bluuebunny/crossref_metadata_2025 huggingface dataset:
FEEDING PREFERENCES OF THE MONKEY MIA DOLPHINS: RESULTS FROM A SIMULTANEOUS CHOICE PROTOCOL
Authors: Dill Lawrence M. , Dill Elizabeth S. , Charles David
Published: August 2006

Abstract

The semiwild beach‐feeding bottlenose dolphins (Tursiops aduncus) of Monkey Mia, Western Australia, provide an unparalleled opportunity to examine prey preference of this species. In a series of binary‐choice feeding experiments, we took advantage of the animals' willingness to be fed by hand, to explore their preferences for fish species, size, and state (freshly caught or previously frozen). At the end of each beach visit, each dolphin was provided with a pair of fish but allowed to eat only the first one chosen. The dolphins appeared indifferent among the three species of fish offered to them (yellowtail trumpeter, Amniataba caudovittatus; striped trumpeter, Pelates sexlineatus; and western butterfish, Pentapodus vitta), which were of similar body form and matched for mass. Overall, the dolphins showed a slight preference for the larger of two yellowtail trumpeter offered, suggesting the capability for rational choice when there was a basis for it (most likely energy in this case), although there was considerable individual variation. The dolphins did not distinguish between freshly caught and previously frozen yellowtail. The methodology we describe can be used to generate data of potential value for understanding food and habitat selection of wild dolphins, and for modifying management practices for semiwild dolphins at Monkey Mia and elsewhere.
A NOVEL BEHAVIOR OBSERVED IN HUMPBACK WHALES ON WINTERING GROUNDS AT ABROLHOS BANK (BRAZIL)
Authors: Morete Maria E. , Freitas Ana , Engel Marcia H. , Pace Richard M. , Clapham Phillip J.
Published: August 2006

Abstract

We describe a novel behavior, termed “tail‐up,” observed in humpback whales (Megaptera novaeangliae) on wintering grounds on Abrolhos Bank, Brazil. The behavior involves the whale positioned vertically in the water column with its tail in the air. With the exception of calves, tail‐up was observed in all social classes, and its frequency increased through the end of the season. Tail‐ups were recorded in 144 (5.8%) of 2,465 groups of whales observed from a shore station, and in 297 (14.9%) of 1,996 groups observed from vessel surveys; biases in each method suggest that the true frequency lies between these sources. One hundred and fifty‐two hours of continuous sampling showed that the dutation of tail‐up events lasted from a few seconds to 12 min and was longest in groups comprised of a single adult. The maximum duration of a recorded period that consistently included tail‐up was 10 h; however, some individuals were observed to engage in the behavior at night and for four consecutive days. Tail‐up movement speed did not vary by social class; however, it varied according to wind direction and speed. The characteristics of tail‐up that we observed showed that it differed from the descriptions of similar behaviors in other cetacean species. The function of tail‐up is unknown, but we suggest that it may be a multifunctional behavior.
EVALUATION OF THE ALASKA HARBOR SEAL (PHOCA VITULINA) POPULATION SURVEY: A SIMULATION STUDY
Authors: Adkison Milo D. , Quinn Terrance J. , Small Robert J.
Published: August 2006

Abstract

We used simulation to investigate robust designs and analyses for detecting trends from population surveys of Alaska harbor seals. We employed an operating model approach, creating simulated harbor seal population dynamics and haul‐out behavior that incorporated factors thought to potentially affect the performance of aerial surveys. The factors included the number of years, the number of haul‐out sites in an area, the number and timing of surveys within a year, known and unknown covariates affecting haul‐out behavior, substrate effects, movement among substrates, and variability in survey and population parameters. We found estimates of population trend were robust to the majority of potentially confounding factors, and that adjusting counts for the effects of covariates was both possible and beneficial. The use of mean or maximum counts by site without covariate correction can lead to substantial bias and low power in trend determination. For covariate‐corrected trend estimates, there was minimal bias and loss of accuracy was negligible when surveys were conducted 20 d before or after peak haul‐out attendance, survey date became progressively earlier across years, and peak attendance fluctuated across years. Trend estimates were severely biased when the effect of an unknown covariate resulted in a long‐term trend in the fraction of the population hauled out. A key factor governing the robustness and power of harbor seal population surveys is intersite variability in trend. This factor is well understood for sites within the Prince William Sound and Kodiak trend routes for which at least 10 consecutive annual surveys have been conducted, but additional annual counts are needed for other areas. The operating model approach proved to be an effective means of evaluating these surveys and should be used to evaluate other marine mammal survey designs.
SPERM WHALES IN THE GULF OF CALIFORNIA: RESIDENCY, MOVEMENTS, BEHAVIOR, AND THE POSSIBLE INFLUENCE OF VARIATION IN FOOD SUPPLY
Authors: Jaquet Nathalie , Gendron Diane , Coakes Amanda
Published: August 2006

