A microsatellite-based multilocus phylogeny of the Drosophila melanogaster species complex.

Uncovering the genealogy of closely related species remains a major challenge for phylogenetic reconstruction. It is unlikely that the phylogeny of a single gene will represent the phylogeny of a species as a whole [1], but DNA sequence data across a large number of loci can be combined in order to obtain a consensus tree [2]. Long sequences are needed, however, to minimize the effect of (infrequent) base substitutions, and sufficient individuals must be sequenced per species to account for intraspecific polymorphisms, an overwhelming task using current DNA sequencing technology. By contrast, microsatellites are easy to type [3], allowing the analysis of many loci in multiple individuals. Despite their successful use in mapping [4,5], behavioural ecology [6] and population genetics [7], their usefulness for the phylogenetic reconstruction of closely related taxa has never been demonstrated, even though microsatellites are often conserved across species [8-10]. One drawback to microsatellite use is their high mutation rate (10(-4)-10(-2)), combined with an incomplete understanding of their mutation patterns. Many microsatellites are available for Drosophila melanogaster, and they are distributed throughout the genome [11]. Most can be amplified in the D. melanogaster species complex [12,13] and have low mutation rates [14, 15]. We show that microsatellite-specific distance measurements [16] correlate with other multilocus distances, such as those obtained from DNA-DNA hybridization data. Thus microsatellites may provide an ideal tool for building multilocus phylogenies. Our phylogenetic reconstruction of the D. melanogaster complex provides strong evidence that D. sechellia arose first, followed by a split between D. simulans and D. mauritiana.

Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation.

Microsatellites are short tandemly repeated DNA sequence motifs that are highly variable in most organisms. In contrast to mammals, long microsatellites (>15 repeats) are extremely rare in the Drosophila melanogaster genome. To investigate this paucity of long microsatellites in Drosophila, we studied 19 loci with exceptionally long microsatellite alleles. Inter- and intraspecific analysis showed that long microsatellite alleles arose in D. melanogaster only very recently. This lack of old alleles with many repeats indicated that long microsatellite alleles have short persistence times. The size distribution of microsatellite mutations in mutation-accumulation lines suggests that long alleles have a mutation bias toward a reduction in the number of repeat units. This bias causes the short persistence times of long microsatellite alleles. We propose that species-specific, size-dependent mutation spectra of microsatellite alleles may provide a general mechanism to account for the observed differences in microsatellite length between species.

Prevalence of Salmonella, Campylobacter, and Escherichia coli on ostrich carcasses and the susceptibility of ostrich-origin E. coli isolates to various antibiotics.

There has been limited research on the prevalence of foodborne pathogens such as Escherichia coli O157:H7, Salmonella, and Campylobacter on ostrich carcasses. Likewise, few studies have been done in ostriches to determine the antimicrobial susceptibilities of common bacteria, like E. coli. In this study, ostrich carcasses were sampled from eight slaughterhouses in Ohio and one in Indiana. Although results demonstrated no E. coli O157:H7 from the carcasses sampled, 91% (116/128) of the dressed carcasses sampled had E. coli present. One carcass sample (1/152) was positive for Salmonella. Campylobacter were detected in 10% (19/191) of the carcasses. Antimicrobial susceptibility testing on 93 carcass E. coli isolates showed resistance to erythromycin (99%), neomycin (65%), netilmicin (2%), oxytetracycline (22%), streptomycin (2%), and trimethoprim (3%). All isolates were resistant to bacitracin, lincomycin, penicillin, and vancomycin. For the large intestinal sampling, 149 of the 217 (69%) samples had E. coli present. Fifty of these 149 samples had E. coli levels ranging from 10(2) to 10(5) colony-forming units/g feces. Campylobacter were isolated from 6 of 201 (3%) samples. No Salmonella colony was detected. Antimicrobial susceptibility testing on 131 intestinal E. coli isolates showed resistance to erythromycin (98%), neomycin (66%), netilmicin (34%), oxytetracycline (34%), streptomycin (40%), and trimethoprim (13%). All isolates were resistant to bacitracin, lincomycin, penicillin, and vancomycin.

