Deadly diving? Physiological and behavioural management of decompression stress in diving mammals.

Decompression sickness (DCS; 'the bends') is a disease associated with gas uptake at pressure. The basic pathology and cause are relatively well known to human divers. Breath-hold diving marine mammals were thought to be relatively immune to DCS owing to multiple anatomical, physiological and behavioural adaptations that reduce nitrogen gas (N(2)) loading during dives. However, recent observations have shown that gas bubbles may form and tissue injury may occur in marine mammals under certain circumstances. Gas kinetic models based on measured time-depth profiles further suggest the potential occurrence of high blood and tissue N(2) tensions. We review evidence for gas-bubble incidence in marine mammal tissues and discuss the theory behind gas loading and bubble formation. We suggest that diving mammals vary their physiological responses according to multiple stressors, and that the perspective on marine mammal diving physiology should change from simply minimizing N(2) loading to management of the N(2) load. This suggests several avenues for further study, ranging from the effects of gas bubbles at molecular, cellular and organ function levels, to comparative studies relating the presence/absence of gas bubbles to diving behaviour. Technological advances in imaging and remote instrumentation are likely to advance this field in coming years.

Tracking apex marine predator movements in a dynamic ocean.

Pelagic marine predators face unprecedented challenges and uncertain futures. Overexploitation and climate variability impact the abundance and distribution of top predators in ocean ecosystems. Improved understanding of ecological patterns, evolutionary constraints and ecosystem function is critical for preventing extinctions, loss of biodiversity and disruption of ecosystem services. Recent advances in electronic tagging techniques have provided the capacity to observe the movements and long-distance migrations of animals in relation to ocean processes across a range of ecological scales. Tagging of Pacific Predators, a field programme of the Census of Marine Life, deployed 4,306 tags on 23 species in the North Pacific Ocean, resulting in a tracking data set of unprecedented scale and species diversity that covers 265,386 tracking days from 2000 to 2009. Here we report migration pathways, link ocean features to multispecies hotspots and illustrate niche partitioning within and among congener guilds. Our results indicate that the California Current large marine ecosystem and the North Pacific transition zone attract and retain a diverse assemblage of marine vertebrates. Within the California Current large marine ecosystem, several predator guilds seasonally undertake north-south migrations that may be driven by oceanic processes, species-specific thermal tolerances and shifts in prey distributions. We identify critical habitats across multinational boundaries and show that top predators exploit their environment in predictable ways, providing the foundation for spatial management of large marine ecosystems.

The Neurospora crassa genome: cosmid libraries sorted by chromosome.

A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.

The Arabidopsis profilin gene family. Evidence for an ancient split between constitutive and pollen-specific profilin genes.

Profilin is a ubiquitous eukaryotic protein that regulates the actin cytoskeleton and recently has been identified as a potent allergen in pollen. We examined the profilin gene family in the model plant, Arabidopsis thaliana, and found that it contained approximately 8 to 10 members. Four distinct profilin sequences, three cDNAs, PRF1, PRF2, and PRF3, and two genomic clones, PRF1 and PRF4, were isolated and characterized. These genes encoded four distinct profilin isoforms of 131 to 134 amino acids. Northern and reverse-transcriptase polymerase chain reaction analyses demonstrated that Arabidopsis PRF1 was expressed in all major plant organs, whereas PRF4 was specifically expressed in mature pollen. Gene trees constructed from amino acid sequence data revealed the presence of two ancient, distinct profilin gene classes in plants. PRF4 was in a class with previously identified pollen-specific profilins from monocot and dicot species. PRF1, PRF2, PRF3, and a distant dicot sequence formed a separate novel class, suggesting an ancient separation of plant profilins based on regulation and perhaps function. The coevolution of plant actin and profilin classes with similar patterns of expression is discussed. The similarity of plant, fungal, protist, insect, and nematode profilins and their extreme divergence from the vertebrate profilins has striking implications for the evolution of fungal-spore- and plant-pollen-profilins as allergens.

Sequence, function, and phylogenetic analysis of an ascovirus DNA polymerase gene.

We have sequenced a 5.5-kb region of the DNA genome of the Spodoptera Ascovirus (SAV) containing a DNA polymerase gene. The gene codes for a 1104-amino-acid polypeptide with seven motifs characteristic of DNA polymerases and three additional motifs associated with polymerases possessing 3' to 5' exonuclease activity. The SAV DNA polymerase gene was able to functionally substitute for a baculovirus DNA polymerase gene in a transient assay that relies on origin-specific reporter plasmid DNA replication. Analysis of the predicted DNA polymerase sequence using neighbor-joining and protein parsimony algorithms indicated that this gene was only distantly related to other known viral and cellular DNA polymerases. The SAV DNA polymerase gene is the first ascovirus gene to be identified and sequenced. The molecular phylogenetic analyses of this gene supports the placement of insect ascoviruses in a separate virus family.

