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Biomedical subjects

D J Ellis

Publications and source records attributed to D J Ellis.

At least 19 recordsLinked to original sources
PubMed2000

A cell-free system for regulated exocytosis in PC12 cells.

We have developed a cell-free system for regulated exocytosis in the PC12 neuroendocrine cell line. Secretory vesicles were preloaded with acridine orange in intact cells, and the cells were sonicated to produce flat, carrier-supported plasma membrane patches with attached vesicles. Exocytosis resulted in the release of acridine orange which was visible as a disappearance of labeled vesicles and, under optimal conditions, produced light flashes by fluorescence dequenching. Exocytosis in vitro requires cytosol and Ca(2+) at concentrations in the micromolar range, and is sensitive to Tetanus toxin. Imaging of membrane patches at diffraction- limited resolution revealed that 42% of docked granules were released in a Ca(2+)-dependent manner during 1 min of stimulation. Electron microscopy of membrane patches confirmed the presence of dense-core vesicles. Imaging of membrane patches by atomic force microscopy revealed the presence of numerous particles attached to the membrane patches which decreased in number upon stimulation. Thus, exocytotic membrane fusion of single vesicles can be monitored with high temporal and spatial resolution, while providing access to the site of exocytosis for biochemical and molecular tools.

Acridine Orange↗
PubMed2000

Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy.

Bacterial type I restriction/modification systems are capable of performing multiple actions in response to the methylation pattern on their DNA recognition sequences. The enzymes making up these systems serve to protect the bacterial cells against viral infection by binding to their recognition sequences on the invading DNA and degrading it after extensive ATP-driven translocation. DNA cleavage has been thought to occur as the result of a collision between two translocating enzyme complexes. Using atomic force microscopy (AFM), we show here that EcoKI dimerizes rapidly when bound to a plasmid containing two recognition sites for the enzyme. Dimerization proceeds in the absence of ATP and is also seen with an EcoKI mutant (K477R) that is unable to translocate DNA. Only monomers are seen when the enzyme complex binds to a plasmid containing a single recognition site. Based on our results, we propose that the binding of EcoKI to specific DNA target sequences is accompanied by a conformational change that leads rapidly to dimerization. This event is followed by ATP-dependent translocation and cleavage of the DNA.

DNA Restriction Enzymes↗
PubMed1999

Investigation of protein partnerships using atomic force microscopy.

The origin of contrast in atomic force microscopy (AFM) lies in the probe's response to forces between itself and the sample. These forces most commonly result from changes in height as the tip is scanned over the surface, but can also originate in properties inherent in the sample. These have been exploited as further means of contrast and have spawned an array of similar imaging techniques, such as chemical force microscopy, magnetic force microscopy, and frictional force microscopy. All of these techniques use AFM as an extremely sensitive gauge to map forces at discrete sites on the surface. A natural extension of this approach is to map forces in an array, in order to create a force map. AFM can be used in aqueous or fluid environments, thus allowing the exploration of forces in biological systems under physiologically relevant conditions. By immobilizing one half of an interacting pair of proteins onto the tip and the other half onto the substrate, it is possible to investigate the electrostatic and hydrophobic interactions between them. We employed these techniques to examine the interaction between a pair of proteins of known affinity that are involved in exocytosis (NSF and alpha-SNAP) and separately to demonstrate how two-dimensional force mapping can be applied to the nuclear envelope to identify nuclear pore complexes.

Animals↗
PubMed1999

Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsenophilum sp. nov., new members of the Sulfurospirillum clade of the epsilon Proteobacteria.

Two strains of dissimilatory arsenate-reducing vibrio-shaped bacteria are assigned to the genus Sulfurospirillum. These two new species, Sulfurospirillum barnesii strain SES-3T and Sulfurospirillum arsenophilum strain MIT-13T, in addition to Sulfurospirillum sp. SM-5, two strains of Sulfurospirillum deleyianum, and Sulfurospirillum arcachonense, form a distinct clade within the epsilon subclass of the Proteobacteria based on 16S rRNA analysis.

Arsenates↗
PubMed1999

Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer.

