Method to estimate genotype probabilities at individual loci in farm livestock

Summary A Bayesian method to estimate genotype probabilities at a single locus using information on the individual and all its relatives and their mates has been developed. The method uses data over several generations, can deal with large numbers of individuals in large livestock families and allows for missing information. It can be extended to multiple alleles and can be used for autosomal or sex-linked loci. The allele frequencies and the form of expression (dominance, penetrance) must be specified. An algorithm using the method and involving an iterative procedure has been developed to calculate the genotype probabilities for practical use in livestock breeding. The method and algorithm were used to determine the accuracy of estimating genotype probabilities of sires for a female sex-limited trait, such as genetic variants of milk proteins. Data were similated and genotype probabilities estimated for 100 sires (20 replicates) with 3, 6 and 12 female offspring per sire, for different population frequencies, for additive and dominance gene action and for variable genotypic expression. Such simulation is useful in the design of testing systems for the use of information on specific genetic loci in selection.Prepared during a leave at Centre for Genetic Improvement of Livestock, Guelph, Canada     

Cytochemical localization of plasma membrane ATPase activity in plant cells

Summary The cytochemical localization of ATPase activity has been investigated in maize root cells using both lead and cerium-based capture methods. With both methods, staining at the plasma membrane was observed in all cells of the root, although the precipitate obtained with cerium was more uniform and granular than that with lead. Controls using no substrate or no magnesium, -glycerophosphate to replace ATP, vanadate or boiled tissue generally showed little or no staining. However, biochemical studies on purified plasma membrane fractions showed that ATPase activity was markedly inhibited by fixation, particularly by glutaraldehyde, and also by lead and cerium ions. Non-enzymic hydrolysis of ATP by cerium was greater than that by lead. The value and limitations of these procedures for the localization of plasma membrane H⁺-ATPase activity are summarized in relation to previous criticisms of these methods.Abbreviations DTT dithiothreitol - EDTA ethylene diaminetetraacetic acid - GP B-glycerophosphate - PCMBS p-chloromercuribenzene sulphonic acid - PMSF phenylmethylsulphonyl fluoride     

Isozyme analysis of progeny derived from (Allium fistulosum ×Allium cepa) ×Allium cepa

Summary Relatively large quantities of seed were obtained from the interspecific backcross (A. fistulosum xA. cepa) ×A. cepa allowing, for the first time, an extensive study of the heritable traits exhibited by backcross progeny. Two backcross populations, BC1034 and BC1040, distinguished by differentA. fistulosum parents, were characterized for the isozyme markersIdh-1, Adh-1, andPgi-1. Statistical methods are described to calculate cell probabilities for a mixed population of F₂ and BC₁ progeny, using an estimate of the fraction of F₂ progeny in the population derived from the isozyme data. Cell probability distributions were calculated for a mixed population with independent pairs of loci and a mixed population with nonindependent pairs of loci. The isozyme lociIdh-1 andPgi-1 appear to be linked, with a map distance estimated at 33 centimorgans (cM) in BC1034 and 42 cM in BC1040. The probability distribution model for linked loci did not account for all of the distorted segregation ratios inIdh-1 ×Adh-1 orPgi-1 ×Adh-1. The cytological literature does not support linkage betweenIdh-1 ×Adh-1 orPgi-1 ×Adh-1. The distorted segregation ratios for these pairs of loci are likely the result of genetic incompatibilities between the two species.Journal Article No. 1578, Agricultural Experiment Station, New Mexico State University, Las Cruces, NM, USA     

On the constancy of the evolutionary rate of cistrons

Summary The variations of evolutionary rates in hemoglobins and cytochrome c among various lines of vertebrates are analysed by estimating the variance. The observed variances appear to be larger than expected purely by chance.If the amino acid substitutions in evolution are the result of random fixation of selectively neutral or nearly neutral mutations, the evolutionary rate of cistrons can be represented by the integral of the product of mutation rate and fixation probability in terms of selective values around the neutral point. This integral is called the effective neutral mutation rate.The influence of effective population number and generation time on the effective neutral mutation rate is discussed. It is concluded that the uniformity of the rate of amino acid substitutions over diverse lines is compatible with random fixation of neutral or very slightly deleterious mutations which have some chance of being selected against during the course of substitution. On the other hand, definitely advantageous mutations will introduce significant variation in the substitution rate among lines. Approximately 10% of the amino acid substitutions of average cistrons might be adaptive and create slight but significant variations in evolutionary rate among vertebrate lines, although the uniformity of evolutionary rate is still valid as a first approximation.Contribution No. 813 from the National Institute of Genetics, Mishima, Shizuokaken 411 Japan. Aided in part by a grant-in-aid from the Ministry of Education, Japan.     

A probabilistic approach to the construction of competing-risk life tables

"This paper aims to identify net and partial-crude probabilities in the competing-risk life table context, by using probabilistic approaches. Five types of lifelength random variables are defined to formulate these nonidentifiable probabilities. General expressions for net and partial-crude probabilities are first derived under independent risks assumptions. Two sets of explicit formulas for estimating the net and partial-crude probabilities are then derived in terms of the identifiable overall and crude probabilities by making the additional assumption of piecewise uniform distribution of the lifelength random variables. A study of the degree to which nonidentifiability can affect the net and partial-crude probabilities in a variety of situations is developed. An example from cross-sectional studies is employed to illustrate the methodology developed."     

