Two nuclei, termed here the medial hypothalamic nucleus and the lateral hypothalamic retinorecipi... more Two nuclei, termed here the medial hypothalamic nucleus and the lateral hypothalamic retinorecipient nucleus, are possible homologs of the mammalian suprachiasmatic nucleus. As the mammalian suprachiasmatic nucleus is characterized by a dense concentration of vasoactive intestinal peptide (VIP)-and neurophysin (NP)-immunoreactive neurons and an absence of acetylcholinesterase (AChE) staining, we decided to examine these factors in the ring dove hypothalamus. Neither
Background: Nonhuman primates are important for both biomedical studies and understanding human e... more Background: Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released marmoset assembly. Findings: RNA was extracted from five tissues: skeletal muscle, bladder and hippocampus from a male common marmoset, and cerebral cortex and cerebellum from a female common marmoset. All five RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the NCBI Sequenc...
Number of variants at splice sites and percent of total splice sites for CDS and UTR exons provid... more Number of variants at splice sites and percent of total splice sites for CDS and UTR exons provided for four rhesus macaques (17573, ON12033, ON22186 and 002T-NHP). (DOCX 11 kb)
List of effects of mutations in four rhesus macaques (17573, ON12033, ON22186 and 002T-NHP) as an... more List of effects of mutations in four rhesus macaques (17573, ON12033, ON22186 and 002T-NHP) as annotated by SnpEff. SNV = single nucleotide variant; Indel = insertion or deletion. Effects are as follows: Intergenic = in the intergenic region. Upstream = upstream of a gene by at most 5kbp. Downstream = downstream of a gene by at most 5kbp. 5' UTR = located in the 5' UTR. 3' UTR = located in the 3' UTR. Intronic = between two exons. Splice Acceptor = two bases before exon start. Splice Donor = two bases after coding exonâ s end. Splice Region = in the putative (Lariat) branch point, located in the intron. Frameshift = indel in the coding region that is not a multiple of 3. Inframe indel = indel in the coding region that is a multiple of 3. Start Lost = start codon is mutated to non-start codon. Stop gained = non-stop codon is mutated to stop codon. Stop Lost = stop codon is mutated to non-stop codon. (DOCX 116 kb)
The problem addressed by this paper is accurate and automatic gene finding following precise iden... more The problem addressed by this paper is accurate and automatic gene finding following precise identification/annotation of exon and intron boundaries for biologically verified nucleotide sequences, using the alignment of human genomic DNA to the curated mRNA transcript. We present a detailed description of a new cDNA/DNA homology gene annotation algorithm combining the results of BLASTN search with spliced alignment. Unambiguous junction of several Genomic DNA sequences is the key feature increasing our annotation quality, comparing to other programs. We also address gene annotation with both non-canonic splice sites and short exons. The approach has been tested on Genie learning subset as well as full-scale human RefSeq, demonstrating performance as high as 97%. Spliced alignments, BLAST, RefSeq, dynamic programming
The trajectory of retinal projections and the location of retinorecipient nuclei in the quail bra... more The trajectory of retinal projections and the location of retinorecipient nuclei in the quail brain was examined after application of horseradish peroxidase (HRP) either to the cut end of the optic nerve or following intraocular injection of HRP. Retinal projections to the hypothalamus, dorsalateral anterior thalamus (rostralateral part, magnocellular part, and lateral part), lateral anterior thalamus, lateroventral geniculate nucleus, lateral geniculate intercalated nuclei (rostral and caudal parts), ventrolateral thalamus, superficial synencephalic nucleus, external nucleus, tectal gray, diffuse pretectal area, pretectal optic area, ectomammillary nucleus, and optic tectum were revealed. Retinal projections observed in quail were compared with results obtained in other avian species and considered in relation to possible anatomic pathways underlying photoperiodism and circadian rhythms.
Determining the connections of neural systems is critical for determining how they function. In t... more Determining the connections of neural systems is critical for determining how they function. In this review, we focus on the use of HSV-1 and HSV-2 as transneuronal tracers. Using HSV to examine neural circuits is technically simple. HSV is injected into the area of interest, and after several days, the animals are perfused and processed for immunohistochemistry with antibodies to HSV proteins. Variables which influence HSV infection include species of host, age of host, titre of virus, strain of virus and phenotype of infected cell. The choice of strain of HSV is critically important. Several strains of HSV-1 and HSV-2 have been utilized for purposes of transneuronal tract-tracing. HSV has been used successfully to study neuronal circuitry in a variety of different neuroanatomical systems including the somatosensory, olfactory, visual, motor, autonomic and limbic systems.
Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investig... more Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investigators studying many species must rely on draft genomes. Using the rhesus macaque as an example, we document the effects of sequencing errors, gaps in sequence and misassemblies on one automated gene model pipeline, Gnomon. The combination of draft genome with automated gene finding software can result in spurious sequences. We estimate that approximately 50% of the rhesus gene models are missing, incomplete or incorrect. The problems identified in this work likely apply to all draft vertebrate genomes annotated with any automated gene model pipeline and thus represent a pervasive challenge to the analysis of draft genomes.
Due to the large geographical overlap of populations exposed to Zika virus (ZIKV) and human immun... more Due to the large geographical overlap of populations exposed to Zika virus (ZIKV) and human immunodeficiency virus (HIV), understanding disease pathogenesis in such coinfections is urgently needed. We used chronically infected simian immunodeficiency virus and chimeric simian human immunodeficiency virus (SIV/SHIV) macaques and inoculated with ZIKV. Plasma viral loads of both SIV/SHIV and ZIKV showed no significant changes as compared to ZIKV alone-infected animals. Tissue clearance of ZIKV was observed similarly. Furthermore, minimal changes in cytokines/chemokines were observed. Collectively, these data suggest that coinfection may not alter disease pathogenesis and warrants large HIV-ZIKV epidemiological studies to validate these findings.
Zika Virus (ZIKV) is primarily transmitted through mosquito bites. It can also be transmitted dur... more Zika Virus (ZIKV) is primarily transmitted through mosquito bites. It can also be transmitted during sexual intercourse and in utero from mother to fetus. To gain preliminary insight into ZIKV pathology and immune responses on route of transmission, rhesus macaques (RMs) were inoculated with ZIKV (PRVABC59) via intravaginal (IVAG) (n = 3) or subcutaneous (sub Q) (n = 2) routes. Systemic ZIKV infection was observed in all RMs, regardless of the route of inoculation. After 9 days postinfection (dpi), ZIKV was not detected in the plasma of IVAG- and sub-Q-inoculated RMs. Importantly, RMs harbored ZIKV up to 60 dpi in various anatomical locations. Of note, ZIKV was also present in several regions of the brain, including the caudate nucleus, parietal lobe, cortex, and amygdala. These observations appear to indicate that ZIKV infection may be systemic and persistent regardless of route of inoculation. In addition, we observed changes in key immune cell populations in response to ZIKV infe...
In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodefi... more In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodeficiency virus (SIV) in macaques, SIV infection of a natural host, sooty mangabeys (Cercocebus atys), is non-pathogenic despite high viraemia. Here we sequenced and assembled the genome of a captive sooty mangabey. We conducted genome-wide comparative analyses of transcript assemblies from C. atys and AIDS-susceptible species, such as humans and macaques, to identify candidates for host genetic factors that influence susceptibility. We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans. One of these sequence divergences, a C-terminal frameshift in the toll-like receptor-4 (TLR4) gene of C. atys, is associated with a blunted in vitro response to TLR-4 ligands. In addition, we found a major structural change in exons 3-4 of the immune-regulatory protein intercellular adhesion molecule 2 (ICAM-2); expression of th...
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particular... more The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct. The rhesus macaque provides a unique opportunity to determine whether an improved genome (MacaM) yields better results than a draft genome (rheMac2) for evolutionary studies. We compared protein-coding genes annotated in the rheMac2 and MacaM genomes with their human orthologs. We found many genes annotated in rheMac2 had apparently spurious sequences not present in genes derived from MacaM. The rheMac2 a...
Rhesus macaques are an important pre-clinical model of human disease. To advance our understandin... more Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model. We detected an average of 131 mutations predicted to severely alter protein coding per animal, and identified 45 such variants that coincide with known pathogenic human variants. These data suggest that expanded screening of existing breeding colonies will identify novel models of human disease, and that increased genomic characterization can help inform research studies in macaques.
