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.     

Temperature dependent model dielectric function of highly disordered Ga0.52In0.48P

We report on the temperature dependence of the dielectric function of Ga_0.52In_0.48P from room temperature to 500°C, and for photon energies from 0.75 eV to 5 eV. The undoped, highly disordered Ga_0.52In_0.48P thin film was grown by metal-organic vapor phase epitaxy lattice matched onto a (001) GaAs substrate. The dielectric function of Ga_0.52In_0.48P was measured by in-situ spectroscopic ellipsometry, and analyzed using Adachi's composite critical point model. We provide a second-order temperature expansion parameter set for calculation of the Ga_0.52In_0.48P dielectric function and its temperature dependence, and which may become useful for in situ growth control or optoelectronic device performance evaluation at elevated temperatures. We discuss the temperature-induced shift of critical point transition energy parameters.     

In Situ Study of Nanostructure and Electrical Resistance of Nanocluster Films Irradiated with Ion Beams

An in situ study is reported on the structural evolution in nanocluster films under He⁺ ion irradiation using an advanced helium ion microscope. The films consist of loosely interconnected nanoclusters of magnetite or iron‐magnetite (Fe‐Fe₃O₄) core‐shells. The nanostructure is observed to undergo dramatic changes under ion‐beam irradiation, featuring grain growth, phase transition, particle aggregation, and formation of nanowire‐like network and nanopores. Studies based on ion irradiation, thermal annealing and electron irradiation have indicated that the major structural evolution is activated by elastic nuclear collisions, while both electronic and thermal processes can play a significant role once the evolution starts. The electrical resistance of the Fe‐Fe₃O₄ films measured in situ exhibits a super‐exponential decay with dose. The behavior suggests that the nanocluster films possess an intrinsic merit for development of an advanced online monitor for fast neutron radiation with both high detection sensitivity and long‐term applicability, which can enhance safety measures in many nuclear operations.     

A monolithic CMOS microhotplate-based gas sensor system

A monolithic CMOS microhotplate-based conductance-type gas sensor system is described. A bulk micromachining technique is used to create suspended microhotplate structures that serve as sensing film platforms. The thermal properties of the microhotplates include a 1-ms thermal time constant and a 10/spl deg/C/mW thermal efficiency. The polysilicon used for the microhotplate heater exhibits a temperature coefficient of resistance of 1.067/spl times/10/sup -3///spl deg/C. Tin(IV) oxide and titanium(IV) oxide (SnO/sub 2/,TiO/sub 2/) sensing films are grown over postpatterned gold sensing electrodes on the microhotplate using low-pressure chemical vapor deposition (LPCVD). An array of microhotplate gas sensors with different sensing film properties is fabricated by using a different temperature for each microhotplate during the LPCVD film growth process. Interface circuits are designed and implemented monolithically with the array of microhotplate gas sensors. Bipolar transistors are found to be a good choice for the heater drivers, and MOSFET switches are suitable for addressing the sensing films. An on-chip operational amplifier improves the signal-to-noise ratio and produces a robust output signal. Isothermal responses demonstrate the ability of the sensors to detect different gas molecules over a wide range of concentrations including detection below 100 nanomoles/mole.     

Children's use of looking behavior as a cue to detect another's goal

Three studies examined children's understanding of the role that looking behavior plays in revealing another's desired goal. In each study, participants were asked which of 2 objects a protagonist wanted to obtain. Four-year-olds did not infer that an object examined via prolonged looking was more likely to be the protagonist's goal than an object that was either glanced at or inadvertently touched. Instead, they were accurate only when the protagonist looked at one of two potential goals. In contrast, the majority of 6-year-olds (and adults in Experiment 1) consistently regarded prolonged looking as the more important cue of the protagonist's goal. These age differences suggest that development is characterized by an increasing appreciation that goal is revealed by comparative differences in the quality of perceptual connectedness to objects in the world. One explanation for these age differences is that preschoolers are limited in their understanding of the difference between perceiving with full attention and without it.     

A review of multivariate control charts

A review of the literature on control charts for multivariate quality control (MQC) is given, with a concentration on developments occurring since the mid-1980s. Multivariate cumulative sum (CUSUM) control procedures and a multivariate exponentially weighted moving average (EWMA) control chart are reviewed and recommendations are made regarding their use. Several recent articles that give methods for interpreting an out-of-control signal on a multivariate control chart are analyzed and discussed. Other topics such as the use of principal components and regression adjustment of variables in MQC, as well as frequently used approximations in MQC, are discussed.     

