The cytodisk: a cytometer based upon a new principle of cell alignment

A new method is described for one-dimensional alignment of small particles such as biological cells. A drop of the particle suspension is spread out on a flat disk or plate equipped with V-shaped grooves such as are present on a gramophone disk. After drying, the particles are located on the bottom of the grooves and are thus aligned in a one-dimensional array. The new alignment procedure is demonstrated with a suspension of fluorescent polystyrene microspheres (diameter 3.8 microns) and a suspension of the unicellular algae chlorella vulgaris (diameter about 3 microns). It appears that the alignment of cells and spheres is very good. When using microspheres, more than 95% of the particles in the grooves are located within +/- 2 microns of the centre line of the groove. Based upon this cell-alignment principle, a new cytometer, named the cytodisk, is proposed. The proposed system has a number of advantages over the flow cytometer, among which is the unique ability of relocating a previously measured cell for further measurement or visual examination. A prototype of a cytodisk, developed for initial test measurements, was built in our laboratory. The apparatus, constructed from a record player and ordinary long-playing records, uses a simple mechanical tracking system and a single optical fiber for fluorescence excitation and detection. With this apparatus it is demonstrated that a cytodisk can indeed perform quite well: A histogram of fluorescing microspheres could be measured with a coefficient of variation of 4.1%. The performance of this prototype is limited by the quality of the mechanical tracking system and the optical system used.(ABSTRACT TRUNCATED AT 250 WORDS)     

A light scattering study on the ion permeabilities of dark-adapted bovine rod outer segment disk membranes

The ion permeability properties of dark adapted bovine rod outer segment disk membranes were studied using light scattering to monitor osmotic responses of disks to various salts and ionophores. A preparation procedure is presented which provides very fresh rod outer segment material with mostly intact stacked disks, but with perforated plasma membrane. It is shown that in this preparation the disks (or rod sacs) are the only osmotically responding compartments and that these responses can be readily monitored by means of light-scattering techniques. The disk membrane is found under the conditions tested, to possess no measurable permeability to cations Na+, Ca2+, Mg2+ nor the the anions Cl-, Br-, NO3-, SO4(2-), H2PO4- and HPO4(2-). There is a considerable K+ permeability, which can be completely abolished by millimolar amounts of divalent cations. The proton permeability of the disk membrane is found to depend dramatically upon the preparation procedure and duration. The fresher the material used the lower is the proton permeability measured. In our freshest preparations, even after freeze-thawing in liquid nitrogen, the disks exhibit an H+ permeability which is so low that it cannot be measured with the techniques used in this study. Even in mitochondrial or chloroplast membmranes, in which proton gradients and therefore a low proton conductance play an essential role, such low proton permeabilities have not been found. This would suggest that proton gradients across the disk membrane could play an important role in the physiological function of the photoreceptor cell. In summary it can be said that the disk membrane, apparently more than any other natural membrane system studied so far, is capable of retaining ion gradients for extended periods of time.     

Detecting Isolation by Distance Using Phylogenies of Genes

We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)2 in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.     

Double-Exposure Optical Sectioning Structured Illumination Microscopy Based on Hilbert Transform Reconstruction

Structured illumination microscopy (SIM) with axially optical sectioning capability has found widespread applications in three-dimensional live cell imaging in recent years, since it combines high sensitivity, short image acquisition time, and high spatial resolution. To obtain one sectioned slice, three raw images with a fixed phase-shift, normally 2π/3, are generally required. In this paper, we report a data processing algorithm based on the one-dimensional Hilbert transform, which needs only two raw images with arbitrary phase-shift for each single slice. The proposed algorithm is different from the previous two-dimensional Hilbert spiral transform algorithm in theory. The presented algorithm has the advantages of simpler data processing procedure, faster computation speed and better reconstructed image quality. The validity of the scheme is verified by imaging biological samples in our developed DMD-based LED-illumination SIM system.     

