Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa

The outer carbohydrate layer, or O antigen, of Pseudomonas aeruginosa varies markedly in different isolates of these bacteria, and at least 20 distinct O-antigen serotypes have been described. Previous studies have indicated that the major enzymes responsible for O-antigen synthesis are encoded in a cluster of genes that occupy a common genetic locus. We used targeted yeast recombinational cloning to isolate this locus from the 20 internationally recognized serotype strains. DNA sequencing of these isolated segments revealed that at least 11 highly divergent gene clusters occupy this region. Homology searches of the encoded protein products indicated that these gene clusters are likely to direct O-antigen biosynthesis. The O15 serotype strains lack functional gene clusters in the region analyzed, suggesting that O-antigen biosynthesis genes for this serotype are harbored in a different portion of the genome. The overall pattern underscores the plasticity of the P. aeruginosa genome, in which a specific site in a well-conserved genomic region can be occupied by any of numerous islands of functionally related DNA with diverse sequences.     

Genetic variation at KIT locus may predispose to melanoma

As loss of KIT frequently occurs in melanoma progression, we hypothesized that KIT is implicated in predisposition to melanoma (MM). Thus, we sequenced the KIT coding region in 112 familial MM cases and 143 matched controls and genotyped tag single‐nucleotide polymorphisms (SNPs) in two cohorts of melanoma patients and matched controls. Five rare KIT substitutions, all predicted possibly or probably deleterious, were identified in five patients, but none in controls [RR = 2.26 (1.26–2.26)]. Expressed in melanocyte lines, three substitutions inhibited KIT signaling. Comparison with exomes database (7020 alleles) confirmed a significant excess of rare deleterious KIT substitutions in patients. Additionally, a common SNP, rs2237028, was associated with MM risk, and 6 KIT variants were associated with nevus count. Our data strongly suggest that rare KIT substitutions predispose to melanoma and that common variants at KIT locus may also impact nevus count and melanoma risk.     

Genetic variation in the porcine myogenin gene locus

The myogenin (MYOG) gene fulfills a key function in muscle differentiation by controlling the onset of myoblast fusion and the establishment of myofibers. In meat-producing animals like pigs and cattle, myofiber numbers have been related to growth capacity. We have characterized the porcine MYOG gene to detect genetic variation at this locus and to relate it to growth characteristics. MYOG gene fragments were isolated by PCR on genomic DNA and by screening a genomic library with a mixture of the four human MyoD cDNA fragments. Both the exons and promoter region were very similar to the human and mouse genes. Southern blot analysis of 105 unrelated pigs revealed three polymorphic MspI sites, located in the promoter region, the second intron, and at the 3′ side of the gene. PCR-RFLP tests detecting four MYOG alleles were developed. PCR analysis of a panel of pig–rodent somatic cell hybrids confirmed the genetic localization of MYOG on pig Chromosome (Chr) 9. The PCR-RFLP tests and microsatellite markers on Chr 9 offer the possibility to genotype large numbers of pigs for studies of genetic linkage to meat deposition and growth characteristics. Received 13 October 1996 / Accepted: 16 March 1992     

Genetic variation at the mitochondrial DNA 9-bp repeat locus in the Sakha of Siberia

Genetic variation at the mitochondrial DNA 9-bp repeat locus was assayed in 779 Sakha from Siberia. Fourteen deletion (1.8%), nine triplication (1.2%), and two 4-repeat alleles (0.26%) were identified. Several of these alleles were also detected as heteroplasmies. Among the four heteroplasmic individuals identified (0.51%), three different combinations of repeat alleles were present: 1/2, 2/3, and 2/3/4 copies. Hypervariable region I (HVRI) sequencing revealed that three different sets of haplogroups were associated with the three most frequent 9-bp polymorphisms: (1) haplo-groups B, T, and W for deletions; (2) haplogroups C, D, and K for triplications; and (3) haplogroups C, D, and T for heteroplasmies. Both of the two 4-repeat alleles were associated with haplogroup D. We detected more types of 9-bp polymorphisms and more genetic variation within classes of polymorphism than previously reported for any single population. We also present the largest and most geographically diverse sampling of the Sakha population to date. No neighboring populations have been reported to carry a non-haplogroup B deletion, triplication, or heteroplasmy, suggesting that shared ancestry or admixture or both are unlikely explanations for the presence of these polymorphisms in the Sakha. The identification of high levels of variation may be a function of the large sample size and the in-depth analysis of all derived polymorphisms. Further study of the Sakha is warranted to determine whether the level of variation is unexpectedly high, especially in light of the presence of different heteroplasmies, which suggests multiple recent events.     

