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Results for “collinearity analysis”

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PubMed1980

Integration of viral DNA sequences in cells transformed by adenovirus 2 or SV40.

We have cloned and propagated in prokaryotic vectors the viral DNA sequences that are integrated in a variety of cells transformed by adenovirus 2 or SV40. Analysis of the clones reveals that the viral DNA sequences sometimes are arranged in a simple fashion, collinear with the viral genome; in other cell lines there are complex arrangements of viral sequences in which tracts of the viral genome are inverted with respect to each other. In several cases the nucleotide sequences at the joints between cell and viral sequences have been determined: usually there is a sharp transition between cellular and viral DNAs. The viral sequences are integrated at different locations within the genomes of different cell lines; likewise there is no specific site on the viral genomes at which integration occurs. Sometimes the viral sequences are integrated within repetitive cellular DNA, and sometimes within unique sequences. In some cases there is evidence that the viral sequences along with the flanking cell DNA have been amplified after integration. The sequences that flank the viral insertion in the line of SV40-transformed rat cells known as 14B have been used as probes to isolate, from untransformed rat cells, clones that carry the region of the chromosome in which integration occurred. Analysis of the structure of these clones by restriction endonculease digestion and heteroduplex formation shows that a rearrangement of cellular sequences has occurred, presumably as a consequence of integration.

Adenoviruses, Human↗

PubMed2006

Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity.

BACKGROUND: At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause tick-borne Lyme disease. Previous work including the genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a highly variable plasmid part. The frequent occurrence of duplicated sequence stretches, the observed plasmid redundancy, as well as the mainly unknown function and variability of plasmid encoded genes rendered the relationships between plasmids within and between species largely unresolvable. RESULTS: To gain further insight into Borreliae genome properties we completed the plasmid sequences of B. garinii PBi, added the genome of a further species, B. afzelii PKo, to our analysis, and compared for both species the genomes of pathogenic and apathogenic strains. The core of all Bbsl genomes consists of the chromosome and two plasmids collinear between all species. We also found additional groups of plasmids, which share large parts of their sequences. This makes it very likely that these plasmids are relatively stable and share common ancestors before the diversification of Borrelia species. The analysis of the differences between B. garinii PBi and B. afzelii PKo genomes of low and high passages revealed that the loss of infectivity is accompanied in both species by a loss of similar genetic material. Whereas B. garinii PBi suffered only from the break-off of a plasmid end, B. afzelii PKo lost more material, probably an entire plasmid. In both cases the vls gene locus encoding for variable surface proteins is affected. CONCLUSION: The complete genome sequences of a B. garinii and a B. afzelii strain facilitate further comparative studies within the genus Borrellia. Our study shows that loss of infectivity can be traced back to only one single event in B. garinii PBi: the loss of the vls cassettes possibly due to error prone gene conversion. Similar albeit extended losses in B. afzelii PKo support the hypothesis that infectivity of Borrelia species depends heavily on the evasion from the host response.

Borrelia↗

PubMed2003

On the dynamics of a spherical scaffold in rotating bioreactors.

We analyze the dynamics of a spherical scaffold in rotating bioreactors (or clinostats). The idealized clinostat environment consists of a purely rotational flow that is perpendicular to a gravitational field. We confirm through a detailed analytical study that lift effects considerably alter the position of the equilibrium point reached by the scaffolds in the (vertical) direction collinear to the gravitational field. This result holds for small particle and shear Reynolds numbers. Our analysis shows that the inertial lift effect is negligible in the horizontal direction. We show that for all rotations of practical interest, and for the range of particle Reynolds number smaller than unity, the vertical coordinate of the equilibrium point is strongly affected by consideration of lift effects. For light (heavy) particles, inclusion of lift in the formation forces the equilibrium position to be below (above) the horizontal plane that contains the axis of rotation. The equilibrium point for light particles is stable and therefore is observable experimentally. The equilibrium point for heavy particles is unstable. We also estimate the stress level applied to the scaffold and derive an algebraic expression that indicates that the stress level acting on the scaffold decreases with increasing shear Reynolds number.

Acceleration↗

PubMed2000

The potential for sparing of parotids and escalation of biologically effective dose with intensity-modulated radiation treatments of head and neck cancers: a treatment design study.