Abstract

Sperm whale movements, residency, population structure, and behavior were investigated in the Gulf of California in 1998 and 1999. Variations in sperm whale movement patterns and behavior were related to changes in prey abundance (jumbo squid, Dosidicus gigas) determined by fishery statistics. Photo‐identification data revealed that seven female sperm whales moved into the Gulf of California from the Galapagos Islands, traveling up to 3,803 km. These are among the longest documented movements for female sperm whales. There were significant differences in speed and distance traveled during a dive cycle between 1998 and 1999 (low and high squid abundance). In 1999 there were also significant differences in small‐scale movements and behavior between the northern and the southern part of the study area (high and low prey abundance). These results suggest that when food resources are low, sperm whales travel in straighter lines, dive for longer periods, travel larger distances during dive cycles, and at higher speed. In 1999 there were significant differences in time spent socializing in areas of high prey abundance versus areas of low abundance. All of these changes in behavior were consistent with increased foraging effort when squid abundance was low. A high proportion of mature males and first‐year calves were observed in the Gulf of California, suggesting that it is an important sperm whale breeding ground.
IMPROVED BODY CONDITION OF WEANED HAWAIIAN MONK SEAL PUPS ASSOCIATED WITH EL Niño EVENTS: POTENTIAL BENEFITS TO AN ENDANGERED SPECIES
Authors: Antonelis George A. , Baker Jason D. , Polovina Jeffrey J.
Published: August 2006

Abstract

Efforts to enhance recovery of endangered Hawaiian monk seals (Monachus schauinslandi) require an understanding of factors influencing population dynamics. This study examines relationships between body condition and survival of monk seal pups at French Frigate Shoals and Laysan Island and El Niño events. Girth measurements and mass estimates were used as indicators of pup body condition, and survival was evaluated from weaning to age 2. Linear models and logistic regression analysis were used to evaluate El Niño effects. Temporal trends in mean girth, mass, and survival were identified at both study sites. After accounting for temporal trends, girths were 3.7 cm and 2.7 cm greater during El Niño years at French Frigate Shoals and Laysan Island, respectively. Average mass estimates were significantly greater during El Niño years at French Frigate Shoals (2.6 kg increase), but were not significantly different at Laysan Island (1.8 kg increase). Weaned pups born at French Frigate Shoals during El Niño years survived significantly better, but this effect was not detected at Laysan Island. El Niño events probably affect pup condition and survival, but these parameters need to be monitored during future El Niño events to clarify these relationships.
POPULATION STRUCTURE IN AN INSHORE CETACEAN REVEALED BY MICROSATELLITE AND mtDNA ANALYSIS: BOTTLENOSE DOLPHINS (TURSIOPS SP.) IN SHARK BAY, WESTERN AUSTRALIA
Authors: Krützen Michael , Sherwin William B. , Berggren Per , Gales Nick
Published: August 2006

Abstract

We examined population substructure of bottlenose dolphins (Tursiops sp). in Shark Bay, Western Australia, using 10 highly polymorphic microsatellite loci, and mitochondrial DNA (mtDNA). For microsatellite analysis, 302 different animals were sampled from seven localities throughout the bay. Analysis of genetic differentiation between sampling localities showed a significant correlation between the number of migrants (Nm) calculated from FST, RST and private alleles, and distance between localities–a pattern of isolation‐by‐distance. For mtDNA, 220 individuals from all seven localities were sequenced for a 351 base pair fragment of the control region, resulting in eight haplotypes, with two distinct clusters of haplotypes. Values of FST and (φ)ST for mtDNA yielded statistically significant differences, mostly between localities that were not adjacent to each other, suggesting female gene flow over a scale larger than the sampled localities. We also observed a significant correlation between the number of female migrants calculated from FST and φST and the distance of sampling localities. Our results indicate that dispersal in female dolphins in Shark Bay is more restricted than that of males.
A PREHISTORIC BREEDING POPULATION OF HARP SEALS (PHOCA GROENLANDICA) IN THE BALTIC SEA
Authors: Storå Jan , Ericson Per G. P.
Published: August 2006

Abstract

The pelagic and gregarious, low Arctic harp seal (Phoca groenlandica) is the most common seal species in most refuse faunas from coastal hunter‐gatherer sites dating from the late Atlantic to the early Subboreal period (ca. 4000‐2000 cal B. C.) in the Baltic Sea. Our main objective was to examine the migration contra breeding population hypotheses regarding the Baltic harp seals. Analyses of epiphyseal fusion data and osteometry of archeological harp seal remains from 25 dwelling‐sites suggest that a local breeding population established itself in the early Subboreal period. In the Middle Neolithic the rookery possibly was situated in the Baltic proper, south of Aland and west of Gotland. The mean adult size of the Baltic harp seals decreased, suggesting minimal genetic exchange with the north Atlantic Ocean population. Genetic drift, interspecific competition, and over‐hunting by humans are all factors likely to have contributed to the eventual extinction of harp seals in the Baltic Sea.
FORAGING DEPTHS OF SEA OTTERS AND IMPLICATIONS TO COASTAL MARINE COMMUNITIES
Authors: Bodkin James L. , Esslinger George G. , Monson Daniel H.
Published: August 2006