An approach to searching protein sequences for superfamily relationships or chance similarities relevant to the molecular mimicry hypothesis: application to the basic proteins of myelin.

A rapid method for similarity searches (FASTP program) was used to identify similarities between a protein database and the human basic proteins from myelin [P2 protein and 17.2K, 18.5K, and 21.5K variants of myelin basic protein (MBP)]. From similarity scores, we concluded that none of the presently known proteins are in a family containing the MBPs. No new members were found for the lipid-binding family of which P2 is a member. Sequence similarities deemed relevant to the molecular mimicry hypothesis for virus-induced autoimmunity were identified in FASTP data with the aid of microcomputer programs. Several MBP/viral protein similarities were found that have not been reported previously. Of note because of their association with demyelinating conditions were proteins from visna and vaccinia. Similarity with visna was specific to the 21.5K and 20.2K MBPs. The most interesting new possibility for mimicry involving the P2 protein was between the influenza A NS2 protein and a sequence region of P2 thought to be neuritogenic in animals and mitogenic for lymphocytes from some patients with Guillain-Barré syndrome (GBS). This may have relevance for some cases of GBS associated with the 1976 U.S.A. swine flu vaccination program. Because FASTP reports only the best similarities between proteins, searches with FASTP may not have detected all the examples of mimicry present in the database. Searches might also be more effective if similarities could be scored on immunological rather than structural relatedness.

An access interface for the MS-DOS diskette format of GenBank(R), a gene sequence database.

An interface program has been developed for users of MS-DOS computers and the GenBank(R) gene sequence files in their diskette format. With the program a user is able to produce keyword, author and entry name listings of GenBank items or to select GenBank sequences for viewing, printing or decoding. The decode option uncompresses sequence data and yields a character file which has the format used on GenBank magnetic tapes. Program options are chosen by selecting items from command menus. While the program is designed primarily for hard disk operation, it also allows users of diskette-based computers to work with GenBank files.

A microcomputer program for hydropathic analysis of proteins with I/O through word processing and graphics software.

A BASIC program has been devised for the hydropathic analysis of protein sequences according to the method of Kyte and Doolittle (1982). The program uses sequence data from input files that are created with a word processor and produces two types of output file: one contains a bar graph of the hydropathic profile in a format that can be easily edited; the other is a tabulation of hydropathic indices along a protein's sequence that can be used as input by the program for the production of a bar graph or as input into other graphics and analysis software. An MS-DOS microcomputer, operating under IBM BASICA or GWBASIC and a dot matrix printer with block graphics capabilities are the only hardware requirements for graphic display of hydropathy profiles. The program is capable of unattended analysis from a list of up to 15 input files.

Globin proteins of the normal and anemic duck.

The red blood cells of normal adult ducks contain two main hemoglobins. The most abundant type, HbA, comprises approximately 80% of the total, with the remaining 20% being made up of HbD. An attempt was made to determine whether during hemolytic anemia a special alpha globin chain (alpha s) replaces the alpha chain of HbA found in normal animals. This special stress alpha globin, whose existence has been seriously questioned, was originally postulated to explain the sequence discrepancies obtained between alpha chains of normal and anemic chickens and ducks. Using gel electrophoresis, isoelectric focusing, and HPLC peptide mapping techniques no qualitative differences between the alpha A globins of normal and anemic animals were found. The nature of the beta globin chains present in adult ducks has also never been rigorously established. In this work, a variety of techniques, including HPLC, gel electrophoresis, and microcolumn amino acid analysis, were used to examine the beta chains from each hemoglobin. Using these methods, no differences were found between the beta globin chains of the two hemoglobins.

Hydrophobic regions in myelin proteins characterized through analysis of "hydropathic" profiles.

