bluuebunny/crossref_metadata_2025 huggingface dataset:
Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium
Authors: Moolhuijzen P. , Dunn D. S. , Bellgard M. , Carter M. , Jia J. , Kong X. , Gill B. S. , Feuillet C. , Breen J. , Appels R.
Published: June 2007

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.
Cytogenetics in the age of molecular genetics
Authors: Zhang Peng , Friebe Bernd , Gill Bikram , Park R. F.
Published: June 2007

From the beginning of the 20th Century, we have seen tremendous advances in knowledge and understanding in almost all biological disciplines, including genetics, molecular biology, structural and functional genomics, and biochemistry. Among these advances, cytogenetics has played an important role. This paper details some of the important milestones of modern cytogenetics. Included are the historical role of cytogenetics in genetic studies in general and the genetics stocks produced using cytogenetic techniques. The basic biological questions cytogenetics can address and the important role and practical applications of cytogenetics in applied sciences, such as in agriculture and in breeding for disease resistance in cereals, are also discussed. The goal of this paper is to show that cytogenetics remains important in the age of molecular genetics, because it is inseparable from overall genome analysis. Cytogenetics complements studies in other disciplines within the field of biology and provides the basis for linking genetics, molecular biology and genomics research.
Avirulence proteins of rust fungi: penetrating the host - haustorium barrier
Authors: Dodds Peter N. , Catanzariti Ann-Maree , Lawrence Greg J. , Ellis Jeffrey G.
Published: June 2007

The continued deployment of resistance genes in Australian wheat varieties plays a crucial role in the prevention of crop losses as a result of rust infection. Resistance genes in plants act as an immune system by recognising specific components of the rust pathogen, encoded by avirulence (Avr) genes, and initiating defence responses. Recent advances in the model rust species, Melampsora lini, which infects cultivated flax (Linum usitatissimum), has led to the identification of several avirulence genes. These encode secreted proteins that are expressed in haustoria, specialised rust structures that penetrate the host cell wall. The AvrL567, AvrM, AvrP4, and AvrP123 proteins are recognised when expressed intracellularly in resistant plants, and the AvrL567 proteins interact directly with the corresponding L5 and L6 cytoplasmic resistance proteins. These observations imply that rusts deliver a range of small effector proteins directly into the plant cytoplasm, which are likely to perform key functions in facilitating pathogen infection. The plants’ resistance protein system has evolved to recognise the presence of these effectors during infection. Selection imposed by host resistance genes has led to the diversification of flax rust Avr genes to escape recognition. Nevertheless, virulent strains of flax rust retain variant forms of the Avr genes, suggesting that they have a positive fitness value to the pathogen. This knowledge is now being applied to develop screens for avirulence and pathogenicity-related proteins from important rust pathogens of wheat.
Wheat leaf and stem rust in the United States
Authors: Kolmer J. A. , Jin Y. , Long D. L.
Published: June 2007

Leaf rust, caused by Puccinia triticina, is a common and widespread disease of wheat in the US. On an annual basis, over 50 races of the leaf rust fungus are detected. There are at least 5 major groups of genetically distinct P. triticina isolates in the US based on allelic variation at microsatellite loci. Distinct regional race populations of P. triticina are found in the US, due to the widespread use of race-specific leaf rust resistance (Lr) genes in different market classes of wheat. In the south-eastern States where soft red winter wheats are grown, races with virulence to Lr9, Lr11, and Lr18 are predominant. In the southern Great Plains region where hard red winter wheats are grown, races with virulence to genes Lr9, Lr17, Lr24, and Lr26 are common. In the northern Great Plains region where hard red spring wheats are grown, races with virulence to Lr2a and Lr16 are common. Due to the wide dispersal of P. triticina, some races are found in all regions of the US. Highly effective durable resistance to leaf rust has been difficult to achieve due to the high degree of virulence variation in the P. triticina population and the rapid selection of races with virulence to effective Lr genes in wheat cultivars. Hard red spring wheat cultivars with genes Lr16, Lr23, and Lr34 have been highly resistant for more than 10 years in Minnesota and the Dakotas. Stem rust, caused by P. graminis f. sp. tritici, has not been a common disease of wheat in the US since the last major epidemics in the 1950s. The low levels of stem rust infections in the US can be attributed to the increasing use of highly resistant winter and spring wheat cultivars, which has greatly reduced the overall level of stem rust urediniospores. Eradication of the alternate host, Berberis vulgaris, has reduced the number of races and slowed the emergence of new races. Resistance genes Sr2, Sr6, Sr17, Sr24, Sr31, Sr36, and SrTmp are common in the winter wheats. Genes Sr6, Sr9b, Sr11, and Sr17 are common in the spring wheats. Spring wheat cultivars may also have adult plant stem rust resistance derived from cv. Thatcher. Many of the winter and spring wheats are susceptible to the new stem rust race from East Africa; however, cultivars with resistance to this race can be found in each of the major wheat classes.
Stem rust of wheat in Australia
Authors: Park R. F.
Published: June 2007

