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PubMed1981

T cell clones reactive with sperm whale myoglobin. Isolation of clones with specificity for individual determinants on myoglobin.

We have been able to isolate clones of sperm whale muscle myoglobin (Mb)-reactive T cells from (C57BL/6 x A/J)F1 [(B6A)F1] mice. Four types of clones were isolated, distinguished by their patterns of recognition of Mb cyanogen bromide (CNBr) fragments and antigen presenting cell (APC) requirements. Individual T cell clones proliferated in response to one of three CNBr fragments of Mb. Dose-response curves of all clones were identical for native Mb and the appropriate fragment. T cell clones reactive to fragment 1-55 did not proliferate in response to peptide 15-22 (a peptide that binds to serum antibody directed against 1-55). These data support previous findings suggesting differences between antigen recognition by T and B cells, i.e., T cells may not recognize antigen in its native conformation and/or T and B cells may recognize distinct epitopes on the same antigen. Using T cell clones to analyze genetic control of responsiveness to Mb, we found that certain (B6A)F1 T cells recognize Mb presented by low responder strain APC. Thus, genetically determined low responsiveness in this case is probably not due to failure of APC function. We also found that responsiveness to certain Mb epitopes mapped to the I-A subregion whereas others mapped, via gene complementation, to the I-A and I-E subregions. We found no examples of responsiveness mapping to the I-C subregion and suggest an alternative explanation for previous reports mapping genetic control of responsiveness to certain Mb determinants to I-C.

Animals↗

PubMed1986

T cell clones specific for an amphipathic alpha-helical region of sperm whale myoglobin show differing fine specificities for synthetic peptides. A multiview/single structure interpretation of immunodominance.

The T cell response to sperm whale myoglobin in the H-2d haplotype has been shown to be largely focused on a limited region around glutamic acid 109 recognized in association with I-Ad. T cell clones 9.27 and 1.2 have been previously (4, 5) shown to reflect this specificity and MHC restriction. In this study we have used a panel of synthetic peptides from the region 102-118 of myoglobin to characterize the specificities of these representative clones. The segment from 106-118 was found to represent a consensus region for recognition by both clones. However, we saw significant differences between clones in the hierarchy of responsiveness to peptides within the panel. In as much as the peptide and the I-Ad molecule remain constant, these differences derive from differences in how each T cell receptor interacts with the antigen. This peptide segment is an amphipathic alpha helix in native myoglobin, meaning that one side is hydrophobic and the other hydrophilic. It is one of the prototype cases that led us to find that amphipathic helices constitute the majority of immunodominant sites recognized by helper T cells (1). It is likely that the peptide will refold into an amphipathic helix stabilized by the interface at the surface of the presenting cell. When such secondary conformation is considered, these data are consistent with a model of multiple T cell specificities arising from multiple views of a single antigen conformation at a single Ia-binding site and do not require postulation of multiple conformations or binding sites. Additionally, the finding of distinct specificities suggests that the immunodominance of this site depends not on the dominance of a single clone, but on the focusing of a polyclonal response on a single region of the molecule in association with I-Ad. The immunodominance of this particular region of the protein may thus depend on intrinsic features of the site, such as potential to form an amphipathic helix, as well as extrinsic factors such as binding properties of the I-A molecule.

Amino Acid Sequence↗

PubMed2001

Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale.

We present a new method for paternity analysis in natural populations that is based on genotypic data that can take the sampling fraction of putative parents into account. The method allows paternity assignment to be performed in a decision theoretic framework. Simulations are performed to evaluate the utility and robustness of the method and to assess how many loci are necessary for reliable paternity inference. In addition we present a method for testing hypotheses regarding relative reproductive success of different ecologically or behaviorally defined groups as well as a new method for estimating the current population size of males from genotypic data. This method is an extension of the fractional paternity method to the case where only a proportion of all putative fathers have been sampled. It can also be applied to provide abundance estimates of the number of breeding males from genetic data. Throughout, the methods were applied to genotypic data collected from North Atlantic humpback whales (Megaptera novaeangliae) to test if the males that appear dominant during the mating season have a higher reproductive success than the subdominant males.

Animals↗

PubMed1985

An approach to estimating population densities of great whales from sighting surveys.

