Pseudogenes as an alternative source of natural antisense transcripts

<p>Abstract</p> <p>Background</p> <p>Naturally occurring antisense transcripts (NATs) are non-coding RNAs that may regulate the activity of sense transcripts to which they bind because of complementarity. NATs that are not located in the gene they regulate (trans-NATs) have better chances to evolve than cis-NATs, which is evident when the sense strand of the cis-NAT is part of a protein coding gene. However, the generation of a trans-NAT requires the formation of a relatively large region of complementarity to the gene it regulates.</p> <p>Results</p> <p>Pseudogene formation may be one evolutionary mechanism that generates trans-NATs to the parental gene. For example, this could occur if the parental gene is regulated by a cis-NAT that is copied as a trans-NAT in the pseudogene. To support this we identified human pseudogenes with a trans-NAT to the parental gene in their antisense strand by analysis of the database of expressed sequence tags (ESTs). We found that the mutations that appeared in these trans-NATs after the pseudogene formation do not show the flat distribution that would be expected in a non functional transcript. Instead, we found higher similarity to the parental gene in a region nearby the 3' end of the trans-NATs.</p> <p>Conclusions</p> <p>Our results do not imply a functional relation of the trans-NAT arising from pseudogenes over their respective parental genes but add evidence for it and stress the importance of duplication mechanisms of genetic material in the generation of non-coding RNAs. We also provide a plausible explanation for the large transcripts that can be found in the antisense strand of some pseudogenes.</p

Design & Optimization of Large Cylindrical Radomes with Subcell and Non-Orthogonal FDTD Meshes Combined with Genetic Algorithms

The word radome is a contraction of radar and dome. The function of radomes is to protect antennas from atmospheric agents. Radomes are closed structures that protect the antennas from environmental factors such as wind, rain, ice, sand, and ultraviolet rays, among others. The radomes are passive structures that introduce return losses, and whose proper design would relax the requirement of complex front-end elements such as amplifiers. The radome consists mostly in a thin dielectric curved shape cover and sometimes needs to be tuned using metal inserts to cancel the capacitive performance of the dielectric. Radomes are in the near field region of the antennas and a full wave analysis of the antenna with the radome is the best approach to analyze its performance. A major numerical problem is the full wave modeling of a large radome-antenna-array system, as optimization of the radome parameters minimize return losses. In the present work, the finite difference time domain (FDTD) combined with a genetic algorithm is used to find the optimal radome for a large radome-antenna-array system. FDTD uses general curvilinear coordinates and sub-cell features as a thin dielectric slab approach and a thin wire approach. Both approximations are generally required if a problem of practical electrical size is to be solved using a manageable number of cells and time steps in FDTD inside a repetitive optimization loop. These approaches are used in the full wave analysis of a large array of crossed dipoles covered with a thin and cylindrical dielectric radome. The radome dielectric has a thickness of ~λ/10 at its central operating frequency. To reduce return loss a thin helical wire is introduced in the radome, whose diameter is ~0.0017λ and the spacing between each turn is ~0.3λ. The genetic algorithm was implemented to find the best parameters to minimize return losses. The inclusion of a helical wire reduces return losses by ~10 dB, however some minor changes of radiation pattern could distort the performance of the whole radome-array-antenna system. A further analysis shows that desired specifications of the system are preserved

Amplification of the Gene Ontology annotation of Affymetrix probe sets

BACKGROUND: The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations which is not always desirable for microarray experiment evaluation. RESULTS: Here we present a protocol to amplify the set of Gene Ontology annotations associated to Affymetrix DNA microarray probe sets using information from related databases. CONCLUSION: Predicted novel annotations and the evidence producing them can be accessed at Probe2GO: . Scripts are available on demand

Analysis of the finite difference time domain technique to solve the Schrödinger equation for quantum devices

