An empirical assessment of the focal species hypothesis.

Biodiversity surrogates and indicators are commonly used in conservation management. The focal species approach (FSA) is one method for identifying biodiversity surrogates, and it is underpinned by the hypothesis that management aimed at a particular focal species will confer protection on co-occurring species. This concept has been the subject of much debate, in part because the validity of the FSA has not been subject to detailed empirical assessment of the extent to which a given focal species actually co-occurs with other species in an assemblage. To address this knowledge gap, we used large-scale, long-term data sets of temperate woodland birds to select focal species associated with threatening processes such as habitat isolation and loss of key vegetation attributes. We quantified co-occurrence patterns among focal species, species in the wider bird assemblage, and species of conservation concern. Some, but not all, focal species were associated with high levels of species richness. One of our selected focal species was negatively associated with the occurrence of other species (i.e., it was an antisurrogate)-a previously undescribed property of nominated focal species. Furthermore, combinations of focal species were not associated with substantially elevated levels of bird species richness, relative to levels associated with individual species. Our results suggest that although there is some merit to the underpinning concept of the FSA, there is also a need to ensure that actions are sufficiently flexible because management tightly focused on a given focal species may not benefit some other species, including species of conservation concern, such of which might not occur in species-rich assemblages.

Susceptibility to spontaneous pneumonitis in an inbred strain of beige and satin mice.

Among mice of strain SB/Le, homozygous for the mutant genes beige (bg), satin (sa), and white-bellied agouti (A(w)), 70% developed progressive pneumonitis by 6 months of age. Among backcross offspring from an outcross to C57BL/6J-A(w-J), 49% of homozygous beige and 11% of nonbeige genotypes developed pneumonitis by 6 months of age. The evidence indicates that a specific action of the beige gene increases susceptibility to progressive pneumonitis. Lymphadenopathy, including reticulum cell neoplasms and atypical lymphoproliferative lesions, was observed in high incidence in sa+/sa bg males, suggesting a closer association with satin than with beige. Beige mice show giant lysosomal granules in the leukocytes and pigment dilution closely analogous to the Chediak-Higashi syndrome in man and similar disorders in mink and cattle. Strain SB/Le provides a convenient model in a laboratory animal for study of the increased susceptibility to infection analogous to that of the Chediak-Higashi syndrome.

Maximization of signal derived from cDNA microarrays.

Microarray technology is a powerful tool for generating expression data on a large number of genes simultaneously. However, as for any assay, it must be reproducible to give confidence in the results. Using a classical statistical method--the factorial design of experiments--we have assessed the effects of different experimental factors in our system. Significant effects on signal were seen when the standard components were substituted with a different enzyme, fluorescent label, or RNA purification method. This has led to the implementation of an improved procedure that maximizes signal without affecting the variability of the system, thus increasing the signal-to-noise ratio. In addition, we were able to quantify the variability between microarrays and replicates within microarrays.

Multifactorial screening design and analysis of SELDI-TOF ProteinChip array optimization experiments.

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry is a powerful tool for rapidly generating protein expression data (peptide and protein profiles) from a large number of samples. However, as with any technology, it must be optimized and reproducible for one to have confidence in the results. Using a classical statistical method called the fractional factorial design of experiments, we assessed the effects of 11 different experimental factors. We also developed several metrics that reflect trace quality and reproducibility. These were used to measure the effect of each individual factor, and the interactions between factors, to determine optimal factor settings and thus ultimately produce the best possible traces. Significant improvements to output traces were seen by simultaneously altering several parameters, either in the sample preparation procedure or during the matrix preparation and application procedure. This has led to the implementation of an improved method that gives a better quality, reproducible, and robust output.

The susceptibility of roots to infection by an arbuscular mycorrhizal fungus in relation to age and phosphorus supply.

