bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence
Authors: Nilsen H. , Hayes B. , Berg P. R. , Roseth A. , Sundsaasen K. K. , Nilsen K. , Lien S. 
Published: February 2008

SummaryA linkage map was constructed for bovine chromosome 6 (BTA6), using 399 single nucleotide polymorphisms (SNPs) detected primarily from PCR‐resequencing. The efficiency of SNP detection was highly dependent on the source of sequence information chosen for primer design (BAC‐end sequences, introns or promoters). The SNPs were used to build a linkage map comprising 104 cM on BTA6. The SNP order in the linkage map corresponded very well with radiation hybrid (RH) maps available for BTA6 as well as with expected positions in the human comparative map, but diverged significantly from the current assembly of the bovine genome (Btau_3.1). When performing linkage analysis with the marker order suggested from the Btau_3.1 we observed an expansion of the genetic map from 104 cM to 137 cM, strongly suggesting a reordering of scaffolds in the current version of the bovine genome assembly. The extent of LD on BTA6 was evaluated by calculating the average r2 for SNP pairs separated by given distances. The decline of LD was rapid with distance, such that r2 was 0.1 at 100 kb. Our results indicate that linkage mapping will be a valuable source of information for correcting errors in the current bovine assembly. These errors were sufficiently frequent to be of concern for the accuracy of mapping QTL with panels of SNPs whose positions are based on the current assembly.
Effects of elevated atmospheric carbon dioxide on amino acid and NH4+‐N cycling in a temperate pine ecosystem
Authors: HOFMOCKEL KIRSTEN S. , SCHLESINGER WILLIAM H. , JACKSON ROBERT B. 
Published: February 2008

AbstractRising atmospheric carbon dioxide (CO2) is expected to increase forest productivity, resulting in greater carbon (C) storage in forest ecosystems. Because elevated atmospheric CO2 does not increase nitrogen (N) use efficiency in many forest tree species, additional N inputs will be required to sustain increased net primary productivity (NPP) under elevated atmospheric CO2. We investigated the importance of free amino acids (AAs) as a source for forest N uptake at the Duke Forest Free Air CO2 Enrichment (FACE) site, comparing its importance with that of better‐studied inorganic N sources. Potential proteolytic enzyme activity was monitored seasonally, and individual AA concentrations were measured in organic horizon extracts. Potential free AA production in soils ranged from 190 to 690 nmol N g−1 h−1 and was greater than potential rates of soil NH4+ production. Because of this high potential rate of organic N production, we determined (1) whether intact AA uptake occurs by Pinus taeda L., the dominant tree species at the FACE site, (2) if the rate of cycling of AAs is comparable with that of ammonium (NH4+), and (3) if atmospheric CO2 concentration alters the aforementioned N cycling processes. A field experiment using universally labeled ammonium (15NH4+) and alanine (13C3H715NO2) demonstrated that 15N is more readily taken up by plants and heterotrophic microorganisms as NH4+. Pine roots and microbes take up on average 2.4 and two times as much NH4+ 15N compared with alanine 15N 1 week after tracer application. N cycling through soil pools was similar for alanine and NH4+, with the greatest 15N tracer recovery in soil organic matter, followed by microbial biomass, dissolved organic N, extractable NH4+, and fine roots. Stoichiometric analyses of 13C and 15N uptake demonstrated that both plants and soil microorganisms take up alanine directly, with a 13C : 15N ratio of 3.3 : 1 in fine roots and 1.5 : 1 in microbial biomass. Our results suggest that intact AA (alanine) uptake contributes substantially to plant N uptake in loblolly pine forests. However, we found no evidence supporting increased recovery of free AAs in fine roots under elevated CO2, suggesting plants will need to acquire additional N via other mechanisms, such as increased root exploration or increased N use efficiency.
Mixed‐conifer understory response to climate change, nitrogen, and fire
Authors: HURTEAU MATTHEW , NORTH MALCOLM 
Published: February 2008