Tissue Fixation for Immunohistochemical Detection of Proliferating Cell Nuclear Antigen with PC10 Monoclonal Antibody

PC10 is a monoclonal antibody to proliferating cell nuclear antigen, a nuclear protein associated with the cell cycle. We have evaluated the effects of tissue fixation on PC10 immunoreactivity in sections of paraffin embedded rat tissues. Immunoreactivity was well preserved in tissues after fixation with alcohol-based solutions for 3-24 hr. Fewer PC10-positive cells were detectable in samples fixed with formaldehydecontaining solutions compared with samples fixed with alcohol for the same time. Loss of PC10 immunoreactivity in formaldehyde fixed tissues was progressive, and quantifiable as early as after 3 hr fixation. Consequently, alcohol-based fixatives are strongly recommended for any immunocytochemical prospective study using PC10 antibody. In contrast, loss of PC10-immunoreactivity is always predictable, but difficult to quantitate, using formaldehyde fixed specimens. This aspect should be considered when using PC10 antibody in retrospective studies with routinely-processed archival material.     

MORTALITY OF SEA OTTERS IN PRINCE WILLIAM SOUND FOLLOWING THE EXXON VALDEZ OIL SPILL

Abstract: This paper presents an estimate of the total number of sea otters that died as a direct consequence of the oil spill that occurred when the T/V Exxon Valdez grounded in Prince William Sound, Alaska on 24 March 1989. We compared sea otter counts conducted from small boats throughout the Sound during the summers of 1984 and 1985 to counts made after the spill during the summer of 1989. We used ratio estimators, corrected for sighting probability, to calculate otter densities and population estimates for portions of the Sound affected by the oil spill. We estimated the otter population in the portion of Prince William Sound affected by the oil was 6,546 at the time of the spill and that the post-spill population in the summer of 1989 was 3,898, yielding a loss estimate of approximately 2,650. Bootstrapping techniques were used to approximate confidence limits on the loss estimate of about 500–5,000 otters. The wide confidence limits are a result of the complex scheme required to estimate losses and limitations of the data. Despite the uncertainty of the loss estimate it is clear that a significant fraction of the otters in the spill zone survived. We observed otters persisting in relatively clean embayments throughout the oil spill zone suggesting that the highly convoluted coastline of Prince William Sound produced refuges that allowed some sea otters in the oil spill area to survive.     

Localisation and measurement of VIP in the genitourinary system of man and animals

VIP is present in the genitourinary system of man and animals. In man the highest concentrations are found in the penis, the uterus and vagina and in the urinary bladder. VIP nerves heavily innervate the erectile tissue of the male external genitalia, the uterine smooth muscle and blood vessels, the seromucous glands of the cervix, and the lamina propria and vaginal epithelium. In the urinary bladder, VIP nerves are located beneath the transitional epithelium, in the lamina propria and in the smooth muscle. Other areas well innervated by VIP nerves include the prostate, seminal vesicles and vasa deferentia. Chemical (phenol- and 6-OHDA) or surgical (hypogastric or pelvic nerve section) extrinsic denervation fail to deplete the genitourinary system of its VIP content, supporting the view that VIP-containing nerves originate from local ganglion cells. Indeed, neuronal cell bodies containing VIP are seen in the paracervical ganglia of the female genitalia, the para- or intramural bladder ganglia and scattered through the base of the cavernosum body, the neck of the bladder and the prostate. The finding of elevated levels of VIP in the local circulation after induced penile erection in man and mammals and the ability of VIP to relax the detrusor muscle of the bladder suggests that the peptide may be involved in penile erection and bladder relaxation, as does the marked VIP depletion in the penis or bladder in patients suffering from diabetic impotence or bladder instability.     

The hydrogenase-nitrogenase relationship in the blue-green algaAnabaena cylindrica

Nitrogen-fixingAnabaena cylindrica cells are found to evolve hydrogen in high quantities in the presence of CO plus C₂H₂. Studies with the inhibitors dichlorophenyldimethylurea (DCMU), disalicylidenepropanediamine (DSPD), dibromothymoquinone (DBMIB), undecylbenzimidazole (UDB) and chloro-carbonyl-cyanide-phenylhydrazone (CCCP) and also withAnabaena grown on nitrate- and ammonia-nitrogen show that the H₂-formation is due to the ATP-dependent H₃O⁺-reduction catalysed by nitrogenase. In control experiments CO plus C₂H₂ inhibited the activities of a cell-free hydrogenase fromClostridium pasteurianum. It is concluded that Anabaena has a hydrogenase whose natural function is to recycle the H₂ lost by the action of nitrogenase.Abbreviations Cl-CCP m-chloro-carbonyl-cyanide-phenylhydrazone - DSPD disalicylidenepropanediamine(1–3) - DBMIB dibromothymoquinone - DCMU N-(3,4-dichlorophenyl) NN-dimethyl-urea - UDB 2-undecyl-benzimidazole     

Soil beidellite and its relation to problems of potassium fertility and poor response to potassium fertilizers

Summary X-ray diffraction studies were made on soils with and without potassium fertility problems. All soils with clay fractions containing dominant beidellite or vermiculite showed potassium deficiency and lack of response to potassium fertilizer applications. All of the soils containing dominant montmorillonite or other clay minerals contained adequate potassium; on none of these, poor potassium response was reported. Special management practices are needed on the beidellitic and vermiculitic soils to increase potassium and ammonium fertilizer efficiency. Dominance of beidellite in the clay fraction should be reflected in soil classification. Establishment of a ‘beidellite’ family differentiating criterion in the Soil Taxonomy is proposed for this purpose.