Biomedical subjects

J K Bowmaker

Publications and source records attributed to J K Bowmaker.

At least 37 records · Page 2Linked to original sources

PubMed1997

Molecular evolution of the cottoid fish endemic to Lake Baikal deduced from nuclear DNA evidence.

Lake Baikal in Eastern Siberia contains a remarkable flock of 29 species of teleost fishes of the suborder Cottoidei (sculpins, bullheads) that are endemic to the lake and its associated rivers and occupy all depth habitats down to over 1500 m. The species are divided into three families, the Cottidae with 7 species, the Abyssocottidae with 20 species, and the Comephoridae with 2 species. Nucleotide sequences of the rod opsin gene from 12 of these species, plus a non-Baikal marine species, have been used to examine the evolutionary relations and the divergence time of the flock. Phylogenetic trees, generated by neighbor-joining and maximum parsimony, indicate that the unique Comephoridae family with its viviparity and unusual appearance is closely related to the Cottidae and Abyssocottidae, whereas the genus Cottocomephorus, at present placed in the Cottidae, was the first to diverge from the ancestral species and forms a separate lineage. The major adaptation to deep water would appear to be of relatively recent origin, and there is evidence that the ancestral species occupied a shallow-water-marine or brackish habitat. Estimates of antiquity obtained from synonymous substitutions place the origin of the species flock at around 4.9 million years ago.

Animals↗

PubMed1997

Visual pigments and oil droplets from six classes of photoreceptor in the retinas of birds.

Microspectrophotometric examination of the retinal photoreceptors of the budgerigar (shell parakeet), Melopsittacus undulatus (Psittaciformes) and the zebra finch, Taeniopygia guttata (Passeriformes), demonstrate the presence of four, spectrally distinct classes of single cone that contain visual pigments absorbing maximally at about 565, 507, 430-445 and 360-380 nm. The three longer-wave cone classes contain coloured oil droplets acting as long pass filters with cut-offs at about 570, 500-520 and 445 nm, respectively, whereas the ultraviolet-sensitive cones contain a transparent droplet. The two species possess double cones in which both members contain the long-wave-sensitive visual pigment, but only the principal member contains an oil droplet, with cut-off at about 420 nm. A survey of the cones of the pigeon, Columba livia (Columbiformes), confirms the presence of the three longer-wave classes of single cone, but also reveals the presence of a fourth class containing a visual pigment with maximum absorbance at about 409 nm, combined with a transparent droplet. No evidence was found for a fifth, ultraviolet-sensitive receptor. In the chicken, Gallus gallus (Galliformes), the cone class with a transparent droplet contains "chicken violet" with maximum absorbance at about 418 nm. The rods of all four species contain visual pigments that are spectrally similar, with maximum absorbance between about 506 and 509 nm. Noticeably, in any given species, the maximum absorbance of the rods is spectrally very similar to the maximum absorbance of the middle-wavelength-sensitive cone pigments.

Animals↗

PubMed1996

Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal.

Lake Baikal in Eastern Siberia is the deepest and one of the largest and most ancient lakes in the world. However, even in the deepest regions, oxygenation levels do not fall below 75-80% of the surface levels. This has enabled a remarkable flock of largely endemic teleost fish of the sub-order Cottoidei to colonize all depth habitats. We have previously shown that species that occupy progressively deeper habitats show a blue shift in the peak wavelength of absorbance (lambda max) of both their rod and cone visual pigments; for the rod pigments, a number of stepwise shifts occur from about 516 nm in littoral species to about 484 nm in abyssal species. By sequencing the rod opsin gene from 11 species of Baikal cottoids that include representatives from all depth habitats, we have been able to identify four amino acid substitutions that would account for these shifts. The effect of each substitution on lambda max is approximately additive and each corresponds to a particular lineage of evolution.

Amino Acid Sequence↗

PubMed1995

The rhodopsin-encoding gene of bony fish lacks introns.

A study of the sequences of the rhodopsin-encoding genes (Rh) in eight fish species from two of the major subdivisions of the teleosts reveals that no introns are present in the coding region. This contrasts with the opsin-encoding genes of all other vertebrates where either four or five introns are invariably found. Phylogenetic analysis shows that this intronless teleost Rh is homologous to the intron-containing Rh of amphibia, birds and mammals. Possible mechanisms for intron loss are discussed, including replacement by homologous conversion of Rh with a processed cDNA.

