Detection of surface differences between two closely related cell populations by partitioning isotopically labeled mixed cell populations in two-polymer aqueous phases

The partition behavior of cells in dextran-poly(ethylene glycol) aqueous phases (i.e., the cells' relative affinity for the top or bottom phase or their adsorption at the interface) is greatly dependent on the polymer concentrations and ionic composition and concentration. Appropriate selection of phase system composition permits detection of differences in either charge-associated or lipid-related surface properties. We have now developed a method that can reveal differences by partitioning that fall within experimental error if one were to compare countercurrent distribution (CCD) curves of two closely related cell populations run separately. One cell population is isotopically labeled in vitro (e.g., with⁵¹Cr-chromate) and is mixed with an excess of the unlabeled cell population with which it is to be compared. The mixture is subjected to CCD and the relative specific radio-activities are determined through the distribution. As control we also examine a mixture of labeled cells and unlabeled cells of the same population. The feasibility of this method was established by use of cell mixtures the relative partition coefficients of which were known. The procedure was then used to test for human erythrocyte subpopulations⁵¹Cr-chromate-labeled human young or old red blood cells were mixed with unfractionated erythrocytes and subjected to CCD in a phase system reflecting charge-associated properties. It was found that older cells had a high, young cells (probably only reticulocytes) a low partition coefficient. Because of the small differences involved these results were not previously obtained. It was further determined, by repartitioning⁵¹Cr-labeled cells from the left or right ends of a CCD of human red blood cells admixed to unlabeled unfractionated erythrocytes, that a subpopulation with higher partition coefficient exists (probably constituting the old red cells). These experiments serve to illustrate (a) that human red blood cells, contrary to a previous report, can be subfractionated by partitioning and (b) the usefulness of this new method in detecting smaller surface differences between closely related cell populations than was heretofore possible by partitioning alone.     

Detection of surface differences between two closely related cell populations by partitioning isotopically labeled mixed cell populations in two-polymer aqueous phases. II. A correction

The partition behavior of cells in dextran-poly(ethylene glycol) aqueous phases (i.e., the cells' relative affinity for the top or bottom phase or their adsorption at the interface) is greatly dependent on the polymer concentrations and ionic composition and concentration. Appropriate selection of phase system composition permits detection of differences in either charge-associated or lipid-related surface properties. We have now developed a method that can reveal differences by partitioning that fall within experimental error if one were to compare countercurrent distribution (CCD) curves of two closely related cell populations run separately. One cell population is isotopically labeled in vitro (e.g., with 51Cr-chromate) and is mixed with an excess of the unlabeled cell population with which it is to be compared. The mixture is subjected to CCD and the relative specific radio-activities are determined through the distribution. As control we also examine a mixture of labeled cells and unlabeled cells of the same population. The feasibility of this method was established by use of cell mixtures the relative partition coefficients of which were known. The procedure was then used to test for human erythrocyte subpopulations. 51Cr-chromate-labeled human young or old red blood cells were mixed with unfractionated erythrocytes and subjected to CCD in a phase system reflecting charge-associated properties. It was found that older cells had a high, young cells (probably only reticulocytes) a low partition coefficient. Because of the small differences involved these results were not previously obtained.(ABSTRACT TRUNCATED AT 250 WORDS)     

Detection of surface differences between two closely related cell populations by partitioning isotopically labeled mixed cell populations in two-polymer aqueous phases. I. Human red blood cell subpopulations

