PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (40)
 

Clipboard (0)
None

Select a Filter Below

Year of Publication
1.  Baboons as a Model to Study Genetics and Epigenetics of Human Disease 
ILAR Journal  2013;54(2):106-121.
A major challenge for understanding susceptibility to common human diseases is determining genetic and environmental factors that influence mechanisms underlying variation in disease-related traits. The most common diseases afflicting the US population are complex diseases that develop as a result of defects in multiple genetically controlled systems in response to environmental challenges. Unraveling the etiology of these diseases is exceedingly difficult because of the many genetic and environmental factors involved. Studies of complex disease genetics in humans are challenging because it is not possible to control pedigree structure and often not practical to control environmental conditions over an extended period of time. Furthermore, access to tissues relevant to many diseases from healthy individuals is quite limited. The baboon is a well-established research model for the study of a wide array of common complex diseases, including dyslipidemia, hypertension, obesity, and osteoporosis. It is possible to acquire tissues from healthy, genetically characterized baboons that have been exposed to defined environmental stimuli. In this review, we describe the genetic and physiologic similarity of baboons with humans, the ability and usefulness of controlling environment and breeding, and current genetic and genomic resources. We discuss studies on genetics of heart disease, obesity, diabetes, metabolic syndrome, hypertension, osteoporosis, osteoarthritis, and intrauterine growth restriction using the baboon as a model for human disease. We also summarize new studies and resources under development, providing examples of potential translational studies for targeted interventions and therapies for human disease.
doi:10.1093/ilar/ilt038
PMCID: PMC3924757  PMID: 24174436
cardiovascular disease; diabetes; genomics resources; hypertension; intrauterine growth restriction; metabolic syndrome; obesity; osteoporosis
2.  Repertoire of Endothelial Progenitor Cells Mobilized by Femoral Artery Ligation – A Nonhuman Primate Study 
To determine in the baboon model the identities and functional characteristics of endothelial progenitor cells mobilized in response to artery ligation, we collected peripheral blood mononuclear cells before and 3 days after a segment of femoral artery was removed. Our goal was to find EPC subpopulations with highly regenerative capacity. We identified 12 subpopulations of putative EPCs that were altered >1.75 fold; two subpopulations (CD146+/CD54-/CD45- at 6.63 fold, and CD146+/UEA-1-/CD45- at 12.21 fold) were dramatically elevated. To investigate the regenerative capacity of putative EPCs, we devised a new assay that maximally resembled their in vivo scenario, we purified CD34+ and CD146+ cells and co-cultured them with basal and mobilized peripheral blood mononuclear cells; both cell types took up Dil-LDL, but purified CD146+ cells exhibited accelerated differentiation by increasing expression of CD31 and CD144, and by exhibiting more active cord-like structure formation by comparison to the CD34+ subpopulation in a co-culture with mobilized PBMNCs. We demonstrate that ischemia due to vascular ligation mobilizes multiple types of cells with distinct roles. Baboon CD146+ cells exhibit higher reparative capacity than CD34+ cells, and thus are a potential source for therapeutic application.
doi:10.1111/j.1582-4934.2011.01501.x
PMCID: PMC3433842  PMID: 22128816
EPC mobilization; nonhuman primate model; ischemia
3.  The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance 
PLoS ONE  2013;8(4):e57563.
The baboon is an invaluable model for the study of human health and disease, including many complex diseases of the kidney. Although scientists have made great progress in developing this animal as a model for numerous areas of biomedical research, genomic resources for the baboon, such as a quality annotated genome, are still lacking. To this end, we characterized the baboon kidney transcriptome using high-throughput cDNA sequencing (RNA-Seq) to identify genes, gene variants, single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (InDels), cellular functions, and key pathways in the baboon kidney to provide a genomic resource for the baboon. Analysis of our sequencing data revealed 45,499 high-confidence SNPs and 29,813 InDels comparing baboon cDNA sequences with the human hg18 reference assembly and identified 35,900 cDNAs in the baboon kidney, including 35,150 transcripts representing 15,369 genic genes that are novel for the baboon. Gene ontology analysis of our sequencing dataset also identified numerous biological functions and canonical pathways that were significant in the baboon kidney, including a large number of metabolic pathways that support known functions of the kidney. The results presented in this study catalogues the transcribed mRNAs, noncoding RNAs, and hypothetical proteins in the baboon kidney and establishes a genomic resource for scientists using the baboon as an experimental model.
doi:10.1371/journal.pone.0057563
PMCID: PMC3634053  PMID: 23637735
4.  Impaired Fitness of Mycobacterium africanum Despite Secretion of ESAT-6 
The Journal of Infectious Diseases  2012;205(6):984-990.
Background. When compared with Mycobacterium tuberculosis, individuals that live in the same household as an active case of smear-positive pulmonary tuberculosis exposed to M. africanum progress less frequently to active disease within 2 years. A putative ESX-1 secretion apparatus member, Rv3879c, is mutated in M. africanum, and individuals infected with M. africanum less frequently demonstrate T-cell responses to the ESX-1–secreted virulence factor ESAT-6 than those infected with M. tuberculosis. We hypothesized that less frequent progression is caused by impaired secretion of ESAT-6.
Methods. We analyzed in vivo growth and in vitro secretion of ESAT-6 and CFP-10, comparing M. tuberculosis to M. africanum and a strain of M. africanum complemented with M. tuberculosis Rv3879c.
