An outbreak of norovirus linked to oysters in Tasmania.

Norovirus is the most commonly reported virus in shellfish related gastroenteritis outbreaks. In March 2013 an investigation was conducted following the receipt of reports of gastroenteritis after the consumption of oysters at private functions in Tasmania. Cases were ascertained through general practitioners, emergency departments, media releases and self-reporting. Of the 306 cases identified in Tasmania, ten faecal specimens were collected for laboratory testing and eight were positive for norovirus (GII.g). The most common symptoms were vomiting (87%), diarrhoea (85%), myalgia (82%) and fever (56%). The implicated oysters were traced to a single lease from which they were harvested and distributed locally and interstate. Nationally 525 cases were identified from Tasmania (306), Victoria (209), New South Wales (8) and Queensland (2). This report highlights the consequences of norovirus outbreaks in shellfish, even with rapid identification, trace back and removal of the implicated product from the market.

Maternal risk-management elucidates the evolution of reproductive adaptations in sharks by means of natural selection.

Maternal investment theory is the study of how breeding females allocate resources between offspring size and brood size to achieve reproductive success. In classical trade-off models, r/K-selection and bet-hedging selection, the primary predictors of maternal investments in offspring are population density and resource stability. In crowded, stable environments, K-selected females invest in large offspring at an equivalent cost in brood size. In uncrowded, unstable environments, r-selected females invest in large broods at an equivalent cost in offspring size. In unpredictable resource environments, bet-hedging females invest moderately in brood size and offspring size. The maternal risk-management model represents a profound departure from classical trade-off models. Maternal investments in offspring size, brood size, and brood number are shaped independently by autonomous risk factors: the duration of gaps in resources during seasonal cycles, rates of predation, and unpredictable catastrophic events. To date, no single model has risen to a position of preeminence. Here in sharks, we show that maternal investments within and across species do not agree with the predictions of trade-off models and instead agree with the predictions of the maternal risk-management model. Within and across shark species, offspring size and brood size were independent maternal investment strategies. The risk of starvation favored investments in larger offspring. The risk of predation favored investments in larger broods. If empirical studies continue to confirm its predictions, maternal-risk management may yet emerge as a unifying model of diverse reproductive adaptations by means of natural selection.

Model-informed drug development of voxelotor in sickle cell disease: Population pharmacokinetics in whole blood and plasma.

Oxbryta (voxelotor) is a small-molecule inhibitor of sickle hemoglobin (Hb) polymerization approved for patients with sickle cell disease (SCD) aged greater than or equal to 12 years at a dose of 1500 mg once daily (q.d.). Voxelotor binds preferentially to Hb, and voxelotor partitioning into red blood cells is an effective predictor of Hb occupancy. The objectives of these analyses were to develop a population pharmacokinetic (PopPK) model for voxelotor in both plasma and whole blood in adults and adolescents to support the dose selection for optimal target engagement and to identify covariates that have a significant effect on voxelotor pharmacokinetics (PK) in plasma and whole blood. An integrated plasma and whole blood PopPK model with two compartments, first-order absorption and elimination, and a site-of-action effect compartment adequately described the concentration-time profiles of voxelotor in plasma and whole blood in patients treated up to 72 weeks. Covariates with significant effects on voxelotor PK included baseline blood volume on apparent volume of the central compartment and time-varying hematocrit and dose on whole blood partitioning, indicating that clinical markers of voxelotor effect can, in turn, influence its PK. Furthermore, the model confirmed that voxelotor PK in plasma and whole blood is linear with dose and time and comparable for adults and adolescents. No clinically important covariate effects on voxelotor PK that warranted dose adjustment were identified in this analysis. Overall, the PopPK analyses contributed significantly to the voxelotor label and support 1500 mg q.d. as the therapeutic dose in adults and adolescents with SCD.

Model-informed drug development of voxelotor in sickle cell disease: Exposure-response analysis to support dosing and confirm mechanism of action.

