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At least 1,243 records · Page 69Linked to original sources
PubMed2003

Phylogenetic and physiological characterization of a heterotrophic, chemolithoautotrophic Thiothrix strain isolated from activated sludge.

The sheathed filamentous bacterium known as strain CT3, isolated by micromanipulation from an activated sludge treatment plant in Italy, is a member of the genus Thiothrix in the gamma-Proteobacteria according to 16S rDNA sequence analysis. The closest phylogenetic neighbours of strain CT3 are strains I and Q(T), which were also isolated from activated sludge and belong to the species Thiothrix fructosivorans. These strains have respectively 99.2 and 99.4 % similarity to CT3 by 16S rDNA sequence comparison. CT3 shows 63-67 % DNA-DNA hybridization with strain I, which is the only currently viable strain of T. fructosivorans. CT3 is the second strain in the genus Thiothrix that has been shown to be capable of growing autotrophically with reduced sulfur compounds as the sole energy source; autotrophy was also confirmed in strain I. The first reported chemolithoautotrophic isolate of this genus was a strain of 'Thiothrix ramosa' that was isolated from a hydrogen sulfide spring and is morphologically distinguishable from all other described strains of Thiothrix, including CT3. CT3 is an aerobic organism that is non-fermentative, not capable of denitrification and able to grow heterotrophically. Autotrophy in the genus Thiothrix should be investigated more fully to better define the taxonomy of this genus.

DNA, Bacterial↗
PubMed2006

Meganema perideroedes gen. nov., sp. nov., a filamentous alphaproteobacterium from activated sludge.

An industrial wastewater treatment plant at Grindsted, Denmark, has suffered from bulking problems for several years caused by filamentous bacteria. Five strains were isolated from the sludge by micromanipulation. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains formed a monophyletic cluster in the Alphaproteobacteria, and they were phenotypically different from their closest relatives and from all hitherto known filamentous bacteria described (closest relative Brevundimonas vesicularis ATCC 11426(T), 89.8 % sequence similarity). In pure culture, the cells (1.5-2.0 microm) in filaments are Gram-negative and contain polyphosphate and polyhydroxyalkanoates. The optimum temperature for growth is 30 degrees C and the strains grow in 2 % NaCl and are oxidase- and catalase-positive. Ubiquinone 10 is the major quinone. The major fatty acid (C(18 : 1)omega7c) and smaller amounts of unsaturated fatty acids, 3-hydroxy fatty acids with a chain length of 16 and 18 carbon atoms and small amounts of 10-methyl-branched fatty acids with 18 carbon atoms (C(19 : 0) 10-methyl) affiliated the strains with the Methylobacterium/Xanthobacter group in the Alphaproteobacteria. The G+C content of the DNA is 42.9 mol% (for strain Gr1(T)). The two most dissimilar isolates by 16S rRNA gene comparison (Gr1(T) and Gr10; 97.7 % identical) showed 71.5 % DNA-DNA relatedness. Oligonucleotide probes specific for the pure cultures were designed for fluorescence in situ hybridization and demonstrated that two filamentous morphotypes were present in the Grindsted wastewater treatment plant. It is proposed that the isolates represent a new genus and species, Meganema perideroedes gen. nov., sp. nov. The type strain of Meganema perideroedes is strain Gr1(T) (=DSM 15528(T)=ATCC BAA-740(T)).

Alphaproteobacteria↗
PubMed2005

Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules.

