Amplification ratio control system for copy number variation genotyping

We describe a generic design for ratiometric analysis suitable for determination of copy number variation (CNV) class of a gene. Following two initial sequence-specific PCR priming cycles, both ends of both amplicons (one test and one reference) in a duplex reaction, are all primed by the same universal primer (UP). Following each amplification denaturation step, the UP target and its reverse complement (UP') in each strand form a hairpin. The bases immediately beyond the 3'-end of the UP and 5' of UP' are chosen such as not to base pair in the hairpin (otherwise priming is ablated). This hairpin creates a single constant environment for priming events and chaperones free 3'-ends of amplicon strands. The resultant 'amplification ratio control system' (ARCS) permits ratiometric representation of amplicons relative to the original template into PCR plateau phase. These advantages circumvent the need for real-time PCR for quantitation. Choice of different %(G+C) content for the target and reference amplicons allows liquid phase thermal melt discrimination and quantitation of amplicons. The design is generic, simple to set up and economical. Comparisons with real-time PCR and other techniques are made and CNV assays demonstrated for haptoglobin duplicon and 'chemokine (C-C motif) ligand 3-like 1' gene.     

Origins of Cdx1 regulatory elements suggest roles in vertebrate evolution

Cdx1, an upstream regulator of Hox genes, is best characterized for its homeotic effects upon the developing axial skeleton, particularly in the neck. It responds to retinoic acid (RA) in both mouse embryos and embryonal carcinoma (EC) cells. By use of beta-galactosidase chemiluminescence, we show that a mouse Cdx1/lacZ reporter expressed in P19 EC cells responds to RA by the combined activities of an intron retinoic acid response element (RARE) and an upstream RARE. In contrast, a chicken Cdx1/lacZ reporter responds only by activity of the intron RARE. Database analyses upon Cdx1 from twenty three vertebrate species reveal that the intron RARE is structurally conserved in amniotes (eutherian mammals, marsupials, birds and Anole lizard), but not in Xenopus or fish. The upstream RARE is structurally conserved only in eutherian mammals. We conclude that the intron RARE originated at around the amphibian/amniote division, and the upstream RARE appeared around the marsupial/eutherian mammal division. In view of the site of action of Cdx1, we propose that acquisition of the intron RARE may have facilitated the substantial changes that occurred in the neck and anterior thorax at the advent of the amniotes. We present evidence that Cdx1 is also a developmental regulator of the female urogenital system, and we suggest that acquisition of the upstream RARE may have contributed to morphological divergence of marsupial and eutherian mammals.     

CONFIRMATION OF CATFISH MORTALITIES RESULTING FROM MICROCYSTIN PRODUCED DURING MICROCYSTIS BLOOMS

Enigmatic deaths of finfish have occurred in freshwater systems for many years. Some of these fish mortalities can be attributed to the accumulation of cyanobacterial toxins during ingestion of floating feeds or passively through opercular ventilation. We recently were able to document the accumulation of microcystin and resulting catastrophic mortality of pond-raised catfish ( Ictalurus punctatus ). The causative organism, Microcystis aeruginosa , was the dominant phytoplankton component within the cooler fall-winter season. Microcystin, a hepatotoxin produced by Microcystis , was detected in water and catfish liver samples. Fish exposed to pond water containing this bloom were killed within 24 h. Necropsy of fish exposed to pond water revealed congested liver and spleen tissues. Environmental conditions associated with several similar bloom events suggest several predictive options to forecast conditions supporting toxin formation, particularly temperature.     

Using genetic variation to disentangle the complex relationship between food intake and health outcomes

Diet is considered as one of the most important modifiable factors influencing human health, but efforts to identify foods or dietary patterns associated with health outcomes often suffer from biases, confounding, and reverse causation. Applying Mendelian randomization in this context may provide evidence to strengthen causality in nutrition research. To this end, we first identified 283 genetic markers associated with dietary intake in 445,779 UK Biobank participants. We then converted these associations into direct genetic effects on food exposures by adjusting them for effects mediated via other traits. The SNPs which did not show evidence of mediation were then used for MR, assessing the association between genetically predicted food choices and other risk factors, health outcomes. We show that using all associated SNPs without omitting those which show evidence of mediation, leads to biases in downstream analyses (genetic correlations, causal inference), similar to those present in observational studies. However, MR analyses using SNPs which have only a direct effect on the exposure on food exposures provided unequivocal evidence of causal associations between specific eating patterns and obesity, blood lipid status, and several other risk factors and health outcomes.     

Gastrulation in the mouse: the role of the homeobox gene goosecoid.

Mouse goosecoid is a homeobox gene expressed briefly during early gastrulation. Its mRNA accumulates as a patch on the side of the epiblast at the site where the primitive streak is first formed. goosecoid-expressing cells are then found at the anterior end of the developing primitive streak, and finally in the anteriormost mesoderm at the tip of the early mouse gastrula, a region that gives rise to the head process. Treatment of early mouse embryos with activin results in goosecoid mRNA accumulation in the entire epiblast, suggesting that a localized signal induces goosecoid expression during development. Transplantation experiments indicate that the tip of the murine early gastrula is the equivalent of the organizer of the amphibian gastrula.     

Surface and internal antigens of rat spermatozoa distinguished using monoclonal antibodies

Fluorescent antibody labeling techniques are frequently used to investigate the topography of antigens on spermatozoa. It is generally assumed that these procedures detect molecules only on the sperm surface but we now show that this assumption is not always valid. Using monoclonal antibodies that recognize either surface or internal antigens we demonstrate how spurious conclusions can be made, and we suggest simple procedures for assigning the position of an antigen to the cell surface or to an intracellular organelle. Antibodies against plasma membrane antigens should stain 100% of normal intact spermatozoa, but this proportion should be greatly reduced if the spermatozoa have previously been demembranated. If ? 100% of spermatozoa are stained but the proportion increases following permeabilization, then the possibility should be considered that the antigens are intracellular. We conclude that assignment of an antigen to a regional domain on the sperm surface using fluorescent antibody techniques should be validated by a demonstration that the antigen is actually located on the cell surface.     