Results. ESAT-6 and CFP-10 secretion were similar for all strains, although these were enriched in M. africanum cell lysates, suggesting a modest ESX-1 secretion defect unrelated to the Rv3879c mutation. In mice, M. africanum demonstrated smaller bacterial population sizes than M. tuberculosis but similar numbers and frequencies of ESAT-6–responsive T cells in the lungs.
Conclusions. These results confirm impaired fitness of M. africanum in vivo and indicate that Rv3879c is not required for secretion of ESAT-6 or for its presentation as an antigen to T cells in vivo.
doi:10.1093/infdis/jir883
PMCID: PMC3282571  PMID: 22301632
5.  Antibiotics in early life alter the murine colonic microbiome and adiposity 
Nature  2012;488(7413):621-626.
Antibiotics administered in low doses have been widely used as growth promoters in the agricultural industry since the 1950s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we hypothesized that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities. We generated a model of adiposity by giving subtherapeutic antibiotic therapy to young mice and evaluated changes in the composition and capabilities of the gut microbiome. Administration of subtherapeutic antibiotic therapy increased adiposity in young mice and increased hormones related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids, increases in colonic short-chain fatty acid levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early-life murine metabolic homeostasis through antibiotic manipulation.
doi:10.1038/nature11400
PMCID: PMC3553221  PMID: 22914093
6.  Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells 
Background
Humans and rodents with impaired phytanic acid (PA) metabolism can accumulate toxic stores of PA that have deleterious effects on multiple organ systems. Ruminants and certain fish obtain PA from the microbial degradation of dietary chlorophyll and/or through chlorophyll-derived precursors. In contrast, humans cannot derive PA from chlorophyll and instead normally obtain it only from meat, dairy, and fish products.
Results
Captive apes and Old world monkeys had significantly higher red blood cell (RBC) PA levels relative to humans when all subjects were fed PA-deficient diets. Given the adverse health effects resulting from PA over accumulation, we investigated the molecular evolution of thirteen PA metabolism genes in apes, Old world monkeys, and New world monkeys. All non-human primate (NHP) orthologs are predicted to encode full-length proteins with the marmoset Phyh gene containing a rare, but functional, GA splice donor dinucleotide. Acox2, Scp2, and Pecr sequences had amino acid positions with accelerated substitution rates while Amacr had significant variation in evolutionary rates in apes relative to other primates.
Conclusions
Unlike humans, diverse captive NHPs with PA-deficient diets rich in plant products have substantial RBC PA levels. The favored hypothesis is that NHPs can derive significant amounts of PA from the degradation of ingested chlorophyll through gut fermentation. If correct, this raises the possibility that RBC PA levels could serve as a biomarker for evaluating the digestive health of captive NHPs. Furthermore, the evolutionary rates of the several genes relevant to PA metabolism provide candidate genetic adaptations to NHP diets.
doi:10.1186/1476-511X-12-10
PMCID: PMC3571895  PMID: 23379307
Phytanic acid; Chlorophyll; Old world monkeys; New world monkeys; Peroxisome
7.  A Custom Rat and Baboon Hypertension Gene Array to Compare Experimental Models 
One challenge in understanding the polygenic disease of hypertension is elucidating the genes involved and defining responses to environmental factors. Many studies focus on animal models of hypertension; however, this does not necessarily extrapolate to humans.
Current technology and cost limitations are prohibitive in fully evaluating hypertension within humans. Thus, we have designed a single array platform that allows direct comparison of genes relevant to hypertension in animal models and non-human primates/human hypertension. The custom array is targeted to 328 genes known to be potentially related to blood pressure control.
Studies compared gene expression in the kidney from normotensive rats and baboons. We found 74 genes expressed in both the rat and baboon kidney, 41 genes expressed in the rat kidney that were not detected in the baboon kidney and 34 genes expression in the baboon kidney that were not detected in the rat kidney.
To begin the evaluation of the array in a pathological condition, kidney gene expression was compared between the salt sensitive DOCA rat model of hypertension and sham animals. Gene expression in renal cortex and medulla from hypertensive DOCA compared with sham rats revealed 3 genes differentially expressed in the renal cortex: Annexin A1 (up-regulated; relative intensity: 1.316 ± 0.321 vs. 2.312 ± 0.283), Glutamate-cysteine ligase (down-regulated; relative intensity: 3.738 ± 0.174 vs. 2.645 ± 0.364) and Glutathione-S transferase (down-regulated; relative intensity: 5.572 ± 0.246 vs. 4.215 ± 0.411) and 21 genes differentially expressed in renal medulla. Interestingly, few genes were differentially expressed in the kidney in the DOCA-salt model of hypertension; this may suggest that the complexity of hypertension may be the result of only a few gene-by-environment responsive events.
doi:10.1258/ebm.2011.011188
PMCID: PMC3557854  PMID: 22228705
hypertension; gene array; kidney; rat; baboon
8.  Vertebrate Endothelial Lipase: Comparative Studies of an Ancient Gene and Protein in Vertebrate Evolution 
Genetica  2011;139(3):291-304.
