bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vivo Induction of Glial Cell Proliferation and Axonal Outgrowth and Myelination by Brain-Derived Neurotrophic Factor
Authors: de Groot Dorien M. , Coenen Anton J. M. , Verhofstad Albert , van Herp François , Martens Gerard J. M.
Published: August 2006

Brain-derived neurotrophic factor (BDNF) belongs to the neurotrophin family of neuronal cell survival and differentiation factors but is thought to be involved in neuronal cell proliferation and myelination as well. To explore the role of BDNF in vivo, we employed the intermediate pituitary melanotrope cells of the amphibian Xenopus laevis as a model system. These cells mediate background adaptation of the animal by producing high levels of the prohormone proopiomelanocortin (POMC) when the animal is black adapted. We used stable X. transgenesis in combination with the POMC gene promoter to generate transgenic frogs overexpressing BDNF specifically and physiologically inducible in the melanotrope cells. Intriguingly, an approximately 25-fold overexpression of BDNF resulted in hyperplastic glial cells and myelinated axons infiltrating the pituitary, whereby the transgenic melanotrope cells became located dispersed among the induced tissue. The infiltrating glial cells and axons originated from both peripheral and central nervous system sources. The formation of the phenotype started around tadpole stage 50 and was induced by placing white-adapted transgenics on a black background, i.e. after activation of transgene expression. The severity of the phenotype depended on the level of transgene expression, because the intermediate pituitaries from transgenic animals raised on a white background or from transgenics with only an approximately 5-fold BDNF overexpression were essentially not affected. In conclusion, we show in a physiological context that, besides its classical role as neuronal cell survival and differentiation factor, in vivo BDNF can also induce glial cell proliferation as well as axonal outgrowth and myelination.
An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision inC. elegans
Authors: Johnston Robert J. , Copeland John W. , Fasnacht Marc , Etchberger John F. , Liu Jun , Honig Barry , Hobert Oliver
Published: August 2006

Gene regulatory networks that control the terminally differentiated state of a cell are, by and large, only superficially understood. In a mutant screen aimed at identifying regulators of gene batteries that define the differentiated state of two left/right asymmetric C. elegansgustatory neurons, ASEL and ASER, we have isolated a mutant, fozi-1,with a novel mixed-fate phenotype, characterized by de-repression of ASEL fate in ASER. fozi-1 codes for a protein that functions in the nucleus of ASER to inhibit the expression of the LIM homeobox gene lim-6,neuropeptide-encoding genes and putative chemoreceptors of the GCY gene family. The FOZI-1 protein displays a highly unusual domain architecture, that combines two functionally essential C2H2 zinc-finger domains, which are probably involved in transcriptional regulation, with a formin homology 2(FH2) domain, normally found only in cytosolic regulators of the actin cytoskeleton. We demonstrate that the FH2 domain of FOZI-1 has lost its actin polymerization function but maintains its phylogenetically ancient ability to homodimerize. fozi-1 genetically interacts with several transcription factors and micro RNAs in the context of specific regulatory network motifs. These network motifs endow the system with properties that provide insights into how cells adopt their stable terminally differentiated states.
TheDrosophilacaspase Ice is important for many apoptotic cell deaths and for spermatid individualization, a nonapoptotic process
Authors: Muro Israel , Berry Deborah L. , Huh Jun R. , Chen Chun Hong , Huang Haixia , Yoo Soon Ji , Guo Ming , Baehrecke Eric H. , Hay Bruce A.
Published: August 2006

Caspase family proteases play important roles in the regulation of apoptotic cell death. Initiator caspases are activated in response to death stimuli, and they transduce and amplify these signals by cleaving and thereby activating effector caspases. In Drosophila, the initiator caspase Nc(previously Dronc) cleaves and activates two short-prodomain caspases, Dcp-1 and Ice (previously Drice), suggesting these as candidate effectors of Nc killing activity. dcp-1-null mutants are healthy and possess few defects in normally occurring cell death. To explore roles for Ice in cell death, we generated and characterized an Ice null mutant. Animals lacking Ice show a number of defects in cell death, including those that occur during embryonic development, as well as during formation of adult eyes, arista and wings. Ice mutants exhibit subtle defects in the destruction of larval tissues, and do not prevent destruction of salivary glands during metamorphosis. Cells from Ice animals are also markedly resistant to several stresses, including X-irradiation and inhibition of protein synthesis. Mutations in Ice also suppress cell death that is induced by expression of Rpr, Wrinkled (previously Hid) and Grim. These observations demonstrate that Ice plays an important non-redundant role as a cell death effector. Finally, we demonstrate that Ice participates in, but is not absolutely required for, the non-apoptotic process of spermatid differentiation.
IKKβ/2 induces TWEAK and apoptosis in mammary epithelial cells
Authors: Baxter Fiona O. , Came Paul J. , Abell Kathrine , Kedjouar Blandine , Huth Marion , Rajewsky Klaus , Pasparakis Manolis , Watson Christine J.
Published: August 2006