Annual pathogenicity surveys of Puccinina graminis f. sp. tritici (Pgt), initiated at the University of Sydney in 1919, have continued without interruption to the present day. The population structure of Pgt over the past 85 years has been strongly influenced by exotic introductions in 1925 (race 126), 1954 (race 21), and 1969 (races 194 and 326), subsequent random mutations to virulence, and selection of genotypes with virulence matching resistance genes in cultivars. Pathotypes detected in Australia over the past 10 years trace back to either races 21, 194, or 326. Based on varietal resistance and pathogenic variability, previous workers identified 3 periods between 1919 and 1970: from 1919 to 1938, cultivars lacked effective resistance genes; from 1938 to 1964, cultivars released with single genes for resistance (Sr6, Sr11, Sr9b, Sr36, Sr17), and new pathotypes with corresponding virulences were detected; from 1965 to 1970, and beyond, cultivars with multiple resistance genes were deployed in many regions, significantly reducing yield losses. During this third phase, and until now, cultivars were protected by resistance genes Sr2, Sr9g, Sr12, Sr13, Sr17, Sr22, Sr24, Sr26, Sr30, Sr36, and Sr38, singly or more commonly in combinations. Overall inoculum levels and pathotype diversity in Pgt have declined in all wheat-growing regions since the mid 1970s, likely as a consequence of the release of cultivars with gene combinations. Despite the low levels of stem rust in Australia over the past 30 years, resistance is still a top priority in many breeding programs. The development of virulence for Sr38 in WA in 2001 was a timely reminder of the need for continued vigilance if the sustained genetic control of the past 30 years is to continue.
A walk on the wild side: mining wild wheat and barley collections for rust resistance genes
Authors: Steffenson Brian J. , Olivera Pablo , Roy Joy K. , Jin Yue , Smith Kevin P. , Muehlbauer Gary J.
Published: June 2007

Leaf rust, stem rust, and stripe rust are among the most important diseases of wheat and barley worldwide and are best controlled using genetic resistance. To increase the diversity of rust resistance in wheat and barley, a project was initiated to identify and characterise rust resistance genes from the wild species of Aegilops sharonensis (Sharon goatgrass) and Hordeum vulgare ssp. spontaneum (wild barley), respectively. One hundred and two accessions of Sharon goatgrass from Israel and 318 Wild Barley Diversity Collection (WBDC) accessions from the Fertile Crescent, Central Asia, North Africa, and the Caucasus region were evaluated for resistance to leaf rust, stem rust, and/or stripe rust. Sharon goatgrass exhibited a wide range of infection types (ITs) in response to leaf rust, stem rust, and stripe rust. The percentage of resistant accessions in Sharon goatgrass was 58.8–78.4% for leaf rust, 11.8–69.6% for stem rust, and 46.1% for stripe rust, depending on the race used and the plant growth stage. Genetic studies with Sharon goatgrass revealed oligogenic resistance to leaf rust and stem rust. Wild barley also exhibited a wide range of ITs to leaf rust and stem rust; however, the overall frequency of resistance was lower than for Sharon goatgrass. The percentage of resistant accessions in wild barley was 25.8% for leaf rust and 5.7–20.1% for stem rust, depending on the race used. Resistance to the new virulent stem rust race TTKS (i.e. Ug99), present in eastern Africa, was found in both Sharon goatgrass (70% of accessions) and wild barley (25% of 20 accessions tested). Association mapping for stem rust resistance was applied in the WBDC using Diversity Arrays Technology (DArT) markers. Using the highly conservative P value threshold of 0.001, 14 and 15 significant marker associations were detected when the number of subpopulations (K value) was set for 10 and 8, respectively. These significant associations were in 9 and 8 unique chromosome bins, respectively. Two significant marker associations were detected for resistance to the wheat stem rust race MCCF in the same bin as the rpg4/Rpg5 complex on chromosome 7(5H). The presence of a major stem rust resistance gene in this bin on chromosome 7(5H) was validated in a bi-parental mapping population (WBDC accession Damon × cv. Harrington) constructed with DArT markers. The results from this study indicate that Sharon goatgrass and wild barley are rich sources of rust resistance genes for cultivated wheat and barley improvement, respectively, and that association mapping may be useful for positioning disease resistance genes in wild barley.
Puccinia striiformis in Australia: a review of the incursion, evolution, and adaptation of stripe rust in the period 1979 - 2006
Authors: Wellings C. R.
Published: June 2007

The wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici; Pst) was first detected in Australia in 1979. The features of the initial pathotype suggested that it was of European origin, and later work provided evidence that it was most likely transmitted as adherent spores on travellers’ clothing. Despite long-held views that this cool temperature pathogen would not adapt to Australian conditions, Pst became endemic and progressively adapted to commercial wheat production through step-wise mutation. Several of these mutant pathotypes became frequent in the Pst population, causing widespread infection and significant costs to production (yield and quality losses; chemical control expenditure) in certain cultivars and seasons. Pathotype evolution, including adaptation to native barley grass (Hordeum spp.) populations, is described. The occurrence of an exotic pathotype of Pst in Western Australia in 2002, and its subsequent spread to eastern Australia, represented a major shift in the pathogen population. This pathotype dominated pathogen populations throughout Australia from 2003, with chemical control expenditure estimated at AU$40–90 million annually. Another exotic introduction was detected in 1998. Initial data indicated that certain isolates collected from barley grass were highly avirulent to wheat differentials, with the exception of partial virulence to Chinese 166. Further seedling tests revealed that these isolates, tentatively designated barley grass stripe rust (BGYR), were virulent on several Australian barleys, notably those of Skiff parentage. Data, including molecular studies, suggest that BGYR is a new forma specialis of P. striiformis. Field nurseries indicate that BGYR is likely to have little impact on commercial barley, although this may change with further pathotype evolution or the release of susceptible cultivars.
PapA1 and PapA2 are acyltransferases essential for the biosynthesis of theMycobacterium tuberculosisvirulence factor Sulfolipid-1
Authors: Kumar Pawan , Schelle Michael W. , Jain Madhulika , Lin Fiona L. , Petzold Christopher J. , Leavell Michael D. , Leary Julie A. , Cox Jeffery S. , Bertozzi Carolyn R.
Published: June 2007