Summary
Endothelial lipase (LIPG; E.C.3.1.1.3) is one of three members of the triglyceride lipase family that contributes to lipoprotein degradation within the circulation system and plays a major role in HDL metabolism in the body. In this study, in silico methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for LIPG genes and encoded proteins using data from several vertebrate genome projects. LIPG is located on human chromosome 18 and is distinct from 15 other human lipase genes examined. Vertebrate LIPG genes usually contained 10 coding exons located on the positive strand for most primates, as well as for horse, bovine, opossum, platypus and frog genomes. The rat LIPG gene however contained only 9 coding exons apparently due to the presence of a ‘stop’ codon’ within exon 9. Vertebrate LIPG protein subunits shared 58–97% sequence identity as compared with 38–45% sequence identities with human LIPC (hepatic lipase) and LIPL (lipoprotein lipase). Four previously reported human LIPG N-glycosylation sites were predominantly conserved among the 10 potential N-glycosylation sites observed for the vertebrate LIPG sequences examined. Sequence alignments and identities for key LIPG amino acid residues were observed as well as conservation of predicted secondary and tertiary structures with those previously reported for horse pancreatic lipase (LIPP) (Bourne et al., 1994). Several potential sites for regulating LIPG gene expression were observed including CpG islands near the 5′-untranslated regions of the human, mouse and rat LIPG genes; a predicted microRNA binding site near the 3′-untranslated region and several transcription factor binding sites within the human LIPG gene. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate LIPG gene subfamily with other neutral triglyceride lipase gene families [LIPC and LIPL], other neutral lipase gene families [LIPP, LIPR1, LIPR2, LIPR3, LIPI, LIPH and LIPS], and the extended family of mammalian acid lipases (LIPA, LIPF, LIPJ, LIPK, LIPM, LIPN and LIPO). It is apparent that the triglyceride lipase ancestral gene for the vertebrate LIPG gene predated the appearance of fish during vertebrate evolution > 500 million years ago.
doi:10.1007/s10709-011-9549-1
PMCID: PMC3482104  PMID: 21267636
Vertebrates; amino acid sequence; endothelial lipase; evolution; gene duplication
9.  Comparative structures and evolution of vertebrate lipase H (LIPH) genes and proteins: a relative of the phospholipase A1 gene families 
3 Biotech  2012;2(4):263-275.
Lipase H (LIPH) is a membrane-bound phospholipase generating 2-acyl lysophosphatidic acid (LPA) in the body. LPA is a lipid mediator required for maintaining homeostasis of diverse biological functions and in activating cell surface receptors such as P2Y5, which plays an essential role in hair growth. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for LIPH genes and encoded proteins using data from several vertebrate genome projects. Vertebrate LIPH genes contained ten coding exons transcribed on either the positive or negative DNA strands. Evidence is presented for duplicated LIPH genes for the chicken and zebra fish genomes. Vertebrate LIPH protein subunits shared 56–97 % sequence identities and exhibited sequence alignments and identities for key LIPH amino acid residues as well as extensive conservation of predicted secondary and tertiary structures with those previously reported for horse pancreatic lipase (LIPP), with ‘N-signal peptide’, ‘lipase,’ and ‘plat’ structural domains. Comparative studies of vertebrate LIPH sequences with other phospholipase A1-like lipases (LIPI and PS-PLA1), as well as vascular and pancreatic lipases, confirmed predictions for LIPH N-terminal signal peptides (residues 1–18); a conserved vertebrate LIPH N-glycosylation site (66NVT for human LIPH); active site ‘triad’ residues (Ser 154; Asp 178; His 248); disulfide bond residues (233–246; 270–281; 284–292; 427–446), and a ‘short’ 12 residue ‘active site lid’, which is comparable to other phospholipases examined. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the vertebrate LIPH family of genes related to, but distinct from other phospholipase A1-like genes (LIPI and PS-PLA1), and from vascular lipase and pancreatic lipase gene families.
Electronic supplementary material
The online version of this article (doi:10.1007/s13205-012-0087-z) contains supplementary material, which is available to authorized users.
doi:10.1007/s13205-012-0087-z
PMCID: PMC3482443
Vertebrates; Amino acid sequence; Lipase H; Evolution; Phylogeny
10.  Differential microRNA response to a high-cholesterol, high-fat diet in livers of low and high LDL-C baboons 
BMC Genomics  2012;13:320.
Background
Dysregulation of microRNA (miRNA) expression has been implicated in molecular genetic events leading to the progression and development of atherosclerosis. We hypothesized that miRNA expression profiles differ between baboons with low and high serum low-density lipoprotein cholesterol (LDL-C) concentrations in response to diet, and that a subset of these miRNAs regulate genes relevant to dyslipidemia and risk of atherosclerosis.
Results
Using Next Generation Illumina sequencing methods, we sequenced hepatic small RNA libraries from baboons differing in their LDL-C response to a high-cholesterol, high-fat (HCHF) challenge diet (low LDL-C, n = 3; high LDL-C, n = 3), resulting in 517 baboon miRNAs: 490 were identical to human miRNAs and 27 were novel. We compared miRNA expression profiles from liver biopsies collected before and after the challenge diet and observed that HCHF diet elicited expression of more miRNAs compared to baseline (chow) diet for both low and high LDL-C baboons. Eighteen miRNAs exhibited differential expression in response to HCHF diet in high LDL-C baboons compared to 10 miRNAs in low LDL-C baboons. We used TargetScan/Base tools to predict putative miRNA targets; miRNAs expressed in high LDL-C baboons had significantly more gene targets than miRNAs expressed in low LDL-C responders. Further, we identified miRNA isomers and other non-coding RNAs that were differentially expressed in response to the challenge diet in both high LDL-C and low LDL-C baboons.