Rapid morphological oscillation of mitochondrion-rich cell in estuarine mudskipper following salinity changes

Morphological changes in the chloride cells or mitochondrion-rich (MR) cells in the skin under the pectoral fin of the estuarine mudskipper (Periophthalmus modestus) were examined in relation to intertidal salinity oscillation in river mouth. MR cells were distinguished between those in contact with the water (cells labeled with both mitochondrial probe DASPEI and Concanavalin-A, an apical surface marker of MR cells) and those that are not (DASPEI-positive only). After transfer of the fish from seawater to freshwater, no difference in the total MR cell density was observed, but the subpopulation of MR cells that are Concanavalin-A-positive decreased dramatically within 30 min. After 6 hr in freshwater, the fish were returned to seawater; the number of Con-A-positive MR cells increased to the initial levels rapidly. Thus, in seawater, mudskippers seem to open the apical crypts of the MR cells to secrete salt; in freshwater, they close the crypt of the MR cells tentatively, and tolerate hypotonicity until the rising tide. This unique response of chloride cells may also be seen in gills of other estuarine species.     

Genetic variation at the omp2 porin locus of the brucellae: species-specific markers

The omp2 locus of Brucella abortus is composed of two closely related genes (omp2a and omp2b) that encode, and potentially both express, homologous porin proteins. Genetic variation at this locus is revealed in the form of restriction-fragment-length polymorphisms which can be used to distinguish the type strains of all six Brucella species. Five of the six species contain single copies of omp2a and omp2b, whereas Brucella ovis appears to have two copies of the omp2a gene. The implications of these results with regard to the physiological functions of the omp2a and the omp2b gene products, phylogeny of the genus, and species-specific adaptation are discussed.     

Genetic variation in sexual and clonal lineages of a freshwater snail

Sexual reproduction within natural populations of most plants and animals continues to remain an enigma in evolutionary biology. That the enigma persists is not for lack of testable hypotheses but rather because of the lack of suitable study systems in which sexual and asexual females coexist. Here we review our studies on one such organism, the freshwater snail Potamopyrgus antipodarum (Gray). We also present new data that bear on hypotheses for the maintenance of sex and its relationship to clonal diversity. We have found that sexual populations of the snail are composed of diploid females and males, while clonal populations are composed of a high diversity of triploid apomictic females. Sexual and asexual individuals coexist in stable frequencies in many ‘mixed’ populations; genetic data indicate that clones from these mixed populations originated from the local population of sexual individuals without interspecific hybridization. Field data show that clonal and sexual snails have completely overlapping life histories, but individual clonal genotypes are less variable than individuals from the sympatric sexual population. Field data also show segregation of clones among depth‐specific habitat zones within a lake, but clonal diversity remains high even within habitats. A new laboratory experiment revealed extensive clonal variation in reproductive rate, a result which suggests that clonal diversity would be low in nature without some form of frequency‐dependent selection. New results from a long‐term field study of a natural, asexual population reveal that clonal diversity remained nearly constant over a 10‐year period. Nonetheless, clonal turnover occurs, and it occurs in a manner that is consistent with parasite‐mediated, frequency‐dependent selection. Reciprocal cross‐infection experiments have further shown that parasites are more infective to sympatric host snails than to allopatric snails, and that they are also more infective to common clones than rare clones within asexual host populations. Hence we suggest that sexual reproduction in these snails may be maintained, at least in part, by locally adapted parasites. Parasite‐mediated selection possibly also contributes to the maintenance of local clonal diversity within habitats, while clonal selection may be responsible for the distribution of clones among habitats. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society 2003, 79 , 165–181.     

