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PubMed1988

Hormone binding globulins undergo serpin conformational change in inflammation.

A surprising recent finding is that thyroxine binding globulin (TBG) and cortisol binding globulin (CBG), are members of the serine protease inhibitor (serpin) superfamily. Apparently evolution has completely adapted the serpin structure for its new role in these proteins as a transport agent, as there is no evidence of any retained protease inhibitory activity. This drastic change in function raises the question as to why such a complex molecular framework has been selected for the relatively simple task of hormone transport? To function as inhibitors the serpins have a native stressed (S) conformation that makes them vulnerable to proteolytic cleavage, the cleavage being accompanied by an irreversible transition to a stable relaxed (R) form. We demonstrate here that TBG and CBG have retained the stressed native structure typical of the inhibitor members of the family and we provide evidence that the S-R transition has been adapted to allow altered hormone delivery at inflammatory sites.

Amino Acid Sequence↗
PubMed2026

Chromosomal-level genome assembly of Trypanosoma carassii, the etiologic agent of a recent outbreak of trypanosomiasis in cage-cultured large yellow croaker (Larimichthys crocea) in China.

Trypanosoma carassii, a typical freshwater fish trypanosome, has recently been identified as the etiological agent of a trypanosomiasis outbreak in cage-cultured large yellow croaker (Larimichthys crocea) in China and has been designated as T. c. larimichthys. To date, publicly available genomic data for trypanosomes have been limited to terrestrial species, particularly those of medical importance. Here, we present a chromosome-level genome assembly of T. carassii, the first genome of an aquatic trypanosome, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding technologies. A preliminary genome survey based on Illumina sequencing data estimated the genome size at 56.38 Mb with a heterozygosity of 1.17%. The final assembled genome spans 48.55 Mb, with contig N50 and scaffold N50 values of 139.15 Kb, and achieves 100.00% BUSCO completeness. Hi-C data resolved the assembly into 34 chromosomes and 9 unanchored scaffolds. Repetitive elements account for 53.29% of the genome (approximately 25.87 Mb). A total of 11,584 protein-coding genes were predicted, 95.36% of which were functionally annotated. Synonymous substitution rates analysis of paralogous genes indicates a recent burst of gene duplication, which likely corresponds to a whole-genome duplications. This high-quality genome assembly provides invaluable resources for understanding the evolution and host adaptation of aquatic trypanosomes.

Animals↗
PubMed2001

For whales and seals the ocean is not blue: a visual pigment loss in marine mammals.

Most terrestrial mammals have colour vision based on two spectrally different visual pigments located in two types of retinal cone photoreceptors, i.e. they are cone dichromats with long-to-middle-wave-sensitive (commonly green) L-cones and short-wave-sensitive (commonly blue) S-cones. With visual pigment-specific antibodies, we here demonstrate an absence of S-cones in the retinae of all whales and seals studied. The sample includes seven species of toothed whales (Odontoceti) and five species of marine carnivores (eared and earless seals). These marine mammals have only L-cones (cone monochromacy) and hence are essentially colour-blind. For comparison, the study also includes the wolf, ferret and European river otter (Carnivora) as well as the mouflon and pygmy hippopotamus (Artiodactyla), close terrestrial relatives of the seals and whales, respectively. These have a normal complement of S-cones and L-cones. The S-cone loss in marine species from two distant mammalian orders strongly argues for convergent evolution and an adaptive advantage of that trait in the marine visual environment. To us this suggests that the S-cones may have been lost in all whales and seals. However, as the spectral composition of light in clear ocean waters is increasingly blue-shifted with depth, an S-cone loss would seem particularly disadvantageous. We discuss some hypotheses to explain this paradox.

Animals↗
PubMed2003

Restoration of blood flow by using continuous perimuscular infiltration of plasmid DNA encoding subterranean mole rat Spalax ehrenbergi VEGF.