The Nuclear Factor-κB (NF-κB) family of transcription factors are ubiquitously expressed and control a wide range of cellular responses,including apoptosis, proliferation, differentiation, inflammation and immunity. Here, we investigated the function of the NF-κB upstream regulator IκB kinase 2/β (IKK2) in apoptosis regulation in the normal physiological setting of regressing mammary gland. Conditional deletion of the gene encoding IKK2 resulted, surprisingly, in delayed apoptosis and remodelling, and abrogation of caspase 3 cleavage. This failure to induce involution was associated with reduced expression, within 24 hours of involution, of the death receptor (DR) ligand TNF and its receptor TNFR1,which are known NF-κB targets. This was associated with elevated levels of active AKT and phosphorylated FOXO3a. Furthermore, we show that expression of TWEAK, another DR ligand, is dramatically downregulated, even in heterozygous IKK2 mammary glands. Unlike other DR ligands, the TWEAK promoter has six consensus FOXO-binding sites, further suggesting that it is differentially regulated. Interestingly, a cleaved form of TWEAK is upregulated during involution. This unexpected function of the IKK2/NF-κB pathway as a regulator of TWEAK expression and inducer of apoptosis has significant consequences for future therapeutic approaches for cancer and inflammatory diseases.
Slug stability is dynamically regulated during neural crest development by the F-box protein Ppa
Authors: Vernon Ann E. , LaBonne Carole
Published: August 2006

The neural crest is a population of stem-cell-like precursors found only in vertebrates. Slug, a member of the Snail family of zincfinger transcriptional repressors, is a critical regulator of neural crest development and has also been implicated in the acquisition of invasive behavior during tumor progression. Despite its central role in these two important processes, little is known about the mechanisms that control the expression and/or activity of Slug. We demonstrate that Slug is a labile protein whose stability is positively reinforced through activation of the neural crest regulatory program. We identify Partner of paired (Ppa) as the F-box component of a modular E3 ligase, and show that it is expressed in neural crest-forming regions, and that it binds to and promotes ubiquitin-mediated proteasomal degradation of Slug. Misexpression of Ppa inhibits the formation of neural crest precursors, and Slug mutants in which Ppa binding has been abrogated rescue this inhibition. These results provide novel insight into the regulation of Slug, a protein that plays a central role in neural crest precursor formation, as well as in developmental and pathological epithelial to mesenchymal transitions.
Primordial germ cell deficiency in the connexin 43 knockout mouse arises from apoptosis associated with abnormal p53 activation
Authors: Francis Richard J. B. , Lo Cecilia W.
Published: August 2006

Connexin 43 knockout (Cx43α1KO) mice exhibit germ cell deficiency,but the underlying cause for the germ cell defect was unknown. Using an Oct4-GFP reporter transgene, we tracked the distribution and migration of primordial germ cells (PGCs) in the Cx43α1KO mouse embryo. Analysis with dye injections showed PGCs are gap-junction-communication competent, with dye coupling being markedly reduced in Cx43α1-deficient PGCs. Time-lapse videomicroscopy and motion analysis showed that the directionality and speed of cell motility were reduced in the Cx43α1KO PGCs. This was observed both in E8.5 and E11.5 embryos. By contrast, PGC abundance did not differ between wild-type and heterozygous/homozygous Cx43α1KO embryos until E11.5, when a marked reduction in PGC abundance was detected in the homozygous Cx43α1KO embryos. This was accompanied by increased PGC apoptosis and increased expression of activated p53. Injection of α-pifithrin, a p53 antagonist, inhibited PGC apoptosis and prevented the loss of PGC. Analysis using a cell adhesion assay indicated a reduction inβ1-integrin function in the Cx43α1KO PGCs. Together with the abnormal activation of p53, these findings suggest the possibility of anoikis-mediated apoptosis. Overall, these findings show Cx43α1 is essential for PGC survival, with abnormal p53 activation playing a crucial role in the apoptotic loss of PGCs in the Cx43α1KO mouse embryos.
DIG-1, a novel giant protein, non-autonomously mediates maintenance of nervous system architecture
Authors: Bénard Claire Y. , Boyanov Alexander , Hall David H. , Hobert Oliver
Published: August 2006

Dedicated mechanisms exist to maintain the architecture of an animal's nervous system after development is completed. To date, three immunoglobulin superfamily members have been implicated in this process in the nematode Caenorhabditis elegans: the secreted two-Ig domain protein ZIG-4, the FGF receptor EGL-15 and the L1-like SAX-7 protein. These proteins provide crucial information for neuronal structures, such as axons, that allows them to maintain the precise position they acquired during development. Yet, how widespread this mechanism is throughout the nervous system, and what other types of factors underlie such a maintenance mechanism, remains poorly understood. Here, we describe a new maintenance gene, dig-1, that encodes a predicted giant secreted protein containing a large number of protein interaction domains. With 13,100 amino acids, the DIG-1 protein is the largest secreted protein identifiable in any genome database. dig-1functions post-developmentally to maintain axons and cell bodies in place within axonal fascicles and ganglia. The failure to maintain axon and cell body position is accompanied by defects in basement membrane structure, as evidenced by electron microscopy analysis of dig-1 mutants. Expression pattern and mosaic analysis reveals that dig-1 is produced by muscles to maintain nervous system architecture, demonstrating that dig-1 functions non-autonomously to preserve the proper layout of neural structures. We propose that DIG-1 is a component of the basement membrane that mediates specific contacts between cellular surfaces and their environment through the interaction with a cell-type specific set of other maintenance factors.
Actin capping protein α maintainsvestigial-expressing cells within theDrosophilawing disc epithelium
Authors: Janody Florence , Treisman Jessica E.
Published: August 2006

