bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Stages of Hepatozoon americanum and of Parasitized Canine Host Cells
Authors: Cummings C. A. , Panciera R. J. , Kocan K. M. , Mathew J. S. , Ewing S. A.
Published: November 2005

American canine hepatozoonosis is caused by Hepatozoon americanum, a protozoan parasite, the definitive host of which is the tick, Amblyomma maculatum. Infection of the dog follows ingestion of ticks that harbor sporulated H. americanum oocysts. Following penetration of the intestinal mucosa, sporozoites are disseminated systemically and give rise to extensive asexual multiplication in cells located predominantly in striated muscle. The parasitized canine cells in “onion skin” cysts and in granulomas situated within skeletal muscle, as well as those in peripheral blood leukocytes (PBL), were identified as macrophages by use of fine structure morphology and/or immunohistochemical reactivity with macrophage markers. Additionally, two basic morphologic forms of the parasite were observed in macrophages of granulomas and PBLs. The forms were presumptively identified as merozoites and gamonts. The presence of a “tail” in some gamonts in PBLs indicated differentiation toward microgametes. Recognition of merozoites in PBLs supports the contention that hematogenously redistributed merozoites initiate repeated asexual cycles and could explain persistence of infection for long periods in the vertebrate host. Failure to clearly demonstrate a host cell membrane defining a parasitophorous vacuole may indicate that the parasite actively penetrates the host cell membrane rather than being engulfed by the host cell, as is characteristic of some protozoans.
Histologic Features Associated with Tritrichomonas foetus-induced Colitis in Domestic Cats
Authors: Yaeger M. J. , Gookin J. L.
Published: November 2005

Tritrichomonas foetus is a venereal pathogen of naturally bred cattle. In domestic cats, T. foetus colonizes the colon, resulting in chronic, large-bowel diarrhea. The infection is prevalent among young, densely housed cats, and there is no effective treatment. To the authors' knowledge, the characteristic microscopic lesions of T. foetus infection in naturally infected cats have not been described. The aim of the study reported here was to characterize the histologic changes in the colon of seven cats with T. foetus infection and chronic diarrhea. All cats were 1 year old or younger (mean, 6.7 ± 1.7 months), and a diagnosis of T. foetus infection was made on the basis of direct fecal smear examination (five cats), fecal culture in InPouch™ TF medium (four cats), single-tube nested polymerase chain reaction (PCR) analysis of DNA extracted from feces (two cats), or observation of trichomonads in sections of colon followed by PCR confirmation on DNA extracted from paraffin-embedded tissue (two cats). The presence of colonic trichomonads was the most diagnostic histologic feature. Organisms were identified in all cats, but in only 24 of 43 (56%) sections of colon. Trichomonads were generally present in close proximity to the mucosal surface and less frequently in the lumen of colonic crypts. The presence of colonic trichomonads was consistently associated with mild-to-moderate lymphoplasmacytic and neutrophilic colitis, crypt epithelial cell hypertrophy, hyperplasia and increased mitotic activity, loss of goblet cells, crypt microabscesses, and attenuation of the superficial colonic mucosa. In two of the cats, histologic lesions were more severe and were associated with invasion of trichomonads into the lamina propria and/or deeper layers of the colon.
Bovine Papillomavirus Type-2 (BPV-2) Infection and Expression of Uroplakin IIIb, a Novel Urothelial Cell Marker, in Urinary Bladder Tumors of Cows
Authors: Roperto S. , Ambrosio V. , Borzacchiello G. , Galati P. , Paciello O. , Russo V. , Roperto F.
Published: November 2005

Several immunohistochemical markers have been used to define the differentiation pattern of urothelial cell tumors of the urinary bladder. We investigated the expression of the recently characterized uroplakin (UP) IIIb, an urothelium-specific and differentiation-dependent protein, in 39 urothelial tumors of the urinary bladder in cows that had suffered from chronic enzootic hematuria for several years. Bovine papillomavirus type 2 DNA was amplified and UP IIIb protein was detected in all these tumors. In papillomas and papillary carcinomas, UP IIIb expression was mostly seen as superficial staining; luminal and peripheral patterns were also observed. In nonpapillary carcinomas, UP IIIb appeared to define clearly the cell membrane lining intercellular and intracellular lumina as well as the cell borders in deeper cell layers. In benign and malignant lesions, an intracytoplasmic immunoreactivity was also detected. Coarse intracytoplasmic UP IIIb-positive material close to the nucleus occurred in some malignant cells. Focally strong membraneous immunostaining that marked single cells with complete ringlike peripheral pattern was seen. Although UP IIIb expression does not seem to correlate with the biological behavior of urothelial tumors, it appears to be a highly sensitive marker for bovine urothelial tumors.
Incidence of Polysaccharide Storage Myopathy: Necropsy Study of 225 Horses
Authors: Valentine B. A. , Cooper B. J.
Published: November 2005