PURPOSE: Conventional radiotherapy for cancers of the head and neck (HN) can yield acceptable locoregional tumor control rates, but toxicity of many normal tissues limits our ability to escalate dose. Xerostomia represents one of the most common complications. The purpose of this study is to investigate the potential of intensity-modulated radiotherapy (IMRT) to achieve adequate sparing of parotids and to escalate nominal and/or biologically-effective dose to achieve higher tumor control without exceeding normal tissue tolerances. METHODS AND MATERIALS: An IMRT optimization system, developed at our institution for research and clinical purposes, and coupled to a commercial radiation treatment planning system, has been applied to a number of cases of HN carcinomas. IMRT plans were designed using dose- and dose-volume-based criteria for 4 and 6 MV coplanar but non-collinear beams ranging in number from 5 to 15 placed at equi-angular steps. Detailed analysis of one of the cases is presented, while the results of the other cases are summarized. For the first case, the IMRT plans are compared with the standard 3D conformal radiation treatment (3DCRT) plan actually used to treat the patient, and with each other. The aim of the 3DCRT plan for this particular case was to deliver 73 Gy to the tumor volume in 5 fractions of 2 Gy and 28 fractions of 2.25 Gy/fx; and 46 Gy to the nodes in 2 Gy/fx while maintaining critical normal tissues to below specified tolerances. The IMRT plans were designed to be delivered as a "simultaneous integrated boost" (SIB) using the "sweeping window" technique with a dynamic MLC. The simultaneous integrated boost strategy was chosen, partly for reasons of efficiency in planning and delivery of IMRT treatments, and partly with the assumption that dose distributions in such treatments are more conformal and spare normal tissues to a greater extent than those with sequential boost strategy. Biologically equivalent dose normalized to 2 Gy/fx, termed here as normalized total dose (NTD), for this strategy was calculated using published head and neck fractionation data. RESULTS: IMRT plans were more conformal than the 3DCRT plans. For equivalent coverage of the tumor and the nodes, and for the dose to the spinal cord and the brainstem maintained within tolerance limits, the dose to parotids was greatly reduced. For the detailed example presented, it was shown that the tumor and the nodes in the 3DCRT plan receive NTDs of 78 and 46 Gy, respectively. For the IMRT plan, a nominal dose of 70 Gy could be delivered to the tumor in 28 fractions of 2.5 Gy each, simultaneously with 50.4 Gy to nodes with 1.8 Gy/fx. The two are biologically equivalent to 82 and 46 Gy, respectively, if delivered in 2 Gy/fx. Similar computations were carried out for other cases as well. The quality of IMRT plans was found to improve with increasing number of beams, up to 9 beams. Dose-volume-based criteria led to a modest improvement in IMRT plans and required less trial and error. CONCLUSION: IMRT has the potential to significantly improve radiotherapy of HN cancers by reducing normal tissue dose and simultaneously allowing escalation of dose. SIB strategy is not only more efficient and yields better dose distributions, but may also be biologically more effective. Dose-volume-based criteria is better than purely dose-based criteria. The quality of plans improves with number of beams, reaching a saturation level for a certain number of beams, which for the plans studied was found to be 9.

Adult↗

PubMed2005

Determining gamma from B --> pi(pi) decays without the CP-asymmetry Cpi(0)pi(0).

Factorization based on the soft-collinear effective theory (SCET) can be used to reduce the number of hadronic parameters in an isospin analysis of B --> pi(pi) decays by one. This gives a theoretically precise method for determining the CP violating phase gamma by fitting to the B --> pi(pi) data without Cpi(0)pi(0). SCET predicts that gamma lies close to the isospin bounds. With the current world averages we find gamma = 75 degrees +/- 2 degrees(+9 degrees)(-13 degrees), where the uncertainties are theoretical, then experimental.

Journal Article↗

PubMed2001

Parametrization of electrophilicity for the prediction of the toxicity of aromatic compounds.