Sickle cell disease (SCD) is characterized by the production of sickle hemoglobin (HbS), which when deoxygenated, polymerizes leading to red blood cell damage and hemolytic anemia, a defining feature of SCD. Voxelotor (Oxbryta) is a small molecule inhibitor of HbS polymerization that disrupts the polymerization mechanism by binding HbS to increase HbS oxygen affinity. Voxelotor is approved in the United States for the treatment of SCD in patients greater than or equal to 12 years of age at a 1500 mg once-daily (q.d.) dose. These exposure-response analyses aimed to evaluate the relationships between voxelotor whole blood concentration and change from baseline (CFB) in clinical measures of anemia and hemolysis and between voxelotor whole blood and plasma concentrations and the incidence of selected safety end points to confirm the voxelotor mechanism of action and to support the clinical dose recommendation. In patients treated with voxelotor up to 72 weeks, CFB hemoglobin (Hb) increased linearly (p < 0.001) with increasing voxelotor concentration and percent Hb occupancy and increases in CFB Hb corresponded to improvements in measures of hemolysis. The target 1 g/dl increase in CFB Hb was achieved with 1500 mg voxelotor q.d. Significant relationships were observed between voxelotor exposures and grade greater than or equal to 1 increased alanine aminotransferase and decreased white blood cell count; however, most events were grade 1. No clinically important covariate effects on voxelotor efficacy or safety were observed. Overall, these analyses support 1500 mg q.d. as the therapeutic dose for voxelotor in adults and adolescents.

Population pharmacokinetics of rucaparib in patients with advanced ovarian cancer or other solid tumors.

PURPOSE: To develop a population pharmacokinetics (PPK) model for rucaparib, an oral poly(ADP-ribose) polymerase inhibitor. METHODS: The PPK analysis used PK data from patients in Study 1014 (NCT01009190, n = 35), Study 10 (NCT01482715, n = 123), and ARIEL2 (NCT01891344, n = 300), including intensive intravenous data (12-40 mg), intensive and sparse oral data (12-360 mg single-dose, 40-500 mg once daily, and 240-840 mg twice daily [BID]), and intensive single-dose oral data under fasted conditions and after a high-fat meal (40, 300, and 600 mg). RESULTS: Rucaparib PK was well described by a two-compartment model with sequential zero-order release and first-order absorption and first-order elimination. A high-fat meal slightly increased bioavailability at 600 mg but not at lower doses; this is not considered clinically significant, and rucaparib can be taken with or without food. Covariate effects of baseline creatinine clearance and albumin on rucaparib clearance were identified. Despite numerical increases in exposure with renal impairment, no dose adjustment is recommended for patients with mild or moderate renal impairment. No statistically significant relationships were detected for demographics, hepatic function (normal versus mild impairment), CYP1A2 and CYP2D6 phenotypes, or strong CYP1A2 or CYP2D6 inhibitors. Concomitant proton pump inhibitors showed no clinically significant effect on absorption. External validation of the model with data from ARIEL3 (NCT01968213) and TRITON2 (NCT02952534) studies showed no clinically meaningful PK differences across indications or sex. CONCLUSION: The PPK model adequately described rucaparib PK, and none of the covariates evaluated had a clinically relevant effect. CLINICALTRIALS: GOV: Study 1014 (NCT01009190), Study 10 (NCT01482715), ARIEL2 (NCT01891344), ARIEL3 (NCT01968213), and TRITON2 (NCT02952534).

Ambient urban N deposition drives increased biomass and total plant N in two native prairie grass species in the U.S. Southern Great Plains.

Remnants of native tallgrass prairie experience elevated atmospheric nitrogen (N) deposition in urban areas, with potential effects on species traits that are important for N cycling and species composition. We quantified bulk (primarily wet) inorganic N (NH4+-N + NO3--N) deposition at six sites along an urban development gradient (6-64% urban) in the Dallas-Fort Worth metropolitan area from April 2014 to October 2015. In addition, we conducted a phytometer experiment with two common native prairie bunchgrass species--one well studied (Schizachyrium scoparium) and one little studied (Nasella leucotricha)--to investigate ambient N deposition effects on plant biomass and tissue quality. Bulk inorganic N deposition ranged from 6.1-9.9 kg ha-1 yr-1, peaked in spring, and did not vary consistently with proportion of urban land within 10 km of the sites. Total (wet + dry) inorganic N deposition estimated using bulk deposition measured in this study and modeled dry deposition was 12.9-18.2 kg ha-1 yr-1. Although the two plant species studied differ in photosynthetic pathway, biomass, and tissue N, they exhibited a maximum 2-3-fold and 2-4-fold increase in total biomass and total plant N, respectively, with 1.6-fold higher bulk N deposition. In addition, our findings indicate that while native prairie grasses may exhibit a positive biomass response to increased N deposition up to ~18 kg ha-1 yr-1, total inorganic N deposition is well above the estimated critical load for herbaceous plant species richness in the tallgrass prairie of the Great Plains ecoregion and thus may negatively affect these plant communities.

There's a frog in my salad! A review of online media coverage for wild vertebrates found in prepackaged produce in the United States.