The optimal vector, regulatory sequences, and method of delivery of angiogenic gene therapy are of considerable interest. The Spalax ehrenbergi superspecies live in subterranean burrows at low oxygen tensions and its tissues are highly vascularized. We tested whether continuous perimuscular administration of Spalax vascular endothelial growth factor (VEGF) DNA could increase tissue perfusion in a murine hindlimb ischemia model. Placebo or VEGF +/- internal ribosome entry site (IRES) was continuously administrated perimuscularly in the ischemic zone by using an infusion pump. None of the mice in the VEGF-treated group (>50 microg) developed visible necrosis vs. 33% of the placebo group. Microscopic necrosis was observed only in the placebo group. Spalax VEGF muscular infiltration resulted in a faster and more complete restoration of blood flow. The restoration of blood flow by VEGF was dose-dependent and more robust and rapid when using the VEGF-IRES elements. The flow restoration using continuous perimuscular infiltration was faster than single i.m. injections. Vessel density was higher in the VEGF and VEGF-IRES (-) groups compared with the placebo. Continuous perimuscular administration of angiogenic gene therapy offers a new approach to restore blood flow to an ischemic limb. Incorporation of an IRES element may assist in the expression of transgenes delivered to ischemic tissues. Further studies are needed to determine whether VEGF from the subterranean mole rat Spalax VEGF is superior to VEGF from other species. If so, 40 million years of Spalax evolution underground, including adaptive hypoxia tolerance, may prove important to human angiogenic gene therapy.

Animals↗
PubMed1990

Isolation of carp genes encoding major histocompatibility complex antigens.

In the evolution of the adaptive immune system unique to vertebrates, teleost fish occupy the critical position. This is the most primitive class of lower vertebrates in which the capacity for acute allograft rejections can be demonstrated, thus suggesting the presence of major histocompatibility complex (MHC) antigens and, therefore, T cells. Here, we report the identification of two putative MHC-antigen-encoding sequences in the carp Cyprinus carpio. One, identified as TLAI alpha-1, had reasonable homology to MHC class I heavy chains of mammalian and avian species, while the other, identified as TLAII beta-1, was homologous to MHC class II beta chain of the aforementioned higher vertebrates. For these isolations of fish MHC genes, we have identified two highly conserved amino acid sequence blocks surrounding two cysteine residues in the second domain of MHC class II beta chains as well as the third domain of class I heavy chains of humans, mice, and chickens. Two kinds of mixed oligonucleotide probes corresponding to these two regions were synthesized. The carp genomic DNA was subjected to amplification by polymerase chain reaction using the above two synthetic DNA fragments as primers. Subsequently, two different DNA sequences sandwiched by these primers were isolated from the amplified products. Their use as secondary probes led to the identification of TLAI alpha-1 and TLAII beta-1. We also discuss the applicability of the above approach for isolation from lower vertebrates of other genes belonging to the immunoglobulin super-family as well as the evolutionary origin of vertebrate MHC antigens.

Amino Acid Sequence↗
PubMed2004

Wavelength dependency of light-induced effects on photoperiodic clock in the migratory blackheaded bunting (Emberiza melanocephala).

The effects of light wavelength on photoperiodic clock were determined in the migratory male blackheaded bunting (Emberiza melanocephala). We constructed an action spectrum for photoperiodic induction (body fattening, gain in body mass, and gonadal recrudescence) by exposing birds for 4.5 weeks to 13 h light per day (L:D = 13:11 h) of white (control), blue (450 nm), or red (640 nm) color at irradiances ranging from 0.028 to 1.4Wm(-2). The threshold light irradiance for photoinduction was about 10-fold higher for blue, compared to red and white light. Phase-dependent effects of light wavelength on the photoperiodic clock were further examined in the next two sets of skeleton photoperiods (SKPs). In the first set of SKPs, birds were exposed for four weeks to asymmetrical light periods (L:D:L:D= 6:6:1:11 h) at 0.25+/-0.01 W m(-2); two light periods applied were of the same (450nm: blue:blue, B:B; 640nm, red:red, R:R) or different (blue:red, B:R or red:blue, R:B) wavelengths, or of white:white (W:W, controls). Photoperiodic induction occurred under R:R and B:R, but not under B:B and R:B light conditions; the W:W condition induced an intermediate response. The second set of SKPs used symmetrical light periods (L:D:L:D = 1:11:1:11 h), and measured effects also on the activity rhythm. Birds were first exposed to one of the four SKPs (R:R, B:B, R:B, or B:R) for three weeks, subsequently were released into dim constant light (LLdim; approximately 0.01 Wm(-2), the night light used in an L:D cycle) for two weeks, and then were returned to respective SKPs for another three weeks. Activity was greater in the R:R compared to B:B, and in B:R compared to R:B light condition. Zugunruhe (intense nighttime activity, indicating migratory restlessness in a caged situation) developed under the R:R and B:R, but not the B:B and R:B, light condition. Under LLdim, all birds free-ran with a period >24h, the Zugunruhe had a circadian period longer than the daytime activity, and the re-entrainment to SKPs was influenced by the position of light periods relative to circadian phase of the activity rhythm. Photoperiodic induction at the end of 8 weeks was found in the R:R and B:R, but not in B:B, light conditions; in the R:B condition only one bird had initiated testes. Taken together, these results suggest that in the blackheaded bunting, the circadian photoperiodic clock is differentially responsive to light wavelengths; this responsiveness is phase-dependent, and the development of Zugunruhe reflects a true circadian function. Wavelength-dependent response of the photoperiodic clock could be part of an adaptive strategy in evolution of the seasonality in reproduction and migration among photoperiodic species under wild conditions.

