeSeCys was heat stable and survived processing of the fruit to tomato juice.     

Norsesquiterpene glycosides in bracken ferns (Pteridium esculentum and Pteridium aquilinum subsp. wightianum) from Eastern Australia: reassessed poisoning risk to animals

Austral bracken Pteridium esculentum contains three unstable norsesquiterpene glycosides: ptaquiloside, ptesculentoside, and caudatoside, in variable proportions. The concentration of each of the glycosides was determined in this study as their respective degradation products, pterosin B, pterosin G and pterosin A, by HPLC-UV analysis. Samples of P. esculentum collected from six sites in eastern Australia contained up to 17 mg of total glycoside/g DW, with both ptaquiloside and ptesculentoside present as major components accompanied by smaller amounts of caudatoside. Ratios of ptaquiloside to ptesculentoside varied from 1:3 to 4:3, but in all Australian samples ptesculentoside was a significant component. This profile differed substantially from that of P. esculentum from New Zealand, which contained only small amounts of both ptesculentoside and caudatoside, with ptaquiloside as the dominant component. A similar profile with ptaquiloside as the dominant glycoside was obtained for Pteridium aquilinum subsp. wightianum (previously P. revolutum ) from northern Queensland and also P. aquilinum from European sources. Ptesculentoside has chemical reactivity similar to that of ptaquiloside and presumably biological activity similar to that of this potent carcinogen. The presence of this additional reactive glycoside in Australian P. esculentum implies greater toxicity for consuming animals than previously estimated from ptaquiloside content alone.     

The influence of NH4 +‐N vs. NO3 ‐‐n nutrition on root reductant release by fe‐stressed sorghum 1

The effect of NH₄ ⁺ ‐N on root reduction capacity developed during Fe stress was investigated in plants grown in a CaCO₃ buffered nutrient solution. After a 3‐day period of Fe stress, reduction capacity was not increased by the presence of NH₄ ⁺ ‐N in the growth medium or in the extracting solution. Since reductant degradation over time was pH dependent, experiments measuring root reductant release into nutrient solution would be confounded by treatments with different solution pH values. In an unbuffered nutrient solution a differential NH₄ ⁺ uptake due to the cultivar would affect solution pH and interfere with a reliable interpretation of reductant measurements.     

Root reductant release as a measure of sorghum cultivar iron efficiency

Measurement of root reductant levels developed during plant Fe stress was tested as a possible assay for sorghum cultivar Fe‐efficiency screening. Iron‐stressed sorghum was shown to release reductants into CaCO₃ buffered nutrient solution; however, considerably more plants could be tested by extracting reductants from excised roots of Fe‐stressed sorghum in 35 ml of pH 3 nutrient solution and 1 mM glucose. An Fe‐efficient cultivar, RT×2536, and an Fe‐inefficient cultivar, BT×378, could be separated by measurement of reductants released into CaCO₃ buffered nutrient solution and by an excised root extraction method; however, neither method was as effective as visual rating methods.     

Cultivar response to bacterial ring rot infection in Maine

An account of several years of testing cultivars for response to bacterial ring rot (BRR) infection is reported. Inoculum was prepared by grinding infected tuber tissue and adding distilled water to make a slurry. Seedpieces of cultivars to be tested were dipped in the slurry, planted and covered immediately in the field. Five hill plots were arranged in a RCB design with four replications and cultivars of known reaction to BRR were included as checks. Assessment of symptom expressions was begun when symptoms were first observed in any entry and repeated weekly for the remainder of the growing season. Results of tests on named cultivars and a few advanced, numbered selections are presented for the years 1983 through 1986.     

Initial Experience with Norepinephrine Infusion in Hypotensive Critically III Foals

Seven critically ill foals that continued to be hypotensive despite fluid resuscitation and the infusion of dobutamine and/or dopamine were treated with an infusion of norepinephrine (noradrenaline). The norepinephrine was administered concurrently with dobutamine, and the combination therapy was titrated by use of indirect mean arterial pressure measurements. The highest dose of norepinephrine used was 1.5 mcg/kg/min. In six foals the administration of norepinephrine was associated with an increase in blood pressure. In one foal the mean arterial pressure did not increase in response to the doses of norepinephrine administered. All of the foals experienced an increase in urine output coincident with the start of the norepinephrine infusion. Three of the foal survived to hospital discharge.