Cloning and sequencing of quail and pigeon prion genes

Quail and pigeon PrP genes were cloned and sequenced. Like mammalian PrP genes, quail and pigeon genes are encoded by a single exon of a single copy gene in the genome. All of the structural features of mammalian PrP genes were found in the quail and pigeon PrP gene. Compared with the nucleotide sequences of mammalian PrP, they display generally 30% similarity. When compared with chicken PrP's DNA sequence, they show a higher homology (90%), and an even higher homology (99%) when compared to each other. A phylogenetic tree was constructed to trace the evolution of the prion gene in animals.     

Avian smooth muscle: Morphometric analysis and comparison of different types

Summary Smooth muscle from the pigeon gizzard and intestine, and quail gizzard were investigated using ultrastructural morphometric analysis and compared on the basis of volume percent mitochondria, dense bodies, sarcoplasmic reticulum, number of mitochondria/m², and fiber diameter. One-way analysis of variance tests showed significant differences in (1) volume percent mitochondria between pigeon intestine and quail gizzard and between pigeon and quail gizzards; (2) mitochondrial number between all three muscles; and (3) fiber diameter between pigeon gizzard and intestine and pigeon intestine and quail gizzard.     

Erythrocytes of Japanese Quail for Hemagglutination by Rubella Virus

Erythrocytes (RBC) of adult Japanese quail, Coturnix coturnix japonica, were found to be as sensitive as day-old chick RBC for rubella virus hemagglutination (HA). Various factors involved in the HA were studied with quail RBC as well as with adult pigeon and day-old chick RBC. Pigeon RBC, unlike chick and quail RBC, tended to show, without hemagglutinin, a pattern of sedimented RBC resembling the HA pattern by the virus at 4 C, to a lesser extent at room temperature, in 0.85% NaCl solution buffered with m/100 phosphate (PBS), and were prevented from doing so by addition of a small amount of bovine plasma albumin to the diluent. A small amount (about 10^?3 m ) of CaCL₂ in PBS gave higher HA titers. The HA titer was higher at 4 C than at room temperature and much reduced at 36 C with chick and quail RBC. With pigeon RBC, addition of bovine plasma albumin to the diluent tended to reduce HA titers. The HA titer was highest at pH 5.8 to 6.8, and was inversely proportional to the RBC concentration. Under the conditions established on the basis of these findings, chick and quail RBC gave similar HA titers, but pigeon RBC gave consistently higher titers. However, these types of RBC gave no significant difference in HA-inhibiting antibody titer when 4 units of hemagglutinin as determined with the homologous RBC was used.     

鹌鹑源鼠伤寒沙门氏菌的分离鉴定与耐药性分析

【背景】在鹌鹑养殖过程中,抗菌药物和消毒剂的不规范使用加剧了耐药菌株在动物、场所和食品之间的相互传播,因此,掌握致病菌株在养殖动物中的耐药状况至关重要。【目的】检测北京周边地区鹌鹑蛋源致病菌株的耐药特征和耐药基因的流行情况。【方法】在天津市武清区部分鹌鹑养殖场采集鹌鹑泄殖腔粪便、鹌鹑蛋表、养殖环境和鹌鹑饮水的样品,通过细菌分离培养、菌落形态观察、染色镜检、生化鉴定、血清分型、沙门氏菌inv A基因序列测定等方法对分离菌株进行鉴定。同时进行小鼠攻毒试验,测定小鼠半数致死量(median lethal dose, LD50)。再通过药敏试验和PCR方法对分离菌的耐药表型、耐药基因及毒力基因进行检测。【结果】分离菌株菌落颜色、镜检形态和生化试验结果符合沙门氏菌特性,沙门氏菌inv A基因序列测定与鼠伤寒沙门氏菌参考株相似度为99.44%,鉴定为鼠伤寒沙门氏菌,血清型为1,4,[5],[12]:i:l,2。该菌株对小鼠有致病作用,小鼠LD50为2.10×107 CFU/mL;药敏试验结果显示该菌株对氨苄西林、阿莫西林/克拉维酸、头孢噻呋、链霉素、磺胺甲啞唑、磺胺异啞唑、诺氟沙星、环丙沙星表现耐...     

Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides

Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studied ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea meleagris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed for turkey, quail and chicken using primers specific for the human apobec-1 gene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, respectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-based STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining analysis of an agc1-based STS that was common to all five species showed phylogenetic relationships consistent with those previously defined using mitochondria DNA sequences and nuclear gene restriction maps. Additionally, several putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chicken when multiple sequences were evaluated from each species. This report describes new STSs that are resources for genetic and physical mapping and genome analysis within and among avian species. These resources should further aid in our understanding of the biology of agriculturally important but little-studied guinea fowl and turkey. This revised version was published online in July 2006 with corrections to the Cover Date.     

Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals

BackgroundAlthough the mammalian X and Y chromosomes evolved from a single pair of autosomes, they are highly differentiated: the Y chromosome is dramatically smaller than the X and has lost most of its genes. The surviving genes are a specialized set with extraordinary evolutionary longevity. Most mammalian lineages have experienced delayed, or relatively recent, loss of at least one conserved Y-linked gene. An extreme example of this phenomenon is in the Japanese spiny rat, where the Y chromosome has disappeared altogether. In this species, many Y-linked genes were rescued by transposition to new genomic locations, but until our work presented here, this has been considered an isolated case.ResultsWe describe eight cases of genes that have relocated to autosomes in mammalian lineages where the corresponding Y-linked gene has been lost. These gene transpositions originated from either the X or Y chromosomes, and are observed in diverse mammalian lineages: occurring at least once in marsupials, apes, and cattle, and at least twice in rodents and marmoset. For two genes - EIF1AX/Y and RPS4X/Y - transposition to autosomes occurred independently in three distinct lineages.ConclusionsRescue of Y-linked gene loss through transposition to autosomes has previously been reported for a single isolated rodent species. However, our findings indicate that this compensatory mechanism is widespread among mammalian species. Thus, Y-linked gene loss emerges as an additional driver of gene transposition from the sex chromosomes, a phenomenon thought to be driven primarily by meiotic sex chromosome inactivation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0667-4) contains supplementary material, which is available to authorized users.     

Characterization of a prion protein (PrP) gene from rabbit; a species with apparent resistance to infection by prions

The prion protein gene (PrP) encodes a cellular protein of unknown function. A conformational isoform of this protein is involved in the neurodegenerative prion diseases. To facilitate the identification of structurally and antigenically important regions within the PrP molecule, the rabbit PrP open reading frame (ORF) was cloned and characterised. There is 82–87% identity at the nucleotide sequence level and 88–93% identity at the amino acid (aa) sequence level, between the rabbit gene and PrP sequences of other mammals. The rabbit gene shares structural and organisational features common to all known PrP genes signifying that it is the rabbit PrP gene. Comparison of the rabbit PrP aa sequence with PrP aa sequences from different species revealed several potential epitopes. Two anti-ovine PrP peptide Ab raised in rabbits, 168-92 and 98-92, confirmed that two separate cross-reacting epitopes segregate with single aa differences between rabbit and sheep PrP at positions 43 and 99 of the rabbit PrP polypeptide. The presence of these epitopes correlates with the species recognition patterns of previously published Ab. The usefulness of the rabbit PrP gene sequence in predicting antigenic regions within the PrP proteins of various species is illustrated. The structure of the rabbit PrP protein in relation to rabbits' apparent resistance to infection by prions is discussed.     

Genes in S. cerevisiae encoding proteins with domains homologous to the mammalian ras proteins

The ras genes, which were first identified by their presence in RNA tumor viruses and which belong to a highly conserved gene family in vertebrates, have two close homologs in yeast, detectable by Southern blotting. We have cloned both genes (RAS1 and RAS2) from plasmid libraries and determined the complete nucleotide sequence of their coding regions. They encode proteins with nearly 90% homology to the first 80 positions of the mammalian ras proteins, and nearly 50% homology to the next 80 amino acids. Yeast RAS1 and RAS2 proteins are more homologous to each other, with about 90% homology for the first 180 positions. After this, at nearly the same position that the mammalian ras proteins begin to diverge from each other, the two yeast ras proteins diverge radically. The yeast ras proteins, like the proteins encoded by the mammalian genes, terminate with the sequence cysAAX, where A is an aliphatic amino acid. Thus the yeast ras proteins have the same overall structure and interrelationship as the family of mammalian ras proteins. The domains of divergence may correspond to functional domains of the ras proteins. Monoclonal antibody directed against mammalian ras proteins immunoprecipitates protein in yeast cells containing high copy numbers of the yeast RAS2 gene.     