Amphibians↗

PubMed1995

Adaptive evolution of color vision genes in higher primates.

The intron 4 sequences of the three polymorphic alleles at the X-linked color photo-pigment locus in the squirrel monkey and the marmoset reveal that the alleles in each species are exceptionally divergent. The data further suggest either that each triallelic system has arisen independently in these two New World monkey lineages, or that in each species at least seven deletions and insertions (14 in the two species) in intron 4 have been transferred and homogenized among the alleles by gene conversion or recombination. In either case, the alleles in each species apparently have persisted more than 5 million years and probably have been maintained by overdominant selection.

Alleles↗

PubMed1995

Sequence and evolution of the blue cone pigment gene in Old and New World primates.

The sequences of the blue cone photopigments in the talapoin monkey (Miopithecus talapoin), an Old World primate, and in the marmoset (Callithrix jacchus), a New World monkey, are presented. Both genes are composed of 5 exons separated by 4 introns. In this respect, they are identical to the human blue gene, and intron sizes are also similar. Based on the level of amino acid identity, both monkey pigments are members of the S branch of pigments. Alignment of these sequences with the human gene requires the insertion/deletion of two separate codons in exon 1. The silent site divergence between these primate blue genes indicates a separation of the Old and New World primate lineages around 43 million years ago.

Amino Acid Sequence↗

PubMed1995

Differences in the temporal properties of human longwave- and middlewave-sensitive cones.

In recent years a number of electrophysiological and psychophysical observations have suggested that the temporal properties of the human longwave- and middlewave-sensitive cones might be different. However, until now the issue has remained unresolved, despite its obvious importance. We have succeeded in probing, electrophysiologically, the temporal properties of the two classes, under a range of adapting conditions, in a normal human observer. Here we present evidence that the temporal properties of these cone types are indeed different and that this difference is constant irrespective of the state of light adaptation, suggesting that light adaptation has little effect on the kinetics of transduction in human cones.

Adaptation, Physiological↗

PubMed1995

The chemistry of John Dalton's color blindness.

John Dalton described his own color blindness in 1794. In common with his brother, he confused scarlet with green and pink with blue. Dalton supposed that his vitreous humor was tinted blue, selectively absorbing longer wavelengths. He instructed that his eyes should be examined after his death, but the examination revealed that the humors were perfectly clear. In experiments presented here, DNA extracted from his preserved eye tissue showed that Dalton was a deuteranope, lacking the middlewave photopigment of the retina. This diagnosis is shown to be compatible with the historical record of his phenotype, although it contradicts Thomas Young's belief that Dalton was a protanope.

Base Sequence↗

PubMed1995

Interspecific variation of photoreceptors in four co-existing haplochromine cichlid fishes.

The photoreceptors of four co-existing haplochromine cichlids have been studied morphometrically and microspectrophotometrically, and the results were interpreted in terms of resolution and sensitivity. Among the three species, Haplochromis argens, H. piceatus and H. ishmaeli, the cone dimensions and the visual pigments differed only slightly, in spite of differences in vertical distribution and feeding behaviour between these species. The fourth species H. pyrrhocephalus showed distinctly different visual properties, with very large double cones at low densities, and its spectral sensitivity shifted to significantly longer wavelengths. To some degree, the photoreceptor morphometrics and visual pigments appeared to be attuned to the photic conditions of the specific habitats. The two species H. piceatus and H. pyrrhocephalus, occupying a dimmer habitat with less penetrating blue light, had reduced blue sensitive single cones, whereas the surface dwelling species H. argens had relatively small red/green sensitive double cones. Also an attempt has been made to relate the visual capacity of the cichlids to their behavioural patterns, focussing on prey detection. The greatest visual differences were observed in the two species H. argens and H. pyrrhocephalus, with resources coincidence and with the highest encounter frequency, which may indicate that visual segregation contributes towards reducing interference competition among co-existing species with a similar diet.

Animals↗

PubMed1994

Visual pigments and the photic environment: the cottoid fish of Lake Baikal.