Tissue patterning must be translated into morphogenesis through cell shape changes mediated by remodeling of the actin cytoskeleton. We have found that Capping protein α (Cpa) and Capping protein β (Cpb), which prevent extension of the barbed ends of actin filaments, are specifically required in the wing blade primordium of the Drosophila wing disc. cpaor cpb mutant cells in this region, but not in the remainder of the wing disc, are extruded from the epithelium and undergo apoptosis. Excessive actin filament polymerization is not sufficient to explain this phenotype, as loss of Cofilin or Cyclase-associated protein does not cause cell extrusion or death. Misexpression of Vestigial, the transcription factor that specifies the wing blade, both increases cpa transcription and makes cells dependent on cpa for their maintenance in the epithelium. Our results suggest that Vestigial specifies the cytoskeletal changes that lead to morphogenesis of the adult wing.
Milton controls the early acquisition of mitochondria byDrosophilaoocytes
Authors: Cox Rachel T. , Spradling Allan C.
Published: August 2006

Mitochondria in many species enter the young oocyte en mass from interconnected germ cells to generate the large aggregate known as the Balbiani body. Organelles and germ plasm components frequently associate with this structure. Balbiani body mitochondria are thought to populate the germ line, ensuring that their genomes will be inherited preferentially. We find that milton, a gene whose product was previously shown to associate with Kinesin and to mediate axonal transport of mitochondria, is needed to form a normal Balbiani body. In addition, germ cells mutant for some milton or Kinesin heavy chain (Khc) alleles transport mitochondria to the oocyte prematurely and excessively, without disturbing Balbiani body-associated components. Our observations show that the oocyte acquires the majority of its mitochondria by competitive bidirectional transport along microtubules mediated by the Milton adaptor. These experiments provide a molecular explanation for Balbiani body formation and, surprisingly,show that viable fertile offspring can be obtained from eggs in which the normal program of mitochondrial acquisition has been severely perturbed.
Analysis of cell migration, transdifferentiation and apoptosis during mouse secondary palate fusion
Authors: Jin Jiu-Zhen , Ding Jixiang
Published: August 2006

Malformations in secondary palate fusion will lead to cleft palate, a common human birth defect. Palate fusion involves the formation and subsequent degeneration of the medial edge epithelial seam. The cellular mechanisms underlying seam degeneration have been a major focus in the study of palatogenesis. Three mechanisms have been proposed for seam degeneration:lateral migration of medial edge epithelial cells; epithelial-mesenchymal trans-differentiation; and apoptosis of medial edge epithelial cells. However,there is still a great deal of controversy over these proposed mechanisms. In this study, we established a [Rosa26↔C57BL/6] chimeric culture system, in which a Rosa26-originated `blue' palatal shelf was paired with a C57BL/6-derived `white' palatal shelf. Using this organ culture system,we observed the migration of medial edge epithelial cells to the nasal side,but not to the oral side. We also observed an anteroposterior migration of medial edge epithelial cells, which may play an important role in posterior palate fusion. To examine epithelial-mesenchymal transdifferentiation during palate fusion, we bred a cytokeratin 14-Cre transgenic line into the R26R background. In situ hybridization showed that the Cretransgene is expressed exclusively in the epithelium. However,β-galactosidase staining gave extensive signals in the palatal mesenchymal region during and after palate fusion, demonstrating the occurrence of an epithelial-mesenchymal transdifferentiation mechanism during palate fusion. Finally, we showed that Apaf1 mutant mouse embryos are able to complete palate fusion without DNA fragmentation-mediated programmed cell death, indicating that this is not essential for palate fusion in vivo.
A microRNA detection system based on padlock probes and rolling circle amplification
Authors: Jonstrup Søren Peter , Koch Jørn , Kjems Jørgen
Published: August 2006

The differential expression and the regulatory roles of microRNAs (miRNAs) are being studied intensively these years. Their minute size of only 19–24 nucleotides and strong sequence similarity among related species call for enhanced methods for reliable detection and quantification. Moreover, miRNA expression is generally restricted to a limited number of specific cells within an organism and therefore requires highly sensitive detection methods. Here we present a simple and reliable miRNA detection protocol based on padlock probes and rolling circle amplification. It can be performed without specialized equipment and is capable of measuring the content of specific miRNAs in a few nanograms of total RNA.
Pokeweed antiviral protein depurinates the sarcin/ricin loop of the rRNA prior to binding of aminoacyl-tRNA to the ribosomal A-site
Authors: Mansouri Sheila , Nourollahzadeh Emad , Hudak Katalin A.
Published: August 2006