Tissue Distribution,Gender- and Genotype-Dependent Expression of Autophagy-Related Genes in Avian Species

As a result of the genetic selection of broiler (meat-type breeders) chickens for enhanced growth rate and lower feed conversion ratio, it has become necessary to restrict feed intake. When broilers are fed ad libitum, they would become obese and suffer from several health-related problems. A vital adaptation to starvation is autophagy, a self-eating mechanism for recycling cellular constituents. The autophagy pathway has witnessed dramatic growth in the last few years and extensively studied in yeast and mammals however, there is a paucity of information in avian (non-mammalian) species. Here we characterized several genes involved in autophagosome initiation and elongation in Red Jungle fowl (Gallus gallus) and Japanese quail (coturnix coturnix Japonica). Both complexes are ubiquitously expressed in chicken and quail tissues (liver, leg and breast muscle, brain, gizzard, intestine, heart, lung, kidney, adipose tissue, ovary and testis). Alignment analysis showed high similarity (50.7 to 91.5%) between chicken autophagy-related genes and their mammalian orthologs. Phylogenetic analysis demonstrated that the evolutionary relationship between autophagy genes is consistent with the consensus view of vertebrate evolution. Interestingly, the expression of autophagy-related genes is tissue- and gender- dependent. Furthermore, using two experimental male quail lines divergently selected over 40 generations for low (resistant, R) or high (sensitive, S) stress response, we found that the expression of most studied genes are higher in R compared to S line. Together our results indicate that the autophagy pathway is a key molecular signature exhibited gender specific differences and likely plays an important role in response to stress in avian species.     

Metabolism of a dieldrin analogue - secondary oxidation by liver microsomes

HCE was metabolised to a monohydroxy epoxide (HHC) by liver microsomes and 11,000g supernatants of the rat, rabbit, pigeon and Japanese quail. After a substantial amount of the substrate had been metabolised HHC began to be hydroxylated to a more polar metabolite that was identified as dihydroxy HCE. Both metabolic conversions were evidently mixed function oxidations since they depended upon NADPH and O₂. Dihydroxy HCE was also produced $\text{in vivo}$ by the rabbit and the quail.     

Evolutionary Descent of Prion Genes from the ZIP Family of Metal Ion Transporters

In the more than twenty years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into a possible function of PrP may be obtained through the characterization of its molecular neighborhood in cells. Quantitative interactome data demonstrated the spatial proximity of two metal ion transporters of the ZIP family, ZIP6 and ZIP10, to mammalian prion proteins in vivo. A subsequent bioinformatic analysis revealed the unexpected presence of a PrP-like amino acid sequence within the N-terminal, extracellular domain of a distinct sub-branch of the ZIP protein family that includes ZIP5, ZIP6 and ZIP10. Additional structural threading and orthologous sequence alignment analyses argued that the prion gene family is phylogenetically derived from a ZIP-like ancestral molecule. The level of sequence homology and the presence of prion protein genes in most chordate species place the split from the ZIP-like ancestor gene at the base of the chordate lineage. This relationship explains structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The phylogenetic and spatial connection to ZIP proteins is expected to open new avenues of research to elucidate the biology of the prion protein in health and disease.     

Differential hepatic gene expression of a dietary specialist (Neotoma stephensi) and generalist (Neotoma albigula) in response to juniper (Juniperus monosperma) ingestion

Dietary specialization is thought to be rare in mammalian herbivores because of limitations of their detoxification system in processing large doses of a single type of plant secondary compound (PSC). Therefore, in order to specialize on a single species of plant, mammalian herbivores must have a highly efficient detoxification system for the particular types of PSCs they ingest. Using microarray technology, we looked at the expression of hepatic genes of a dietary specialist, Neotoma stephensi, and a sympatric generalist, Neotoma albigula, in response to diets containing different levels of one-seeded juniper (Juniperus monosperma). We found large between species differences in gene expression, as well as large within species differences when specialists fed a low juniper diet (25% juniper) were compared to specialists fed their ecologically relevant level of juniper (70% juniper). We also tested the hypothesis that the specialist relies on less costly phase I detoxification enzymes more than phase II compared to the generalist. Although we found that the specialist had higher cumulative as well as average expression of phase I versus phase II enzymes, the generalist had a similar pattern of expression for phase I versus phase II enzymes.     