The aim of this study was to determine which descriptor best parametrized the electrophilicity of aromatic compounds with regard to their acute toxicity. To achieve this, toxicity data for 203 substituted aromatic compounds containing a nitro- or cyano group were evaluated in the 40-h Tetrahymena pyriformis population growth impairment assay. Quantitative structure-activity relationships (QSARs) were developed relating toxic potency [log(IGC(50)(-1))] with hydrophobicity quantified by the 1-octanol/water partition coefficient (log P) and electrophilic reactivity quantified by the molecular orbital parameters, either the energy of the lowest unoccupied molecular orbital (E(LUMO)) or maximum acceptor superdelocalizability (A(max)) was developed. For the full data set, E(LUMO) and A(max) were collinear (r = 0.87). A comparison of the QSARs [log(IGC(50)(-1)) = 0.40 log P - 0.94E(LUMO) - 1.27; n = 203, r(2) = 0.60, s = 0.49, F = 151] and [log(IGC(50)(-1)) = 0.37 log P + 13.1A(max) - 4.30; n = 203, r(2) = 0.70, s = 0.42, F = 237] reveals A(max) to be the better electrophilic parameter for modeling these data. Analysis of outliers indicates a preponderance of 4-subsituted nitrophenols and nitroanilines. Smaller datasets (51 and 102 compounds) selected in order to reduce the collinearity between A(max) and E(LUMO) were also evaluated. Results indicate A(max) to be the superior descriptor of electrophilicity for the purpose of toxicological QSARs for aromatic compounds. Development of QSARs using partial least-squares yielded similar results.

Aniline Compounds↗

PubMed2005

QSAR by LFER model of cytotoxicity data of anti-HIV 5-phenyl-1-phenylamino-1H-imidazole derivatives using principal component factor analysis and genetic function approximation.

Cytotoxicity data of anti-HIV 5-phenyl-1-phenylamino-1H-imidazole derivatives were subjected to quantitative structure-activity relationship (QSAR) study using linear free energy related (LFER) model of Hansch using electronic (Hammett sigma), hydrophobicity (pi) and steric (molar refractivity and STERIMOL L, B1, B2, B3 and B4) parameters of phenyl ring substituents of the compounds, along with appropriate indicator variables. Principal component factor analysis (FA) was used as the data-preprocessing step to identify the important predictor variables contributing to the response variable and to avoid collinearities among them. The generated multiple linear regression (MLR) equations were statistically validated using leave-one-out technique. Genetic function approximation (GFA) was also used on the same data set to develop QSAR equations, which produced the same best equation as obtained with FA-MLR. The final equation is of acceptable statistical quality (explained variance 80.2%) and predictive potential (leave-one-out predicted variance 74%). The analysis explores the structural and physicochemical contributions of the compounds for cytotoxicity. A thiol substituent at 2 position of the imidazole nucleus decreases cytotoxicity when compared to the corresponding unsubstituted congener. Presence of hydrogen bond donor group at meta position of the phenyl ring present at 5 position of the imidazole nucleus also reduces cytotoxicity. Additionally, absence of any substituent at 2 and 3 positions of the phenyl ring of 1-phenylamino fragment reduces the cytotoxicity. The negative coefficient of sigmap indicates that presence of electron-withdrawing substituents at the para position of the phenyl ring of the 1-phenylamino fragment is not favourable for the cytotoxicity. Again, lipophilicity of meta substituents of the 5-phenyl ring increases cytotoxicity. The coefficients of molar refractivity (MRm) and STERIMOL parameters for meta substituents (Lm, B1m and B4m) of the phenyl ring of 1-phenylamino fragment indicate that the length, width and overall size of meta substituents are conducive factors for the cytotoxicity.

Algorithms↗

PubMed2006

High prevalence of renal dysfunction in long-term survivors after pediatric liver transplantation.

OBJECTIVE: To determine the prevalence and identify variables associated with renal dysfunction in long-term survivors of pediatric liver transplantation. STUDY DESIGN: Data from 117 patients who survived>or=3 years after liver transplantation were analyzed. Demographic and clinical information was obtained from chart review and from a clinical care database. The dependent variable was renal function as determined by measured glomerular filtration rate (mGFR). Univariate and multivariate analyses were performed to identify independent variables associated with renal dysfunction (mGFR<70 mL/min per 1.73 m2). RESULTS: The average time since liver transplant was 7.6+/-3.4 years (range, 3 to 14.6 years). When the last available mGFR for all patients was analyzed, renal dysfunction was present in 32%. In the univariate analysis, mGFR at 1 year after transplant, cyclosporine immunosuppression, and time since transplant were significant; the second two were strongly collinear. Using multiple logistic regression modeling excluding time since transplant, cyclosporine and mGFR at 1 year after transplant were strongly associated with renal dysfunction. CONCLUSIONS: Renal dysfunction is a common complication in children who survive liver transplantation. Our observations are of critical importance because children may live long enough to move from a stage of renal insufficiency characterized by asymptomatic decreased GFR to symptomatic end-stage renal disease.

