Beta‐globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B

Domestic sheep (Ovis aries) can be divided into two groups with significantly different responses to hypoxic environments, determined by two allelic beta‐globin haplotypes. Haplotype A is very similar to the goat beta‐globin locus, whereas haplotype B has a deletion spanning four globin genes, including beta‐C globin, which encodes a globin with high oxygen affinity. We surveyed the beta‐globin locus using resequencing data from 70 domestic sheep from 42 worldwide breeds and three Ovis canadensis and two Ovis dalli individuals. Haplotype B has an allele frequency of 71.4% in O. aries and was homozygous (BB) in all five wild sheep. This shared ancestry indicates haplotype B is at least 2–3 million years old. Approximately 40 kb of the sequence flanking the ~37‐kb haplotype B deletion had unexpectedly low identity between haplotypes A and B. Phylogenetic analysis showed that the divergent region of sheep haplotype B is remarkably distinct from the beta‐globin loci in goat and cattle but still groups with the Ruminantia. We hypothesize that this divergent ~40‐kb region in haplotype B may be from an unknown ancestral ruminant and was maintained in the lineage to O. aries, but not other Bovidae, evolving independently of haplotype A. Alternatively, the ~40‐kb sequence in haplotype B was more recently acquired by an ancestor of sheep from an unknown non‐Bovidae ruminant, replacing part of haplotype A. Haplotype B has a lower nucleotide diversity than does haplotype A, suggesting a recent bottleneck, whereas the higher frequency of haplotype B suggests a subsequent spread through the global population of O. aries.     

In pursuit of the functions of the Wnt family of developmental regulators: Insights from Xenopus laevis

Wnts are a recently described family of secreted glycoproteins related to the Drosophila segment polarity gene, wingless, and to the proto-oncogene, int-1. Wnts are thought to function as developmental modulators, with signalling distances of only a few cell diameters. In Xenopus, at least six Wnts, including Xwnts-1, -3A, and -4, are expressed initially in the developing central nervous system, with some regions expressing multiple Xwnts. Xwnt-8 is expressed by mid-blastula stage, in ventral and lateral mesoderm. Xwnt-5A mRNAs are stored in the egg, and later are expressed throughout the embryo in both ectoderm and mesoderm, but with a pronounced enrichment in the head and tail. Recent studies in Xenopus have pursued the diverse roles of Xwnts in early development, the mechanisms by which Xwnts signal information between cells, and the cell physiological responses to Xwnt signals.     

Cloning of the mating-type gene MATA of the yeast Yarrowia lipolytica

Summary The mating type gene MA TA of the dimorphic yeast Yarrowia lipolytica was cloned. The strategy used was based on the presumed function of this gene in the induction of sporulation. A diploid strain homozygous for the mating type B was transformed with an integrative gene bank from an A wild-type strain. A sporulating transformant was isolated, which contained a plasmid with an 11.6 kb insert. This sequence was rescued from the chromosomal DNA of the transformant and deletion mapping was performed to localize the MAT insert. The MAT gene conferred both sporulating and non-mating phenotypes on a B/B diploid. A LEU2 sequence targeted to this locus segregated like a mating type-linked gene. The A strain did not contain silent copies of the MAT gene.     

GABA modulation of SVZ‐derived progenitor ventral cell migration

The subventricular zone (SVZ) is a proliferative region that provides neurons to olfactory bulb throughout life. The new neurons undergo cell migration from SVZ and travel until they reach their final destination. We previously showed in the early postnatal mouse a ventral migratory subpopulation from SVZ targets the Islands of Calleja (ICC) in the basal forebrain. However, unlike the well‐characterized rostral migratory stream, little is known about the guidance mechanisms operating in the ventrally directed migratory pathway. In this study, we examined the role of neurotransmitter γ‐aminobutyric acid (GABA) in SVZ‐derived progenitor ventral migration and the involvement of this neurotransmitter in the cytoarchitectual organization of dispersed cells into the tight clusters of the ICC. Our results show that the ventral SVZ cell migration rate was enhanced by GABA acting through a GABA_A receptor and that GABA acts as a directional guidance cue for ventral migrating cells. Furthermore, disruption of GABA signaling inhibited the formation of Island clusters in vitro. Taken together, these data suggest that GABA is an important guidance and organizational cue for the Island of Calleja. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 75: 791–804, 2015     

