Physiological ecology of the arctic ground squirrel: Energy metabolism, torpor, and behavioral endocrinology

Thesis (Ph.D.) University of Alaska Fairbanks, 1998I monitored seasonal changes in body condition and dates of immergence into and emergence from hibernation in a natural population of arctic ground squirrels (Sphermophilus parryii kennicottii) living on the North Slope of Alaska. Age and sex differences in changes of body condition and hibernation chronology are attributable to sex differences in energetic costs associated with preparation for reproduction and differences in reproductive status within males. While winters are long and environmental conditions faced by arctic ground squirrels in northern Alaska are extreme, the timing of hibernation did not differ appreciably from patterns observed in Sciurid populations living in temperate latitudes. To determine the environmental conditions faced by S. parryii during hibernation and to investigate the effect of overwinter temperature on change in body condition of the individual, I instrumented 18 burrow sites with temperature-sensitive data loggers to record soil temperature at hibernacula depth. Burrow sites did not differ significantly in soil temperature over years, but significant thermal differences were observed among burrows. Burrows with more shrubby vegetation accumulated deeper snow and had higher overwinter temperatures than did windswept sites. Females hibernated at warmer sites than did males and adults hibernated at warmer sites than juveniles. Repeated measures of overwinter changes in body condition were not significantly correlated with winter soil temperatures for any age or sex class. To determine the energetic cost associated with hibernation under arctic conditions, I measured metabolic rate, respiratory quotient, and body temperature of arctic ground squirrels in steady-state torpor. At ambient temperatures below 0\sp\circC, body temperature remained constant and metabolic rate increased proportional to the gradient between body and ambient temperatures. With increased metabolic rate associated with decreased ambient temperature, animals switched from catabolism of exclusively lipid fuel to mixed fuels. To test the effects of male-male aggressive behavior on circulating testosterone and corticosterone concentrations during the breeding season, I staged encounters between free-living males and sampled them for blood following the interaction. Levels of testosterone and corticosterone significantly increased following the encounter compared to in control animals, and the magnitude of increase significantly correlated with the intensity of the interaction

Lifetime glucocorticoid profiles in baleen of right whale calves: Potential relationships to chronic stress of repeated wounding by Kelp Gulls

Baleen tissue accumulates stress hormones (glucocorticoids, GC) as it grows, along with other adrenal, gonadal and thyroid hormones. The hormones are deposited in a linear fashion such that a single plate of baleen allows retrospective assessment and evaluation of long-term trends in the whales´ physiological condition. In whale calves, a single piece of baleen contains hormones deposited across the lifespan of the animal, with the tip of the baleen representing prenatally grown baleen. This suggests that baleen recovered from stranded carcasses of whale calves could be used to examine lifetime patterns of stress physiology. Here we report lifetime profiles of cortisol and corticosterone in baleen of a North Atlantic right whale ("NARW" - Eubalaena glacialis) calf that died from a vessel strike, as well as four southern right whale ("SRW" - Eubalaena australis) calves that were found dead with varying severity of chronic wounding from Kelp Gull (Larus dominicanus) attacks. In all five calves, prenatally grown baleen exhibited a distinctive profile of elevated glucocorticoids that declined shortly before birth, similar to GC profiles reported from baleen of pregnant females. After birth, GC profiles in calf baleen corresponded with the degree of wounding. The NARW calf and two SRW calves with no or few gull wounds had relatively low and constant GC content throughout life, while two SRW calves with high numbers of gull wounds had pronounced elevations in baleen GC content in postnatal baleen followed by a precipitous decline shortly before death, a profile suggestive of prolonged chronic stress. Baleen samples may present a promising and valuable tool for defining the baseline physiology of whale calves and may prove useful for addressing conservation-relevant questions such as distinguishing acute from chronic stress and, potentially, determining cause of death.Fil: Ajó, Alejandro A. Fernández. Northern Arizona University; Estados UnidosFil: Hunt, Kathleen E.. Northern Arizona University; Estados UnidosFil: Uhart, Marcela María. University of California at Davis; Estados UnidosFil: Rowntree, Victoria. University of Utah; Estados UnidosFil: Sironi, Mariano. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Diversidad Biológica y Ecológica; Argentina. Instituto de Conservación de Ballenas; ArgentinaFil: Marón, Carina Flavia. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Diversidad Biológica y Ecológica; Argentina. Instituto de Conservación de Ballenas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Di Martino, Matias. Southern Right Whale Health Monitoring Program; ArgentinaFil: Buck, Charles Loren. Northern Arizona University; Estados Unido

GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes

BACKGROUND: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb. RESULTS: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences. CONCLUSIONS: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." Availability: and

Day and night in the subterranean: measuring daily activity patterns of subterranean rodents (Ctenomys aff. knighti) using bio-logging