Crop impaction resulting from feather ball formation in caged layers.

Abnormal behaviors in commercial poultry, including feather pulling and pica, have been known to occur when birds are exposed to an unfamiliar environment. We report here the development of crop impactions resulting from feather ball formation. Twelve specific-pathogen-free (SPF) chickens were placed in one of three cages housed among a commercial layer flock in three different buildings on a farm site. Three weeks after placement, the birds were removed from the cages and given a physical exam. Chickens were thin, and one bird in each of the three caged groups had a palpable mass at the level of the thoracic inlet. At necropsy, a mass was noted in the crop. Upon further dissection, a wet, foul-smelling mass consisting of feathers and feed debris was recovered. Results from our case indicate that unfamiliar surroundings can cause pica in birds. Hence, avian researchers and veterinarians planning to introduce new birds into a flock, i.e., SPF birds, should consider the birds' previous environmental conditions prior to placement because sudden placement in unfamiliar surroundings can result in pica.

Serologic survey of slaughter-age ostriches (Struthio camelus) for antibodies to selected avian pathogens.

Serum samples from 163 slaughter-age ostriches (Struthio camelus) in Ohio and Indiana were tested for antibodies to avian influenza virus (AIV), Newcastle disease virus (NDV), paramyxovirus (PMV) 2, PMV3, PMV7, infectious bursal disease virus (IBDV), Bordetella avium, Mycoplasma synoviae, Mycoplasma gallisepticum, Ornithobacterium rhinotracheale, Salmonella pullorum, Salmonella gallinarum, and Salmonella typhimurium. One ostrich had antibodies to AIV H5N9, 57% of the ostriches had antibodies to NDV, four ostriches had antibodies to both NDV and PMV2, and one ostrich had antibodies to NDV, PMV2, PMV3, and PMV7. None of the ostriches had antibodies to IBDV, B. avium, M. synoviae, M. gallisepticum, O. rhinotracheale, S. pullorum, S. gallinarum, and S. typhimurium. This is the first report of antibodies to avian influenza and PMV7 in ostriches in the United States.

Evaluation of an avian-specific probiotic to reduce the colonization and shedding of Campylobacter jejuni in broilers.

Campylobacter jejuni has often been responsible for human gastroenteritis. Poultry have often been implicated as a source for these human infections. Intestinal colonization of C. jejuni in the chicken plays a role in carcass contamination during slaughter. Thus, reducing C. jejuni colonization in chickens can potentially reduce the incidence of C. jejuni infections in humans. The use of probiotics to competitively exclude the colonization of intestinal pathogens has been proposed for poultry. Hence, the purpose of this study was to evaluate the use of an avian-specific probiotic containing Lactobacillus acidophilus and Streptococcus faecium for reducing the shedding and colonization of C. jejuni in the chicken intestinal tract. Day-old chicks were randomly allocated into either a probiotic-treated group or a control group. The treated group was given probiotic from day 1 to day 3, and the control group was not given any probiotic. Six hours after the first oral administration of probiotics (treatment) or double distilled water (control), these chicks were challenged with C. jejuni. The frequency of the C. jejuni shedding was monitored until market age. Intestinal colonization was determined for the two experimental groups at slaughter. Results indicated that chickens given probiotics from day 1 to day 3 had a 70% reduction in the frequency of C. jejuni shedding in colonized chicks (P = 0.0001) and a 27% reduction in jejunal colonization in colonized chicks (P = 0.0001) at slaughter when compared with the control group. Thus, the use of the avian-specific probiotic containing L. acidophilus and S. faecium can reduce the colonization and frequency of fecal shedding of C. jejuni in market-aged broilers.