An apparatus in which plant roots may be challenged uniformly with inoculum of arbuscular mycorrhizal fungi is described. Seedlings of leek (Allium porrum L.) or clover (Trifolium repens L.) were first grown non-symbiotically in the apparatus for 21 d at three rates of phosphorus (P) addition to soil (150 (P1), 450 (P3) and 750 (P5) mg P kg-1 soil). The positions of individual root tips were recorded, and the root systems then challenged with inoculum of Glomus mosseae (Nicol & Gerd.) Gerdemann & Trappe. Roots were excised 14 d later, and the probability of occurrence of internal infection in successive 3 mm (clover) or 5 mm (leek) sections of root was estimated in first-order laterals (clover) or main axes (leek) from the proportion of sections at each location of replicate roots that bore internal fungal structures. Only in the region of a root proximal to the position of the root tips at inoculation could data be used to investigate change of probability of infection with cell age. Here, there were sharp declines in probability of infection with proximal distance, in both hosts and in all P treatments. The decline of probability was greater in clover: when expressed in terms of cell age at the time of challenge, there was no infection at PI in cells ≤ 10 d old in leek and none in cells ≤ 7 d old in clover. Models of the form loge , [p1 /(1 -p1 )] =α+ß× distance, where p1 is the estimated probability of infection and a and α are constants, were fitted to these data. The odds on infection are [p1 /(1 -p1 )]. For leek, ß was unaltered by P addition (P3 and P5 curves were parallel to P1) but from a it could be calculated that on average the odds on successful infection at any particular distance were reduced by 37% and 70% by P3 and P5 rates of P addition respectively. In clover the curves for the three P treatments were not parallel. Addition of P appeared to reduce the odds on infection of clover much more than those of leek. We conclude that the simplest explanation for the patterns of infection in leek is that P addition increased the time taken for soil inoculum of G. mosseae to infect roots: the mechanism in clover might be more complex.

Neuronal ceroid lipofuscinosis (nclf), a new disorder of the mouse linked to chromosome 9.

The neuronal ceroid lipofuscinoses (NCLs) comprise a set of at least 6 distinct human and an unknown number of animal diseases characterized by storage of proteolipids in lysosomes of many cell types. By unknown mechanisms, this accumulation leads to or is associated with severe neuronal and retinal degeneration. The genes for 3 human NCLs, infantile, late infantile, and juvenile, have been cloned. The first murine form of NCL, the motor neuron degeneration (mnd) mouse, has been described and mapped to proximal Chromosome 8. Here we describe a second genetic variant of NCL in the mouse, neuronal ceroid lipofuscinosis, nclf. These mice exhibited a phenotype that was almost exactly the same as that observed in mnd/mnd mice. Homozygous nclf mice developed progressive retinal atrophy early in life and become paralyzed at around 9 months of age. They accumulated luxol fast blue staining material in cytoplasm of neurons and many other cell types. Ultrastructurally, affected lysosomes had a "finger print pattern" with membranous material arranged in "pentalaminar" patterns. Affected mice developed severe cerebral gliosis in late stages of their disease. They also had severe Wallerian degeneration of long tracts in spinal cord and brain stem, lesions that accounted for the distinctive upper motor neuron signs displayed by both nclf/nclf and mnd/mnd mice. By crossing nclf/nclf mice with CAST/Ei mice, linkage analysis of nclf with respect to SSLP markers was performed, showing that nclf is located on Chromosome 9 between D9Mit164 and D9Mit165, in a region that is homologous with human Ch 15q21, where the gene for one variant of late infantile NCL, CLN6, recently has been mapped. The genes for two proteolipids known to be stored in lysosomes of animals and people with NCL were also mapped in this study and found not to map to the mnd or nclf loci nor to any mouse locus homologous to any known human NCL disease locus.

Vibrator (vb): a spinocerebellar system degeneration with autosomal recessive inheritance in mice.

Vibrator (gene symbol vb), an autosomal recessive mutation, occurred spontaneously in the DBA/2J strain of mice, was rescued by a single cross to C57BL/6J and subsequent brother X sister mating, and has been mapped near shaker-2 (sh-2) and vestigial tail (vt) on chromosome 11. The name emphasizes the unusually rapid (18-20 Hz) postural action tremor expressed in juvenile homozygotes. Selected neurons in spinal cord, and later in brainstem and cerebellum, show progressive degenerative changes featuring dilated cisternae of endoplasmic reticulum in cell bodies, dendrites and axons, with eventual severe intracellular vacuolation and some cell death.

Hydrocephalus with hop gait (hyh): a new mutation on chromosome 7 in the mouse.