A third allele of serum esterases in domestic fowl and the strain distribution of six phenotypes*

A starch gel electrophoretic technique has been described which utilized a pH 8.9 Tris-citrate gel buffer and facilitated the resolution of a new serum esterase zone of fowl. This zone was shown to be controlled by allele Es^C, the third in the series Es^A, Es^B, and Es^C. Allelic frequencies were determined in five egg-type strains and seven meat-type strains. Es^A was predominant in egg-type birds while Es^B was the most frequent allele in meat-type birds.     

The Evolution of Parasite Recognition Genes in the Innate Immune System: Purifying Selection on <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> Peptidoglycan Recognition Proteins

Genes involved in the recognition of parasites by the acquired immune system are often subject to intense selection pressures. In some cases, selection to recognize a diverse range of parasites has resulted in high levels of polymorphism, while elsewhere the protein sequence has changed rapidly under directional selection. We tested whether parasite recognition genes in the innate immune system show similar patterns of evolution. We sequenced seven peptidoglycan recognition protein genes (PGRPs) from 12 lines of Drosophila melanogaster and one line of D. simulans and used a variety of tests to determine whether the observed mutations were selectively neutral. We were unable to detect either balancing or directional selection. This suggests that the molecular cues used by insects to detect parasites are highly conserved and probably under strong functional constraints which prevent their evolving to evade the host immune response. Therefore, interactions between these genes are unlikely to be the focus of host–parasite coevolution, at least in Drosophila. We also found evidence of gene conversion occurring between two genes, PGRP-SC1A and PGRP-SC1B.     

Tissue-specific interplay between copper uptake and efflux in Drosophila

The vinegar fly Drosophila melanogaster is proving to be an excellent system to study the in vivo regulation of the essential metal copper. The Ctr1A/B and DmATP7 copper transport proteins have well-established roles in Drosophila copper uptake and efflux, respectively. Both Ctr1A and DmATP7 are essential genes, whereas Ctr1B mutants are viable but die in excess or depleted copper conditions. Less is known about the tissue-specific requirements for these three genes and how they interact to maintain copper homeostasis in different cell types. Here, we use targeted overexpression and suppression of each gene to examine these questions in vivo. We find that in the epidermal cells that form the adult thoracic and abdominal cuticle, Ctr1A plays a major role in copper uptake, whereas Ctr1B plays only a minor supporting role and DmATP7, as previously shown, is essential for transfer of copper to the trans-Golgi network. We also find that the copper chaperone dSco1 appears necessary for supplying the mitochondria with copper in these tissues. In contrast, in the developing Drosophila eye, DmATP7 appears to be non-essential unless copper levels in these cells are artificially elevated. Again, Ctr1A is the main copper uptake gene in the eye, but when ectopically expressed, Ctr1B has greater phenotypic effects than Ctr1A. Furthermore, Ctr1A and Ctr1B show a dramatic synergistic interaction, indicating their relationship is more complicated than a simply additive one and that they may in fact act cooperatively for optimal copper import.     