An extension of the finite difference time domain is applied to solve the Schrödinger equation. A systematic analysis of stability and convergence of this technique is carried out in this article. The numerical scheme used to solve the Schrödinger equation differs from the scheme found in electromagnetics. Also, the unit cell employed to model quantum devices is different from the Yee cell used by the electrical engineering community. A bound for the time step is derived to ensure stability. Several numerical experiments in quantum structures demonstrate the accuracy of a second order, comparable to the analysis of electromagnetic devices with the Yee cell.a!Electronic mail: [email protected] b!Electronic mail: [email protected] c!Electronic mail: [email protected] d!Electronic mail: [email protected]

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. leprae’s genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. leprae’s pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3′ (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1 × 10−7). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5′ (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts

Tumor de partes blandas en la vecindad de una prótesis de cadera no cementada

Presentamos el caso de un varón de 63 años de edad que fue diagnosticado de un sarcoma de partes blandas en la cara posterior del muslo seis meses después de implantarle una prótesis total de cadera no cementada. Se discute la posible asociación etiológica entre los tumores malignos y el implante de materiales.We present the case of a 63-year-old man who was diagnosed of a soft tissue sarcoma in the posterior side of the thigh six months after a cementless hip replacement. The possible etiological association between malignant tumours and implant materials is discussed

An overview on the Prus-Szczepanik condition

In 2005 Prus and Sczcepanik introduced a large class of Banach spaces with the fixed point property for nonexpansive mappings. We say that this class satisfies the PSz condition. Checking that a given Banach space belongs to this class is not an easy task. Here we study the relationship between the PSz condition and other well-known geometrical properties of Banach spaces, and we give easier sufficient conditions for a Banach space to satisfy it.Consejo Nacional de Ciencia y Tecnologia (México)Ministerio de Economía y Competitivida

Molten salt attack on multilayer and functionally-graded YSZ coatings

Thermal barrier coatings have been extensively studied in the last years in order to increase the operational temperature of the current gas turbines as well as to improve the coating lifetime. Many coating characteristics must be met to achieve these requirements (low thermal conductivity, high thermal fatigue resistance…); therefore, complex systems have been engineered for these purposes. One of the possibilities to optimise the different properties deals with the design of multilayer or functionally-graded coatings where various types of microstructures with different characteristics are combined. One of the most important cause of gas turbines degradation relates to the attack of different type of particles which are suspended in the atmosphere (sand, fly ash…). These solid particles are molten at the operational temperatures and then, the molten salts chemically react with the coating. For this reason, the present research was focused on this type of attack. In the present work, the molten salt attack of various YSZ coatings with multilayer and functionally-graded design was addressed. Two different type of microstructures were specifically combined for this design: the APS coating microstructure obtained from conventional (microstructured) powder and a bimodal structure with nanozones obtained from nanostructured feedstock. Besides, different salts were used to simulate different attack environments (desert sand and volcanic fly ash). Findings show that nanozones act as barrier against the penetration of molten salts toward deeper layer. However, a layer formed by nanozones can detach when the salt attack is too aggressive. Hence, functionally-graded coatings, where two types of microstructures are combined through the whole coating, become ideal to diminish the molten salt attack

ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation

<p>Abstract</p> <p>Background</p> <p>SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments.</p> <p>Results</p> <p>Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes.</p> <p>Conclusion</p> <p>The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip) will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.</p

Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6

In order to clarify their physiological functions, we have undertaken a characterization of the three-membered gene families SNZ13 and SNO13. In media lacking vitamin B6, SNZ1 and SNO1 were both required for growth in certain conditions, but neither SNZ2, SNZ3, SNO2 nor SNO3 were required. Copies 2 and 3 of the gene products have, in spite of their extremely close sequence similarity, slightly different functions in the cell. We have also found that copies 2 and 3 are activated by the lack of thiamine and that the Snz proteins physically interact with the thiamine biosynthesis Thi5 protein family. Whereas copy 1 is required for conditions in which B6 is essential for growth, copies 2 and 3 seem more related with B1 biosynthesis during the exponential phase