Effects of Patch-Burn Management on Dickcissel Nest Success in a Tallgrass Prairie

Abstract Grassland birds have declined more than any other North American habitat-associated bird community. Because most species of grassland birds evolved within heterogeneous landscapes created by the interaction of fire and grazing, traditional rangeland management that promotes homogeneity, including annual dormant-season burning combined with early-intensive grazing, might be partly responsible for these declines, especially in some regions of the Great Plains, USA. Recently, an alternative grassland management practice known as patch-burning has been promoted as a means of restoring heterogeneity to grasslands by mimicking the grazing-fire interaction that once occurred on the prairie before European settlement. From 2003 to 2004, we examined effects of patch-burning and traditional management (annual burning followed by early-intensive grazing) on the reproductive success of dickcissels (Spiza americana) in tallgrass prairie in Oklahoma. We monitored 296 dickcissel nests and found that dickcissel nesting phenology differed between traditional and patch-burned pastures. Specifically, dickcissels tended to initiate their nests later in the traditional pasture. Mean number of eggs laid and fledglings produced were similar between the treatments, but nest densities were higher in traditional pastures. Predation was the predominant cause of nest failure and was higher in traditional pastures than in patch-burned pastures. Brown-headed cowbird (Molothrus ater) parasitism was higher in traditional pastures than in patch-burned pastures. Overall, dickcissel nest success was higher in patch-burned pastures than in traditional pastures. The positive response of dickcissel nest success to patch-burn management provides further evidence that this practice can be a useful tool for grassland bird conservation. By creating a mosaic of different stature vegetation, patch-burn management enhances productivity of grassland bird species by providing a refuge area in the unburned patches that affords dickcissels and other nesting grassland birds some protection from the direct (e.g., trampling) and indirect (e.g., cowbird parasitism and predation) effects of grazing, which are not available under traditional management. Patch-burn management should be encouraged as a conservation strategy for grassland birds throughout the Great Plains.     

A three-dimensional model of the U1 small nuclear ribonucleoprotein particle

Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes.     

Intestinal Transit Time During Infection with Eimeria nieschulzi in Rats*

SYNOPSIS. Experiments were designed to test whether or not intestinal transit time increases significantly during severe coccidiosis in the rat. Intraduodenal catheters were surgically implanted into 25 rats. Six to 12 days after surgery 11 rats were inoculated orally with 10⁴ sporulated oocysts of Eimeria nieschulzi Dieben, and 11 were inoculated with 10⁶ oocysts; 3 rats were retained as uninfected controls. At 2, 4, 8, 9, and 16 days postinoculation (PI) Na₂⁵¹CrO₄ was injected through the catheter into the duodenum of fasted rats and allowed to progress through the small bowel for 15 min, at which time the rats were killed. The distribution of ⁵¹Cr in the gut was plotted as a function of gut length. The leading edge of radioactivity traversed 70% of the gut length in controls, and ～ 50–60% in parasitized rats on days 2, 4, 8, and 9 PI. Also, a reflux of gut contents, as evidenced by radioactivity in the stomach, occurred early (PI days 2 & 4) in rats infected with 10⁴ oocysts and throughout patency in rats infected with 10⁶ oocysts. A 2nd study was undertaken to determine if chemically induced suppression of gut transit time during early infection would enhance infectivity as measured by increased parasite fecundity. Nine rats were injected subcutaneously with an antidiarrheal agent, Loperamide®, known to slow small bowel motility significantly. Another group of 9 control rats was injected with the ethanol-propylene glycol solvent. Ten min after injection, all rats were inoculated per os with 10⁴E. nieschulzi oocysts. The daily number of oocysts discharged/rat was followed from PI days 5–11. Patency began for all rats on PI day 7. The total number of oocysts discharged by the drugged rats as compared with controls was not significantly different.     

