Fast optimal genome tiling with applications to microarray design and homology search.

In this paper, we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size-bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a number of computational biology applications such as selecting genomic DNA fragments for PCR-based amplicon microarrays and performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we first discuss the solution to a basic online interval maximum problem via a sliding-window approach and show how to use this solution in a nontrivial manner for many of the tiling problems introduced. We also discuss NP-hardness results and approximation algorithms for generalizing our basic tiling problem to higher dimensions. Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported.     

Culture and Rights: Anthropological Perspectives.

Culture and Rights: Anthropological Perspectives. Jane K. Cowan. Marie-Bénédicte Dembour. and Richard A. Wilson. eds. Cambridge: Cambridge University Press, 2001. 258 pp.     

Soft-tissue accumulation of lead in the blue tilapia,Oreochromis aureus (steindachner), and the modifying effects of cadmium and mercury

The interaction of mercury and cadmium with lead was investigated by exposingOreochromis aureus to two heavy metals simulataneously. The chronic accumulation prolife of lead was determined by analyzing the liver, brain, gill filaments, intestine, caudal muscle, spleen, trunk kidney, and gonads following exposure to lead alone and in mixtures with mercury and cadmium. Nominal exposure concentrations of lead were 0.05, 0.10, 0.50, and 1.00 mg/L. Mixtures of lead (0.50 or 0.05 mg/L) with cadmium (0.05 mg/L) and lead (0.50 or 0.05 mg/L) with mercury (0.05 mg/L) were also used. Following 140 d of exposure to lead, the highest concentrations of lead consistently accumulated in the trunk kidney. The concentration of lead in the kidney was decreased by coexposure to mercury or cadmium, but increased in the muscle and liver. Under all exposure regimes, the median concentration of lead in the muscle exceeded safety levels recommended for human consumption. In a food fish, such asO. aureus, a knowledge of toxic metal accumulation patterns is of great importance.     

Homosexual behavior in primates: A review of evidence and theory

Homosexual behavior is defined as genital contact, genital manipulation or both between same-sex individuals. Available data indicate that this behavior is phylogenetically widespread among the anthropoid primates, but totally absent among prosimians. The majority of the 33 species that demonstrate homosexual behavior do so rarefy, but for a substantial number (N =12) it appears to be a more common pattern under free-ranging conditions. I summarize data on homosexual behavior as it relates to form, living condition, age, sex, social organization, and ecological context, and discuss hormonal, demographic, and sociosexual theories for primate homosexual behavior. Among adult primates, the behavior is not the product of abnormal excesses or deficiencies in androgens. Prenatal excesses of androgens may have some effect on the expression of female homosexual behavior, but these effects might vary over the life span, and data are equivocal at present. Demographic processes that result in skewed sex ratios can favor the expression of homosexual behavior in a population, which causes intraspecific variation. I examine several sociosexual explanations, including (a) proceptivity enhancement, (b) receptivity reduction, (c) dominance assertion, (d) practice for heterosexual copulation, (e) tension regulation, (f) reconciliation, and (g) alliance formation. An evolutionary scenario highlights the transformations this behavior underwent during the evolution of the anthropoid primates. I suggest exaptation as a theoretical framework for interpreting homosexual behavior and conclude that future consideration of sexual selection among primates should address homosexual components of this process.     

Origin of deoxycorticosterone sulfate (DOC-SO4) in plasma of pregnant women: Pregnenolone-3,21-disulfate is a placental precursor of DOC-SO4

The plasma levels of deoxycorticosterone sulfate (DOC-SO₄) in near-term pregnant women are 100 times those in plasma of men or non-pregnant women. Yet, neither the tissue site of synthesis nor the precursor of DOC-SO₄ that enters maternal plasma is known. Several potential sources have been excluded: plasma DOC-SO₄ is not derived from plasma DOC; and the secretion of C₂₁-steroids (other than aldosterone) from the maternal adrenals during human pregnancy is not increased. Similarly, the transfer of DOC-SO₄ from fetal plasma cannot account for the high level of DOC-SO₄ in the maternal compartment, and a reduced clearance of plasma DOC-SO₄ during pregnancy cannot account for the high levels of DOC-SO₄. Indeed, the rate of clearance of DOC-SO₄ from plasma is 10–100 times that of most other steroid sulfates. To address this question further, we evaluated the possibility that fetal plasma pregnenolone-3,21-disulfate serves as a precursor for DOC-SO₄ formation in the placenta. The preferential hydrolysis of the 3β-sulfate of pregnenolone-3,21-disulfate in placenta would give rise to pregnenolone-21-monosulfate, which, if acted upon by placental 3β-hydroxysteroid dehydrogenase/Δ^{5 → 4} isomerase, could give DOC-SO₄. [³H]Pregnenolone-3,21-disulfate was incubated with minces of human placental tissue for 5, 20, 60 and 120 min. Radiolabelled DOC-SO₄, DOC, and pregnenolone-21-monosulfate were isolated from the incubation media and quantified. After a 5 min incubation, 7.5% of substrate was converted to DOC-SO₄; and after 20, 60 and 120 min 30% of the [³H]pregnenolone-3,21-disulfate was recovered from the media of these incubations as [³H]DOC-SO₄. [³H]DOC was also present in the incubation media and the concentrations of this product increased as a function of incubation time. Therefore, pregnenolone-3,21-disulfate, which is present in very high concentrations in fetal plasma (1000 ng/ml), is metabolized in the placenta to DOC-SO₄. Because of the fetal and maternal vascular arrangements of the hemochorioendothelial placenta of human pregnancy, steroids produced in syncytiotrophoblasts preferentially enter the intervillous space; thus, fetal plasma pregnenolone-3,21-disulfate may serve as a placental precursor of maternal plasma DOC-SO₄.     

Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains

The universal genetic code is determined by the aminoacylation of tRNAs. In spite of the universality of the code, there are barriers to aminoacylation across taxonomic domains. These barriers are thought to correlate with the co-segregation of sequences of synthetases and tRNAs into distinct taxonomic domains. By contrast, we show here examples of eukaryote-like synthetases that are found in certain prokaryotes. The associated tRNAs have retained their prokaryote-like character in each instance. Thus, co-segregation of domain-specific synthetases and tRNAs does not always occur. Instead, synthetases make adaptations of tRNA-protein contacts to cross taxonomic domains.