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.

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.

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.

Downeast anemia (dea), a new mouse model of severe nonspherocytic hemolytic anemia caused by hexokinase (HK(1)) deficiency.

A new spontaneous mutation in the A/J inbred mouse strain, downeast anemia (dea), causes severe hemolytic anemia with extensive tissue iron deposition and marked reticulocytosis. The anemia is present at birth and persists throughout life. The defect is inherited as an autosomal recessive and is transferable through bone marrow stem cells. The red cell morphology is consistent with a nonspherocytic hemolytic anemia, suggestive of a red cell enzymopathy. In linkage analysis, dea is nonrecombinant with the hexokinase-1 gene (Hk1) on mouse Chromosome 10. Expression of Hk1 is markedly decreased in dea erythroid tissues, and the transcript produced is larger than normal. Hexokinase enzyme activity is significantly decreased in dea tissues, including red cells, spleen, and kidney. Southern blot analyses revealed approximately 5.5 kb of additional sequence in the 5' portion of the dea Hk1 gene, which was identified by direct sequencing as an early transposon (ETn) insertion in intron 4. ETn insertions disrupt genes in several mouse models by a variety of mechanisms, including aberrant splicing of ETn sequences into the mRNA. We conclude that the primary gene defect in the dea mutation is in Hk1 and that dea is a model of generalized hexokinase deficiency, the first such model identified to date.

Juvenile bare: a new hair loss mutation on chromosome 7 of the mouse.

We describe a new juvenile hair loss mutant in the mouse in which the hair follicle follows irregular pathways to the surface and generally becomes dystrophic when the mouse is about 23 days of age. Skin from mutant mice older than 1 month of age is histologically normal, although adult mutant mice show a slightly more sparse coat than normal. Grafts of mutant littermates skin to SCID hosts indicate that the condition is probably a systemic response rather than one of the follicle per se. The hair loss is caused by a recessive mutation, which we have named juvenile bare (jb), located on proximal chromosome 7.

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.

Patchy fur, a mouse coat mutation associated with X-Y nondisjunction, maps to the pseudoautosomal boundary region.

Patchy fur is a semidominant X-linked mutation in the mouse, resulting in a sparse coat. The Paf mutation also alters the normal segregation of the X and the Y chromosomes during male meiosis by causing nondisjunction at anaphase I. Analysis of 1139 female meioses from an intersubspecific backcross using 15 PCR-based markers localizes Paf to an approximately 0.2-cM interval that includes the pseudoautosomal boundary. The meiotic nondisjunction phenotype may result from a chromosomal rearrangement that includes pseudoautosomal sequences and affects XY pairing.

Mapping the mouse dactylaplasia mutation, Dac, and a gene that controls its expression, mdac.

Dactylaplasia is an inherited mouse limb malformation whose manifestation is clearly dependent on the interaction of two genes and thus represents an excellent model system for studying such gene interactions in vivo. The Dac mutation is inherited as a semidominant trait and may be a model for some forms of human ectrodactyly. Heterozygotes show absence of digits on each foot; the long bones are normal. On the SM/Ckc background on which the mutation occurred, Dac homozygotes die around birth. We mapped Dac to the distal end of Chr 19 by backcross segregation analysis A closely linked marker was then used to distinguish +/+, Dac/+, and Dac/Dac genotypes of embryos and adults. When intercrossed with the NZB/BINJ strain, Dac homozygotes were shown to be viable and fertile, but had a more severe limb malformation (only a single remaining digit) than heterozygotes. Expression of the abnormal limb phenotypes of Dac/+ and Dac/Dac mice also depends on homozygosity for a recessive allele of another unlinked gene, mdac, that is polymorphic among inbred mouse strains. We mapped mdac to the middle of Chr 13 by segregation analysis of both recombinant inbred strains and backcross progeny.

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.

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.

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.

Rostral cerebellar malformation, (rcm): a new recessive mutation on chromosome 3 of the mouse.

