The outer membrane porin from Yersinia enterocolitica in yersiniosis diagnostics

The diagnostic test system based on a species-specific antigen, pore-forming protein from the outer membrane of Yersinia enterocolitica, for yersiniosis verification by the method of ELISA has been developed and approved. The proposed ELISA test system is characterized by high sensitivity (95%) and specificity (89%) and provides a differential diagnostics of yersiniosis from other acute enteric infections with similar clinical manifestations. In comparison with the commercial diagnostics based on indirect hemagglutination reaction, which is conventionally used in clinical practice, the porin-based ELISA provides the high level (90–95%) of yersiniosis identification at early (1st week) and late (2nd–4th week) stages of infection process. It has been found that the ELISA test system reveals antibodies to the Y. enterocolitica porin in patient’s serum irrespective of the serological variant of causative agent.     

Highly sensitive field test lateral flow immunodiagnostics of PVX infection

A test system is described and expanded upon for mass field immunochromatography assay on porous membrane carriers for rapid diagnostics of potato virus X (PVX) in potato leaf tissue and sprout extracts using colloidal gold nanoparticles as a marker. Sensitivity of the assay developed for PVX identification is found to be comparable to the sensitivity of solid-phase sandwich-ELISA. Complete assay time does not exceed 15 min, and the lower limit of the PVX detection in non-clarified leaf extract is 2 ng/ml. A single measurement requires 0.1–0.2 ml (3–5 drops) of tested solution only (extracted from 10–20 mg of potato leaf tissue or sprouts). The simplicity and reliability of the method makes it especially efficient in direct rapid monitoring of many infected potato specimens in the field, as verified by field trials of 360 clones of 28 domestic and foreign cultivars of potato. A diagnostic kit for routine analyses of potato viral infections both in the laboratory and in the field is described and expanded upon.     

Biomarkers for Diagnosis of Candidal Infections

Candidemia and invasive candidiasis are associated with significant mortality, in part because of inadequate diagnostic tests. The current gold standard is blood culture, which is negative in 50% of cases. As such, development of novel diagnostics is a top priority. In Europe, studies of combined mannan antigen and anti-mannan antibody detection assays have demonstrated sensitivity of 71–100% and specificity of 86–93%. In the United States, there is more experience with (1 → 3)-β-D-glucan detection as a broad-spectrum assay for fungal pathogens. Sensitivity and specificity for diagnosing invasive candidiasis have ranged widely in studies (47–95% and 76–100%, respectively). Nucleic acid detection assays such as polymerase chain reaction (PCR) are potentially powerful tools that are now approaching the clinic. Overall, optimized PCR assays have sensitivities and specificities for candidemia and proven or probable invasive candidiasis that exceed 90%. Studies to determine the precise clinical roles of non–culture-based diagnostics are in progress.     

Micro-nano-technology for biomedical application

Nanomedical developments range from nanoparticles for molecular diagnostics, imaging and therapy to integrated medical nanosystems, which may perform complex repair actions at the cellular level inside the body in the future. There are three categories where MNT are applied in biomedicine

Distribution of matter in the current-carrying plasma and dense core of the discharge channel formed upon electrical wire explosion

Distribution of matter in the discharge channel formed upon a nanosecond electrical explosion of a single wire in air and vacuum was studied experimentally. Simultaneous use of optical, UV, and X-ray diagnostics made it possible to distinguish qualitatively different regions of the discharge channel, such as the current-carrying layers and the region occupied by a weakly conducting cold plasma. Several series of experiments with 25-μm-diameter 12-mm-long wires made of different materials were performed. The charging voltage and the current amplitude were varied in the ranges of U ₀ = 10–20 kV and I _max ∼ 5–10 kA, respectively. Explosion regimes with a current pause and with and without current interruption, as well as with wire preheating in air and vacuum, were studied. Shadow and schlieren images of the discharge channel were obtained using optical probing at the second harmonic of a YAG: Nd⁺³ laser (λ = 0.532 μm, τ ∼ 10 ns). In the experiments carried out in vacuum, X-ray images of the discharge channel were also obtained using an X-pinch as a point source of probing radiation and UV images were recorded using a four-frame MCP camera.     