AbstractCalifornia's Sierra Nevada mountains are predicted to experience greater variation in annual precipitation according to climate change models, while nitrogen deposition from pollution continues to increase. These changes may significantly affect understory communities and fuels in forests where managers are attempting to restore historic conditions after a century of altered fire regimes. The objective of this research was to experimentally test the effects of increasing and decreasing snowpack depth, increasing nitrogen, and applying prescribed fire to mixed‐conifer forest understories at two sites in the central and southern Sierra Nevada. Understory response to treatments significantly differed between sites with herb biomass increasing in shrub‐dominated communities when snowpack was reduced. Fire was a more important factor in post‐treatment species richness and cover than either snowpack addition or reduction. Nitrogen additions unexpectedly increased herbaceous species richness. These varied findings indicate that modeling future climatic influences on biodiversity may be more difficult than additive prediction based on increasing the ecosystem's two limiting growth resources. Increasing snowpack and nitrogen resulted in increased shrub biomass production at both sites and increased herb production at the southern site. This additional understory biomass has the potential to increase fuel connectivity in patchy Sierran mixed‐conifer forests, increasing fire severity and size.
Global characterization of fire activity: toward defining fire regimes from Earth observation data
Authors: CHUVIECO EMILIO , GIGLIO LOUIS , JUSTICE CHRIS 
Published: February 2008

AbstractThere is interest in the global community on how fire regimes are changing as a function of changing demographics and climate. The ground‐based data to monitor such trends in fire activity are inadequate at the global scale. Satellite observations provide a basis for such a monitoring system. In this study, a set of metrics were developed from 6 years of MODIS active fire data. The metrics were grouped into eight classes representing three axes of fire activity: density, season duration and interannual variability. These groups were compared with biophysical and human explanatory variables on a global scale. We found that more than 30% of the land surface has a significant fire frequency. The most extensive fire class exhibited high fire density, low duration and high variability and was found in boreal and tropical wet and dry environments. A high association was found between population distribution and fire persistence. Low GDP km−2 was associated with fire classes with high interannual variability and low seasonal duration. In areas with more economic resources, fires tend to be more regular and last longer. High fire duration and low interannual variability were associated with croplands, but often with low fire density. The study was constrained by the limited length of satellite data record but is a first step toward developing a comprehensive global assessment of fire regimes. However, more attention is needed by the global observing systems to provide the underpinning socio‐economic observations to better quantify and analyze the human characteristics of fire regimes.
Myxoid tumours of soft tissue: the so‐called myxoid extracellular matrix is heterogeneous in composition
Authors: Willems S M , Schrage Y M , Baelde J J , Briaire‐de Bruijn I , Mohseny A , Sciot R , Bovée J V M G , Hogendoorn P C W 
Published: February 2008

Aim: Myxoid tumours of soft tissue are characterized by their so‐called ‘myxoid’ extracellular matrix. The aim was to investigate the composition and possible function of this matrix which is poorly understood.Methods and results: Using Alcian Blue staining with and without pretreatment with hyaluronidase and application of the critical electrolyte concentration method followed by densitometry, the glycosaminoglycan composition of three different myxoid tumours was studied. The composition of glycosaminoglycans varied with tumour type and grade, despite their general characterization as myxoid tumours. Intramuscular myxoma contained similar amounts of the various glycosaminoglycans as grade I myxofibrosarcoma; grade III myxofibrosarcoma contained less hyaluronic acid and more heparan sulphate, whereas extraskeletal myxoid chondrosarcoma contained predominantly chondroitin‐4 and ‐6 sulphates. Western blot identified albumin as a major protein in tumour lysates, and its presence in the extracellular matrix and cytoplasm of the majority of tumours was demonstrated by immunohistochemistry; production of albumin by the tumour cells was confirmed by quantitative polymerase chain reaction.Conclusions: The extracellular matrix of myxoid tumours of soft tissue has a heterogeneous composition consisting of, amongst others, glycosaminoglycans and albumin, which appear to play an active role in their morphogenesis.
Synergism between entomopathogenic nematodes and Bacillus thuringiensis crops: integrating biological control and resistance management
Authors: Gassmann Aaron J. , Stock S. Patricia , Sisterson Mark S. , Carrière Yves , Tabashnik Bruce E. 
Published: February 2008