Abstract

We visually observed 1,251 dives, of 14 sea otters instrumented with TDRs in southeast Alaska, and used attribute values from observed dives to classify 180,848 recorded dives as foraging (0.64), or traveling (0.36). Foraging dives were significantly deeper, with longer durations, bottom times, and postdive surface intervals, and greater descent and ascent rates, compared to traveling dives. Most foraging occurred in depths between 2 and 30 m (0.84), although 0.16 of all foraging was between 30 and 100 m. Nine animals, including all five males, demonstrated bimodal patterns in foraging depths, with peaks between 5 and 15 m and 30 and 60 m, whereas five of nine females foraged at an average depth of 10 m. Mean shallow foraging depth was 8 m, and mean deep foraging depth was 44 m. Maximum foraging depths averaged 61 m (54 and 82 for females and males, respectively) and ranged from 35 to 100 m. Female sea otters dove to depths ≤20 m on 0.85 of their foraging dives while male sea otters dove to depths ≥45 m on 0.50 of their foraging dives. Less than 0.02 of all foraging dives were >55 m, suggesting that effects of sea otter foraging on nearshore marine communities should diminish at greater depths. However, recolonization of vacant habitat by high densities of adult male sea otters may result in initial reductions of some prey species at depths >55 m.
THE LIKELIHOOD OF SPERM COMPETITION IN MANATEES‐EXPLAINING AN APPARENT PARADOX
Authors: Reynolds JOHN E. , Rommel Sentiel A. , Pitchford Meghan E.
Published: August 2006

Abstract

Florida manatees (Trichechus manatus latirostris) are promiscuous, with multiple males mating with individual females. This suggests manatees are sperm competitors. Surprisingly, manatee testes are not relatively large. For adult males in non‐winter, testicular size is approximately twice what is expected, based on allometry, for “typical” (i. e., non‐sperm competitor) male mammals of similar size; for these manatees, combined testicular weight represents 0.19% of the body weight (n= 27 manatees). Testicular weight was generally largest in manatees older than 7 yr in non‐winter. Testicular size of some sperm competitors is as much as an order of magnitude (or more) larger than expected in a “typical” species. Perhaps in compensation for the testes not being remarkably large, the seminal vesicles of mature manatees may be larger than the testes. Production of notably large volumes of seminal fluid characterizes sperm competitor primate species and may have positive energy consequences for species such as the manatee that have extremely low metabolic rates. Another possible explanation for the observed relationship between testicular mass and body mass in manatees is that selection for a greatly expanded hindgut and extremely dense, heavy integument could make the body mass of manatees “artificially” high, and the relative testicular mass “artificially” low.
AERIAL SURVEYS FOR COASTAL DOLPHINS: ABUNDANCE OF HECTOR'S DOLPHINS OFF THE SOUTH ISLAND WEST COAST, NEW ZEALAND
Authors: Slooten Elisabeth , Dawson Stephen Michael , Rayment William Jacob
Published: August 2006

Abstract

Line‐transect surveys of abundance depend critically on the estimation of detection probability, which includes corrections for availability and visibility. In this aerial line‐transect survey for Hector's dolphin (Cephalorhynchus hectori) we recorded dive times from a helicopter to estimate the proportion of time that dolphins could be seen at or near the water surface and were therefore “available” to be counted. The proportion of available sightings that were counted on transect lines was estimated by comparing sightings by two independent teams of two observers in the fixed‐wing plane. The survey covered the area between Farewell Spit and Milford Sound, off the west coast of the South Island of New Zealand. Survey effort was stratified according to existing distribution data. A total of 142 separate sightings was made on 1,355 km of trackline. Average availability for fifty Hector's dolphin groups observed from the helicopter (161 dive/surface cycles) was 46.3% (CV = 4.2%). Data from the two independent observer teams indicated that 96.2% (CV = 2.3%) of the dolphin groups that were at the surface and on the trackline were seen. The abundance estimate for the South Island west coast, corrected for visibility and availability, was 5,388 Hector's dolphins (CV = 20.6%). The total population estimate for South Island Hector's dolphins is 7,270 (CV = 16.2%).
DIETS OF COASTAL BOTTLENOSE DOLPHINS FROM THE U. S. MID‐ATLANTIC COAST DIFFER BY HABITAT
Authors: Gannon Damon P. , Waples Danielle M.
Published: August 2006

Abstract

We recorded 31 species in the stomachs of 146 coastal bottlenose dolphins (Tursiops truncatus) from North Carolina, U. S. A. Sciaenid fishes were the most common prey (frequency of occurrence = 95%). By mass, Atlantic croaker (Micropogonias undulatus) dominated the diet of dolphins that stranded inside estuaries, whereas weakfish (Cynosicon regalis) was most important for dolphins in the ocean. Inshore squid (Loligo sp.) was eaten commonly by dolphins in the ocean, but not by those in the estuaries. There was no significant pattern in prey size associated with dolphin demography, but the proportion of the diet represented by croaker was higher for males than for females, and mature dolphins ate more croaker than did juveniles. Dietary differences between dolphins that stranded in the estuaries and those that stranded on ocean beaches support the hypothesis that some members of the population inhabit the ocean primarily while others reside principally in estuaries. The overwhelming majority of prey were soniferous species (75% of numerical abundance), which is consistent with the hypothesis that bottlenose dolphins use passive listening to locate noise‐making fishes. However, spatiotemporal patterns in consumption of Sciaenid fishes did not coincide with their spawning, which is when peak sound production is thought to occur.
ABUNDANCE AND POPULATION TREND (1978‐2001) OF WESTERN ARCTIC BOWHEAD WHALES SURVEYED NEAR BARROW, ALASKA
Authors: George J. C. “CRAIG” , Zeh J. , Suydam R. , Clark C.
Published: August 2006

