Phylogenetic screening of the human genome: identification of differentially hybridizing repetitive sequence families

The phi-screen, a method of phylogenetic screening, can be employed to detect repetitive sequence families that differentially hybridize between closely related species. Such differences may involve sequence divergence or variations in copy number, including total presence versus absence of a family of repeated DNA. We present the results of a phi-screen comparing the human genome to that of the prosimian, Galago crassicaudatus. Three human repetitive families that are divergent or not present in galago have been detected. One of these families is described in detail; it is similar among the anthropoids but is present in a lower copy number and/or divergent form in prosimians. The family is clearly related to the transposon-like human element (THE) described by Paulson et al. (1985). THEs have long terminal repeats reminiscent of retroviruses but are unique in that they have no sequence similarity to known mammalian retroviruses. The sequence of a solo long terminal repeat, found unassociated with THE internal sequence, is presented. This family member, THE p2, is bordered by a 5-bp target-site repeat and is interrupted by the insertion of an Alu element. A solo THE element sequenced by Wiginton et al. (1986) contains an insertion of Alu at precisely the same position as does THE p2.      

The solution conformation of the Le chi group

The solution conformation of the non-reducing terminal Gal beta 1----4 (Fuc alpha 1----3)GlcNAc (Lewis X or Le chi) group in the oligosaccharide Lacto-N-fucopentaose (LNFP) III has been determined by high resolution 1H NMR spectroscopy and semi-empirical quantum mechanical calculations. The two methods give the same single conformer for the Le chi group showing close packing of the Gal and Fuc rings. The metal binding properties and homotypic oligomer formation of LNFP III have also been investigated by NMR spectroscopy. No evidence for metal binding or high-affinity homotypic oligomer formation has been found.     

Cultured human hepatocytes. Evidence for metabolism of low density lipoproteins by a pathway independent of the classical low density lipoprotein receptor

Studies of low density lipoprotein (LDL) metabolism in nonhuman model systems have indicated that the mammalian liver has dual mechanisms for the uptake and regulation of the concentration of plasma LDL. Heretofore, direct evaluation of lipoprotein uptake mechanisms in human hepatocytes has not been possible. In order to compare hepatocyte LDL uptake with fibroblast LDL metabolism, human hepatocytes were isolated and cultured from small biopsy specimens obtained from normolipidemic and homozygous familial hypercholesterolemic patients. Cells cultured in serum-free culture medium retained the morphological and biochemical characteristics of hepatocytes for at least 7 days. The uptake and degradation of LDL by hepatocytes was compared to that of the cultured human fibroblasts. Like fibroblasts, hepatocytes bound, internalized, and degraded LDL. In both cell types, uptake approached saturation at a concentration of 50 micrograms of LDL protein/ml. Competition for LDL binding by LDL, high density lipoprotein, and modified LD revealed that the hepatocyte binding was specific for LDL. Cellular cholesterol loading by incubation in LDL-enriched culture medium resulted in diminished LDL uptake in both cell types. Chemical modification of LDL by acetoacetylation, acetylation, and reductive methylation abolished LDL uptake and degradation by fibroblasts. However, hepatocytes bound and degraded the modified LDL at 30-50% the level of native LDL. Homozygous familial hypercholesterolemic hepatocytes were devoid of the LDL receptor pathway but metabolized native LDL to the extent observed with modified LDL uptake by normal hepatocytes. In contrast to the classic LDL receptor pathway, the second or alternate pathway does not lead to regulation of 3-hydroxy-3-methylglutaryl-CoA reductase activity. These findings indicate the presence of two separate pathways of LDL uptake in human hepatocytes which have different effects on hepatocytic cholesterol metabolism.     