The partition behavior of cells in dextran-poly(ethylene glycol) aqueous phases (i.e., the cells' relative affinity for the top or bottom phase or their adsorption at the interface) is greatly dependent on the polymer concentrations and ionic composition and concentration. Appropriate selection of phase system composition permits detection of differences in either charge-associated or lipid-related surface properties. We have now developed a method that can reveal differences by partitioning that fall within experimental error if one were to compare countercurrent distribution (CCD) curves of two closely related cell populations run separately. One cell population is isotopically labeled in vitro (e.g., with 51Cr-chromate) and is mixed with an excess of the unlabeled cell population with which it is to be compared. The mixture is subjected to CCD and the relative specific radio-activities are determined through the distribution. As control we also examine a mixture of labeled cells and unlabeled cells of the same population. The feasibility of this method was established by use of cell mixtures the relative partition coefficients of which were known. The procedure was then used to test for human erythrocyte subpopulations. 51Cr-chromate-labeled human young or old red blood cells were mixed with unfractionated erythrocytes and subjected to CCD in a phase system reflecting charge-associated properties. It was found that older cells had a high, young cells (probably only reticulocytes) a low partition coefficient. Because of the small differences involved these results were not previously obtained. It was further determined, by repartitioning 51Cr-labeled cells from the left or right ends of a CCD of human red blood cells admixed to unlabeled unfractionated erythrocytes, that a subpopulation with higher partition coefficient exists (probably constituting the old red cells). These experiments serve to illustrate (a) that human red blood cells, contrary to a previous report, can be subfractionated by partitioning and (b) the usefulness of this new method in detecting smaller surface differences between closely related cell populations than was heretofore possible by partitioning alone.     

Testing for ancient admixture between closely related populations

One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.     

Fractionation of K-562 cells on the basis of their surface properties by partitioning in two-polymer aqueous-phase systems

The K-562 cell line is a culture of human leukemia stem cells originally derived from a patient with chronic myelogenous leukemia in blast crisis. We have subjected such cells, in the log phase of growth, to countercurrent distribution in a charge-sensitive dextran-polyethylene glycol aqueous-phase system, a method that fractionates cells on the basis of subtle differences in their surface properties, and found that: (1) The cell population is heterogeneous since it is composed of cells with different partition ratios. (2) There is a correlation between increasing cell partition ratios and increasing cell electrophoretic mobilities. (3) Cells under different parts of the distribution curve have dissimilar ratios of cells in different parts of the cell cycle, a phenomenon that may, at least partially, be the basis for the subfractionation of these cells. There is a clear tendency for cells in G₀+G₁+early S to decrease and for those in late S+G₂+M to increase with increasing partition ratios. (4) Sialic acid is a major surface charge component of the cells as evidenced by a dramatic drop in their partition ratios after treatment with neuraminidase.     

Fractionation of K-562 cells on the basis of their surface properties by partitioning in two-polymer aqueous-phase systems

The K-562 cell line is a culture of human leukemia stem cells originally derived from a patient with chronic myelogenous leukemia in blast crisis. We have subjected such cells, in the log phase of growth, to countercurrent distribution in a charge-sensitive dextran-polyethylene glycol aqueous-phase system, a method that fractionates cells on the basis of subtle differences in their surface properties, and found that: (1) The cell population is heterogeneous since it is composed of cells with different partition ratios. (2) There is a correlation between increasing cell partition ratios and increasing cell electrophoretic mobilities. (3) Cells under different parts of the distribution curve have dissimilar ratios of cells in different parts of the cell cycle, a phenomenon that may, at least partially, be the basis for the subfractionation of these cells. There is a clear tendency for cells in G0 + G1 + early S to decrease and for those in late S + G2 + M to increase with increasing partition ratios. (4) Sialic acid is a major surface charge component of the cells as evidenced by a dramatic drop in their partition ratios after treatment with neuraminidase.     