Conjugal transfer at natural population densities in a microcosm simulating an estuarine environment

Abstract Estuarine microcosms were used to follow conjugal transfer of a broad host range IncP1 plasmid from a Pseudomonas putida donor to indigenous bacteria. Donor cells were added at a concentration similar to the natural abundance of bacteria in the water column (10⁶ cells ml⁻¹). Transfer was not detected in any of the test microcosms (calculated limit of detection of 10⁻⁷ and 10⁻⁴ transconjugants donor⁻¹ in water column and sediment, respectively), with the exception of transfer to an isogenic recipient (added at 10⁵ cells ml⁻¹) in sediments of controls that had been inoculated with both donors and recipients. The same plasmid was transferred with high efficiencies (10⁻¹ to 10⁻³) to a variety of recipients in filter and broth matings. These results suggest that if conjugal gene transfer occurred, it was at efficiencies that were not detectable in estuarine microcosms simulating natural population densities.     

Hemolymph ammonia, urea and uric acid levels and nitrogenous excretion of Marsupenaeus japonicus at different salinity levels

Arginase specific activity, hemolymph ammonia, urea and uric acid levels and nitrogenous excretion were measured in Kuruma shrimp Marsupenaeus japonicus (7.29±1.16 g) acclimated to different salinities of 18‰, 26‰, 34‰ and 42‰. Arginase activity in the gill, midgut, hepatopancreas and muscle were higher and lower for the shrimp in 42‰ and 18‰, respectively. Arginase specific activity of hemolymph was higher at 34‰. Hemolymph ammonia, urea and uric acid increased directly with salinity, and excretions of total nitrogen (total-N), organic nitrogen (organic-N) and urea-N increased directly with salinity. However, ammonia-N excretion and nitrite-N excretion were inversely related to salinity. Ammonia-N accounted for 90.9%, 75.0%, 67.9% and 38.5% of total-N, whereas urea-N accounted for 3.1%, 4.5%, 7.9% and 10.9%, and organic accounted for 4.2%, 19.8%, 23.1% and 50.4% of total-N excreted by the shrimp in 18‰, 26‰, 34‰ and 42‰, respectively. Significantly higher levels of hemolymph urea and uric acid together with an increase in arginase activity indicated that ureogenesis and uricogenesis are activated for M. japonicus in hyperosmotic conditions.     

Genetic variation among laboratory strains of the planorbid snail Biomphalaria glabrata

Isozymes of laboratory strains of Biomphalaria glabrata have been studied by starch gel electrophoresis. Methods are outlined for adaptation of this technique to the genetic study of these snails. Twenty-eight presumptive gene loci have been identified. Twelve invariant enzymes were observed. Sixteen loci displayed some polymorphism within or among the strains. These polymorphisms were generally widespread among strains from Brazil, Puerto Rico, St. Lucia, and the Dominican Republic. A high degree of intrastrain polymorphism was noted even in some presumably inbred laboratory strains. Crosses between strains were used to demonstrate the genetic basis for the patterns observed at 9 of the 16 polymorphic loci.     

