A critical appreciation of pathway analysis in atherosclerotic disease. Cellular phenotypic plasticity as an illustrative example.

The rapid advancements in genome-scale (omics) techniques has created significant opportunities to investigate complex disease mechanisms in tissues and cells. Nevertheless, interpreting -omics data can be challenging, and pathway enrichment analysis is a frequently used method to identify candidate molecular pathways that drive gene expression changes. With a growing number of -omics studies dedicated to atherosclerosis, there has been a significant increase in studies and hypotheses relying on enrichment analysis. This brief review discusses the benefits and limitations of pathway enrichment analysis within atherosclerosis research. We highlight the challenges of identifying complex biological processes, such as cell phenotypic switching, within -omics data. Additionally, we emphasize the need for more comprehensive and curated gene sets that reflect the biological complexity of atherosclerosis. Pathway enrichment analysis is a valuable tool for gaining insights into the molecular mechanisms of atherosclerosis. Nevertheless, it is crucial to remain aware of the intrinsic limitations of this approach. By addressing these weaknesses, enrichment analysis in atherosclerosis can lead to breakthroughs in identifying the mechanisms of disease progresses, the identification of key driver genes, and consequently, advance personalized patient care.

Different end-points to assess effects in systemic lupus erythematosus patients exposed to pesticide mixtures.

Systemic Lupus Erythematosus (SLE) is an autoimmune disease with high female predominance in reproductive years. It is characterized by a pronounced inflammation and production of a variety of autoantibodies. SLE pathogenesis is influenced by genes, hormones and environmental agents. The aim of this study was assess the possible effect of environmental pesticide mixtures in SLE patients. Oxidative DNA damage was measured using the comet assay modified by enzyme Endo III for detection of oxidized bases (Endo Sites), and oxidative stress by the measurement of the activity of catalase (CAT), superoxide dismutase (SOD) and lipid peroxidation (TBARS). Eighty-nine patients with diagnosis of SLE were included, 46% of them came from areas highly sprayed with pesticides and were compared with patients from urban areas with the same clinical and socio-demographic characteristics (p≥0.155). In order to identify factors that could predict DNA damage and oxidative stress, a binary logistic regression model with independent variables was developed: place of residence (p=0.007) have 75% of positive predictive value while smoking habit (p=0.186) have a 56% negative predictive value. The Odd Ratio (OR) obtained indicate that lupus patients living in rural areas presented 3.52 times more oxidative DNA damage compared to those living in the city. The prospects of applying biomarkers to assess exposure and biological effects, such as DNA damage and oxidative stress in autoimmune diseases, allow improving the characterization of individual risk.

Deconvolution of the EPR spectra of vanadium oxide nanotubes.

In this work we report results of continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy of vanadium oxide nanotubes. The observed EPR spectra are composed of a weak well-resolved spectrum of isolated V(4+) ions on top of an intense and broad structure-less line shape, attributed to spin-spin exchanged V(4+) clusters. With the purpose to deconvolute the structured weak spectrum from the composed broad line, a new approach based on the Krylov basis diagonalization method (KBDM) is introduced. It is based on the discrimination between broad and sharp components with respect to a selectable threshold and can be executed with few adjustable parameters, without the need of a priori information on the shape and structure of the lines. This makes the method advantageous with respect to other procedures and suitable for fast and routine spectral analysis, which, in conjunction with simulation techniques based on the spin Hamiltonian parameters, can provide a full characterization of the EPR spectrum. Results demonstrate and characterize the coexistence of two V(4+) species in the nanotubes and show good progress toward the goal of obtaining high fidelity deconvoluted spectra from complex signals with overlapping broader line shapes.

Manifestaciones inusuales de histoplasmosis en enfermedades del tejido conectivo / Unusual manifestation of histoplasmosis in connective tissue diseases

Este artículo describe la coexistencia de siete pacientes con enfermedades reumáticas: lupus eritematoso sistémico, artritis reumatoide y dermatomiositis e infección concomitante por Histoplasma capsulatum. Las enfermedades del tejido conectivo y la histoplasmosis comparten varios hallazgos clínicos. Por lo tanto, la histoplasmosis puede ser mal diagnosticada como enfermedades del tejido conectivo o como un brote de estas enfermedades. Estos casos resaltan la importancia de la concientización sobre la histoplasmosis en pacientes inmunocomprometidos, especialmente en aquellos procedentes de zonas endémicas.(AU)

Manifestaciones inusuales de histoplasmosis en enfermedades del tejido conectivo / Unusual manifestation of histoplasmosis in connective tissue diseases

Este artículo describe la coexistencia de siete pacientes con enfermedades reumáticas: lupus eritematoso sistémico, artritis reumatoide y dermatomiositis e infección concomitante por Histoplasma capsulatum. Las enfermedades del tejido conectivo y la histoplasmosis comparten varios hallazgos clínicos. Por lo tanto, la histoplasmosis puede ser mal diagnosticada como enfermedades del tejido conectivo o como un brote de estas enfermedades. Estos casos resaltan la importancia de la concientización sobre la histoplasmosis en pacientes inmunocomprometidos, especialmente en aquellos procedentes de zonas endémicas.