Prevalence and characteristics of Pasteurella multocida in commercial turkeys.

The oropharyngeal regions of 680 meat turkeys and 55 breeder turkeys from nine outbreak farms, three history-outbreak farms, and 19 nonoutbreak farms in Ohio, Indiana, and Pennsylvania were cultured to determine the prevalence of Pasteurella multocida in turkeys. Pasteurella multocida was recovered from 32 out of 105 turkeys belonging to outbreak farms. Pasteurella multocida was not recovered from either history-outbreak or nonoutbreak farms. Characterization via capsular and somatic serotyping, biotyping, restriction endonuclease analysis, and antimicrobial susceptibility testing was performed on all recovered P. multocida isolates. Pasteurella multocida serotype A:1 and somatic serotype 1 with an un-typable capsular serogroup (UT:1) were the most common serogroups found. All isolates belonged to biotype P. multocida ssp. multocida. EcoRI, HpaII, and HindIII restriction enzyme digestions identified three, five, and five restriction fragment length polymorphism profiles, respectively. A majority of the isolates were susceptible to amikacin, ampicillin, ceftiofur, cephalothin, enrofloxacin, florfenicol, gentamicin, neomycin, novobiocin, oxacillin with 2% NaCl, sarafloxacin, tilmicosin, and trimethoprim with sulphadiazine and resistant to clindamicin, penicillin, tiamulin, and tylosin.

Survey of pathogens and blood parasites in free-living passerines.

To determine the disease prevalence of free-living passerines, 1709 passerines were sampled from 38 different field sites in Ohio. Choanal and cloacal swabs were collected from each bird and cultured for the presence of Pasteurella multocida, Salmonella spp., and Escherichia coli by standard microbiologic techniques. In addition, the serum from each bird was analyzed for the presence of antibodies to Mycoplasma gallisepticum, Mycoplasma synoviae, Newcastle disease virus, and avian influenza virus. A blood smear was also made to examine for the presence of blood parasites. Results indicated that the isolation of E. coli varied with bird species, with the European starling having a higher (21.4%) isolation of E. coli. Salmonella spp. were also isolated from these free-living passerines. Pasteurella multocida was not isolated from any of the sampled passerines. These birds did not have antibodies to M. gallisepticum, M. synoviae, Newcastle disease virus, or avian influenza virus. Blood parasites were not detected in any of the birds sampled.

Induction of vitamin A deficiency in turkeys.

The objective of this study was to determine the relationship between the hepatic vitamin A (VitA) level and the pathologic changes in the oropharynx and esophagus of VitA-deficient turkeys. Study turkeys were provided with a diet sufficient (11,000 IU/kg) or deficient (2750 IU/kg) in VitA from 4 to 17 wk of age. Body weight, bacterial culture, and tissues from internal organs were collected at weekly intervals. VitA deficiency causes epithelial tissue damage in poultry. This epithelial damage was seen grossly as white plaques in the oropharynx and esophagus and histologically as squamous metaplasia of mucosal glands and keratinization of epithelium. No significant difference in body weights was seen among the groups. Moreover, no pathogenic bacteria was isolated during sampling periods. Liver VitA levels declined significantly after consumption of low VitA diet for 3 wk and were depleted after 5 wk. Squamous metaplasia due to VitA deficiency developed in the esophagus after 3 wk and in the oropharynx after 4 wk of consuming a VitA-deficient diet.

The effect of route of inoculation on the virulence of raptorial Pasteurella multocida isolates in Pekin ducks (Anas platyrhynchos).

The purpose of this study was to determine the virulence of raptorial Pasteurella multocida for ducks and the effect of various routes of inoculation on virulence. Four-week-old Pekin ducks (Anas platyrhynchos) were challenged with one of three raptorial isolates (RTHA-2, RTHA-4, or WESO-1) by one of five inoculation routes (intranasal, intraocular, intravenous, oral, and subcutaneous). Ducks were monitored daily for mortality until 2 wk postchallenge. Results indicated that the intravenous route caused the most mortality for all isolates and that significant variation existed in the virulence among the sources of P. multocida, with WESO-1 causing the least mortality of the isolates tested.