Niche partitioning of closely related symbiotic dinoflagellates

Reef-building corals are fundamental to the most diverse marine ecosystems, yet a detailed understanding of the processes involved in the establishment, persistence and ecology of the coral-dinoflagellate association remains largely unknown. This study explores symbiont diversity in relation to habitat by employing a broad-scale sampling regime using ITS2 and denaturing gradient gel electrophoresis. Samples from Pocillopora damicornis, Stylophora pistillata and Seriatopora hystrix all harboured host-specific clade C symbiont types at Heron Island (Great Barrier Reef, Australia). While Ser. hystrix associated with a single symbiont profile along its entire depth distribution, both P. damicornis and Sty. pistillata associated with multiple symbiont profiles that showed a strong zonation with depth. It is shown that, with an increased sampling effort, previously identified 'rare' symbiont types within this group of host species are in fact environmental specialists. A multivariate approach was used to expand on the common distinction of symbionts by a single genetic identity. It shows merit in its capacity not only to include all the variability present within the marker region but also to reliably represent ecological diversification of symbionts. Furthermore, the cohesive species concept is explored to explain how niche partitioning may drive diversification of closely related symbiont lineages. This study provides thus evidence that closely related symbionts are ecologically distinct and fulfil their own niche within the ecosystem provided by the host and external environment.     

Assessing the degree of stratification between closely related Holstein-Friesian populations

Genomic information is an important part of the routine evaluation of dairy cattle and provides the wide availability of animals genotyped using single nucleotide polymorphism (SNP) microarrays. We analyzed 2243 Polish and 2294 German Holstein-Friesian bulls genotyped using the Illumina BovineSNP50 BeadChip. For each bull, estimated breeding values (EBVs) calculated from national routine genetic evaluation were available for production traits and for somatic cell score (SCS). Separately for each population, we estimated SNP haplotypes, pairwise linkage disequilibrium (LD), and SNP effects. The SNP genetic covariance between both populations was estimated using a bivariate mixed model. The average LD was lower in the Polish than in the German population and, with increasing genomic distance, LD decays 1.7 times more rapidly in German than in Polish cattle. The comparison of SNP allele frequencies for base populations estimated separately using Polish and German data revealed a very good agreement. The comparison of genetic effects corresponding to various window lengths defined in bp emerged a systematic pattern: regardless of the length of the compared region, few significant differences were found for production traits, while many were observed for SCS. For each trait, the German population had much higher SNP variances than the Polish population and the genetic covariance estimates were all positive. Depending on traits’ inheritance mode, the additive genetic variation can be stored in many genes following the infinitesimal model (like for SCS) or distributed between genes with high effects and the polygenic “background” (like for production traits). Accounting for those differences has implications on the prospective international genomic evaluation.     

Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatases

The Chlorella virus RNA triphosphatase (cvRTPase) is involved in the formation of the RNA cap structure found at the 5′-end of the viral mRNAs and requires magnesium ions to mediate its catalytic activity. To extend our studies on the role of metal ions in phosphohydrolysis, we have used a combination of fluorescence spectroscopy, circular dichroism, denaturation studies and thermodynamic analyses to monitor the binding of magnesium ions to the cvRTPase. Using these techniques, the thermodynamic forces responsible for the interaction of metal ions with an RNA triphosphatase were also evaluated for the first time. Our thermodynamic analyses indicate that the initial association of magnesium with the cvRTPase is dominated by a favorable entropic effect and is accompanied by the release of eight water molecules from the enzyme. Moreover, both fluorescence spectroscopy and circular dichroism assays indicated that minor conformational changes were occurring upon magnesium binding. Mutational studies were also performed and confirmed the importance of three specific glutamate residues located in the active site of the enzyme for the binding of magnesium ions. Finally, in contrast to the yeast RNA triphosphatase, we demonstrate that the binding of magnesium ions to the cvRTPase does not lead to the stabilization of the ground state binding of the RNA substrate. Based on the results of the present study, we hypothesize that the binding of magnesium ions induces local conformational perturbations in the active site residues that ultimately positions the lateral chains of critical amino acids involved in catalysis. Our results highlight fundamental differences in the role of magnesium ions in the phosphohydrolase reactions catalyzed by the cvRTPase and the closely related yeast RNA triphosphatase.     