Hydrocephalus with hop gait (hyh) is a new lethal recessive mouse mutation that arose in the C57BL/10J strain at The Jackson Laboratory. It has been mapped to the proximal end of Chromosome 7 close to the Gpi-1 locus. This homozygous mutant is characterized clinically by a domed head and a hopping gait observable at 2 weeks of age and death between 4 and 10 weeks of age. The affected mice have dilated lateral ventricles and a large third ventricular cyst, patent through narrowed rostral cerebral aqueduct, cystic caudal aqueduct and no communication of the aqueduct with the fourth ventricle. The cerebellum has a mild cortical malformation.

An explanation for the apparent losses of metals in a long-term field experiment with sewage sludge.

Large losses of metals applied to soil in metal-contaminated sewage sludge have been reported. The potential pathways of loss, including lateral movement from treated plot areas, have not been examined. A field experiment, which started in 1942, was investigated to determine the amount of lateral movement of zinc, cadmium, copper, nickel, chromium and lead due to conventional cultivation processes. A two-dimensional 'dispersion' model (i.e. movement of soil due to cultivation) fitted well to the observed movement of metals, and gave coefficients for movement of 0.24 and 0.13 m(2) per tillage operation in dimensions parallel or perpendicular to the direction of ploughing, respectively. For testing purposes, the model was used to predict the concentrations of metals in specific areas of a plot or average concentrations for whole plots at different points in time. The concentrations measured in soil samples agreed well with the predicted values. Finally, the model was also used to estimate the proportion of the metal load applied between 1942 and 1961 that remained in the 0-27 cm cultivated layer in 1985. About 80% was accounted for: this large recovery is of great relevance to the long-term disposal of metal-contaminated wastes to land. Detailed analyses of soil profile samples showed that approximately 1% of the metals applied had moved 3.5 cm below the plough layer or less, but there was no evidence of accumulation of metals in deeper horizons down to 46 cm. These results are discussed in relation to the other potential losses of metals in the experiment.

Assignment of LH XVI to chromosome 3 in the mouse.

We have presented evidence that the mouse loci comprising linkage group XVI are located on chromosome 3 distal to the my locus such that the order of genes is: Car-1, Car-2--my--ma--soc--Amy-1, Amy-2--Va. The genetic length for chr 3 is now estimated to be 82 recombination units. The genetic location of the breakpoint in the reciprocal translocation T(2:3)24H is placed between the Amy-1 and Va loci. A new simplified method for determining the Amy-1 and Amy-2 genotype of mice is presented.

Gene order in linkage group XVI of the house mouse.

Data have been presented to show the linkages and most probable order of eight loci in LG XVI. The map of LG XVI is as follows: spa-3-ma-2-ft-1-soc-6-op-3-(Amy-1, Amy-2)-20-Va with the position of de known to be on the ma side of Va. Data from a 3-point cross with ma, Va, and the Robertsonian translocation, Rb5, showed no linkage with the centromere of Chr 12 with either end, ma or Va. We conclude that LG XVI is not carried on Chr 12, and preliminary data indicates it is most likely carried on Chr 3.

X-linked polydactyly (Xpl), a new mutation in the mouse.

A new X-linked dominant mutation in the mouse exhibiting preaxial polydactyly and tibial hemimelia is described and named X-linked polydactyly (Xpl). Linkage tests show that Xpl is located on the distal end of the X chromosome with the order Ta--13--jp--15--Xpl.

Spontaneous renal artery thrombosis associated with altered mental status.

Renal artery thrombosis is much less common than renal artery occlusion by emboli. When it does occur, it is usually a result of blunt abdominal trauma or a thrombus superimposed on an atherosclerotic plaque. Numerous other factors have been associated with renal artery thrombosis. Spontaneous renal artery thrombosis is a rare phenomenon in itself. This case represents spontaneous renal artery thrombosis associated with an altered mental status. Clinical features with suspected etiologies are reviewed. Recommendations for future evaluations are given.

Location of plucked (pk) on chromosome 18 of the mouse.

Plucked (pk), a recessive hair-type mutation in the mouse, has been assigned to chromosome 18 at a location between Tw and syfp. The Robertsonian translocation Rb(7.18)9Lub was found to suppress crossing over in the proximal half of this chromosome.

Analysis of covariance and standardization as instances of prediction.