Low abundance of Escherichia coli microsatellites is associated with an extremely low mutation rate.

It is widely assumed that microsatellites are generated by replication slippage, a mutation process specific to repetitive DNA. Consistent with their high mutation rate, microsatellites are highly abundant in most eukaryotic genomes. In Escherichia coli, however, microsatellites are rare and short despite the fact that a high microsatellite mutation rate was described. We show that this high microsatellite instability depends on the presence of the F-plasmid. E. coli cells lacking the F-plasmid have extremely low microsatellite mutation rates. This result provides a possible explanation for the genome-wide low density of microsatellites in E. coli. Furthermore, we show that the F-plasmid induced microsatellite instability is independent of the mismatch repair pathway.

A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus.

Changes in gene expression are known to occur between closely related species, but it is not yet clear how many of these are due to random fixation of allelic variants or due to adaptive events. In a microarray survey between subspecies of the Mus musculus complex, we identified the mitogen-activated protein-kinase-kinase MKK7 as a candidate for change in gene expression. Quantitative PCR experiments with multiple individuals from each subspecies confirmed a specific and significant up-regulation in the testis of M. m. domesticus. Northern blot analysis shows that this is due to a new transcript that is not found in other tissues, nor in M. m. musculus. A cis-trans test via allele specific expression analysis of the MKK7 gene in F1 hybrids between domesticus and musculus shows that the expression change is mainly caused by a mutation located in cis. Nucleotide diversity was found to be significantly reduced in a window of at least 20 kb around the MKK7 locus in domesticus, indicative of a selective sweep. Because the MKK7 gene is involved in modulating a kinase signalling cascade in a stress response pathway, it seems a plausible target for adaptive differences between subspecies, although the functional role of the new testis-specific transcripts will need to be further studied.

Drosophila virilis has long and highly polymorphic microsatellites.

Comparative genomics is a powerful approach to inference of the dynamics of genome evolution. Most information about the evolution of microsatellites in the genus Drosophila has been obtained from Drosophila melanogaster. For comparison, we collected microsatellite data for the distantly related species Drosophila virilis. Screening about 0.5 Mb of nonredundant genomic sequence from GenBank, we identified 239 dinucleotide microsatellites. On average, D. virilis dinucleotides were significantly longer than D. melanogaster microsatellites (7.69 repeats vs. 6.75 repeats). Similarly, direct cloning of microsatellites resulted in a higher mean repeat number in D. virilis than in D. melanogaster (12.7 repeats vs. 12.2 repeats). Characterization of 11 microsatellite loci mapping to division 40-49 on the fourth chromosome of D. virilis indicated that D. virilis microsatellites are more variable than those of D. melanogaster.

Parturition care planning.

Nursing care planning is not a new concept, but in contemporary nursing, this tool is taking on new meaning. In an area such as labor and delivery, the concept of the nursing process must be scrutinized and adapted to facilitate its usefulness in providing optimum care of the parturient. A perspective on the scope of care planning, its benefits to the parturient, and its value and implications is presented.

Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila.

Microsatellites are tandem repetitions of short (1-6 bp) motifs. It is widely assumed that microsatellites degenerate through the accumulation of base substitutions in the repeat array. Using a phylogenetic framework, we studied the evolutionary dynamics of interruptions in three Drosophila microsatellite loci. For all three loci, we show that the interruptions in a microsatellite can be lost, resulting in a longer uninterrupted microsatellite stretch. These results indicate that mutations in the microsatellite array do not necessarily lead to decay but may represent only a transition state during the evolution of a microsatellite. Most likely, this purification of interrupted microsatellites is caused by DNA replication slippage.

Creative intervention strategies in the management of perinatal loss.