The Relationship Between FST and the Frequency of the Most Frequent Allele

F_ST is frequently used as a summary of genetic differentiation among groups. It has been suggested that F_ST depends on the allele frequencies at a locus, as it exhibits a variety of peculiar properties related to genetic diversity: higher values for biallelic single-nucleotide polymorphisms (SNPs) than for multiallelic microsatellites, low values among high-diversity populations viewed as substantially distinct, and low values for populations that differ primarily in their profiles of rare alleles. A full mathematical understanding of the dependence of F_ST on allele frequencies, however, has been elusive. Here, we examine the relationship between F_ST and the frequency of the most frequent allele, demonstrating that the range of values that F_ST can take is restricted considerably by the allele-frequency distribution. For a two-population model, we derive strict bounds on F_ST as a function of the frequency M of the allele with highest mean frequency between the pair of populations. Using these bounds, we show that for a value of M chosen uniformly between 0 and 1 at a multiallelic locus whose number of alleles is left unspecified, the mean maximum F_ST is ∼0.3585. Further, F_ST is restricted to values much less than 1 when M is low or high, and the contribution to the maximum F_ST made by the most frequent allele is on average ∼0.4485. Using bounds on homozygosity that we have previously derived as functions of M, we describe strict bounds on F_ST in terms of the homozygosity of the total population, finding that the mean maximum F_ST given this homozygosity is 1 − ln 2 ≈ 0.3069. Our results provide a conceptual basis for understanding the dependence of F_ST on allele frequencies and genetic diversity and for interpreting the roles of these quantities in computations of F_ST from population-genetic data. Further, our analysis suggests that many unusual observations of F_ST, including the relatively low F_ST values in high-diversity human populations from Africa and the relatively low estimates of F_ST for microsatellites compared to SNPs, can be understood not as biological phenomena associated with different groups of populations or classes of markers but rather as consequences of the intrinsic mathematical dependence of F_ST on the properties of allele-frequency distributions.DIFFERENTIATION among groups is one of the fundamental subjects of the field of population genetics. Comparisons of the level of variation among subpopulations with the level of variation in the total population have been employed frequently in population-genetic theory, in statistical methods for data analysis, and in empirical studies of distributions of genetic variation. Wright’s (Wright 1951) fixation indices, and F_ST in particular, have been central to this effort.Wright’s F_ST was originally defined as the correlation between two randomly sampled gametes from the same subpopulation when the correlation of two randomly sampled gametes from the total population is set to zero. Several definitions of F_ST or F_ST-like quantities are now available, relying on a variety of different conceptual formulations but all measuring some aspect of population differentiation (e.g., Charlesworth 1998; Holsinger and Weir 2009). Many authors have claimed that one or another formulation of F_ST is affected by levels of genetic diversity or by allele frequencies, either because the range of F_ST is restricted by these quantities or because these quantities affect the degree to which F_ST reflects population differentiation (e.g., Charlesworth 1998; Nagylaki 1998; Hedrick 1999, 2005; Long and Kittles 2003; Jost 2008; Ryman and Leimar 2008; Long 2009; Meirmans and Hedrick 2011). For example, Nagylaki (1998) and Hedrick (1999) argued that measures of F_ST may be poor measures of genetic differentiation when the level of diversity is high. Charlesworth (1998) suggested that F_ST can be inflated when diversity is low, arguing that F_ST might not be appropriate for comparing loci with substantially different levels of variation. In a provocative recent article, Jost (2008) used the diversity dependence of forms of F_ST to question their utility as differentiation measures at all.One definition that is convenient for mathematical assessment of the relationship of an F_ST-like quantity and allele frequencies is the quantity labeled G_ST by Nei (1973), which for a given locus measures the difference between the heterozygosity of the total (pooled) population, h_T, and the mean heterozygosity across subpopulations, h_S, divided by the heterozygosity of the total population:GST=hT−hShT.(1)In terms of the homozygosity of the total population, H_T = 1 − h_T, and the mean homozygosity across subpopulations, H_S = 1 − h_S, we can writeGST=HS−HT1−HT.(2)The Wahlund (1928) principle guarantees that H_S ≥ H_T and, therefore, because H_S ≤ 1 and for a polymorphic locus with finitely many alleles, 0 < H_T < 1, G_ST lies in the interval [0,1].Using G_ST for their definition of F_ST, Hedrick (1999, 2005) and Long and Kittles (2003) pointed out that because h_T < 1, F_ST cannot exceed the mean homozygosity across subpopulations, H_S:F_ST = 1 ? h_S/h_T < 1 ? h_S = H_S.(3)Hedrick (2005) obtained this result by considering a set of K equal-sized subpopulations, in which each allele is private to a single subpopulation. In the limit as K → ∞, a stronger upper bound on F_ST as a function of H_S and K reduces to Equation 3 (see also Jin and Chakraborty 1995 and Long and Kittles 2003).While Hedrick (1999, 2005) and Long and Kittles (2003) have clarified the relationship between F_ST and the mean homozygosity H_S across subpopulations, their approaches do not easily illuminate the connection between F_ST and allele frequencies themselves. A formal understanding of the relationship between F_ST and allele frequencies would make it possible to more fully understand the behavior of F_ST in situations where markers of interest differ substantially in allele frequencies or levels of genetic diversity. Our recent work on the relationship between homozygosity and the frequency of the most frequent allele (Rosenberg and Jakobsson 2008; Reddy and Rosenberg 2012) provides a mathematical approach for formal investigation of bounds on population-genetic statistics in terms of allele frequencies. In this article, we therefore seek to thoroughly examine the dependence of F_ST on allele frequencies by investigating the upper bound on F_ST in terms of the frequency M of the most frequent allele across a pair of populations. We derive bounds on F_ST given the frequency of the most frequent allele and bounds on the frequency of the most frequent allele given F_ST. We consider loci with arbitrarily many alleles in a pair of subpopulations. Using theory for the bounds on homozygosity given the frequency of the most frequent allele, we obtain strict bounds on F_ST given the homozygosity of the total population. Our analysis clarifies the relationships among F_ST, allele frequencies, and homozygosity, providing explanations for peculiar observations of F_ST that can be attributed to allele-frequency dependence.     