Mycobacterium tuberculosisproduces numerous exotic lipids that have been implicated as virulence determinants. One such glycolipid, Sulfolipid-1 (SL-1), consists of a trehalose-2-sulfate (T2S) core acylated with four lipid moieties. A diacylated intermediate in SL-1 biosynthesis, SL1278, has been shown to activate the adaptive immune response in human patients. Although several proteins involved in SL-1 biosynthesis have been identified, the enzymes that acylate the T2S core to form SL1278and SL-1, and the biosynthetic order of these acylation reactions, are unknown. Here we demonstrate that PapA2 and PapA1 are responsible for the sequential acylation of T2S to form SL1278and are essential for SL-1 biosynthesis.In vitro, recombinant PapA2 converts T2S to 2′-palmitoyl T2S, and PapA1 further elaborates this newly identified SL-1 intermediate to an analog of SL1278. Disruption ofpapA2andpapA1inM. tuberculosisconfirmed their essential role in SL-1 biosynthesis and their order of action. Finally, the ΔpapA2and ΔpapA1mutants were screened for virulence defects in a mouse model of infection. The loss of SL-1 (and SL1278) did not appear to affect bacterial replication or trafficking, suggesting that the functions of SL-1 are specific to human infection.
Single-molecule observation of DNA charge transfer
Authors: Takada Tadao , Fujitsuka Mamoru , Majima Tetsuro
Published: June 2007

DNA charge transfer highly depends on the electronic interaction between base pairs and reflects the difference in the base composition and sequence. For the purpose of investigating the charge transfer process of individual DNA molecules and the optical readout of DNA information at the single-molecule level, we performed single-molecule observation of the DNA charge transfer process by using single-molecule fluorescence spectroscopy. The DNA charge transfer process, leading to the oxidation of the fluorescent dye, was explored by monitoring the on–off signal of the dye after the charge injection by the excitation of a photosensitizer. The photobleaching efficiency of the dyes by the DNA charge transfer specifically depended on the base sequence and mismatch base pair, demonstrating the discrimination of the individual DNA information. Based on this approach, the optical readout of a single-base mismatch contained in a target DNA was performed at the single-molecule level.
The syntaxin SYP132 contributes to plant resistance against bacteria and secretion of pathogenesis-related protein 1
Authors: Kalde Monika , Nühse Thomas S. , Findlay Kim , Peck Scott C.
Published: June 2007

In contrast to many mammalian pathogens, potential bacterial pathogens of plants remain outside the host cell. The plant must, therefore, promote an active resistance mechanism to combat the extracellular infection. How this resistance against bacteria is manifested and whether similar processes mediate basal, gene-for-gene, and salicylate-associated defense, however, are poorly understood. Here, we identify a specific plasma membrane syntaxin,
Nb
SYP132, as a component contributing to gene-for-gene resistance in
Nicotiana benthamiana
. Silencing
NbSYP132
but not
NbSYP121
, the apparent orthologue of a syntaxin required for resistance to powdery mildew fungus, compromised AvrPto-Pto resistance. Because syntaxins may play a role in secretion of proteins to the extracellular space, we performed a limited proteomic analysis of the apoplastic fluid. We found that
NbSYP132
-silenced plants were impaired in the accumulation of at least a subset of pathogenesis-related (PR) proteins in the cell wall. These results were confirmed by both immunoblot analysis and imunolocalization of a PR protein, PR1a. These results implicate
Nb
SYP132 as the cognate target soluble
N
-ethylmaleimide-sensitive factor attachment protein receptor for exocytosis of vesicles containing antimicrobial PR proteins.
Nb
SYP132 also contributes to basal and salicylate-associated defense, indicating that SYP132-dependent secretion is a component of multiple forms of defense against bacterial pathogens in plants.
Measurement of 7,8-dihydro-8-oxo-2′-deoxyguanosine metabolism in MCF-7 cells at low concentrations using accelerator mass spectrometry
Authors: Hah Sang Soo , Mundt Janna M. , Kim Hyung M. , Sumbad Rhoda A. , Turteltaub Kenneth W. , Henderson Paul T.
Published: June 2007