Adolescent↗

PubMed2005

A study on the prognostic value of cyclins D1 and E expression levels in resectable gastric cancer and on some correlations between cyclins expression, histoclinical parameters and selected protein products of cell-cycle regulatory genes.

Cyclins condition the course of a cell cycle through the activation of appropriate serine-threonine kinases. Any variation in the cyclins' expression result in pathologies of the cell division, including neoplastic proliferation. Activity of the complexes of cyclins D1 and E with appropriate cyclin-dependent kinases may be inhibited by protein P21 (WAF1/CIP1) which functions as a cell growth cycle inhibitor. As yet, there have been rather few reports on the prognostic value of this cyclin expression assessment in gastric cancer, the kind of neoplasm still characterized by very poor prognosis. The study aimed at the assessment of expression levels of cyclins D1 and E in surgically removed gastric cancers, including the analysis of this prognostic value parameter, and attempted to determine some correlations between the expression of the examined cyclins and selected histoclinical and molecular parameters such as: patients' age and gender, histological type according to the Lauren classification, cancer stage (TNM), degree of histological malignancy (G) and level of expression of the cell-cycle regulatory genes protein products--P53, P21, P27. Immunohistochemical analysis was performed on specimens obtained from radical stomach resections of 80 patients treated in the period 1992-1997 for gastric cancer stage I-IIIB (TNM-UICC) at the Department of Surgical Oncology, Medical University of Lodz. For immunohistochemical examinations, the LSAB system was used, designed for assessment of antigen expression. In statistical analysis, Fisher's exact test was applied to evaluate correlations between the analyzed variables and Mantel-Haenschel's test to evaluate their collinearity. For the evaluation of the effect of the analyzed variables on postoperation survival and recurrence-free survival the Cox regression model was used. When analyzing the prognostic value and survival period in association to the cyclins D1 and E expression levels, a statistically significant correlation was found only in relation to cyclin E expression: a survival period of minimum 5 year duration was significantly higher in the group displaying a negative, or only faintly positive, reaction to the presence of cyclin E, than in the group with a strongly positive response. Moreover, the analysis showed statistically significant non-linear dependence between the histological type of cancer in the Lauren classification as well as a degree of histological malignancy and the level of cyclin E expression, and a negative correlation between the level of cyclin E expression and the stage of cancer; In addition, a positive correlation between the level of P53 and cyclin E expression as well as statistically significant non-linear correlation between the level of cyclin E expression and the level of protein P21 expression was observed. However, no statistically significant correlations were found between the level of expression of the two cyclins and the level of protein P27 expression or between the levels of cyclin D1 and E expression in gastric cancer. Out of the two types of evaluated cyclins only cyclin E can be considered a significant regulatory factor and a useful prognostic parameter in gastric cancer.

Cell Cycle↗

PubMed2006

Competing magnetic interactions in Na10Co4O10, studied by neutron diffraction.

Na(10)Co(4)O(10) was investigated by neutron powder diffraction at 230, 70, and 4 K. The crystal structure, determined previously by X-ray diffraction on single crystals, was confirmed. Na(10)Co(4)O(10) orders magnetically below 37 K. All observed magnetic reflections could be indexed by integers (hkl) with respect to the chemical unit cell and the magnetic propagation vector q=0. The refinement was performed in the Shubnikov space group C2/c and indicated a collinear antiferromagnetic spin structure. The determined spin arrangement is consistent with the magnetic intratetramer interactions suggested previously from the analysis of magnetic susceptibility data: the magnetic moments of the central Co(III) ions of the Co(4)O(10) tetramer lie parallel to each other and couple in an antiparallel fashion to the terminal Co(II) moments. The Rietveld analysis shows that the net moments of 0.64 mu(B) per tetramer form ferromagnetic layers parallel to the ab plane. Adjacent layers are coupled antiferromagnetically along c. The spins are aligned in the ac plane along the line connecting adjacent Co(II) and Co(III) ions of the tetramer. We have determined unusually low values for the ordered magnetic moments of 2.43(5) mu(B) and 2.11(6) mu(B) for Co(III) and Co(II), respectively. The occurrence of spontaneous magnetization below 37 K indicates a slight canting of 2.2 degrees of the antiferromagnetic structure. A representation analysis shows that a weak ferromagnetic component along b is compatible with the determined antiferromagnetic structure.