Interspecific differences in photosensitivity between three closely related species of pigeons

It is known from field observations that vernal gonad recrudescence begins in January for the Stock dove, a month later at the end of February for the Wood pigeon, while many town pigeons ( Columba livia ) have active gonads throughout the year.
Photostimulation experiments demonstrate that spermatogenesis can be stimulated in the Stock dove by exposure to an artificial daylength regimeincreasing from 9.1 to 10.8 hours over 28 days. This photoperiod is the approximate equivalent of natural daylength changes occurring from late January onwards at 52° N. The same phototreatment, however, was not stimulatory for the testes of Wood pigeons, which required the equivalent of a March photoperiod. Natural daylength changes occurring in late November and December failed to evoke gametogenetic recovery in Stock dove controls.
The gonads of feral pigeons in full breeding condition were unaffected when the subjects were transferred from full summer photoperiods to those found in midwinter and spermatogenesis was maintained in birds kept under winter daylengths for four months.
The discussion mentions the problem of intraspecific geographical variation in photosensitivity. Scottish Wood pigeons begin their gonad recovery earlier and by March have considerably larger testes than birds in the south of England. Furthermore, they achieve this more advanced condition before the vernal equinox when daylengths are shorter in Scotland than in the south of England.     

High throughput characterization of structural differences between closely related proteins in solution

Partitioning of a protein in an aqueous two-phase system (ATPS) is governed by interactions of the protein with aqueous media in the two phases. Here we describe how partitioning of proteins in a set of ATPS of different compositions can be used to quantify differences between 3D structures of closely related proteins. We also provide perspective on practical applications of the technology when comparative analysis of the higher-order structure of proteins is desired.     

Difference in B cell mitogen responsiveness between closely related strains of mice.

Spleen cells from C3H/HeJ mice respond very poorly to the mitogenic action of endotoxin (LPS) in vitro whereas cells from a very closely related strain, C3H/HeN respond very well. An analysis of the genetic similarity of these two strains was performed. There is no significant MLR measurable between cells of these strains under a variety of culture conditions. They do not manifest a significant graft-vs-host response nor do they reject reciprocal skin grafts. Because of this genetic similarity, it is possible to reconstitute the LPS response of nonresponder mice by an adoptive transfer of spleen cells from C3H/HeN mice. This strain pair should therefore prove useful in analyzing the genetic and cellular basis of endotoxin reactivity.     

Detection and resolution of closely related satellite DNA sequences by molecular cloning.

Highly repeated satellite DNAs often consist of mixtures of DNAs with closely related repeating sequences. By cloning individual molecules we have resolved the 1.705 g/cm³ satellite DNA of Drosophila melanogaster into two distinct components: poly$\text{d}\text{A-A-G-A-G}\text{T-T-C-T-C}$ and poly$\text{d}\text{A-A-G-A-G-A-G}\text{T-T-C-T-C-T-C}$. The presence of two distinct sequences within this physically homogeneous satellite DNA had not previously been detected by standard physical, chemical, or sequencing techniques. Both cloning and direct sequence analysis suggest that the five-base-pair and seven-base-pair repeating units reside on separate molecules and are not interspersed with each other.     

The partitioning behavior of K-562 cells associated with different stages of culture growth

Partitioning behavior of cells in dextran-poly(ethylene glycol) aqueous phase systems is a sensitive reflection of the cells' surface properties. A decrease in partition ratio, in charge-sensitive phases, of a variety of cell lines as a function of culture growth has been reported by a number of investigators. The basis for this phenomenon remains unclear. We have now studied the surface properties of K-562 cells (a human cell line originally derived from a patient with chronic myelogenous leukemia in blast crisis) during suspension culture growth by countercurrent distribution. The mean partition ratio of viable cells remained constant during 220 h of culture (i.e., well into stationary phase). The decrease in mean partition ratio of the cell population as a whole during culture, previously observed and reported by others, is attributed to the lower partition ratio of non-viable cells which increase with time of culture.     

Differentiation of closely related and distant human populations by multilocus DNA fingerprinting

Using multilocus DNA fingerprinting with phage M13 DNA as a probe, we have investigated a heterogeneous group of four human populations from Eastern Europe and Northeastern Asia. These populations belong to two language families: Indo-European (Eastern Slavonic branch: Russians, Belarussians) and Altaian (Turkic branch: Yakuts). The experimental results were treated by different statistical techniques: cluster analysis, multidimensional scaling, and multiple correspondence analysis. Coefficients of genetic differentiation were estimated using similarity indices and heterozygosities. The results of our study demonstrated similarity of Belarussian populations and significant differences between the group of Slavonic populations and Yakuts.     