Two DNA Aptamers against Avian Influenza H9N2 Virus Prevent Viral Infection in Cells

New antiviral therapy for pandemic influenza mediated by the H9N2 avian influenza virus (AIV) is increasingly in demand not only for the poultry industry but also for public health. Aptamers are confirmed to be promising candidates for treatment and prevention of influenza viral infections. Thus, we studied two DNA aptamers, A9 and B4, selected by capillary electrophoresis-based systemic evolution of ligands by exponential enrichment (CE-SELEX) procedure using H9N2 AIV purified haemagglutinin (HA) as target. Both aptamers had whole-virus binding affinity. Also, an enzyme-linked aptamer assay (ELAA) confirmed binding affinity and specificity against other AIV subtypes. Finally, we studied aptamer-inhibitory effects on H9N2 AIV infection in Madin–Darby canine kidney (MDCK) cells and quantified viral load in supernatant and in cell with quantitative PCR (qPCR). Our data provide a foundation for future development of innovative anti-influenza drugs.     

Load sharing among spinal elements of a motion segment in extension and lateral bending

A linear optimization model was formulated using a semi-experimental protocol to estimate the forces in the spinal elements of a lumbar motion segment subjected to an extension or lateral bending moment with and without a 120 N compressive preload. A morphometer was used to acquire the three-dimensional locations of the disk center, facet centers and ligament origin and insertion sites with the specimen in a "neutral" position. The relative motion of the superior vertebra, under the loading conditions tested, was monitored using a Selspot II system. These data allowed the formulation of the static equilibrium equations for the superior vertebra at each of the loading conditions mentioned above. A linear optimization technique was used, along with a suitable cost function, to find an optimum solution for the set of equations and imposed constraints. Results showed that for 6.9 Nm of extension moment, each facet carried a load of 52 N, with the disk carrying an axial tensile load of 104 N. At the 6.9 Nm extension moment coupled with 120 N preload, each facet carried a load of 77.2 N and the disk an axial tensile load of 37 N. In right lateral bending, with and without preload, the load was distributed among the right facet, the disk, the left ligamentum flavum and the left capsular ligament. At the 6.9 Nm load step without preload the right facet carried an axial load of 127.01 N with the disk carrying an axial compressive load of 7.8 N. Ligament forces for this step for the left ligamentum flavum and capsular ligament, respectively, were 61.03 N and 65.14 N. The addition of 120 N of preload reduced the load on the right facet to 83.5 N. The compressive load in the disk increased to 107.5 N. The corresponding ligament forces were 43.2 N (left ligamentum flavum) and 50.7 N (left capsular ligament).     

Rapid determination of EUF-extractable nitrogen and boron

Summary A procedure for the rapid determination of EUF-extractable nitrogen (NH₄ ⁺, NO₃ ⁻ and easily soluble organic N compounds) is described. In this procedure the EUF-N fractions are oxidized to NO₃. The oxidation with peroxodisulfate is accelerated by ultraviolet (UV) radiation. This reduces the time of digestion to about 15 minutes. The contents of EUF-extractable N are on the average only between 2–8 mg/100 g soil. Their determination by the new procedure in the form of NO₃ is more precise than the results obtained by digestion according to Kjeldahl. The sum of EUF-extractable N fractions obtained by the new procedure allows to assess the N fertilizer requirements more precisely than is possible when using the EUF-NO₃ fractions alone. Therefore this new procedure constitutes a considerable advantage when working out fertilizer recommendations for agricultural practice.     