Growing evidence suggests that oxidative damage to cells generates mutagenic 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-oxodG), which may initiate diseases related to aging and carcinogenesis. Kinetic measurement of 8-oxodG metabolism and repair in cells has been hampered by poor assay sensitivity and by difficulty characterizing the flux of oxidized nucleotides through the relevant metabolic pathways. We report here the development of a sensitive and quantitative approach to characterizing the kinetics and metabolic sources of 8-oxodG in MCF-7 human breast cancer cells by accelerator mass spectrometry. We observed that [
14
C]8-oxodG at medium concentrations of up to 2 pmol/ml was taken up by MCF-7 cells, phosphorylated to mono-, di-, and triphosphate derivatives, and incorporated into DNA. Oxidative stress caused by exposure of the cells to 17β-estradiol resulted in a reduction in the rate of [
14
C]8-oxodG incorporation into DNA and an increase in the ratio of 8-oxodG monophosphate (8-oxodGMP) to 8-oxodG triphosphate (8-oxodGTP) in the nucleotide pool. 17β-Estradiol-induced oxidative stress up-regulated the nucleotide pool cleansing enzyme MTH1 and possibly other Nudix-related pyrophosphohydrolases. These data support the conclusion that 8-oxodGTP is formed in the nucleotide pool by both 8-oxodG metabolism and endogenous reactive oxygen species. The metabolism of 8-oxodG to 8-oxodGTP, followed by incorporation into DNA is a mechanism by which the cellular presence of this oxidized nucleoside can lead to mutations.
Endothelin-converting enzyme 1 degrades neuropeptides in endosomes to control receptor recycling
Authors: Roosterman Dirk , Cottrell Graeme S. , Padilla Benjamin E. , Muller Laurent , Eckman Christopher B. , Bunnett Nigel W. , Steinhoff Martin
Published: June 2007

Neuropeptide signaling requires the presence of G protein-coupled receptors (GPCRs) at the cell surface. Activated GPCRs interact with β-arrestins, which mediate receptor desensitization, endocytosis, and mitogenic signaling, and the peptide–receptor–arrestin complex is sequestered into endosomes. Although dissociation of β-arrestins is required for receptor recycling and resensitization, the critical event that initiates this process is unknown. Here we report that the agonist availability in the endosomes, controlled by the membrane metalloendopeptidase endothelin-converting enzyme 1 (ECE-1), determines stability of the peptide–receptor–arrestin complex and regulates receptor recycling and resensitization. Substance P (SP) binding to the tachykinin neurokinin 1 receptor (NK1R) induced membrane translocation of β-arrestins followed by trafficking of the SP–NK1R–β-arrestin complex to early endosomes containing ECE-1a–d. ECE-1 degraded SP in acidified endosomes, disrupting the complex; β-arrestins returned to the cytosol, and the NK1R, freed from β-arrestins, recycled and resensitized. An ECE-1 inhibitor, by preventing NK1R recycling in endothelial cells, inhibited resensitization of SP-induced inflammation. This mechanism is a general one because ECE-1 similarly regulated NK3R resensitization. Thus, peptide availability in endosomes, here regulated by ECE-1, determines the stability of the peptide–receptor–arrestin complex. This mechanism regulates receptor recycling, which is necessary for sustained signaling, and it may also control β-arrestin-dependent mitogenic signaling of endocytosed receptors. We propose that other endosomal enzymes and transporters may similarly control the availability of transmitters in endosomes to regulate trafficking and signaling of GPCRs. Antagonism of these endosomal processes represents a strategy for inhibiting sustained signaling of receptors, and defects may explain the tachyphylaxis of drugs that are receptor agonists.
Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in
Drosophila melanogaster
Authors: Bergman Casey M. , Bensasson Douda
Published: June 2007

LTR and non-LTR retrotransposons exhibit distinct patterns of abundance within the
Drosophila melanogaster
genome, yet the causes of these differences remain unknown. Here we investigate whether genomic differences between LTR and non-LTR retrotransposons reflect systematic differences in their insertion history. We find that for 17 LTR and 10 non-LTR retrotransposon families that evolve under a pseudogene-like mode of evolution, most elements from LTR families have integrated in the very recent past since colonization of non-African habitats (≈16,000 years ago), whereas elements from non-LTR families have been accumulating in overlapping waves since the divergence of
D. melanogaster
from its sister species,
Drosophila simulans
(≈5.4 Mya). LTR elements are significantly younger than non-LTR elements, individually and by family, in regions of high and low recombination, and in genic and intergenic regions. We show that analysis of transposable element (TE) nesting provides a method to calculate transposition rates from genome sequences, which we estimate to be one to two orders of magnitude lower than those that are based on mutation accumulation studies. Recent LTR integration provides a nonequilibrium alternative for the low population frequency of LTR elements in this species, a pattern that is classically interpreted as evidence for selection against the transpositional increase of TEs. Our results call for a new class of population genetic models that incorporate TE copy number, allele frequency, and the age of insertions to provide more powerful and robust inferences about the forces that control the evolution of TEs in natural populations.
Electrical stimulation of the rostral medial prefrontal cortex in rabbits inhibits the expression of conditioned eyelid responses but not their acquisition
Authors: Leal-Campanario Rocío , Fairén Alfonso , Delgado-García José M. , Gruart Agnès
Published: June 2007