Muscle samples were obtained at necropsy from 225 horses and ponies 1 year of age or older. Samples were processed in routine manner and were stained with hematoxylin and eosin and with periodic acid-Schiff for glycogen. Sections were examined for abnormal glycogen content and amylase- resistant complex polysaccharide and for chronic myopathic change (excessive fiber size variation, increase in number of internal nuclei). A total of 101 horses and ponies with lesions of polysaccharide storage myopathy were identified. Age of affected horses ranged from one to 30 years, with a mean of 14.7 years. Mean age of nonaffected horses was 12 years. Incidence of polysaccharide storage myopathy varied depending on breed; Thoroughbreds had the lowest (27%) and draft-related horses had the highest (86%) incidence. Chronic myopathic changes were more severe in polysaccharide storage myopathy-affected horses than in nonaffected horses. Results of this study indicate that polysaccharide storage myopathy is a common disorder of many breeds of horses and ponies.
Erythropoietin Receptor Expression in Canine Mammary Tumor: An Immunohistochemical Study
Authors: Sfacteria A. , Mazzullo G. , Bertani C. , Calabrò P. , Vico G. De , Macrì B.
Published: November 2005

Erythropoietin (EPO) is a cytokine primarily involved in the regulation of the erythropoiesis. Recently, it has been demonstrated that EPO and its receptor (EPOR) are expressed in several neoplastic cell lines and solid tumors. Furthermore, in vitro and in vivo studies have shown that EPO could promote human breast carcinoma growth by means of the binding with its receptor, although a clear function for EPO in this setting has not been yet established. While the human medical literature has been accumulating strong evidence on EPO's role in oncogenesis, to date, there are no veterinary reports focusing on such an issue. The aim of the present study was to investigate the immunohistochemical expression of EPOR in canine mammary gland dysplastic and neoplastic lesions. Our results show a weak to moderate EPOR expression in dysplastic glands, being immunoreactivity enhanced as the lesion shows an increasing malignant pattern. On the basis of these findings, this study describes, for the first time, the evidence for EPOR expression in canine mammary gland tumor and suggests a feasible EPO's role for canine mammary tumor progression.
Peripheral Nerve Pathology in Two Rottweilers with Neuronal Vacuolation and Spinocerebellar Degeneration
Authors: Salvadori C. , Tartarelli C. L. , Baroni M. , Mizisin A. , Cantile C.
Published: November 2005

Neuronal vacuolation and spinocerebellar degeneration in young Rottweiler dogs is a neurodegenerative condition characterized by neuronal vacuolation of several nuclei in the central nervous system and degeneration of the spinal cord white matter. Here, we describe the morphologic and ultrastructural findings in laryngeal muscles and peripheral nerves of a 16-week-old female and a 32-week-old female Rottweiler dog affected by progressive ataxia and tetraparesis associated with laryngeal paralysis. Lesions were characterized by neurogenic muscle atrophy of the intrinsic laryngeal muscles, and a loss of large myelinated fibers in the recurrent laryngeal nerve, accompanied by demyelinating/remyelinating features affecting the small myelinated fibers. No significant changes were detected in the cranial laryngeal, vagus, phrenic, ulnar, or peroneal nerves. These findings were indicative of a selective distal neuropathy of the recurrent laryngeal nerve with early severe axonal degeneration, mainly of the large myelinated fibers.
Meningoencephalitis Tuberculosa in a Holstein Cow
Authors: Oruç E.
Published: November 2005

The gross and histopathologic lesions of meningoencephalitis tuberculosa in a 4-year-old Holstein cow showing clinical signs compatible with bovine spongiform encephalopathy are described in this report. Grossly, numerous gray to yellow, firm and caseous nodules were seen on the ventral surfaces of the brain and in the lateral and fourth ventricles. Histopathologically, foci of caseation and dystrophic mineralization were surrounded by multinucleated giant cells, epitheloid macrophages, plasma cells, lymphocytes and fibrous proliferation. Ziehl-Neelsen stains of the lesions revealed masses of slender acid-fast bacilli in the necrotic centers of lesions and within surrounding giant cells.
Choroid Plexus Megalin Is Involved in Neuroprotection by Serum Insulin-Like Growth Factor I
Authors: Carro Eva , Spuch Carlos , Trejo Jose Luis , Antequera Desiré , Torres-Aleman Ignacio
Published: November 2005

The involvement of circulating insulin-like growth factor I (IGF-I) in the beneficial effects of physical exercise on the brain makes this abundant serum growth factor a physiologically relevant neuroprotective signal. However, the mechanisms underlying neuroprotection by serum IGF-I remain primarily unknown. Among many other neuroprotective actions, IGF-I enhances clearance of brain amyloid β (Aβ) by modulating transport/production of Aβ carriers at the blood-brain interface in the choroid plexus. We found that physical exercise increases the levels of the choroid plexus endocytic receptor megalin/low-density lipoprotein receptor-related protein-2 (LRP2), a multicargo transporter known to participate in brain uptake of Aβ carriers. By manipulating choroid plexus megalin levels through viral-directed overexpression and RNA interference, we observed that megalin mediates IGF-I-induced clearance of Aβ and is involved in IGF-I transport into the brain. Through this dual role, megalin participates in the neuroprotective actions of IGF-I including prevention of tau hyperphosphorylation and maintenance of cognitive function in a variety of animal models of cognitive loss. Because we found that in normal aged animals, choroid plexus megalin/LRP2 is decreased, an attenuated IGF-I/megalin input may contribute to increased risk of neurodegeneration, including late-onset Alzheimer's disease.
Spatiotemporal Gating of Sensory Inputs in Thalamus during Quiescent and Activated States
Authors: Aguilar Juan R. , Castro-Alamancos Manuel A.
Published: November 2005

