The genetic ancestry of African Americans, Latinos, and European Americans across the United States.

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.

Short communication: Parameters of abomasal emptying and glucose-insulin dynamics in Holstein-Friesian calves at 2 ages and 2 levels of milk replacer intake.

Elevated planes of nutrition in the preweaning period of dairy calf management can increase average daily gain, shorten age at puberty, and increase milk yield. In a previous study, 12 Holstein calves were fed 2 meals/d of 4 or 2 L milk replacer up to 7 wk of age. The objective of the current study was to estimate parameters of abomasal emptying and glucose-insulin dynamics in these calves by fitting a mechanistic model to postprandial appearances of plasma glucose, insulin, and the abomasal emptying marker acetaminophen measured at 4 and 7 wk of age. Higher intake of milk replacer resulted in longer bouts of abomasal emptying at a slower rate. Parameters of glucose and insulin dynamics were not affected by milk replacer intake. However, older calves had decreased insulin-stimulated glucose utilization indicating impaired insulin sensitivity, as well as increased pancreatic responsiveness. Neither of these effects were apparent from i.v. glucose tolerance tests on the calves and may have been related to postprandial gut hormone release. Effects of age on parameters of glucose-insulin dynamics were larger than effects of milk replacer intake. Conversely, effects of milk replacer intake on abomasal emptying were larger than effects of age.

Effect of plane of milk replacer intake and age on glucose and insulin kinetics and abomasal emptying in female Holstein Friesian dairy calves fed twice daily.

The objective of this study was to investigate how preweaning plane of milk replacer intake and age can affect insulin and glucose kinetics as well as abomasal emptying rate in dairy calves fed twice a day. A total of 12 female Holstein Friesian calves were blocked by cow parity, paired by colostrum origin, and were randomly assigned to a high plane of milk replacer intake (8 L/d, 1.2kg of milk replacer/d; n=6) or a low plane of nutrition (4 L/d, 0.6kg of milk replacer/d; n=6). All calves received 4 L of colostrum over 2 meals (1 and 6h after birth) and were then directly transferred to their assigned feeding plans until they were stepped-down from milk by 50% during wk 7 and weaned on wk 8. Milk replacer (24% crude protein, 18% crude fat) was fed at 150g/L twice daily (0700 and 1700h) and all calves had ad libitum access to pelleted calf starter, chopped wheat straw, and water. Jugular catheters were placed in all calves at 4, 7, and 10wk of age. Then, postprandial response to plasma glucose, insulin, and acetaminophen (supplied with the meal) were determined to measure abomasal emptying. The next day, a glucose tolerance test was conducted by infusing glucose via the jugular catheter. At 4 and 7wk of age, the rate constant (%/h) for abomasal emptying of the meal was lower in high calves (0.21±0.02 in wk 4; 0.27±0.02 in wk 7) compared with low (0.34±0.02 in wk 4; 0.47±0.02 in wk 7). The postprandial plasma insulin area under the curve over 420min was greater in high calves (18,443±7,329; low=5,834±739 µU/mL) compared with low. We found no differences in glucose tolerance test kinetics between the high and low dairy calves at 4, 7, or 10wk of age. The findings from this study suggest that feeding dairy calves an elevated plane of nutrition in 2 meals of milk replacer per day does not decrease insulin sensitivity.

Clinical potential of gene therapy: towards meeting the demand.

Since the discovery that new genetic material could be transferred into human cells resulting in induced expression of genes and proteins, clinicians and scientists have been working to harness the technology for clinical outcomes. This article provides a summary of the current status of developments within the broad discipline of clinical gene therapy. In pursuing the treatment of diverse clinical conditions, a wide variety of therapeutics, each tailor-made, may be required. Gene therapy offers the possibility of accurately and specifically targeting particular genetic abnormalities through gene correction, addition or replacement. It represents a compelling idea that adds a new dimension to our portfolio of credible therapeutic choices.

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.

Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

Patient-maintained propofol sedation using reaction time monitoring: a volunteer safety study.

Previous volunteer studies of an effect-site controlled, patient-maintained sedation system using propofol have demonstrated a risk of over-sedation. We have incorporated a reaction-time monitor into the handset of the patient-maintained sedation system to add an individualised patient-feedback mechanism. This study assessed if such reaction-time feedback modification would reduce the risk of over-sedation in 20 healthy volunteers deliberately attempting to over-administer themselves propofol. All the volunteers successfully sedated themselves without reaching any unsafe endpoints. All volunteers maintained verbal contact throughout, in accordance with the definition of conscious sedation. The mean (SD) lowest S(p) O(2) was 97 (1.7) % when breathing room air and no volunteer required supplementary oxygen. The mean (SD) maximum effect-site propofol concentration reached was 1.7 (0.4) µg.ml(-1) . The present system was found to be safer than its predecessors, allowing conscious sedation, but preventing over-sedation.