We have studied the role of rostral medial prefrontal cortex (mPFC) on reflexively evoked blinks and on classically conditioned eyelid responses in alert-behaving rabbits. The rostral mPFC was identified by its afferent projections from the medial half of the thalamic mediodorsal nuclear complex. Classical conditioning consisted of a delay paradigm using a 370-ms tone as the conditioned stimulus (CS) and a 100-ms air puff directed at the left cornea as the unconditioned stimulus (US). The CS coterminated with the US. Electrical train stimulation of the contralateral rostral mPFC produced a significant inhibition of air-puff-evoked blinks. The same train stimulation of the rostral mPFC presented during the CS–US interval for 10 successive conditioning sessions significantly reduced the generation of conditioned responses (CRs) as compared with values reached by control animals. Interestingly, the percentage of CRs almost reached control values when train stimulation of the rostral mPFC was removed from the fifth conditioning session on. The electrical stimulation of the rostral mPFC in well conditioned animals produced a significant decrease in the percentage of CRs. Moreover, the stimulation of the rostral mPFC was also able to modify the kinematics (latency, amplitude, and velocity) of evoked CRs. These results suggest that the rostral mPFC is a potent inhibitor of reflexively evoked and classically conditioned eyeblinks but that activation prevents only the expression of CRs, not their latent acquisition. Functional and behavioral implications of this inhibitory role of the rostral mPFC are discussed.
Dispersing biofilms with engineered enzymatic bacteriophage
Authors: Lu Timothy K. , Collins James J.
Published: June 2007

Synthetic biology involves the engineering of biological organisms by using modular and generalizable designs with the ultimate goal of developing useful solutions to real-world problems. One such problem involves bacterial biofilms, which are crucial in the pathogenesis of many clinically important infections and are difficult to eradicate because they exhibit resistance to antimicrobial treatments and removal by host immune systems. To address this issue, we engineered bacteriophage to express a biofilm-degrading enzyme during infection to simultaneously attack the bacterial cells in the biofilm and the biofilm matrix, which is composed of extracellular polymeric substances. We show that the efficacy of biofilm removal by this two-pronged enzymatic bacteriophage strategy is significantly greater than that of nonenzymatic bacteriophage treatment. Our engineered enzymatic phage substantially reduced bacterial biofilm cell counts by ≈4.5 orders of magnitude (≈99.997% removal), which was about two orders of magnitude better than that of nonenzymatic phage. This work demonstrates the feasibility and benefits of using engineered enzymatic bacteriophage to reduce bacterial biofilms and the applicability of synthetic biology to an important medical and industrial problem.
Computing the distribution of the maximum in balls-and-boxes problems with application to clusters of disease cases
Authors: Ewens Warren J. , Wilf Herbert S.
Published: June 2007

We present a rapid method for the exact calculation of the cumulative distribution function of the maximum of multinomially distributed random variables. The method runs in time
O(mn)
, where
m
is the desired maximum and
n
is the number of variables. We apply the method to the analysis of two situations in which an apparent clustering of cases of a disease in some locality has raised epidemiological concerns, and these concerns have been discussed in the recent literature. We conclude that one of these clusters may be explained on purely random grounds, namely the leukemia cluster in Niles, IL, in 1956–1960; whereas the other, a leukemia cluster in Fallon, NV, in 1999–2001, may not.
Evolution of Na,K-ATPase βm-subunit into a coregulator of transcription in placental mammals
Authors: Pestov Nikolay B. , Ahmad Nisar , Korneenko Tatiana V. , Zhao Hao , Radkov Rossen , Schaer Danièle , Roy Sophie , Bibert Stéphanie , Geering Käthi , Modyanov Nikolai N.
Published: June 2007

Change in gene functions (gene cooption) is one of the key mechanisms of molecular evolution. Genes can acquire new functions via alteration in properties of encoded proteins and/or via changes in temporal or spatial regulation of expression. Here we demonstrate radical changes in the functions of orthologous ATP1B4 genes during evolution of vertebrates. Expression of ATP1B4 genes is brain-specific in teleost fishes, whereas it is predominantly muscle-specific in tetrapods. The encoded βm-proteins in fish, amphibian, and avian species are β-subunits of Na,K-ATPase located in the plasma membrane. In placental mammals βm-proteins lost their ancestral functions, accumulate in nuclear membrane of perinatal myocytes, and associate with transcriptional coregulator Ski-interacting protein (SKIP). Through interaction with SKIP, eutherian βm acquired new functions as exemplified by regulation of TGF-β-responsive reporters and by augmentation of mRNA levels of Smad7, an inhibitor of TGF-β signaling. Thus, orthologous vertebrate ATP1B4 genes represent an instance of gene cooption that created fundamental changes in the functional properties of the encoded proteins.
Ceramide transfer protein function is essential for normal oxidative stress response and lifespan
Authors: Rao Raghavendra Pralhada , Yuan Changqing , Allegood Jeremy C. , Rawat Satinder S. , Edwards Michael Beth , Wang Xin , Merrill Alfred H. , Acharya Usha , Acharya Jairaj K.
Published: June 2007

