Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers.

Normal tissues are essential for studying disease-specific differential gene expression. However, healthy human controls are typically available only in postmortal/autopsy settings. In cancer research, fragments of pathologically normal tissue adjacent to tumor site are frequently used as the controls. However, it is largely underexplored how cancers can systematically influence gene expression of the neighboring tissues. Here we performed a comprehensive pan-cancer comparison of molecular profiles of solid tumor-adjacent and autopsy-derived "healthy" normal tissues. We found a number of systemic molecular differences related to activation of the immune cells, intracellular transport and autophagy, cellular respiration, telomerase activation, p38 signaling, cytoskeleton remodeling, and reorganization of the extracellular matrix. The tumor-adjacent tissues were deficient in apoptotic signaling and negative regulation of cell growth including G2/M cell cycle transition checkpoint. We also detected an extensive rearrangement of the chemical perception network. Molecular targets of 32 and 37 cancer drugs were over- or underexpressed, respectively, in the tumor-adjacent norms. These processes may be driven by molecular events that are correlated between the paired cancer and adjacent normal tissues, that mostly relate to inflammation and regulation of intracellular molecular pathways such as the p38, MAPK, Notch, and IGF1 signaling. However, using a model of macaque postmortal tissues we showed that for the 30 min - 24-hour time frame at 4ºC, an RNA degradation pattern in lung biosamples resulted in an artifact "differential" expression profile for 1140 genes, although no differences could be detected in liver. Thus, such concerns should be addressed in practice.

The Effect of the Position Determination Error for Flexible Linear Array Elements on the Tomogram Focusing.

In the article, the study of the quality of tomogram focusing during the inspection of objects with curved surfaces by flexible acoustic array was described. The main goal of the study was theoretically and experimentally define the acceptable deviation limits of the elements' coordinates values. The tomogram reconstruction was performed by the total focusing method. The Strehl ratio was chosen as a criterion for assessing the quality of tomogram focusing. The ultrasonic inspection procedure were simulated and validated experimentally by means of convex and concave curved arrays. In the study, it was proven that the elements coordinates of the flexible acoustic array were determined with an error of no more than 0.18λ and the tomogram image was obtained in sharp focus.

Studies of Angular Resolution for Acoustic Arc Arrays.

Currently, phased arrays are increasingly used in ultrasonic nondestructive testing. One of the most important parameters of ultrasonic nondestructive testing with the application of phased arrays is the angular resolution. This paper presents the results of studies of the angular resolution of concave and convex acoustic arrays in ultrasonic testing with the application of the total focusing method. Computer modeling of concave and convex acoustic arrays consisting of 16, 32 and 64 elements with distances between elements of 0.5 and 1 mm and arc radii of 30 and 60 mm have been performed. The results obtained by computer modeling were confirmed via in situ experiments.

Structural evolution and tissue-specific expression of tetrapod-specific second isoform of secretory pathway Ca2+-ATPase.

Secretory pathway Ca-ATPases are less characterized mammalian calcium pumps than plasma membrane Ca-ATPases and sarco-endoplasmic reticulum Ca-ATPases. Here we report analysis of molecular evolution, alternative splicing, tissue-specific expression and subcellular localization of the second isoform of the secretory pathway Ca-ATPase (SPCA2), the product of the ATP2C2 gene. The primary structure of SPCA2 from rat duodenum deduced from full-length transcript contains 944 amino acid residues, and exhibits 65% sequence identity with known SPCA1. The rat SPCA2 sequence is also highly homologous to putative human protein KIAA0703, however, the latter seems to have an aberrant N-terminus originating from intron 2. The tissue-specificity of SPCA2 expression is different from ubiquitous SPCA1. Rat SPCA2 transcripts were detected predominantly in gastrointestinal tract, lung, trachea, lactating mammary gland, skin and preputial gland. In the newborn pig, the expression profile is very similar with one remarkable exception: porcine bulbourethral gland gave the strongest signal. Upon overexpression in cultured cells, SPCA2 shows an intracellular distribution with remarkable enrichment in Golgi. However, in vivo SPCA2 may be localized in compartments that differ among various tissues: it is intracellular in epidermis, but enriched in plasma membranes of the intestinal epithelium. Analysis of SPCA2 sequences from various vertebrate species argue that ATP2C2 gene radiated from ATP2C1 (encoding SPCA1) during adaptation of tetrapod ancestors to terrestrial habitats.

A Caenorhabditis elegans mutant lacking functional nicotinamide nucleotide transhydrogenase displays increased sensitivity to oxidative stress.

Proton-translocating mitochondrial nicotinamide nucleotide transhydrogenase (NNT) was investigated regarding its physiological role in Caenorhabditis elegans. NNT catalyzes the reduction of NADP(+) by NADH driven by the electrochemical proton gradient, Deltap, and is thus a potentially important source of mitochondrial NADPH. Mitochondrial detoxification of reactive oxygen species (ROS) by glutathione-dependent peroxidases depends on NADPH for regeneration of reduced glutathione. Transhydrogenase may therefore be directly involved in the defense against oxidative stress. nnt-1 deletion mutants of C. elegans, nnt-1(sv34), were isolated and shown to grow essentially as wild type under normal laboratory conditions, but with a strongly lowered GSH/GSSG ratio. Under conditions of oxidative stress, caused by the superoxide-generating agent methyl viologen, growth of worms lacking nnt-1 activity was severely impaired. A similar result was obtained by using RNAi. Reintroducing nnt-1 in the nnt-1(sv34) knockout mutant led to a partial rescue of growth under oxidative stress conditions. These results provide evidence for the first time that nnt-1 is important in the defense against mitochondrial oxidative stress.

