Conodonts from the upper Ordovician siliceous rocks of Central Kazakhstan

Several conodont localities of the upper Sandbian Stage are known in siliceous deposits of Central Kazakhstan. All of them produced similar assemblages overwhelmingly dominated by Periodon grandis with insignificant admixture of Scabbardella altipes, Hamarodus europaeus, Pygodus anserinus, Protopanderodus sp., and Drepanodus sp. The main feature of this fauna is in the co-occurrence of H. europaeus and P. grandis, forms characteristic for deep-water facies at shelf or microcontinents margins of temperate and warm-water paleobiogeographic provinces. The Ordovician paleo-oceanic basin of Kazakhstan and southern Urals were parts of the uniform biogeographic area as indicated by similarity of Ordovician conodont assemblages in siliceous deposits of these regions.     

MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study

Background  

The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quantify the importance of multi-SNP interactions, few of them could handle the genome wide data due to the combinatorial explosive search space and the difficulty to statistically evaluate the high-order interactions given limited samples.     

A simple method to introduce marker-free genetic modifications into the chromosome of naturally nontransformable Bacillus amyloliquefaciens strains

A simple method to introduce marker-free deletions, insertions, and point mutations into the chromosomes of naturally nontransformable Bacillus amyloliquefaciens strains has been developed. The method is efficient and fast, and it allows for the generation of genetic modifications without the use of a counter-selectable marker or a special prerequisite strain. This method uses the combination of the following: the effective introduction of a delivery plasmid into cells for gene replacement; a two-step replacement recombination procedure, which occurs at a very high frequency due to the use of a thermosensitive rolling-circle replication plasmid; and colony polymerase chain reaction (PCR) analysis for screening. Using PCR primers with mismatches at the 3′ end enables the selection of strains that contain a single nucleotide substitution in the target gene. This approach can be used as a routine method for the investigation of complex physiological pathways and for the metabolic engineering of food-grade industrial B. amyloliquefaciens and other Bacillus strains.     

Diversity of lactic acid bacteria of the bioethanol process

Background  

Bacteria may compete with yeast for nutrients during bioethanol production process, potentially causing economic losses. This is the first study aiming at the quantification and identification of Lactic Acid Bacteria (LAB) present in the bioethanol industrial processes in different distilleries of Brazil.     

Supramolecular diversity and magnetic properties of novel heterometallic Cu(II)/Cr(III) complexes prepared from copper powder, Reineckes salt and ethylenediamine

Three novel heterometallic complexes [Cu(en)₂Cr(NCS)₄(NH₃)₂][Cr(NCS)₄(NH₃)₂] · 6dmf (1), [Cu(en)₂Cr(NCS)₄(NH₃)₂](OAc) (2) and [{Cu(en)₂}₃{Cr(NCS)₄(NH₃)₂}₂(NCS)₂](NCS)₂ (3) have been synthesized in a one-pot reaction from copper powder, Reineckes salt, NH₄X [X⁻ = OAc⁻ (2), NCS⁻ (3)] in a dmf (1) or CH₃CN (2, 3) solution of ethylenediamine (en). X-ray studies showed that 1 and 2 consist of cationic polymeric chains, formed by and building blocks that bridged through thiocyanate anions. In both complexes, distinct hydrogen bonds are present and serve to increase the dimensionality of the compound from one to two (in 1) or three (in 2). The main structural feature of 3 is the pentanuclear Cu₃Cr₂ cation which is H-bonded with uncoordinated thiocyanate groups generating a 3D supramolecular assembly. The shortest Cu?Cr distances are 5.840(1) Å for 1, 5.856(1) and 6.018(3) Å for 2 and 6.009(9) and 6.465(9) Å for 3. Compounds 1 and 2 are essentially paramagnets whereas compound 3 shows a weak antiferromagnetic coupling. The magnetic properties are simulated and discussed in terms of the structural features.     