In an attempt to understand better the micro-organisms involved in anaerobic degradation of aromatic hydrocarbons in the Fe(III)-reducing zone of petroleum-contaminated aquifers, Fe(III)-reducing micro-organisms were isolated from contaminated aquifer material that had been adapted for rapid oxidation of toluene coupled to Fe(III) reduction. One of these organisms, strain H-5T, was enriched and isolated on acetate/Fe(III) medium. Strain H-5T is a Gram-negative strict anaerobe that grows with various simple organic acids such as acetate, propionate, lactate and fumarate as alternative electron donors with Fe(III) as the electron acceptor. In addition, strain H-5T also oxidizes long-chain fatty acids such as palmitate with Fe(III) as the sole electron acceptor. Strain H-5T can also grow by fermentation of citrate or fumarate in the absence of an alternative electron acceptor. The primary end-products of citrate fermentation are acetate and succinate. In addition to various forms of soluble and insoluble Fe(III), strain H-5T grows with nitrate, Mn(IV), fumarate and the humic acid analogue 2,6-anthraquinone disulfonate as alternative electron acceptors. As with other organisms that can oxidize organic compounds completely with the reduction of Fe(III), cell suspensions of strain H-5T have absorbance maxima indicative of a c-type cytochrome(s). It is proposed that strain H-5T represents a novel genus in the Holophaga-Acidobacterium phylum and that it should be named Geothrix fermentans sp. nov., gen. nov.

Biodegradation, Environmental↗
PubMed1998

Carbohydrate oxidation coupled to Fe(III) reduction, a novel form of anaerobic metabolism.

An isolate, designated GC-29, that could incompletely oxidize glucose to acetate and carbon dioxide with Fe(III) serving as the electron acceptor was recovered from freshwater sediments of the Potomac River, Maryland. This metabolism yielded energy to support cell growth. Strain GC-29 is a facultatively anaerobic, gram-negative motile rod which, in addition to glucose, also used sucrose, lactate, pyruvate, yeast extract, casamino acids or H2 as alternative electron donors for Fe(III) reduction. Stain GC-29 could reduce NO3(-), Mn(IV), U(VI), fumarate, malate, S2O3(2-), and colloidal S0 as well as the humics analog, 2,6-anthraquinone disulfonate. Analysis of the almost complete 16S rRNA sequence indicated that strain GC-29 belongs in the Shewanella genus in the epsilon subdivision of the Proteobacteria. The name Shewanella saccharophilia is proposed. Shewanella saccharophilia differs from previously described fermentative microorganisms that metabolize glucose with the reduction of Fe(III) because it transfers significantly more electron equivalents to Fe(III); acetate and carbon dioxide are the only products of glucose metabolism; energy is conserved from Fe(III) reduction; and glucose is not metabolized in the absence of Fe(III). The metabolism of organisms like S. saccharophilia may account for the fact that glucose is metabolized primarily to acetate and carbon dioxide in a variety of sediments in which Fe(III) reduction is the terminal electron accepting process.

Journal Article↗
PubMed1998

Recovery of humic-reducing bacteria from a diversity of environments.

To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments.

Acetic Acid↗
PubMed1997

Dissimilatory arsenate and sulfate reduction in Desulfotomaculum auripigmentum sp. nov.

A newly discovered arsenate-reducing bacterium, strain OREX-4, differed significantly from strains MIT-13 and SES-3, the previously described arsenate-reducing isolates, which grew on nitrate but not on sulfate. In contrast, strain OREX-4 did not respire nitrate but grew on lactate, with either arsenate or sulfate serving as the electron acceptor, and even preferred arsenate. Both arsenate and sulfate reduction were inhibited by molybdate. Strain OREX-4, a gram-positive bacterium with a hexagonal S-layer on its cell wall, metabolized compounds commonly used by sulfate reducers. Scorodite (FeAsO42. H2O) an arsenate-containing mineral, provided micromolar concentrations of arsenate that supported cell growth. Physiologically and phylogenetically, strain OREX-4 was far-removed from strains MIT-13 and SES-3: strain OREX-4 grew on different electron donors and electron acceptors, and fell within the gram-positive group of the Bacteria, whereas MIT-13 and SES-3 fell together in the epsilon-subdivision of the Proteobacteria. Together, these results suggest that organisms spread among diverse bacterial phyla can use arsenate as a terminal electron acceptor, and that dissimilatory arsenate reduction might occur in the sulfidogenic zone at arsenate concentrations of environmental interest. 16S rRNA sequence analysis indicated that strain OREX-4 is a new species of the genus Desulfotomaculum, and accordingly, the name Desulfotomaculum auripigmentum is proposed.

Arsenates↗
PubMed1997

GST-lamin fusion proteins act as dominant negative mutants in Xenopus egg extract and reveal the function of the lamina in DNA replication.