The personal grief experienced by a mother who has lost her child is profound. Coping with the sadness and incomprehensibility of the loss predisposes her to feelings of increased vulnerability and isolation. As the woman externalizes her internal experience of grief, she is better able to manage and deal with the situational crises that surround and emerge from the pregnancy loss. This article presents a number of creative, non-traditional approaches that can be utilized to bring about wholeness and well-being in the mother as she shares her loss story.

High mutation rate of a long microsatellite allele in Drosophila melanogaster provides evidence for allele-specific mutation rates.

Within recent years, microsatellite have become one of the most powerful genetic markers in biology. For several mammalian species, microsatellite mutation rates have been estimated on the order of 10(-3)-10(-5). A recent study, however, demonstrated mutation rates in Drosophila melanogaster of at least one order of magnitude lower than those in mammals. To further test this result, we examined mutation rates of different microsatellite loci using a larger sample size. We screened 24 microsatellite loci in 119 D. melanogaster lines maintained for approximately 250 generations and detected 9 microsatellite mutations. The average mutation rate of 6.3 x 10(-6) is identical to the mutation rate from a previous study. Most interestingly, all nine mutations occurred at the same allele of one locus (DROYANETSB). This hypermutable allele has 28 dinucleotide repeats and is among the longest microsatellite reported in D. melanogaster. The allele-specific mutation rate of 3.0 x 10(-4) per generation is within the range of mammalian mutation rates. Future microsatellite analyses will have to account for the dramatic differences in allele-specific mutation rates.

Multiple mating in wild Drosophila melanogaster revisited by microsatellite analysis.

The occurrence of multiple mating in Drosophila melanogaster is of particular interest to evolutionary biologists, as seminal fluid has some toxic effects for females. Thus, it has been predicted that the number of matings per females should be low. We have tested this prediction with seven highly polymorphic microsatellite loci in inseminated females from a Viennese D. melanogaster population. In contrast to the predicted low number of matings and previous studies in natural populations, we identified the genotypes of four to six different males fertilizing the offspring of each female tested. Potential causes and consequences are discussed.

Microsatellite analysis reveals substantial genetic differentiation between contemporary New World and Old World Holstein Friesian populations.

Genotypic data from 39 microsatellite loci typed in 211 animals were used to assess the genetic differentiation between Old World and New World Holstein Friesian cattle populations. Gene diversities were similar in all five Holstein Friesian populations surveyed, ranging from 0.43 to 0.48. A tree of individuals based on the proportion of shared alleles indicated a clear distinction between Old World and New World Holstein Friesian populations. Similarly, genetic differentiation between populations, as measured by FST, was highly significant. Using the split decomposition method, we were able to visualize the significant introgression of New World Holstein Friesian into European Holstein Friesian populations.

Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular analysis of the candidate gene GLABROUS1.

GLABROUS1 (GL1) belongs to the large family of MYB transcription factors and is known to play a central role in trichome initiation. We studied trichome distribution and the molecular variation of GL1 in 28 A. thaliana accessions. Trichome density on rosette leaves was highly variable among those accessions. On the molecular level, we detected substantial sequence variation in a 3-kb fragment which included the complete coding region of the GL1 locus (pi = 0.01). Phylogenetic analysis of GL1 indicates the presence of two diverged clades among 28 accessions. Using ANOVA, we show that the phenotypic variation in trichome density cannot be explained by the sequence divergence between the two phylogenetic lineages. Sequence analysis of wild-type Arabidopsis thaliana and Arabidopsis lyrata accessions indicates that all amino acid substitutions are located outside of the conserved helix-turn-helix DNA-binding domains R2 and R3. Using plants of A. thaliana and A. lyrata with either naturally occurring or ethyl methane sulfonate--induced glabrous phenotypes, we demonstrate that the last 14 C-terminal amino acids of the GL1 gene have no major impact on the initiation of trichomes.