The main role of the thalamus is to relay sensory inputs to the neocortex according to the regulations dictated by behavioral state. Hence, changes in behavioral state are likely to transform the temporal and spatial properties of thalamocortical receptive fields. We compared the receptive fields of single cells in the ventroposterior medial thalamus (VPM) of urethane-anesthetized rats during quiescent states and during aroused (activated) states. During quiescent states, VPM cells respond to stimulation of a principal whisker (PW) and may respond modestly to one or a few adjacent whiskers (AWs). During either generalized forebrain activation or selective thalamic activation caused by carbachol infusion in the VPM, the responses to AWs enhance so that VPM receptive fields become much larger. Such enlargement is not observed at the level of the principal trigeminal nucleus, indicating that it originates within the thalamus. Interestingly, despite the increase in AW responses during activation, simultaneous deflection of the PW and AWs produced VPM responses that resembled the PW response, as if the AWs were not stimulated. This nonlinear summation of sensory responses was present during both quiescent and activated states. In conclusion, the thalamus suppresses the excitatory surround (AWs) of the receptive field during quiescent states and enlarges this surround during arousal. But, thalamocortical cells represent only the center (PW) of the receptive field when the center (PW) and surround (AWs) are stimulated simultaneously.
Prediction and Decoding of Retinal Ganglion Cell Responses with a Probabilistic Spiking Model
Authors: Pillow Jonathan W. , Paninski Liam , Uzzell Valerie J. , Simoncelli Eero P. , Chichilnisky E. J.
Published: November 2005

Sensory encoding in spiking neurons depends on both the integration of sensory inputs and the intrinsic dynamics and variability of spike generation. We show that the stimulus selectivity, reliability, and timing precision of primate retinal ganglion cell (RGC) light responses can be reproduced accurately with a simple model consisting of a leaky integrate-and-fire spike generator driven by a linearly filtered stimulus, a postspike current, and a Gaussian noise current. We fit model parameters for individual RGCs by maximizing the likelihood of observed spike responses to a stochastic visual stimulus. Although compact, the fitted model predicts the detailed time structure of responses to novel stimuli, accurately capturing the interaction between the spiking history and sensory stimulus selectivity. The model also accounts for the variability in responses to repeated stimuli, even when fit to data from a single (nonrepeating) stimulus sequence. Finally, the model can be used to derive an explicit, maximum-likelihood decoding rule for neural spike trains, thus providing a tool for assessing the limitations that spiking variability imposes on sensory performance.
The Suppressive Field of Neurons in Lateral Geniculate Nucleus
Authors: Bonin Vincent , Mante Valerio , Carandini Matteo
Published: November 2005

The responses of neurons in lateral geniculate nucleus (LGN) exhibit powerful suppressive phenomena such as contrast saturation, size tuning, and masking. These phenomena cannot be explained by the classical center-surround receptive field and have been ascribed to a variety of mechanisms, including feedback from cortex. We asked whether these phenomena might all be explained by a single mechanism, contrast gain control, which is inherited from retina and possibly strengthened in thalamus. We formalized an intuitive model of retinal contrast gain control that explicitly predicts gain as a function of local contrast. In the model, the output of the receptive field is divided by the output of a suppressive field, which computes the local root-mean-square contrast. The model provides good fits to LGN responses to a variety of stimuli; with a single set of parameters, it captures saturation, size tuning, and masking. It also correctly predicts that responses to small stimuli grow proportionally with contrast: were it not for the suppressive field, LGN responses would be linear. We characterized the suppressive field and found that it is similar in size to the surround of the classical receptive field (which is eight times larger than commonly estimated), it is not selective for stimulus orientation, and it responds to a wide range of frequencies, including very low spatial frequencies and high temporal frequencies. The latter property is hardly consistent with feedback from cortex. These measurements thoroughly describe the visual properties of contrast gain control in LGN and provide a parsimonious explanation for disparate suppressive phenomena.
Relative Influences of Crossing Over and Gene Conversion on the Pattern of Linkage Disequilibrium in Arabidopsis thaliana
Authors: Plagnol Vincent , Padhukasahasram Badri , Wall Jeffrey D , Marjoram Paul , Nordborg Magnus
Published: November 2005