Conclusions
We sequenced and annotated baboon liver miRNAs from low LDL-C and high LDL-C responders using high coverage Next Gen sequencing methods, determined expression changes in response to a HCHF diet challenge, and predicted target genes regulated by the differentially expressed miRNAs. The identified miRNAs will enrich the database for non-coding small RNAs including the extent of variation in these sequences. Further, we identified other small non-coding RNAs differentially expressed in response to diet. Our discovery of differentially expressed baboon miRNAs in response to a HCHF diet challenge that differ by LDL-C phenotype is a fundamental step in understating the role of non-coding RNAs in dyslipidemia.
doi:10.1186/1471-2164-13-320
PMCID: PMC3536563  PMID: 22809019
11.  Comparative Studies of Vertebrate Lipoprotein Lipase: A Key Enzyme of Very Low Density Lipoprotein Metabolism 
Lipoprotein lipase (LIPL or LPL; E.C.3.1.1.34) serves a dual function as a triglyceride lipase of circulating chylomicrons and very-low-density lipoproteins (VLDL) and facilitates receptor-mediated lipoprotein uptake into heart, muscle and adipose tissue. Comparative LPL amino acid sequences and protein structures and LPL gene locations were examined using data from several vertebrate genome projects. Mammalian LPL genes usually contained 9 coding exons on the positive strand. Vertebrate LPL sequences shared 58–99% identity as compared with 33–49% sequence identities with other vascular triglyceride lipases, hepatic lipase (HL) and endothelial lipase (EL). Two human LPL N-glycosylation sites were conserved among seven predicted sites for the vertebrate LPL sequences examined. Sequence alignments, key amino acid residues and conserved predicted secondary and tertiary structures were also studied. A CpG island was identified within the 5'-untranslated region of the human LPL gene which may contribute to the higher than average (x4.5 times) level of expression reported. Phylogenetic analyses examined the relationships and potential evolutionary origins of vertebrate lipase genes, LPL, LIPG (encoding EL) and LIPC (encoding HL) which suggested that these have been derived from gene duplication events of an ancestral neutral lipase gene, prior to the appearance of fish during vertebrate evolution. Comparative divergence rates for these vertebrate sequences indicated that LPL is evolving more slowly (2–3 times) than for LIPC and LIPG genes and proteins.
doi:10.1016/j.cbd.2011.04.003
PMCID: PMC3102144  PMID: 21561822
Vertebrates; amino acid sequence; lipoprotein lipase; evolution; gene duplication
12.  Moderate Global Reduction in Maternal Nutrition Has Differential Stage of Gestation Specific Effects on β1- and β2-Adrenergic Receptors in the Fetal Baboon Liver 
Reproductive Sciences  2011;18(4):398-405.
Hepatic β-adrenergic receptors (β-ARs) play a pivotal role in mobilization of reserves via gluconeogenesis and glycogenolysis to supply the animal with its energy needs during decreased nutrient availability. Using a unique nutrient-deprived baboon model, we have demonstrated for the first time that immunoreactive hepatic β1- and β2-AR subtypes are regionally distributed and localized on cells around the central lobular vein in 0.5 and 0.9 gestation (G) fetuses of ad libitum fed control (CTR) and maternal nutrient restricted (MNR) mothers. Furthermore, MNR decreased fetal liver immunoreactive β1-AR and increased immunoreactive β2-AR at 0.5G. However, at 0.9G, immunohistochemistry and Western blot analysis revealed a decrease in β1-AR and no change in β2-AR levels. Thus, MNR in a nonhuman primate species has effects on hepatic β1- and β2-ARs that are receptor- and gestation stage-specific and may represent compensatory systems whose effects would increase glucose availability in the presence of nutrient deprivation.
doi:10.1177/1933719110386496
PMCID: PMC3343058  PMID: 21079239
β-adrenergic receptor; immunolocalization; gene expression; protein expression; baboon
13.  Vertebrate hepatic lipase genes and proteins: a review supported by bioinformatic studies 
Open access bioinformatics  2011;2011(3):85-95.
Hepatic lipase (gene: LIPC; enzyme: HL; E.C.3.1.1.3) is one of three members of the triglyceride lipase family that contributes to vascular lipoprotein degradation and serves a dual role in triglyceride hydrolysis and in facilitating receptor-mediated lipoprotein uptake into the liver. Amino acid sequences, protein structures, and gene locations for vertebrate LIPC (or Lipc for mouse and rat) genes and proteins were sourced from previous reports and vertebrate genome databases. Lipc was distinct from other neutral lipase genes (Lipg encoding endothelial lipase and Lpl encoding lipoprotein lipase [LPL]) and was located on mouse chromosome 9 with nine coding exons on the negative strand. Exon 9 of human LIPC and mouse and rat Lipc genes contained “stop codons” in different positions, causing changes in C-termini length. Vertebrate HL protein subunits shared 58%–97% sequence identities, including active, signal peptide, disulfide bond, and N-glycosylation sites, as well as proprotein convertase (“hinge”) and heparin binding regions. Predicted secondary and tertiary structures revealed similarities with the three-dimensional structure reported for horse and human pancreatic lipases. Potential sites for regulating LIPC gene expression included CpG islands near the 5″-untranslated regions of the mouse and rat LIPC genes. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate LIPC gene family with other neutral triglyceride lipase gene families (LIPG and LPL). We conclude that the triglyceride lipase ancestral gene for vertebrate neutral lipase genes (LIPC, LIPG, and LPL) predated the appearance of fish during vertebrate evolution.
doi:10.2147/OAB.S18401
PMCID: PMC3298411  PMID: 22408368
vertebrates; amino acid sequence; hepatic lipase; evolution; gene duplication
14.  Comparative Structures and Evolution of Vertebrate Carboxyl Ester Lipase (CEL) Genes and Proteins with a Major Role in Reverse Cholesterol Transport 
Cholesterol  2011;2011:781643.