A Gram-positive bacterium, designated strain AG019(T), was isolated by micromanipulation from aerobic granules obtained from a laboratory-scale sequencing batch reactor. This isolate grew axenically as cocci clustered predominantly in tetrads, and was morphologically similar to the dominant organisms observed in the biomass. The morphology also resembled that of the tetrad-forming organisms commonly seen in activated sludge samples. Strain AG019(T) was found to be an oxidase-negative, catalase-positive, non-motile aerobe that does not reduce nitrate and grows at temperatures between 15 and 40 degrees C, with an optimum at 37 degrees C. The pH range for growth was 5.0-9.0, with an optimum at pH 7.5. Strain AG019(T) contained a peptidoglycan with directly cross-linked meso-diaminopimelic acid (type A1gamma) and lacked mycolic acids. The G+C content of the DNA was 75 mol%. Menaquinone MK-8(H(2)) was the major isoprenoid quinone. The bacterium stained positively for intracellular polyphosphate granules but not for poly-beta-hydroxyalkanoates. It produced capsular material and showed autoaggregation ability. Phenotypic and 16S rRNA gene analyses showed that the bacterium differed sufficiently from its closest phylogenetic relatives, namely members of the suborder Frankineae, which includes the genera Geodermatophilus, Blastococcus, Frankia, Sporichthya, Acidothermus and Microsphaera, that it is proposed that it be placed in a novel genus, Quadrisphaera, as Quadrisphaera granulorum gen. nov., sp. nov. The type strain is AG019(T) (=ATCC BAA-1104(T)=DSM 44889(T)).

Actinomycetales↗
PubMed2006

Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam.

Three strains of non-motile, Gram-positive, filamentous actinomycetes, isolates J4(T), J5 and J59, initially recognized microscopically in activated sludge foam by their distinctive branching patterns, were isolated by micromanipulation. The taxonomic positions of the isolates were determined using a polyphasic approach. Almost-complete 16S rRNA gene sequences of the isolates were aligned with corresponding sequences of representatives of the suborder Corynebacterineae and phylogenetic trees were inferred using three tree-making algorithms. The organisms formed a distinct phyletic line in the Gordonia 16S rRNA gene tree. The three isolates showed 16S rRNA gene sequence similarities within the range 96.9-97.2 % with their nearest phylogenetic neighbours, namely Gordonia bronchialis DSM 43247(T) and Gordonia terrae DSM 43249(T). Strain J4(T) was shown to have a chemotaxonomic profile typical of the genus Gordonia and was readily distinguished from representatives of the genus on the basis of Curie-point pyrolysis mass spectrometric data. The isolates shared nearly identical phenotypic profiles that distinguished them from representatives of the most closely related Gordonia species. It is evident from the genotypic and phenotypic data that the three isolates belong to a novel Gordonia species. The name proposed for this taxon is Gordonia defluvii sp. nov.; the type strain is J4(T) (=DSM 44981(T)=NCIMB 14149(T)).

Bacterial Typing Techniques↗
PubMed2006

Integrated confocal and scanning probe microscopy for biomedical research.

Atomic force microscopy (AFM) continues to be developed, not only in design, but also in application. The new focus of using AFM is changing from pure material to biomedical studies. More frequently, it is being used in combination with other optical imaging methods, such as confocal laser scanning microscopy (CLSM) and fluorescent imaging, to provide a more comprehensive understanding of biological systems. To date, AFM has been used increasingly as a precise micromanipulator, probing and altering the mechanobiological characteristics of living cells and tissues, in order to examine specific, receptor-ligand interactions, material properties, and cell behavior. In this review, we discuss the development of this new hybrid AFM, current research, and potential applications in diagnosis and the detection of disease.

Animals↗
PubMed1999

Different statistical mechanical ensembles for a stretched polymer.

Imposing to a single polymer chain of N monomers either a fixed pair of forces +/-f acting at the chain ends (stress ensemble) or a fixed end-to-end vector R (strain ensemble) does correspond to the use of different statistical mechanical ensembles. In particular, the two elasticity laws, R(f)=g(f) and f(R)=h(R), where R(f) is the length of the average end-to-end vector (f) in the stress ensemble and f(R) is the intensity of the average internal force (R) in the strain ensemble, are not equivalent. For these conjugated ensembles, the quantity Delta(f)=f-h(g(f)) and more generally Delta(O)= (f)- (R) where O is an arbitrary observable, is studied systematically in this paper for a wide class of polymer models corresponding to chains at temperatures equal or above the theta point. The leading term Delta((2))(O) of an expansion of Delta(O) in terms of the successive moments of the end-to-end vector fluctuations in the stress ensemble can be used to analyze the scaling properties of Delta(f). For the Gaussian and the freely jointed chain models, Delta(O) proportional to 1/N for large N with the particularity that, for the elasticity law, Delta(f) strictly vanishes for the Gaussian chain at any finite N. For chains in good solvent, the usual result Delta(f) proportional to 1/N at fixed f is only valid in the highly stretched chain regime (Pincus regime). N independent large ensemble differences of the order of 20% on Delta(f) are noticed when the chain is stretched over a distance of the order of the unstretched chain average end-to-end distance R0. These effects decrease to the 1% level for R(f)>3R(0). Monte Carlo calculations for a chain model containing both excluded volume and finite extensibility features illustrate the distinction between the elasticity laws in the two ensembles over all stretching regimes. Our study suggests that the nature of the constraints used in single chain micromanipulations could be relevant to the interpretation of experimental elasticity law data.