In this paper, prediction provides the basis for unifying the procedures of covariances adjustment and standardization. Analysis of covariance is a method of forming predictions from a linear model; it is used when qualitative effects are to be studied and the effects of continuous variables are to be adjusted for. An essential feature is the division into effects of interest and effects for which adjustment is required. Covariates may also be qualitative: as such, they are used implicitly in experimental designs with blocks, where treatment effects are adjusted for the effect of blocks. The technique of standardization is well-known in epidemiology and demography as a method of adjusting explicitly for qualitative effects. The same division of effects applies when an analysis that uses generalized linear models is summarized. Two distinct types of prediction, which give identical results in classical linear models, are available: prediction may be conditional on a fixed value of a covariate, or marginal on a distribution of values such as the distribution in the set of data being analysed. Prediction methods are illustrated by the analysis of a table of proportions by use of a logit model.

Osteopetrosis, a new recessive skeletal mutation on chromosome 12 of the mouse.

Osteopetrosis (op/op) is a new mutation in the mouse that is transmitted as an autosomal recessive linked with variant waddler (Va) on chromosome 12. Compared with normal littermates, young op/op mice have excessive accumulations of bone without marrow cavities, increases in bone matrix formation and concentrations of parafollicular cells of the thyroid, and are hypophosphatemic. Osteoclasts from op/op mice are small, few in number and have an abnormal cytoplasmic distribution of the lysosomal enzyme acid phosphatase. In contrast to the three other mutations that transmit osteopetrosis in mice, the skeletal signs of the disease slowly disappear in op/op animals after bone matrix formation declines about 6 weeks after birth from 145 percent to 20 percent of that in normal siblings. The main skeletal defect in op/op mice appears to be a severe restriction in bone remodeling that is capable of slowly removing the excessive skeletal mass characteristic of the disease only after bone formation has declined to one-fifth that of normal littermates.

Patchy fur (Paf), a semidominant X-linked gene associated with a high level of X-Y nondisjunction in male mice.

Several X-linked mutations that have associated sex chromosomal nondisjunction have been identified in the mouse. We describe a new semidominant X-linked mutation called patchy fur (Paf) that produces an abnormal coat. It maps to the distal end of the murine X chromosome very near the XY pseudoautosomal region. The degree of severity in affected mice is hemizygous males greater than homozygous females greater than heterozygous females. An unusual feature of Paf is that either the mutation itself or an inseparable chromosomal abnormality causes delayed disjunction of the X and Y chromosomes at meiotic metaphase I, which in turn results in approximately 19% XO progeny and slightly less than 1% XXY progeny from Paf/Y males. The effect occurs only in male carriers and thus must extend into the proximal end of the XY pairing region.

Urogenital syndrome (us): a developmental mutation on chromosome 2 of the mouse.

Urogenital syndrome (us) is a recessive mutation in mice characterized primarily by abnormalities of the axial skeleton and urogenital organs. We established linkage of us with the centromeric end of Chromosome (Chr) 2, using the Robertsonian Chr Rb(2.8)2Lub. Analysis of progeny from crosses using the Chr 2 markers Danforth's short tail (Sd) and ulnaless (Ul) positioned us near two loci that have recently been mapped by RFLPs, nonerythroid alpha-spectrin (Spna-2) and the paired-box-containing-gene-8 (Pax-8). The position of us relative to these loci was established by analysis of progeny from interspecific backcrosses between the us strains and Mus spretus. The estimated map distances and most likely gene order are centromere-Pax-8-2.1 +/- 1.2-us-0.7 +/- 0.7-Spna-2; however, the reverse order cannot be ruled out. Our data make it unlikely that us is a mutation in either Spna-2 or Pax-8. Spna-2 is close enough to us, however, to be a useful marker for positional cloning of the us gene. The human mutation Nail-patella-syndrome (NPS1) maps to the region of human Chr 9 (9q34) that is homologous to the us region of mouse Chr 2. Phenotypic similarities between the two syndromes suggest the possibility that they are caused by mutations at homologous loci.

Association of megacolon with a new dominant spotting gene (Dom) in the mouse.

A new semidominant mutation in the mouse is described. In heterozygotes it produces white spotting and a deficiency of myenteric ganglion cells in the colon and, in homozygotes it is lethal prior to 13 days of gestation. The mutation, called dominant megacolon, symbol Dom, is located on chromosome (chr) 15, 20.6 +/- 1.6 units proximal to Ca. Hairy ears, Eh, a semidominant gene also on chr 15 is shown to have a suppressing effect on crossing over in this section of chr 15.