FASTA barcodes: a simple method for the identification of yeast ORF deletions

A consortium of yeast geneticists have created -6000 individual ORF deletions, representing > 96% of the currently verified or predicted ORFs in S. cerevisiae. Importantly, molecular barcodes (each a unique 20 bp sequence termed either Uptag or Downtag) were used as identifiers for every ORF deletion. Microarray analyses of pooled yeast deletions has been used to identify thousands of genes involved in general fitness, haploinsufficiency, drug resistance and DNA damage repair. However, application of this powerful technology requires considerable expense, expertise and specialized equipment. While standard PCR techniques and specifically designed PCR primers can be used to confirm that a given ORF is in fact deleted, this procedure cannot be used to identify unknown deletions. In theory, every ORF deletion could be determined by barcode sequencing. However, neither a consolidated barcode database nor a reliable search engine is currently available for this purpose. To address this need, we have adapted a FASTA sequence program that utilizes the unique barcode database to allow users to identify individual ORF deletions, based upon simple sequencing reactions of PCR amplifications of either Uptag or Downtag barcodes. In silico and practical testing of this application reveals that it is an inexpensive, reliable and reproducible method for rapidly identifying unknown deletions. This approach allows laboratories to conduct small- or large-scale genetic screens with pooled yeast deletion strains and identify or verify any ORF deletion without the need for microarray technology.     

Maternal folate supply and sex influence gene‐specific DNA methylation in the fetal gut

Scope : Epidemiological evidence supports the developmental origins of health and disease hypothesis that developmental under/over‐nutrition increases adulthood disease risk. Epigenetic markings are one potential mechanism mediating these effects. Altered folate supply may influence methyl group availability for DNA methylation. We reported low folate supply in utero was associated with reduced global DNA methylation in the murine small intestine of adult offspring. We hypothesised that aberrant methylation would be observed during early development. Methods and results : Female C57BL/6J mice were fed diets containing 2 mg folic acid/kg or 0.4 mg folic acid/kg 4 wk before mating and during pregnancy. At 17.5 day gestation, gene methylation in fetal gut was analysed by Pyrosequencing^®. Low folate reduced overall methylation of Slc394a by 3.4% (p=0.038) but did not affect Esr1 or Igf2 differentially methylated region (DMR) 1. There were sex‐specific differences in Slc394a and Esr1 methylation (2.4% higher in females (p=0.002); 4% higher in males (p=0.0014), respectively). Conclusion : This is the first study reporting causal effects of maternal folate depletion on gene‐specific methylation in fetal gut. These observations support reports that altered methyl donor intake during development affects DNA methylation in the offspring. The consequences of epigenetic changes for health throughout the life course remain to be investigated.     

Report of the U.S. Department of Energy Fusion Energy Sciences Advisory Committee (FESAC) Panel Reviewing the Theory and Computing Program

This Panel was set up by the Fusion Energy Sciences Advisory Committee (FESAC) at its November 2000 meeting for the purpose of addressing questions from the Department of Energy concerning the theory and computing/simulation program of the Office of Fusion Energy Sciences. Although the Panel primarily addressed programmatic questions, it acknowledges that the theory and computing in fusion energy sciences has a stellar record of research successes. (A recent FESAC report entitled Opportunities in the Fusion Energy Sciences Program listed a number of theory and computing research highlights.) Last year the National Research Council performed an assessment of the quality of the fusion energy sciences program—including theory and computing—and concluded that the quality of its research is on a par with that of other leading areas of contemporary physical science.     

Effect of preweaning disease on the reproductive performance and first-lactation milk production of heifers in a large dairy herd