Salinity related physiological and genetic differences between populations of Mytilus edulis

Aminopeptidase-I, the enzymatic product of the Lap locus, liberates N-terminal neutral and aromatic amino acids from oligopeptides. The enzyme is associated with the brush border of the intestine and the extensive lysosomal system in the digestive tubule cells; the enzyme functions in oligopeptide degradation and possibly amino acid transport. The Lap locus is genetically polymorphic and allele frequencies differ between populations according to environmental salinities.
Using cell-free lysosomes, we show salinity related differences in both lysosomal membrane latency and lysosomal and cytosolic free-amino acid concentrations. Differences in the response of the lysosomal aminopeptidase-I enzyme to differences or changes in salinity are discussed.
Antibodies against aminopeptidase-I enzyme were used to demonstrate that alleles of the Lap locus exhibit different specific activities per unit enzyme concentration. In oceanic populations, the concentrations of aminopeptidase-I enzyme of individual phenorypes are equal, suggesting that variation of specific activity among phenorypes is due to allele specific differences in catalytic efficiency. In estuarine populations, total enzyme activity is lower, which is partially due to a significantly lower concentration of aminopeptidase-I enzyme of one homozygote genotype.
The consequences of a change in environmental salinity can be measured on the biochemical, physiological, and population genetic levels. We discuss the possible mechanisms by which salinity variations are responsible for the genetic polymorphism of aminopeptidase-I.     

Cell kinetics of the K-562 cell line in microculture

The cell kinetic parameters of K-562 leukemia cells were studied using microwell cultures in which growth was initiated from a single cell. Total population growth was studied by direct enumeration, 3H-thymidine labelling, and flow cytometry. Clonogenic cell growth was studied by replating and 3H-thymidine suicide. In 7-day clones of K-562 cells, durations of the total cell cycle, G1, S, G2, and M phases were 20.8 h, 3.5 h, 12.9 h, 3.3 h, and 1.1 h, respectively; the growth fraction was 0.92 and the cell loss factor was 0.084. Study of colony-forming cells by replating indicated that clonogenic cells comprised 40% of total cells. 3H-Thymidine suicide showed that cell-cycle duration for these cells was 22.5 h and that S-phase duration was 11.7 h.     

Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes

A technique for genome-wide detection of differences in the integration site positions of interspersed repeats in related genomes (DiffIR) is described. The technique is based on a whole- genome selective PCR amplification of the repeats’ flanking regions followed by a differential hybridization screening of the arrayed library of the selected amplicons. The technique was successfully applied to the comparison of the integration sites in the human and chimpanzee genomes, allowing us to discover 11 new human-specific integrations of human endogenous retrovirus, K family (HML-2) long terminal repeats.     

Ultrastructure of the cell walls of two closely related clostridia that possess different regular arrays of surface subunits.

Cell walls of Clostridium thermohydrosulfuricum and C. thermosaccharolyticum have a two-layered structure, consisting of a thin, lysozyme-sensitive murein layer and a surface (S) layer composed of hexagonally or tetragonally arranged subunits. The subunits can be removed from the murein layer by treatment of cell wall preparations, are composed of a fragile, pH-sensitive monolayer of macromolecular subunits. In both organisms the first stage of the cell division process involves only the plasma membrane and the murein layer. During the subsequent cell separation, a surplus of S-layer subunits appears at the site of division, and consequently the newly formed cell poles remain completely covered by the s layer throughout the separation process. In autolyzed cells an additional layer of subunits assembles on extended areas of the inside of the mucopeptide layer. These observations indicate that the biological function of the S layer depends on its ability to maintain a complete covering of the cell surface at all stages of cell growth and division.