Ribosome-inactivating proteins, such as the pokeweed antiviral protein (PAP), inhibit translation by depurinating the conserved sarcin/ricin loop of the large ribosomal RNA. Depurinated ribosomes are unable to bind elongation factor 2, and, thus, the translocation step of the elongation cycle is inhibited. Though the consequences of depurination are well characterized, the ribosome conformation required for depurination to take place has not been described. In this report, we correlate biochemical and genetic data to conclude that pokeweed antiviral protein depurinates the sarcin/ricin loop when the A-site of the ribosomal peptidyl-transferase center is unoccupied. We show that prior incubation of ribosomes with puromycin, an analog of the 3′-terminus of aminoacyl-tRNA, inhibits both binding and depurination by PAP in a concentration-dependent manner. Expression of PAP in the yeast strain mak8-1 results in little depurination unless the cells are lysed, a process that would promote loss of aminoacyl-tRNA from the ribosome. The mak8-1 strain is known to exhibit a higher affinity for aminoacyl-tRNA compared with wild-type cells, and therefore, its ribosomes are more resistant to PAP in vivo. These data contribute to the mechanism of action of pokeweed antiviral protein; specifically, they have uncovered the ribosomal conformation required for depurination that leads to subsequent translation inhibition.
Prosecution Interviews of Witnesses: What More Will Be Sacrificed to ‘Narrow the Justice Gap’?
Authors: McGowan Laura
Published: August 2006

It seems that prosecutors will be entitled to interview complainants and other prosecution witnesses in criminal cases. How these interviews will be conducted and at what stage of proceedings is not clear. This article considers what effect prosecution interviews may have on various stages of a criminal investigation and prosecution. It concludes that interviews for the purpose of screening out weak charges may be welcome, but great caution should be exercised when interviewing witnesses later in prosecution proceedings and that the objectivity of prosecutors and prosecution counsel should not be sacrificed in an attempt to ‘narrow the justice gap’.
A Multiplex Assay for the Detection and Mapping of Complex Glycerol Kinase Deficiency
Authors: Klein Roger D , Thorland Erik C , Gonzales Patrick R , Beck Patricia A , Dykas Daniel J , McGrath James M , Bale Allen E
Published: August 2006

Background: Glycerol kinase deficiency (GKD) is an X-linked recessive disorder that presents in both isolated and complex forms. The contiguous deletion that leads to GKD also commonly affects NR0B1 (DAX1), the gene associated with adrenal hypoplasia congenita, and DMD, the Duchenne muscular dystrophy gene. Molecular testing to delineate this deletion is expensive and has only limited availability.

Methods: We designed a multiplex PCR assay for the detection and mapping of a contiguous deletion potentially affecting the IL1RAPL1, NR0B1, GK, and DMD genes in a 29-month-old male patient with GKD.

Results: Multiplex PCR detected a contiguous deletion that involved the IL1RAPL1, NR0B1, GK, and DMD genes. Although the patient had a creatine kinase concentration within the reference interval, further mapping with PCR revealed that exon 74 was the last intact exon at the 3′ end of the DMD gene.

Conclusions: Multiplex PCR is an effective and inexpensive way to detect and map the contiguous deletion in cases of complex GKD. The extension of a deletion to include DMD exon 75 in a patient with a creatine kinase concentration within the reference interval suggests that this region of the gene may not be essential for protein function.
Genetic Variation inDrosophila melanogasterResistance to Infection: A Comparison Across Bacteria
Authors: Lazzaro Brian P , Sackton Timothy B , Clark Andrew G
Published: August 2006

Insects use a generalized immune response to combat bacterial infection. We have previously noted that natural populations of D. melanogaster harbor substantial genetic variation for antibacterial immunocompetence and that much of this variation can be mapped to genes that are known to play direct roles in immunity. It was not known, however, whether the phenotypic effects of variation in these genes are general across the range of potentially infectious bacteria. To address this question, we have reinfected the same set of D. melanogaster lines with Serratia marcescens, the bacterium used in the previous study, and with three additional bacteria that were isolated from the hemolymph of wild-caught D. melanogaster. Two of the new bacteria, Enterococcus faecalis and Lactococcus lactis, are gram positive. The third, Providencia burhodogranaria, is gram negative like S. marcescens. Drosophila genotypes vary highly significantly in bacterial load sustained after infection with each of the four bacteria, but mean loads are largely uncorrelated across bacteria. We have tested statistical associations between immunity phenotypes and nucleotide polymorphism in 21 candidate immunity genes. We find that molecular variation in some genes, such as Tehao, contributes to phenotypic variation in the suppression of only a subset of the pathogens. Variation in SR-CII and 18-wheeler, however, has effects that are more general. Although markers in SR-CII and 18-wheeler explain >20% of the phenotypic variation in resistance to L. lactis and E. faecalis, respectively, most of the molecular polymorphisms tested explain <10% of the total variance in bacterial load sustained after infection.
Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.)
Authors: Schlueter Jessica A , Scheffler Brian E , Schlueter Shannon D , Shoemaker Randy C
Published: August 2006

The paleopolyploid soybean genome was investigated by sequencing homeologous BAC clones anchored by duplicate N-hydroxycinnamoyl/benzoyltransferase (HCBT) genes. The homeologous BACs were genetically mapped to linkage groups C1 and C2. Annotation of the 173,747- and 98,760-bp BACs showed that gene conservation in both order and orientation is high between homeologous regions with only a single gene insertion/deletion and local tandem duplications differing between the regions. The nucleotide sequence conservation extends into intergenic regions as well, probably due to conserved regulatory sequences. Most of the homeologs appear to have a role in either transcription/DNA binding or cellular signaling, suggesting a potential preference for retention of duplicate genes with these functions. Reverse transcriptase–PCR analysis of homeologs showed that in the tissues sampled, most homeologs have not diverged greatly in their transcription profiles. However, four cases of changes in transcription were identified, primarily in the HCBT gene cluster. Because a mapped locus corresponds to a soybean cyst nematode (SCN) QTL, the potential role of HCBT genes in response to SCN is discussed. These results are the first sequenced-based analysis of homeologous BACs in soybean, a diploidized paleopolyploid.
Marker-Based Prediction of the Parental Genome Contribution to Inbred Lines Derived From Biparental Crosses
Authors: Frisch Matthias , Melchinger Albrecht E
Published: August 2006