Thermozymes: biotechnology and structure–function relationships

Recent findings on the biochemical and molecular features of the following thermozymes are presented, based on their biotechnological use: α-amylase and amylopullulanase, used in starch processing; glucose isomerase, used in sweetener production; alcohol dehydrogenase, used in chemical synthesis; and alkaline phosphatase, used in diagnostics. The corresponding genes and recombinant proteins have been characterized in terms of sequence similarities, specific activities, thermophilicity, and unfolding kinetics. Site-directed and nested deletion mutagenesis were used to understand structure–function relationships. All these thermozymes display higher stability and activity than their counterparts currently used in the biotechnology industry. Received: January 22, 1998 / Accepted: February 16, 1998     

Diagnostics of plasma produced by femtosecond laser pulse impact upon a target with an internal nanostructure

X-ray diagnostics of the interaction of femtosecond laser pulses with intensities of 10¹⁶–10¹⁸ W/cm² with CO₂ clusters and frozen nanosize water particles is carried out. The stage of cluster expansion and the formation of a plasma channel, which governs the parameters of the formed X-ray radiation source and accelerated ion flows, is studied. The measurements are based on recording spatially resolved X-ray spectra of H- and He-like oxygen ions. Utilization of Rydberg transitions for spectra diagnostics makes it possible to determine plasma parameters on a time scale of t ∼ 10 ps after the beginning of a femtosecond pulse. The role of the rear edge of the laser pulse in sustaining the plasma temperature at a level of ∼100 eV in the stage of a nonadiabatic cluster expansion is shown. The analysis of the profiles and relative intensities of spectral lines allows one to determine the temperature and density of plasma electrons and distinguish the populations of “thermal” ions and ions that are accelerated up to energies of a few tens of kiloelectronvolts. It is shown that the use of solid clusters made of frozen nanoscale water droplets as targets leads to a substantial increase in the number of fast He-like ions. In this case, however, the efficiency of acceleration of H-like ions does not increase, because the time of their ionization in plasma exceeds the time of cluster expansion.     

Magnesium,Calcium, and Trace Elements Excretion in 24-h Urine

Urine is a clinical specimen often used in medical diagnostics for monitoring of elements concentrations and kidneys function. We determined the contents of magnesium (Mg), calcium (Ca), zinc (Zn), copper (Cu), iron (Fe), lead (Pb), and cadmium (Cd) in 74 samples of 24-h urine (from 46 women and 28 men). The measurements were realized by the atomic absorption spectrometry (AAS) with atomization in the flame (FAAS) and in the graphite furnace (GFAAS). The received results were the subject of statistical analysis including the sex and age of volunteers. Moreover, correlations between the elements and the relationships between age and amounts of excreted elements with urine were tested. We found the statistically significant higher content of Zn in men’s urine than in women^’s one. Moreover, both adult women and men (>18 years) excreted much more Ca in urine in comparison to young subjects. Only in case of Pb the significant positive correlation between its amount in 24-h urine of all donors and age was stated. The correlation analysis has shown the significant positive relationships between Ca–Mg, Ca–Fe, Mg–Fe, Cu–Fe, Cu–Cd, Fe–Cd, and Pb–Cd in total samples of urine. Basing on our results, we concluded that the gender and age of donors may impact on the elemental status of 24-h urine.     