Web-based, participant-driven studies yield novel genetic associations for common traits.

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here we report initial results from a participant-driven study of 22 traits. Replications of associations (in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP, and MC1R) for hair color, eye color, and freckling validate the Web-based, self-reporting paradigm. The identification of novel associations for hair morphology (rs17646946, near TCHH; rs7349332, near WNT10A; and rs1556547, near OFCC1), freckling (rs2153271, in BNC2), the ability to smell the methanethiol produced after eating asparagus (rs4481887, near OR2M7), and photic sneeze reflex (rs10427255, near ZEB2, and rs11856995, near NR2F2) illustrates the power of the approach.

Pervasive hitchhiking at coding and regulatory sites in humans.

Much effort and interest have focused on assessing the importance of natural selection, particularly positive natural selection, in shaping the human genome. Although scans for positive selection have identified candidate loci that may be associated with positive selection in humans, such scans do not indicate whether adaptation is frequent in general in humans. Studies based on the reasoning of the MacDonald-Kreitman test, which, in principle, can be used to evaluate the extent of positive selection, suggested that adaptation is detectable in the human genome but that it is less common than in Drosophila or Escherichia coli. Both positive and purifying natural selection at functional sites should affect levels and patterns of polymorphism at linked nonfunctional sites. Here, we search for these effects by analyzing patterns of neutral polymorphism in humans in relation to the rates of recombination, functional density, and functional divergence with chimpanzees. We find that the levels of neutral polymorphism are lower in the regions of lower recombination and in the regions of higher functional density or divergence. These correlations persist after controlling for the variation in GC content, density of simple repeats, selective constraint, mutation rate, and depth of sequencing coverage. We argue that these results are most plausibly explained by the effects of natural selection at functional sites -- either recurrent selective sweeps or background selection -- on the levels of linked neutral polymorphism. Natural selection at both coding and regulatory sites appears to affect linked neutral polymorphism, reducing neutral polymorphism by 6% genome-wide and by 11% in the gene-rich half of the human genome. These findings suggest that the effects of natural selection at linked sites cannot be ignored in the study of neutral human polymorphism.

High rate of recent transposable element-induced adaptation in Drosophila melanogaster.

Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that many of these TEs are in fact adaptive by demonstrating that the regions flanking five of these TEs display signatures of partial selective sweeps. Furthermore, we show that eight out of the 13 putatively adaptive elements show population frequency heterogeneity consistent with these elements playing a role in adaptation to temperate climates. We conclude that TEs have contributed considerably to recent adaptive evolution (one TE-induced adaptation every 200-1,250 y). The majority of these adaptive insertions are likely to be involved in regulatory changes. Our results also suggest that TE-induced adaptations arise more often from standing variants than from new mutations. Such a high rate of TE-induced adaptation is inconsistent with the number of fixed TEs in the D. melanogaster genome, and we discuss possible explanations for this discrepancy.

Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures.

Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.

A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster.

A recent genomewide screen identified 13 transposable elements that are likely to have been adaptive during or after the spread of Drosophila melanogaster out of Africa. One of these insertions, Bari-Juvenile hormone epoxy hydrolase (Bari-Jheh), was associated with the selective sweep of its flanking neutral variation and with reduction of expression of one of its neighboring genes: Jheh3. Here, we provide further evidence that Bari-Jheh insertion is adaptive. We delimit the extent of the selective sweep and show that Bari-Jheh is the only mutation linked to the sweep. Bari-Jheh also lowers the expression of its other flanking gene, Jheh2. Subtle consequences of Bari-Jheh insertion on life-history traits are consistent with the effects of reduced expression of the Jheh genes. Finally, we analyze molecular evolution of Jheh genes in both the long- and the short-term and conclude that Bari-Jheh appears to be a very rare adaptive event in the history of these genes. We discuss the implications of these findings for the detection and understanding of adaptation.

Inferring the strength of selection in Drosophila under complex demographic models.