Prepackaged leafy green vegetables represent one of the fastest growing segments of the fresh-produce industry in the United States. Several steps in the production process have been mechanized to meet the downstream demand for prebagged lettuces. The growth in this market, however, has come with drawbacks, and chief among them are consumers finding wild animals in prepackaged crops. These incidents may signal an overburdened produce supply chain, but we currently lack the information needed to determine if this is a food-safety problem or food-quality concern. Here, we address this gap by reviewing online media coverage of wild vertebrates found in prepackaged produce items by customers in the United States. We discovered 40 independent incidents since 2003 with 95% having occurred during 2008-2018, suggesting that the frequency of incidents may have increased during the last decade. The minority of incidents included wild animals found in organic produce (27.5%), whereas the majority involved conventionally grown crops (72.5%). Most incidents involved amphibians (52.5%) and reptiles (22.5%), while fewer contained mammals (17.5%) and birds (7.5%). Frogs and toads made up all of the amphibian-related incidents, with more than 60% comprising small-bodied treefrogs found in various types of fresh leafy greens. At least seven incidents involved Pacific Treefrogs (Hyliola regilla) and three comprised Green Anoles (Anolis carolinensis). One lizard and nine frogs were found alive, and at least two frogs were released into non-native areas. This is the first review quantifying incidents of vertebrates found by customers in prepackaged produce, yet it remains unclear whether these occurrences indicate a food-safety crisis or a complaint against food quality. Nevertheless, wild animals can spread diseases to humans via contaminated produce, therefore we contend that industry professionals can reduce the potential health risk to their consumers and negative economic consequences to themselves through increased attention to this matter.

Ceftazidime-Avibactam Population Pharmacokinetic Modeling and Pharmacodynamic Target Attainment Across Adult Indications and Patient Subgroups.

Ceftazidime-avibactam is a novel ß-lactam/ß-lactamase inhibitor combination for the treatment of serious infections caused by resistant gram-negative pathogens. Population pharmacokinetic (PopPK) models were built to incorporate pharmacokinetic (PK) data from five phase III trials in patients with complicated intra-abdominal infection (cIAI), complicated urinary tract infection (cUTI), or nosocomial (including ventilator-associated) pneumonia. Ceftazidime and avibactam pharmacokinetics were well-described by two-compartment disposition models, with creatinine clearance (CrCL) the key covariate determining clearance variability. Steady-state ceftazidime and avibactam exposure for most patient subgroups differed by ≤ 20% vs. healthy volunteers. Probability of PK/pharmacodynamic (PD) target attainment (free plasma ceftazidime > 8 mg/L and avibactam > 1 mg/L for ≥ 50% of dosing interval) was ≥ 94.9% in simulations for all patient subgroups, including indication and renal function categories. No exposure-microbiological response relationship was identified because target exposures were achieved in almost all patients. These modeling results support the approved ceftazidime-avibactam dosage regimens (2000-500 mg every 8 hours, adjusted for CrCL ≤ 50 mL/min).

Using genome-context data to identify specific types of functional associations in pathway/genome databases.

BACKGROUND: Hundreds of genes lacking homology to any protein of known function are sequenced every day. Genome-context methods have proved useful in providing clues about functional annotations for many proteins. However, genome-context methods detect many biological types of functional associations, and do not identify which type of functional association they have found. RESULTS: We have developed two new genome-context-based algorithms. Algorithm 1 extends our previous algorithm for identifying missing enzymes in predicted metabolic pathways (pathway holes) to use genome-context features. The new algorithm has significantly improved scope because it can now be applied to pathway reactions to which sequence similarity methods cannot be applied due to an absence of known sequences for enzymes catalyzing the reaction in other organisms. The new method identifies at least one known enzyme in the top ten hits for 58% of EcoCyc reactions that lack enzyme sequences in other organisms. Surprisingly, the addition of genome-context features does not improve the accuracy of the algorithm when sequences for the enzyme do exist in other organisms. Algorithm 2 uses genome-context methods to predict three distinct types of functional relationships between pairs of proteins: pairs that occur in the same protein complex, the same pathway, or the same operon. This algorithm performs with varying degrees of accuracy on each type of relationship, and performs best in predicting pathway and protein complex relationships.

Influence of the geographic distribution of prion protein gene sequence variation on patterns of chronic wasting disease spread in white-tailed deer (Odocoileus virginianus).