Node-derived cultures with high-morphogenic competence in barley and wheat

A successful regeneration system is presented for elite cultivars in barley and wheat based on nodes. Nodal explants were excised from in vitro and ex vitro grown plants. A combination of 8.28 μM 4-amino-3,5,6-trichloropicolinic acid and 4.54 μM to 22.71 μm thidiazuron (TDZ) used in MS-based medium containing 60 g l⁻¹ maltose favoured induction of clumps of multiple shoots/buds with or without callus formation in the primary cultures. Within 8–10 weeks upon further subcultures, the proliferation into callus with rapid and continuously forming adventitious buds containing clusters of meristemoids, termed meristematic bulk tissue (MBT) was obtained. Lowering the levels of growth regulators resulted in redifferentiation of shoots, which elongated, rooted, developed into morphologically normal plants and set seeds normally. With a frequency ranging between 37 and 82% the nodes raised from in vitro grown plants were proliferated into MBT independent of TDZ concentration, cultivar and species. The average number of shoots per responding node in different cultivars was 7–15 in barley and 1–6 in wheat after 12–14 weeks. Nodes from greenhouse grown plants mainly responded for callus formation with poor development of MBT.     

Surface-bound selectin–ligand binding is regulated by carrier diffusion

Two-dimensional (2D) kinetics of receptor–ligand interactions governs cell adhesion in many biological processes. While the dissociation kinetics of receptor–ligand bond is extensively investigated, the association kinetics has much less been quantified. Recently receptor–ligand interactions between two surfaces were investigated using a thermal fluctuation assay upon biomembrane force probe technique (Chen et al. in Biophys J 94:694–701, 2008). The regulating factors on association kinetics, however, are not well characterized. Here we developed an alternative thermal fluctuation assay using optical trap technique, which enables to visualize consecutive binding–unbinding transition and to quantify the impact of microbead diffusion on receptor–ligand binding. Three selectin constructs (sLs, sPs, and PLE) and their ligand P-selectin glycoprotein ligand 1 were used to conduct the measurements. It was indicated that bond formation was reduced by enhancing the diffusivity of selectin-coupled carrier, suggesting that carrier diffusion is crucial to determine receptor–ligand binding. It was also found that 2D forward rate predicted upon first-order kinetics was in the order of sPs > sLs > PLE and bond formation was history-dependent. These results further the understandings in regulating association kinetics of surface-bound receptor–ligand interactions.     

Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics

The application of gas chromatography–mass spectrometry (GC–MS) to the ‘global’ analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project’s (METAbolomics for Plants Health and OutReach: ) priorities towards robust technology development, a GC–MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GC×GC–TOF/MS was compared with 1 dimensional GC–TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise.     

Optimizing the biodegradation of two keratinous wastes through a Bacillus subtilis recombinant strain using a response surface methodology

Statistical optimization of the biodegradation of two keratinous wastes directed by Bacillus subtilis recombinant cells was carried out by means of a response surface methodology. A Box–Behnken design was employed to predict the optimal levels of three variables namely, keratin percent, incubation time and inoculum size. Analysis of variance revealed that, only keratin percent had the highest significant effect. Canonical analysis and ridge max analysis were used to get the optimal levels of the three predictors along with the optimum levels of the responses. The optimal sets of predicted and validated levels of the three variables were [7.69% (w/v) feathers, 96.58 h and 1.28% (v/v) inoculum size] and [8% (w/v) feathers, 98.45 h, 3.9% (v/v) inoculum size] to achieve the highest levels of soluble proteins (1.25–1.7 mg/ml) and NH₂-free amino groups (245.82–270.0 μmol leucine/ml), respectively upon using three optimized feathers-based media. These values represented 83.67–100% and 100% adequacy for the models of soluble proteins and NH₂-free amino groups, respectively. While, [8.23% (w/v) sheep wool, 5.52% (v/v) inoculum size and 46.58 h] and [8.33% (w/v) sheep wool, 5.89% (v/v) inoculum size and 63.46 h] were the optimal sets of predicted and validated levels of the above variables to achieve the highest yields of soluble proteins (3.4–4.6 mg/ml) and NH₂-free amino groups (290.9–302.0 μmol leucine/ml), respectively upon using three optimized sheep wool-based media. These values represented 100% adequacy for the models of soluble proteins and NH₂-free amino groups. By the end of the optimization strategy, a fold enhancement (2.14–2.43 and 1.78–2.12) in the levels of released soluble proteins and NH₂-free amino groups, respectively was obtained upon using three optimized feathers-based media. However, a fold enhancement (4.25–5.75 and 2.42–2.5) in the levels of soluble proteins and NH₂-free amino groups, respectively was obtained upon using three optimized sheep wool-based media. Data would encourage pilot scale optimization of the biodegradation of these wastes.     