Transposable elements (TEs) constitute a substantial fraction of the genomes of many species, and it is thus important to understand their population dynamics. The strength of natural selection against TEs is a key parameter in understanding these dynamics. In principle, the strength of selection can be inferred from the frequencies of a sample of TEs. However, complicated demographic histories, such as found in Drosophila melanogaster, could lead to a substantial distortion of the TE frequency distribution compared with that expected for a panmictic, constant-sized population. The current methodology for the estimation of selection intensity acting against TEs does not take into account demographic history and might generate erroneous estimates especially for TE families under weak selection. Here, we develop a flexible maximum likelihood methodology that explicitly accounts both for demographic history and for the ascertainment biases of identifying TEs. We apply this method to the newly generated frequency data of the BS family of non-long terminal repeat retrotransposons in D. melanogaster in concert with two recent models of the demographic history of the species to infer the intensity of selection against this family. We find the estimate to differ substantially compared with a prior estimate that was made assuming a model of constant population size. Further, we find there to be relatively little information about selection intensity present in the derived non-African frequency data and that the ancestral African subpopulation is much more informative in this respect. These findings highlight the importance of accounting for demographic history and bear on study design for the inference of selection coefficients generally.

Growth and morphology control of carbon nanotubes at the apexes of pyramidal silicon tips.

We describe the development of catalysed chemical vapour deposition (cCVD) growth schemes suitable for the production of carbon nanotube atomic force microscopy (CNT-AFM) probes. Growth and sample processing conditions are utilized that both incorporate safety in the process, e.g. the use of ethanol (EtOH) vapour as a carbon feedstock and hydrogen at only 4% (flow proportion), and simplicity, e.g. no catalyst patterning is required. Cobalt is employed as the growth catalyst and thin films of aluminium on silicon as the substrate material. Purpose-fabricated silicon substrates containing large numbers of tip structures are used as models of AFM probes. This enables growth to be carried out on many tips at once, facilitating a thorough investigation of the effect of different growth schemes on yields. cCVD growth schemes are chosen which produce stabilizing high density networks of carbon nanotubes on the sidewalls of the pyramidal tips to aid in anchoring the apex protruding carbon nanotube(s) in place. This results in long-lasting AFM imaging tips. We demonstrate that through rational tailoring of cCVD conditions it is possible to tune the growth conditions such that CNTs which protrude straight from tip apexes can be obtained at yields of greater than or equal to 78%. Application of suitable growth schemes to CNT growth on commercially available AFM probes resulted in CNT-AFM probes which were found to be extremely useful for extended lifetime metrological profiling of complex structures.

Nonadaptive explanations for signatures of partial selective sweeps in Drosophila.

A beneficial mutation that has nearly but not yet fixed in a population produces a characteristic haplotype configuration, called a partial selective sweep. Whether nonadaptive processes might generate similar haplotype configurations has not been extensively explored. Here, we consider 5 population genetic data sets taken from regions flanking high-frequency transposable elements in North American strains of Drosophila melanogaster, each of which appears to be consistent with the expectations of a partial selective sweep. We use coalescent simulations to explore whether incorporation of the species' demographic history, purifying selection against the element, or suppression of recombination caused by the element could generate putatively adaptive haplotype configurations. Whereas most of the data sets would be rejected as nonneutral under the standard neutral null model, only the data set for which there is strong external evidence in support of an adaptive transposition appears to be nonneutral under the more complex null model and in particular when demography is taken into account. High-frequency, derived mutations from a recently bottlenecked population, such as we study here, are of great interest to evolutionary genetics in the context of scans for adaptive events; we discuss the broader implications of our findings in this context.

Effects of feeding frequency of an elevated plane of milk replacer and calf age on behavior, and glucose and insulin kinetics in male Holstein calves.