Abstract

The 2001 survey of western Arctic (Bering, Chukchi, and Beaufort seas) bowhead whales was conducted from 5 April to 7 June near Barrow, Alaska. Visual observers recorded a total of 3,295 “new” (not seen before) and 532 “conditional” (possibly seen before) whales in 1,130 h of watch effort, including 121 new calves (3.7% of the new whales). Concurrent with the visual survey, passive acoustic surveillance was conducted almost continuously from 16 April to 31 May, resulting in 27,023 locations of vocalizing bowhead whales. The estimated number of whales within 4 km of the perch (N4) was 7,025 (SE = 1,068). The estimated proportion of the whales within 4 km of the perch (P4) was 0.862 (SE = 0.044, computed by a moving blocks bootstrap). Combining these, the abundance estimate (N4/P4) for 2001 is 10,470 (SE = 1, 351) with a 95% confidence interval of 8, 100–13, 500. The estimated annual rate of increase (ROI) of the population from 1978 to 2001 is 3.4% (95% CI 1.7%‐5%). Reports from hunters and results of an aerial survey in June 2001 indicate whales continued to pass Barrow after the survey had ended. In 2001 51% (572 h) of the watch was scored as occurring during “fair‐excellent” visibility conditions, somewhat lower than the average for all surveys since 1978. Sea ice in the leads and fog were the principle environmental factors affecting visibility for all years. The estimated rate of increase and the fact that the number of calves counted in 2001 is the highest ever recorded suggest a steady recovery of this population. Other populations of large balaenids, notably the North Atlantic right whale, have failed to recover despite 70 yr of protection. The recovery of the howhead whale is likely attributable to low anthropogenic mortality, a relatively pristine habitat, and a well‐managed subsistence hunt. Nonetheless, offshore oil development, increasing shipping traffic, changes in the Bering Sea ecosystem, sea ice retreat, and possibly killer whale predation within its range could impact this bowhead population and should be carefully monitored.
CHANGES IN ABUNDANCE OF HARBOR SEALS IN MAINE, 1981–2001
Authors: Gilbert James R. , Waring Gordon T. , Wynne Kate M. , Guldager Nikolina
Published: August 2006

Abstract

Aerial counts of harbor seals (Pboca vitulina concolor) on ledges along the Maine coast were conducted during the pupping season in 1981, 1986, 1993, 1997, and 2001. Between 1981 and 2001, the uncorrected counts of seals increased from 10,543 to 38,014, an annual rate of 6.6 percent. In 2001 30 harbor seals were captured and radio‐tagged prior to aerial counts. Of these, 19 harbor seals (six adult males, two adult females, seven juvenile males, and four juvenile females) were available during the survey to develop a correction factor for the fraction of seals not observed. The corrected 2001 abundance estimate was 99,340 harbor seals. Productivity in this population has increased since 1981 from 6.4% pups to 24.4% pups. The number of gray seals (Halichoerus grypus) counted during the harbor seal surveys increased from zero in both 1981 and 1986 to 1,731 animals in 2001.
Oxygen Isotope Variation in Stony-Iron Meteorites
Authors: Greenwood R. C. , Franchi I. A. , Jambon A. , Barrat J. A. , Burbine T. H.
Published: August 2006

Asteroidal material, delivered to Earth as meteorites, preserves a record of the earliest stages of planetary formation. High-precision oxygen isotope analyses for the two major groups of stony-iron meteorites (main-group pallasites and mesosiderites) demonstrate that each group is from a distinct asteroidal source. Mesosiderites are isotopically identical to the howardite-eucrite-diogenite clan and, like them, are probably derived from the asteroid 4 Vesta. Main-group pallasites represent intermixed core-mantle material from a single disrupted asteroid and have no known equivalents among the basaltic meteorites. The stony-iron meteorites demonstrate that intense asteroidal deformation accompanied planetary accretion in the early Solar System.
Decreased xanthine oxidoreductase is a predictor of poor prognosis in early-stage gastric cancer
Authors: Linder N , Haglund C , Lundin M , Nordling S , Ristimäki A , Kokkola A , Mrena J , Wiksten J-P , Lundin J
Published: August 2006

Background:Xanthine oxidoreductase (XOR) is a key enzyme in the degradation of DNA, RNA and high-energy phosphates. About half of the patients with breast cancer have a decrease in XOR expression. Patients with breast cancer with unfavourable prognosis are independently identified by the loss of XOR.

Aim:To assess the clinical relevance of XOR expression in gastric cancer.

Methods:XOR levels were studied by immunohistochemistry in tissue microarray specimens of 337 patients with gastric cancer and the relation between XOR expression and a series of clinicopathological variables, as well as disease-specific survival, was assessed.

Results:XOR was moderately decreased in 41% and was undetectable in another 14% of the tumours compared with the corresponding normal tissue. Decreased XOR was associated with advanced stage, deep tumour penetration, diffusely spread tumour location, positive lymph node status, large tumour size, non-curative disease, cellular aneuploidy, high S-phase fraction and high cyclooxygenase-2 expression, but not with p53 expression or Borrmann classification. Down regulation of XOR was associated with unfavourable outcome, and the cumulative 5-year gastric cancer-specific survival in patients with strong XOR expression was 47%, compared with 22% in those with moderate to negative expression (p<0.001). This was also true in patients with stage I–II (p = 0.01) and lymph node-negative (p = 0.02) disease, as well as in patients with smaller (⩽5 cm) tumours (p = 0.02).