The distribution of lead within ancient and modern human teeth: implications for long-term and historical exposure monitoring

The preservation of lead within human tissue makes it possible to monitor long-term exposure to the element and to model changing sources of lead pollution throughout the lifetime of an individual. Dental tissues have recently been shown to be particularly useful for this purpose. Enamel, for instance, forms at known stages of life and is chemically stable in vivo whereas dentine is remodelled in a predictable fashion. The relative stability of enamel is reflected in its excellent post-mortem preservation. This raises the possibility of using historical or archaeological material to reconstruct long-term trends and establish baseline data relating to exposure among pre-industrial or even prehistoric populations. The use of archaeological material is currently problematic, however, because of the site-specific nature of diagenesis and incomplete understanding of its chemistry, particularly in respect of lead uptake into dental tissue from the burial environment. A detailed study of lead distribution within both ancient and modern human teeth is presented. Conclusions are drawn on the pattern of lead distribution resulting from tissue formation and the manner of its alteration in the burial environment. In particular, attention is drawn to a consistent enrichment of lead within the outer 30 microns of the enamel of both ancient and modern teeth which appears to be unrelated to diagenesis. The implications for current approaches to long-term monitoring and for the reconstruction of historical and archaeological exposure patterns are discussed.     

Bioavailability and pharmacokinetic disposition of tacrine in elderly patients with Alzheimer''s disease

PURPOSE: The Baerveldt glaucoma implant is an aqueous shunting device with large surface area that is installed through a single-quadrant conjunctival incision. A rabbit model of the Baerveldt implant was created to obtain serial histology and clinical information over 1 year. METHODS: Modified versions of the Baerveldt implant (110 or 160 mm2) were implanted in 18 normal New Zealand white rabbit eyes. The rabbits were examined periodically and their intraocular pressures (IOPs) recorded. They were killed at monthly intervals to obtain histology of the bleb capsules. RESULTS: Thin capsules were present at 1 month, which consisted of lamellar collagen deposition surrounded by a granulomatous reaction with multinucleate giant cells. Inflammatory cells (probably macrophages) were scattered on the inner bleb surface. The granulomatous reaction resolved after 4 months. Subsequently, capsule thickness and cellularity remained relatively stable, although the collagen stroma became less compact over time. Sixteen rabbit eyes had initial IOP reductions of > or = 3 mm Hg compared with fellow eyes, which persisted up to 4 weeks postoperatively. Seven eyes (39%) exhibited a hypertensive phase (IOP exceeded that of fellow eye by > or = 3 mm Hg) from 2 weeks to 3 months postoperatively. CONCLUSION: The Baerveldt explant is surrounded by a fibrous capsule that matures over time. The bleb histology in the rabbit model is similar to that described with the Molteno implant in primates and humans, except for the eventual development of a fibroblastic inner lining in the rabbit model. This contrasts with primate and human models, in which the inner lining remains an open mesh.     

Entry of Borrelia burgdorferi into macrophages is end-on and leads to degradation in lysosomes

Blastocyst-derived pluripotent mouse embryonic stem cells can differentiate in vitro to form so-called embryoid bodies (EBs), which recapitulate several aspects of murine embryogenesis. We used this in vitro model to study oxygen supply and consumption as well as the response to reduced oxygenation during the earliest stages of development. EBs were found to grow equally well when cultured at 20% (normoxia) or 1% (hypoxia) oxygen during the first 5 days of differentiation. Microelectrode measurements of pericellular oxygen tension within 13- to 14-day-old EBs (diameter 510-890 micron) done at 20% oxygen revealed efficient oxygenation of the EBs' core region. Confocal laser scanning microscopy analysis of EBs incubated with fluorescent dyes that specifically stain living cells confirmed that the cells within an EB were viable. To determine the EBs' capability to sense low oxygen tension and to specifically respond to low ambient oxygen by modulating gene expression we quantified aldolase A and vascular endothelial growth factor (VEGF) mRNAs, since expression of these genes is upregulated by hypoxia in a variety of cells. Compared with the normoxic controls, we found increased aldolase A and VEGF mRNA levels after exposing 8- to 9-day-old EBs to 1% oxygen. We propose that EBs represent a powerful tool to study oxygen-regulated gene expression during the early steps of embryogenesis, where the preimplantation conceptus resides in a fluid environment with low oxygen tension until implantation and vascularization allow efficient oxygenation.