Ceramide transfer protein (CERT) transfers ceramide from the endoplasmic reticulum to the Golgi complex, a process critical in synthesis and maintenance of normal levels of sphingolipids in mammalian cells. However, how its function is integrated into development and physiology of the animal is less clear. Here, we report thein vivoconsequences of loss of functional CERT protein. We generatedDrosophila melanogastermutant flies lacking a functional CERT (Dcert) protein using chemical mutagenesis and a Western blot-based genetic screen. The mutant flies die early between days 10 and 30, whereas controls lived between 75 and 90 days. They display >70% decrease in ceramide phosphoethanolamine (the sphingomyelin analog inDrosophila) and ceramide. These changes resulted in increased plasma membrane fluidity that renders them susceptible to reactive oxygen species and results in enhanced oxidative damage to cellular proteins. Consequently, the flies showed reduced thermal tolerance that was exacerbated with aging and metabolic compromise such as decreasing ATP and increasing glucose levels, reminiscent of premature aging. Our studies demonstrate that maintenance of physiological levels of ceramide phosphoethanolamine by CERTin vivois required to prevent oxidative damages to cellular components that are critical for viability and normal lifespan of the animal.
Differential phosphorylation of NG2 proteoglycan by ERK and PKCα helps balance cell proliferation and migration
Authors: Makagiansar Irwan T. , Williams Scott , Mustelin Tomas , Stallcup William B.
Published: June 2007

Two distinct Thr phosphorylation events within the cytoplasmic domain of the NG2 proteoglycan help regulate the cellular balance between proliferation and motility. Protein kinase Cα mediates the phosphorylation of NG2 at Thr2256, resulting in enhanced cell motility. Extracellular signal–regulated kinase phosphorylates NG2 at Thr2314, stimulating cell proliferation. The effects of NG2 phosphorylation on proliferation and motility are dependent on β1-integrin activation. Differential cell surface localization of the two distinctly phosphorylated forms of NG2 may be the mechanism by which the NG2–β1-integrin interaction promotes proliferation in one case and motility in the other. NG2 phosphorylated at Thr2314 colocalizes with β1-integrin on microprotrusions from the apical cell surface. In contrast, NG2 phosphorylated at Thr2256 colocalizes with β1-integrin on lamellipodia at the leading edges of cells. Thus, phosphorylation and the resulting site of NG2–integrin localization may determine the specific downstream effects of integrin signaling.
The RGD motif in fibronectin is essential for development but dispensable for fibril assembly
Authors: Takahashi Seiichiro , Leiss Michael , Moser Markus , Ohashi Tomoo , Kitao Tomoe , Heckmann Dominik , Pfeifer Alexander , Kessler Horst , Takagi Junichi , Erickson Harold P. , Fässler Reinhard
Published: June 2007

Fibronectin (FN) is secreted as a disulfide-bonded FN dimer. Each subunit contains three types of repeating modules: FN-I, FN-II, and FN-III. The interactions of α5β1 or αv integrins with the RGD motif of FN-III repeat 10 (FN-III10) are considered an essential step in the assembly of FN fibrils. To test this hypothesis in vivo, we replaced the RGD motif with the inactive RGE in mice. FN-RGE homozygous embryos die at embryonic day 10 with shortened posterior trunk, absent tail bud–derived somites, and severe vascular defects resembling the phenotype of α5 integrin–deficient mice. Surprisingly, the absence of a functional RGD motif in FN did not compromise assembly of an FN matrix in mutant embryos or on mutant cells. Matrix assembly assays and solid-phase binding assays reveal that αvβ3 integrin assembles FN-RGE by binding an isoDGR motif in FN-I5, which is generated by the nonenzymatic rearrangement of asparagines (N) into an iso-aspartate (iso-D). Our findings demonstrate that FN contains a novel motif for integrin binding and fibril formation whose activity is controlled by amino acid modification.
DNA polymerase β is able to repair breaks in switch regions and plays an inhibitory role during immunoglobulin class switch recombination
Authors: Wu Xiaoming , Stavnezer Janet
Published: June 2007

Immunoglobulin (Ig) class switch recombination (CSR) is initiated by activation-induced cytidine deaminase (AID), which converts cytosines to uracils in switch (S) regions. Subsequent excision of dU by uracil DNA glycosylase (UNG) of the base excision repair (BER) pathway is required to obtain double-strand break (DSB) intermediates for CSR. Since UNG normally initiates faithful repair, it is unclear how the AID-instigated S region lesions are converted into DSBs rather than correctly repaired by BER. Normally, DNA polymerase β (Polβ) would replace the dC deaminated by AID, leading to correct repair of the single-strand break, thereby preventing CSR. We address the question of whether Polβ might be specifically down-regulated during CSR or inhibited from accessing the AID-instigated lesions, or whether the numerous AID-initiated S region lesions might simply overwhelm the BER capacity. We find that nuclear Polβ levels are induced upon activation of splenic B cells to undergo CSR. When Polβ−/− B cells are activated to switch in culture, they switch slightly better to IgG2a, IgG2b, and IgG3 and have more S region DSBs and mutations than wild-type controls. We conclude that Polβ attempts to faithfully repair S region lesions but fails to repair them all.
Aggressive mimics profit from a model–signal receiver mutualism
Authors: Cheney Karen L , Côté Isabelle M
Published: June 2007