The endemic cottoid fish of Lake Baikal in Eastern Siberia offer a singular opportunity for examining within a number of closely related species, the relationships of visual pigments, photoreceptor complements and depth within a deep freshwater environment. The lake, the deepest (1600 m) and one of the largest and most ancient in the world, is unique in that the oxygen levels at the bottom are only reduced to about 80% of the surface levels. We have studied, by light microscopy, microspectrophotometry and visual pigment extraction, the retinas from 17 species of Baikal cottoids that live at different depths within the lake. Generally the retinas contain, in addition to rods, large green-sensitive double cones and small blue-sensitive single cones: surprisingly for freshwater fish, the visual pigments are based on Vitamin A1. The lambda max of both rods and cones are displaced to shorter wavelengths with increasing depth. Surface species have cones with lambda max at about 546, 525 and 450 nm and rods at 523 nm, deeper living species retain cones, but with lambda max shifting towards 500 and 425 nm and with rods at 480 nm, whereas the deepest living fish possess only rods (lambda max 480-500 nm). These data clearly show a correlation between photoreceptor complement, visual pigment lambda max and depth, but question the hypothesis that there is a correlation of pigment lambda max with water colour since, in contrast to oceanic waters, the maximum transmission of Baikal water is between 550 and 600 nm.

Animals↗

PubMed1994

Sequence divergence, polymorphism and evolution of the middle-wave and long-wave visual pigment genes of great apes and Old World monkeys.

In man, the spectral shift between the middle-wave (MW) and long-wave (LW) visual pigments is largely achieved by amino acid substitution at two codons, both located in exon 5. A third amino acid site coded by exon 3 is polymorphic between pigments. We have studied the equivalent regions of the cone opsin genes in two members of the Hominidea (the gorilla, Gorilla gorilla and the chimpanzee, Pan troglodytes) and in three members of the Cercopithecoidea family of Old World primates (the diana monkey, Cercopithecus diana, the talapoin monkey, Miopithecus talapoin, and the crab-eating macaque, Macaca fascicularis). No variation in the codons that specify the amino acids involved in spectral tuning were found. We predict therefore that the MW and LW pigments of gorilla and chimpanzee have similar spectral characteristics to those of man. Multiple copies of the same opsin gene sequence were identified in the chimpanzee, talapoin and macaque and we also show that non-human Old World primates are similar to man in showing a bunching of polymorphic sites in exon 3. We discuss the ancestry of the separate MW and LW genes of Old World primates and the equivalent polymorphic gene of the marmoset, a New World primate.

Amino Acid Sequence↗

PubMed1993

The molecular basis of a spectral shift in the rhodopsins of two species of squid from different photic environments.

The molecular basis of spectral tuning of rhodopsin pigments in two squid species is examined. The absorbance spectra of rhodopsin extracts from Alloteuthis subulata (lambda max 499 nm) showed a 5 nm red shift compared with Loligo forbesi (lambda max 494 nm). The rhodopsin gene sequence of A. subulata opsin was determined from polymerase chain reaction (PCR) amplified fragments by using genomic DNA as template. The deduced amino acid sequence was compared with that obtained from the previously published cDNA sequence of Loligo forbesi. A total of 22 amino acid differences are present, although only seven can be considered to be non-homologous substitutions. Three of these changes occur in helical transmembrane regions but only one, the substitution of phenylalanine by serine at site 270 in Alloteuthis subulata, involves the replacement of an apolar with a hydroxyl-bearing residue at a site located near the centre of helix VI and on the inner face of the retinal-binding pocket. The equivalent site is also used for the spectral tuning of primate cone pigments, an example of convergent evolution. It is proposed that substitution at this site is responsible for the 5 nm red shift. The relation between this spectral shift and the maximum depth distribution of Alloteuthis subulata of about 200 m, compared with about 360 m for Loligo forbesi, is discussed. An unexpected finding was that the rhodopsin gene of both species appears to lack introns.

Amino Acid Sequence↗

PubMed1993

Structure and evolution of the polymorphic photopigment gene of the marmoset.

The marmoset Callithrix jacchus jacchus, is typical of a New World monkey in exhibiting a polymorphism of photopigments in the middlewave to longwave (535-565 nm) region of the spectrum. The single X-linked opsin gene that encodes the protein component of these pigments is present in three allelic forms producing, in marmosets, pigments with maximum sensitivities at about 543, 556 and 563 nm. All male monkeys are dichromats, whereas females may be either dichromats or trichromats. A cDNA sequence corresponding to the 563 form of this gene is reported, together with partial genomic DNA sequences of exons 2, 3, 4 and 5 of all three alleles. The origin of these sequences and their divergence from the middlewave- and longwave-sensitive pigments of man is discussed from both a functional and an evolutionary standpoint.

Amino Acid Sequence↗

PubMed1992

The spatial arrangement of cones in the primate fovea.