Managing and controlling the spread of diseases in wild animal populations is challenging, especially for social and mobile species. Effective management benefits from information about disease susceptibility, allowing limited resources to be focused on areas or populations with a higher risk of infection. Chronic wasting disease (CWD), a transmissible spongiform encephalopathy that affects cervids, was detected in Colorado in the late 1960s. CWD was detected in Illinois and Wisconsin in 2002 and has since spread through many counties. Specific nucleotide variations in the prion protein gene (PRNP) sequence have been associated with reduced susceptibility to CWD in white-tailed deer. Though genetic resistance is incomplete, the frequency of deer possessing these mutations in a population is an important factor in disease spread (i.e. herd immunity). In this study we sequenced 625 bp of the PRNP gene from a sampling of 2433 deer from Illinois and Wisconsin. In north-central Illinois where CWD was first detected, counties had a low frequency of protective haplotypes (frequency <0.20); whereas in northwestern Illinois counties, where CWD cases have only more recently been detected, the frequency of protective haplotypes (frequency >0.30) was much higher (p < 0.05). Protective haplotype frequencies varied significantly among infected and uninfected geographic areas. The frequency of protective PRNP haplotypes may contribute to population level susceptibility and may shape the way CWD has spread through Illinois. Analysis of PRNP haplotype distribution could be a useful tool to assess CWD risk and allocate resources to contain and reduce the spread of infection.

Exodus! Large-scale displacement and social adjustments of resident Atlantic spotted dolphins (Stenella frontalis) in the Bahamas.

Over the last 20 years, significant habitat shifts have been documented in some populations of cetaceans. On Little Bahama Bank (LBB) there are sympatric communities of resident Atlantic spotted dolphins (Stenella frontalis) and bottlenose dolphins (Tursiops truncatus), monitored since 1985. The size and social structure (three clusters: Northern, Central, Southern) have been stable among the spotted dolphin community with little immigration/emigration, even after large demographic losses (36%) following two major hurricanes in 2004. In 2013 an unprecedented exodus of over 50% (52 individuals) of the spotted dolphin community was documented. The entire Central cluster and a few Northern and Southern individuals relocated 161 km south to Great Bahama Bank (GBB), also home to two sympatric resident communities of spotted dolphins and bottlenose dolphins. During the late summer of 2013 and the summers of 2014 and 2015 both sites were regularly monitored but no former LBB dolphins returned to LBB. Uncharacteristic matriline splits were observed. Social analyses revealed random associations for those spotted dolphins and very little integration between spotted dolphins that moved to GBB (MGBB) and those dolphin resident to GBB (RGBB). Male alliances among spotted dolphins were present, with some altered patterns. On LBB, the operational sex ratio (OSR) was reduced (.40 to .25). OSR for MGBB and RGBB dolphins were similar (.45 and .43). A significant steady decrease in sea surface temperature and chlorophyll a (a proxy for plankton production) occurred on LBB leading up to this exodus. Similar trends were not present over the same period on GBB. The sudden large-scale shift of spotted dolphins from LBB to GBB in association with the gradual decline in certain environmental factors suggests that a possible "tipping point" was reached in prey availability. This study provides a unique view into social and genetic implications of large-scale displacement of stable dolphin communities.

Reproductive characteristics of female white-tailed deer (Odocoileus virginianus) in the Midwestern USA.

Knowledge of reproductive characteristics of wild populations is necessary to inform responsible management decisions that promote herd health. As management, goals, and free-ranging populations change over time and landscapes, updated knowledge of reproductive characteristics are needed to inform responsible management practices. We estimated reproductive characteristics of female white-tailed deer in Illinois, including pregnancy rate, litter size, fetal growth and fetal sex ratio. We found maternal age to have an important influence on several reproductive factors. Approximately 66% of tested females (n = 3884) were pregnant and pregnancy rates increased with increasing maternal age, from 20.5% in fawns to 85.8% in adult deer. Litter size ranged from 1 to 5 fetuses per pregnant female. The average litter size was 1.9 ± 0.54 fetuses per pregnant female and also increased with age, from 1.2 in fawns to 2.0 in adults, respectively. Breeding season peaked in November with the mean estimated conception dates of fetuses varying with maternal age. Fawns conceived fetuses later in the breeding season (December 2) compared to yearlings and adults (November 11 and 8, respectively). We measured the body mass index (BMI) of all fetuses and found that litter size and female age influence fetal size. We found no bias in fetal sex ratio (average 1.0:1.0, male:female) but we observed a sex bias in fetal size (mean BMI male = 0.71, female 0.67) across all maternal age classes. A comparison of the current study and previous reports indicate that variation in maternal age within a population is an important driver of reproductive metrics, likely because maternal age and body size or condition are related. Furthermore, variation in resource availability will influence reproductive rates, especially among fawn females.