In this article we infer the rates of gene conversion and crossing over in Arabidopsis thaliana from population genetic data. Our data set is a genomewide survey consisting of 1347 fragments of length 600 bp sequenced in 96 accessions. It has several orders of magnitude more markers than any previous nonhuman study. This allows for more accurate inference as well as a detailed comparison between theoretical expectations and observations. Our methodology is specifically set to account for deviations such as recurrent mutations or a skewed frequency spectrum. We found that even if some components of the model clearly do not fit, the pattern of LD conforms to theoretical expectations quite well. The ratio of gene conversion to crossing over is estimated to be around one. We also find evidence for fine-scale variations of the crossing-over rate.
Genetic Addiction: Selfish Gene's Strategy for Symbiosis in the Genome
Authors: Mochizuki Atsushi , Yahara Koji , Kobayashi Ichizo , Iwasa Yoh
Published: November 2005

The evolution and maintenance of the phenomenon of postsegregational host killing or genetic addiction are paradoxical. In this phenomenon, a gene complex, once established in a genome, programs death of a host cell that has eliminated it. The intact form of the gene complex would survive in other members of the host population. It is controversial as to why these genetic elements are maintained, due to the lethal effects of host killing, or perhaps some other properties are beneficial to the host. We analyzed their population dynamics by analytical methods and computer simulations. Genetic addiction turned out to be advantageous to the gene complex in the presence of a competitor genetic element. The advantage is, however, limited in a population without spatial structure, such as that in a well-mixed liquid culture. In contrast, in a structured habitat, such as the surface of a solid medium, the addiction gene complex can increase in frequency, irrespective of its initial density. Our demonstration that genomes can evolve through acquisition of addiction genes has implications for the general question of how a genome can evolve as a community of potentially selfish genes.
Constructing the Parental Linkage Phase and the Genetic Map Over Distances <1 cM Using Pooled Haploid DNA
Authors: Gasbarra Dario , Sillanpää Mikko J
Published: November 2005

A new statistical approach for construction of the genetic linkage map and estimation of the parental linkage phase based on allele frequency data from pooled gametic (sperm or egg) samples is introduced. This method can be applied for estimation of recombination fractions (over distances <1 cM) and ordering of large numbers (even hundreds) of closely linked markers. This method should be extremely useful in species with a long generation interval and a large genome size such as in dairy cattle or in forest trees; the conifer species have haploid tissues available in megagametophytes. According to Mendelian expectation, two parental alleles should occur in gametes in 1:1 proportions, if segregation distortion does not occur. However, due to mere sampling variation, the observed proportions may deviate from their expected value in practice. These deviations and their dependence along the chromosome can provide information on the parental linkage phase and on the genetic linkage map. Usefulness of the method is illustrated with simulations. The role of segregation distortion as a source of these deviations is also discussed. The software implementing this method is freely available for research purposes from the authors.
Estimating Selection on Nonsynonymous Mutations
Authors: Loewe Laurence , Charlesworth Brian , Bartolomé Carolina , Nöel Véronique
Published: November 2005

The distribution of mutational effects on fitness is of fundamental importance for many aspects of evolution. We develop two methods for characterizing the fitness effects of deleterious, nonsynonymous mutations, using polymorphism data from two related species. These methods also provide estimates of the proportion of amino acid substitutions that are selectively favorable, when combined with data on between-species sequence divergence. The methods are applicable to species with different effective population sizes, but that share the same distribution of mutational effects. The first, simpler, method assumes that diversity for all nonneutral mutations is given by the value under mutation-selection balance, while the second method allows for stronger effects of genetic drift and yields estimates of the parameters of the probability distribution of mutational effects. We apply these methods to data on populations of Drosophila miranda and D. pseudoobscura and find evidence for the presence of deleterious nonsynonymous mutations, mostly with small heterozygous selection coefficients (a mean of the order of 10−5 for segregating variants). A leptokurtic gamma distribution of mutational effects with a shape parameter between 0.1 and 1 can explain observed diversities, in the absence of a separate class of completely neutral nonsynonymous mutations. We also describe a simple approximate method for estimating the harmonic mean selection coefficient from diversity data on a single species.
Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila melanogaster
Authors: Thornton Kevin , Andolfatto Peter
Published: November 2005

Genome-wide nucleotide variation in non-African populations of Drosophila melanogaster is a subset of variation found in East sub-Saharan African populations, suggesting a bottleneck in the history of the former. We implement an approximate Bayesian approach to infer the timing, duration, and severity of this putative bottleneck and ask whether this inferred model is sufficient to account for patterns of variability observed at 115 loci scattered across the X chromosome. We estimate a recent bottleneck 0.006Ne generations ago, somewhat further in the past than suggested by biogeographical evidence. Using various proposed statistical tests, we find that this bottleneck model is able to predict the majority of observed features of diversity and linkage disequilibrium in the data. Thus, while precise estimates of bottleneck parameters (like inferences of selection) are sensitive to model assumptions, our results imply that it may be unnecessary to invoke frequent selective sweeps associated with the dispersal of D. melanogaster from Africa to explain patterns of variability in non-African populations.
Primate Chaperones Hsc70 (Constitutive) and Hsp70 (Induced) Differ Functionally in Supporting Growth and Prion Propagation in Saccharomyces cerevisiae
Authors: Tutar Yusuf , Song Youtao , Masison Daniel C
Published: November 2005

