ICTV Virus Taxonomy Profile: Arteriviridae 2021.

The family Arteriviridae comprises enveloped RNA viruses with a linear, positive-sense genome of approximately 12.7 to 15.7 kb. The spherical, pleomorphic virions have a median diameter of 50-74 nm and include eight to eleven viral proteins. Arteriviruses infect non-human mammals in a vector-independent manner. Infections are often persistent and can either be asymptomatic or produce overt disease. Some arteriviruses are important veterinary pathogens while others infect particular species of wild rodents or African non-human primates. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Arteriviridae, which is available at ictv.global/report/arteriviridae.

Transmission electron microscopy artifacts in characterization of the nanomaterial-cell interactions.

We investigated transmission electron microscopy artifacts obtained using standard sample preparation protocols applied to the investigation of Escherichia coli cells exposed to common nanomaterials, such as TiO2, Ag, ZnO, and MgO. While the common protocols for some nanomaterials result only in known issues of nanomaterial-independent generation of anomalous deposits due to fixation and staining, for others, there are reactions between the nanomaterial and chemicals used for post-fixation or staining. Only in the case of TiO2 do we observe only the known issues of nanomaterial-independent generation of anomalous deposits due to exceptional chemical stability of this material. For the other three nanomaterials, different artifacts are observed. For each of those, we identify causes of the observed problems and suggest alternative sample preparation protocols to avoid artifacts arising from the sample preparation, which is essential for correct interpretation of the obtained images and drawing correct conclusions on cell-nanomaterial interactions. Finally, we propose modified sample preparation and characterization protocols for comprehensive and conclusive investigations of nanomaterial-cell interactions using electron microscopy and for obtaining clear and unambiguous revelation whether the nanomaterials studied penetrate the cells or accumulate at the cell membranes. In only the case of MgO and ZnO, the unambiguous presence of Zn and Mg could be observed inside the cells.

Mechanisms of antibacterial activity of MgO: non-ROS mediated toxicity of MgO nanoparticles towards Escherichia coli.

The toxicity of metal oxide nanomaterials and their antimicrobial activity is attracting increasing attention. Among these materials, MgO is particularly interesting as a low cost, environmentally-friendly material. The toxicity of MgO, similar to other metal oxide nanomaterials, is commonly attributed to the production of reactive oxygen species (ROS). We investigated the toxicity of three different MgO nanoparticle samples, and clearly demonstrated robust toxicity towards Escherichia coli bacterial cells in the absence of ROS production for two MgO nanoparticle samples. Proteomics data also clearly demonstrate the absence of oxidative stress and indicate that the primary mechanism of cell death is related to the cell membrane damage, which does not appear to be due to lipid peroxidation.

Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas--Erysipelothrix rhusiopathiae SY1027.

BACKGROUND: Erysipelothrix rhusiopathiae is the causative agent of animal erysipelas and, to a fewer occurrences, human erysipeloid. It is ubiquitous in nature and commensal in diverse species of animals, wild or domestic, from mammals and birds to reptiles and fish. Mechanisms of its virulence and pathogenicity are poorly understood. RESULTS: Making use of the complete genome sequencing of E. rhusiopathiae strain SY1027 and comparative genome analysis between the three highly pathogenic strains (SY1027, Fujisawa and ATCC19414), the genomic structure and putative functional elements, such as pathogenicity island (PAI)-like regions, potential virulence factors and horizontal transferring genes of the bacteria are identified. Strain SY1027 genome is 1,752,910 base pairs long, just 30 kilobases smaller than strain Fujisawa, with the same GC level of 36.36%. It contains 1,845 open reading frames (ORF) predicted by GLIMMER 3.02, of which 1,775 were annotated by PGAAP, 1,757 (~95.23%) were annotated by NCBI nr blast, 1,209 by COG database and 1,076 by KEGG database. 37 potential virulence factors were annotated in strain SY1027 by VFDB, while 19 (~51.35%) of them are common in the 2 strains, 7 of which are potentially related to antibiotic resistance and highly conserved (~98-100% match identity (ID)) amongst the three strains of E. rhusiopathiae and modestly homologous to other gastrointestinal tract-inhabiting Firmicutes (~40% match ID), e.g. Clostridium spp., Enterococcus spp. Genomic island- and pathogenicity island-like regions were also predicted, in which some showed association with tRNA and potential virulence factors. CONCLUSION: Complete genome sequencing of Erysipelothrix rhusiopathiae, the causative agent of animal erysipelas, was performed. Molecular identification of various genomic elements pave the way to the better understanding of mechanisms underlying metabolic capabilities, pathogenicity of swine erysipelas and prospective vaccine targets besides the widely used SpaA antigens.