Bile-salt activated carboxylic ester lipase (CEL) is a major triglyceride, cholesterol ester and vitamin ester hydrolytic enzyme contained within pancreatic and lactating mammary gland secretions. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures and gene locations for CEL genes, and encoded proteins using data from several vertebrate genome projects. A proline-rich and O-glycosylated 11-amino acid C-terminal repeat sequence (VNTR) previously reported for human and other higher primate CEL proteins was also observed for other eutherian mammalian CEL sequences examined. In contrast, opossum CEL contained a single C-terminal copy of this sequence whereas CEL proteins from platypus, chicken, lizard, frog and several fish species lacked the VNTR sequence. Vertebrate CEL genes contained 11 coding exons. Evidence is presented for tandem duplicated CEL genes for the zebrafish genome. Vertebrate CEL protein subunits shared 53–97% sequence identities; demonstrated sequence alignments and identities for key CEL amino acid residues; and conservation of predicted secondary and tertiary structures with those previously reported for human CEL. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the vertebrate CEL family of genes which were related to a nematode carboxylesterase (CES) gene and five mammalian CES gene families.
doi:10.1155/2011/781643
PMCID: PMC3227413  PMID: 22162806
15.  Comparative studies of glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1: evidence for a eutherian mammalian origin for the GPIHBP1 gene from an LY6-like gene 
3 Biotech  2011;2(1):37-52.
Glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPIHBP1) functions as a platform and transport agent for lipoprotein lipase (LPL) which functions in the hydrolysis of chylomicrons, principally in heart, skeletal muscle and adipose tissue capillary endothelial cells. Previous reports of genetic deficiency for this protein have described severe chylomicronemia. Comparative GPIHBP1 amino acid sequences and structures and GPIHBP1 gene locations were examined using data from several mammalian genome projects. Mammalian GPIHBP1 genes usually contain four coding exons on the positive strand. Mammalian GPIHBP1 sequences shared 41–96% identities as compared with 9–32% sequence identities with other LY6-domain-containing human proteins (LY6-like). The human N-glycosylation site was predominantly conserved among other mammalian GPIHBP1 proteins except cow, dog and pig. Sequence alignments, key amino acid residues and conserved predicted secondary structures were also examined, including the N-terminal signal peptide, the acidic amino acid sequence region which binds LPL, the glycosylphosphatidylinositol linkage group, the Ly6 domain and the C-terminal α-helix. Comparative and phylogenetic studies of mammalian GPIHBP1 suggested that it originated in eutherian mammals from a gene duplication event of an ancestral LY6-like gene and subsequent integration of exon 2, which may have been derived from BCL11A (B-cell CLL/lymphoma 11A gene) encoding an extended acidic amino acid sequence.
Electronic supplementary material
The online version of this article (doi:10.1007/s13205-011-0026-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s13205-011-0026-4
PMCID: PMC3339605  PMID: 22582156
Mammals; Amino acid sequence; GPIHBP1; LY6-like; BCL11A; Evolution; Chylomicronemia; Chemistry; Bioinformatics; Agriculture; Stem Cells; Biomaterials; Biotechnology; Cancer Research
16.  Comparative studies of glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1: evidence for a eutherian mammalian origin for the GPIHBP1 gene from an LY6-like gene 
3 Biotech  2011;2(1):37-52.
Glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPIHBP1) functions as a platform and transport agent for lipoprotein lipase (LPL) which functions in the hydrolysis of chylomicrons, principally in heart, skeletal muscle and adipose tissue capillary endothelial cells. Previous reports of genetic deficiency for this protein have described severe chylomicronemia. Comparative GPIHBP1 amino acid sequences and structures and GPIHBP1 gene locations were examined using data from several mammalian genome projects. Mammalian GPIHBP1 genes usually contain four coding exons on the positive strand. Mammalian GPIHBP1 sequences shared 41–96% identities as compared with 9–32% sequence identities with other LY6-domain-containing human proteins (LY6-like). The human N-glycosylation site was predominantly conserved among other mammalian GPIHBP1 proteins except cow, dog and pig. Sequence alignments, key amino acid residues and conserved predicted secondary structures were also examined, including the N-terminal signal peptide, the acidic amino acid sequence region which binds LPL, the glycosylphosphatidylinositol linkage group, the Ly6 domain and the C-terminal α-helix. Comparative and phylogenetic studies of mammalian GPIHBP1 suggested that it originated in eutherian mammals from a gene duplication event of an ancestral LY6-like gene and subsequent integration of exon 2, which may have been derived from BCL11A (B-cell CLL/lymphoma 11A gene) encoding an extended acidic amino acid sequence.