Genome-wide identification and mapping of variable sequences in the genomes of Burkholderia mallei and Burkholderia pseudomallei.

Burkholderia mallei and Burkholderia pseudomallei, closely related Gram-negative bacteria, are the causative agents of such serious infectious diseases of humans and animals as glanders and melioidosis, respectively. Despite numerous studies of these pathogens, the detailed mechanisms of their pathogenesis is still poorly understood. One of the serious obstacles to revealing factors responsible for pathogenicity lies in the considerable natural variability of B. pseudomallei and B. mallei, which is also a challenge to development of rapid and efficient diagnostic tools facilitating unambiguous identification of the infectious agents. To gain a deeper insight into B. mallei and B. pseudomallei interspecies divergence and intraspecies polymorphism, we compared the genomes of B. mallei C-5 and B. pseudomallei C-141 strains using a subtractive hybridization technique. A library of DNA fragments specific for B. mallei C-5 and absent from B. pseudomallei C-141 was obtained and analyzed. Some of the differential sequences detected were also not found in the recently sequenced genome of B. pseudomallei K96243. However, a multitude of B. mallei C-5 sequences absent from the B. pseudomallei C-141 genome were detected in the genome of B. pseudomallei K96243. On the other hand, some sequences identified as constituents of the B. mallei C-5 genome were not found in the genome of B. mallei ATCC 23344. Some of the differential DNA fragments displayed similarity to different mobile elements that have not yet been described for B. mallei, whereas the others matched fragments of various prophages, or, when translated into protein sequences, components of active transport systems and different enzymes. A substantial proportion of the differential clones had no database matches either at the nucleotide or amino acid sequence level. The results suggest great genome-wide intra- and interspecies variability of B. mallei and B. pseudomallei. The differences identified may be useful as molecular signatures for identification of B. mallei strains.

Genome-wide comparison reveals great inter- and intraspecies variability in B. pseudomallei and B. mallei pathogens.

Burkholderia mallei and B. pseudomallei, closely related Gram-negative bacteria, are causative agents of serious infectious diseases of humans and animals: glanders and melioidosis, respectively. Despite numerous studies of these pathogens, the detailed mechanism of their pathogenesis is still unknown. The problem is even more complicated due to natural variability of B. pseudomallei and B. mallei strains, the understanding of which is a prerequisite for rational design of tools for diagnostics, prophylaxis and therapy of the diseases. Using a subtractive hybridization technique, we compared the genomes of B. pseudomallei C-141 and B. mallei C-5 strains. A subtracted library of DNA fragments specific for B. pseudomallei C-141 and absent from B. mallei C-5 was obtained and analyzed. A variety of differences have been detected and mapped on the recently sequenced genome of B. pseudomallei K96243. A comparative sequence analysis also revealed considerable genomic differences between B. pseudomallei C-141 and B. mallei ATCC 23344 strains sequenced at The Institute for Genomic Research (TIGR). We also observed significant genomic differences between B. pseudomallei C-141 and B. pseudomallei K96243. Some of the differential DNA fragments displayed similarity to different mobile elements which have not yet been described for B. pseudomallei, whereas the others matched various prophage components, components of active transport systems, different enzymes and transcription regulators. A substantial proportion of the differential clones had no database matches either at the nucleotide or protein level. The results provide evidence for great genome-wide variability of B. pseudomallei, further confirmed by Southern blot analysis of various B. pseudomallei strains. The data obtained can be useful for future development of efficient diagnostic tools allowing rapid identification of species, strains and isolates of B. mallei and B. pseudomallei.

Purification of a recombinant membrane protein tagged with a calmodulin-binding domain: properties of chimeras of the Escherichia coli nicotinamide nucleotide transhydrogenase and the C-terminus of human plasma membrane Ca2+ -ATPase.

A Ca2+ -dependent calmodulin-binding peptide (CBP) is an attractive tag for affinity purification of recombinant proteins, especially membrane proteins, since elution is simply accomplished by removing/chelating Ca2+. To develop a single-step calmodulin/CBP-dependent purification procedure for Escherichia coli nicotinamide nucleotide transhydrogenase, a 49 amino acid large CBP or a larger 149 amino acid C-terminal fragment of human plasma membrane Ca2+ -ATPase (hPMCA) was fused C-terminally to the beta subunit of transhydrogenase. Fusion using the 49 amino acid fragment resulted in a dramatic loss of transhydrogenase expression while fusion with the 149 amino acid fragment gave a satisfactory expression. This chimeric protein was purified by affinity chromatography on calmodulin-Sepharose with mild elution with EDTA. The purity and activity were comparable to those obtained with His-tagged transhydrogenase and showed an increased stability. CBP-tagged transhydrogenase contained a 4- to 10-fold higher amount of the alpha subunit relative to the beta subunit as compared to wild-type transhydrogenase. To determine whether the latter was due to the CBP tag, a double-tagged transhydrogenase with both an N-terminal 6x His-tag and a CBP-tag, purified by using either tag, gave no significant increase in purity as compared to the single-tagged protein. The reasons for the altered subunit composition are discussed. The results suggest that, depending on the construct, the CBP-tag may be a suitable affinity purification tag for membrane proteins in general.