Expressed sequence tag analysis of the emu (Dromaius novaehollandiae) pituitary by 454 GS Junior pyrosequencing.

Emus (Dromaius novaehollandiae) are farmed for their oil for pharmaceutical and cosmetic uses. This emu pituitary expressed sequence tag study was undertaken to identify novel transcripts in the emu pituitary to propel their identification and functional studies. By mapping reads derived from the Roche 454 GS Junior pyrosequencer to 8 reference species (human, mouse, chicken, zebra finch, fruit fly, turkey, round worm, and Carolina anole lizard) from the UniGene database, a total of 81,788 reads (53,312 mapped reads) were obtained and assembled with Reference Sequence (RefSeq). We annotated 6,676 potential emu genes by referencing 7 species (excluding lizard) and identified 1,232 potential genes common among 3 species (human, mouse, and chicken) with complete available reference genomes. Gene Ontology analysis revealed 376 Gene Ontology terms showing, with the highest counts, their involvements in biological processes, metabolism, and cellular components. These potential genes were detected to associate with 20 pathways including mitogen-activated protein kinase, insulin, neurotrophin signaling pathways, and carbohydrate digestion and absorption pathway. We also revealed a panel of tissue-specific genes including regulator of G-protein signaling protein (RGS), glucagon-like peptide receptor (GLPR), and growth hormone-inducible transmembrane protein (GHITM). Additionally, fatty acid binding protein (FABP), fatty acid desaturase (FAS), and stearoyl-coenzyme A desaturase (SCD), key enzyme genes in fat metabolism, were found to be also expressed in emu pituitary. This expressed sequence tag study represents the first step in functional characterization of emu pituitary gene expression and SNP identification for the improvement of fat production in the emu.

Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae).

Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.

Molecular characterization of prostaglandin F receptor (FP) and E receptor subtype 3 (EP3) in chickens.

Prostaglandin E and F regulate diverse physiological functions including gastrointestinal motility, fever induction and reproduction. This multitude of biological effects is mediated via their four E receptor subtypes (EP(1), EP(2), EP(3) and EP(4)) and F receptor (FP), respectively. Majority of these studies was performed in mammalian species, while investigations on their roles were impeded by inadequate information on their receptors in avian species. In present study, full-length cDNAs of chicken EP(3) (cEP(3)) and two isoforms of FP - cFPa and cFPb - were cloned from adult hen ovary. The putative cEP(3) and cFPa share high amino acid sequence identity with their respective orthologs, while the predicted cFPb is a novel middle-truncated splice variant which lacks 107 amino acids between transmembrane domains 4 and 6. RT-PCR showed that cEP(3), cFPa and cFPb are widely expressed in adult tissues examined, including ovary and oviduct. Using a pGL3-CRE luciferase reporter system, cEP(3)-expressing DF1 cells inhibited forskolin-induced luciferase activity (EC(50): <1.9 pM) upon PGE(2) treatment, suggesting that cEP(3) may functionally couple to Gi protein. Upon PGF(2α) addition, cFPa was shown to potentially couple to intracellular Ca(2+)-signaling pathway by pGL3-NFAT-RE reporter assay (EC(50): 2.9 nM), while cFPb showed no response. Using a pGL4-SRE reporter system, both cEP(3) and cFPa exhibited potential MAPK activation by PGE(2) and PGF(2α) at EC(50) 0.34 and 13 nM, respectively. Molecular characterization of these receptors paved the road to the better understanding of PGE(2) and PGF(2α) roles in avian physiology and comparative endocrinology studies.