Computer-generated "hydropathic" profiles were constructed for graphic comparison of the amino acid sequences for P2 protein, 18.5 kilodalton (kDa) myelin basic protein (BP), and myelin proteolipid protein (PLP). Profiles were also obtained for cytochrome b5, a membrane protein known to be capable of reversible association with lipid bilayers and of a size comparable to that of the myelin BPs. Analysis of the PLP sequence produced profiles generally compatible with the suggestions that PLP has three transbilayer and two bilayer intercalating segments. Profiles for P2 and 18.5 kDa BP were found to contain hydrophilic segments separated by relatively short hydrophobic regions. Whereas hydropathic indices in hydrophobic regions of P2, 18.5 kDa BP, and PLP fall in the value ranges recently reported for cores of globular proteins and intrabilayer domains of membrane proteins, hydrophobic sections of P2 and 18.5 kDa BP have hydropathic indices similar to those in the hydrophobic core (transprotein) regions of globular proteins. None of them are comparable to the region of cytochrome b5 known to anchor that protein in its membrane or to the segments of PLP sequence proposed as intrabilayer domains. This comparison suggests that neither BP has structural characteristics compatible with insertion into the hydrocarbon core of the myelin lipid bilayer, a conclusion that is consistent with a recently published study that identified the bilayer penetrating proteins of myelin with a hydrophobic probe. The above findings suggest an enhancement for some details of myelin architecture and a cautious approach to interpreting data for BP intercalation into bilayers.

Protein composition of PNS myelin: developmental comparison of control and quaking mice.

Protein compositions were determined for sciatic nerve myelin isolated from young and adult control and quaking (Qk) mice. Age-related changes in the relative amounts of large (Pl) and small (Pr) basic proteins were found. In control animals, the ratio Pr/Pl increased with age, a change similar to that observed for the large (Bl) and small (Bs) CNS myelin basic proteins of adult mice. Pr/Pl also increased with age in the Qk mouse sciatic nerve, but only to the point that the value in the adult Qk mouse was similar to that observed for young control animals, a situation reminiscent of the effect of the Qk mutation on CNS basic proteins. Thus, our data suggest that the Qk mutation has a similar effect on peripheral nervous system (PNS) and CNS basic proteins. Our findings are consistent with recent electrophoretic and immunochemical data showing that PNS and CNS myelin basic proteins in rodents are analogous, and they suggest that the genetic program controlling basic protein expression is common to oligodendroglia and Schwann cells.

Basic proteins of rodent peripheral nerve myelin: immunochemical identification of the 21.5K, 18.5K, 17K, 14K, and P2 proteins.

Proteins in peripheral nervous system and central nervous system myelin and homogenates of sciatic nerve and brain from young and adult mice and rats were characterized with affinity-purified anti-P2 and anti-myelin basic protein sera after electrophoretic transfer from sodium dodecyl sulfate-polyacrylamide gels to nitrocellulose sheets. Using this method we have identified a component of rodent peripheral nervous system myelin as P2 protein. Peripheral nervous system myelin also showed the presence of four basic proteins in addition to P2 protein. These were found to be analogous to the 14, 17, 18.5, and 21.5K species found in the central nervous system myelin. A number of high-molecular-weight proteins were also detected with anti-myelin basic protein serum in peripheral nervous system, as well as central nervous system myelin. In addition, we report the presence of a high-molecular-weight P2 cross-reactive protein in rodent brain stem homogenates, but not in central nervous system myelin. Key Words: Basic proteins--PNS myelin--CNS myelin--Immunocharacterization. Greenfield S. et al. Basic proteins of rodent peripheral nerve myelin: Immunochemical identification of the 21.5K, 18.5K, 17K, 14K, and P2 proteins.

Conformation of bovine nerve root P2 protein: characteristics of the molecule from circular dichroism spectra.

Circular dichroism (CD) was used to study the conformations of bovine nerve root P2 basic protein, its reduced and carboxymethylated derivative (RCM-P2), and its large cyanogen bromide fragment (CN1). Data in the far UV show that both the parent protein and RCM-P2 have conformations dominated by a large amount of beta structure. However, the CN1 peptide appears to exist in a largely unordered conformation. Since CN1 lacks short (20 residue) amino- and carboxy-terminal segments of the P2 protein, the spectral data suggest that these regions are important for determining and/or maintaining folding of the P2 protein in aqueous solutions. The P2 protein was found to have a distinctive CD spectrum in the near UV. The characteristics of molar ellipticities indicate that the spectrum contains significant contributions from tyrosine residues, and that these contributions suggest different environments for the two tyrosines in P2 protein. Both environments depend on protein conformation, since CD side chain absorptions are lost when P2 protein is denatured with 5 M urea.

Structure of bovine P2 basic protein: sequence of a carboxyterminal segment that is a neuritogen in rabbits.