Ultrastructural localization of giardins to the edges of disk microribbons of Giarida lamblia and the nucleotide and deduced protein sequence of alpha giardin

The giardins are a group of 29-38-kD proteins in the ventral disk of the protozoan parasite Giardia lamblia. The disk attaches the parasite to the host's intestinal epithelium and is composed of parallel, coiled microtubules that are adjacent to the ventral plasma membrane and from which processes called microribbons extend into the cytoplasm; the microribbons are connected by crossbridges. G. lamblia cytoskeletons, consisting of disks and attached flagella, were isolated and used to show that the 29-38-kD proteins separate into five bands by one-dimensional electrophoresis and into 23 species by two-dimensional analysis. Rabbit antibodies raised against a 33-kD protein band, purified by one-dimensional gel electrophoresis and shown to contain three proteins by two-dimensional electrophoresis, recognized 17 proteins by two-dimensional immunoblot analysis. By immunofluorescence these antibodies reacted with the ventral disk but not with the flagella in isolated cytoskeletons. Electron microscopy revealed that the anti-giardin antibodies bound to the edges of the microribbons but not to the microtubules, crossbridges, or other, nondisk structures. Antibodies to tubulin reacted with both the disk and flagella in isolated cytoskeletons but bound only to the microtubules in these structures. The amino-terminal sequence of the 33-kD immunogen was determined and used to construct a DNA oligomer, and the oligomer was used to isolate the alpha giardin gene. The gene was used to hybrid select RNA, and the in vitro translation product from this RNA was precipitated by the antibodies against the 33-kD immunogen. The gene sequence was a single open reading frame of 885 nucleotides that predicted a protein of 33.8 kD. The protein sequence is unique, having no significant homology to two other giardin sequences or to any sequences within the Protein Identification Resource. It is predicted to be 82% alpha helical. The downstream sequence of the gene indicates that the sequence AGT-PuAA is located six to nine nucleotides beyond the stop codon in all protein-encoding genes of G. lamblia that have been sequenced and reported to date.     

Oblong,a program to analyse phylogenomic data sets with millions of characters,requiring negligible amounts of RAM

Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.     

The occurrence of Chlamydia spp. in pigs with and without clinical disease

Background

Disk-associated cervical spondylomyelopathy (DA-CSM) is a multifactorial neurological disorder in which progressive caudal cervical spinal cord compression is mainly caused by one or more intervertebral disk protrusions. The Doberman pinscher breed seems predisposed for this condition. The underlying cause and pathophysiology of DA-CSM are currently unknown. Recently, wider intervertebral disks have been put forward as a risk factor for development of clinically relevant DA-CSM. However, little is known about other factors affecting intervertebral disk width. Therefore the aim of this study was to assess the association between intervertebral disk width, measured on magnetic resonance imaging (MRI), and clinical status, age, gender and intervertebral disk location in dogs with and without clinical signs of DA-CSM.

Methods

Doberman pinschers with clinical signs of DA-CSM (N=17),clinically normal Doberman pinschers (N=20), and clinically normal English Foxhounds (N=17), underwent MRI of the cervical vertebral column. On sagittal T2-weighted images, intervertebral disk width was measured from C2-C3 to C6-C7. Intra ?Cand interobserver agreement were assessed on a subset of 20 of the 54 imaging studies.

Results

Intervertebral disk width was not significantly different between Doberman pinschers with clinical signs of DA-CSM, clinically normal Doberman pinschers or clinically normal English Foxhounds (p=0.43). Intervertebral disk width was positively associated with increasing age (p=0.029). Each monthly increase in age resulted in an increase of disk width by 0.0057mm. Intervertebral disk width was not significantly affected by gender (p=0.056), but was significantly influenced by intervertebral disk location (p <0.0001). The assessed measurements were associated with a good intra ?Cand interobserver agreement.

Conclusions

The present study does not provide evidence that wider intervertebral disks are associated with clinical status in dogs with and without DA-CSM. Instead, it seems that cervical intervertebral disk width in dogs is positively associated with increase in age.     