Estimates of population densities for great whales have been obtained from sighting surveys using line transect sampling and subsequent analysis based on the perpendicular distances of sightings from the trackline. This paper considers the use of a sighting process model to allow distances to sightings parallel to the trackline to be incorporated, in the hope of relaxing certain assumptions required by the usual line transect analysis. A number of theoretical and methodological problems with this approach and he conventional analysis are noted. An alternative sampling procedure is suggested which avoids many of these problems.

Animals↗

PubMedDate not supplied

Low genetic variation among killer whales (Orcinus orca) in the eastern north Pacific and genetic differentiation between foraging specialists.

Killer whales from the coastal waters off California through Alaska were compared for genetic variation at three nuclear DNA markers and sequenced for a total of 520 bp from the mitochondrial control region. Two putative sympatric populations that range throughout this region were compared. They can be distinguished by social and foraging behavior and are known as "residents" and "transients". We found low levels of variation within populations compared to other cetacean species. Comparisons between fish (resident) versus marine mammal (transient) foraging specialists indicated highly significant genetic differentiation at both nuclear and mitochondrial loci. This differentiation is at a level consistent with intraspecific variation. A comparison between two parapatric resident populations showed a small but fixed mtDNA haplotype difference. Together these data suggest low levels of genetic dispersal between foraging specialists and a pattern of genetic differentiation consistent with matrifocal population structure and small effective population size.

Alleles↗

PubMed1990

Characterization of ganglioside GM4 lactones isolated from the whale brain.

Two novel ganglioside lactones were isolated from the brain of Bryde's whale (Balaenoptera edeni) and characterized. These gangliosides migrated above GM4 and were designated M4-1 and M4-2 in the order of location from the bottom of the TLC plate. These gangliosides were converted to GM4 by mild alkali treatment. Although M4-1 and M4-2 contained 1 mol each of N-acetylneuraminic acid and galactose, they behaved as neutral lipids on ion-exchange chromatography. Inner ester linkages were found in these gangliosides by secondary ion mass spectrometry and infrared spectroscopy. Two-dimensional J-correlated proton NMR spectra revealed that an inner ester linkage was formed in M4-1 between the sialic acid carboxyl group and the C-4 hydroxyl group of the galactosyl residue and another inner ester linkage was formed in M4-2 between the sialic acid carboxyl group and the C-2 hydroxyl group of galactose.

Animals↗

PubMed1982

Occurrence of 2-O-acyl galactosyl ceramide in whale brain.

Four glycolipids (Fr. I, II, III, and IV) were isolated from whale brain and three (Fr. I, II, and III) of them were demonstrated to be galactosyl ceramide combined with fatty acid by ester linkage. Fr. IV was shown to be a monoalkyl monoacyl galactosyl glycerol. For determining the substituted position of the acyl group on the galactose moiety, free hydroxyl groups of ester cerebrosides were protected with dihydropyran, deacylated by mild alkali treatment, and then subjected to permethylation. Finally, the methylated galactitol acetates obtained by hydrolysis and reduction were detected by gas chromatography and identified by gas chromatography-mass spectrometry. By this procedure, Fr. I was shown to be an acyl ester of kerasine, with the ester group at the 6-position of galactose. Fr. II and III were demonstrated to be acyl esters of phrenosine, in which the acyl groups were attached to the 6- and 2-position of the galactose, respectively. While the ester-linked acyl group of Fr. I, II, and III was composed of only normal fatty acids, predominantly palmitic acid, and the amide-linked fatty acids showed a heterogeneous composition of normal and hydroxy fatty acids, C16 to C24.

Animals↗

PubMed1997

Microsatellite genetic distances between oceanic populations of the humpback whale (Megaptera novaeangliae).