Journal Article↗

PubMed2005

Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6.

On pig chromosome 6, the SW71 microsatellite is located in the region corresponding to several quantitative trait loci (QTL), such as those for intramuscular fat content and for body weight at 4 weeks of age. The genomic sequence of approximately 909 kb was obtained from seven BAC clones encompassing the SW71 region corresponding to human 18q11.21-q11.22. By searching the NCBI GenBank using BLASTX and BLASTN, this 909-kb segment was found to contain eight genes, RAB31, TXNDC2, VAPA, APCDD1, NAPG, FAM38B, C18orf30, and C18orf58, and one putative gene (DN119777). The average G + C content in the sequence of this contig was 45.75% and 33 CpG islands were detected. CpG islands were scattered throughout the region in which most of the putative genes were located. Dense CpG islands of approximately 840 bp were observed, including within the 5' UTR and exon 1 of the orthologs of the RAB31, VAPA, APCDD1, and NAPG genes. Comparative analysis of conserved segments of six species showed that K(a)/K(s) ratios of the TXNDC2 gene in collinear and rearranged segments were significantly different at 4.1 and 1.3, respectively. In conclusion, we demonstrated the genomic organization of pig chromosome 6, including the gene order surrounding SW71, which provides important information for comparative mapping. Moreover, the genes revealed in this study may be positional candidate genes associated with QTL on chromosome 6 that affect fat deposition in pigs.

Adiposity↗

PubMed2025

Polyploidy-mediated variations in glutamate receptor proteins linked to Fusarium wilt resistance in upland cotton.

Cotton production in the US faces a serious threat from Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4), a soil-borne fungus causing Fusarium wilt by infecting the roots and vascular system of susceptible cotton, leading to rapid wilting and death. Here, we investigate genetic mechanisms of resistance to FOV4 in the highly resistant upland cotton genotype "U1" using an early-generation segregating biparental population ("U1" × "CSX8308") with comprehensive genomic resources. Reference-grade genomic assemblies of the parents revealed minor structural variations between "U1" haplotypes, a high degree of collinearity at chromosome synteny and micro-synteny levels, and significant divergence from "CSX8308" with 8.9 million SNPs. QTL analysis identified significant markers on chromosomes D03 and A02 linked to reduced Fusarium wilt severity. Within these regions, two glutamate-receptor-like (GLR) genes showed structural variation and overlapped between translocated segments on A02 and D03, suggesting a rare but important reinforcing effect of parallel evolution between susceptible and resistant genotypes. Transcriptome profiles of "U1" under FOV4 infection reveal activation of calcium-binding proteins and transcription factors regulating plant hormones (ethylene, abscisic acid, jasmonic acid, and salicylic acid), along with enzymes involved in cell wall remodeling and phytoalexin production. Advancing cotton improvement depends on incorporating durable genetic disease resistance into high-yielding, high-quality cultivars.

Fusarium↗

PubMed2002

Spin densities in two-component relativistic density functional calculations: noncollinear versus collinear approach.