Molecular characterization of prostaglandin F receptor (FP) and E receptor subtype 1 (EP1) in zebrafish.

Prostaglandins E (PGE) and F (PGF) mediate diverse physiological functions via their cell surface receptors - prostaglandin E receptor (EP) subtypes 1, 2, 3 and 4 (EP(1); EP(2); EP(3); EP(4)) and F receptor (FP). In teleost fishes, PGE was implicated in gill epithelium ion transport, while both PGE and PGF were involved in oocyte maturation, follicular rupture and coordination of reproductive behaviors. However, little is known about the mechanisms behind their actions. In present study, we first identified the full-length ORF cDNA clones of three zebrafish prostaglandin E receptor subtype 1 (zEP(1)) isoforms - zEP(1a), zEP(1b) and zEP(1c) - and FP (zFP) from adult ovary. RT-PCR showed that zEP(1a), zEP(1b) and zFP are widely expressed in adult tissues, while zEP(1c) mRNA expression is mainly confined in brain and kidney. Using a pGL3-NFAT-RE luciferase reporter system, both zEP(1a) and zEP(1b) expressed in DF-1 cells were shown to be activated by PGE(2) potently while zEP(1c) and zFP were activated by PGF(2a) effectively, suggesting that the four receptors are functionally coupled to intracellular Ca(2+)-signaling pathway. Furthermore, EP1a and EP1b, but not EP1c were suggested to couple to cAMP-PKA signaling pathway using a pGL3-CRE luciferase reporter assay. Although zEP(1c) might originate as a paralog to zEP(1a) and zEP(1b), its functional coupling to PGF(2α) instead of PGE(2) suggested that zEP(1) isoforms might have sub-functionalized in their ligand binding and G protein coupling specificity, in addition to differential tissue distribution. Characterization of these receptors undoubtedly furthered our understanding on the diverse yet highly target-specific responses of prostaglandins in teleosts.

Identification and characterization of the chicken galanin receptor GalR2 and a novel GalR2-like receptor (GalR2-L).

In mammals, the neuropeptide galanin exerts a variety of physiological roles in the neuroendocrine system through its interactions with three galanin receptor subtypes (GalR1, GalR2 and GalR3). However, little is known about the characteristics of galanin receptors in birds, and it is only recently that avian GalR1 and a novel GalR1-like receptor were first identified in chickens. In this study, we report the cDNA cloning and characterization of the other two chicken galanin receptors, the galanin type II receptor (cGalR2) and a novel GalR2-like receptor (GalR2-L), which share high degrees of similarity in sequence identity, gene structure and signaling properties. cGalR2 and cGalR2-L cDNAs encode two putative receptors of 371 and 370 amino acids, in which they show considerable amino acid sequence identities (65-67%, and 53-55%, respectively) with the mammalian GalR2. RT-PCR assays revealed that cGalR2 and cGalR2-L mRNA were widely expressed in the adult chicken tissues including the whole brain, intestine, lung, ovary, pituitary and different regions of the oviduct. As assayed with different luciferase reporter systems, chicken galanin (cGal 1-29) and human galanin-like peptide (hGALP 1-60) were demonstrated to stimulate the luciferase activities in Chinese hamster ovary cells expressing cGalR2 and cGalR2-L through the activations of cAMP/PKA, Ca(2+)/calcineurin and MAPK/ERK signaling pathways, hence suggesting that both receptors are functionally coupled to the G(s) and G(q) proteins. Furthermore, the previously identified cGalR1 and cGalR1-L were found to be solely coupled to the G(i/o) proteins, and the hGALP (1-60) exhibited only a low potency to cGalR1, cGalR1-L, cGalR2 and cGalR2-L activations.

Genetic diversity and multiple introductions of porcine reproductive and respiratory syndrome viruses in Thailand.