Journal Article↗
PubMed2000

Dynamics and lateral interactions of dipolar chains

The dynamics and lateral interactions of dipolar chains in magnetorheological suspensions determine the long-time microscopic structure and resulting rheological response. In this paper we characterize proposed lateral interaction mechanisms and their implications for long-time coarsening of structure and compare them to direct measurements of the lateral interaction of dipolar chains using optical trap micromanipulation. We observe a long-range far-field attraction between flexible chains, while the near-field interaction can be repulsive or attractive. At high field strengths, we observe the short-range attraction of rigid chains. Chain dynamics measured with videomicroscopy and diffusing wave spectroscopy are described by a local-mode model and are consistent with fluctuation-mediated interaction theories. The subdiffusive behavior at intermediate and long times scales as t(0.75), identical to semiflexible molecules. Finally, we show examples of how defects in chains can create lateral attractions or repulsions.

Journal Article↗
PubMed2002

Single molecule statistics and the polynucleotide unzipping transition.

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force value of order 10 pN, with different critical behavior for homopolymers and for random heteropolymers. We extend results on the disorder-averaged behavior of DNA's with random sequences [D. K. Lubensky and D. R. Nelson, Phys. Rev. Lett. 85, 1572 (2000)] to the more experimentally accessible problem of unzipping a single DNA molecule. As the applied force approaches the critical value, the double-stranded DNA unravels in a series of discrete, sequence-dependent steps that allow it to reach successively deeper energy minima. Plots of extension versus force thus take the striking form of a series of plateaus separated by sharp jumps. Similar qualitative features should reappear in micromanipulation experiments on proteins and on folded RNA molecules. Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior. Above the transition, the dynamics of the unzipping fork is related to that of a particle diffusing in a random force field; anomalous, disorder-dominated behavior is expected until the applied force exceeds the critical value for unzipping by roughly 5 pN.

Base Pairing↗
PubMed2002

Fluid-membrane tethers: minimal surfaces and elastic boundary layers.

Thin cylindrical tethers are common lipid bilayer membrane structures, arising in situations ranging from micromanipulation experiments on artificial vesicles to the dynamic structure of the Golgi apparatus. We study the shape and formation of a tether in terms of the classical soap-film problem, which is applied to the case of a membrane disk under tension subject to a point force. A tether forms from the elastic boundary layer near the point of application of the force, for sufficiently large displacement. Analytic results for various aspects of the membrane shape are given.

Cytoplasmic Vesicles↗
PubMed2000

Pulling pinned polymers and unzipping DNA.

We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA. When the pulling force is increased to a critical value, an "unzipping" transition occurs. For random DNA sequences with short-ranged correlations, we obtain exact results for the number of monomers liberated and the specific heat, including the critical behavior at the transition. Related systems include a random heteropolymer pulled away from an adsorbing surface and a vortex line in a type II superconductor tilted away from a fragmented columnar defect.

Animals↗
PubMed2001

Buckling of actin-coated membranes under application of a local force.

The mechanical properties of composite membranes obtained by self-assembly of actin filaments with giant fluid vesicles are studied by micromanipulation with optical tweezers. These complexes exhibit typical mechanical features of a solid shell, including a finite in-plane shear elastic modulus ( approximately 10(-6) N/m). A buckling instability is observed when a localized force of the order of 0.5 pN is applied perpendicular to the membrane plane. Although predicted for polymerized vesicles, this is the first evidence of such an instability.