Electronic supplementary material
The online version of this article (doi:10.1007/s13205-011-0026-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s13205-011-0026-4
PMCID: PMC3339605  PMID: 22582156
Mammals; Amino acid sequence; GPIHBP1; LY6-like; BCL11A; Evolution; Chylomicronemia
17.  Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins 
Mammalian carboxylesterase (CES or Ces) genes encode enzymes that participate in xenobiotic, drug, and lipid metabolism in the body and are members of at least five gene families. Tandem duplications have added more genes for some families, particularly for mouse and rat genomes, which has caused confusion in naming rodent Ces genes. This article describes a new nomenclature system for human, mouse, and rat carboxylesterase genes that identifies homolog gene families and allocates a unique name for each gene. The guidelines of human, mouse, and rat gene nomenclature committees were followed and “CES” (human) and “Ces” (mouse and rat) root symbols were used followed by the family number (e.g., human CES1). Where multiple genes were identified for a family or where a clash occurred with an existing gene name, a letter was added (e.g., human CES4A; mouse and rat Ces1a) that reflected gene relatedness among rodent species (e.g., mouse and rat Ces1a). Pseudogenes were named by adding “P” and a number to the human gene name (e.g., human CES1P1) or by using a new letter followed by ps for mouse and rat Ces pseudogenes (e.g., Ces2d-ps). Gene transcript isoforms were named by adding the GenBank accession ID to the gene symbol (e.g., human CES1_AB119995 or mouse Ces1e_BC019208). This nomenclature improves our understanding of human, mouse, and rat CES/Ces gene families and facilitates research into the structure, function, and evolution of these gene families. It also serves as a model for naming CES genes from other mammalian species.
doi:10.1007/s00335-010-9284-4
PMCID: PMC3127206  PMID: 20931200
18.  Comparative Studies of Mammalian Acid Lipases: Evidence for a New Gene Family in Mouse and Rat (Lipo) 
At least six families of mammalian acid lipases (E.C. 3.1.1.-) catalyse the hydrolysis of triglycerides in the body, designated as LIPA (lysosomal), LIPF (gastric), LIPJ (testis) and LIPK, LIPM and LIPN (epidermal), which belong to the AB hydrolase superfamily. In this study, in silico methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for acid lipase genes and encoded proteins using data from several mammalian genome projects. Mammalian acid lipase genes were located within a gene cluster for each of the 8 mammalian genomes examined, including human (Homo sapiens), chimpanzee (Pons troglodytes), rhesus monkey (Macacca mulatta), mouse (Mus musculus), rat (Rattus norvegicus), cow (Bos taurus), horse (Equus caballus) and dog (Canis familaris), with each containing 9 coding exons. Human and mouse acid lipases shared 44-87% sequence identity and exhibited sequence alignments and identities for key amino acid residues and conservation of predicted secondary and tertiary structures with those previously reported for human gastric lipase (LIPF) (Roussel et al., 1999). Evidence for a new family of acid lipase genes is reported for mouse and rat genomes, designated as Lipo. Mouse acid lipase genes are subject to differential mRNA tissue expression, with Lipa showing wide tissue expression, while others have a more restricted tissue expression in the digestive tract (Lipf), salivary gland (Lipo) and epidermal tissues (Lipk, Lipm and Lipn). Phylogenetic analyses of the mammalian acid lipase gene families suggested that these genes are products of gene duplication events prior to eutherian mammalian evolution and derived from an ancestral vertebrate LIPA gene, which is present in the frog, Xenopus tropicalis.
doi:10.1016/j.cbd.2010.05.004
PMCID: PMC2917524  PMID: 20598663
Mammals; amino acid sequence; acid lipases; evolution; gene duplication
19.  Genomics and proteomics of vertebrate cholesterol ester lipase (LIPA) and cholesterol 25-hydroxylase (CH25H) 
3 Biotech  2011;1(2):99-109.
Cholesterol ester lipase (LIPA; EC 3.1.1.13) and cholesterol 25-hydroxylase (CH25H; EC 1.14.99.48) play essential role in cholesterol metabolism in the body by hydrolysing cholesteryl esters and triglycerides within lysosomes (LIPA) and catalysing the formation of 25-hydroxycholesterol from cholesterol (CH25H) which acts to repress cholesterol biosynthesis. Bioinformatic methods were used to predict the amino acid sequences, structures and genomic features of several vertebrate LIPA and CH25H genes and proteins, and to examine the phylogeny of vertebrate LIPA. Amino acid sequence alignments and predicted subunit structures enabled the identification of key sequences previously reported for human LIPA and CH25H and transmembrane structures for vertebrate CH25H sequences. Vertebrate LIPA and CH25H genes were located in tandem on all vertebrate genomes examined and showed several predicted transcription factor binding sites and CpG islands located within the 5′ regions of the human genes. Vertebrate LIPA genes contained nine coding exons, while all vertebrate CH25H genes were without introns. Phylogenetic analysis demonstrated the distinct nature of the vertebrate LIPA gene and protein family in comparison with other vertebrate acid lipases and has apparently evolved from an ancestral LIPA gene which predated the appearance of vertebrates.
