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PubMed1992

Simultaneous electroelution of proteins from denaturing or native gels into a well matrix.

An electroelution device that is based on a semidry blotter and that allows the simultaneous elution of proteins or other charged macromolecules from one-dimensional gels is described. It consists of a central plate that has a matrix of oblong wells arranged in eight columns of 32 wells each, such that when a gel is placed on the plate each lane of bands is underlaid by a column of wells. The plate is placed between the electrodes of a semidry blotter and the wells are sealed by a dialysis membrane resting on polyacrylamide gel block, prior to being filled with transfer buffer. Using radiolabeled molecular weight standards resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, elution is shown to require 30-60 min for 90% or better of proteins between 10 and 120 kDa to be removed from the gel. The recovery volume is 200 microliters per well and losses due to adsorption onto the dialysis membrane are minimal. beta-Galactosidase eluted from a nonreducing, nondenaturing gel was shown to be quantitatively active. The advantages of the device include its ease of assembly and operation, its speed, its reproducibility, and the fact that no gel slicing is required since all proteins are eluted simultaneously, allowing large-scale screening of multiple protein fractions.

Electrophoresis, Polyacrylamide Gel↗
PubMed1993

An inexpensive microdrive for chronic single-unit recording.

A microdrive and microelectrode costing about $2.67 is described. The assembly is lightweight, compact, and versatile and is ideal for chronic single-unit recording from behaving rats. It is easy to assemble and operate and has been used successfully by undergraduates in the teaching and research laboratory.

Animals↗
PubMed2004

Three's company: component structures bring a closer view of tripartite drug efflux pumps.

Bacterial multidrug resistance is a serious clinical problem and is commonly conferred by tripartite efflux 'pumps' in the prokaryotic cell envelope. Crystal structures of the three components of a drug efflux pump have now been solved: the outer membrane TolC exit duct in the year 2000, the inner membrane AcrB antiporter in 2002 and the periplasmic adaptor MexA in 2004. These structures have enhanced our understanding of the principles underlying pump assembly and operation, and present pumps as new drug targets.

Animals↗
PubMed1997

Preparation for emergency relief after biological warfare.

Upon invitation by the World Health Organization during the Gulf War, a task force "Scorpio" independent from the nations involved in the armed conflict was formed whose task was to determine whether, which and to what extent biological warfare agents had been used. risk assessment concluded that anthrax and Clostridium botulinum toxin were the major risks. The 21 civilian experts had rapidly to decide on the doctrine of operation, to assemble material which could be used and to be immunized or protected otherwise against the potential risks. Biological warfare agents may be used anywhere any time, be it by terrorists or during open or clandestine hostilities. The general population cannot rely on the military to take care of civilian relief, thus international and national organizations may wish to establish similar task forces basing on the "Scorpio" model on a national or regional basis.

Anthrax↗
PubMed2001

Trade-offs in miniature quadrupole designs.

Pressing needs for miniature mass spectrometers became apparent during the last decade in process monitoring and control, space exploration, and environmental screening. Besides the small footprint, common requirements include low cost, low power consumption, field portability, reliability, autonomy, and ease-of-use. Design concepts and construction technologies of miniaturized quadrupole sensors were guided by cost reduction requirements without sacrifice of performance. The first miniature and complete quadrupole mass spectrometer system was introduced as the Micropole sensor. The concept featured a novel technique to assemble and operate multiple miniature quadrupoles in parallel. The short analyzer length offers a significant advantage by enabling direct mass filtering at pressures up in the 10(-2) torr range. High voltages at higher frequencies (10-20 MHz) are required for acceptable mass resolving powers. Additional trade-offs were uncovered in miniature sensors leading to designs optimized for each class of applications. Real time ray tracing of ions injected and filtered in the quadrupole field is used early in the design stage to predict the performance and reliability of the device.

Journal Article↗
PubMed2004

Positive ion transmission mode ion/ion reactions in a hybrid linear ion trap.