Finite element simulation of an artificial intervertebral disk using fiber reinforced laminated composite model

Degeneration of intervertebral disk (IVD) has been increased in recent years. The lumbar herniation can be cured using conservative and surgical procedures. Surgery is considered after failure of conservative treatment. Partial discectomy, fusion, and total disk replacement (TDR) are also common surgical treatments for degenerative disk disease. However, due to limitations and disadvantages of the current treatments, many studies have been carried out to approach the best design of mimicking natural disk. Recently, a new method of TDRs has been introduced using nature deformation of IVD by reinforced fibers of annulus fibrosis. Nonetheless, owing to limitations of experimental works on the human body, numerical studies of IVD may help to understand load transfer and biomechanical properties within the disks with reinforced fibers. In this study, a three-dimensional (3D) finite element model of the L2-L3 disk vertebrae unit with 12 vertical fibers embedded into annulus fibrosis was constructed. The IVD was subjected to compressive force, bending moment, and axial torsion. The most important parameters of disk failures were compared to that of experimental data. The results showed that the addition of reinforced fibers into the disk invokes a significant decrease of stress in the nucleus and annulus. The findings of this study may have implications not only for developing IVDs with reinforced fibers but also for the application of fiber reinforced IVD in orthopedics surgeries as a suitable implant.     

A novel ferromagnetic coupling one-dimensional complex {Cu(II)(NIT3Py)2[N(CN)2]2(H2O)2}

The novel ferromagnetic coupling one-dimensional complex {Cu(NIT3Py)₂[N(CN)₂]₂(H₂O)₂} (NIT3Py=2-(3^′-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) was synthesized and characterized structurally and magnetically. It crystallizes in the monoclinic space group C2/c. The Cu(II) ion is in a distorted octahedral environment. The units of {Cu(NIT3Py)₂[N(CN)₂]₂(H₂O)₂} were connected as one-dimensional structure by the intermolecular hydrogen bonds. Magnetic measurements show that there are intramolecular ferromagnetic interactions and intermolecular antiferromagnetic interactions within the chain.     

Nickel(II) complexes with Schiff-base ligands derived from epimeric pyranose backbones as 2,3-chelators: modeling the coordination chemistry of chitosan

Two mononuclear nickel(II) complexes with Schiff-base ligands derived from the epimeric sugars glucosamine and mannosamine have been synthesized. The X-ray crystal structure reveals a distorted octahedral geometry at the nickel(II) ions with an N4O2 donor set and the rare 2,3-chelation of the donor atoms of the carbohydrate backbone. Upon complexation only the glucopyranose ring maintains the 4C1 chair conformation, whereas the mannopyranose ring adopts the OS5 screw-boat conformation. Dimeric units of complex cations are formed by intermolecular hydrogen bonding which are further assembled by pi-stacking affording one-dimensional chains with a twofold screw symmetry.     

Functional interaction between the two halves of the photoreceptor-specific ATP binding cassette protein ABCR (ABCA4). Evidence for a non-exchangeable ADP in the first nucleotide binding domain

ABCR, also known as ABCA4, is a member of the superfamily of ATP binding cassette transporters that is believed to transport retinal or retinylidene-phosphatidylethanolamine across photoreceptor disk membranes. Mutations in the ABCR gene are responsible for Stargardt macular dystrophy and related retinal dystrophies that cause severe loss in vision. ABCR consists of two tandemly arranged halves each containing a membrane spanning segment followed by a large extracellular/lumen domain, a multi-spanning membrane domain, and a nucleotide binding domain (NBD). To define the role of each NBD, we examined the nucleotide binding and ATPase activities of the N and C halves of ABCR individually and co-expressed in COS-1 cells and derived from trypsin-cleaved ABCR in disk membranes. When disk membranes or membranes from co-transfected cells were photoaffinity labeled with 8-azido-ATP and 8-azido-ADP, only the NBD2 in the C-half bound and trapped the nucleotide. Co-expressed half-molecules displayed basal and retinal-stimulated ATPase activity similar to full-length ABCR. The individually expressed N-half displayed weak 8-azido-ATP labeling and low basal ATPase activity that was not stimulated by retinal, whereas the C-half did not bind ATP and exhibited little if any ATPase activity. Purified ABCR contained one tightly bound ADP, presumably in NBD1. Our results indicate that only NBD2 of ABCR binds and hydrolyzes ATP in the presence or absence of retinal. NBD1, containing a bound ADP, associates with NBD2 to play a crucial, non-catalytic role in ABCR function.     