STUDIES ON THE PRODUCTION AND PHYSIOLOGICAL EFFECTS OF ASYMMETRIN

In shake-flask culture asymmetrin was produced by PenicIlliumthomiiaud Byssochlamys niveaduring autolysis. A bioassay wasdevised to estimate relative concentrations of this compound.Culture filtrates of P. thomiicontaining asymmetrin caused adecrease in wet weight, dry weight, and total nitrogen of Phaseolusvulgarisup to 18 days after treatment. At certain intervalsafter treatment with culture filtrate of B. nivea,respirationwas inhibited, and changes were observed in isotope ratio valuesof plants supplied with glucose-¹⁴ C. Plants treated previouslywith culture filtrates of B. nivearesponded but little to gibberelhcacid. High concentrations of mdoleacetic acid inhibited growthof control plants but stimulated growth of plants treated withculture filtrate of B. nivea. ¹Present address: United Fruit Company, Norwood, Massachusetts.Supported in part by a Public Health Service Fellowship No.GF 13,776 from the division of General Medical Sciences, PublicHealth Service, National Institutes of Health, and Grant G 20989from the National Science Foundation. ²Journal Paper No. 2170 of the Purdue Agricultural ExperimentStation.     

Protein and Ribonucleic Acid Synthesis by Plant Mitochondrial Systems

The incorporation of ¹⁴C-labelled phenylalanine into proteins of the mitochondrial systems obtained from 48-h germinating seeds of Vigna sinensis (L.) Savi can be stimulated by polyuridylic acid [poly (U)] and depressed by rifampicin, which is, however, ineffective if poly (U) is allowed to interact with the incorporating system before the antibiotic has access to it. A system consisting of a mitochondrial S-100 fraction and ribosomes from the same source with other cofactors can bring about polymerization of phenylalanine. The incorporation of ¹⁴C-labelled uracil into RNA by the plant mitochondria is greatly dependent on the exogenous addition of adenine, guanine, cytosine and also on 5-phosphoribosyl-l-pyrophosphate (5-PRPP). It is greatly suppressed by rifampicin and ethidium bromide.     

Endemic evolutionary radiation of Rhagada land snails (Pulmonata: Camaenidae) in a continental archipelago in northern Western Australia

In the Dampier Archipelago of Western Australia's Pilbara Region, several locally endemic, morphologically distinctive species of Rhagada land snails occur, contrasting with the morphologically conservative species with wider distributions on the adjacent mainland. To test alternative origins of this unusual local diversity in a continental archipelago, we examined sequences of the cytochrome oxidase subunit 1 and 16S mitochondrial genes in 22 described species and eight undescribed forms, including all known morphospecies from the Pilbara Region's Dampier Archipelago and adjacent mainland. Phylogenetic analyses consistently resolved four, deep clades within the Pilbara Region, with a mean sequence divergence of 15–18%. All but one of the species from the Dampier Archipelago formed one of the major clades, indicating that the morphological radiation in the archipelago evolved locally, rather than through multiple, relictual mainland lineages. Morphological divergence spanning almost that of the entire genus was within a subclade with sequence divergence < 4%, highlighting the disconnection between morphological diversification and levels of molecular genetic divergence. This in situ morphological radiation in the Dampier Archipelago, which transcends variation seen over much larger distances on the mainland, is unusual for a continental archipelago, and may relate to local heterogeneity of land forms. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 316–327.     

C/C++ Coding for Matrix Pseudo Inverses in Clinical Near Infrared Spectroscopy

Near infrared spectroscopy is used clinically to investigate patterns of change in cerebral oxygenation. We have shown that differences reported between authors are likely the result of computer encoding errors in the manipulation of matrices. Current methods compute the inverse of a non-square matrix to derive chromophore concentration values, and solution of another non-square matrix to derive polynomial coefficients of a least squares best fit curve from which the first derivative can be used to estimate blood flow values. Encoding of these pseudo inverses involves too many nested looping steps to easily identify encoding errors. We have given C/C++ source code along with sample numerical values at the termination of each loop within the algorithm. This provides counter checking for future software development by other programmers, and also permits other investigators to report whether the software used for their experiments agrees with previously published material.