A triple quadrupole mass spectrometer capable of ion trapping experiments has been adapted for ion/ion reaction studies. The instrument is based on a commercially available linear ion trap (LIT) tandem mass spectrometer (i.e., an MDS SCIEX 2000 Q TRAP) that has been modified by mounting an atmospheric sampling glow discharge ionization (ASGDI) source to the side of the vacuum manifold for production of singly charged anions. The ASGDI source is located line of sight to the side of the third quadrupole of the triple quadrupole assembly (Q3). Anions are focused into the side of the rod array (i.e., anion injection occurs orthogonal to the normal ion flight path). A transmission mode method to perform ion/ion reactions has been developed whereby positive ions are transmitted through the pressurized collision quadrupole (Q2) while anions are stored in Q2. The Q2 LIT is used to trap negative ions whereas the Q3 LIT is used to accumulate positive ions transmitted from Q2. Anions are injected to Q3 and transferred to Q2, where they are stored and collisionally cooled. Multiply charged protein/peptide ions, formed by electrospray, are then mass selected by the first quadrupole assembly (Q1) operated in the rf/dc mode and injected into Q2. The positive ions, including the residual precursor ions and the product ions arising from ion/ion proton-transfer reactions, are accumulated in Q3 until they are analyzed via mass-selective axial ejection for mass analysis. The parameters that affect ion/ion reactions are discussed, including pressure, nature of the gas in Q2, and operation of Q2 as a linear accelerator. Ion/ion reactions in this mode can be readily utilized to separate ions with the same m/z but largely different mass and charge, e.g., +1 bradykinin and +16 myoglobin, in the gas phase.

Animals↗
PubMed2001

Continuous and stopped flow injection for catalytic determination of total iodine in urine.

This paper describes the use of flow injection (FI) techniques for the determination of iodine in urine, based on the catalytic effect of iodide in the redox reaction between Ce(IV) and As(III). The proposed procedures minimize errors in the conventional batch method arising from the reading of absorbance at a fixed time after addition of Ce(IV) reagent. Two FI systems, for the continuous and stopped modes of operation were assembled. In the continuous-FI system, a thermostated bath was used to increase the sensitivity. However this is not necessary for the stopped-FI system. The two systems are comparable in terms of sensitivity, sample throughput and detection limit. The continuous-FI and the stopped-FI exhibited detection limits (3 sigma) of 2.3 and 3 micrograms I l-1 respectively. Both systems have equal sample throughputs of 35 samples h-1. Calibration plots for both techniques are linear. The FI procedures provide very short analysis times compared to the batch procedure. Using the linear regression test, there is no significant difference between the results from the four methods, i.e., continuous-FI, stopped-FI, conventional method and ICP-MS. The proposed methods are readily applicable for automation and can be an alternative to the conventional procedure for the survey of the iodine deficiency disorder. A condition for sample digestion is also proposed to reduce the amount of chloric acid required for complete digestion. Kinetic information of the reaction can also be obtained from the stopped flow mode.

Flow Injection Analysis↗
PubMed2003

Parental occupations and other risk factors associated with nonchromosomal single, chromosomal single, and multiple birth defects: a population-based study in Singapore from 1994 to 1998.

OBJECTIVE: The purpose of this study was to evaluate the association between the prevalence of birth defects among maternal and paternal occupation groups in Singapore for live births between January 1, 1994, and December 31, 1998, and to determine whether there are certain demographic risk factors and maternal and/or paternal occupation groups that are associated with an increased risk for birth defects versus chromosomal single birth defect, nonchromosomal single birth defect, and multiple birth defects. STUDY DESIGN: This was a retrospective study. Information on live births (Singapore National Registry of Births and Deaths) and birth defect cases (National Birth Defects Register) were studied. Other information included the mother's date of birth, ethnic group, highest educational qualification, and the occupation of the mother and the father. Cox regression analysis was used to determine whether certain demographic and occupational factors were associated with the three groups of birth defects. RESULTS: Of a total of 237,755 live births, there were 3276 birth defect cases (nonchromosomal single birth defect, 1869 cases; chromosomal single birth defect, 197 cases; and multiple birth defects, 1210 cases). Increased risks for all types of birth defects were observed with advancing gestational age. Occurrence of nonchromosomal single birth defect and multiple birth defects were significantly higher for multiple births compared to singleton births. Significant associations were found with the use of "legislators, senior officers, and managers" as reference: Maternal occupation of "cleaners, laborers, and related workers" with chromosomal single birth defect anomalies (adjusted risk ratio, 4.86; 95% CI, 1.07-22.14); paternal occupation of "plant and machine operators and assemblers" (adjusted risk ratio, 1.50; 95% CI, 1.14-1.98) with nonchromosomal single birth defect; "production craftsmen and related workers" and "cleaners and laborers and related workers" with nonchromosomal single birth defect (adjusted risk ratio, 1.42; 95% CI, 1.10-1.82; and adjusted risk ratio, 1.43; 95% CI, 1.07-1.91 respectively); and multiple birth defects (adjusted risk ratio, 1.42; 95% CI, 1.03-1.94; and adjusted risk ratio, 1.47; 95% CI, 1.03-2.09, respectively). CONCLUSION: Maternal delivery age is an important risk factor for all birth defects. Mothers and fathers who work as "cleaners and laborers and related workers" appear to have a higher risk of giving birth to children with chromosomal single birth defect and nonchromosomal single birth defect and multiple birth defects, respectively. Further in-depth study would be needed to confirm these observations.