Molecular markers can be employed to predict the parental genome contribution to inbred lines. The proportion α of alleles originating from parent P1 at markers polymorphic between the parental lines P1 and P2 is commonly used as a predictor for the genome contribution of parent P1 to an offspring line. Our objectives were to develop a new marker-based predictor ξ for the parental genome contribution, which takes into account not only the alleles at marker loci but also their map distance, and to compare the prediction precision of ξ with that of alternative methods. We derived formulas for ξ for inbreds derived from biparental crosses (F1 and backcrosses) with the single-seed descent or double-haploid method and presented an extension ξ* possessing statistical optimum properties. In a simulation study, α showed a systematic overestimation of large parental genome contribution that was not observed for ξ. The mean squared prediction error of ξ was at least 50% smaller than that of α for linkage maps with unequal distances between adjacent markers. A data set from a study on plant variety protection in maize was used to illustrate the application of ξ. We conclude that ξ provides substantially greater prediction precision than the commonly used predictor α in a broad range of applications in genetics and breeding.
Marker Genotypes and Population Admixture and Their Association With Body Weight, Height and Relative Body Mass in United States Federal Bison Herds
Authors: Musani Solomon K , Halbert Natalie D , Redden David T , Allison David B , Derr James N
Published: August 2006

Elucidating genetic influences on bison growth and body composition is of interest, not only because bison are important for historical, cultural, and agricultural reasons, but also because their unusual population history makes them valuable models for finding influential loci in both domestic cattle and humans. We tested for trait loci associated with body weight, height, and bison mass index (BMI) while controlling for estimated ancestry to reduce potential confounding effects due to population admixture in 1316 bison sampled from four U.S. herds. We used 60 microsatellite markers to model each phenotype as a function of herd, sex, age, marker genotypes, and individual ancestry estimates. Statistical significance for genotype and its interaction with ancestry was evaluated using the adaptive false discovery rate. Of the four herds, two appeared to be admixed and two were nonadmixed. Although none of the main effects of the loci were significant, estimated ancestry and its interaction with marker loci were significantly associated with the phenotypes, illustrating the importance of including ancestry in the models and the dependence of genotype–phenotype associations on background ancestry. Individual loci contributed ∼2.0% of variation in weight, height, and BMI, which confirms the utility and potential importance of adjusting for population stratification.
Drosophila mus301/spindle-C Encodes a Helicase With an Essential Role in Double-Strand DNA Break Repair and Meiotic Progression
Authors: McCaffrey Ruth , St Johnston Daniel , González-Reyes Acaimo
Published: August 2006

mus301 was identified independently in two genetic screens, one for mutants hypersensitive to chemical mutagens and another for maternal mutants with eggshell defects. mus301 is required for the proper specification of the oocyte and for progression through meiosis in the Drosophila ovary. We have cloned mus301 and show that it is a member of the Mus308 subfamily of ATP-dependent helicases and the closest homolog of human and mouse HEL308. Functional analyses demonstrate that Mus301 is involved in chromosome segregation in meiosis and in the repair of double-strand-DNA breaks in both meiotic and mitotic cells. Most of the oogenesis defects of mus301 mutants are suppressed by mutants in the checkpoint kinase Mei41 and in MeiW68, the Spo11 homolog that is thought to generate the dsDNA breaks that initiate recombination, indicating that these phenotypes are caused by activation of the DNA damage checkpoint in response to unrepaired Mei-W68-induced dsDNA breaks. However, neither mei-W68 nor mei-41 rescue the defects in oocyte specification of mus301 mutants, suggesting that this helicase has another function in oocyte selection that is independent from its role in meiotic recombination.
Variable Populations Within Variable Populations: Quantifying Mitochondrial Heteroplasmy in Natural Populations of the Gynodioecious PlantSilene vulgaris
Authors: Welch Mark E , Darnell Michael Z , McCauley David E
Published: August 2006

Populations of mitochondria reside within individuals. Among angiosperms, these populations are rarely considered as genetically variable entities and typically are not found to be heteroplasmic in nature, leading to the widespread assumption that plant mitochondrial populations are homoplasmic. However, empirical studies of mitochondrial variation in angiosperms are relatively uncommon due to a paucity of sequence variation. Recent greenhouse studies of Silene vulgaris suggested that heteroplasmy might occur in this species at a level that it is biologically relevant. Here, we use established qualitative methods and a novel quantitative PCR method to study the intraindividual population genetics of mitochondria across two generations in natural populations of S. vulgaris. We show incidences of heteroplasmy for mitochondrial atpA and patterns of inheritance that are suggestive of more widespread heteroplasmy at both atpA and cox1. Further, our results demonstrate that quantitative levels of mitochondrial variation within individuals are high, constituting 26% of the total in one population. These findings are most consistent with a biparental model of mitochondrial inheritance. However, selection within individuals may be instrumental in the maintenance of variation because S. vulgaris is gynodioecious. Male sterility is, in part, regulated by the mitochondrial genome, and strong selection pressures appear to influence the frequency of females in these populations.
Assessing the Significance of Quantitative Trait Loci in Replicable Mapping Populations
Authors: Zou Fei , Xu Zongli , Vision Todd
Published: August 2006