Hsp70's are highly conserved essential protein chaperones that assist protein folding and prevent protein aggregation. They have modular structures consisting of ATPase, substrate-binding, and C-terminal domains. Substrate binding and release is regulated by ATP hydrolysis and nucleotide exchange, which in turn are regulated by cochaperones. Eukaryotes have constitutive (Hsc70) and stress-inducible (iHsp70) isoforms, but their functions have not been systematically compared. Using a yeast system to evaluate heterologous Hsp70's we find that primate Hsc70 supported growth but iHsp70 did not. Plant Hsc70 and iHsp70 counterparts behaved similarly, implying evolutionary conservation of this distinction. Swapping yeast and primate Hsp70 domains showed that (i) the Hsc70–iHsp70 distinction resided in the ATPase domain, (ii) substrate-binding domains of Hsp70's within and across species functioned similarly regarding growth, (iii) C-terminal domain function was important for growth, and (iv) Hsp70 functions important for cell growth and prion propagation were separable. Enzymatic analysis uncovered a correlation between substrate affinity and prion phenotype and showed that ATPase and protein-folding activities were generally similar. Our data support a view that intrinsic activities of Hsp70 isoforms are comparable, and functional differences in vivo lie mainly in complex interactions of Hsp70 with cochaperones.
eae36, a Locus on Mouse Chromosome 4, Controls Susceptibility to Experimental Allergic Encephalomyelitis in Older Mice and Mice Immunized in the Winter
Authors: Teuscher Cory , Doerge R W , Fillmore Parley D , Blankenhorn Elizabeth P
Published: November 2005

Genetic factors are believed to contribute to multiple sclerosis (MS) susceptibility; however, strong evidence implicating intrinsic and environmental factors in the etiopathogenesis of MS also exists. Susceptibility to experimental allergic encephalomyelitis (EAE), the principal animal model of MS, is also influenced by nongenetic factors, including age and season at immunization. This suggests that age- and season-by-gene interactions exist and that different susceptibility loci may influence disease as a function of the two parameters. In this study, linkage analysis based on genome exclusion mapping was carried out using age and season at immunization restricted cohorts of (B10.S × SJL/J) F2 intercross mice in an effort to identify such linkages. Significant linkage of EAE to eae4 and eae5 was detected with 6- to 12-week-old and summer cohorts. In contrast, significant linkage of EAE to eae4 and eae5 was not detected with the >12-week-old and winter/spring populations. Rather, significant linkage to D4Mit203 at 128.50 Mb on chromosome 4 was detected with animals that were >12 weeks old at the time of immunization or were immunized in the winter. This previously unidentified locus has been designated eae36. These results support the existence of age- and season-by-gene-specific interactions in the genetic control of susceptibility to autoimmune inflammatory disease of the central nervous system and suggest that late-onset MS may be immunogenetically distinct.
Estimating the “Effective Number of Codons”: The Wright Way of Determining Codon Homozygosity Leads to Superior Estimates
Authors: Fuglsang Anders
Published: November 2005

In 1990, Frank Wright introduced a method for measuring synonymous codon usage bias in a gene by estimation of the “effective number of codons,” Nc. Several attempts have been made recently to improve Wright's estimate of Nc, but the methods that work in cases where a gene encodes a protein not containing all amino acids with degenerate codons have not been tested against each other. In this article I derive five new estimators of Nc and test them together with the two published estimators, using resampling under rigorous testing conditions. Estimation of codon homozygosity, F, turns out to be a key to the estimation of Nc. F can be estimated in two closely related ways, corresponding to sampling with or without replacement, the latter being what Wright used. The Nc methods that are based on sampling without replacement showed much better accuracy at short gene lengths than those based on sampling with replacement, indicating that Wright's homozygosity method is superior. Surprisingly, the methods based on sampling with replacement displayed a superior correlation with mRNA levels in Escherichia coli.
Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes
Authors: Binladen Jonas , Wiuf Carsten , Gilbert M Thomas P , Bunce Michael , Barnett Ross , Larson Greger , Greenwood Alex D , Haile James , Ho Simon Y W , Hansen Anders J , Willerslev Eske
Published: November 2005

To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine → guanine and thymine → cytosine) and type 2 transitions (cytosine → thymine and guanine → adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.
High Mobility Group Proteins HMGD and HMGZ Interact Genetically With the Brahma Chromatin Remodeling Complex in Drosophila
Authors: Ragab Anan , Thompson Elizabeth C , Travers Andrew A
Published: November 2005

