The effect of the physiological state of Escherichia coli on the nucleoid ultrastructure under stress exposures]

The energetic state and activity of polyamine-synthesizing system of E. coli were studied under conditions of aerobic-anaerobic and pH transitions, nutrition shifts, osmotic and heat shocks. The electron microscopy of cells showed a correlation between cell physiological state and nucleoid ultrastructure. The role of energetic status and polyamines in the regulation of DNA supercoiling is discussed which is a putative cause for the changes observed in the nucleoid ultrastructure.     

Multiplex PCR for Identification of Bacterial Pathogens of Infectious Pneumonia

Russian Journal of Bioorganic Chemistry - A multiplex PCR system has been developed and optimized for rapid detection of the five main pathogens of bacterial pneumonia. The system can be expanded...     

In vitro formation of triple-stranded DNA structures in the human alpha1-antitrypsin gene

We analyzed the possibility of triplex formation in the human alpha 1-antitrypsin gene. Conditions and nucleotide sequence dependence of triplex formation and thermostability of the product were determined.     

Fluorescence data analysis on gel-based biochips

A series of biochip readers developed for gel-based biochips includes three imaging models and a novel nonimaging biochip scanner. The imaging readers, ranging from a research-grade versatile reader to a simple portable one, use wide-field objectives and 12-bit digital large-coupled device cameras for parallel addressing of multiple array elements. This feature is valuable for monitoring the kinetics of sample interaction with immobilized probes. Depending on the model and the label used, the sensitivity of these readers approaches 0.3 amol of a labeled sample per gel element. In the selective scanner, both the spot size of the excitation laser beam and the detector field of view match the size of the biochip array elements so that the whole row of the array can be read in a single scan. The portable version reads 50-mm long, 150-element, one-dimensional arrays in 5 s. With a dynamic range of 4000:1, a sensitivity of 1-5 amol of a labeled sample per gel element, and a data format facilitating online processing, the scanner is an attractive, inexpensive solution for biomedical diagnostics. Fluorophores for sample labeling were compared experimentally in terms of detection sensitivity, influence on duplex stability, and suitability for multilabel analysis and thermodynamic studies. Texas Red and tetracarboxyphenylporphyn proved to be the best choice for two-wavelength analysis using the imaging readers.     

Identification of Mycobacterium tuberculosis strains and a simultaneous identification of their drug resistance by the hybridization method on oligonucleotide microchips

A method of multiplex polymerase chain reaction (PCR) with subsequent hyoridization on oligonucleotide microchips was worked out to identify the Mycobacterium tuberculosis complex and to determine simultaneously the bacterial sensitivity to 2 first-line drugs, i.e. rifampin and isoniazid. The method provides for detecting above 95% of rifampin-resistant and around 80% of isoniazid-resistant strains within 1 day.     

Tooth replacement rates in early chondrichthyans: a qualitative approach

The continuous replacement of teeth throughout their lifetime is a common characteristic of most chondrichthyans. This process was already present in the earliest representatives of the group. It has been well established that different species of extant sharks show rapid tooth replacement rates; however, some authors have suggested that in early chondrichthyans this rate might have been much slower. Here we present a qualitative approach to analyse tooth replacement rates in the Early Devonian shark Leonodus carlsi , the earliest tooth-bearing shark known to date. For this, we have examined 1,103 isolated teeth from Celtiberia, Spain. Our study provides strong evidences of an extremely slow dental replacement in this primitive chondrichthyan based on three independents analyses: (1) statistical analysis of the wear degree, demonstrating that teeth remain functional for a long period of time; (2) analysis of both the histological and the morphological features of the teeth cusps suggests that this chondrichthyan used a maturation process that optimizes its function, thus worn teeth show an efficient working shape that implies their teeth remained functional for a long time after being modelled by use; and (3) estimations of size increments between teeth (Δs) of the same dental family for some recent sharks whose rates of replacement were known prove that Δs is inversely proportional to the rate of replacement ( R ² = 0.8327). The estimated values of tooth replacement rates obtained from Δs for L. carlsi and for some Late Devonian cladoselachian sharks are significatively slower than those observed in current sharks.     