Replicable populations, such as panels of recombinant inbred or doubled haploid lines, are convenient resources for the mapping of QTL. To increase mapping power, replications are often collected within each RI line and a common way to analyze such data is to include in the QTL model only a single measurement from each line that represents the average among the replicates (a line means model). An obvious, but seldom explored, alternative, is to include every replicate in the model (a full data model). Here, we use simulations to compare these two approaches. Further, we propose an extension of the standard permutation procedure that is required to correctly control the type I error in mapping populations with nested structure.
Inheritance Patterns of Transcript Levels in F1 Hybrid Mice
Authors: Cui Xiangqin , Affourtit Jason , Shockley Keith R , Woo Yong , Churchill Gary A
Published: August 2006

Genetic analysis of transcriptional regulation is a rapidly emerging field of investigation that promises to shed light on the regulatory networks that control gene expression. Although a number of such studies have been carried out, the nature and extent of the heritability of gene expression traits have not been well established. We describe the inheritance of transcript levels in liver tissue in the first filial (F1) generation of mice obtained from reciprocal crosses between the common inbred strains A/J and C57BL/6J. We obtain estimates of genetic and technical variance components from these data and demonstrate that shrinkage estimators can increase detectable heritability. Estimates of heritability vary widely from transcript to transcript, with one-third of transcripts showing essentially no heritability (<0.01) and one-quarter showing very high heritability (>0.50). Roughly half of all transcripts are differentially expressed between the two parental strains. Most transcripts show an additive pattern of inheritance. Dominance effects were observed for 20% of transcripts and a small number of transcripts were identified as showing an overdominance mode of inheritance. In addition, we identified 314 transcripts with expression levels that differ between the reciprocal F1 animals. These genes may be related to maternal effect.
Repair of DNA Damage Induced by Bile Salts in Salmonella enterica
Authors: Prieto Ana I , Ramos-Morales Francisco , Casadesús Josep
Published: August 2006

Exposure of Salmonella enterica to sodium cholate, sodium deoxycholate, sodium chenodeoxycholate, sodium glychocholate, sodium taurocholate, or sodium glycochenodeoxycholate induces the SOS response, indicating that the DNA-damaging activity of bile resides in bile salts. Bile increases the frequency of GC → AT transitions and induces the expression of genes belonging to the OxyR and SoxRS regulons, suggesting that bile salts may cause oxidative DNA damage. S. enterica mutants lacking both exonuclease III (XthA) and endonuclease IV (Nfo) are bile sensitive, indicating that S. enterica requires base excision repair (BER) to overcome DNA damage caused by bile salts. Bile resistance also requires DinB polymerase, suggesting the need of SOS-associated translesion DNA synthesis. Certain recombination functions are also required for bile resistance, and a key factor is the RecBCD enzyme. The extreme bile sensitivity of RecB−, RecC−, and RecA− RecD− mutants provides evidence that bile-induced damage may impair DNA replication.
The Drosophila Fragile X Protein dFMR1 Is Required During Early Embryogenesis for Pole Cell Formation and Rapid Nuclear Division Cycles
Authors: Deshpande Girish , Calhoun Gretchen , Schedl Paul
Published: August 2006

The FMR family of KH domain RNA-binding proteins is conserved from invertebrates to humans. In humans, inactivation of the X-linked FMR gene fragile X is the most common cause of mental retardation and leads to defects in neuronal architecture. While there are three FMR family members in humans, there is only a single gene, dfmr1, in flies. As in humans, inactivation of dfmr1 causes defects in neuronal architecture and in behavior. dfmr1 has other functions in the fly in addition to neurogenesis. Here we have analyzed its role during early embryonic development. We found that dfmr1 embryos display defects in the rapid nuclear division cycles that precede gastrulation in nuclear migration and in pole cell formation. While the aberrations in nuclear division are correlated with a defect in the assembly of centromeric/centric heterochromatin, the defects in pole cell formation are associated with alterations in the actin–myosin cytoskeleton.
Joining timber with glass fibre and epoxy
Authors: Claisse P. , Masse B.
Published: August 2006

Wood-glass-epoxy joints are made by wetting glass fibre cloth with epoxy resin and bonding it to the sides of the timbers. They represent an economic alternative to punched metal plates or bolts in a variety of applications, including those where high durability, waterproofing or an attractive appearance are required. They may also be used to enhance the properties of the timber members themselves. Previously published work has shown that these joints perform well in fatigue. This paper presents test results for strength and stiffness for various different joint configurations with the timbers parallel and at 30°, 60° and 90° to each other. The results indicated that uniaxial glass cloth performs better than biaxial glass cloth in all joints. Misaligning the glass with the direction of loading has a significant detrimental effect on performance. For the non-parallel joints the unavoidable effect of loading at an angle to the grain reduced both the failure loads and the stiffness.
A fracture-based model for the compressive strength of masonry
Authors: Roberts T. M. , Hughes T. G.
Published: August 2006