Production in <Emphasis Type="Italic">Trichoderma reesei</Emphasis> of three xylanases from <Emphasis Type="Italic">Chaetomium thermophilum</Emphasis>: a recombinant thermoxylanase for biobleaching of kraft pulp

Three endoxylanase genes were cloned from the thermophilic fungus Chaetomium thermophilum CBS 730.95. All genes contained the typical consensus sequence of family 11 glycoside hydrolases. Genomic copies of Ct xyn11A, Ct xyn11B, and Ct xyn11C were expressed in the filamentous fungus T. reesei under the control of the strong T. reesei cel7A (cellobiohydrolase 1, cbh1) promoter. The molecular masses of the Ct Xyn11A, Ct Xyn11B, and Ct Xyn11C proteins on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were 27, 23, and 22 kDa, respectively. Ct Xyn11A was produced almost as efficiently as the homologous xylanase II from a corresponding single-copy transformant strain. Ct Xyn11B production level was approximately half of that of Ct Xyn11A. The amount of Ct Xyn11C was remarkably lower. Ct Xyn11A had the highest temperature optimum and stability of the recombinant xylanases and the highest activity at acid-neutral pH (pH 5–7). It was the most suitable for industrial bleaching of kraft pulp at high temperature.     

Genetic characterization and fine mapping of a yellow-seeded gene in Dahuang (a <Emphasis Type="Italic">Brassica rapa</Emphasis> landrace)

The development of yellow-seeded cultivars in Brassica rapa (B. rapa) would improve the quality and quantity of available oil. The identification and mapping of the seed coat color gene may aid in the development of yellow-seeded cultivars and facilitate introgression of the yellow-seeded gene into desirable Brassica napus (B. napus) lines through marker-assisted selection. In the current study, we investigated the inheritance of a yellow-seeded landrace in B. rapa, “Dahuang”, originating from the Qinghai-Tibetan plateau. Genetic analysis revealed that the phenotype of the yellow-seeded trait in Dahuang is controlled by one recessive gene, termed Brsc1. Mapping of the Brsc1 gene was subsequently conducted in a BC₁ population comprised 456 individuals, derived from (Dahuang × 09A-126) × Dahuang. From a survey of 256 amplified fragment length polymorphism (AFLP) primer combinations, 10 tightly linked AFLP markers were obtained. The closest AFLP markers flanking Brsc1, Y10 and Y06, were 0.2 and 0.4 cM away, respectively. Subsequently, using simple sequence repeat (SSR) markers in the reference map, the Brsc1 gene was mapped on A09 in B. rapa. Blast analysis revealed that seven AFLP markers showed sequence homology to A09 of B. rapa, wherein six AFLP markers in our map were in the same order as those in A09 of B. rapa. The two closest markers, Y10 and Y06, delimited the Brsc1 gene within a 2.8 Mb interval. Furthermore, Y05 and Y06, the two closest AFLP markers on one side linked to Brsc1, were located in scaffold000059 on A09 of B. rapa, whereas the closet AFLP marker on the opposite side of Brsc1, Y10, was located in scaffold000081 on A09 of B. rapa. Molecular markers developed from these studies may facilitate marker-assisted selection (MAS) of yellow-seeded lines in B. rapa and B. napus and expedite the process of map-based cloning of Brsc1.     

Fish are like flies are like frogs: Conservation of dorsal-ventral patterning mechanisms

Genetic analysis of Drosophila has shown that a morphogenetic gradient of the Transforming Growth Factor-β family member dpp patterns the embryonic dorsalventral axis. Molecular and embryological evidence from Xenopus has strongly suggested a similar role for Bmp-4, the dpp homolog, in patterning the dorsalventral axis of chordates. A recent report has now identified mutations in two genes, dino and swirl, that disrupt dorsal-ventral patterning in the zebrafish Danio rerio⁽¹⁾. Characterization of these mutations parallels findings from Drosophila, thus establishing a genetic framework for the analysis of dorsalventral patterning in a vertebrate.     