The retinae of Old World primates contain three classes of light-sensitive cone, which exhibit peak absorption in different spectral regions. But how are the different types of cone arranged in the hexagonal mosaic of the fovea? This question has often been answered with artists' impressions, but never with direct measurements. Staining for antibodies specific to the short-wave photopigment has revealed a sparse, semiregular array of cones; but nothing is known about the arrangement of the more numerous long- and middle-wave cones. Are they randomly distributed, with chance aggregations of one type, as Hartridge postulated in these columns nearly 50 years ago? Or do they exhibit a regular alteration, recalling the systematic mosaics seen in some non-mammalian species? Or, conversely, is there positive clumping of particular cone types, as might be expected if local patches of cones were descended from a single precursor cell? We have made direct microspectrophotometric measurements of patches of foveal retina from Old World monkeys, and report here that the distribution of long- and middle-wave cones is locally random. These two cone types are present in almost equal numbers, and not in the ratio of 2:1 that has been postulated for the human fovea.

Animals↗

PubMed1992

Sequence divergence and copy number of the middle- and long-wave photopigment genes in Old World monkeys.

We have studied the sequence and organization of the genes for the middle-wave (MW) and long-wave (LW) cone photopigment genes in six species of Old World monkeys. Previous studies have shown that the MW and LW pigments of all six species exhibit peak sensitivities near 535 nm and 565 nm, respectively, and thus resemble the equivalent human pigments. In the case of man, the protein components of the MW and LW photopigments differ by 15 amino acids, although only seven of these differences involve non-homologous substitutions and are therefore candidates for a role in spectral tuning. Regions corresponding to exons 4 and 5 of these genes, and including five such candidate sites, were sequenced in the Old World monkeys. In contrast to the equivalent human genes, substitutions were found at two of these sites, position 233 and 309 of the MW gene in all six species. The role of amino acid substitutions in the spectral tuning of these photopigments is discussed. A comparison of the nucleotide sequences of the MW and LW genes provides evidence for sequence homogenization within species; the role of gene conversion in the evolution of these genes is discussed. The close juxtaposition and homology of the MW and LW genes on the X chromosome is thought to underlie the high frequency of colour vision defects in man and the presence in many individuals of extra copies of the MW gene. A study of a group of talapoin (Ceropithecus talapoin) monkeys has revealed a similar numerical polymorphism for this gene to that present in man. In contrast to the situation in man, where the MW and LW genes may contain a shortened first intron, restriction digests of genomic DNA showed that the size of this intron does not differ across the six species of Old World monkeys examined.

Amino Acid Sequence↗

PubMed1992

The polymorphic photopigments of the marmoset: spectral tuning and genetic basis.

The marmoset (Callithrix jacchus jacchus), a South American monkey, is polymorphic for the middle- to long-wave cone photopigments: the three variant pigments have spectral peaks at 543, 556 and 563 nm. Comparisons of the deduced amino acid sequences of these pigments indicate that the variations in spectral sensitivity are associated with the presence or absence of hydroxyl-bearing residues at sites 180 and 285; but, in contrast to the additive hypothesis of Neitz et al. (1991), we propose that adjustments at site 233 may also be required to produce viable long-wave and middle-wave pigments. Within a family group of monkeys, we find that a restriction site polymorphism in the photopigment gene segregates in a way that is consistent with the single X-linked gene hypothesis previously proposed on the basis of the photopigment types present in male and female marmosets.

Amino Acid Sequence↗

PubMed1992

The relationship between cone pigments and behavioural sensitivity in a New World monkey (Callithrix jacchus jacchus).

Microspectrophotometric measurements of visual pigments and behavioural measurements of spectral sensitivity are reported for individual marmosets from 3 family groups. The sex differences and polymorphism that characterise the long-wave cone pigments in this species are well reflected by variations in the behavioural sensitivities. With one exception, the pattern of inheritance is compatible with a genetic model in which the long-wave pigment is specified by a single polymorphic locus on the X-chromosome. Measurements are also reported for the spectral absorbance of the marmoset lens, and these are used to reconstruct short-wave behavioural sensitivity from the microspectrophotometric measurements of the short-wave cones.

Animals↗

PubMed1991

Ultraviolet-sensitive cones in the goldfish.

Goldfish have been shown behaviourally to have ultraviolet sensitivity. We have now identified by microspectrophotometry a population of small single cones in the goldfish retina that contain a visual pigment maximally sensitive around 355-360 nm.

Animals↗