Presence of sulfate in N-glycosidically linked carbohydrate units of calf thyroid plasma membrane glycoproteins

Calf thyroid slices were found to incorporate [35S] sulfate into two major plasma membrane glycoproteins, which have been previously designated as GP-1 and GP-3 (Okada, Y., and Spiro, R. G. (1980) J. Biol. Chem. 255, 8865-8872). The 35S-glycoproteins were identified on the basis of their characteristic solubility and electrophoretic migration as well as their affinity for Bandeiraea simplicifolia I lectin. After pronase digestion of these glycoproteins, the 35S-label remained associated with the glycopeptides primarily on asparagine-linked carbohydrate units which were released by hydrazinolysis. Examination of the reduced radio-labeled products obtained by nitrous acid cleavage of the hydrazine-liberated oligosaccharides indicated that sulfate esters of N-acetylglucosamine occurred at three locations on the carbohydrate units; two 35S-monosaccharides (2,5-anhydromannitol 4- and 6-sulfate) and one 35S-disaccharide (beta-Gal(1----4)-2,5-anhydromannitol(6-SO4] were formed. The disaccharide is believed to be derived from an internal sulfated N-acetyllactosamine sequence while the monosaccharides most likely originate from 4- and 6-sulfated N-acetylglucosamine residues situated, respectively, at the non-reducing and reducing termini of the oligosaccharide units. Quantitation by NaB[3H]4 reduction of the sulfated saccharides obtained by nitrous acid treatment of hydrazine-released oligosaccharides from unlabeled GP-3 indicated that about 20% of the asparagine-linked carbohydrate units contain sulfate substituents.     

Ion-exchange high-performance liquid chromatography of oligodeoxyribonucleotides using formamide

The superiority of buffer systems containing formamide for the ion-exchange high-performance liquid chromatographic separation of oligodeoxyribonucleotide mixtures generated in solid-phase syntheses is illustrated. The resolutions achieved are compared to those achieved with the same mixtures in other eluting solvents. The use of formamide systems is recommended for oligodeoxyribonucleotide purification in general and is particularly valuable where the oligonucleotide of interest is highly self-complementary and/or rich in deoxyguanosine residues.