Electronic supplementary material
The online version of this article (doi:10.1007/s13205-011-0013-9) contains supplementary material, which is available to authorized users.
doi:10.1007/s13205-011-0013-9
PMCID: PMC3324826  PMID: 22582164
Vertebrates; Lipase A; Cholesterol 25-hydroxylase; Cholesterol metabolism; Chemistry; Biomaterials; Bioinformatics; Cancer Research; Stem Cells; Agriculture; Biotechnology
20.  Genomics and proteomics of vertebrate cholesterol ester lipase (LIPA) and cholesterol 25-hydroxylase (CH25H) 
3 Biotech  2011;1(2):99-109.
Cholesterol ester lipase (LIPA; EC 3.1.1.13) and cholesterol 25-hydroxylase (CH25H; EC 1.14.99.48) play essential role in cholesterol metabolism in the body by hydrolysing cholesteryl esters and triglycerides within lysosomes (LIPA) and catalysing the formation of 25-hydroxycholesterol from cholesterol (CH25H) which acts to repress cholesterol biosynthesis. Bioinformatic methods were used to predict the amino acid sequences, structures and genomic features of several vertebrate LIPA and CH25H genes and proteins, and to examine the phylogeny of vertebrate LIPA. Amino acid sequence alignments and predicted subunit structures enabled the identification of key sequences previously reported for human LIPA and CH25H and transmembrane structures for vertebrate CH25H sequences. Vertebrate LIPA and CH25H genes were located in tandem on all vertebrate genomes examined and showed several predicted transcription factor binding sites and CpG islands located within the 5′ regions of the human genes. Vertebrate LIPA genes contained nine coding exons, while all vertebrate CH25H genes were without introns. Phylogenetic analysis demonstrated the distinct nature of the vertebrate LIPA gene and protein family in comparison with other vertebrate acid lipases and has apparently evolved from an ancestral LIPA gene which predated the appearance of vertebrates.
Electronic supplementary material
The online version of this article (doi:10.1007/s13205-011-0013-9) contains supplementary material, which is available to authorized users.
doi:10.1007/s13205-011-0013-9
PMCID: PMC3324826  PMID: 22582164
Vertebrates; Lipase A; Cholesterol 25-hydroxylase; Cholesterol metabolism
21.  MOLECULAR PATHWAYS MEDIATING DIFFERENTIAL RESPONSES TO LIPOPOLYSACCHARIDE BETWEEN HUMAN AND BABOON ARTERIAL ENDOTHELIAL CELLS 
SUMMARY
1. Vascular inflammation plays a critical role in atherogenesis. Previously, we showed that baboon arterial endothelial cells (BAEC) were hyporesponsive to lipopolysaccharide (LPS) compared with human arterial endothelial cells (HAEC).
2. In the present study, we investigated mechanisms underlying differential responses between HAEC and BAEC to tumour necrosis factor (TNF)-α and LPS.
3. Both HAEC and BAEC responded similarly to TNF-α. However, BAEC showed retarded responses to LPS in expression of E-selectin, intercellular adhesion molecule-1 (ICAM-1), monocyte chemotactic protein-1 (MCP-1) and interleukin-8 (P < 0.05). These changes were confirmed at the mRNA level. Tumour necrosis factor-α activated nuclear factor-κB members such as p50, p52, p65, c-rel and RelB in both HAEC and BAEC. In contrast, LPS activated p50 and p65 only in HAEC. Using microarray assays, we found that TNF receptor-associated factor 2 (TRAF-2), TNF receptor superfamily member 1A -associated via death domain (TRADD) and nuclear factors such as nuclear factor of kappa in B-cells inhibitor, α (NFKBIA) and nuclear factor of kappa in B-cells inhibitor, β (NFKBIB) were upregulated by LPS only in HAEC. Although the baseline expression of Toll-like receptor (TLR) 4 was low in both HAEC and BAEC, TNF-α activated TLR4 expression in both cell types. Although LPS increased TLR4 expression only in HAEC, human and baboon peripheral blood mononuclear cells exhibited similar TLR4 expression and response to LPS. Transfecting BAEC with TLR4/myeloid differentiation protein-2 (MD-2) overexpression vector conferred BAEC responsiveness to LPS.
4. The findings of the present study indicate that an altered TLR4 system may be responsible for the resistance of baboon endothelial cells to LPS. Given the importance of TLR4 in human immune responses and vascular diseases, the natural resistance of baboons to LPS/TLR4-initiated inflammation could make the baboon a valuable animal model in which to study how inflammation affects atherogenesis.
doi:10.1111/j.1440-1681.2009.05260.x
PMCID: PMC3148808  PMID: 19650795
baboons; endothelial cells; inflammatory reactions; lipopolysaccharide; Toll-like receptor
22.  Mammalian carboxylesterase 3: comparative genomics and proteomics 
Genetica  2010;138(7):695-708.