Raising replacement heifers represents a substantial cost in dairy farms, with reproductive efficiency being one of the main factors driving the total rearing cost. Diseases during the preweaning period, such as diarrhea or bovine respiratory disease (BRD), are reported at high incidence risks worldwide. However, the long-term effects of disease before weaning on productive and reproductive performance remain controversial. This retrospective cohort study explored the extent to which diseases such as diarrhea or BRD during the preweaning period affected average daily gain (ADG), herd removal, reproductive indices, and 305-d mature equivalent milk production (305ME) of replacement heifers. The health, growth, and production records of 2,272 female calves from a large dairy herd were used; 487 and 926 of the calves had BRD and diarrhea, respectively, before weaning. The reproductive variables age at first service, age at successful service, age at calving, and pregnancies per artificial insemination were calculated. Associations of disease status with reproduction indices, removal from herd, ADG, and 305ME were evaluated by survival analysis and mixed models. Heifers with a history of BRD before weaning were less likely to be inseminated or achieve first calving than heifers without BRD. However, BRD status did not change the age at first insemination of calving among those being inseminated or reaching first calving, respectively. There were also no differences in ADG, 305ME, and pregnancies per artificial insemination between heifers with and without a history of BRD. A history of diarrhea preweaning was not associated with changes in the probability of being inseminated, having a confirmed pregnancy, or reaching first calving. However, heifers affected by diarrhea required more inseminations to become pregnant. Diarrhea status was also associated with a 325-kg reduction in 305ME in the first lactation and a 50 g/d reduction in ADG. Collectively, our results demonstrate some long-term effects of diseases before weaning on the reproductive efficiency of heifers and first-lactation 305ME production, but with limited effect on the time to achieve critical reproductive performance indicators.     

Noncontact measurement of electrostatic fields: verification of modeled potentials within ion mobility spectrometer drift tube designs

The heart of an ion mobility spectrometer is the drift region where ion separation occurs. While the electrostatic potentials within a drift tube design can be modeled, no method for independently validating the electrostatic field has previously been reported. Two basic drift tube designs were modeled using SIMION 7.0 to reveal the expected electrostatic fields: (1) A traditional alternating set of electrodes and insulators and (2) a truly linear drift tube. One version of the alternating electrode/insulator drift tube and two versions of linear drift tubes were then fabricated. The stacked alternating electrodes/insulators were connected through a resistor network to generate the electrostatic gradient in the drift tube. The two linear drift tube designs consisted of two types of resistive drift tubes with one tube consisting of a resistive coating within an insulating tube and the other tube composed of resistive ferrites. The electrostatic fields within each type of drift tube were then evaluated by a noncontact method using a Kelvin-Zisman type electrostatic voltmeter and probe (results for alternative measurement methods provided in supplementary material). The experimental results were then compared with the electrostatic fields predicted by SIMION. Both the modeling and experimental measurements reveal that the electrostatic fields within a stacked ion mobility spectrometer drift tube are only pseudo-linear, while the electrostatic fields within a resistive drift tube approach perfect linearity.     

Coagulation dynamics of fractal flocs induced by enmeshment and electrostatic patch mechanisms

The size and structure of flocs during floc formation were monitored for various coagulation mechanisms. Two distinctive mechanisms, namely, enmeshment and electrostatic patch, govern the dynamics of kaolin particles coagulation by polyaluminum chloride (PACl). They were investigated by small angle static light scattering (SASLS) and solid-state ²⁷Al NMR. In addition, a novel wet SEM (WSEM) was used in-situ to image the morphology of the aggregate in aqueous solution. Synthetic suspended particles were coagulated by two PACl products, a commercial product (PACl) and one laboratory product (PACl-E). The PACl-E contained more than 60% Al₁₃ while the PACl contained only 7% Al₁₃, with large percentage of colloidal Al. For coagulation by PACl at neutral pH and high dosage where the strong repulsion between particles occurs, the enmeshment ruled by reaction-limited aggregation (RLA) results in larger sweep flocs as well as higher fractal dimensional structure. For coagulation by PACl-E at alkaline pH and low dosage, the flocs were coagulated predominately by electrostatic patch with Al₁₃ aggregates. At such condition, it is likely that diffusion-limited aggregation (DLA) predominately rule PACl-E coagulation. The fractal dimension (D_s) values of PACl and PACl-E flocs formed at enmeshment and electrostatic patch increased with dosage, respectively. When breakage of flocs occurs, the breakage rate of PACl-E flocs is slower than that of sweep flocs. By WSEM imaging, the adsorption of spherical Al precipitates onto the particles was observed to form sweep flocs with a rough and ragged contour, while the PACl-E flocs were formed with a smooth and glossy structure.     

Packaging postponement: a global packaging strategy

Postponement applications have been growing in recent years as international firms increasingly develop global products that are customized for local markets. The purpose of this article is to provide an understanding of the logistical principles of postponement and speculation. It explores the factors that favour packaging postponement: (a) modular products that can be customized for local markets; (b) products that gain volume, weight or value from packing; (c) unpredictable demand; (d) a large number of market‐based variations for a single formulation; and (e) situations where economies of scale in packaging and logistics can be optimized. Examples are presented. Copyright © 2000 John Wiley & Sons, Ltd.