A cDNA encoding Xlamin B1 was cloned from a whole ovary mRNA by RT-PCR. GST-lamin fusion constructs were generated from this cDNA by first creating convenient restriction sites within the Xlamin B1 coding sequence, using PCR directed mutagenesis, and then sub-cloning relevant sequences into pGEX-4T-3. Two expression constructs were made, the first, termed delta 2+ lacked sequences encoding the amino-terminal 'head domain' of lamin B1 but included sequences encoding the nuclear localization signal sequence (NLS). The second expression construct, termed delta 2-, lacked sequences encoding the amino-terminal 'head domain' as well as sequences encoding the NLS. Purified fusion proteins expressed from these constructs, when added to egg extracts prior to sperm pronuclear assembly, formed hetero-oligomers with the endogenous lamin B3. The delta 2+ fusion protein prevented nuclear lamina assembly but not nuclear membrane assembly. The resulting nuclei were small (approximately 10 microns in diameter), did not assemble replication centers and failed to initiate DNA replication. When the delta 2- fusion protein was added to egg extracts prior to sperm pronuclear assembly, lamina assembly was delayed but not prevented. The resulting nuclei although small (approximately 12 microns), did form replication centers and initiated DNA replication. When added to egg extracts after sperm pronuclear assembly was completed delta 2+, but not delta 2-, entered the pre-formed nuclei causing lamina disassembly. However, the disassembly of the lamina by delta 2+ did not result in the disruption of replication centers and indeed these centres remained functional. These results are consistent with the hypothesis that lamina assembly precedes and is required for the formation of replication centers but does not support those centers directly.

Animals↗
PubMed1995

Lower intestinal hemorrhage.

Lower intestinal hemorrhage, defined as bleeding originating below the ligament of Treitz, is a common clinical problem frequently requiring hospital admission. The two chief causes, vascular ectasia and diverticulosis, are degenerative diseases usually found in the elderly. This article focuses on those disease entities that potentially can result in significant lower intestinal blood loss. It also discusses a generalized approach to the diagnostic evaluation leading to specific management of the patient presenting with this problem.

Colonic Diseases↗
PubMed1994

Mesenteric venous thrombosis.

Mesenteric venous thrombosis (MVT) and its clinical expressions have become better defined as a result of improvements in both diagnostic imaging and our understanding of the various intestinal ischemic syndromes. Acute, subacute, and chronic forms of MVT are currently recognized, and these forms may differ in the symptoms they produce, the methods by which they are diagnosed, and the treatments they may require. Moreover, an underlying disease that predisposes a patient to MVT can be found in most instances.

Animals↗
PubMed1993

Assisting the breastfeeding mother: a problem-solving process.

At the Vancouver Breastfeeding Centre (VBC), breastfeeding is facilitated through a process of assessment, analysis, diagnosis, care and counsel, and evaluation. This process is described and related to phases of breastfeeding kinetics by considering two presenting problems: sore nipples, and inadequate production of milk.

Consultants↗
PubMed1992

Distribution, Frequency, and Diversity of Bacillus thuringiensis in an Animal Feed Mill.

Bacillus thuringiensis was isolated from 36 of 50 residue samples obtained from an animal feed mill (a stored-product environment). Of 710 selected colonies having Bacillus cereus-B. thuringiensis morphology isolated from the samples, 477 were classified as B. thuringiensis because of production of parasporal delta-endotoxin crystals. There was a diverse population of B. thuringiensis, as revealed by differentiation of the isolates into 36 subgroups by using (i) their spectra of toxicity to the lepidopterans Heliothis virescens, Pieris brassicae, and Spodoptera littoralis and the dipteran Aedes aegypti and (ii) their parasporal crystal morphology. A total of 55% of the isolates were not toxic to any of these insects at the concentrations used in the bioassays; 40% of all isolates were toxic to one or more of the Lepidoptera; and 20, 1, and 1% of the isolates were toxic to only P. brassicae, H. virescens, and S. littoralis, respectively. The most frequent toxicity was toxicity to P. brassicae (36% of all isolates); 18% of the isolates were toxic to A. aegypti (5% exclusively), 10% were toxic to H. virescens, and 4% were toxic to S. littoralis. Toxicity to P. brassicae was more often linked with toxicity to H. virescens than with toxicity to S. littoralis. The frequency of toxicity was significantly greater in isolates that produced bipyramidal crystals than in isolates that produced irregular pointed, irregular spherical, rectangular, or spherical crystals.

Journal Article↗
PubMed1992

The impact of agency policies and protocols on breastfeeding.

Health care agency policies and protocols exert a considerable effect on the initiation and continuation of breastfeeding. Supportive practices, protocols, policies, and philosophies are outlined, and the most prevalent nonsupportive practices are described. Other agency factors affecting the support of breastfeeding, such as diagnostic procedures and medical and surgical interventions, are discussed.

Adult↗