Structure and genomic organization of centromeric repeats in<Emphasis Type="Italic"> Arabidopsis</Emphasis> species

Centromeric repetitive sequences were isolated from Arabidopsis halleri ssp. gemmifera and A. lyrata ssp. kawasakiana. Two novel repeat families isolated from A. gemmifera were designated pAge1 and pAge2. These repeats are 180 bp in length and are organized in a head-to-tail manner. They are similar to the pAL1 repeats of A. thaliana and the pAa units of A. arenosa. Both A. gemmifera and A. kawasakiana possess the pAa, pAge1 and pAge2 repeat families. Sequence comparisons of different centromeric repeats revealed that these families share a highly conserved region of approximately 50 bp. Within each of the four repeat families, two or three regions showed low levels of sequence variation. The average difference in nucleotide sequence was approximately 10% within families and 30% between families, which resulted in clear distinctions between families upon phylogenetic analysis. FISH analysis revealed that the localization patterns for the pAa, pAge1 and pAge2 families were chromosome specific in A. gemmifera and A. kawasakiana. In one pair of chromosomes in A. gemmifera, and three pairs of chromosomes in A. kawasakiana, two repeat families were present. The presence of three families of centromeric repeats in A. gemmifera and A. kawasakiana indicates that the first step toward homogenization of centromeric repeats occurred at the chromosome level.Communicated by W. R. McCombie     

Evolution and arrangement of the <Emphasis Type="Italic">hsp70</Emphasis> gene cluster in two closely related species of the <Emphasis Type="Italic">virilis</Emphasis> group of <Emphasis Type="Italic">Drosophila</Emphasis>

To investigate the genetic basis of differing thermotolerance in the closely related species Drosophila virilis and Drosophila lummei, which replace one another along a latitudinal cline, we characterized the hsp70 gene cluster in multiple strains of both species. In both species, all hsp70 copies cluster in a single chromosomal locus, 29C1, and each cluster includes two hsp70 genes arranged as an inverted pair, the ancestral condition. The total number of hsp70 copies is maximally seven in the more thermotolerant D. virilis and five in the less tolerant D. lummei, with some strains of each species exhibiting lower copy numbers. Thus, maximum hsp70 copy number corresponds to hsp70 mRNA and Hsp70 protein levels reported previously and the size of heat-induced puffs at 29C1. The nucleotide sequence and spacing of the hsp70 copies are consistent with tandem duplication of the hsp70 genes in a common ancestor of D. virilis and D. lummei followed by loss of hsp70 genes in D. lummei. These and other data for hsp70 in Drosophila suggest that evolutionary adaptation has repeatedly modified hsp70 copy number by several different genetic mechanisms.     

Affinity chromatography without immobilized ligands; A new method for studying macromolecular interactions using high-performance liquid chromatography

A new method for studying macromolecular interactions was devised. The principle is based on affinity chromatography with a mobile zone of affinity ligand instead of a column with immobilized ligand. In this method, the difference in migration velocities between the moving zone of affinity ligand and a sample in a conventional gel-permeation column is utilized. The fast migrating zone (A zone), which is later injected into the column, and the slow migrating zone (B zone), which is injected beforehand, interfere with each other at the passing point in the column if A and B interact such as A + B ? AB. The zone interference deforms each elution profile of A and B, because the complex AB has a migration velocity different from the others. The elution profiles in zone-interference chromatography are calculated by computer simulation in the framework of the plate theory. The binding constant is calculated from the peak shift of elution volume of B in the zone-interference chromatogram. The interaction between single-strand DNA (A zone) and ribonuclease A (B zone) was studied.     

Cloning,sequencing, and expression of the genomic DNA encoding the protein phosphatase cdc25 in <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis>

A genomic DNA (Dd-cdc25) encoding the protein phosphatase cdc25 was isolated from the cellular slime mold Dictyostelium discoideum. The Dd-cdc25 DNA sequence, with a length of 2,958 bp, encodes a protein consisting of 986 amino acid (aa) residues. The sequence shares significant identities with cdc25 from human, mouse, Xenopus, Drosophila, and Shizosaccharomyces pombe, particularly at the C-terminal region including the catalytic site for phosphatase activity. The deduced Dictyostelium cdc25 protein (Dd-cdc25) has the highest molecular mass (109.9 kDa) in several cdc25 species so far reported and contains four regions consisting of unusually long asparagine repeats (22–31) in the sequence. Unexpectedly, however, Western blot analysis using a specific antibody raised against the C terminus (aa 892–986) of Dd-cdc25 demonstrated that the protein exists as a short form (56 kDa), which has the C-terminal active site of phosphatase, during the course of Dictyostelium development. The Western blot analysis also revealed marked changes in the phosphorylated state of the Dd-cdc25, coupling with cellular development.Electronic Supplementary Material Supplementary material to this paper is available in electronic form at The sequence reported in this paper has been deposited in the DDBJ/EMBL/GenBank database with the accession number AB039883Edited by N. Satoh     