Multinuclear magnetic resonance studies of the 2Fe.2S* ferredoxin from Anabaena species strain PCC 7120. 3. Detection and characterization of hyperfine-shifted nitrogen-15 and hydrogen-1 resonances of the oxidized form

All the nitrogen signals from the amino acid side chains and 80 of the total of 98 backbone nitrogen signals of the oxidized form of the 2Fe.2S* ferredoxin from Anabaena sp. strain PCC 7120 were assigned by means of a series of heteronuclear two-dimensional experiments [Oh, B.-H. Mooberry, E. S., & Markley, J. L. (1990) Biochemistry (second paper of three in this issue )]. Two additional nitrogen signals were observed in the one-dimensional 15N NMR spectrum and classified as backbone amide resonances from residues whose proton resonances experience paramagnetic broadening. The one-dimensional 15N NMR spectrum shows nine resonances that are hyperfine shifted and broadened. From this inventory of diamagnetic nitrogen signals and the available X-ray coordinates of a related ferredoxin [Tsukihara, T., Fukuyama, K., Nakamura, M., Katsube, Y., Tanaka, N., Kakudo, M., Wada, K., Hase, T., & Matsubara, H. (1981) J. Biochem. 90, 1763-1773], the resolved hyperfine-shifted 15N peaks were attributed to backbone amide nitrogens of the nine amino acids that share electrons with the 2Fe.2S* center or to backbone amide nitrogens of two other amino acids that are close to the 2Fe.2S* center. The seven 15N signals that are missing and unaccounted for probably are buried under the envelope of amide signals. 1H NMR signals from all the amide protons directly bonded to the seven missing and nine hyperfine-shifted nitrogens were too broad to be resolved in conventional 2D NMR spectra.(ABSTRACT TRUNCATED AT 250 WORDS)     

Mechanical properties of spruce and beech wood grown in elevated CO2

Biomechanical responses of stems of 6- to 7-year-old spruce [Picea abies (L.) Karst.] and beech (Fagus sylvatica L) trees were studied after 4 years of growth in elevated atmospheric CO₂ in combination with a nitrogen treatment and on two different soil types. At the end of the treatment, stems were harvested and tested in fresh and air-dried status. Bending characteristics of juvenile wood (modulus of elasticity, termed rigidity) were determined by bending tests. Fracture characteristics (termed toughness) were determined by stroke-pendulum tests. From the base disk of each stem densitometric data were obtained. In spruce, wood produced under elevated CO₂ was tougher on both soil types; enhanced N deposition made wood less rigid only on acidic soils. In contrast, beech wood samples showed no significant reaction to CO₂ but were significantly tougher under high nitrogen depositions on acidic soil. Effects on wood density of both CO₂ and N treatments were not significant, but wood density was higher on acidic soil and so were rigidity and toughness (soil effect). Different genotypes of spruce and beech reacted significantly differently to the treatments. Some genotypes reacted strongly to CO₂ or N, whereas others did not react or showed interactions between CO₂ and N. This underlines the importance of genetic diversity in tree communities.     

Single-species models of the Allee effect: extinction boundaries,sex ratios and mate encounters

We critically review and classify models of single-species population dynamics subject to the demographic Allee effect with emphasis on non-spatial, deterministic approach. Inclusion of spatial movement and stochastic phenomena does not substantially change the behaviour; stochasticity only "blurs" step-like character of the Allee effect into a sigmoidal form. The outcome of all non-spatial, deterministic models is either unconditional extinction, extinction-survival scenario (ES), or unconditional survival. Three major model classes are recognized: (1) one-dimensional heuristic models, (2) one-dimensional models with mating probability and fixed sex ratio, and (3) two-sex models with variable adult sex ratio. Each class is characterized by the shape of extinction boundary which separates extinction from survival in the ES scenario. The latter two classes may give better predictions of extinction thresholds than heuristic models but require specific information and are data intensive. In one-dimensional models with fixed sex ratio, population cannot survive if density/number of males decreases below some threshold while there is no such restriction on females. Individual-based models seem to be most capable of explaining mechanisms leading to the Allee effect.     