Porcine reproductive and respiratory syndrome virus (PRRSV) is prevalent in Thailand, causing a huge impact on the country's swine industry. Yet the diversity and origin of these Thai PRRSVs remained vague. In this context, we collected all the Thai PRRSV sequences described earlier and incorporated them into the global diversity. The results indicated that PRRSVs in Thailand were originated from multiple introductions involving both Type 1 and Type 2 PRRSVs. Many of the introductions were followed by extensive geographic expansion, causing regional co-circulation of diverse PRRSV variants in three major pig-producing provinces. Based on these results, we suggest (1) to avoid blind vaccination and to apply vaccines tailor-made for target diversity, (2) to monitor pig importation and transportation, and (3) to implement a better biosecurity to reduce horizontal transmissions as three potentially effective strategies of controlling PRRS in Thailand.

Characterization of the chicken galanin type I receptor (GalR1) and a novel GalR1-like receptor (GalR1-L).

Galanin is a multi-functional neuropeptide that is widely distributed in the mammalian central nervous system and peripheral tissues. It exerts multiple physiological functions through interaction with 3 known G protein-coupled receptors (GPCR), namely, galanin type I, II and III (GalR1, 2 and 3) receptors, which have only been identified in mammals. In this study, we reported the cloning and characterization of chicken galanin type I receptor (GalR1) and a novel galanin receptor with considerable homology to chicken GalR1, which herein is designated as galanin type I-like receptor (GalR1-L). Chicken GalR1 and GalR1-L full-length cDNAs were cloned from chicken brain and small intestine tissue, respectively. The former encodes a protein of 357 amino acids that shares 84-86% amino acid sequence identities with its mammalian counterparts, whereas the latter encodes a 363-amino acid protein with comparatively lower identities (55-56%) to the mammalian GalR1. Using reverse transcription (RT)-PCR assays, we examined the expression of both receptors in adult chicken tissues. Both receptors were found to be widely distributed in the tissues examined, including brain, small intestine, kidney, ovary, pancreas, pituitary and spleen. Interestingly, cGalR1 expression was detected in different regions of chicken oviduct, while cGalR1-L expression was restricted to the vagina. Using a pGL3-CRE luciferase reporter system, chicken galanin peptide (1-29) was demonstrated to inhibit both basal and forskolin-stimulated luciferase activities, in dose-dependent manners, through the cAMP-mediated signaling pathway in Chinese hamster ovary (CHO) cells expressing either cGalR1 or cGalR1-L, thus suggesting the functional couplings of both receptors to G(i) proteins. Together, the characterization of chicken GalR1 and GalR1-L provides a better understanding of the physiological roles of galanin in avian species.

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals.

Evolutionary change in gene regulation can result from changes in cis-regulatory elements, leading to differences in the temporal and spatial expression of genes or in the coding region of transcription factors leading to novel functions or both. Although there is a growing body of evidence supporting the importance of cis-regulatory evolution, examples of protein-mediated evolution of novel developmental pathways have not been demonstrated. Here, we investigate the evolution of prolactin (PRL) expression in endometrial cells, which is essential for placentation/pregnancy in eutherian mammals and is a direct regulatory target of the transcription factor HoxA-11. Here, we show that (i) endometrial PRL expression is a derived feature of placental mammals, (ii) the PRL regulatory gene HoxA-11 experienced a period of strong positive selection in the stem-lineage of eutherian mammals, and (iii) only HoxA-11 proteins from placental mammals, including the reconstructed ancestral eutherian gene, are able to up-regulate PRL from the promoter used in endometrial cells. In contrast, HoxA-11 from the reconstructed therian ancestor, opossum, platypus, and chicken are unable to up-regulate PRL expression. These results demonstrate that the evolution of novel gene expression domains is not only mediated by the evolution of cis-regulatory elements but can also require evolutionary changes of transcription factor proteins themselves.

A novel prolactin-like protein (PRL-L) gene in chickens and zebrafish: cloning and characterization of its tissue expression.