Iatrogenic and sporadic Creutzfeldt-Jakob disease in 2 sisters without mutation in the prion protein gene

ABSTRACT

Human genetic prion diseases have invariably been linked to alterations of the prion protein (PrP) gene PRNP. Two sisters died from probable Creutzfeldt-Jakob disease (CJD) in Switzerland within 14 y. At autopsy, both patients had typical spongiform change in their brains accompanied by punctuate deposits of PrP. Biochemical analyses demonstrated proteinase K-resistant PrP. Sequencing of PRNP showed 2 wild-type alleles in both siblings. Retrospectively, clinical data revealed a history of dural transplantation in the initially deceased sister, compatible with a diagnosis of iatrogenic CJD. Clinical and familial histories provided no evidence for potential horizontal transmission. This observation of 2 siblings suffering from CJD without mutations in the PRNP gene suggests potential involvement of non-PRNP genes in prion disease etiology.     

Molecular Cloning of Pigeon UDP-galactose:��-d-Galactoside ��1,4-Galactosyltransferase and UDP-galactose:��-d-Galactoside ��1,4-Galactosyltransferase, Two Novel Enzymes Catalyzing the Formation of Gal��1�C4Gal��1�C4Gal��1�C4GlcNAc Sequence

We previously found that pigeon IgG possesses unique N-glycan structures that contain the Galα1–4Galβ1–4Galβ1–4GlcNAc sequence at their nonreducing termini. This sequence is most likely produced by putative α1,4- and β1,4-galactosyltransferases (GalTs), which are responsible for the biosynthesis of the Galα1–4Gal and Galβ1–4Gal sequences on the N-glycans, respectively. Because no such glycan structures have been found in mammalian glycoproteins, the biosynthetic enzymes that produce these glycans are likely to have distinct substrate specificities from the known mammalian GalTs. To study these enzymes, we cloned the pigeon liver cDNAs encoding α4GalT and β4GalT by expression cloning and characterized these enzymes using the recombinant proteins. The deduced amino acid sequence of pigeon α4GalT has 58.2% identity to human α4GalT and 68.0 and 66.6% identity to putative α4GalTs from chicken and zebra finch, respectively. Unlike human and putative chicken α4GalTs, which possess globotriosylceramide synthase activity, pigeon α4GalT preferred to catalyze formation of the Galα1–4Gal sequence on glycoproteins. In contrast, the sequence of pigeon β4GalT revealed a type II transmembrane protein consisting of 438 amino acid residues, with no significant homology to the glycosyltransferases so far identified from mammals and chicken. However, hypothetical proteins from zebra finch (78.8% identity), frogs (58.9–60.4%), zebrafish (37.1–43.0%), and spotted green pufferfish (43.3%) were similar to pigeon β4GalT, suggesting that the pigeon β4GalT gene was inherited from the common ancestors of these vertebrates. The sequence analysis revealed that pigeon β4GalT and its homologs form a new family of glycosyltransferases.     

A comparison of the protective action of added egg yolks from five avian species to the cryopreservation of bull sperm

Cryopreservation of domestic animal sperm has been widely used for artificial insemination (AI), and egg yolk is one of the most commonly used cryoprotectants during the freezing-thawing process. The objectives of this study were to compare the effectiveness of egg yolk from five avian species (domestic chicken, domestic duck, domestic goose, Japanese quail or domestic pigeon) and to optimize the concentration of egg yolk on the cryopreservation of bull sperm in terms of frozen-thawed sperm progressive motility and viability. The results were two-fold. First, they showed that pigeon egg yolk provided the best cryoprotective effects on the cryopreservation of bull sperm, compared with egg yolk of chicken, quail, goose or duck. Second, the best concentration of pigeon egg yolk in extender was 20% during cryopreservation among five concentrations of 5, 10, 20, 30 or 40%. The results suggest that pigeon egg yolk could be used as an alternative to chicken egg yolk in extender but requires further testing in fertility trials.     