With present day exchange-correlation functionals, accurate results in nonrelativistic open shell density functional calculations can only be obtained if one uses functionals that do not only depend on the electron density but also on the spin density. We consider the common case where such functionals are applied in relativistic density functional calculations. In scalar-relativistic calculations, the spin density can be defined conventionally, but if spin-orbit coupling is taken into account, spin is no longer a good quantum number and it is not clear what the "spin density" is. In many applications, a fixed quantization axis is used to define the spin density ("collinear approach"), but one can also use the length of the local spin magnetization vector without any reference to an external axis ("noncollinear approach"). These two possibilities are compared in this work both by formal analysis and numerical experiments. It is shown that the (nonrelativistic) exchange-correlation functional should be invariant with respect to rotations in spin space, and this only holds for the noncollinear approach. Total energies of open shell species are higher in the collinear approach because less exchange energy is assigned to a given Kohn-Sham reference function. More importantly, the collinear approach breaks rotational symmetry, that is, in molecular calculations one may find different energies for different orientations of the molecule. Data for the first ionization potentials of Tl, Pb, element 113, and element 114, and for the orientation dependence of the total energy of I+2 and PbF indicate that the error introduced by the collinear approximation is approximately 0.1 eV for valence ionization potentials, but can be much larger if highly ionized open shell states are considered. Rotational invariance is broken by the same amount. This clearly indicates that the collinear approach should not be used, as the full treatment is easily implemented and does not introduce much more computational effort.

Journal Article↗

PubMed2001

Idiosyncratic profiles of collinearity error using segments and dot pairs.

It is well known that judgments of oblique line segments are more variable and less accurate than are judgments of horizontal or vertical segments, i.e., the "oblique effect." A prior study from our laboratories confirmed these differentials for a task in which the collinearity of segments at various angular positions was judged. Further, that study found that each observer manifests a distinct, idiosyncratic profile of errors across the 360 degrees range. These error tendencies are conspicuous in models derived by harmonic analysis, and we describe significant excursions of a given model as "delta errors." The present experiments found complex profiles of delta error with various stimulus and test conditions. A given subject manifested similar models of delta error when judging collinearity of dot pairs versus line segments. In the prior work the segments to be judged were asymmetrically positioned upon the test sheet. However, the asymmetric positioning is not responsible for the errors, as the present work found errors excursions with a round display field. Similar profiles of delta error were found when subjects were allowed to mark an open space, versus being required to respond at a specific distance (indicated by a target circle). This addresses questions of whether the error should be measured as an angle. In the two final experiments, we present evidence that the source of delta error within the nervous system is at the point of binocular synthesis of the information from the two eyes, or beyond, and the effects are not due to errors of reaching. Potential neural substrates for these complex, idiosyncratic error tendencies are discussed.

Discrimination Learning↗

PubMed2002

Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.

Sequence analysis of the BcnI restriction-modification system from Bacillus centrosporus revealed four open reading frames (bcnIC, bcnIR, bcnIB and bcnIA) that are arranged as two converging collinear pairs. One pair encodes a putative small regulatory protein, C.BcnI, and the restriction endonuclease R.BcnI. The other two gene products are the DNA cytosine-N4 methyltransferases M.BcnIA and M.BcnIB, which differ by circular permutation of conserved sequence motifs. The BcnI methyltransferases are isospecific on double-stranded DNA [methylation specificity CC(C/G)GG], but M.BcnIA can also methylate the target sites in single-stranded DNA. Functional analysis shows that bcnIA is dispensable (bcnIB is capable of protecting the DNA against the in vivo activity of bcnIR); in contrast, no stable clones were obtained if bcnIB alone was deleted from the system. By analogy with the DpnII system, the second methylase M.BcnIA may play a role in the transformation proficiency of its gram-positive host. The interchangeability of homologous elements in the beta class of cytosine-N4 methylases was probed by hybrid formation between M.BcnIB and its closest homolog M.Cfr9I (CCCGGG) employing a novel semi-random strategy combined with selection for catalytic activity. The fusion points in the active hybrids mapped in a narrow region located between sequence motifs X and I. Our data illustrate that recombination of two related sequences by circular permutation may serve as an evolutionary mechanism for creating new specificities of amino MTases.

Amino Acid Sequence↗

PubMed2026

Reference-Guided Chromosome-Scale Genome Assembly With Insights on Population Genomics of the Atlantic Goliath Grouper (Epinephelus itajara), Islas del Rosario, Colombia.