Actins↗
PubMed2005

Microsphere manipulation using ferroelectric liquid crystals.

We propose a strategy for a micromanipulation method using SSFLC (surface stabilized ferroelectric liquid crystals). By adjusting the frequency of the applied ac electric field, the surface layers that cannot follow an applied ac electric field are constructed in SSFLC. In addition, by applying a sawtooth wave voltage, net flow along the smectic layer is generated. The flow direction is reversed by changing the polarity of the sawtooth wave. Consequently, the particles dispersed in SSFLC can be driven bidirectionally along the smectic layer. The particle velocity depends on the temperature, amplitude, and frequency of the applied voltage.

Journal Article↗
PubMed1990

Ventricular volume measurement from a multiplanar transesophageal ultrasonic imaging system: an in vitro study.

We have developed a system to assess the feasibility of using multiple transesophageal ultrasonic images to measure left-ventricular volume, an important variable in patient management. The system includes a special transesophageal probe with a micromanipulator for acquiring cardiac images in multiple planes with known interplanar spatial relationship and an off-line processing system to compute the volume. In vitro studies with the probe demonstrated that the distance between two targets in space can be identified within 2 mm (SD = 0.4 mm) for points in the imaging plane 3.4 mm (SD = 0.5 mm) for points not lying in the imaging plane. This gives an average accuracy of +/- 6.5% for distances greater than 4.5 cm. Comparison of ultrasonic measurements of the volume of water-filled balloons and excised hearts to the volume required to fill them, revealed a correlation coefficient of 0.992, a regression line having a slope of 1.0 and an ordinate intercept at 0.2 mL, and a standard error of the estimate of 8 mL.

Calibration↗
PubMed2004

Vision-based force measurement.

This paper demonstrates a method to visually measure the force distribution applied to a linearly elastic object using the contour data in an image. The force measurement is accomplished by making use of the result from linear elasticity that the displacement field of the contour of a linearly elastic object is sufficient to completely recover the force distribution applied to the object. This result leads naturally to a deformable template matching approach where the template is deformed according to the governing equations of linear elasticity. An energy minimization method is used to match the template to the contour data in the image. This technique of visually measuring forces we refer to as vision-based force measurement (VBFM). VBFM has the potential to increase the robustness and reliability of micromanipulation and biomanipulation tasks where force sensing is essential for success. The effectiveness of VBFM is demonstrated for both a microcantilever beam and a microgripper. A sensor resolution of less than +/- 3 nN for the microcantilever and +/- 3 mN for the microgripper was achieved using VBFM. Performance optimizations for the energy minimization problem are also discussed that make this algorithm feasible for real-time applications.

Algorithms↗
PubMed2004

Combining Ar ion milling with FIB lift-out techniques to prepare high quality site-specific TEM samples.

Focused ion beam (FIB) techniques can prepare site-specific transmission electron microscopy (TEM) cross-section samples very quickly but they suffer from beam damage by the high energy Ga+ ion beam. An amorphous layer about 20-30 nm thick on each side of the TEM lamella and the supporting carbon film makes FIB-prepared samples inferior to the traditional Ar+ thinned samples for some investigations such as high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). We have developed techniques to combine broad argon ion milling with focused ion beam lift-out methods to prepare high-quality site-specific TEM cross-section samples. Site-specific TEM cross-sections were prepared by FIB and lifted out using a Narishige micromanipulator onto a half copper-grid coated with carbon film. Pt deposition by FIB was used to bond the lamellae to the Cu grid, then the coating carbon film was removed and the sample on the bare Cu grid was polished by the usual broad beam Ar+ milling. By doing so, the thickness of the surface amorphous layers is reduced substantially and the sample quality for TEM observation is as good as the traditional Ar+ milled samples.

Journal Article↗
PubMed1992

Direct detection of Epstein-Barr virus DNA from a single Reed-Sternberg cell of Hodgkin's disease by polymerase chain reaction.