Optimizing feeding regimens in early life to maximize lifelong growth and production are essential in the dairy industry. This study investigated the effects of milk replacer (MR) feeding frequency and calf age on behavior, and glucose and insulin kinetics of pre- and post-weaned calves fed an elevated plane of MR. Ten male Holstein calves (42.2±1.8 kg BW) were blocked by BW and randomly assigned to two treatments offering 8 l MR/day (150 g/l) in two (2×; meal size 4 l) or four (4×; meal size 2 l) feedings via an automated calf feeder. Milk replacer was gradually stepped down by 1 l/day during week 8, with calves being weaned by week 9. Water and pelleted calf starter were offered ad libitum. Individual intake of MR and starter were recorded daily, and BW was recorded weekly. The number of visits to the MR feeder (rewarded and unrewarded), and behaviors such as lying, cross-sucking, non-nutritive sucking and occupancy time in the feeder were recorded for individual calves from weeks 4 to 10. Jugular catheters were placed on weeks 4, 7 and 10 to facilitate postprandial blood sampling and glucose tolerance tests. Statistical analysis was conducted using the PROC GLIMMIX procedure (SAS) for behavioral observations, and the MIXED procedure (SAS) with repeated measures for BW, intake, plasma glucose and plasma insulin data. Final BW, starter and MR intake did not differ between treatments. There were no differences in observed calf behaviors; with the exception that 2× calves visited the MR feeder more often (P<0.01; total: unrewarded and rewarded). Baseline concentrations (mmol/l) and the maximum change in glucose (delta, mmol/l) were greater and lower (P=0.02) in 4×compared to 2×calves, respectively. Postprandial insulin AUC240 tended (P=0.09) to be greater in 2×calves, compared to 4×calves at week 7. Similarly, T max (min), AUC240 and delta values (µU/ml) were greater (P⩽0.05) in 2×calves, compared to 4×calves. No treatment ×age interactions were observed for glucose or insulin during the glucose tolerance tests. Therefore, we conclude that feeding an elevated plane of MR (8 l/day) at a lower frequency (2× v. 4×) increased feeder visits, but not other hunger-related behaviors, and while postprandial glucose and insulin parameters varied, insulin sensitivity remained stable in Holstein dairy calves up to 10 weeks of age in calves consuming similar levels of calf starter.

ABCB1 genetic polymorphism influences the pharmacology of the new pyrrolobenzodiazepine derivative SJG-136.

ATP-binding cassette transporter P-glycoprotein (ABCB1) is responsible for the multidrug resistance (MDR1) phenotype observed in cancer cells. SJG-136, a new pyrrolobenzodiazepine dimer, is a sequence-dependent DNA crosslinking agent and substrate of ABCB1. We previously showed that colon cancer cell lines expressing high levels of ABCB1 showed a lower sensitivity to SJG-136. Here, we show that in 3T3 isogenic fibroblasts, ABCB1 genetic polymorphism differentially affects ABCB1 gene expression and transport function. However, this genotype-phenotype relationship was not observed in immortalized lymphocytes, which expressed 10- to 1000-fold less ABCB1 than colon cancer cell lines. Consistent with this, the cytotoxicity of SJG-136 in 3T3 fibroblasts was affected by ABCB1 genetic polymorphism but not in immortalized lymphocytes. ABCB1 genetic polymorphism is therefore likely to affect drug sensitivity in tissues expressing high levels of the transporter and in which significant variability is observed.

Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila.

The effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. The pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. Because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. Thus, the spatial correspondence between neutral polymorphism and nonsynonymous divergence may be especially informative about the process of adaptation. Here we study this correspondence using genomewide polymorphism data from Drosophila simulans and the divergence between D. simulans and D. melanogaster. Focusing on highly recombining portions of the autosomes, at a spatial scale appropriate to the study of selective sweeps, we find that neutral polymorphism is both lower and, as measured by a new statistic Q(S), less homogeneous where nonsynonymous divergence is higher and that the spatial structure of this correlation is best explained by the action of strong recurrent selective sweeps. We introduce a method to infer, from the spatial correspondence between polymorphism and divergence, the rate and selective strength of adaptation. Our results independently confirm a high rate of adaptive substitution (approximately 1/3000 generations) and newly suggest that many adaptations are of surprisingly great selective effect (approximately 1%), reducing the effective population size by approximately 15% even in highly recombining regions of the genome.

Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster.

BACKGROUND: Levels of molecular diversity in Drosophila have repeatedly been shown to be higher in ancestral, African populations than in derived, non-African populations. This pattern holds for both coding and noncoding regions for a variety of molecular markers including single nucleotide polymorphisms and microsatellites. Comparisons of X-linked and autosomal diversity have yielded results largely dependent on population of origin. RESULTS: In an attempt to further elucidate patterns of sequence diversity in Drosophila melanogaster, we studied nucleotide variation at putatively nonfunctional X-linked and autosomal loci in sub-Saharan African and North American strains of D. melanogaster. We combine our experimental results with data from previous studies of molecular polymorphism in this species. We confirm that levels of diversity are consistently higher in African versus North American strains. The relative reduction of diversity for X-linked and autosomal loci in the derived, North American strains depends heavily on the studied loci. While the compiled dataset, comprised primarily of regions within or in close proximity to genes, shows a much more severe reduction of diversity on the X chromosome compared to autosomes in derived strains, the dataset consisting of intergenic loci located far from genes shows very similar reductions of diversities for X-linked and autosomal loci in derived strains. In addition, levels of diversity at X-linked and autosomal loci in the presumably ancestral African population are more similar than expected under an assumption of neutrality and equal numbers of breeding males and females. CONCLUSION: We show that simple demographic scenarios under assumptions of neutral theory cannot explain all of the observed patterns of molecular diversity. We suggest that the simplest model is a population bottleneck that retains an ancestral female-biased sex ratio, coupled with higher rates of positive selection at X-linked loci in close proximity to genes specifically in derived, non-African populations.