Aquatic insects in an estuarine environment: densities, distribution and salinity tolerance

1. Aquatic insects were quantitatively surveyed at five sites along the tidally influenced section of a river-dominated estuary in North Wales. Site 1 was the furthest upstream and was established as a reference site as it was never inundated by salt water. Site 5 was the furthest downstream and was inundated by all incoming tides. Numerically, insects made up 32% of the estuarine invertebrate fauna. 2. Although the densities of most insect taxa decreased towards the estuary mouth, there were significant numbers present downstream for much of the year; for example, in April at site 4 (which was inundated by 81% of all high tides), a mean of 3514 chironomid larvae were recorded per m² of estuary bed. Even at site 5, which was inundated twice daily, there were 747 larvae per m². Among the larger aquatic insects, caddisfly and elmid beetle larvae, together with stonefly nymphs, were consistently taken at site 4 (e.g. maxima of forty-eight caddisfly larvae m^–2 in December and seventy elmids m^–2 in April), although their densities were lower than upstream. 3. There were seasonal shifts in the longitudinal distribution of several taxa, most notably the extension of chironomids down the estuary in April and July, and the concentration of simuliid larvae and mayfly nymphs at site 2 in July. The total freshwater benthos showed a downstream shift between September and December, which was maintained through April and into the summer. The latter was despite peak saltwater inundation (highest tides) in October, November and April. In June and July, when saltwater intrusion was lowest, the ranges of many aquatic insects had contracted to sites 1 and 2. 4. Laboratory experiments showed that virtually all individuals of nineteen species of insects collected from site 1 (freshwater) survived a 4-h immersion in 8.75‰ saltwater (25% strength seawater). Immersion in progressively more saline solutions reduced the survivorship of first the mayflies, followed by the caddisflies Glossosoma conformis and Hydropsyche instabilis. After 4 h in full strength seawater, all specimens of the stonefly Dinocras cephalotes, over half of the Perla bipunctata, and some individuals of nine species of caddisfly were alive. Four species of caddisfly (Sericostoma personatum, Odontocerum albicorne, Potamophylax cingulatus and Adicella reducta) survived a 24-h simulated tidal cycle of immersion. With the exception of P. cingulatus, a few individuals of these caddisfly species survived immersion in full-strength seawater for 24 h. For some individual species there was good agreement between their observed longitudinal distribution in the estuary and laboratory-measured salinity tolerance; however, there was no significant correlation, overall, for the fauna.     

Genetic variation at pig plasma protein locus PLP1 and its assignment to chromosome 5

A new genetic polymorphism of an unidentified plasma protein (PLP1) in pigs was described by using a method of two-dimensional gel electrophoresis and protein staining. Two codominant alleles, with frequencies of 0.83 and 0.17, were found in the Swedish Yorkshire breed. The PLP1 marker was typed in a three-generation pedigree and tested for linkage against a set of 128 markers. The PLP1 locus showed significant LOD score values with three different microsatellite markers (S0092, DAGK and S005), previously assigned to chromosome 5.     

Genetic variation at the Pgi locus in the mosquito fish Gambusia affinis (Poecilidae) and a possible effect on susceptibility to an insecticide

Although some studies have been completed on genetic variation in relation to tolerance to heavy metals, none have considered pesticide pollution. This study examines the relationship between genotypes at the glucose phosphate isomerase ( Pgi ) locus in Gambusia and susceptibility to the organophosphate insecticide chlorpyrifos. Laboratory toxicity tests show significant differences in genotype frequencies between susceptible and tolerant groups offish from one site but not at others. A field survey examined genotype frequencies and levels of pesticide in the fish at seven sites. No chlorpyrifos was found at any of the sites, but a number of organochlorines were recorded. Significant correlations were found between three organochlorines (DDT/DDD, DDE and lindane) and frequences of particular genotypes. There were also significant differences in tolerance between populations and between size classes. These results are discussed in relation to previous work with heavy metals.     

Allelic variation at the frizzled locus of Drosophila

The epidermis of Drosophila has a tissue polarity that is manifested by a parallel array of polarized structures (primarily hairs and bristles). The production of normal tissue polarity requires the function of the frizzled (fz) locus. We have isolated a large number of alleles at this locus and have phenotypically characterized more than 25 of them. We have found extensive allelic variation that a previous study failed to detect. Most of the alleles fall into a hypomorphic to amorphic series. Two alleles, however, have unusual properties. These alleles, which in general are moderately strong alleles, fail to produce a rough eye phenotype that is characteristic of all the other moderate or strong fz alleles. Thus, these two alleles are tissue specific in effect. Furthermore, these two alleles also have a neomorphic or antimorphic effect on hair polarity in one region of the wing.     