Many pleiotropic roles have been ascribed to small abundant HMG–Box (HMGB) proteins in higher eukaryotes but their precise function has remained enigmatic. To investigate their function genetically we have generated a defined deficiency uncovering the functionally redundant genes encoding HMGD and HMGZ, the Drosophila counterparts of HMGB1–3 in mammals. The resulting mutant is a strong hypomorphic allele of HmgD/Z. Surprisingly this allele is viable and exhibits only minor morphological defects even when homozygous. However, this allele interacts strongly with mutants of the Brahma chromatin remodeling complex, while no interaction was observed with mutant alleles of other remodeling complexes. We also observe genetic interactions between the HmgD/Z deficiency and some, but not all, known Brahma targets. These include the homeotic genes Sex combs reduced and Antennapedia, as well as the gene encoding the cell-signaling protein Rhomboid. In contrast to more general structural roles previously suggested for these proteins, we infer that a major function of the abundant HMGB proteins in Drosophila is to participate in Brahma-dependent chromatin remodeling at a specific subset of Brahma-dependent promoters.
Differential Usage of Alternative Pathways of Double-Strand Break Repair in Drosophila
Authors: Preston Christine R , Flores Carlos C , Engels William R
Published: November 2005

Double-strand DNA breaks can be repaired by any of several alternative mechanisms that differ greatly in the nature of the final repaired products. We used a reporter construct, designated “Repair reporter 3” (Rr3), to measure the relative usage of these pathways in Drosophila germ cells. The method works by creating a double-strand break at a specific location such that expression of the red fluorescent protein, DsRed, in the next generation can be used to infer the frequency at which each pathway was used. A key feature of this approach is that most data come from phenotypic scoring, thus allowing large sample sizes and considerable precision in measurements. Specifically, we measured the proportion of breaks repaired by (1) conversion repair, (2) nonhomologous end joining (NHEJ), or (3) single-strand annealing (SSA). For conversion repair, the frequency of mitotic crossing over in the germ line indicates the relative prevalence of repair by double Holliday junction (DHJ) formation vs. the synthesis-dependent strand annealing (SDSA) pathway. We used this method to show that breaks occurring early in germ-line development were much more frequently repaired via single-strand annealing and much less likely to be repaired by end joining compared with identical breaks occurring later in development. Conversion repair was relatively rare when breaks were made either very early or very late in development, but was much more frequent in between. Significantly, the changes in relative usage occurred in a compensatory fashion, such that an increase in one pathway was accompanied by decreases in others. This negative correlation is interpreted to mean that the pathways for double-strand break repair compete with each other to handle a given breakage event.
The Maize aberrant pollen transmission 1 Gene Is a SABRE/KIP Homolog Required for Pollen Tube Growth
Authors: Xu Zhennan , Dooner Hugo K
Published: November 2005

Maize (Zea mays) pollen tubes grow in the styles at a rate of >1 μm/sec. We describe here a gene required to attain that striking rate. The aberrant pollen transmission 1 (apt1) gene of maize was identified by an Ac-tagged mutation that displayed a severe pollen transmission deficit in heterozygotes. Rare apt1 homozygotes can be recovered, aided by phenotypic selection for Ac homozygotes. Half of the pollen in heterozygotes and most of the pollen in homozygotes germinate short and twisted pollen tubes. The apt1 gene is 26 kb long, makes an 8.6-kb pollen-specific transcript spliced from 22 exons, and encodes a protein of 2607 amino acids. The APT1 protein is homologous to SABRE and KIP, Arabidopsis proteins of unknown function involved in the elongation of root cortex cells and pollen tubes, respectively. Subcellular localization analysis demonstrates that APT1 colocalizes with a Golgi protein marker in growing tobacco pollen tubes. We hypothesize that the APT1 protein is involved in membrane trafficking and is required for the high secretory demands of tip growth in pollen tubes. The apt1-m1(Ac) mutable allele is an excellent tool for selecting Ac transpositions because of the strong negative selection pressure operating against the parental Ac site.
Transposon Insertions ofmagellan-4That Impair Social Gliding Motility inMyxococcus xanthus
Authors: Youderian Philip , Hartzell Patricia L
Published: November 2005

Myxococcus xanthus has two different mechanisms of motility, adventurous (A) motility, which permits individual cells to glide over solid surfaces, and social (S) motility, which permits groups of cells to glide. To identify the genes involved in S-gliding motility, we mutagenized a ΔaglU (A−) strain with the defective transposon, magellan-4, and screened for S− mutants that form nonmotile colonies. Sequence analysis of the sites of the magellan-4 insertions in these mutants and the alignment of these sites with the M. xanthus genome sequence show that two-thirds of these insertions lie within 27 of the 37 nonessential genes known to be required for social motility, including those necessary for the biogenesis of type IV pili, exopolysaccharide, and lipopolysaccharide. The remaining insertions also identify 31 new, nonessential genes predicted to encode both structural and regulatory determinants of S motility. These include three tetratricopeptide repeat proteins, several regulators of transcription that may control the expression of genes involved in pilus extension and retraction, and additional enzymes involved in polysaccharide metabolism. Three insertions that abolish S motility lie within genes predicted to encode glycolytic enzymes, suggesting that the signal for pilus retraction may be a simple product of exopolysaccharide catabolism.
Relaxation of Selection With Equalization of Parental Contributions in Conservation Programs: An Experimental Test With Drosophila melanogaster
Authors: Rodríguez-Ramilo S T , Morán P , Caballero A
Published: November 2005