Ligands of boron in Pisum sativum nodules are involved in regulation of oxygen concentration and rhizobial infection

Boron (B) is an essential nutrient for N₂‐fixing legume–rhizobia symbioses, and the capacity of borate ions to bind and stabilize biomolecules is the basis of any B function. We used a borate‐binding‐specific resin and immunostaining techniques to identify B ligands important for the development of Pisum sativum–Rhizobium leguminosarum 3841 symbiotic nodules. arabinogalactan–extensin (AGPE), recognized by MAC 265 antibody, appeared heavily bound to the resin in extracts derived from B‐sufficient, but not from B‐deficient nodules. MAC 265 stained the infection threads and the extracellular matrix of cortical cells involved in the oxygen diffusion barrier. In B‐deprived nodules, immunolocalization of MAC 265 antigens was significantly reduced. Leghaemoglobin (Lb) concentration largely decreased in B‐deficient nodules. The absence of MAC 203 antigens in B‐deficient nodules suggests a high internal oxygen concentration, as this antibody detects an epitope on the lipopolysaccharide (LPS) of bacteroids typically expressed in micro‐aerobically grown R. leguminosarum 3841. However, B‐deprived nodules did not accumulate oxidized lipids and proteins, and revealed a decrease in the activity of the major antioxidant enzyme ascorbate peroxidase (APX). Therefore, B deficiency reduced the stability of nodule macromolecules important for rhizobial infection, and for regulation of oxygen concentration, resulting in non‐functional nodules, but did not appear to induce oxidative damage in low‐B nodules.     

Long-term exposure of Boeckellagibbosa (Copepoda, Calanoida) to in situ levels of solar UVB radiation

1. The freshwater calanoid copepod Boeckella gibbosa is typical of high elevation lakes and ponds in Patagonia (Argentina). Previous studies have shown that this species is highly tolerant to short-term exposure to natural and artificial UVB radiation, and that its tolerance is due to photoreactivation by longer wavelength radiation. In this study, we investigate the potential sublethal effects of solar radiation after prolonged exposure.
2. We incubated B. gibbosa at 1 m depth in oligotrophic Lake Toncek for 24 days. The incubation chambers were 1.2 l acrylic cylinders covered with appropriate filters in order to obtain three radiation treatments: visible radiation only, visible radiation + UVA and visible radiation + UVA + UVB.
3. The three treatments did not differ significantly in variables considered as indicators of survival (number of individuals), reproduction (proportion of ovigerous females, clutch size) and development (instar composition). Although resistance to solar UVB radiation is certainly a requisite to live in transparent high elevation habitats, the fact of being effectively exposed to natural levels of UVB radiation does not seem to have measurable consequences on an already adapted species, such as B. gibbosa     

New triphosphate conjugates bearing reporter groups: labeling of DNA fragments for microarray analysis

A simple and convenient method for incorporation of fluorescent or ligand groups into 3'-termini of DNA fragments is proposed. A set of triphosphoric acid monoesters bearing fluorescent groups or biotin attached to the triphosphate fragment through linkers of different lengths and structures was synthesized. All the compounds were substrates for calf thymus terminal deoxynucleotidyltransferase and were used for incorporation of marker groups into 3'-termini of DNA fragments. The compounds were successfully applied for DNA labeling during post-PCR target preparation for microarray analysis.     

Study of Multiple Enzymatic Incorporation of Modified Nucleotides of Purine and Pyrimidine Nature in the Growing DNA Chain

Molecular Biology - The substrate properties of nitrogen-base modified derivatives of purine and pyrimidine deoxynucleoside triphosphates during their simultaneous pairwise insertion into the...