Conclusion:XOR expression in gastric cancer may be a new marker for a more aggressive gastric cancer biology, similar to that previously reported for breast cancer.
Myalgic encephalomyelitis: a review with emphasis on key findings in biomedical research
Authors: Hooper M
Published: August 2006

This review examines research findings in patients with myalgic encephalomyelitis in light of the current debate about this chronic multiple-symptom, multiorgan, multisystem illness and the conflicting views in medicine. These issues cannot be separated from the political opinions and assertions that conflict with science and medicine, and will be part of this review as they have enormous consequences for scientific and medical research, patients, clinicians, carers and policy makers.
Fluctuating asymmetry in certain morphological traits in laboratory populations of Drosophila ananassae
Authors: Vishalakshi C , Singh B N
Published: August 2006

Fluctuating asymmetry (FA, subtle random deviations from perfect bilateral symmetry) is often used as a measure of developmental instability (DI), which results from perturbations in developmental pathways caused by genetic or environmental stressors. During the present study, we estimated FA in 5 morphological traits, viz. wing length (WL), wing to thorax ratio (W:T), sternopleural bristle number (SBN), sex-comb tooth number (SCTN), and ovariole number (ON) in 18 laboratory populations of Drosophila ananassae. FA levels of measured traits differed significantly among populations except for SBN (in males and females) and W:T ratio (in females). Positional fluctuating asymmetry (PFA), a sensitive measure of DI, also varied significantly among the populations for SBN in females and SCTN in males. Interestingly, both males and females were similar for nonsexual traits. However, when FA across all traits (sexual and nonsexual) was combined into a single composite index (CFA), significant differences were found for both populations and sexes. Males showed higher CFA values than females, suggesting that males are more prone to developmental perturbations. The magnitude of FA differed significantly among traits, being lowest for nonsexual traits (SBN, WL, W:T ratio) and highest for sexual traits (SCTN and ON). The trait size of sexual traits (SCTN and ON) was positively correlated with their asymmetry. The possible reasons for variation in FA both among traits and among populations, and the usefulness of FA as an indicator of developmental stress and phenotypic quality in D. ananassae are discussed.Key words: fluctuating asymmetry, developmental instability, morphological traits, laboratory populations, D. ananassae.
Cross-species microsatellite amplification inVasconcelleaand related genera and their use in germplasm classification
Authors: Kyndt T , Droogenbroeck B Van , Haegeman A , Roldán-Ruiz I , Gheysen G
Published: August 2006

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea × heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.Key words: Carica, Jacaratia, Vasconcellea, simple sequence repeats, cross-species amplification, classification, interspecific hybrids.
Identification and isolation of a BTB–POZ-containing gene expressed in oocytes and early embryos of the zebrafish Danio rerio
Authors: Smith T H.L , Stedronsky K , Morgan B , McGowan R A
Published: August 2006

In this report, we describe the cloning of a cDNA from the zebrafish Danio rerio encoding a protein containing a BTB–POZ domain closely resembling the BTBD1 and BTBD2 proteins previously identified in mammals. However, unlike other BTB–POZ-containing genes, expression of this gene in adults is most abundant in oocytes, where the RNA can be detected at all stages of oogenesis examined. The presence of the RNA persists through early cleavage, but is decreased significantly by gastrulation. Although the function of this gene has yet to be determined, its resemblance to the BTB–POZ family of genes coupled with its expression pattern suggests that it may have an important function in oogenesis and (or) early zebrafish development.Key words: BTBD1, BTBD2, BTB–POZ domain, kelch superfamily, PHR domain.
Long-range histone acetylation: biological significance, structural implications, and mechanismsThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.
Authors: Calestagne-Morelli Alison , Ausió Juan
Published: August 2006

Genomic characterization of various euchromatic regions in higher eukaryotes has revealed that domain-wide hyperacetylation (over several kb) occurs at a range of loci, including individual genes, gene family clusters, compound clusters, and more general clusters of unrelated genes. Patterns of long-range histone hyperacetylation are strictly conserved within each unique cellular system studied and they reflect biological variability in gene regulation. Domain-wide histone acetylation consists generally of nonuniform peaks of enriched hyperacetylation of specific core histones, histone isoforms, and (or) histone variants against a backdrop of nonspecific acetylation across the domain in question. Here we review the characteristics of long-range histone acetylation in some higher eukaryotes and draw special attention to recent literature on the multiple effects that histone hyperacetylation has on chromatin’s structural integrity and how they affect transcription. These include the thermal, ionic, cumulative, and isoform-specific (H4 K16) consequences of acetylation that result in a more dynamic core complex and chromatin fiber.
Reuniting the contrasting functions of H2A.ZThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.
Authors: Guillemette Benoît , Gaudreau Luc
Published: August 2006

It is now well established that cells modify chromatin to set transcriptionally active or inactive regions. Such control of chromatin structure is essential for proper development of organisms. In addition to the growing number of histone post-translational modifications, cells can exchange canonical histones with different variants that can directly or indirectly change chromatin structure. Moreover, enzymatic complexes that can exchange specific histone variants within the nucleosome have now been identified. One such variant, H2A.Z, has recently been the focus of many studies. H2A.Z is highly conserved in evolution and has many different functions, while defining both active and inactive chromatin in different contexts. Advanced molecular techniques, such as genome-wide binding assays (chromatin immunoprecipitation on chip) have recently given researchers many clues as to how H2A.Z is targeted to chromatin and how it affects nuclear functions. We wish to review the recent literature and summarize our understanding of the mechanisms and functions of H2A.Z.
The role of chromatin structure in regulating stress-induced transcription inSaccharomyces cerevisiaeThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.
Authors: Uffenbeck Shannon R. , Krebs Jocelyn E.
Published: August 2006