Two nuclei, termed here the medial hypothalamic nucleus and the lateral hypothalamic retinorecipi... more Two nuclei, termed here the medial hypothalamic nucleus and the lateral hypothalamic retinorecipient nucleus, are possible homologs of the mammalian suprachiasmatic nucleus. As the mammalian suprachiasmatic nucleus is characterized by a dense concentration of vasoactive intestinal peptide (VIP)-and neurophysin (NP)-immunoreactive neurons and an absence of acetylcholinesterase (AChE) staining, we decided to examine these factors in the ring dove hypothalamus. Neither
Background: Nonhuman primates are important for both biomedical studies and understanding human e... more Background: Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released marmoset assembly. Findings: RNA was extracted from five tissues: skeletal muscle, bladder and hippocampus from a male common marmoset, and cerebral cortex and cerebellum from a female common marmoset. All five RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the NCBI Sequenc...
Number of variants at splice sites and percent of total splice sites for CDS and UTR exons provid... more Number of variants at splice sites and percent of total splice sites for CDS and UTR exons provided for four rhesus macaques (17573, ON12033, ON22186 and 002T-NHP). (DOCX 11 kb)
List of effects of mutations in four rhesus macaques (17573, ON12033, ON22186 and 002T-NHP) as an... more List of effects of mutations in four rhesus macaques (17573, ON12033, ON22186 and 002T-NHP) as annotated by SnpEff. SNV = single nucleotide variant; Indel = insertion or deletion. Effects are as follows: Intergenic = in the intergenic region. Upstream = upstream of a gene by at most 5kbp. Downstream = downstream of a gene by at most 5kbp. 5' UTR = located in the 5' UTR. 3' UTR = located in the 3' UTR. Intronic = between two exons. Splice Acceptor = two bases before exon start. Splice Donor = two bases after coding exonâ s end. Splice Region = in the putative (Lariat) branch point, located in the intron. Frameshift = indel in the coding region that is not a multiple of 3. Inframe indel = indel in the coding region that is a multiple of 3. Start Lost = start codon is mutated to non-start codon. Stop gained = non-stop codon is mutated to stop codon. Stop Lost = stop codon is mutated to non-stop codon. (DOCX 116 kb)
The problem addressed by this paper is accurate and automatic gene finding following precise iden... more The problem addressed by this paper is accurate and automatic gene finding following precise identification/annotation of exon and intron boundaries for biologically verified nucleotide sequences, using the alignment of human genomic DNA to the curated mRNA transcript. We present a detailed description of a new cDNA/DNA homology gene annotation algorithm combining the results of BLASTN search with spliced alignment. Unambiguous junction of several Genomic DNA sequences is the key feature increasing our annotation quality, comparing to other programs. We also address gene annotation with both non-canonic splice sites and short exons. The approach has been tested on Genie learning subset as well as full-scale human RefSeq, demonstrating performance as high as 97%. Spliced alignments, BLAST, RefSeq, dynamic programming
The trajectory of retinal projections and the location of retinorecipient nuclei in the quail bra... more The trajectory of retinal projections and the location of retinorecipient nuclei in the quail brain was examined after application of horseradish peroxidase (HRP) either to the cut end of the optic nerve or following intraocular injection of HRP. Retinal projections to the hypothalamus, dorsalateral anterior thalamus (rostralateral part, magnocellular part, and lateral part), lateral anterior thalamus, lateroventral geniculate nucleus, lateral geniculate intercalated nuclei (rostral and caudal parts), ventrolateral thalamus, superficial synencephalic nucleus, external nucleus, tectal gray, diffuse pretectal area, pretectal optic area, ectomammillary nucleus, and optic tectum were revealed. Retinal projections observed in quail were compared with results obtained in other avian species and considered in relation to possible anatomic pathways underlying photoperiodism and circadian rhythms.
Determining the connections of neural systems is critical for determining how they function. In t... more Determining the connections of neural systems is critical for determining how they function. In this review, we focus on the use of HSV-1 and HSV-2 as transneuronal tracers. Using HSV to examine neural circuits is technically simple. HSV is injected into the area of interest, and after several days, the animals are perfused and processed for immunohistochemistry with antibodies to HSV proteins. Variables which influence HSV infection include species of host, age of host, titre of virus, strain of virus and phenotype of infected cell. The choice of strain of HSV is critically important. Several strains of HSV-1 and HSV-2 have been utilized for purposes of transneuronal tract-tracing. HSV has been used successfully to study neuronal circuitry in a variety of different neuroanatomical systems including the somatosensory, olfactory, visual, motor, autonomic and limbic systems.
Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investig... more Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investigators studying many species must rely on draft genomes. Using the rhesus macaque as an example, we document the effects of sequencing errors, gaps in sequence and misassemblies on one automated gene model pipeline, Gnomon. The combination of draft genome with automated gene finding software can result in spurious sequences. We estimate that approximately 50% of the rhesus gene models are missing, incomplete or incorrect. The problems identified in this work likely apply to all draft vertebrate genomes annotated with any automated gene model pipeline and thus represent a pervasive challenge to the analysis of draft genomes.
Due to the large geographical overlap of populations exposed to Zika virus (ZIKV) and human immun... more Due to the large geographical overlap of populations exposed to Zika virus (ZIKV) and human immunodeficiency virus (HIV), understanding disease pathogenesis in such coinfections is urgently needed. We used chronically infected simian immunodeficiency virus and chimeric simian human immunodeficiency virus (SIV/SHIV) macaques and inoculated with ZIKV. Plasma viral loads of both SIV/SHIV and ZIKV showed no significant changes as compared to ZIKV alone-infected animals. Tissue clearance of ZIKV was observed similarly. Furthermore, minimal changes in cytokines/chemokines were observed. Collectively, these data suggest that coinfection may not alter disease pathogenesis and warrants large HIV-ZIKV epidemiological studies to validate these findings.
Zika Virus (ZIKV) is primarily transmitted through mosquito bites. It can also be transmitted dur... more Zika Virus (ZIKV) is primarily transmitted through mosquito bites. It can also be transmitted during sexual intercourse and in utero from mother to fetus. To gain preliminary insight into ZIKV pathology and immune responses on route of transmission, rhesus macaques (RMs) were inoculated with ZIKV (PRVABC59) via intravaginal (IVAG) (n = 3) or subcutaneous (sub Q) (n = 2) routes. Systemic ZIKV infection was observed in all RMs, regardless of the route of inoculation. After 9 days postinfection (dpi), ZIKV was not detected in the plasma of IVAG- and sub-Q-inoculated RMs. Importantly, RMs harbored ZIKV up to 60 dpi in various anatomical locations. Of note, ZIKV was also present in several regions of the brain, including the caudate nucleus, parietal lobe, cortex, and amygdala. These observations appear to indicate that ZIKV infection may be systemic and persistent regardless of route of inoculation. In addition, we observed changes in key immune cell populations in response to ZIKV infe...
In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodefi... more In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodeficiency virus (SIV) in macaques, SIV infection of a natural host, sooty mangabeys (Cercocebus atys), is non-pathogenic despite high viraemia. Here we sequenced and assembled the genome of a captive sooty mangabey. We conducted genome-wide comparative analyses of transcript assemblies from C. atys and AIDS-susceptible species, such as humans and macaques, to identify candidates for host genetic factors that influence susceptibility. We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans. One of these sequence divergences, a C-terminal frameshift in the toll-like receptor-4 (TLR4) gene of C. atys, is associated with a blunted in vitro response to TLR-4 ligands. In addition, we found a major structural change in exons 3-4 of the immune-regulatory protein intercellular adhesion molecule 2 (ICAM-2); expression of th...
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particular... more The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct. The rhesus macaque provides a unique opportunity to determine whether an improved genome (MacaM) yields better results than a draft genome (rheMac2) for evolutionary studies. We compared protein-coding genes annotated in the rheMac2 and MacaM genomes with their human orthologs. We found many genes annotated in rheMac2 had apparently spurious sequences not present in genes derived from MacaM. The rheMac2 a...
Rhesus macaques are an important pre-clinical model of human disease. To advance our understandin... more Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model. We detected an average of 131 mutations predicted to severely alter protein coding per animal, and identified 45 such variants that coincide with known pathogenic human variants. These data suggest that expanded screening of existing breeding colonies will identify novel models of human disease, and that increased genomic characterization can help inform research studies in macaques.
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