Eleven cases of Hodgkin's disease (HD) were examined for the presence of the Epstein-Barr virus (EBV) genome, using the polymerase chain reaction (PCR) to detect EBV DNA in whole paraffin-embedded tissue specimens and in single cells picked out from the specimens with a micromanipulator. The EBV genome was detected in 5 of the 11 cases by conventional PCR. Single cell PCR demonstrated the EBV genome in Reed-Sternberg cells from all the EBV-positive cases, but not from any of the EBV-negative cases. Background lymphocytes and lysozyme-positive histiocytes from EBV-positive cases did not contain the EBV genome. These results indicate an etiological association of EBV with some cases of HD.

Adult↗
PubMed1995

Diagnostic and clinical features in azoospermia.

BACKGROUND AND OBJECTIVE: The recent advances in assisted fertilization and gamete micromanipulation techniques have enabled fertilization in some forms of azoospermia; for example, epididymal sperm aspiration in obstructive azoospermia. Therefore knowledge of the specific degree of testicular damage is of primary importance, since other clinical parameters, such as FSH plasma levels and testicular volume, do not discriminate between the different testiculopathies. In order to further characterize the specific testicular conditions present in azoospermia, we have examined a large group of azoospermic subjects on the basis of testicular cytological analysis obtained by fine needle aspiration. DESIGN AND PATIENTS: One hundred and twenty-two infertile, azoospermic men were studied by physical examination, FSH radioimmunoassay, testicular ultrasound examination and fine needle aspiration of the testes. Thirty-five infertile normozoospermic subjects were studied as controls. RESULTS: The cytological analysis identified five different sub-types in azoospermic subjects: I, Sertoli cell-only syndrome; II, hypospermatogenesis; III, spermatogonial and/or spermatocytic arrest; IV, spermatidic arrest; and V, normal germ line. The testicular volume was reduced in groups I and II, while the FSH plasma levels were increased in groups I, II and III, suggesting a primary role of spermatids in the control of FSH secretion. CONCLUSIONS: In azoospermic subjects, testicular cytological analysis permits the identification of different sub-types and this classification may be very important in determining therapy, particularly the choice between surgical treatment and the hypothetical use of assisted fertilization techniques by retrieval of epididymal or intratesticular spermatozoa or spermatids.

Adult↗
PubMed1995

Bulk sperm collection by epididymal micropuncture and stimulation of the spermatic nerve; a novel method for sperm retrieval for IVF for surgically irreparable vasal obstruction.

We have developed a new sperm collection method by epididymal micropuncture in conjunction with perivascular nerve stimulation to obtain as many uncontaminated spermatozoa as possible for IVF for patients with surgically unreconstructable vasal obstruction. Fifteen azoospermic men with congenital absence of the vas deferens or vasal obstruction not amenable to surgical repair enrolled in this study. Under general anaesthesia the testis and epididymis were retrieved and stabilized in a testicular holder with the aid of 2% agar. The epididymal micropuncture was performed using a micropipette placed in a micromanipulator. A pair of Ag-AgCl ring electrodes were placed around the spermatic cord for perivascular nerve stimulation with DC (intensity 136 V, frequency 20 Hz) for 30 s. Electrical stimulation was repeated every 1 min until no further fluid was obtained. Epididymal fluid obtained ranged from 78 to 980 microliters (mean 169 microliters). Sperm concentration ranged from 0.7 to 200 million (mean 53.5 million). Sperm motility ranged from 0.5% to 70% (mean: 19.9%). The percentage of spermatozoa with normal morphology ranged from 3% to 32% (mean 16.4%). Of 16 cycles in which spermatozoa and oocytes were retrieved, 56% (9/16) resulted in fertilization and 18.8% (3/16) developed clinical pregnancies. The clinical pregnancy rate per couple was 20% (3/15). This is the first clinical experience of the bulk sperm collection system for IVF for the treatment of unreconstructable obstructive azoospermia. Our results indicate that our new technique, in conjunction with IVF, is clinically useful for patients with surgically irreparable vasal obstruction.

Cell Separation↗