Summary

The past decade has witnessed a continual increase in the use of crops genetically modified to produce insecticidal toxins from the bacterium Bacillus thuringiensis (Bt). This presents the challenge of designing agricultural systems to manage pests and the evolution of resistance to Bt.
We tested whether entomopathogenic nematodes might act synergistically with Bt crops by killing pests in non‐Bt refuges and by increasing the fitness costs of resistance to Bt. We also tested whether insect mortality and fitness costs were affected by the cotton phytochemical gossypol.
The entomopathogenic nematode Steinernema riobrave increased the fitness cost of Bt resistance, indicating that its presence in refuges may slow pest adaptation to Bt crops. No effect on fitness costs was detected for the nematode Heterorhabditis bacteriophora. Gossypol did not alter nematode‐imposed fitness costs.
Simulation modelling supported the hypothesis that nematodes in refuges may slow resistance evolution.
The effects of gossypol on insect mortality from nematodes and nematode reproduction differed between nematode species. Gossypol increased insect mortality caused by H. bacteriophora but did not affect mortality caused by S. riobrave. Gossypol enhanced reproduction of H. bacteriophora and decreased reproduction of S. riobrave.
Synthesis and applications. Our results point to the value of developing integrated pest management strategies for Bt crops that include non‐Bt refuges in which entomopathogenic nematodes are used as a pest‐management agent. Because entomopathogenic nematodes can magnify fitness costs of Bt resistance, their presence in refuges may delay resistance by pests to Bt crops. Moreover, entomopathogenic nematodes can serve as biological control agents thereby decreasing dependence on conventional insecticides to manage pest populations in refuges.
A population genomic analysis of species boundaries: neutral processes, adaptive divergence and introgression between two hybridizing plant species
Authors: MINDER A. M. , WIDMER A. 
Published: February 2008

AbstractLittle is known about the nature of species boundaries between closely related plant species and about the extent of introgression as a consequence of hybridization upon secondary contact. To address these topics we analyzed genome‐wide differentiation between two closely related Silene species, Silene latifolia and S. dioica, and assessed the strength of introgression in sympatry. More than 300 AFLP markers were genotyped in three allopatric and three sympatric populations of each species. Outlier analyses were performed separately for sympatric and allopatric populations. Both positive and negative outlier loci were found, indicating that divergent and balancing selection, respectively, have shaped patterns of divergence between the two species. Sympatric populations of the two species were found to be less differentiated genetically than allopatric populations, indicating that hybridization has led to gene introgression. We conclude that differentiation between S. latifolia and S. dioica has been shaped by a combination of introgression and selection. These results challenge the view that species differentiation is a genome‐wide phenomenon, and instead support the idea that genomes can be porous and that species differentiation has a genic basis.
Cytogenetic and molecular characterization of the Abies alba genome and its relationship with other members of the Pinaceae
Authors: Puizina J. , Sviben T. , Krajačić‐Sokol I. , Zoldoš‐Pećnik V. , Siljak‐Yakovlev S. , Papeš D. , Besendorfer V. 
Published: February 2008

AbstractGenome size, karyotype structure, heterochromatin distribution, position and number of ribosomal genes, as well as the ITS2 sequence of the internal transcribed spacer (ITS) were analysed in silver fir (Abies alba Mill.). The analysis also included characterization of the Arabidopsis‐type of telomeric repeats in silver fir and in related species. The results were compared with results from other species of the Pinaceae, to evaluate phylogeny and chromosomal and molecular evolution in the Pinaceae. Integrated chromosomal data provided insights into chromosome and karyotype evolution in the Pinaceae. The evolutionary trend for GC‐rich heterochromatic blocks seems to involve loss of blocks that are not associated with rDNA. Similarly, numerous large blocks of interstitial plant telomeric repeats that are typical for all analysed species of the genus Pinus were not observed in the evolutionarily younger genera, such as Abies, Picea and Larix. On the contrary, the majority of telomeric sequences in these three genera appeared confined to the chromosome ends. We confirmed the current position of Abies and Tsuga in subfamily Abietoideae and the position of Pinus in the subfamily Pinoideae based on ITS2 sequences. Pseudotsuga is placed together with Larix into the subfamily Laricoideae. We conclude that the current position of the genus Picea in the subfamily Abietoideae should be reconsidered and, possibly, the genus Picea should be reclassified as a separate subfamily, Piceoideae, as recently proposed.
14‐3‐3 proteins regulate the potassium channel KAT1 by dual modes
Authors: Sottocornola B. , Gazzarrini S. , Olivari C. , Romani G. , Valbuzzi P. , Thiel G. , Moroni A. 
Published: February 2008