A comparative analysis of chromosome pairing at metaphase I in interspecific hybrids between durum wheat (Triticum turgidum L.) and the most widespread Aegilops species.

Homoeologous metaphase I (MI) associations in hybrids between durum wheat and its wild allotetraploid relatives Aegilops neglecta, Ae. triuncialis and Ae. ventricosa have been characterized by a genomic in situ hybridization procedure that allows simultaneous discrimination of A, B and wild species genomes. Earlier results in equivalent hybrids with the wild species Ae. cylindrica and Ae. geniculata have also been considered to comparatively assay the MI pairing pattern of the durum wheat x Aegilops interspecific combinations more likely to occur in nature. The general picture can be drawn as follows. A and B wheat genomes pair with each other less than the 2 wild constituent genomes do in any of the hybrid combinations examined. Interspecific wheat-wild associations account for 60-70% of total MI pairing in all hybrids, except in that derived from Ae. triuncialis, but the A genome is always the wheat partner most frequently involved in MI pairing with the wild homoeologues. Hybrids with Ae. cylindrica, Ae. geniculata and Ae. ventricosa showed similar reduced levels of MI association and virtually identical MI pairing patterns. However, certain recurrent differences were found when the pattern of homoeologous pairing of hybrids from either Ae. triuncialis or Ae. neglecta was contrasted to that observed in the other durum wheat hybrid combinations. In the former case, a remarkable preferential pairing between the wild species constituent genomes U(t) and C(t) seems to be the reason, whereas a general promotion of homoeologous pairing, qualitatively similar to that observed under the effect of the ph1c mutation, appears to occur in the hybrid with Ae. neglecta. It is further discussed whether the results reported here can be extrapolated to the corresponding bread wheat hybrid combinations.

The use of cytogenetic tools for studies in the crop-to-wild gene transfer scenario.

Interspecific hybridization in plants is an important evolutionary phenomenon involved in the dynamics of speciation that receives increasing interest in the context of possible gene escapes from transgenic crop varieties. Crops are able to cross-pollinate with a number of wild related species and exchange chromosome segments through homoeologous recombination. In this paper, we review a set of cytogenetic techniques that are appropriate to document the different steps required for the stable introgression of a chromosome segment from a donor species (i.e., the crop) into a recipient species (i.e., the wild). Several examples in hybrids and derivatives are given to illustrate how these approaches may be used to evaluate the potential for gene transfer between crops and wild relatives. Different techniques, from classical chromosome staining methods to recent developments in molecular cytogenetics, can be used to differentiate genomes and identify the chromosome regions eventually involved in genetic exchanges. Some clues are also given for the study of fertility restoration in the interspecific hybrid forms.

The relation between pairing preference and chiasma frequency in tetrasomics of rye.

The association pattern of marked tetrasomes of Secale chromosome 1R at meiotic first metaphase was analyzed. Two of the four chromosomes were identical with terminal C-bands at both arms; the other two were also identical but lacked C-bands and were homologous or homeologous with the first two. Four different types of heterozygotes for 1R were studied: (i). autotetraploid hybrids between genetic variants within Secale cereale subsp. cereale, (ii). tetraploid hybrids between subspecies of Secale cereale, (iii). tetraploid hybrids between species of Secale, and (iv). autotetrasomes of S. cereale in a wheat background. Earlier observations that heterozygous associations (banded with unbanded) had consistently higher chiasma frequencies than homozygous associations were extended and confirmed. To analyze this phenomenon more closely, the possible relations between this correlation and several other meiotic phenomena were studied. For this analysis, three genetically different autotetraploid hybrids within S. cereale were selected that differed with respect to the relation between pairing type and chiasma frequency. Special attention was given to different patterns of interference and other meiotic phenomena in the two chromosome arms of chromosome 1R. No relations between such phenomena and the relation between pairing type and chiasma frequency could be established. A hypothesis is formulated assuming that long-distance homologue attraction is concentrated in a limited number of sites and that in different genotypes, different patterns of active sites are present. Moderately weak attraction sites can pair with strong homologous sites under favorable genetic conditions, but two weak sites cannot. Then, heterozygotes have more effective pairing initiation and consequently chiasma formation than homozygotes. Under less favorable conditions, only strong sites are effective, and then, homozygotes pair better, but the chiasma frequency is lower. A model of the forces involved in homologue attraction is presented.