A new recessive mutation in the mouse that causes a disorderly arrangement of Purkinje and granule cells in the rostral portion of the cerebellum is described. The mutation, called rostral cerebellar malformation, rcm, has been located on chromosome (Chr) 3 between the alcohol dehydrogenase-3 (Adh-3) complex and varitint waddler-J (VaJ).

Hairpatches, a single gene mutation characterized by progressive renal disease and alopecia in the mouse. A potential model for a newly described heritable human disorder.

A new murine mutation, hairpatches (Hpt), is on chromosome 4, 18.1 recombination units distal to brown near the interferon alpha and beta chain structural gene complex. On the inbred HPT/Le strain background, Hpt is semi-dominant, and Hpt/Hpt mice die in utero by 6 to 8 days of gestation. Such death in utero is associated with abnormalities of embryonic ectodermal derivatives. However on the (C57BL/6J x C3HeB/FeJ-a/a) segregating hybrid background, Hpt is a fully dominant mutation. HPT/Le Hpt/+ mice can be recognized by 3 to 4 days of age by patches of lightly pigmented skin. These mice show reduced numbers of hair follicles, abnormalities in hair follicle structure, and patchy absence of hair throughout life. By 2 weeks of age, abnormal hair follicle development is accompanied by thickening of the epidermis, reduction in levels of subcutaneous fat, and dermal inflammation. Progressive glomerulosclerosis, resulting in chronic kidney failure, is accompanied by increases in glomerular mesangial matrix, deposition of immune complexes, and glomerular enlargement. Scanning electron microscopic studies revealed abnormalities of podocytes including disorganization, swelling, and fusion of the foot processes. Increase in serum blood urea nitrogen levels accompanies conspicuous renal histopathologic changes. Cardiovascular changes in Hpt/+ mice are evidenced by hypertrophy of the left heart ventricle. Increased systolic blood pressure in these animals was found by 3 months of age. Anemia occurs in Hpt/+ mice by 40 weeks. The Hpt/+ mutation provides a valuable new animal model for chronic kidney disease accompanied by skin abnormalities and ventricular hypertrophy. The pathologic changes caused by this mutation are similar to those reported in affected family members with a newly described autosomal dominant human disease.

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.

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.

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.

New mutation causing sterility in the mouse.

A new murine mutation, skeletal fusions with sterility, sks, has been identified. This mutation causes arrest during the pachytene stage of virtually all spermatogenic cells. Defects in chromosome pairing and appearance of the synaptonemal complex during meiosis in the male are apparent, but defective pairing is probably not the cause of sterility. Affected females are functionally infertile. Oocytes are capable of undergoing meiotic maturation in vitro but cannot be fertilized in vitro. Affected individuals of both sexes are characterized by fusions of vertebrae and of ribs. The sks gene has been mapped to Chromosome 4, 16.6 cM distal to the brown locus.

Spasmodic, a mutation on chromosome 11 in the mouse.

A new recessive mutation, spasmodic (spd), producing behavior that mimics that of the neurological mutation spastic (spa) with rapid tremors, stiff posture, and difficulty in righting, arose spontaneously in strain A/HeJ at the Jackson Laboratory in 1979. It is not an allele of spa and linkage tests show that this mutation is located close to vestigial tail (vt) near the center of chromosome 11. Additional genetic tests show that it is not an allele of trembler (Tr), shaker-2 (sh-2), nor vibrator (vb), all neurological mutations located in the same region of chromosome 11. No differences were observed in the levels of the major CNS and PNS myelin proteins or lipids of spd/spd mice versus littermate controls, suggesting that, unlike several closely linked mutations, the spd mutation does not affect myelination. Pharmacological studies reported here show that aminooxyacetic acid improves the behavioral abnormalities of affected spd/spd mice in the same way it improves the behavior of affected spa/spa mice. However, unlike the spa/spa mice, there are no changes in the postsynaptic receptors for glycine, GABA, or benzodiazepines in spd/spd mice.

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.