While most studies of the impacts of climate change have investigated shifts in the spatial distribution of organisms, temporal shifts in the time of activity is another important adjustment made by animals in a changing world. Due to the importance of light and temperature cycles in shaping activity patterns, studies of activity patterns of organisms that inhabit extreme environments with respect to the 24-hour cyclicity of Earth have the potential to provide important insights into the interrelationships among abiotic variables, behaviour and physiology. Our previous laboratory studies with Argentinean tuco-tucos from the Monte desert (Ctenomys aff. knighti) show that these subterranean rodents display circadian activity/rest rhythms that can be synchronized by artificial light/dark cycles. Direct observations indicate that tuco-tucos emerge mainly for foraging and for removal of soil from their burrows. Here we used bio-logging devices for individual, long-term recording of daily activity/rest (accelerometry) and time on surface (light-loggers) of six tuco-tucos maintained in outdoor semi-natural enclosures. Environmental variables were measured simultaneously. Activity bouts were detected both during day and night but 77% of the highest values happened during the daytime and 47% of them coincided with time on surface. Statistical analyses indicate time of day and temperature as the main environmental factors modulating time on surface. In this context, the total duration that these subterranean animals spent on surface was high during the winter, averaging 3 h per day and time on surface occurred when underground temperature was lowest. Finally, transport of these animals to the indoor laboratory and subsequent assessment of their activity rhythms under constant darkness revealed a switch in the timing of activity. Plasticity of activity timing is not uncommon among desert rodents and may be adaptive in changing environments, such as the desert where this species lives.Fil: Jannetti, Milene G.. Universidade de Sao Paulo. Departamento de Fisiología. Instituto de Biociencias; BrasilFil: Buck, Charles Loren. Northern Arizona University.; Estados UnidosFil: Valentinuzzi, Verónica Sandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de Catamarca. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Secretaría de Industria y Minería. Servicio Geológico Minero Argentino. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Provincia de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja; ArgentinaFil: Oda, Gisele Akemi. Universidade de Sao Paulo. Departamento de Fisiología. Instituto de Biociencias; Brasi

Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource

The Poxvirus Bioinformatics Resource Center (PBRC) has been established to provide informational and analytical resources to the scientific community to aid research directed at providing a better understanding of the Poxviridae family of viruses. The PBRC was specifically established as the result of the concern that variola virus, the causative agent of smallpox, as well as related viruses, might be utilized as biological weapons. In addition, the PBRC supports research on poxviruses that might be considered new and emerging infectious agents such as monkeypox virus. The PBRC consists of a relational database and web application that supports the data storage, annotation, analysis and information exchange goals of the project. The current release consists of over 35 complete genomic sequences of various genera, species and strains of viruses from the Poxviridae family. Sequence and annotation information for these viruses has been obtained from sequences publicly available from GenBank as well as sequences not yet deposited in GenBank that have been obtained from ongoing sequencing projects. In addition to sequence data, the PBRC provides comprehensive annotation and curation of virus genes; analytical tools to aid in the understanding of the available sequence data, including tools for the comparative analysis of different virus isolates; and visualization tools to help better display the results of various analyses. The PBRC represents the initial development of what will become a more comprehensive Viral Bioinformatics Resource Center for Biodefense that will be one of the National Institute of Allergy and Infectious Diseases' ‘Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases’. The PBRC website is available at http://www.poxvirus.org

Determining the Quantitative Principles of T Cell Response to Antigenic Disparity in Stem Cell Transplantation

Alloreactivity compromising clinical outcomes in stem cell transplantation is observed despite HLA matching of donors and recipients. This has its origin in the variation between the exomes of the two, which provides the basis for minor histocompatibility antigens (mHA). The mHA presented on the HLA class I and II molecules and the ensuing T cell response to these antigens results in graft vs. host disease. In this paper, results of a whole exome sequencing study are presented, with resulting alloreactive polymorphic peptides and their HLA class I and HLA class II (DRB1) binding affinity quantified. Large libraries of potentially alloreactive recipient peptides binding both sets of molecules were identified, with HLA-DRB1 generally presenting a greater number of peptides. These results are used to develop a quantitative framework to understand the immunobiology of transplantation. A tensor-based approach is used to derive the equations needed to determine the alloreactive donor T cell response from the mHA-HLA binding affinity and protein expression data. This approach may be used in future studies to simulate the magnitude of expected donor T cell response and determine the risk for alloreactive complications in HLA matched or mismatched hematopoietic cell and solid organ transplantation

Global estimates of mineral dust aerosol iron and aluminum solubility that account for particle size using diffusion-controlled and surface-area-controlled approximations

Mineral aerosol deposition is recognized as the dominant source of iron to the open ocean and the solubility of iron in the dust aerosol is highly variable, with measurements ranging from 0.01–80%. Global models have difficulty capturing the observed variations in solubility, and have ignored the solubility dependence on aerosol size. We introduce two idealized physical models to estimate the size dependence of mineral aerosol solubility: a diffusion‐controlled model and a surface‐area‐controlled model. These models produce differing time‐ and space‐varying solubility maps for aerosol Fe and Al given the dust age at deposition, size‐resolved dust entrainment fields, and the aerosol acidity. The resulting soluble iron deposition fluxes are substantially different, and more realistic, than a globally uniform solubility approximation. The surface‐area‐controlled solubility varies more than the diffusion‐controlled solubility and better captures the spatial pattern of observed solubility in the Atlantic. However, neither of these two models explains the large solubility variation observed in the Pacific. We then examine the impacts of spatially variable, size‐dependent solubility on marine biogeochemistry with the Biogeochemical Elemental Cycling (BEC) ocean model by comparing the modeled surface ocean dissolved Fe and Al with observations. The diffusion‐based variable solubility does not significantly improve the simulation of dissolved Fe relative to a 5% globally uniform solubility, while the surface‐area‐based variable solubility improves the simulation in the North Atlantic but worsens it in the Pacific and Indian Oceans

TAMEE: data management and analysis for tissue microarrays

BACKGROUND: With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. RESULTS: TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. CONCLUSION: We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from

Lubrication

Discussion Grou