Change in the content of salicylic acid and activities of phenylalanine ammonia-lyase and catalase in wheat seedling roots under the influence of Azospirilium lectins

The time course of changes in the endogenous content of salicylic acid, the ratio between the acid’s free and bound forms, and changes in the activities of phenylalanine ammonia-lyase and catalase in wheat seedling roots under the effect of lectins of two strains of the associative nitrogen-fixing bacterium Azospirillum (A. brasilense Sp7 and its mutant defective in lectin activity, A. brasilense Sp7.2.3) is investigated. Differences in plant response to the action of the lectins from these two strains are established. On the basis of the obtained data, a model is proposed for lectin-assisted induction of resistance, according to which the lectin effect on the roots of seedlings results in the accumulation of free salicylic acid, which inhibits catalase activity, ultimately leading to accumulation of hydrogen peroxide and formation of induced resistance.     

Mtb-Specific CD27(low) CD4 T Cells as Markers of Lung Tissue Destruction during Pulmonary Tuberculosis in Humans

Background

Effector CD4 T cells represent a key component of the host’s anti-tuberculosis immune defense. Successful differentiation and functioning of effector lymphocytes protects the host against severe M. tuberculosis (Mtb) infection. On the other hand, effector T cell differentiation depends on disease severity/activity, as T cell responses are driven by antigenic and inflammatory stimuli released during infection. Thus, tuberculosis (TB) progression and the degree of effector CD4 T cell differentiation are interrelated, but the relationships are complex and not well understood. We have analyzed an association between the degree of Mtb-specific CD4 T cell differentiation and severity/activity of pulmonary TB infection.

Methodology/Principal Findings

The degree of CD4 T cell differentiation was assessed by measuring the percentages of highly differentiated CD27^low cells within a population of Mtb- specific CD4 T lymphocytes (“CD27^lowIFN-γ⁺” cells). The percentages of CD27^lowIFN-γ+ cells were low in healthy donors (median, 33.1%) and TB contacts (21.8%) but increased in TB patients (47.3%, p<0.0005). Within the group of patients, the percentages of CD27^lowIFN-γ⁺ cells were uniformly high in the lungs (>76%), but varied in blood (12–92%). The major correlate for the accumulation of CD27^lowIFN-γ⁺ cells in blood was lung destruction (r = 0.65, p = 2.7×10⁻⁷⁾. A cutoff of 47% of CD27^lowIFN-γ⁺ cells discriminated patients with high and low degree of lung destruction (sensitivity 89%, specificity 74%); a decline in CD27^lowIFN-γ⁺cells following TB therapy correlated with repair and/or reduction of lung destruction (p<0.01).

Conclusions

Highly differentiated CD27^low Mtb-specific (CD27^lowIFN-γ⁺) CD4 T cells accumulate in the lungs and circulate in the blood of patients with active pulmonary TB. Accumulation of CD27^lowIFN-γ⁺ cells in the blood is associated with lung destruction. The findings indicate that there is no deficiency in CD4 T cell differentiation during TB; evaluation of CD27^lowIFN-γ⁺ cells provides a valuable means to assess TB activity, lung destruction, and tissue repair following TB therapy.     

A new DNA reporter construct for immuno-PCR

A new DNA reporter construct has been designed for protein quantification by immuno-PCR. It has been shown that the amplification efficiency of a reporter that contains a fragment of human adenovirus 2 flanked by homoprimer sequences is much higher than standard PCR format based on two different primers. The further application of the new construct and its homoprimer-based detection could represent new ways to increase the sensitivity of the immuno-PCR and the efficiency of single-molecule PCR.     

Biodegradation of an Organoselenium Compound to Elemental Selenium by Lentinula edodes (Shiitake) Mushroom

The present paper reports for the first time the transformation of an organic selenium compound into red selenium (Se), which causes the intense red pigmentation of Lentinula edodes (shiitake mushroom) mycelia. The biotransformation of 1,5-diphenyl-3-selenopentanedione-1,5 (diacetophenonyl selenide, preparation DAPS-25) was studied in liquid- and solid-phase cultures of L. edodes. In liquid culture medium, a red color develops in the mycelium at initial DAPS-25 concentrations equal to or higher than 0.1?mmol/l. The intensity and initiation time of coloration is Se concentration-dependent. Semiquantitative data obtained by physicochemical methods on the extent of Se and acetophenone production suggest that L. edodes is able to absorb and/or destruct this organic Se xenobiotic.