Equalization of parental contributions is one of the most simple and widely recognized methods to maintain genetic diversity in conservation programs, as it halves the rate of increase in inbreeding and genetic drift. It has, however, the negative side effect of implying a reduced intensity of natural selection so that deleterious genes are less efficiently removed from the population with possible negative consequences on the reproductive capacity of the individuals. Theoretical results suggest that the lower fitness resulting from equalization of family sizes relative to that for free contribution schemes is expected to be substantial only for relatively large population sizes and after many generations. We present a long-term experiment with Drosophila melanogaster, comparing the fitness performance of lines maintained with equalization of contributions (EC) and others maintained with no management (NM), allowing for free matings and contributions from parents. Two (five) replicates of size N = 100 (20) individuals of each type of line were maintained for 38 generations. As expected, EC lines retained higher gene diversity and allelic richness for four microsatellite markers and a higher heritability for sternopleural bristle number. Measures of life-history traits, such as egg-to-adult viability, mating success, and global fitness declined with generations, but no significant differences were observed between EC and NM lines. Our results, therefore, provide no evidence to suggest that equalization of family sizes entails a disadvantage on the reproductive capacity of conserved populations in comparison with no management procedures, even after long periods of captivity.
Pleiotropic Costs of Niche Expansion in the RNA Bacteriophage Φ6
Authors: Duffy Siobain , Turner Paul E , Burch Christina L
Published: November 2005

Natural and experimental systems have failed to universally demonstrate a trade-off between generalism and specialism. When a trade-off does occur it is difficult to attribute its cause to antagonistic pleiotropy without dissecting the genetic basis of adaptation, and few previous experiments provide these genetic data. Here we investigate the evolution of expanded host range (generalism) in the RNA virus Φ6, an experimental model system allowing adaptive mutations to be readily identified. We isolated 10 spontaneous host range mutants on each of three novel Pseudomonas hosts and determined whether these mutations imposed fitness costs on the standard laboratory host. Sequencing revealed that each mutant had one of nine nonsynonymous mutations in the Φ6 gene P3, important in host attachment. Seven of these nine mutations were costly on the original host, confirming the existence of antagonistic pleiotropy. In addition to this genetically imposed cost, we identified an epigenetic cost of generalism that occurs when phage transition between host types. Our results confirm the existence in Φ6 of two costs of generalism, genetic and environmental, but they also indicate that the cost is not always large. The possibility for cost-free niche expansion implies that varied ecological conditions may favor host shifts in RNA viruses.
Efficacy of Formalin as an Egg Disinfectant for Improving Hybrid Catfish (Channel Catfish × Blue Catfish) Hatching Success
Authors: Small Brian C , Chatakondi Nagaraj
Published: November 2005

Formalin is currently the only aquaculture drug approved by the U.S. Food and Drug Administration for the control of fungi on the eggs of all finfish. The efficacy of formalin for disinfecting hybrid catfish (channel catfish Ictalurus punctatus × blue catfish I. furcatus) eggs was examined and compared with that of three other potential chemotherapeutants. Two experiments were conducted to evaluate treatment dose and frequency on the hatching success of the hybrid catfish. In the first experiment, hybrid catfish egg masses were divided and assigned to 1 of 13 treatments administered as daily 15-min baths. The treatments were as follows: (1) control (no treatment), (2) 50 ppm (mg/L) formalin (F), (3) 100 ppm F, (4) 200 ppm F, (5) 125 ppm hydrogen peroxide (HP), (6) 250 ppm HP, (7) 500 ppm HP, (8) 50 ppm povidone iodine (PI), (9) 100 ppm PI, (10) 200 ppm PI, (11) 2.5 ppm copper sulfate (CS), (12) 5 ppm CS, and (13) 10 ppm CS. Hatching success tended to be highest among eggs treated with 100 ppm F (87.7%), 2.5 ppm CS (87.0%), or 100 ppm PI (85.2%), although these success rates were not significantly (P > 0.05) different from that in the control treatment (82.8%). Treatment with 500 ppm HP resulted in a significant (P < 0.05) decrease in hatching success (31.5%). In the second experiment, the optimal frequency of formalin treatments was assessed by treating hybrid catfish eggs zero, two, three, or four times daily. Eggs treated three times daily with 100 ppm F had the highest (P < 0.05) percentage of hatched eggs. To maximize hatching success, three daily treatments of hybrid catfish eggs with 100 ppm F as a 15-min bath is recommended.
A Three-Year Survey of Penaeid Shrimp and Callinectid Crabs from Texas Coastal Waters for Signs of Disease Caused by White Spot Syndrome Virus or Taura Syndrome Virus
Authors: Dorf Barbara A. , Hons Charlene , Varner Patricia
Published: November 2005