AbstractKAT1 is a cloned plant potassium channel belonging to the superfamily of Shaker‐like Kv channels. Previous studies have shown that 14‐3‐3 proteins significantly increase KAT1 current by modifying the channel open probability. Employing a 14‐3‐3 scavenger construct to lower the long‐term availability of endogenous 14‐3‐3 proteins, we found that 14‐3‐3 proteins not only control the voltage dependency of the channel but also the number of channels in the plasma membrane.
The apparent temperature response of leaf respiration depends on the timescale of measurements: a study of two cold climate species
Authors: Bruhn D. , Schortemeyer M. , Edwards E. J. , Egerton J. J. G. , Hocart C. H. , Evans J. R. , Ball M. C. 
Published: February 2008

AbstractProductivity and climate models often use a constant Q10 for plant respiration, assuming tight control of respiration by temperature. We studied the temperature response of leaf respiration of two cold climate species (the Australian tree Eucalyptus pauciflora and the subantarctic megaherb Pringlea antiscorbutica, both measured in a field setting) on a short timescale (minutes) during different times within a diel course, and on a longer timescale, using diel variations in ambient temperature. There were great variations in Q10 depending on measuring day, measuring time and measuring method. When Q10 was calculated from short‐term (15 min) manipulations of leaf temperature, the resulting values were usually markedly smaller than when Q10 was calculated from measurements at ambient leaf temperatures spread over a day. While for E. pauciflora, Q10 estimates decreased with rising temperature (corroborating the concept of a temperature‐dependent Q10), the opposite was the case for P. antiscorbutica. Clearly, factors other than temperature co‐regulate both leaf respiration rates and temperature sensitivity and contribute to diel and seasonal variation of respiration.
Colocalization of Androgen Binding Protein, Oxytocin Receptor, Caveolin 1 and Proliferation Marker p21 in Benign Prostate Hyperplasia
Authors: Sendemir E. , Herbert Z. , Sivukhina E. , Zermann D.‐H. , Arnold R. , Jirikowski G. F. 
Published: February 2008

SummaryAndrogen‐binding protein (ABP) and oxytocin (OT) are among the factors that control smooth muscle proliferation and tumour growth through oxytocin receptor (OTR). A close functional interaction of OTR and caveolin 1 has been shown to modulate cell growth and proliferation. We investigated samples from 10 patients (mean age 68.3) who underwent transurethral prostate resection because of benign prostate hyperplasia (BPH) by immunohistochemistry. Post‐mortem prostate samples of three young men (age 18, 28, 33) were used as controls. Tissue samples were embedded in epoxy resin and cut into serial 1 μm sections for colocalization of ABP, OTR, proliferation marker p21 and caveolin 1. ABP was found in stroma of the smooth muscle cells in all studied samples. OTR staining occurred in most of these cells in BPH while controls contained only scattered cells positive for OTR. There were no apparent differences in immunostaining for p21 while immunoreactivity for caveolin 1 was observed in most cells in BPH and only in few cells in controls. Caveolin 1 was mostly colocalized with ABP and OTR in BPH samples while controls did only occasionally show this colocalization. Our observations indicate an interaction of ABP and OTR, associated with caveolin 1, which may account in part for known non‐genomic actions of gonadal steroids. Androgen dependent prostate growth in BPH may be linked to these mechanisms.
Histological and immunohistochemical evaluation of duodenal and colonic biopsies after oral bovine lactoferrin supplementation in beagle puppies
Authors: Handl S. , Wehr U. , Zentek J. , Krammer‐Lukas S. 
Published: February 2008

SummaryLactoferrin is a natural compound in the milk of mammals and was shown to influence the intestinal micro‐flora and the immune system in mice, calves, dogs and man. The present study was carried out to investigate the effect of orally administered bovine lactoferrin (0, 30, 60 and 120 mg/kg DM feed) on the intestinal morphology and lymphocyte colonization in 36 motherless raised puppies. Endoscopic biopsies from duodenum and colon, taken in week 14, were scored histologically after staining with haematoxylin and eosin (H&E) and lymphocytes (CD3+, CD4+, CD8+) and plasma cells (IgA+, IgG+, IgM+) were enumerated after immunohistochemical staining by computer‐aided quantification. Histological scoring revealed no significant differences amongst the groups. IgG+plasma cells were reduced (p < 0.05) in the lamina propria of the colon of the 30 and the 60 mg group. The number of CD8+lymphocytes was higher (p < 0.05) in the epithelium of the colon of the lactoferrin groups. In conclusion, this study indicated only minimal effects of bovine lactoferrin on the population of selected immune cells in the gut mucosa of puppies. More investigations are needed to describe the impact of lactoferrin on the digestive physiology of puppies.
TRANSIENT RECEPTOR POTENTIAL (TRP) CHANNELS, VASCULAR TONE AND AUTOREGULATION OF CEREBRAL BLOOD FLOW
Authors: Brayden Joseph E , Earley Scott , Nelson Mark T , Reading Stacey 
Published: February 2008