Abnormalities, Multiple↗
PubMed2006

Conformational suppression of inter-receptor signaling defects.

Motile bacteria follow gradients of attractant and repellent chemicals with high sensitivity. Their chemoreceptors are physically clustered, which may enable them to function as a cooperative array. Although native chemoreceptor molecules are typically transmembrane homodimers, they appear to associate through their cytoplasmic tips to form trimers of dimers, which may be an important architectural element in the assembly and operation of receptor clusters. The five receptors of Escherichia coli that mediate most of its chemotactic and aerotactic behaviors have identical trimer contact residues and have been shown by in vivo crosslinking methods to form mixed trimers of dimers. Mutations at the trimer contact sites of Tsr, the serine chemoreceptor, invariably abrogate Tsr function, but some of those lesions (designated Tsr*) are epistatic and block the function of heterologous chemoreceptors. We isolated and characterized mutations (designated Tar()) in the aspartate chemoreceptor that restored function to Tsr* receptors. The suppressors arose at or near the Tar trimer contact sites and acted in an allele-specific fashion on Tsr* partners. Alone, many Tar() receptors were unable to mediate chemotactic responses to aspartate, but all formed clusters with varying efficiencies. Most of those Tar() receptors were epistatic to WT Tsr, but some regained Tar function in combination with a suppressible Tsr* partner. Tar()-Tsr* suppression most likely occurs through compensatory changes in the conformation or dynamics of a mixed receptor signaling complex, presumably based on trimer-of-dimer interactions. These collaborative teams may be responsible for the high-gain signaling properties of bacterial chemoreceptors.

Bacterial Proteins↗
PubMed1999

The essential role of Saccharomyces cerevisiae CDC6 nucleotide-binding site in cell growth, DNA synthesis, and Orc1 association.

Saccharomyces cerevisiae Cdc6 is a protein required for the initiation of DNA replication. The biochemical function of the protein is unknown, but the primary sequence contains motifs characteristic of nucleotide-binding sites. To study the requirement of the nucleotide-binding site for the essential function of Cdc6, we have changed the conserved Lys114 at the nucleotide-binding site to five other amino acid residues. We have used these mutants to investigate in vivo roles of the conserved lysine in the growth rate of transformant cells and the complementation of cdc6 temperature-sensitive mutant cells. Our results suggest that replacement of Lys with Glu (K114E) and Pro (K114P) leads to loss-of-function in supporting cell growth, replacement of the Lys with Gln (K114Q) or Leu (K114L) yields partially functional proteins, and replacement with Arg yields a phenotype equivalent to wild-type, a silent mutation. To investigate what leads to the growth defects derived from the mutations at the nucleotide-binding site, we evaluated its gene functions in DNA replication by the assays of the plasmid stability and chromosomal DNA synthesis. Indeed, the K114P and K114E mutants showed the complete retraction of DNA synthesis. In order to test its effect on the G1/S transition of the cell cycle, we have carried out the temporal and spatial studies of yeast replication complex. To do this, yeast chromatin fractions from synchronized culture were prepared to detect the Mcm5 loading onto the chromatin in the presence of the wild-type Cdc6 or mutant cdc6(K114E) proteins. We found that cdc6(K114E) is defective in the association with chromatin and in the loading of Mcm5 onto chromatin origins. To further investigate the molecular mechanism of nucleotide-binding function, we have demonstrated that the Cdc6 protein associates with Orc1 in vitro and in vivo. Intriguingly, the interaction between Orc1 and Cdc6 is disrupted when the cdc6(K114E) protein is used. Our results suggest that a proper molecular interaction between Orc1 and Cdc6 depends on the functional ATP-binding of Cdc6, which may be a prerequisite step to assemble the operational replicative complex at the G1/S transition.