Short hairpin RNAs targeting Bcl-xL modulate senescence and apoptosis following SN-38 and irinotecan exposure in a colon cancer model.

Bcl-xL is an anti-apoptotic protein over-expressed in colorectal cancers acting on both the intrinsic and extrinsic pathways. We stably expressed four different short hairpin RNA (pSNG-xL1-4) targeting Bcl-xL in HCT 116 cells. HCT 116 pSNG-xL#1 produced a modest (30%) decrease in Bcl-xL expression whilst Bcl-2 levels were similar to the parental cell line, HCT 116 pSNG-xL#2 and 3 showed 50% decrease in Bcl-xL and stable Bcl-2. HCT 116 pSNG-xL#3 showed a concomitant decrease (50%) in Bcl-2. A decrease in Bcl-xL sensitised cells to the small molecule inhibitor of Bcl-xL, Antimycin A3 and the DNA topoisomerase I inhibitors, SN-38 and camptothecin, but not to doxorubicin. HCT 116 pSNG-xL#1 produced a moderate increase in both senescence and apoptosis and a limited increase in SN-38 induced cell death while HCT 116 pSNG-xL#2 produced an increase in apoptosis but reduced senescence. Finally, when both Bcl-xL and Bcl-2 were decreased to a similar degree (HCT 116 pSNG-xL#3), senescence was significantly increased but apoptosis was limited. This effect was confirmed in vivo after administration of irinotecan and was associated with greater anti-tumour effect. Optimal growth inhibitory effect was therefore observed when both Bcl-xL and Bcl-2 were decreased to a similar extent. Antimycin A3, in combination with SN-38 recapitulated this phenotype in HCT 116 cells, suggesting a potential role for small molecule inhibitors of Bcl-xL/Bcl-2 in the treatment of colorectal cancer, potentially in combination with irinotecan.

Formation of nitric oxide-derived oxidants by myeloperoxidase in monocytes: pathways for monocyte-mediated protein nitration and lipid peroxidation In vivo.

Protein nitration and lipid peroxidation are implicated in the pathogenesis of atherosclerosis; however, neither the cellular mediators nor the reaction pathways for these events in vivo are established. In the present study, we examined the chemical pathways available to monocytes for generating reactive nitrogen species and explored their potential contribution to the protein nitration and lipid peroxidation of biological targets. Isolated human monocytes activated in media containing physiologically relevant levels of nitrite (NO(2)(-)), a major end product of nitric oxide ((*)NO) metabolism, nitrate apolipoprotein B-100 tyrosine residues and initiate LDL lipid peroxidation. LDL nitration (assessed by gas chromatography-mass spectrometry quantification of nitrotyrosine) and lipid peroxidation (assessed by high-performance liquid chromatography with online tandem mass spectrometric quantification of distinct products) required cell activation and NO(2)(-); occurred in the presence of metal chelators, superoxide dismutase (SOD), and scavengers of hypohalous acids; and was blocked by myeloperoxidase (MPO) inhibitors and catalase. Monocytes activated in the presence of the exogenous (*)NO generator PAPA NONOate (Z-[N-(3-aminopropyl)-N-(n-propyl)amino]diazen-1-ium-1,2- diolate) promoted LDL protein nitration and lipid peroxidation by a combination of pathways. At low rates of (*)NO flux, both protein nitration and lipid peroxidation were inhibited by catalase and peroxidase inhibitors but not SOD, suggesting a role for MPO. As rates of (*)NO flux increased, both nitrotyrosine formation and 9-hydroxy-10,12-octadecadienoate/9-hydroperoxy-10,12-octadecadieno ic acid production by monocytes became insensitive to the presence of catalase or peroxidase inhibitors, but they were increasingly inhibited by SOD and methionine, suggesting a role for peroxynitrite. Collectively, these results demonstrate that monocytes use distinct mechanisms for generating (*)NO-derived oxidants, and they identify MPO as a source of nitrating intermediates in monocytes.