Deletion diagnostics for alternating logistic regressions

Deletion diagnostics are introduced for the regression analysis of clustered binary outcomes estimated with alternating logistic regressions, an implementation of generalized estimating equations (GEE) that estimates regression coefficients in a marginal mean model and in a model for the intracluster association given by the log odds ratio. The diagnostics are developed within an estimating equations framework that recasts the estimating functions for association parameters based upon conditional residuals into equivalent functions based upon marginal residuals. Extensions of earlier work on GEE diagnostics follow directly, including computational formulae for one‐step deletion diagnostics that measure the influence of a cluster of observations on the estimated regression parameters and on the overall marginal mean or association model fit. The diagnostic formulae are evaluated with simulations studies and with an application concerning an assessment of factors associated with health maintenance visits in primary care medical practices. The application and the simulations demonstrate that the proposed cluster‐deletion diagnostics for alternating logistic regressions are good approximations of their exact fully iterated counterparts.     

Simple Formation of an Abiotic Porphyrinogen in Aqueous Solution

Porphyrins have long been proposed as key ingredients in the emergence of life yet plausible routes for forming their essential pyrrole precursor have heretofore not been identified. Here we show that the anaerobic reaction of δ-aminolevulinic acid (ALA, 1–5 mM) with the β-ketoester methyl 4-methoxyacetoacetate (2–40 mM) in water (pH 5–7) at 70–100°C for >6 h affords the porphyrinogen, which upon chemical oxidation gives the corresponding porphyrin in overall yield of up to 10%. The key intermediate is the α-methoxymethyl-substituted pyrrole, which undergoes tetramerization and macrocycle formation under kinetic control. The resulting type-I porphyrin bears four propionic acid and four carbomethoxy groups, is distinct from porphyrins (e.g., uroporphyrin or coproporphyrin) derivable from ALA alone via the extant universal biosynthetic path to tetrapyrroles, and is photoactive upon assembly into cationic micelles in aqueous solution. The simple self-organization of eight acyclic molecules into a tetrapyrrole macrocycle, from which a porphyrin is derived that is photoactive in lipid assemblies, augurs well for the spontaneous origin of catalysts and pigments essential for prebiotic metabolism and proto-photosynthesis.     

Three-dimensional finite element modeling of pericellular matrix and cell mechanics in the nucleus pulposus of the intervertebral disk based on in situ morphology

Nucleus pulposus (NP) cells of the intervertebral disk (IVD) have unique morphological characteristics and biologic responses to mechanical stimuli that may regulate maintenance and health of the IVD. NP cells reside as single cell, paired or multiple cells in a contiguous pericellular matrix (PCM), whose structure and properties may significantly influence cell and extracellular matrix mechanics. In this study, a computational model was developed to predict the stress–strain, fluid pressure and flow fields for cells and their surrounding PCM in the NP using three-dimensional (3D) finite element models based on the in situ morphology of cell–PCM regions of the mature rat NP, measured using confocal microscopy. Three-dimensional geometries of the extracellular matrix and representative cell–matrix units were used to construct 3D finite element models of the structures as isotropic and biphasic materials. In response to compressive strain of the extracellular matrix, NP cells and PCM regions were predicted to experience volumetric strains that were 1.9–3.7 and 1.4–2.1 times greater than the extracellular matrix, respectively. Volumetric and deviatoric strain concentrations were generally found at the cell/PCM interface, while von Mises stress concentrations were associated with the PCM/extracellular matrix interface. Cell–matrix units containing greater cell numbers were associated with higher peak cell strains and lower rates of fluid pressurization upon loading. These studies provide new model predictions for micromechanics of NP cells that can contribute to an understanding of mechanotransduction in the IVD and its changes with aging and degeneration.     