All cells, whether free-living or part of a multicellular organism, must contend with a variety of environmental fluctuations that can be harmful or lethal to the cell. Cells exposed to different kinds of environmental stress rapidly alter gene transcription, resulting in the immediate downregulation of housekeeping genes, while crucial stress-responsive transcription is drastically increased. Common cis-acting elements within many stress-induced promoters, such as stress response elements and heat shock elements, allow for coordinated expression in response to many different stresses. However, specific promoter architectures, i.e., specific combinations of high- and low-affinity stress-responsive cis elements embedded in a particular chromatin environment, allow for unique expression patterns that are responsive to the individual type and degree of stress. The coordination of transcriptional stress responses and the role that chromatin structure plays in the regulation and kinetics of such responses is discussed. The interplay among global and gene-specific stress responses is illustrated using the constitutive and stress-induced transcriptional regulation of HSP82 as a model. This review also investigates evidence suggesting that stress-induced transcription is globally synchronized with the stress-induced repression of housekeeping gene via 2 distinct mechanisms of facilitating the binding of TATA-binding protein (TBP): TFIID and SAGA-mediated TBP binding.
The relationship between histone H3 phosphorylation and acetylation throughout the mammalian cell cycleThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.
Authors: McManus Kirk J. , Hendzel Michael J.
Published: August 2006

During interphase, histone amino-terminal tails play important roles in regulating the extent of DNA compaction. Post-translational modifications of the histone tails are intimately associated with regulating chromatin structure: phosphorylation of histone H3 is associated with proper chromosome condensation and dynamics during mitosis, while multiple H2B, H3, and H4 tail acetylations destabilize the chromatin fiber and are sufficient to decondense chromatin fibers in vitro. In this study, we investigate the spatio-temporal dynamics of specific histone H3 phosphorylations and acetylations to better understand the interplay of these post-translational modifications throughout the cell cycle. Using a panel of antibodies that individually, or in combination, recognize phosphorylated serines 10 and 28 and acetylated lysines 9 and 14, we define a series of changes associated with histone H3 that occur as cells progress through the cell cycle. Our results establish that mitosis appears to be a period of the cell cycle when many modifications are highly dynamic. Furthermore, they suggest that the upstream histone acetyltransferases/deacetylases and kinase/phosphatases are temporally regulated to alter their function globally during specific cell cycle time points.
Spatial and temporal variability in the fish diet of Antarctic fur seal (Arctocephalus gazella) in the Atlantic sector of the Southern Ocean
Authors: Davis Dexter , Staniland Iain J. , Reid Keith
Published: August 2006

The spatial and temporal variability in the fish component of the diet of Antarctic fur seals (Arctocephalus gazella (Peters, 1875)) in the Atlantic sector of the Southern Ocean was examined using diet data from 10 sites in the region including a 13-year time series from South Georgia. The fish species composition in the diet at each site showed a strong relationship with the local marine habitat / topography. The absence of formerly harvested fish species indicates a lack of recovery of stocks of Notothenia rossii Richardson, 1844 at South Georgia and Champsocephalus gunnari Lönnberg, 1905 at the South Orkney Islands. At South Georgia, Protomyctophum choriodon Hulley, 1981, Lepidonotothen larseni (Lönnberg, 1905), and C. gunnari were the most important species in the diet between 1991 and 2004. Variability in the occurrence of C. gunnari was driven mainly by annual scale processes, particularly those that influence the availability of Antarctic krill (Euphausia superba (Dana, 1852)). The occurrence of the pelagic P. choriodon was primarily influenced by shorter-term water mass changes within the foraging range of the seals. The fish composition in the diet reflects differences in marine habitat / topography, as well as variability, at a range of time scales that reflect environmental variability and harvesting.
Limits to the Adaptive Potential of Small Populations
Authors: Willi Yvonne , Van Buskirk Josh , Hoffmann Ary A.
Published: August 2006

Small populations are predicted to have reduced capacity to adapt to environmental change for two reasons. First, population genetic models indicate that genetic variation and potential response to selection should be positively correlated with population size. The empirical support for this prediction is mixed: DNA markers usually reveal low heterozygosity in small populations, whereas quantitative traits show reduced heritability only in the smallest and most inbred populations. Quantitative variation can even increase in bottlenecked populations although this effect seems unlikely to increase the adaptive potential of populations. Second, individuals in small populations have lower fitness owing to environmental stress and genetic problems such as inbreeding, which can substantially increase the extinction probability of populations in changing environments. This second reason has not been included in assessments of critical population size assuring evolvability and makes it likely that many small threatened populations have a decreased potential for adaptation.
Pleiotropic functions of TNF-α determine distinct IKKβ-dependent hepatocellular fates in response to LPS
Authors: Dajani Rana , Sanlioglu Salih , Zhang Yulong , Li Qiang , Monick Martha M. , Lazartigues Eric , Eggleston Timothy , Davisson Robin L. , Hunninghake Gary W. , Engelhardt John F.
Published: August 2006