Mitochondrial DNA haplotypes of humpback whales show strong segregation between oceanic populations and between feeding grounds within oceans, but this highly structured pattern does not exclude the possibility of extensive nuclear gene flow. Here we present allele frequency data for four microsatellite loci typed across samples from four major oceanic regions: the North Atlantic (two mitochondrially distinct populations), the North Pacific, and two widely separated Antarctic regions, East Australia and the Antarctic Peninsula. Allelic diversity is a little greater in the two Antarctic samples, probably indicating historically greater population sizes. Population subdivision was examined using a wide range of measures, including Fst, various alternative forms of Slatkin's Rst, Goldstein and colleagues' delta mu, and a Monte Carlo approximation to Fisher's exact test. The exact test revealed significant heterogeneity in all but one of the pairwise comparisons between geographically adjacent populations, including the comparison between the two North Atlantic populations, suggesting that gene flow between oceans is minimal and that dispersal patterns may sometimes be restricted even in the absence of obvious barriers, such as land masses, warm water belts, and antitropical migration behavior. The only comparison where heterogeneity was not detected was the one between the two Antarctic population samples. It is unclear whether failure to find a difference here reflects gene flow between the regions or merely lack of statistical power arising from the small size of the Antarctic Peninsula sample. Our comparison between measures of population subdivision revealed major discrepancies between methods, with little agreement about which populations were most and least separated. We suggest that unbiased Rst (URst, see Goodman 1995) is currently the most reliable statistic, probably because, unlike the other methods, it allows for unequal sample sizes. However, in view of the fact that these alternative measures often contradict one another, we urge caution in the use of microsatellite data to quantify genetic distance.

Alleles↗

PubMed1994

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales.

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.

Animals↗

PubMed2006

Killer whales are capable of vocal learning.

The production learning of vocalizations by manipulation of the sound production organs to alter the physical structure of sound has been demonstrated in only a few mammals. In this natural experiment, we document the vocal behaviour of two juvenile killer whales, Orcinus orca, separated from their natal pods, which are the only cases of dispersal seen during the three decades of observation of their populations. We find mimicry of California sea lion (Zalophus californianus) barks, demonstrating the vocal production learning ability for one of the calves. We also find differences in call usage (compared to the natal pod) that may reflect the absence of a repertoire model from tutors or some unknown effect related to isolation or context.

Animals↗

PubMed1999

Abiotrophia balaenopterae sp. nov., isolated from the minke whale (Balaenoptera acutorostrata).

Phenotypic and phylogenetic studies were performed on a hitherto undescribed micro-organism isolated from a minke whale (Balaenoptera acutorostrata). Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strain constituted a new subline close to, but distinct from, Abiotrophia adiacens and Abiotrophia elegans. The unknown bacterium was readily distinguished from these two Abiotrophia species by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Abiotrophia balaenopterae sp. nov., the type strain of which is M1975/96/1T (= CCUG 37380T).

Animals↗

PubMed1999

Conformational properties of native sperm whale apomyoglobin in solution.

Apomyoglobin from sperm whale is often used for studies of ligand binding, protein folding, and protein stability. In an effort to describe its conformational properties in solution, homonuclear and heteronuclear (13C and 15N) NMR methods were applied to the protein in its native state. Assignments were confirmed for nuclear Overhauser effects (NOEs) involving side chain and backbone protons in the folded regions of the structure. These NOEs were used to derive distance restraints. The shifts induced by the hydrophobic dye 8-anilino-1-naphthalenesulfonic acid (ANS) were inspected in the regions remote from its binding site and served as an indicator of conformational flexibility. 3JalphaH-NH values were obtained to assess dihedral angle averaging and to provide additional restraints. A family of structures was calculated with X-PLOR and an ab initio simulated annealing protocol using holomyoglobin as a template. Where the structure appeared well defined by chemical shift, line width, ANS perturbation, and density of NOEs, the low resolution model of apomyoglobin provides a valid approximation for the structure. The new model offers an improved representation of the folded regions of the protein, which encompass the A, B, E, helices as well as parts of the G and H helices. Regions that are less well defined at this stage of calculations include the CD corner and the end of the H-helix. The EF-F-FG segment remains uncharacterized.

Animals↗

PubMed2000

Amide proton hydrogen exchange rates for sperm whale myoglobin obtained from 15N-1H NMR spectra.

The hydrogen exchange behavior of exchangeable protons in proteins can provide important information for understanding the principles of protein structure and function. The positions and exchange rates of the slowly-exchanging amide protons in sperm whale myoglobin have been mapped using 15N-1H NMR spectroscopy. The slowest-exchanging amide protons are those that are hydrogen bonded in the longest helices, including members of the B, E, and H helices. Significant protection factors were observed also in the A, C, and G helices, and for a few residues in the D and F helices. Knowledge of the identity of slowly-exchanging amide protons forms the basis for the extensive quench-flow kinetic folding experiments that have been performed for myoglobin, and gives insights into the tertiary interactions and dynamics in the protein.

Amides↗

PubMed2003

Abundance estimation from multiple photo surveys: confidence distributions and reduced likelihoods for bowhead whales off Alaska.