The two genes encoding protein synthesis initiation factor eIF-5A in Saccharomyces cerevisiae are members of a duplicated gene cluster

Summary Translation initiation factor eIF-5A is an abundant protein in which a lysine residue is modified by spermidine to form the amino acid derivative, hypusine. The factor is encoded by two genes in Saccharomyces cerevisiae, called TIF51A and TIF51B, which are regulated reciprocally by oxygen and by heme. TIF51B, also called ANBI, is located on chromosome X in a region called COR. We physically mapped TIF51A and its associated serine tRNA₂ gene by the method of chromosome fragmentation and pulsed-field gel electrophoresis. TIF5IA maps 90 kb from the left end of chromosome V in a region called ARC. The COR and ARC regions contain CYCI and CYC7, respectively, and appear to be duplications carrying numerous related genes. The arrangements of related genes in the two regions are incompatible with a duplication mechanism involving a circular intermediate.     

Distinct expression patterns for two Xenopus Bar homeobox genes

The BarH1 and BarH2 homeobox genes are coexpressed in cells of the fly retina and in the central and peripheral nervous systems. The fly Bar genes are required for normal development of the eye and external sensory organs. In Xenopus we have identified two distinct vertebrate Bar-related homeobox genes, XBH1 and XBH2. XBH1 is highly related in sequence and expression pattern to a mammalian gene, MBH1, suggesting that they are orthologues. XBH2 has not previously been identified but is clearly related to the Drosophila Bar genes. During early Xenopus embryogenesis XBH1 and XBH2 are expressed in overlapping regions of the central nervous system. XBH1, but not XBH2, is expressed in the developing retina. By comparing the expression of XBH1 with that of hermes, a marker of differentiated retinal ganglion cells, we show that XBH1 is expressed in retinal ganglion cells during the differentiation process, but is down-regulated as cells become terminally differentiated. Received: 12 August 1999 / Accepted: 5 October 1999     

Retrotransposon <Emphasis Type="Italic">gtwin</Emphasis>: Structural analysis and distribution in <Emphasis Type="Italic">Drosophila</Emphasis> strains

A search for noncanonical variants of the gypsy retrotransposon ( MDG4 ) in the genome of the Drosophila melanogaster strain G32 led to the cloning of four copies of the poorly studied 7411-bp gtwin element. Sequence analysis showed that gtwin belongs to a family of endogeneous retroviruses, which are widespread in the Drosophila genome and have recently been termed insect erantiviruses. The gtwin retrotransposon is evolutionarily closest to MDG4, as evident from a good alignment of their nucleotide sequences including ORF2 (the pol gene) and ORF3 (the env gene), as well as the amino acid sequences of their protein products. These regions showed more than 75% homology. The distribution of gtwin was studied in several strains of the genus Drosophila. While strain G32 contained more than 20 copies of the element, ten other D. melanogaster strains carried gtwin in two to six copies per genome. The gtwin element was not detected in D. Hydei or D. Virilis. Comparison of the cloned gtwin sequences with the gtwin sequence available from the D. melanogaster genome database showed that the two variants of the mobile element differ by the presence or absence of a stop codon in the central region of ORF3. Its absence from the gtwin copies cloned from the strain G32 may indicate an association between the functional state of ORF3 and amplification of the element.Translated from Genetika, Vol. 41, No. 1, 2005, pp. 23–29.Original Russian Text Copyright © 2005 by Kotnova, Karpova, Feoktistova, Lyubomirskaya, Kim, Ilyin.