SUMMARY

Members of the transient receptor potential (TRP) channel superfamily are present in vascular smooth muscle cells and play important roles in the regulation of vascular contractility.
The TRPC3 and TRPC6 channels are activated by stimulation of several excitatory receptors in vascular smooth muscle cells. Activation of these channels leads to myocyte depolarization, which stimulates Ca2+ entry via voltage‐dependent Ca2+ channels (VDCC), leading to vasoconstriction. The TRPV4 channels in arterial myocytes are activated by epoxyeicosatrienoic acids, and activation of the channels enhances Ca2+ spark and transient Ca2+‐sensitive K+ channel activity, thereby hyperpolarizing and relaxing vascular smooth muscle cells.
The TRPC6 and TRPM4 channels are activated by mechanical stimulation of cerebral artery myocytes. Subsequent depolarization and activation of VDCC Ca2+ entry is directly linked to the development of myogenic tone in vitro and to autoregulation of cerebral blood flow in vivo.
These findings imply a fundamental importance of TRP channels in the regulation of vascular smooth muscle tone and suggest that TRP channels could be important targets for drug therapy under conditions in which vascular contractility is disturbed (e.g. hypertension, stroke, vasospasm).
EFFECT OF THE ENDOTHELIN RECEPTOR ANTAGONIST CPU0213, AND ITS MODULATION BY RIFAMPIN, ON CARDIAC AND VASCULAR TISSUE FOLLOWING CHRONIC ISOPROTERENOL TREATMENT
Authors: Luo Lu , Dai De‐Zai , Dai Yin 
Published: February 2008

SUMMARY

The aim of the present study was to investigate the effects of the endothelin (ET) receptor antagonist CPU0213 on cardiac and vascular tissues after impairment by chronic isoproterenol treatment. Because rifampin reduces plasma concentrations of CPU0213, the modulation of the effects of CPU0213 by rifampin was also investigated.
Thirty rats were randomly divided into five groups as follows: (i) control; (ii) isoproterenol treated (1 mg/kg, s.c., for 10 days); (iii) isoproterenol treated with a single injection of CPU0213 (30 mg/kg, s.c., on Day 11); (iv) isoproterenol treated with a single injection of rifampin (50 mg/kg, p.o., on Day 11); and (v) isoproterenol treated with rifampin gvien 3 h before CPU0213 on Day 11. Serum concentrations of CPU0213, haemodynamic and biochemical parameters, mRNA and protein expression levels of the ETA receptor (ETAR), calstabin 2 (FKBP12.6) and sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCA2a), and vasoactivity of the thoracic aorta were determined.
Haemodynamic parameters, serum creatine phosphokinase, lactate dehydrogenase and malondialdehyde levels, mRNA and protein expression of FKBP12.6, SERCA2a and vascular responses were altered following isoproterenol treatment for 10 days. These effects were significantly reversed by CPU0213. Rifampin caused a reduction in serum concentrations of CPU0213 to 36% of control values. However, this reduction in the serum concentrations of CPU0213 did not affect its effects on the heart, but did eliminate its beneficial action on vascular responses. Rifampin alone had no effect these paramters.
The data suggest that isoproterenol acts on the myocardium to cause cardiac insufficiency by upregulating ETAR and downregulating FKBP12.6 and SERCA2a. These effects were ameliorated by CPU0213, but were resistant to rifampin‐induced decreases in plasma CPU0213 concentrations. In vascular tissue, the pathological effects of isoproterenol were ameliorated by CPU0213; however, lowering plasma CPU0213 concentrations with rifampin did partly eliminate the amelioration in vascular activity in respones to CPU0213.