Mimetic species have evolved to resemble other species to avoid predation (protective mimicry) or gain access to food (aggressive mimicry). Mimicry systems are frequently tripartite interactions involving a mimic, model and ‘signal receiver’. Changes in the strength of the relationship between model and signal receiver, owing to shifting environmental conditions, for example, can affect the success of mimics in protective mimicry systems. Here, we show that an experimentally induced shift in the strength of the relationship between a model (bluestreak cleaner fish,
Labroides dimidiatus
) and a signal receiver (staghorn damselfish,
Amblyglyphidodon curacao
) resulted in increased foraging success for an aggressive mimic (bluestriped fangblenny,
Plagiotremus rhinorhynchos
). When the parasite loads of staghorn damselfish clients were experimentally increased, the attack success of bluestriped fangblenny on damselfish also increased. Enhanced mimic success appeared to be due to relaxation of vigilance by parasitized clients, which sought cleaners more eagerly and had lower overall aggression levels. Signal receivers may therefore be more tolerant of and/or more vulnerable to attacks from aggressive mimics when the net benefit of interacting with their models is high. Changes in environmental conditions that cause shifts in the net benefits accrued by models and signal receivers may have important implications for the persistence of aggressive mimicry systems.
Disordered Eating: Young Women's Search for Control and Connection
Authors: Budd Geraldine
Published: June 2007

PROBLEM:  Approximately 5% of American women suffer from eating disorders and scores more exhibit signs of disordered eating. The purpose of this study was to gain an understanding of disordered eating in adolescence.

METHODS:  Grounded theory method was employed. In‐depth interviews were conducted with 15 college women to explore their experiences with disordered eating.

FINDINGS:  Choosing disordered eating behaviors as a method of control occurred when the young women lacked connected and close relationships with others. Conversely, when meaningful relationships were present in their lives, the dysfunction abated.

CONCLUSIONS:  Psychosocial and dietary assessments are necessary to identify youngsters without connected relationships and/or predispositions to disordered eating.
Salmonid microarrays identify intestinal genes that reliably monitor P deficiency in rainbow trout aquaculture1
Authors: Kirchner S. , McDaniel N. K. , Sugiura S. H. , Soteropoulos P. , Tian B. , Fletcher J. W. , Ferraris R. P.
Published: June 2007

Nutrient‐responsive genes can identify important metabolic pathways and evaluate optimal dietary levels. Using a 16K Salmo salar microarray, we identified in rainbow trout (Oncorhynchus mykiss) 21 potential phosphorus (P)‐responsive genes, mainly involved in immune response, proteolysis or transport, whose expression levels changed in the intestine after 5 days of feeding a low‐P (LP) diet. Diet‐induced changes in the expression levels of several genes in each fish were tightly correlated with changes in serum P, and the changes persisted for an additional 15 days after dietary P deficiency. We then evaluated these and previously identified P‐responsive genes under simulated farm conditions, and monitored the intestinal gene expression from 6 h to 7 days after the trout were switched from a sufficient‐P (SP) diet to a LP diet (SP→LP), and from a LP diet to a SP diet (LP→SP). After 7 days, mean serum P decreased 0.14 mM/day for SP→LP and increased 0.10 mm/day for LP→SP. The mRNA abundance of the metalloendopeptidase meprin 1α (MEP1α), the Na+‐dependent phosphate co‐transporter (NaPi2b,SLC34A2), the sulfotransferase SULT2β1 and carbonic anhydrase XIII genes all increased after SP→LP and decreased after LP→SP, suggesting that adaptive expression is reversible and correlated with dietary P. The duration of change in gene expression in response to SP→LP was generally shorter than that of LP→SP, suggesting potentially different mechanisms of adaptation to deficiency as opposed to excess. Diet‐induced changes in mRNA abundance of other genes were either transient or modest. We identified, by heterologous microarray hybridization, new genes sensitive to perturbations in dietary P, and then showed that these genes can reliably monitor P deficiency under field conditions. Simultaneous changes in the expression of these P biomarkers could predict either P deficiency (to prevent economic losses to the farmers) or P excess (to prevent inadvertent pollution of nearby waters).
Tracing genetic change over time using nuclear SNPs in ancient and modern cattle
Authors: Svensson E. M. , Anderung C. , Baubliene J. , Persson P. , Malmström H. , Smith C. , Vretemark M. , Daugnora L. , Götherström A.
Published: June 2007

Ancient DNA has the potential of adding the dimension of time to genetic studies. With a suitable sample set it should be possible to follow genetic changes over time as they occur. To date, only a limited number of ancient DNA studies that cover a large time span have been published, and all of these studies have used mitochondrial DNA. Here, we explore SNP typing as a way to access ancient coding nuclear genes. By targeting fragments of minimal size, we typed three polymorphic sites in 111 ancient cattle remains spanning some 4000 years. We showed that there has been a decrease in heterozygosity over time, especially since the late Middle Ages. We conclude that SNPs can be used to generate a time series for nuclear markers from ancient material, and thereby to study selection on genes over time.
The first linkage map of the American mink (Mustela vison)
Authors: Anistoroaei R. , Menzorov A. , Serov O. , Farid A. , Christensen K.
Published: June 2007

Described herein, the first microsatellite linkage map for the American mink consists of 85 microsatellite markers resolved into 17 linkage groups. The map was constructed using 92 F1 progeny from five sire families created by crossing mink with different colour types. The linkage groups ranged from 0 to 137 cM. These linkage groups were assigned to 12 of the 14 mink autosomes using a somatic cell hybrid panel. The total map covered 690 sex‐averaged Kosambi units with an average marker spacing of 8 cM. This map will facilitate further genetic mapping of monogenic characters and QTL.
Fluorescence analysis of copper(II) and zinc(II) binding behaviour of fulvic acids from pig slurry and amended soils
Authors: Hernández D. , Plaza C. , Senesi N. , Polo A.
Published: June 2007