Animals↗
PubMed2000

A B cell superantigen-induced persistent "Hole" in the B-1 repertoire.

The bacterial toxin protein A from Staphylococcus aureus (SpA) interacts with B cell antigen receptors encoded by variable region heavy chain (V(H)) clan III genes via a V region framework surface that has been highly conserved during the evolution of the adaptive immune system. We have investigated the consequences of exposure to this prototypic B cell superantigen, and found that treatment of neonates or adults induces a T cell-independent deletion of a large supraclonal set of susceptible B cells that includes clan III/V(H) S107 family-expressing lymphocytes. In studies of different SpA forms, the magnitude of the induced deletion directly correlated with the V(H)-specific binding affinity/avidity. Upon cessation of SpA exposure, the representation of conventional splenic (B-2 subset) lymphocytes normalized; however, we found that the V(H) family-restricted deficit of peritoneal B-1 cells persisted. SpA treatment also induced a persistent loss of splenic S107-mu transcripts, with a loss of certain natural antibodies and specific tolerance to phosphorylcholine immunogens that normally recruit protective antimicrobial responses dominated by the S107-expressing B-1 clone, T15. These studies illustrate how a B cell superantigen can exploit a primordial Achilles heel in the immune system, for which B-1 cells, an important source of natural antibodies and host immune responses, have special susceptibility.

Adult↗
PubMedDate not supplied

Variation in the production and distribution of substituted benzoquinone compounds among genetic strains of the confused flour beetle, Tribolium confusum.

Insects often produce chemicals, such as defensive compounds, whose quantity and distribution can affect their fitness. For evolution to produce adaptations, chemical production must be genetically variable. Here we report the results of a study using high-performance liquid chromatography to quantify two important chemical secretions of the flour beetle Tribolium confusum, methyl-1, 4-benzoquinone (MBQ) and ethyl-1,4-benzoquinone (EBQ). Our results show a distinct difference in the production of the compounds among four genetically distinct strains of T. confusum (b-+, b-I, b-IV, b-Pakistan) with an unusually high amount measured for the b-Pakistan strain. By measuring internal and external benzoquinone levels separately, we were also able to detect differences in production and distribution of the compounds between the strains. Some strains secrete more of the chemicals, whereas other strains appear to sequester the compounds within their bodies. The sexes also differ in total quinone production as well as in their internal to external benzoquinone ratios, suggesting the trait is sex influenced. Finally, a consistent correlation in the amounts of MBQ to EBQ in individual beetles suggests that the substituted benzoquinones share a common precursor or pathway.

Animals↗
PubMed1999

The nutrient-toxin dosage continuum in human evolution and modern health.