TNF-α influences morbidity and mortality during the course of endotoxemia. However, the complex pleiotropic functions of TNF-α remain poorly understood. We evaluated how hepatic induction of NF-κB and TNF-α influence survival and hepatocellular death in a lethal murine model of endotoxic shock. Using dominant-negative viral vectors to inhibit the IKK complex, we demonstrate through this study that the liver is a major source of TNF-α during the course of lethal endotoxemia and that IKKβ (but not IKKα) is predominantly responsible for activating NF-κB and TNF-α in the liver after LPS administration. Using TNF-α knockout mice and hepatic-specific inhibition of IKKβ, we demonstrate that the status of TNF-α and NF-κB balances necrotic and apoptotic fates of hepatocytes in the setting of endotoxemia. In the presence of TNF-α, inhibiting hepatic IKKβ resulted in increased survival, reduced serum proinflammatory cytokines, and reduced hepatocyte necrosis in response to a lethal dose of endotoxin. In contrast, inhibiting hepatic IKKβ in TNF-α knockout mice resulted in decreased survival and increased caspase 3-mediated hepatocyte apoptosis after endotoxin challenge, despite a reduced proinflammatory cytokine response. In the presence of TNF-α, NF-κB-dependent hepatocellular necrosis predominated, while in the absence of TNF-α, NF-κB primarily influenced apoptotic fate of hepatocytes. Changes in JNK phosphorylation after LPS challenge were also dynamically affected by both IKKβ and TNF-α; however, this pathway could not solely explain the differential outcomes in hepatocellular fates. In conclusion, our studies demonstrate that induction of NF-κB and TNF-α balances protective (antiapoptotic) and detrimental (proinflammatory) pathways to determine hepatocellular fates during endotoxemia.
Alltrans-retinoic acid induces apoptosis via p38 and caspase pathways in metaplastic Barrett's cells
Authors: Hormi-Carver Kathy , Feagins Linda A. , Spechler Stuart J. , Souza Rhonda F.
Published: August 2006

Retinoids such as all trans-retinoic acid (ATRA) have been used as chemopreventive agents for a number of premalignant conditions. To explore a potential role for retinoids as chemopreventive agents for Barrett's esophagus, we studied ATRA's effects on apoptosis in a nonneoplastic, telomerase-immortalized, metaplastic Barrett's cell line. We treated the Barrett's cells with ATRA in the presence and absence of inhibitors to p53 (pSRZ-siRNA-p53), p38 (SB-203580 and p38 siRNA), and the caspase cascade (z-Val-Ala-Asp-fluoromethyl ketone). We determined the effects of ATRA and the various inhibitors on apoptosis using cell morphology, terminal deoxynucleotidyltransferase-mediated dUTP nick-end labeling staining, cleaved caspase-3 immunofluorescence, and Annexin V staining. We also determined how ATRA in the presence and absence of the inhibitors affected apoptosis following low-dose UV-B irradiation. ATRA induced apoptosis and increased the expression of p53 protein in a dose-dependent fashion. The apoptotic effect of ATRA was abolished by treatment with inhibitors of both p38 and caspase, but not by p53 interfering RNA (RNAi). Inhibition of p38 also prevented expression of cleaved caspase-3, suggesting that ATRA activates p38 upstream of the caspase cascade. We found that ATRA sensitized immortalized Barrett's cells to apoptosis induced by low-dose UV-B irradiation via a similar mechanism. ATRA induces apoptosis in Barrett's epithelial cells and sensitizes them to apoptosis induced by UV-B irradiation via activation of p38 and the caspase cascade, but not through p53. This study elucidates molecular pathways whereby retinoid treatment might prevent carcinogenesis in Barrett's metaplasia and suggests a potential role for the use of safer retinoids for chemoprevention in Barrett's esophagus.
Iron absorption and hepatic iron uptake are increased in a transferrin receptor 2 (Y245X) mutant mouse model of hemochromatosis type 3
Authors: Drake S. F. , Morgan E. H. , Herbison C. E. , Delima R. , Graham R. M. , Chua A. C. G. , Leedman P. J. , Fleming R. E. , Bacon B. R. , Olynyk J. K. , Trinder D.
Published: August 2006

Hereditary hemochromatosis type 3 is an iron (Fe)-overload disorder caused by mutations in transferrin receptor 2 (TfR2). TfR2 is expressed highly in the liver and regulates Fe metabolism. The aim of this study was to investigate duodenal Fe absorption and hepatic Fe uptake in a TfR2 (Y245X) mutant mouse model of hereditary hemochromatosis type 3. Duodenal Fe absorption and hepatic Fe uptake were measured in vivo by 59Fe-labeled ascorbate in TfR2 mutant mice, wild-type mice, and Fe-loaded wild-type mice (2% dietary carbonyl Fe). Gene expression was measured by real-time RT-PCR. Liver nonheme Fe concentration increased progressively with age in TfR2 mutant mice compared with wild-type mice. Fe absorption (both duodenal Fe uptake and transfer) was increased in TfR2 mutant mice compared with wild-type mice. Likewise, expression of genes participating in duodenal Fe uptake ( Dcytb, DMT1) and transfer (ferroportin) were increased in TfR2 mutant mice. Nearly all of the absorbed Fe was taken up rapidly by the liver. Despite hepatic Fe loading, hepcidin expression was decreased in TfR2 mutant mice compared with wild-type mice. Even when compared with Fe-loaded wild-type mice, TfR2 mutant mice had increased Fe absorption, increased duodenal Fe transport gene expression, increased liver Fe uptake, and decreased liver hepcidin expression. In conclusion, despite systemic Fe loading, Fe absorption and liver Fe uptake were increased in TfR2 mutant mice in association with decreased expression of hepcidin. These findings support a model in which TfR2 is a sensor of Fe status and regulates duodenal Fe absorption and liver Fe uptake.
Differentiation of the Gastric Mucosa IV. Role of trefoil peptides and IL-6 cytokine family signaling in gastric homeostasis
Authors: Giraud A. S. , Jackson C. , Menheniott T. R. , Judd L. M.
Published: August 2006