Analysis of karyotypic stability of homoeologous-pairing (ph) mutants in allopolyploid wheats.

Karyotypic analysis of wheat lines with different genotypes for the homoeologous-pairing loci Ph1 and Ph2 was carried out by means of a genomic in situ hybridization method that allowed unequivocal identification of the A, B and D genomes. Chromosomal rearrangements mainly affecting the A and D genomes were found in all plants of allohexaploid wheat (AABBDD) lacking Ph1 activity. The frequency of intergenomic exchanges per plant in ph1b mutant and nulli-5B lines was 4.31 and 3.40, respectively. In addition, an unbalanced genomic constitution was found in a few plants, some even showing a euploid chromosomal number. By contrast, rearranged karyotypes were detected neither in the ph1 mutant line (ph1c) of allotetraploid wheat (AABB) nor in the allohexaploid wheat lines lacking Ph2 activity, namely ph2b mutant and nulli-3D lines. These results were compared with the chromosomal pairing behaviour displayed by mutant lines ph1c, ph1b and ph2b at first meiotic metaphase. Despite the finding of standard, nonrearranged karyotypes in the phlc tetraploid mutant, the frequency of A-B homoeologous metaphase I association was similar to that observed in the ph1b hexaploid mutant. The results presented clearly demonstrate that inactivity of the Ph1 locus induces karyotypic instability in wheat. Intergenomic exchanges have probably been accumulating since the original ph1 mutant and aneuploid lines were obtained, which should be taken into account when it is planned to use these lines for basic research on Ph1 function or in applied wheat breeding programmes.

Simultaneous identification of A, B, D and R genomes by genomic in situ hybridization in wheat-rye derivatives.

Multicolour genomic in situ hybridization was carried out in wheat-rye hybrids and in a wheat-rye translocation line. Different hybridization conditions and mixture compositions were used, and A, B and D genomes of hexaploid wheat as well as the R genome of rye were distinguished simultaneously in somatic cells. Combination of genomic and rDNA probes in multicolour in situ hybridization was also performed to identify chromosomes within a specific genome.

Relationship between the levels of wheat-rye metaphase I chromosomal pairing and recombination revealed by GISH.

The metaphase I and anaphase I stages of meiosis of wheat x rye hybrids carrying the ph1b mutation were analyzed by genomic in situ hybridization. This technique allows distinction between three different types of wheat-rye associations in metaphase I configurations as well as detection of wheat-rye recombinant chromosomes in anaphase I cells. The frequency of associations between wheat and rye chromosomes greatly exceeded the level of wheat-rye recombination found in the three hybrids examined. Extremely distal associations, which account for about 50% of the total wheat-rye metaphase I chromosomal pairing, can explain such a discrepancy between metaphase I and anaphase I data. It is further discussed whether these associations reflect very distally located chiasmata or nonchiasmatic pairing. The sizes of the segments exchanged in wheat-rye recombinant chromosomes provide cytological evidence that wheat-rye recombination is restricted to the distal chromosomal regions.

Meiotic pairing in wheat-rye derivatives detected by genomic in situ hybridization and C-banding--A comparative analysis.

Meiosis of triticalextetraploid rye hybrids (genome constitution ABRRR) was analysed by genomic in situ hybridization (GISH) and C-banding. The results obtained reveal a considerable difference between these techniques with regard to their efficiency in detecting any type of pairing, either homologous or homoeologous. Thus the percentage of pollen mother cells containing wheat/rye homoeologous associations determined by C-banding and GISH was 2.5 and 9.2, respectively. Such a discrepancy can be ascribed to a certain proportion of wheat/rye associations not being identified by C-banding. The potential and limitations of the two techniques for meiotic analysis are discussed.

Meiotic behavior of rye heterozygous for ditelocentric substitutions.