A mechanical model for explaining and quantifying the uniaxial compressive strength of masonry has been developed. The mechanical model is based on the development of tensile cracks from shear plane flaws in the units and the stress intensity factor resulting from the applied loading and tensile stresses induced by lateral straining of the mortar. Calibration of the model requires knowledge of only the compressive strength of the units, and the corresponding compressive strength of the masonry for a single mortar compressive strength. Theoretical predictions are compared and show close correlation with characteristic compressive strengths given in codes of practice.
Briefing: Sustainable timber procurement
Authors: McGregor A.
Published: August 2006

Demand for forest products with chain of custody certification—the unbroken path which products take from an independently certified forest to the consumer—has grown dramatically in the last three years, from all fronts, not least from central government. This briefing note outlines how the various certification schemes have evolved and discusses the issues surrounding them.
Passing ability and segregation stability of self-consolidating concrete with different aggregate proportions
Authors: Ng I. Y. T. , Wong H. H. C. , Kwan A. K. H.
Published: August 2006

An extensive experimental programme has been carried out to study the effects of fine:10 mm:20 mm aggregate proportions on the passing ability and segregation stability of self-consolidating concrete. A total of 18 trial concrete mixes with water/cementitious materials ratios ranging from 0·30 to 0·36 and different combinations of fine and coarse aggregates were produced. In each mix, the paste volume was set at 35%, and pulverised fuel ash, condensed silica fume and a third-generation superplasticiser were added at dosages of 25%, 5% and 3% respectively. All the mixes were tested to have slump flow well above 700 mm. However, not all have satisfactory passing ability and segregation stability, as revealed by J-ring, U-box and sieve segregation tests. The cohesiveness and coarse aggregate content appeared to be the major factors as the passing ability and segregation stability were generally better for mixes with higher cohesiveness and lower coarse aggregate content. Nevertheless, some of the mixes may be considered for making high-strength, self-consolidating concrete. They have the common characteristics of 20 mm aggregate content ≤ 10 mm aggregate content and coarse aggregate content ≤ fine aggregate content.
Green Manure as Nitrogen Source for Sweet Corn in a Warm–Temperate Environment
Authors: Cherr C. M. , Scholberg J. M. S. , McSorley R.
Published: August 2006

Legumes utilized as GM may provide on‐farm organic N. Nonetheless, data regarding GM use on sandy soils in warm‐temperate environments remains scarce. We conducted a 2‐yr field study to evaluate growth and decomposition of sunn hemp (Crotalaria juncea L.), blue lupin (Lupinus angustifolius L., winter 2001–2002), and Cahaba white vetch (Vicia sativa L., winter 2002–2003) used as GM to provide N for sweet corn (Zea mays L. var Rugosa) in a reduced tillage system in northern Florida. Intercepted solar radiation accounted for most variability in total GM dry weight and N content regardless of species or year. Sunn hemp exhibited substantial growth and N accumulation (≤12.2 Mg ha−1 and 172 kg N ha−1 in 14 wk). However, rapid N loss (45–58% within 4 wk after death) occurred after sunn hemp death. Winter GM growth (2.0–4.0 Mg ha−1 and 51–104 kg N ha−1 in 18–20 wk) appeared limited by low LAI response to growing degree days (GDD) and was not affected by previous sunn hemp GM. Sunn hemp residues and living winter legume together contained 120 to 125 kg N ha−1 at time of final sampling before sweet corn planting. Corn rotated with sunn hemp plus winter GM and supplemented with 133 kg synthetic N ha−1 produced marketable ear yields similar to monoculture corn fertilized with 200 kg synthetic N ha−1, but the practical value of this benefit is low. In northern Florida, winter and/or summer GM use may substitute only for a relatively small portion of synthetic N rates.
An Automated Template Approach for Generating Web‐Based Conservation Planning Worksheets
Authors: Steiner Jeffrey J. , Minoura Toshimi , Imaeda Mariko
Published: August 2006

An automated web‐form generator system was created to rapidly produce dynamic web‐based inventory and assessment worksheets that are used by the USDA Natural Resources Conservation Service (NRCS) to describe the condition of natural resources on farms and ranches. These worksheets are used by NRCS as part of the criteria for creating a conservation plan to qualify landowners for payments under the USDA Farm Bill Conservation Title. Presently, most worksheets are filled out by hand or in personal computer spreadsheets. If worksheets such as these were available over the web, landowners could also self‐assess the conditions on their farms or ranches before requiring assistance of NRCS conservation planners or technical service providers. Because many conservation worksheets have a similar style and behavior, we created an automated web‐script generator that produces a dynamic web‐page worksheet from a common template file and a configuration file. A worksheet‐specific configuration file provides the details for the worksheet. The template, configuration files, and web scripts are all in PHP (PHP hypertext processor). Each configuration file required approximately 5 h to program, a savings of more than 4 d compared with a web‐based worksheet programmed individually with a scripting language. In this way, various conservation worksheets can be quickly created for the web, as well as be easily maintained. As an example, we produced a suite of assessment worksheets used by Oregon NRCS with our automated web‐form conservation worksheet system. Those worksheets are accessible at: http://yukon.een.orst.edu/ms_apps/wq_indexes/forms/index_menu.html (verified 5 May 2006).
Whole Plant Photosynthesis, Development, and Carbon Partitioning in Potato as a Function of Temperature
Authors: Timlin Dennis , Lutfor Rahman S. M. , Baker Jeffery , Reddy V. R. , Fleisher David , Quebedeaux Bruno
Published: August 2006