In this study, a full-length cDNA encoding a prolactin-like protein (PRL-L) was cloned from chicken brain tissues using RT-PCR. This putative PRL-L precursor has 225 amino acids in length and shares 30-35% amino acid sequence identity with prolactin (PRL) of chicken, zebrafish, Xenopus, rat and human. Using RT-PCR, the mRNA expression of PRL-L in chicken tissues was further examined. Unlike the predominant expression of PRL in pituitary, PRL-L was found to be widely expressed in adult chicken extra-pituitary tissues with only minimal expression detected in pituitary. In day-7 chicken embryos, the expression of PRL-L, but not PRL, was also detected in all extra-pituitary tissues examined. In line with this finding, the 5'-flanking region of chicken PRL-L (cPRL-L) gene, but not PRL gene, displayed a strong promoter activity in cultured DF-1 cell (a chicken embryo fibroblast cell line), suggesting that the basal expression of PRL-L gene is controlled by a transcriptional regulatory mechanism different from that of PRL gene. As the same findings in chickens, PRL-like protein(s), which share high amino acid sequence (42-86%) identity with chicken PRL-L, was identified in several non-mammalian vertebrate species including zebra finch, tiger puffer, green puffer and zebrafish. RT-PCR assay demonstrated that zebrafish PRL-L, similar to chicken PRL-L, is expressed in extra-pituitary tissues including brain, gill, muscle, ovary and testis. Taken together, these findings strongly suggest that a novel PRL-like protein exists in some non-mammalian vertebrates and may play an important role in target tissues, such as extra-pituitary tissues of chickens and zebrafish.

Discovery of a long inverted repeat in human POTE genes.

POTE gene family is tightly related to prostate, ovary, testis and placenta cancers. We recently identified an intronic long inverted repeat (LIR) in some members of the POTE gene family. Due to the capacity of inducing gene amplification, the POTE intronic LIRs may be involved in over-expression of the POTE genes. Our study aimed to understand the origin of the LIR in primates. We collected the LIR and its flanking sequences within rhesus monkey, chimpanzee and human genomes. The rhesus monkey genome only has half-sized LIRs (lack one repeat copy), whereas the human and chimpanzee genomes contain both full-sized and half-sized LIRs. Phylogenetic tree indicates that the LIR is formed after divergence of rhesus monkey and the common ancestor of human and chimpanzee. The POTE genes containing a full-sized LIR were amplified in the human genome.

In silico prediction of two classes of honeybee genes with CpG deficiency or CpG enrichment and sorting according to gene ontology classes.

Two honeybee DNA methyltransferase genes have recently been identified and confirmed to be functional. The honeybee genes under regulation by DNA methylation may therefore be CpG deficient, due to natural deamination of methylated DNA. In this report, we show that <39% of the known honeybee genes are likely to be methylated on the basis of their low CpG obs/exp ratios. In contrast, orthologues of these genes in the fruitfly do not show CpG deficiency. Classes of function as determined by Gene Ontology were obtained for the honeybee genes with significantly low and high CpG obs/exp ratios. Overrepresented classes in the low CpG[obs/exp] genes are involved in transcription, translation, protein folding, protein localization, protein transportation, cell cycle, and DNA and RNA metabolism.

Acquisition of inverted GSTM exons by an intron of primate GSTM5 gene.

The human GSTM gene family is composed of five gene members, GSTM1-5, and plays an important role in detoxification. In this study, the human GSTM5 gene was found to have a long inverted repeat (LIR) in intron 5. The LIR is able to form a stem-loop structure with a 31-bp stem and a 9-nt loop. The intronic LIR was also identified in other primates but not in non-primates. The human and chimpanzee LIRs had undergone compensating mutations that make the stem loop more stable, suggesting a functional role for the LIR. Sequence homology showed that the LIR was actually a part of inverted exons acquired by the intron. Results of phylogenetic analysis indicate that the inverted exons were derived from exon 5 of GSTM4 and exon 5 of GSTM1. The intronic LIR and inverted GSTM exons can probably introduce complexity in the expression of GSTM gene family.

Molecular cloning and characterization of chicken prostaglandin E receptor subtypes 2 and 4 (EP2 and EP4).