Adenosine Triphosphate↗
PubMed2004

Partial proteolysis of simian virus 40 T antigen reveals intramolecular contacts between domains and conformation changes upon hexamer assembly.

Simian virus 40 large tumor antigen (Tag) is a multi-functional viral protein that binds specifically to SV40 origin DNA, serves as the replicative DNA helicase, and orchestrates the assembly and operation of the viral replisome. Tag associated with Mg-ATP forms hexamers and, in the presence of SV40 origin DNA, double hexamers. Limited tryptic digestion of monomeric Tag revealed three major stable structural domains. The N-terminal domain spans amino acids 1-130, the central domain comprises amino acids 131-476, and the C-terminal domain extends from amino acid 513 to amino acid 698. Co-immunoprecipitation of digestion products of monomeric Tag suggests that the N-terminal domain associates stably with sequences located in the central region of the same Tag molecule. Hexamer formation protected the tryptic cleavage sites in the exposed region between the central and C-terminal domains. Upon hexamerization, this exposed region also became less accessible to a monoclonal antibody whose epitope maps in that region. The tryptic digestion products of the soluble hexamer and the DNA-bound double hexamer were indistinguishable. A low-resolution model of the intramolecular and intermolecular interactions among Tag domains in the double hexamer is proposed.

Animals↗
PubMed2000

Loss control of Mcm5 interaction with chromatin in cdc6-1 mutated in CDC-NTP motif.

Saccharomyces cerevisiae Cdc6 plays an essential role in establishing and maintaining the prereplicative complex (pre-RC) by interacting with the origin recognition complex (ORC) and associating with chromatin origins. These interactions are required to load minichromosome maintenance proteins (MCMs) and other initiator proteins onto replication origins. Although the temperature-sensitive cdc6 mutant, cdc6-1, has been widely used for these studies, the molecular mechanism of the cdc6-1 mutation has been unclear. In this study, we have identified a base substitution at Gly260-->Asp, near the CDC-NTP motif. Using a chromatin immunoprecipitation assay (CHIP), we found that cdc6-1 fails to load Mcm5 onto the replication origins. Chromatin fractions were used to study Mcm5 binding in both the wildtype and mutant background. These studies indicated that Cdc6 is also involved in unloading Mcm5 from chromatin. Specifically, the cdc6-1 mutation protein, cdc6(G260D), which failed to load Mcm5 onto replication origins, also failed to unload the Mcm5 protein. Furthermore, the overexpression of wildtype CDC6 accelerated the unloading of Mcm5 from chromatin fractions. In the absence of functional Cdc6, the Mcm5 protein showed nonorigin binding to chromatin with the cell cycle arrested at the G1S phase transition. Our results suggested that the cdc6(G260D) mutant protein fails to assemble an operational replicative complex and that wildtype Cdc6 plays a role in preventing re-replication by controlling the unloading the MCMs from chromatin origins.

Amino Acid Substitution↗
PubMed1987

Instrumentation and separation results of medium pressure liquid chromatography.

This paper describes the assembly, usage, operation, and separation results of a medium pressure liquid chromatography (MPLC) instrument. Its ability to separate compounds with high resolution makes it a powerful tool for many chemistry laboratories. This equipment can be easily built from inexpensive commercially available materials. Due to the constant reuse of packing materials and infrequent maintenance, MPLC provides a simple, reliable, and economical means of purification.

Chromatography, Liquid↗
PubMed2004

A population-based study on the association between parental occupations and some common birth defects in singapore (1994-1998).