Recent findings support the long-recognized principle that nutritive and toxic effects of an ingested material depend not only on its nature but very much on its quantity. The well known observation that essential nutrients can be toxic at high dosages suggests that the same reversal of effect may be true of many substances that could be beneficial but not essential at low dosages (the phenomenon of hormesis). This has been demonstrated for many well known toxins. We suggest a mathematical model that describes these dosage effects as an expected result of the evolution of human metabolic and dietary adaptations for maximizing benefits and minimizing costs of the ingestion or other intake of any substance. Evolved mechanisms for achieving benefits may be unrelated to those for reducing costs. These evolutionary considerations suggest important consequences demonstrable by experimental or epidemiological studies. They also suggest ways in which our evolved dietary adaptations may be currently maladaptive, and individual development of taste preferences poorly calibrated by early experience in modern environments. The apparent reality of hormesis raises the possibility of counterproductive effects of current dosage recommendations and limits for nutrients and pollutants. We propose that some conceptual and factual problems are urgently in need of resolution. Fundamental to evolutionary biology is the tendency for organisms to become increasingly adapted to those environments to which they are most commonly exposed (Parsons 1990).

Adaptation, Physiological↗
PubMed2004

Signatures of selection and gene conversion associated with human color vision variation.

Trichromatic color vision in humans results from the combination of red, green, and blue photopigment opsins. Although color vision genes have been the targets of active molecular and psychophysical research on color vision abnormalities, little is known about patterns of normal genetic variation in these genes among global human populations. The current study presents nucleotide sequence analyses and tests of neutrality for a 5.5-kb region of the X-linked long-wave "red" opsin gene (OPN1LW) in 236 individuals from ethnically diverse human populations. Our analysis of the recombination landscape across OPN1LW reveals an unusual haplotype structure associated with amino acid replacement variation in exon 3 that is consistent with gene conversion. Compared with the absence of OPN1LW amino acid replacement fixation since divergence from chimpanzee, the human population exhibits a significant excess of high-frequency OPN1LW replacements. Our results suggest that subtle changes in L-cone opsin wavelength absorption may have been adaptive during human evolution.

Africa↗
PubMed1992

Protein requirements of adults from an evolutionary perspective.

It is argued that the observed minimum needs for protein and individual amino acids by adult humans and animals may merely reflect the diet that their predecessors consumed in the course of their evolution. The ability to adapt to diets with a lower proportion of protein than was ever encountered in practice would have given no competitive advantage. This can explain the limited ability to reduce rates of amino acid catabolism. The protein requirement of domestic cats, obligate carnivores, corresponds to approximately 20% of their energy requirement. Humans adapt to lower levels (approximately 6%). Some urge that higher protein intakes, resulting in higher rates of protein synthesis and turnover, are desirable and that, in general, the more prosperous and successful groups eat more protein. But cause and effect may be reversed. Are higher rates of turnover and catabolism necessarily beneficial? Objective data are still not available.

Adaptation, Physiological↗
PubMed1994

SORTEZ: a relational translator for NCBI's ASN.1 database.

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Algorithms↗
PubMed1995

RTM1: a member of a new family of telomeric repeated genes in yeast.

We have isolated a new yeast gene called RTM1 whose overexpression confers resistance to the toxicity of molasses. The RTM1 gene encodes a hydrophobic 34-kD protein that contains seven potential transmembrane-spanning segments. Analysis of a series of industrial strains shows that the sequence is present in multiple copies and in variable locations in the genome. RTM loci are always physically associated with SUC telomeric loci. The SUC-RTM sequences are located between X and Y' subtelomeric sequences at chromosome ends. Surprisingly RTM sequences are not detected in the laboratory strain X2180. The lack of this sequence is associated with the absence of any SUC telomeric gene previously described. This observation raises the question of the origin of this nonessential gene. The particular subtelomeric position might explain the SUC-RTM sequence amplification observed in the genome of yeasts used in industrial biomass or ethanol production with molasses as substrate. This SUC-RTM sequence dispersion seems to be a good example of genomic rearrangement playing a role in evolution and environmental adaptation in these industrial yeasts.

Amino Acid Sequence↗
PubMed2026

Reference genomes of Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica).