Prostaglandin E(2) (PGE(2)) is an important chemical mediator responsible for regulation of many vital physiological processes. Four receptor subtypes have been identified to mediate its biological actions. Among these subtypes, prostaglandin E receptor subtypes 2 and 4 (EP(2) and EP(4)), both coupled to cAMP-protein kinase A (cAMP-PKA) signaling pathway, are proposed to play crucial roles under both physiological and pathological conditions. Though both receptors were extensively studied in mammals, little is known about their functionality and expression in non-mammalian species including chicken. In present study, the full-length cDNAs for chicken EP(2) and EP(4) receptors were first cloned from adult chicken ovary and testis, respectively. Chicken EP(2) is 356 amino acids in length and shows high amino acid identity to that of human (61%), mouse (63%), and rat (61%). On the other hand, the full-length cDNA of EP(4) gene encodes a precursor of 475 amino acids with a high degree of amino acid identity to that of mammals, including human (87%), mouse (86%), rat (84%), dog (85%), and cattle (83%), and a comparatively lower sequence identity to zebrafish (52%). RT-PCR assays revealed that EP(2) mRNA was expressed in all tissues examined including the oviduct, while EP(4) expression was detected only in a few tissues. Using the pGL3-CRE-luciferase reporter system, we also demonstrated that PGE(2) could induce luciferase activity in DF-1 cells expressing EP(2) and EP(4) in dose-dependent manners (EC(50): <1 nM), confirming that both receptors could be activated by PGE(2) and functionally coupled to the cAMP-PKA signaling pathway. Together, our study establishes a molecular basis to understand the physiological roles of PGE(2) in target tissues of chicken.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Vertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5' T to 5' A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5' Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5' T and 5' A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.

Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet.

Our previous study has shown that genetic selection for susceptibility/resistance to diet-induced atherosclerosis has affected the Japanese quail's cecal environment to accommodate distinctly different cecal microbiota. In this study, we fed the Atherosclerosis-resistant (RES) and -susceptable (SUS) quail a regular and a cholesterol enriched diet to examine the interaction of host genotype and diet on the diversity, composition, and metabolic functions of the duodenal and ileal microbiota with relations to atherosclerosis development. In the duodenal content, 9 OTUs (operational taxonomic units) were identified whose abundance had significant positive correlations with plasma total cholesterol, LDL level and/or LDL/HDL ratio. In the ileal content, 7 OTUs have significant correlation with plasma HDL. Cholesterol fed RES hosted significantly less Escherichia and unclassified Enterobacteriaceae (possibly pathogenic) in their duodenum than SUS fed the same diet. Dietary cholesterol significantly decreased the duodenal microbiome of SUS's biosynthesis of Ubiquinone and other terpenoid-quinone. Cholesterol fed RES had significantly more microbiome genes for Vitamin B6, selenocompound, taurine and hypotaurine, and Linoleic acid metabolism; Bisphenol degradation; primary bile acid, and butirosin and neomycin biosynthesis than SUS on the same diet. Microbiome in the ileum and ceca of RES contributed significantly towards the resistance to diet induced atherosclerosis.

Database for chicken full-length cDNAs.

The generation of full-length cDNA databases is essential for functional genomics studies as well as for correct annotation of species genomic sequences. Human and mouse full-length cDNA projects have provided the biomedical research community with a large amount of gene information. Recent completion of the chicken genome sequence draft now enables a similar full-length cDNA project to be initiated for this species. In this report, we introduce the development of a chicken full-length cDNA database, which will facilitate future research work in this biological system. In this project, chicken expressed sequence tags (ESTs) were aligned onto human and mouse full-length cDNAs (or open reading frames) on the basis of their similarity. More than 588,000 chicken ESTs were aligned to approximately 170,000 full-length human and mouse templates obtained from the NEDO, RIKEN, and MGC databases. Many of these templates have known biological functions, and their orthologous chicken genes in the EMBL database are also provided in our database, which is available at http://bioinfo.hku.hk/chicken/. We will continue to collect known chicken full-length cDNAs to update the database for public use. The cDNA alignment results presented herein and on our database will be useful for animal science and veterinary researchers wishing to clone and to confirm full-length chicken cDNAs of interest.