The sequence of the carboxyterminal 18 amino acids released by cyanogen bromide digestion of the bovine P2 protein was determined. It has several interesting structural and immunological properties. It contains the only two half-cystines in the molecule that have the capacity to form an intrachain disulfide bond. Using the rabbit as a test animal, this carboxyterminal peptide was capable of producing experimental allergic neuritis. The sequence of this peptide is Val-Val-Glu-Cys-Lys-Met-Lys-Asp-Val-Val-Cys-Thr-Arg-Ile-Tyr-Glu-Lys-Val.

An immunological characterization of the basic proteins of rodent sciatic nerve myelin.

Radioimmunoassays (RIA) for the myelin basic protein (MBP) and P2 protein together with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were used to establish the identities of and relationships between the basic proteins (BP) of rodent peripheral nervous system (PNS) myelin. The PNS myelin proteins studied, in order of increasing mobility of SDS-PAGE, are P1, PR (R = rodent) and PB (B = breakdown). The majority of the acid extractable proteins of rodent PNS myelin are MBP related as shown by MBP-RIA. When tested individually, rodents P1, PR and PB were each found to cross-react in the RIA for MBP but not that for P2. The acid extracts of rodent PNS myelin were found to contain P2, although in minute quantities. P2 accounts for approximately 0.05-1.0% of the acid extractable protein in rodent PNS myelin.

Experimental allergic neuritis. I. Rat strain differences in the response to bovine myelin antigens.

Strain differences among rats to the induction and severity of experimental allergic neuritis (EAN) in response to whole PNS myelin were observed. Lewis rats were highly susceptible and developed severe EAN without central nervous system lesions (EAE), while Brown Norway rats were most resistant. Wistar, Sprague-Dawley, and Buffalo rats were susceptible but developed less severe disease than Lewis rats. Only Lewis rats consistantly developed EAN in response to isolated P2 protein. The severity of EAN was enhanced by treatment of the P2 with mercaptoethanol prior to injection. None of the strains developed EAN in response to galactocerebroside and none developed the lesions of EAE in response to any of the bovine myelin antigens tested. Myelin protein profiles from these rat strains were similar which suggests that factors other than target tissue differences, such as genetically determined immune responses to bovine myelin antigens, must be involved in these differing responses.

Bovine peripheral nervous system myelin P2 protein: chemical and immunological characterization of the cyanogen bromide peptides.

Cleavage of bovine P2 protein by cyanogen bromide (CNBr) produced peptide fractions CN1, CN2, and CN3 which were isolated by gel filtration chromatography. CN2 was found to contain two NH2-terminals (lysine and valine) and accounted for both of the cysteine residues of P2. When reduced carboxymethylated P2 (RCM-P2) was digested with CNBr, peptides CN1 and CN3 were obtained as were (1) a peptide with NH2-terminal lysine (Lys) that contained no homoserine and only one cysteine residue and (2) a peptide with NH2-terminal valine (Val) that was co-eluted with CN3. These data and the chemical characterization of all the CNBr peptides obtained from P2 and RCM-P2 suggest that isolated P2 protein has a structure composed of the CNBr peptides in the order CN3-CN1-CN2(Val)-CN2(Lys) with an intrachain disulfide bond between the cysteine residues located in the two constituent peptides of CN2, CN2(Lys) and CN2(Val). To locate the neuritogenic region(s) within the P2 protein structure, CN1, CN2, and CN3 were tested for the ability to induced experimental allergic neuritis (EAN) in Lewis rats. The disease-inducing sites of P2 protein were found only in CN1; neither CN2 nor CN3 produced disease. EAN induced by CN1 was comparable to that induced with P2 protein as determined by disease onset, clinical symptoms, and histologic lesions.

Bovine P2 protein: sequence at the NH2-terminal of the protein.

Sequence data from key fragments of the P2 protein established the order of cyanogen bromide (CNBr) peptides in the structure of the protein and the primary structure for approximately one-half of the molecule. Data were obtained from the three tryptic peptides of blocked NH2-terminal CNBr peptide (CN3), the large CNBr peptide of P2 protein (CN1), and a fragment obtained from P2 by cleavage at tryptophan with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine. This last fragment was found to contain an over-lapping sequence that proved the juxtaposition of CN1 and CN3 in P2 protein. Thus, based on this fact and the characteristics of the CNBr peptides, the P2 structure is composed of CNBr peptides in the order: CN3-CN1-CN2(Val)-CN2(Lys). A comparison was made between the partial sequence of P2 protein and the equivalent portion of the structure of bovine myelin basic protein. The structures of these two proteins were found to be distinctly different although certain similarities are found.