At least five families of mammalian carboxylesterases (CES) catalyse the hydrolysis or transesterification of a wide range of drugs and xenobiotics and may also participate in fatty acyl and cholesterol ester metabolism. In this study, in silico methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for CES3 genes and encoded proteins using data from several mammalian genome projects. Mammalian CES3 genes were located within a CES gene cluster with CES2 and CES6 genes, usually containing 13 exons transcribed on the positive DNA strand. Evidence is reported for duplicated CES3 genes for the chimp and mouse genomes. Mammalian CES3 protein subunits shared 58–97% sequence identity and exhibited sequence alignments and identities for key CES amino acid residues as well as extensive conservation of predicted secondary and tertiary structures with those previously reported for human CES1. The human genome project has previously reported CES3 mRNA isoform expression in several tissues, particularly in colon, trachea and in brain. Predicted human CES3 isoproteins were apparently derived from exon shuffling and are likely to be secreted extracellularly or retained within the cytoplasm. Mouse CES3-like transcripts were localized in specific regions of the mouse brain, including the cerebellum, and may play a role in the detoxification of drugs and xenobiotics in neural tissues and other tissues of the body. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the mammalian CES3 family of genes which were related to but distinct from other mammalian CES gene families.
doi:10.1007/s10709-010-9438-z
PMCID: PMC2896070  PMID: 20422440
Mammals; Amino acid sequence; Carboxylesterase; Evolution; Gene duplication
23.  Identification of a QTL for adipocyte volume and of shared genetic effects between adipocyte volume with aspartate aminotransferase 
Biochemical genetics  2010;48(5-6):538-547.
Plasma levels of Aspartate aminotransferase (AST), a liver enzyme, are elevated in patients with visceral obesity. The purpose of this study was to examine if adipocyte volume is under the influence of genetic factors and to evaluate its genetic correlations with AST. Fasting plasma of 374 pedigreed baboons from the Southwest National Primate Research Center at the Southwest Foundation for Biomedical Research, San Antonio, TX were assayed for AST. Adipocyte volume was measured using biopsies of omental adipose tissue. Adipocyte volume, body weight and plasma AST were heritable. Genetic correlations between the measured adiposity - related phenotypes and AST were significant. A QTL (LOD score of 3.2) for adipocyte volume was identified on the baboon homologue of human chromosome 6 near marker D6S1028. These results suggest that omental adipocyte volume is under genetic regulation and that shared genetic factors influence adiposity associated traits and AST.
doi:10.1007/s10528-010-9337-0
PMCID: PMC2869397  PMID: 20390338
non-alcholic fatty liver disease; obesity; adipocyte size; genome scan; QTL; aspartate aminotransferase
24.  Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms 
BMC Physiology  2011;11:9.
Background
The infrarenal abdominal aorta exhibits increased disease susceptibility relative to other aortic regions. Allograft studies exchanging thoracic and abdominal segments showed that regional susceptibility is maintained regardless of location, suggesting substantial roles for embryological origin, tissue composition and site-specific gene expression.
Results
We analyzed gene expression with microarrays in baboon aortas, and found that members of the HOX gene family exhibited spatial expression differences. HOXA4 was chosen for further study, since it had decreased expression in the abdominal compared to the thoracic aorta. Western blot analysis from 24 human aortas demonstrated significantly higher HOXA4 protein levels in thoracic compared to abdominal tissues (P < 0.001). Immunohistochemical staining for HOXA4 showed nuclear and perinuclear staining in endothelial and smooth muscle cells in aorta. The HOXA4 transcript levels were significantly decreased in human abdominal aortic aneurysms (AAAs) compared to age-matched non-aneurysmal controls (P < 0.00004). Cultured human aortic endothelial and smooth muscle cells stimulated with INF-γ (an important inflammatory cytokine in AAA pathogenesis) showed decreased levels of HOXA4 protein (P < 0.0007).
Conclusions
Our results demonstrated spatial variation in expression of HOXA4 in human aortas that persisted into adulthood and that downregulation of HOXA4 expression was associated with AAAs, an important aortic disease of the ageing population.
doi:10.1186/1472-6793-11-9
PMCID: PMC3125234  PMID: 21627813
25.  Phosphatase and tensin homologue/protein kinase B pathway linked to motor neuron survival in human superoxide dismutase 1-related amyotrophic lateral sclerosis 
Brain  2011;134(2):506-517.
Gene expression profiling has been used previously with spinal cord homogenates and laser capture microdissected motor neurons to determine the mechanisms involved in neurodegeneration in amyotrophic lateral sclerosis. However, while cellular and animal model work has focused on superoxide dismutase 1-related amyotrophic lateral sclerosis, the transcriptional profile of human mutant superoxide dismutase 1 motor neurons has remained undiscovered. The aim of this study was to apply gene expression profiling to laser captured motor neurons from human superoxide dismutase 1-related amyotrophic lateral sclerosis and neurologically normal control cases, in order to determine those pathways dysregulated in human superoxide dismutase 1-related neurodegeneration and to establish potential pathways suitable for therapeutic intervention. Identified targets were then validated in cultured cell models using lentiviral vectors to manipulate the expression of key genes. Microarray analysis identified 1170 differentially expressed genes in spinal cord motor neurons from superoxide dismutase 1-related amyotrophic lateral sclerosis, compared with controls. These genes encoded for proteins in multiple functional categories, including those involved in cell survival and cell death. Further analysis determined that multiple genes involved in the phosphatidylinositol-3 kinase signalling cascade were differentially expressed in motor neurons that survived the disease process. Functional experiments in cultured cells and primary motor neurons demonstrate that manipulating this pathway by reducing the expression of a single upstream target, the negative phosphatidylinositol-3 kinase regulator phosphatase and tensin homology, promotes a marked pro-survival effect. Therefore, these data indicate that proteins in the phosphatidylinositol-3 kinase pathway could represent a target for therapeutic manipulation in motor neuron degeneration.
doi:10.1093/brain/awq345
PMCID: PMC3030763  PMID: 21228060
amyotrophic lateral sclerosis; SOD1; PTEN; PI3K; AKT

Results 1-25 (40)