Spatial heterogeneity in size and parasitism: How it arises in an estuarine snail population

Populations of Ilyanassa obsoleta, a snail abundant in estuaries along the Atlantic coast of North America, exhibit much unobvious spatial heterogeneity. Lifetime dispersal of snails stands to be great, as they live for decades and can make daily moves of tens of meters. They could distribute uniformly, but in many populations there are characteristic spatial distributions of differently sized and trematode-infected snails. This is the case where this work was done in the Savages Ditch habitat of Rehoboth Bay, Delaware, U.S.A.. The study was designed to explain how the spatial heterogeneity in that habitat arises as a consequence of snail movements. Individually marked snails were tested for trematode infections and released from five well-separated positions. Snails released from each position were in three groups: (1) natives, collected from the position area, and (2) large and (3) small “outlanders”, collected from a site in the habitat that was separated from all release positions, had enhanced tidal currents, and where both size classes were available. Locations of found, released snails were noted for up to four years. Depending on collection site, many native snails were parasitized. In any case, they always tended to disperse in the vicinity where initially collected. Large outlanders (∼ 21% infected) dispersed variably, moving back toward their source area from certain release positions, but not from others. Small outlanders (∼ 4% infected), almost regardless of where released, tended to disperse back toward their source area. Dispersals of these snail groups from the five release positions explains much about how the pattern of spatial heterogeneity seen in the habitat arises.     

Intestinal transport following transfer to increased salinity in an anadromous fish (Oncorhynchus mykiss)

The ability to transition from freshwater to seawater environments is an intrinsic requirement of the life history of some fish species, including the anadromous rainbow trout (Oncorhynchus mykiss). The differences between hyper- and hypoosmoregulation are developed quickly (in hours to days), and at all scales, from gene expression to organ function. In this study, intestinal ion and water transport was examined in O. mykiss following acute transfer from freshwater (FW) to 70% seawater (SW). Plasma [Mg2+] increased at 24h post-transfer but recovered by 72 h. In the intestinal fluids, total CO? was found to increase with SW exposure/acclimation, while [Na+] decreased after 24h of SW exposure. Overall, in vitro experiments demonstrated the importance of base secretion to epithelial water uptake, and suggested that the primary physiological adjustments occurred 24-72 h after acute SW transfer. The mRNA expression of ion transporters important for intestinal osmoregulation and maintenance of acid-base balance was also investigated. A Na+/H+ exchanger (NHE2) and anion exchanger (SLC26a6) were hypothesized to be involved in the transport of acid-base equivalents, Na+, and Cl?, but were not uniformly expressed across tissue samples, and expression, where present, did not change following salinity transfer. NHE1, however, was expressed in all examined tissues (gill, kidney, anterior intestine, and pyloric cecae), but exhibited no changes in expression following acute salinity transfer.     

Genetic variation at the alcohol dehydrogenase locus in Drosophila melanogaster in relation to environmental variation: Ethanol levels in breeding sites and allozyme frequencies

Summary Ethanol levels in Drosophila breeding sites in seepages of unfortified wine inside wineries have been found to be similar to those in many decaying fruits and vegetables. Fortified wine seepages inside wineries have ethanol levels on average three times as high as other breeding sites. However there was no evidence that this variation in ethanol levels was associated with differences in Adh ^F frequencies in D. melanogaster at sites either within wineries or outside wineries. D. simulans was at lower frequencies at sites inside wineries compared to sites outside although this difference may not be related to ethanol levels. It is concluded that adaptation to natural levels of environmental ethanol by D. melanogaster does not necessarily modify Adh frequencies.