Gastric trefoil peptides mediate mucosal repair by stimulating cell migration, inhibiting apoptosis and inflammation, and likely augmenting the barrier function of mucus. One of these, tff1, is a gastric-specific tumor suppressor gene, which when repressed is associated with gastric cancer progression. IL-6 family cytokines play an important role in maintaining gastric homeostasis by regulating tff1 and other mediators of mucosal proliferation, inflammation, angiogenesis, and apoptosis. In this review the signaling cascades downstream of the common IL-6 cytokine family coreceptor gp130 that contribute to control of this homeostasis are described, as are the pathological outcomes of imbalancing these pathways.
Growth-dependent changes in endothelial factors regulating arteriolar tone
Authors: Samora Julie Balch , Frisbee Jefferson C. , Boegehold Matthew A.
Published: August 2006

Previous studies from this laboratory suggest that during maturation, rapid microvascular growth is accompanied by changes in the mechanisms responsible for regulation of tissue blood flow. To further define these changes, we studied isolated gracilis muscle arterioles from weanling (∼25 days) and juvenile (∼44 days) Sprague-Dawley rats to test the hypothesis that endothelial mechanisms for the control of arteriolar tone are altered with growth. Responses to the endothelium-dependent dilator acetylcholine (ACh) were greater in weanling arterioles (WA) than in juvenile arterioles (JA), whereas there were no consistent differences between age groups in arteriolar responses to other endothelium-dependent agonists (A-23187, vascular endothelial growth factor, and simvastatin). Inhibition of nitric oxide synthase (NOS) with Nω-nitro-l-arginine methyl ester (l-NAME) attenuated ACh-induced dilation in JA but not in WA. In JA, combined inhibition of NOS and cyclooxygenase (with indomethacin) reduced the dilator responses to ACh and simvastatin by ∼90% and ∼70%, respectively, but had no effect in WA. Cytochrome P450 epoxygenase inhibition [with 2-(propargyloxyphenyl) hexanoic acid] had no effect on responses to ACh or simvastatin in either age group. Inhibition of Ca2+-activated or ATP-dependent potassium channels (with tetraethylammonium or glibenclamide, respectively) reduced these arteriolar responses in JA but not those in WA. These findings suggest that in fully grown microvascular networks, endothelium-dependent arteriolar dilation is mediated by the combined release of endothelial nitric oxide and vasodilator prostanoids, and in part through activation of Ca2+-activated and ATP-dependent potassium channels. However, during earlier microvascular growth, this dilation is mediated by other factors yet to be identified. This may have significant implications for the regulation of tissue perfusion during microvascular development.
Frequency encoding of cholinergic- and purinergic-mediated signaling to mouse urinary bladder smooth muscle: modulation by BK channels
Authors: Werner Matthias E. , Knorn Anna-Maria , Meredith Andrea L. , Aldrich Richard W. , Nelson Mark T.
Published: August 2006

In the urinary bladder, contractions of the detrusor muscle and urine voiding are induced by the neurotransmitters ACh and ATP, released from parasympathetic nerves. Activation of K+ channels, in particular the large-conductance Ca2+-activated K+ (BK) channels, opposes increases in excitability and contractility of urinary bladder smooth muscle (UBSM). We have shown that deleting the gene mSlo1 in mice ( Slo−/−), encoding the BK channel, leads to enhanced nerve-mediated and neurotransmitter-dependent contractility of UBSM ( 38 ). Here, we examine the location of the BK channel in urinary bladder strips from mouse. Immunohistochemical analysis revealed that the channel is expressed in UBSM but not in nerves that innervate the smooth muscle. The relationship between electrical field stimulation and force generation of the cholinergic and purinergic pathways was examined by applying blockers of the respective receptors in UBSM strips from wild-type and from Slo−/− (knockout) mice. In wild-type strips, the stimulation frequency required to obtain a half-maximal force was significantly lower for the purinergic (7.2 ± 0.3 Hz) than the cholinergic pathway (19.1 ± 1.5 Hz), whereas the maximum force was similar. Blocking BK channels with iberiotoxin or ablation of the Slo gene increased cholinergic- and purinergic-mediated force at low frequencies, i.e., significantly decreased the frequency for a half-maximal force. Our results indicate that the BK channel has a very significant role in reducing both cholinergic- and purinergic-induced contractility and suggest that alterations in BK channel expression or function could contribute to pathologies such as overactive detrusor.