Genome scanning for resistance-gene analogs in rice, barley, and wheat by high-resolution electrophoresis

 Genes cloned from diverse plants for resistance to different pathogens have sequence similarities in domains presumably involved in pathogen recognition and signal transduction in triggering the defense response. Primers based on the conserved regions of resistance genes often amplify multiple fragments that may not be separable in an agarose gel. We used denaturing polyacrylamide-gel electrophoresis to detect PCR products of plant genomic DNA amplified with primers based on conserved regions of resistance genes. Depending upon the primer pairs used, 30–130 bands were detected in wheat, rice, and barley. As high as 47%, 40%, and 27% of the polymorphic bands were detected in rice, barley, and wheat, respectively, and as high as 12.5% of the polymorphic bands were detected by certain primers in progeny from a cross of the wheat cultivars ‘Stephens’ and ‘Michigan Amber’. Using F₆ recombinant inbred lines from the ‘Stephens’בMichigan Amber’ cross, we demonstrated that polymorphic bands amplified with primers based on leucine-rich repeats, nucleotide-binding sites and protein kinase genes, were inherited as single loci. Linkages between molecular markers and stripe rust resistance genes were detected. This technique provides a new way to develop molecular markers for assessing the genetic diversity of germplasm based upon potential candidate resistance genes in diverse species. Received : 5 September 1997 / Accepted : 6 November 1997     

Soluble HLA-G induces NF–кB activation in natural killer cells

Human leukocyte antigen (HLA)-G is an immunomodulatory molecule discovered for the first time in the maternal–fetal interface. In cancer context, where high number of natural killer (NK) cells is described, the presence of HLA-G in its soluble form is thought to be essential for NK cells signaling. To evaluate intracellular signaling in NK cells upon HLA-G soluble forms stimulation, we investigate the role of soluble HLA-G (HLA-G5- and HLA-G1 shedding form) stimulation on classical nuclear factor (NF)–κB pathway activation. We reported that these two forms of soluble HLA-G could activate NF–κB in NK cells. NF–κB activation in NK cells does implicate neither phosphatidylinositol 3-kinase (PI3K) nor MEK (MAP kinase kinase) as demonstrated after specific inhibition experiments. We demonstrated elsewhere that NF–κB activation in NK cells is not implicated in cytotoxicity inhibition by HLA-G. Our findings may suggest the important role played by NF–κB activation after soluble HLA-G stimulation in other NK cells function.     

Molecular authentication of ginseng cultivars by comparison of internal transcribed spacer and 5.8S rDNA sequences

Molecular authentication among three Panax species and within cultivars and accessions of P. ginseng was investigated using the DNA sequence in the ribosomal ITS1–5.8S–ITS2 region. Four single-nucleotide polymorphisms were identified between P. ginseng and other Panax species. In the electrophoresis profile, obtained after digestion with the enzyme TaqI, three fingerprinting patterns were obtained from cultivars and accessions of Panax species. Consequently, this authentication procedure based upon the restriction fragment length polymorphism in the ribosomal ITS1–5.8S–ITS2 region can now be utilized to differentiate these Panax species as well as major Korean cultivars such as Gopoong and Kumpoong from other cultivars and accessions in Panax species at the DNA level. O. T. Kim and K. H. Bang contributed equally to this paper.     

Backbone assignment of the UHM domain of Puf60 free and bound to five ligands

U2AF homology motifs (UHM) are protein domains that bind peptidic UHM ligand motifs (ULM) and thus form an intricate network of interactions involved in splicing regulation. Here, we report the backbone assignment of the UHM domain of the splicing factor Puf60 as well as ¹H, ¹⁵N chemical shifts upon binding of the ULM peptides U2AF⁶⁵ (85–112), SF1 (1–25), SF3b155 (194–229), SF3b155 (317–357), and Prp16 (201–238).