Maximum likelihood estimates of abundance are obtained from repeated photographic surveys of a closed stratified population with naturally marked and unmarked individuals. Capture intensities are assumed log-linear in stratum, year, and season. In the chosen model, an approximate confidence distribution for total abundance of bowhead whales, with an accompanying likelihood reduced of nuisance parameters, is found from a parametric bootstrap experiment. The confidence distribution depends on the assumed study protocol. A confidence distribution that is exact (except for the effect of discreteness) is found by conditioning in the unstratified case without unmarked individuals.

Aging↗

PubMed2000

Species recognition as a possible function for variations in position and shape of the sexually dimorphic tusks of Mesoplodon whales.

Beaked whales of the genus Mesoplodon are characterized by the presence of a single pair of sexually dimorphic tusks. Variation in the position and shape of these tusks was examined in four sympatric species and was found to be consistent with the hypothesis that these differences may have evolved to aid species recognition between sympatric and otherwise morphologically similar species of this genus.

Animals↗

PubMed2001

Historical population size change of bowhead whales inferred from DNA sequence polymorphism data.

Nucleotide sequence data from the mitochondrial control region were used from a phylogenetic context to investigate the long-term history of a population of bowhead whales (Balaena mysticetus). In addition, the coalescence time of these sequences was used to estimate the age of the inferred patterns of population size change. The results indicate that mitochondrial genetic polymorphism was not affected by a recent bottleneck that occurred near the turn of the 20th century, thereby preserving the signature of historical population size change in the mitochondrial genome. Further analysis showed that this population underwent an expansion initiated in the Middle to Late Pleistocene. As such, early Holocene changes in Arctic sea ice distribution appear to have had little influence on patterns of genetic variability in this population.

Animals↗

PubMed1992

Conservation genetics of whales and dolphins.

Whales and dolphins (cetaceans) are found in all the world's oceans and in some of the major rivers, yet little is known about the distribution and behaviour of many species. At the same time, cetaceans are under threat from a variety of pressures including direct and indirect takes, pollution, and competition for habitat and prey. To ensure their long-term survival it will be necessary to preserve genetic diversity through the identification and protection of differentiated populations, the assessment of variation within local populations, and through a better understanding of reproductive and dispersal behaviour. The application of molecular genetic techniques is helping to provide answers to some of these previously intractable questions. Early results suggest few consistent patterns. Obvious geographic boundaries correlate to genetic distance in some species, and not in others. Furthermore, morphological variation within species can be fairly extensive without correlating to genetic distance, or relatively minor between morphotypes that are as genetically distinct as some species. These examples emphasize the need for further study.

Animals↗

PubMed1991

Fluorescence study of the conformational properties of myoglobin structure. 1. pH-dependent changes of tryptophanyl fluorescence in intact and chemically modified sperm whale apomyoglobins.

The pH-dependent fluorescence of intact sperm whale apomyoglobin (apo-Mb) containing two tryptophans at positions 7 and 14, and of apo-Mb derivatives modified on Trp7 by 2-hydroxy-5-nitrobenzyl bromide (Koshland reagent) and o-nitrophenylsulphenyl chloride, has been studied. The fluorescence of apomyoglobins modified at His residues by iodoacetamide and bromoacetate, and at the N-terminal alpha-NH2 group by methylisothiocyanate, has also been investigated. The individual fluorescent properties of both tryptophans and their contributions to the total spectrum of apo-Mb have been resolved within the pH range 2-12.5. The quantum yield of the 'buried' Trp14 (lambda max at 326 nm) is shown to be twofold higher at pH greater than 8.5 than that of the 'exposed' Trp7 (lambda max at 333 nm). At pH 8.5-5.5 the fluorescence of Trp14 diminished approximately twofold due to quenching by the ionized His residue, most probably His119. The quenching is evidently dynamic because the fluorescence lifetime is shown to be linearly proportional to quantum yield in this pH range. The fluorescence of Trp7 practically does not change between pH 5.5 and 10.0 but increases 2.5-3-fold in the pH range 5.5-4.3 while the contribution of Trp14 remains constant. The conformational changes at the N-terminal and in the region adjacent to it, as well as in the whole apo-Mb molecule in acidic, alkaline and neutral pH ranges, are considered. A relationship is revealed between conformational states of the heme crevice and the N-terminal part of apo-Mb.

Animals↗