Topology of beef heart cytochrome c oxidase from studies on reconstituted membranes

The orientation of purified beef heart cytochrome c oxidase, incorporated into vesicles by the cholate dialysis procedure [Carroll, R.C., & Racker, E. (1977) J. Biol. Chem. 252, 6981], has been investigated by functional and structural approaches. The level of heme reduction obtained by using cytochrome c along with the membrane-impermeant electron donor ascorbate was 78 +/- 2% of that obtained with cytochrome c and the membrane-permeant reagent N,N,N',N'-tetramethyl-p-phenylenediamine. Electron transfer from cytochrome c is known to occur exclusively from the outer surface of the mitochondrial inner membrane (C side), implying that at least 78% of the oxidase molecules are oriented in the same way in these vesicles as in the intact mitochondria. Trypsin, which cleaves subunit IV near its N terminus, modifies only 5-7% of this subunit in intact vesicles. This removal of the N-terminal residues has been shown to occur only in mitochondrial membranes with their inner side (M side) exposed. Diazobenzene [35S]sulfonate [( 35S]DABS) likewise modifies subunit IV only in submitochondrial particles. Labeling of intact membranes with [35S]DABS resulted in incorporation of only 4-8% of the total counts that could be incorporated into this subunit in membranes made leaky to the reagent by addition of 2% Triton X-100. Therefore, both the functional and structural data show that at least 80% and probably more of the cytochrome c oxidase molecules are oriented with their C domain outermost and M domains in the lumen of vesicles prepared by the cholate dialysis method.(ABSTRACT TRUNCATED AT 250 WORDS)     

A multiple testing procedure for clinical trials.

A multiple testing procedure is proposed for comparing two treatments when response to treatment is both dichotomous (i.e., success or failure) and immediate. The proposed test statistic for each test is the usual (Pearson) chi-square statistic based on all data collected to that point. The maximum number (N) of tests and the number (m1 + m2) of observations collected between successive tests is fixed in advance. The overall size of the procedure is shown to be controlled with virtually the same accuracy as the single sample chi-square test based on N(m1 + m2) observations. The power is also found to be virtually the same. However, by affording the opportunity to terminate early when one treatment performs markedly better than the other, the multiple testing procedure may eliminate the ethical dilemmas that often accompany clinical trials.     

The proteomic study of Danio rerio embryos using one-dimensional electrophoresis and mass-spectrometry

Using one-dimensional proteomic mapping (combination of one-dimensional gel electrophoresis (1DE) with subsequent mass spectrometry MALDI-TOF-PMF) the protein profile of Danio rerio embryos has been investigated. The fish species Danio rerio is the most effective alternative model of vertebrates used for studies of drug toxicity (e.g. doxorubicin) due to its high degree of homology with human genome. The proteomic profiling resulted in identification of 84 proteins, including 15 vitellogenins. Using the procedure of preparation of homogenates of Danio rerio embryos optimized by ultrasonic treatment promoting removal of yolk basic proteins (vitellogenin) we have registered changes in the proteome profile of D. rerio embryos induced by doxorubicin (DOX). Growth D. rerio embryos in the medium with DOX caused the decrease in the number of vitellogenins, disappearance of cardiac troponins, and induction of caspase-3. All these observations are consistent with the literature data on doxorubicin-induced cardiotoxicity. The proposed method of 1D proteomic mapping may be used not only for protein identification but also for registration of changes in embryonic proteomic profile caused by drugs or any toxic compound for studying the mechanisms underlying induced toxicity.