Knowledge of temperature effects on whole canopy photosynthesis, growth, and development of potato (Solanum tuberosum L.) is important for crop model development and evaluation. The objective of this study was to quantify the effects of temperature on canopy photosynthesis, development, growth, and partitioning of potato cv. Atlantic under elevated atmospheric CO2 concentration (700 μL L−1 CO2). Potato plants were grown in day‐lit plant growth chambers at six constant day/night temperatures, (12, 16, 20, 24, 28, and 32°C) during a 52‐d experimental period in 1999 in Beltsville, MD. Main stem length and main stem expanded leaf number were measured nondestructively at 4 d intervals while leaf, stem, root, and tuber weights were obtained by destructive harvesting at biweekly time intervals. Canopy level net photosynthesis (PN) was obtained from gas exchange measurements. The optimum temperature for canopy photosynthesis was 24°C early in the growth period and shifted to lower temperatures as the plants aged. Total end‐of‐season biomass was highest in the 20°C treatment. End‐of‐season tuber mass and the ratio of tuber to total biomass decreased with increasing temperature above 24°C. Accumulated biomass was a linear function of total C gain with a common slope for all treatments. However, the proportion of C allocated to tubers decreased with increasing temperatures. High respiration losses decreased total C gain at higher temperatures. When simulating photosynthesis and C assimilation in crop models, source–sink relationships with temperature and photosynthesis need to be accounted for.
Impact of Tillage and Rotation on Yield and Economic Performance in Corn‐Based Cropping Systems
Authors: Meyer‐Aurich Andreas , Janovicek Ken , Deen William , Weersink Alfons
Published: August 2006

The objective of our research was to identify economically efficient corn (Zea mays L.) based tillage‐rotation combinations using a 20‐yr data set from a long‐term experiment in Ontario, Canada. Seven rotations in two tillage systems (moldboard and chisel plow) were analyzed. We found multiple benefits associated with diversifying rotations in both tillage systems The integration of soybean [Glycine max (L.) Merr.] or soybean and wheat (Triticum aestivum L.) resulted in 7 to 11% higher corn yields in the chisel tillage system. In the plow tillage system corn yield in rotation with soybean and wheat increased by 5%, when wheat was underseeded with red clover (Trifolium pratense L.). These diversified rotations resulted in an increase in yearly net returns of $51 to $64 in the moldboard tillage system and $96 to $108 in the chisel tillage system. The diversification of rotations reduces variance of net return and thus makes the rotations attractive to risk averse producers. Furthermore diversified rotations showed less response to price changes. Diversified rotations evaluated in this study also proved to be less affected by increasing energy costs. Red clover seeded into wheat resulted in 5% higher yields for the following corn crop in the moldboard system. Rotations that included red clover cover lowered production risk but did not have higher net returns than comparable rotations without red clover. However, the potential for red clover to reduce N fertilization requirements for the following corn, was not considered in this study. Yield penalties due to chisel plowing with financial consequences were only observed in continuous corn. In all other rotations the effect of tillage was negligible. An increase in energy costs forces farmers to switch to crops with lower inputs rather than switch to reduced tillage.
Evaluating Techniques for Determining Tillage Regime in the Southeastern Coastal Plain and Piedmont
Authors: Sullivan Dana G. , Truman Clint C. , Schomberg Harry H. , Endale Dinku M. , Strickland Timothy C.
Published: August 2006

Reduced tillage and residue management can have significant impacts on soil and water quality, primarily through the accumulation of soil organic C. Yet, methods of tillage and residue cover assessment are time and resource intensive, and often do not yield spatially representative results. A major goal of this study was to compare new remote sensing (RS) indices with the current line‐transect approach for differentiating between conventional (CT) and conservation tillage systems. Experimental plots were located in two physiographic regions in Georgia: the Southern Piedmont and Southern Coastal Plain. Treatments consisted of no tillage (NT) or CT at the Piedmont site, and strip‐tillage (ST) or CT at the Coastal Plain site. Remotely sensed data were acquired three times prior to canopy closure, using a handheld multispectral radiometer (485–1650 nm) and thermal imager (7000–14 000 nm). Soil texture and soil water content were measured to assess the impact of changes in soil background reflectance on crop residue assessments. Results showed that differences in spectral response between CT and conservation tillage systems were best observed using a normalized difference ratio of near infrared (NIR) (1650 ± 100 nm) and blue (485 ± 45 nm) spectra under dry conditions and low canopy cover (<25%). Differences in soil texture and color were the primary limiting factors in differentiating between tillage treatments. However, using readily available soil survey data, our data indicate that visible and NIR spectra can be used to rapidly differentiate between CT and conservation tillage systems in the Georgia Southeastern Coastal Plain and Piedmont physiographic regions.