The evaluation of the mechanisms and extent of interaction of Cu(II) and Zn(II) with fulvic acids (FAs) is of importance for understanding the mobility and bioavailability of these metals in pig slurry (PS)‐amended soils. In this work, a fluorescence titration method and a single site model were used to characterize the interaction of Cu(II) and Zn(II) with FAs isolated from PS, from soils amended with 90 and 150 m3ha−1year−1of PS for 7 years and from the corresponding unamended soil. The binding capacities of FAs and the strengths of metal ion‐FA complexes were larger for Cu(II) than for Zn(II). With respect to the unamended control soil FA, PS‐FA was characterized by smaller binding capacities and stability constants. The binding capacities and affinities of PS‐amended soil FA were intermediate between those of unamended soil FA and PS‐FA, and tended to decrease with increasing amounts of PS applied to soil, thus suggesting a partial incorporation of FA fractions of PS into native soil FA.
Interaction of naphthalene derivatives with soil: an experimental and theoretical case study
Authors: Winkler P. , Novoszad M. , Gerzabek M. H. , Haberhauer G. , Tunega D. , Lischka H.
Published: June 2007

This study provides insight into the relevance of the chemical functional groups of soil organic matter (aromatic, paraffinic, O‐alkyl, carboxyl and carbonyl carbon), as determined by CPMAS 13C NMR, on adsorption processes. Batch adsorption experiments with eight naphthalene derivatives were conducted with soils from a long‐term field experiment and model sorbents. Although the adsorption of some derivatives was mainly affected by the paraffinic organic carbon content in soil, the relation between the C‐distribution and adsorption was complex. This casts doubt on the use of such NMR data to estimate sorption behaviour. Additionally, sorption experiments were performed with six model sorbents representing typical soil components. Considerable adsorption of naphthalene derivatives was observed for montmorillonite and lignin; the smallest values were for kaolinite and cellulose. A quantum chemical approach was used to calculate a local polarity parameter as a molecular property of the naphthalene derivatives. This parameter was correlated with the logarithm of the adsorption coefficients, logKd. Here, clear trends were observed for three of the model sorbents (kaolinite, montmorillonite and lignin).
Structure, reactivity and spectroscopic properties of minerals from lateritic soils: insights from ab initio calculations
Authors: Balan E. , Lazzeri M. , Mauri F. , Calas G.
Published: June 2007

We review here some recent applications of ab initio calculations to the modelling of spectroscopic and energetic properties of minerals, which are key components of lateritic soils or govern their geochemical properties. Quantum mechanical ab initio calculations are based on density functional theory and density functional perturbation theory. Among the minerals investigated, zircon is a typical resistant primary mineral. Its resistance to weathering is at the origin of the peculiar geochemical behaviour of Zr, an element often used in mass balance calculations of continental weathering. Numerical modelling gives a unique picture of the origin of the chemical durability and radiation‐induced amorphization of zircon. We also present several applications of ab initio calculations to the description of properties of secondary minerals, such as kaolinite‐group minerals and gibbsite. Special attention is given to the calculation of infrared and Raman spectra. Surface properties and particle shape are major properties of finely‐divided materials such as clay minerals. We show how theoretical modelling of infrared spectroscopic data provides information on natural samples at both the microscopic (atomic structure) and macroscopic (particle shape) length‐scale. The systematic comparison of experimental and theoretical data significantly improves our understanding of mineral transformations during soil formation and evolution in lateritic environments.
Assessment of early postoperative pain and haemorrhage in young children undergoing dental extractions under general anaesthesia
Authors: McWILLIAMS PENELOPE A. , RUTHERFORD JOHN S.
Published: June 2007

Background.  There have been a lot of guidelines issued about dental extractions under general anaesthesia. There is a considerable body of research about the use of local anaesthetic as an adjunct. Some of this research appears to be contradictory about the use of local anaesthetic in addition to general anaesthesia in very young children. This study attempts to clarify the issue.

Aim.  To determine whether postoperative pain/distress in the early recovery period was different for those children who did or did not have local infiltration anaesthesia for extractions under general anaesthetic, and whether the incidence of clinically significant postoperative bleeding was different for the two groups.

Design.  Children aged 2–6 years, admitted for extraction of deciduous posterior teeth under general anaesthetic, were randomized to groups that were or were not given local infiltration anaesthesia during the procedure. The children were premedicated with paracetamol and ibuprofen, and had absorbable haemostatic packs inserted during the operation. Staff blinded to treatment allocation made observations in the recovery period of pain and any interventions for bleeding.

Results.  There was no difference in postoperative pain, as measured using CHEOPS scale between the two groups, but an increase in post operative bleeding in the group who did not have local anaesthetic administered 5/38 compared to 0/38, P = 0.02.

Conclusions.  As use of local anaesthetic reduces bleeding without altering pain or distress in young children undergoing posterior deciduous tooth extraction, we should consider using as an adjunct to general anaesthesia.