The Gulf of Mexico has the largest shrimp industry in the United States, including both natural fisheries and aquaculture resources. Aquaculture production comes primarily from Texas shrimp farms. With intensification of the farmed shrimp industry and international commerce in aquatic species, the incidence of infectious disease outbreaks has become a growing problem. In 1995, the Texas farmed shrimp industry suffered heavy losses during an outbreak of Taura syndrome virus. Rapid disease transmission, in conjunction with high pond mortalities during the grow-out season, revealed the need for a structured preventive health plan with stringent biosecurity measures. In addition, native indigenous shrimp and crab species have never been systematically evaluated for infectious disease agents. Concern for these native species prompted the Texas Parks and Wildlife Department to initiate a survey to evaluate the general health status of select indigenous marine invertebrate species along the Texas coast. From October 1997 through September 2000, 5,399 commercially important wild penaeid shrimp (2,009 white shrimp Litopenaeus setiferus, 2,868 brown shrimp Farfantepenaeus aztecus, and 522 pink shrimp F. duorarum) and 935 crabs (630 blue crabs Callinectes sapidus and 305 lesser blue crabs C. similis) were collected from randomly selected locations in nine Texas coastal bay systems and evaluated for known viral pathogens with the use of histopathology and in situ hybridization. In this study, only the virus Baculovirus penaei was detected in three brown shrimp. Taura syndrome virus and white spot syndrome virus were not detected within the testing limitations of this study.
Identification and Prediction of Fish Assemblages in Streams of the Mid‐Atlantic Highlands, USA
Authors: Cyterski Michael , Barber Craig
Published: November 2005

Management of aquatic resources requires meaningful assessment endpoints on which to base decisions. In freshwater streams, assessment endpoints are often defined as fish communities. Given the limited resources available for environmental monitoring, having a means of predicting fish assemblages in streams where no sampling has yet occurred would be useful. Such a tool could be used for regional screening‐level analyses of fish communities and could be input into local‐scale model applications for evaluating management scenarios of stream degradation or restoration. In this study, a set of fish assemblages (a list of fish species and their corresponding relative abundances) representative of different stream types in the Mid‐Atlantic Highlands region of the United States was defined by use of a k‐means cluster analysis performed on relative abundance estimates. The cluster analysis produced 18 fish assemblages, and the following 14 species had the greatest relative abundance in at least one of the 18 assemblages: Eastern blacknose dace Rhinichthys atratulus, bluehead chub Nocomis leptocephalus, bluntnose minnow Pimephales notatus, brook trout Salvelinus fontinalis, central stoneroller Campostoma anomalum, creek chub Semotilus atromaculatus, fantail darter Etheostoma flabellare, mottled sculpin Cottus bairdii, mountain redbelly dace Phoxinus oreas, redbreast sunfish Lepomis auritus, rosyside dace Clinostomus funduloides, slimy sculpin Cottus cognatus, striped shiner Luxilus chrysocephalus, and white sucker Catostomus commersonii. A discriminant analysis was then used to predict a stream's potential fish assemblage based on stream and watershed characteristics. The discriminant function had a 42% success rate using the following predictors: Latitude, longitude, mean stream depth, percent urban area of the watershed, and percent fine gravel on the stream bottom. The discriminant function was validated with an independent data set from a regional data collection effort in West Virginia, resulting in 44% success when classifying observed stream fish communities.
Reliability of Linear Measurements on a Virtual Bilateral Cleft Lip and Palate Model
Authors: Oosterkamp Barbara C. M. , van der Meer Wicher J. , Rutenfrans Majelle , Dijkstra Pieter U.
Published: November 2005

Objective:

To assess the reliability and validity of measurements performed on three-dimensional virtual models of neonatal bilateral cleft lip and palate patients, compared with measurements performed on plaster cast models.

Materials and Methods:

Ten high-quality plaster cast models of bilateral cleft lip and palate patients were scanned with an LDI-scanner to obtain a three-dimensional virtual model. Linear measurements were performed on the plaster cast models using a digital caliper and also on the three-dimensional virtual model using Viscam RP version 2.1 software. The measurements were performed by two observers on two occasions.

Results:

Intraclass correlations ranging from .81 to .96 were found for all measurements except the measurement between the constructed reference point pr and reference point i (intraclass correlation = .40). A post hoc procedure in which top-view screen prints of the three-dimensional virtual model were used to perform the measurement between reference points pr and i demonstrated an intraclass coefficient of .90.

Conclusions:

Three-dimensional virtual models obtained by laser scanning neonatal cast models of bilateral cleft lip and palate patients can be used reliably and validly to perform linear measurements between existing reference points on the surface of the model using Viscam RP version 2.1 software. Measurements between reference points constructed outside the surface of the model cannot be validly performed on the three-dimensional virtual model with the software used in this study. For these measurements, top-view screen prints of the three-dimensional virtual model can be used.