Meiotic behavior has been investigated in rye plants carrying a heterozygous ditelocentric substitution for chromosomes 1R and 3R. Such a chromosomal rearrangement replaces a biarmed chromosome with two telocentrics, a situation karyotypically comparable to a Robertsonian translocation. As in Robertsonian translocation heterozygotes, delayed pairing characterizes the centromeric region in the rye pachytene heteromorphic trivalents. In addition, telocentric axes appear to be frequently engaged in nonhomologous synapsis (e.g., fold-back loops and two-by-two heterosynapsis) at their centromeric ends. Unlike those in Robertsonian translocation heterozygotes, the synaptic abnormalities detected here cannot be due to lack of partner homology. Rather, the chromosomal rearrangement itself appears to interfere with normal synaptonemal complex (SC) progression. The synaptic irregularities, which often result in complex pachytene multivalents, seem to have no effect on chiasma formation, since the rearranged pairs behave properly at metaphase I. Finally, differences in both SC length and progression patterns between plants and animals could explain the trans configurations of telocentric centromeres in plants, whereas only cis configurations of acrocentric kinetochores have been described in animals.

Chromosome differentiation and pairing behavior of polyploids: an assessment on preferential metaphase I associations in colchicine-induced autotetraploid hybrids within the genus Secale.

Preferential chromosome association at metaphase I has been analyzed and compared in autotetraploid cells obtained by colchicine treatment of hybrid diploid rye plants with different degrees of chromosomal divergence between homologs. The tendency to identical over homologous, but not identical, pairing preferences detected when homologous partners are contributed by less related parental lines indicates that chromosome differentiation may play an important role on preferential pairing behavior of polyploids. However, associations between more similar (identical) partners are not always favored, thus suggesting that additional factors must be considered. Other hypotheses for explaining pairing preferences in competitive situations are discussed. No clear relationship has been found between multivalent frequencies at metaphase I and chromosome differentiation between homologs or preferential pairing behavior. Therefore evolutionary divergences among related genomes should be carefully stated when evaluated from metaphase I configuration frequencies.

Deteccion de portadores de Salmonella Typhi mediante la prueba de hemaglutinacion indirecta con antigeno Vi muy purificado / Screening of Salmonella Typhi carriers by indirect hemagglutination using highly purified Vi antigen

A study was carrried out to determine the predictive value and the cost-effectiveness of the indirect hemagglutination test using highly purified Vi antigen as a means of screening Salmonella Typhi carrriers in a high-risk group living in an área where typhoid fever is emdemic. The group consisted of women over age 30 who were participating in a municipal sanitary control program for food handlers in Lima, Perú. Test yielding an anti-Vi antibody titer= 1:40 were considered positive (79 percent sensitivity, and 99 percent and 100 percent specificity for the local population). On this basis, 29 women (1.5 percent) tested positive out of a total of 1 931. A follow-up bacteriological study demonstrated that 26 of these 29 women were carriers of S. typhi; thus, the test had a predictive value of 15 percent. The prevalence of carriers in this group was estimated at 292 per 100 000 population. The test cost $US 0.30 per person. In comparison, the method that requires a series of three fecal cultures to isolate the causative agent would have cost $US 1.72. It can be concluded that the test studied is suficiently sensitive, that it is highly specific, and that it is cost-effective when used to detect S. typhi carriers in áreas where typhoid fever is endemic

Detection of salmonella typhi carriers in food handlers by Vi serology in Lima, Peru

This article has previously been published in Spanish in the Boletín de la Oficina Sanitaria Panamericana, Vol. 105, No. 3, pp. 283-9, 1988

Detección de portadores de Salmonella Typhi mediante la prueba de hemaglutinación indirecta con antigeno Vi muy purificado / Screening of Salmonella Typhi carriers by indirect hemagglutination using highly purified Vi antigen

A study was carrried out to determine the predictive value and the cost-effectiveness of the indirect hemagglutination test using highly purified Vi antigen as a means of screening Salmonella Typhi carrriers in a high-risk group living in an area where typhoid fever is emdemic. The group consisted of women over age 30 who were participating in a municipal sanitary control program for food handlers in Lima, Peru. Test yielding an anti-Vi antibody titer= 1:40 were considered positive (79 percent sensitivity, and 99 percent and 100 percent specificity for the local population). On this basis, 29 women (1.5 percent) tested positive out of a total of 1 931. A follow-up bacteriological study demonstrated that 26 of these 29 women were carriers of S. typhi; thus, the test had a predictive value of 15 percent. The prevalence of carriers in this group was estimated at 292 per 100 000 population. The test cost $US 0.30 per person. In comparison, the method that requires a series of three fecal cultures to isolate the causative agent would have cost $US 1.72. It can be concluded that the test studied is suficiently sensitive, that it is highly specific, and that it is cost-effective when used to detect S. typhi carriers in areas where typhoid fever is endemic