Bacteriophage ?29 infection of Bacillus subtilis minicells

Summary Labelled chloroplast rRNAs from Spinacia oleracea were hybridized to restriction endonuclease digests of chloroplast DNA from Oenothera hookeri and Euglena gracilis, to mitochondrial DNA of Acanthamoeba castellanii, and to DNA of the E. coli rrn B operon in the transducing phage lambda rif^d18. The degree of homology is greatest for the 16S rRNA gene. Greater than 90% occurs between the two higher plant genes, 80% homology to the lower plant gene, 60%–70% homology to the bacterial gene, and 20% homology to the mitochondrial gene. The degree of hybridization varied considerably for the 23S and the 5S rRNA genes. Very high homology exists between the two higher plant genes, only about 50% homology for both the Euglena and bacterial genes, and no significant homology for the mitochondrial genes. These results show that any chloroplast (or E. coli) rRNA may be used as a probe to identify rRNA genes in other ctDNAs.Two RNA populations, each enriched for a different ctDNA-encoded mRNA, proved useful in the location of these genes on both higher plant ctDNAs. No significant hybridization was obtained using these probes to the Euglena ctDNA which seems to be too distantly related.Abbreviations Md megadalton, 10⁶ dalton - bp, kbp base pair, kilo base pair - SSC Standard saline citrate, 1 times SSC is 0.15M sodium, chloride, 0.015 M trisodium citrate, pH, 6.8 - mtDNA mitochondrial DNA - ctDNA chloroplast DNA - ctrRNA chloroplast ribosomal RNA     

Prion protein-related proteins from zebrafish are complex glycosylated and contain a glycosylphosphatidylinositol anchor

A hallmark of prion diseases in mammals is a conformational transition of the cellular prion protein (PrP(C)) into a pathogenic isoform termed PrP(Sc). PrP(C) is highly conserved in mammals, moreover, genes of PrP-related proteins have been recently identified in fish. While there is only little sequence homology to mammalian PrP, PrP-related fish proteins were predicted to be modified with N-linked glycans and a C-terminal glycosylphosphatidylinositol (GPI) anchor. We biochemically characterized two PrP-related proteins from zebrafish in cultured cells and show that both zePrP1 and zeSho2 are imported into the endoplasmic reticulum and are post-translationally modified with complex glycans and a C-terminal GPI anchor.     

Identification of a Novel Bacterial K<Superscript>+</Superscript> Channel

In an attempt to explore unknown K⁺ channels in mammalian cells, especially ATP-sensitive K⁺ (K_ATP) channels, we compared the sequence homology of Kir6.1 and Kir6.2, two pore-forming subunits of mammalian K_ATP channel genes, with bacterial genes that code for selective proteins with confirmed or putative ion transport properties. BLAST analysis revealed that a prokaryotic gene (ydfJ) expressed in Escherichia coli K12 strain shared 8.6% homology with Kir6.1 and 8.3% with Kir6.2 genes. Subsequently, we cloned and sequenced ydfJ gene from E. coli K12 and heterologously expressed it in mammalian HEK-293 cells. The whole-cell patch-clamp technique was used to record ion channel currents generated by ydfJ-encoded protein. Heterologous expression of ydfJ gene in HEK-293 cells yielded a novel K⁺ channel current that was inwardly rectified and had a reversal potential close to K⁺ equilibrium potential. The expressed ydfJ channel was blocked reversibly by low concentration of barium in a dose-dependent fashion. Specific K_ATP channel openers or blockers did not alter the K⁺ current generated by ydfJ expression alone or ydfJ coexpressed with rvSUR1 or rvSUR2B subunits of K_ATP channel complex. Furthermore, this coexpressed ydfJ/rvSUR1 channels were not inhibited by ATP dialysis. On the other hand, ydfJ K⁺ currents were inhibited by protopine (a nonspecific K⁺ channel blocker) but not by dofetilide (a HERG channel blocker). In summary, heterologously expressed prokaryotic ydfJ gene formed a novel functional K⁺ channel in mammalian cells.