We sought to study the association between some common birth defects and parental occupations. The live births and congenital malformation born between January 1994 and December 1998 were obtained from the Singapore National Registry of Births and Deaths (the National Birth Defect Registry). The prevalence of overall birth defects among Singapore live births during the study period is 13.9 per 1,000 live births. The most frequent single coding defects were "bulbus cordis anomalies and anomalies of cardiac septal closure (BCA)," "congenital anomalies of urinary system (CUS)," "cleft palate and cleft lip (CPL)," and "certain congenital musculoskeletal deformities (CMD)." Using the "Legislators, Senior Officers & Managers" as reference and adjusting for possible confounders, there were significant associations for: (1) paternal "clerical workers" (adjusted RR 2.25) with the BCA; (2) maternal "professionals" with CUS (adjusted risk ratio [RR] 3.58); (3) paternal "production craftsmen and related workers" with both the BCA (adjusted RR 2.04), and the CMD (adjusted RR 2.83); (4) paternal "plant and machine operators and assemblers" with the BCA (adjusted RR 2.49), and the CUS (adjusted RR 5.19), and the CMD (adjusted RR 3.01). Paternal rather than maternal exposure might be more important in the causation of some common birth defects in Singapore.

Abnormalities, Multiple↗
PubMed1960

Mitotic arrest by deuterium oxide.

In marine invertebrate eggs, where cell divisions occur without growth, deuterium oxide produces arrest of, or serious delay in, mitosis and cytokinesis. All stages requiring assembly or operation of mechanical structures in the cytoplasm are sensitive to D.O. The block is reversible in some cells.

Cell Division↗
PubMed1997

Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity.

Circadian rhythmicity is universally associated with the ability to perceive light, and the oscillators ("clocks") giving rise to these rhythms, which are feedback loops based on transcription and translation, are reset by light. Although such loops must contain elements of positive and negative regulation, the clock genes analyzed to date-frq in Neurospora and per and tim in Drosophila-are associated only with negative feedback and their biochemical functions are largely inferred. The white collar-1 and white collar-2 genes, both global regulators of photoresponses in Neurospora, encode DNA binding proteins that contain PAS domains and are believed to act as transcriptional activators. Data shown here suggest that wc-1 is a clock-associated gene and wc-2 is a clock component; both play essential roles in the assembly or operation of the Neurospora circadian oscillator. Thus DNA binding and transcriptional activation can now be associated with a clock gene that may provide a positive element in the feedback loop. In addition, similarities between the PAS-domain regions of molecules involved in light perception and circadian rhythmicity in several organisms suggest an evolutionary link between ancient photoreceptor proteins and more modern proteins required for circadian oscillation.

Amino Acid Sequence↗
PubMed1999

Action of DNA repair endonuclease ERCC1/XPF in living cells.

To study the nuclear organization and dynamics of nucleotide excision repair (NER), the endonuclease ERCC1/XPF (for excision repair cross complementation group 1/xeroderma pigmentosum group F) was tagged with green fluorescent protein and its mobility was monitored in living Chinese hamster ovary cells. In the absence of DNA damage, the complex moved freely through the nucleus, with a diffusion coefficient (15 +/- 5 square micrometers per second) consistent with its molecular size. Ultraviolet light-induced DNA damage caused a transient dose-dependent immobilization of ERCC1/XPF, likely due to engagement of the complex in a single repair event. After 4 minutes, the complex regained mobility. These results suggest (i) that NER operates by assembly of individual NER factors at sites of DNA damage rather than by preassembly of holocomplexes and (ii) that ERCC1/XPF participates in repair of DNA damage in a distributive fashion rather than by processive scanning of large genome segments.

Animals↗
PubMed2006

Role of intimin-tir interactions and the tir-cytoskeleton coupling protein in the colonization of calves and lambs by Escherichia coli O157:H7.

Intimin facilitates intestinal colonization by enterohemorrhagic Escherichia coli O157:H7; however, the importance of intimin binding to its translocated receptor (Tir) as opposed to cellular coreceptors is unknown. The intimin-Tir interaction is needed for optimal actin assembly under adherent bacteria in vitro, a process which requires the Tir-cytoskeleton coupling protein (TccP/EspF(U)) in E. coli O157:H7. Here we report that E. coli O157:H7 tir mutants are at least as attenuated as isogenic eae mutants in calves and lambs, implying that the role of intimin in the colonization of reservoir hosts can be explained largely by its binding to Tir. Mutation of tccP uncoupled actin assembly from the intimin-Tir-mediated adherence of E. coli O157:H7 in vitro but did not impair intestinal colonization in calves and lambs, implying that pedestal formation may not be necessary for persistence. However, an E. coli O157:H7 tccP mutant induced typical attaching and effacing lesions in a bovine ligated ileal loop model of infection, suggesting that TccP-independent mechanisms of actin assembly may operate in vivo.

Adhesins, Bacterial↗