We established primary fibroblast cultures from a Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica) and generated highly contiguous reference genome assemblies using Oxford Nanopore Technologies PromethION long-read sequencing. The Japanese raccoon dog assembly spanned 2.69 Gb in 813 scaffolds, with a scaffold N50 of 52 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 98.2%. The Japanese red fox assembly spanned 2.47 Gb in 903 scaffolds, with a scaffold N50 of 139 Mb and a BUSCO completeness score of 97.5%. Phylogenomic analysis placed the Japanese raccoon dog in a lineage distinct from the continental raccoon dog, supporting its evolutionary differentiation within Nyctereutes. The Japanese red fox formed a distinct lineage within the red fox clade, consistent with its recognized regional differentiation. These genome assemblies and associated fibroblast cultures provide resources for studies of canid systematics, population history, local adaptation, comparative genome evolution, and conservation genetics.

Canidae↗
PubMed2004

A simple hierarchical approach to modeling distributions of substitution rates.

Genetic sequence data typically exhibit variability in substitution rates across sites. In practice, there is often too little variation to fit a different rate for each site in the alignment, but the distribution of rates across sites may not be well modeled using simple parametric families. Mixtures of different distributions can capture more complex patterns of rate variation, but are often parameter-rich and difficult to fit. We present a simple hierarchical model in which a baseline rate distribution, such as a gamma distribution, is discretized into several categories, the quantiles of which are estimated using a discretized beta distribution. Although this approach involves adding only two extra parameters to a standard distribution, a wide range of rate distributions can be captured. Using simulated data, we demonstrate that a "beta-" model can reproduce the moments of the rate distribution more accurately than the distribution used to simulate the data, even when the baseline rate distribution is misspecified. Using hepatitis C virus and mammalian mitochondrial sequences, we show that a beta- model can fit as well or better than a model with multiple discrete rate categories, and compares favorably with a model which fits a separate rate category to each site. We also demonstrate this discretization scheme in the context of codon models specifically aimed at identifying individual sites undergoing adaptive or purifying evolution.

Animals↗
PubMed2003

Modelling infection as a two-step process combining gene-for-gene and matching-allele genetics.

The genetic basis of infection determines the dynamics of host-parasite coevolution and associated phenomena such as local adaptation and the evolution of sex and recombination. Here, we present parasite resistance as a two-step process in which hosts must first detect parasites and then eradicate them; failure at either step results in infection. The model incorporates 'matching-allele' (MA) genetics for detection and 'gene-for-gene' (GFG) genetics for eradication. We found that the oscillatory dynamics were similar to pure GFG genetics when the cost of 'virulence' alleles was low, but resembled pure MA genetics when the cost was high. The magnitude of the cost that switched the dynamics from GFG dominated to MA dominated depended on the genetic architecture of defence (i.e. the number of GFG and MA loci).

Alleles↗
PubMed2003

Exhaustive sample set among Viverridae reveals the sister-group of felids: the linsangs as a case of extreme morphological convergence within Feliformia.

Although molecular studies have helped to clarify the phylogeny of the problematic family Viverridae, a recent phylogenetic investigation based on cytochrome b (cyt b) has excluded the Asiatic linsangs (genus Prionodon) from the family. To assess the phylogenetic position of the Asiatic linsangs within the Feliformia, we analysed an exhaustive taxonomic sample set with cyt b and newly produced transthyretin intron I sequences (TR-I-I). TR-I-I alone and cyt b +TR-I-I combined (maximum-likelihood analysis) highly support the position of Asiatic linsangs as sister-group of the Felidae. The estimation of minimum divergence dates from molecular data suggests a splitting event ca. 33.3 million years (Myr) ago, which lends support to historical assertions that the Asiatic linsangs are "living fossils" that share a plesiomorphic morphotype with the Oligocene feliform Paleoprionodon. The African linsang is estimated to appear more than 20 Myr later and represents the sister-group of the genus Genetta. Our phylogenetic results illustrate numerous morphological convergences of "diagnostic" characters among Feliformia that might be problematic for the identification of fossil taxa. The morphotype reappearance from the Asiatic to the African linsangs suggests that the genome of the Feliformia conserved its potential ability of expression for a peculiar adaptive phenotype throughout evolution, in this case arboreality and hypercarnivory in tropical forest.

Animals↗