Nathaniel Kenneth Jue

California State University, Monterey Bay | CSUMB · Biology and Chemistry

Ectonucleotide phosphatase/phosphodiesterase 1 (ENPP1) deficiency results in either lethal arterial calcifications ('Generalized Arterial Calcification of Infancy' - GACI), phosphate wasting rickets ('Autosomal Recessive Hypophosphatemic Rickets type 2' - ARHR2), early onset osteoporosis, or progressive spinal rigidity (Ossification of the Posterio...

Ecologists and evolutionary biologists use RNAseq to study population genomics and differential gene expression in non model species. Without a genome, a de novo transcriptome assembly must be created from short sequence reads to create full length genes. Goal: Use RNAseq data from Sebastes auriculatus (brown rockfish) to identify transcriptome ass...

Rockfish placed in control (pH 8.0, pCO2~500 atm) and experimental (pH 7.2, pCO2~2600 atm) treatment for 0H, 12H, 24H, 48H, 120H. Gill, liver, brain, and white muscle were dissected at each time point (n=3). Homogenized 8-14 mg of white muscle for 100X CS and 200X LDH assays. CS (412nm) LDH (340nm) assays performed on TECAN Infinite m200 at 30C

The white shark ( Carcharodon carcharias ; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. T...

Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression...

Ohno's hypothesis predicts that the expression of the single X chromosome in males needs compensatory upregulation to balance its dosage with that of the diploid autosomes. Additionally, X chromosome inactivation ensures that quadruple expression of the two X chromosomes is avoided in females. These mechanisms have been actively studied in mice and...

The evolution of the placenta is an excellent model to examine the evolutionary processes underlying adaptive complexity due to the recent, independent derivation of placentation in divergent animal lineages. In fishes, the family Poeciliidae offers the opportunity to study placental evolution with respect to variation in degree of post-fertilizati...

The evolution of the placenta is an excellent model to examine the evolutionary processes underlying adaptive complexity due to the recent, independent derivation of placentation in divergent animal lineages. In fishes, the family Poeciliidae offers the opportunity to study placental evolution with respect to variation in degree of post-fertilizati...

Deviations from proper gene dosage of the autosome range from severe to lethal consequences in mammals. Eutherian males (XY), however, have reduced gene dosage compared with females (XX) due to a single X and deteriorating Y chromosome. This dosage imbalance is resolved through X chromosome dosage compensation, according to Ohno’s hypothesis: X-lin...

The maintenance of a proper gene dosage is essential in cellular networks. To resolve the dosage imbalance between eutherian females (XX) and male (XY), X chromosome inactivation (XCI) occurs in females, while X-chromosome dosage compensation up-regulates the active X to balance its expression with that of autosome pairs [Ohno’s hypothesis; Ohno 19...

A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S....

The Bornean elephant population in Sabah, with only 2000 individuals, is currently mainly restricted to a limited number of forest reserves. The main threats to the species' survival are population fragmentation and isolation of the existing herds. To support and help monitor future conservation and management measures, we assessed the genetic dive...

In human and mouse diploid cells and gametes, expression levels of X-linked genes are hypothesised to balance with those of autosomal genes (Ohno’s “dosage compensation”). Such a phenomenon, however, has not been systematically studied in cattle or compared between in vivo and in vitro embryos. Using RNA-seq data, we compared dosage compensation an...

Describing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test wh...

Wide-ranging marine species are often described as having a low effective population size (N e) to census size (N) ratio. This genetic phenomenon is typically attributed to large variation among individuals in reproductive success because of the high mortality rates and unpredictable environments associated with larval dispersal. In this study, we...

Background An enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation has been observed in a variety of organisms. Incongruence in the conclusions reached in some recent reports has been attributed to...

Abstract Many inferences about contemporary rates of gene flow are based on the assumption that the observed genetic structure among populations is stable. Recent studies have uncovered several cases in which this assumption is tenuous. Most of those studies have focused on the effects that regular environmental fluctuations can have on genetic str...

High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering gen...

List of RAD tags/loci with genotypes. A complete list (vcf file) of all RAD tag/loci where genotypes were obtained for all individuals (100%) for 1,200 loci/RAD tags, and for 75% of the individuals (i.e. six or more) for 1,700 loci. For the remaining 400 loci, the SNPs were shared by less than six individuals. Eight E. m. borneensis samples were us...

Gene Ontology (GO) term representation of 454-contigs. The GO terms were obtained for 454 contigs containing SNPs using Ensembl gene annotation of L. africana. In these 454-contigs, 24 unique GO terms were represented. (XLSX)

Gene Ontology (GO) term representation of RAD-seq contigs. The GO terms were obtained for RAD-contigs containing SNPs using Ensembl gene annotation of L. africana. In these RAD-seq contigs, 35 unique GO terms were represented. (XLSX)

Summary of SSRs (simple sequence repeats) identified in the Bornean elephant sequence dataset. The number of SSRs or microsatellite loci identified in E. m. borneensis (n = 2) using the 454 shotgun sequencing approach, and the subset of these that are potentially amplifiable (containing suitable PCR priming sites) and validated. The di- and tri-nuc...

Estimation of genetic diversity and genotyping error rates. Comparison of observed heterozygosity (Ho), missing genotypes, allelic dropout, number of positive PCRs, false alleles, and mean number of allele (MNA) for the genotyped samples of E. m. borneensis (n = 7) and E. m. indicus (n = 3). Multiplex assays (five plexes) targeting 194 unique SNPs...

Recent SNP discovery efforts in non-model species. A literature review of recent SNP discovery efforts in non-model species using high throughput sequencing platforms. (XLSX)

Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their i...

Aim  To elucidate the historical phylogeography of the dusky pipefish (Syngnathus floridae) in the North American Atlantic and Gulf of Mexico ocean basins.Location  Southern Atlantic Ocean and northern Gulf of Mexico within the continental United States.Methods  A 394-bp fragment of the mitochondrial cytochrome b gene and a 235-bp fragment of the m...

The role of larval dispersal in ecology and evolution is still largely undescribed in many marine organisms. Larval recruitment has long been viewed as being dominated by unpredictable, highly variable processes but also as a significant driver of population ecology and genetics. Without any knowledge about the directionality and magnitudes of larv...

Gag (Mycteroperca microlepis) from the eastern Gulf of Mexico and northwestern Atlantic are managed as separate stocks, although evidence for their demographic isolation remains equivocal. Several hundred individuals were geno-typed at 11 microsatellite loci and it was found that gag across these regions were genetically indistinguishable (FST <0.0...

Using 11 microsatellite markers, genetic analyses of three successive year-classes of gag Mycteroperca microlepis juveniles across the north-eastern Gulf of Mexico revealed a lack of spatial structure and very little temporal variation between year-classes. These results are consistent with long-term effective population sizes on the order of 30 00...

This study compared catches of Panulirus argus pueruli and very young juveniles between Hunt and Sandwich collectors at Long and Big Munson Keys, Florida, United States. Catch comparisons were made over the peak puerulus settlement period between February and July 2002, using six Sandwich and six Hunt collectors at each site. The collectors were se...