Epinephelus itajara, commonly known as the Atlantic Goliath grouper, is the largest species among the western North Atlantic groupers and is critically endangered. This species plays a crucial ecological, cultural, and economic role and has been the focus of captive breeding efforts at the Oceanario of the Rosario Islands, Colombia. However, despite its ecological and conservation importance, genomic resources and population genomic data for E. itajara remain scarce, particularly in the Colombian Caribbean. This study presents a reference-guided chromosome-scale genome assembly and an analysis of the population genomic structure of E. itajara using PacBio HiFi sequencing and Illumina technologies. The assembled genome has a total size of 1.12 Gb, with a contig N50 of 42.69 Mb and a scaffold N50 of 46.30 Mb. A total of 22,692 protein-coding genes were identified after masking 46% of the genome, which consists of repetitive elements. Comparative genomic analyses revealed a high degree of collinearity with closely related Epinephelus species and identified E. lanceolatus as the closest relative, supporting recent divergence and conserved genome architecture within the genus. Additionally, a population genomics analysis was conducted using 7706 high-quality SNPs to assess the genomic structure of captive populations. The results revealed four distinct genomic lineages, with moderate genetic differentiation among the sampled individuals. In the Colombian Caribbean, two unique lineages were identified, associated with the localities of Bahía Cispatá and Bahía Barbacoas, suggesting possible geographic isolation. These genomic resources provide valuable tools and new opportunities to better understand the genomic diversity, evolutionary history, and reproductive mechanisms of E. itajara. Moreover, they serve as a foundation for conservation strategies, including selective breeding programs aimed at increasing genomic diversity in captive populations and guiding restoration efforts in its natural habitat.

Epinephelus itajara↗

PubMed2001

Metabolic syndrome and ischemic heart disease in elderly men and women.

Associations between metabolic syndrome components and prevalent ischemic heart disease (IHD) were investigated in a cross-sectional, community-based study of elderly men (n = 1,015) and women (n = 1,259) in Rancho Bernardo, California, in 1984-1987. In both sexes, there were significant positive associations between IHD defined by resting electrocardiogram criteria and age, systolic blood pressure, fasting and postchallenge hyperglycemia, total cholesterol/high density lipoprotein cholesterol (HDL cholesterol) ratio, and triglycerides and an inverse significant association with HDL cholesterol. High collinearity and interactions between serum insulin and metabolic syndrome variables were accounted for by uncorrelated principal components identified by factor analysis. In both men and women, three uncorrelated principal components were identified, representing a central metabolic factor (body mass index, fasting and 2-hour serum insulin, high serum triglycerides, and low HDL cholesterol), a glucose factor, and a blood pressure factor. In a multivariate model with age and sex, all three factors were significantly associated with IHD by electrocardiogram criteria; central metabolic factor (odds ratio (OR) = 1.6, p = 0.001), glucose factor (OR = 1.4, p < 0.001), blood pressure factor (OR = 1.2, p = 0.005), age (10 years) (OR = 1.8, p < 0.001), and female sex (OR = 0.5, p < 0.02). Similar results were obtained in analyses using clinically manifest IHD as the outcome. These results support the thesis that the metabolic syndrome exerts effects through different risk factors by different mechanisms.

Aged↗

PubMed1990

[Cloning of clusters of erythromycin biosynthesis genes of Streptomyces erythraeus (Saccharopolyspora erythraea)].

The erythromycin resistance gene (ermE) and part of erythromycin biosynthesis genes located in the same cluster with the ermE gene were cloned from S. erythraeus 3 subjected to improvement with respect to erythromycin production. For isolating the erythromycin biosynthesis genes, the plasmid vector pUC18 and the phage vector lambda EMBL3 were used. The ermE gene DNA was used as a labeled probe for analysis of the recombinant plasmids and phages. The recombinant phages lambda ermE1 and ermE4 containing fragments of the chromosomal DNA collinear to the genome DNA of S. erythraeus 3 were analyzed. The size of the cloned fragment of the chromosomal DNA of S. erythraeus 3 was about 20 kb. Subcloning with the vector pUS18 resulted in isolation of plasmids pSU235-pSU244 containing BamHI fragments of chromosomal DNA from S. erythraeus 3. The restriction map of the chromosomal region of S. erythraeus 3 containing the ermE gene was constructed. The cloned genes of erythromycin biosynthesis are useful in the study of their structure and functions, construction of integrative vectors, improvement of cultures producing macrolide antibiotics and isolation of genes responsible for biosynthesis of other polyketide antibiotics.

Bacteriophage lambda↗