Metabolism of 4-chloro-2-methylphenoxyacetate by a soil pseudomonad. Preliminary evidence for the metabolic pathway

1. A pseudomonad capable of utilizing the herbicide 4-chloro-2-methylphenoxyacetate as a sole carbon source was isolated from soil and cultured in liquid medium. 2. Analysis of induction patterns of 4-chloro-2-methylphenoxyacetate-grown cells suggests that 5-chloro-o-cresol and 5-chloro-3-methylcatechol are early intermediates in the oxidation of 4-chloro-2-methylphenoxyacetate. Cells were not adapted to oxidize 4-chloro-6-hydroxy-2-methylphenoxyacetate. 3. In culture, 4-chloro-2-methylphenoxyacetate rapidly disappeared and the chlorine in the molecule was quantitatively released as Cl(-) ion. 4. A lactone (gamma-carboxymethylene-alpha-methyl-Delta(alphabeta)-butenolide) was isolated from cultures and established as an intermediate. 5. The following metabolic pathway is suggested: 4-chloro-2-methylphenoxyacetate --> 5-chloro-o-cresol --> 5-chloro-3-methylcatechol --> cis-cis-gamma-chloro-alpha-methylmuconate --> gamma-carboxymethylene-alpha-methyl-Delta(alphabeta)-butenolide --> gamma-hydroxy-alpha-methylmuconate. 6. The tentative identification of 5-chloro-o-cresol, a gamma-chloro-alpha-methylmuconate and gamma-hydroxy-alpha-methylmuconate in culture extracts supports this scheme. However, the catechol was never observed to accumulate in cultures. 7. The detection of 4-chloro-6-hydroxy-2-methylphenoxyacetate, 2-methyl-phenoxyacetate, a dehalogenated cresol and oxalate in culture extracts is discussed in relation to the proposed metabolic pathway.     

A study of genetic polymorphisms of milk β-lactoglobulin, αS1-casein, β-casein,and κ-casein in five dairy breeds

Gene frequencies of the milk -lactoglobulin, _S1-casein, -casein, and -casein loci have been estimated from 1663 cows of five dairy breeds. Departure from Hardy-Weinberg equilibrium was found only in the -casein system in Jerseys. However, chance alone could have accounted for this single significant finding. Results of pairwise comparisons among the five breeds of allele frequencies at these milk protein loci indicate that of the 40 possible tests, only six comparisons are not significant at the 5% probability level. It would appear that these breeds are characterizable in terms of the gene frequencies of these milk protein loci. Nonindependent assortment of genotypes among these milk protein loci was also studied. The closely linked casein loci were not independent in almost all the breeds where tests could be carried out. The only exception was between the _S1-casein and -casein loci in Holsteins. -Lactoglobulin was independent of the casein loci in all breeds except Brown Swiss, where it was found to be significantly associated with -casein. Close linkage is proposed as an important factor for maintaining the observed milk protein polymorphisms.This paper represents a portion of a doctoral dissertation submitted by the first author as partial fulfillment of the requirements for the degree of Doctor of Philosophy at the University of Massachusetts at Amherst.     

PHLOEM OF SPHENOPHYLLUM

The phloem of most fossil plants, including that of Sphenophyllum, is very poorly known. Sphenophyllum was a relatively small type of fossil arthrophyte with jointed stems bearing whorls of leaves ranging in form from wedge or fan-shaped to bifid, to linear. The aerial stem systems of the plant exhibited determinate growth involving progressive reduction in the dimensions of the stem primary bodies, fewer leaves per whorl, and smaller and simpler leaves distally. The primary phloem occurs in three areas alternating in position with the arms of the triarch centrally placed primary xylem. Cells of the primary phloem, presumably sieve elements, are axially elongate with horizontal to slightly tapered end walls. In larger stems with abundant secondary xylem and secondary cortex or periderm, a zone of secondary phloem occurs whose structure varies in the three areas opposite the arms of the primary xylem, as opposed to the three areas lying opposite the concave sides of the primary xylem. The axial system of the secondary phloem consists of vertical series of sieve elements with horizontal end walls. In the areas opposite the protoxylem the parenchyma is present as a prominent ray system showing dilation peripherally. Sieve elements in the areas opposite the protoxylem arms have relatively small diameters. In the areas between the protoxylem poles the secondary phloem sieve elements have large diameters and are less obviously in radial files, while the parenchyma resembles that of the secondary xylem in these areas in that it consists of strands of cells extending both radially and tangentially. An actively meristematic vascular cambium has not been found, indicating that this layer changed histologically after the cessation of growth in the determinate aerial stem systems and was replaced by a post-meristematic parenchyma sheath made up of axially elongate parenchyma lacking cells indicative of being either fusiform or ray initials. A phellogen arose early in development in a tissue believed to represent pericycle and produced tissue comparable to phellem externally. Normally, derivatives of the phellogen underwent one division prior to the maturation of the cells. Concentric bands of cells with dark contents apparently represent secretory tissue in the periderm and cell arrangements indicate that a single persistent phellogen was present. Sphenophyllum is compared with other arthrophytes as to phloem structure and is at present the best documented example of a plant with a functionally bifacial vascular cambium in any exclusively non-seed group of vascular plants.