Clay content and pH: soil characteristic associations with the persistent presence of chronic wasting disease in northern Illinois.

Environmental reservoirs are important to infectious disease transmission and persistence, but empirical analyses are relatively few. The natural environment is a reservoir for prions that cause chronic wasting disease (CWD) and influences the risk of transmission to susceptible cervids. Soil is one environmental component demonstrated to affect prion infectivity and persistence. Here we provide the first landscape predictive model for CWD based solely on soil characteristics. We built a boosted regression tree model to predict the probability of the persistent presence of CWD in a region of northern Illinois using CWD surveillance in deer and soils data. We evaluated the outcome for possible pathways by which soil characteristics may increase the probability of CWD transmission via environmental contamination. Soil clay content and pH were the most important predictive soil characteristics of the persistent presence of CWD. The results suggest that exposure to prions in the environment is greater where percent clay is less than 18% and soil pH is greater than 6.6. These characteristics could alter availability of prions immobilized in soil and contribute to the environmental risk factors involved in the epidemiological complexity of CWD infection in natural populations of white-tailed deer.

Molecular assessment of mating strategies in a population of Atlantic spotted dolphins.

Similar to other small cetacean species, Atlantic spotted dolphins (Stenella frontalis) have been the object of concentrated behavioral study. Although mating and courtship behaviors occur often and the social structure of the population is well-studied, the genetic mating system of the species is unknown. To assess the genetic mating system, we genotyped females and their progeny at ten microsatellite loci. Genotype analysis provided estimates of the minimum number of male sires necessary to account for the allelic diversity observed among the progeny. Using the estimates of male sires, we determined whether females mated with the same or different males during independent estrus events. Using Gerud2.0, a minimum of two males was necessary to account for the genetic variation seen among progeny arrays of all tested females. ML-Relate assigned the most likely relationship between offspring pairs; half or full sibling. Relationship analysis supported the conservative male estimates of Gerud2.0 but in some cases, half or full sibling relationships between offspring could not be fully resolved. Integrating the results from Gerud2.0, ML-Relate with previous observational and paternity data, we constructed two-, three-, and four-male pedigree models for each genotyped female. Because increased genetic diversity of offspring may explain multi-male mating, we assessed the internal genetic relatedness of each offspring's genotype to determine whether parent pairs of offspring were closely related. We found varying levels of internal relatedness ranging from unrelated to closely related (range -0.136-0.321). Because there are several hypothesized explanations for multi-male mating, we assessed our data to determine the most plausible explanation for multi-male mating in our study system. Our study indicated females may benefit from mating with multiple males by passing genes for long-term viability to their young.

Prion protein gene sequence and chronic wasting disease susceptibility in white-tailed deer (Odocoileus virginianus).

The sequence of the prion protein gene (PRNP) affects susceptibility to spongiform encephalopathies, or prion diseases in many species. In white-tailed deer, both coding and non-coding single nucleotide polymorphisms have been identified in this gene that correlate to chronic wasting disease (CWD) susceptibility. Previous studies examined individual nucleotide or amino acid mutations; here we examine all nucleotide polymorphisms and their combined effects on CWD. A 626 bp region of PRNP was examined from 703 free-ranging white-tailed deer. Deer were sampled between 2002 and 2010 by hunter harvest or government culling in Illinois and Wisconsin. Fourteen variable nucleotide positions were identified (4 new and 10 previously reported). We identified 68 diplotypes comprised of 24 predicted haplotypes, with the most common diplotype occurring in 123 individuals. Diplotypes that were found exclusively among positive or negative animals were rare, each occurring in less than 1% of the deer studied. Only one haplotype (C, odds ratio 0.240) and 2 diplotypes (AC and BC, odds ratios of 0.161 and 0.108 respectively) has significant associations with CWD resistance. Each contains mutations (one synonymous nucleotide 555C/T and one nonsynonymous nucleotide 286G/A) at positions reported to be significantly associated with reduced CWD susceptibility. Results suggest that deer populations with higher frequencies of haplotype C or diplotypes AC and BC might have a reduced risk for CWD infection--while populations with lower frequencies may have higher risk for infection. Understanding the genetic basis of CWD has improved our ability to assess herd susceptibility and direct management efforts within CWD infected areas.

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.

BACKGROUND: The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to assign function to 40-60% of sequences. In addition, large numbers of sequences may have non-specific annotations (e.g., thiolase family protein). Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. RESULTS: We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. Our algorithm emulates the manual sequence annotation process, considering not only evidence from homology searches, but also considering evidence from genomic context (i.e., is the gene part of an operon?) and functional context (e.g., are there functionally-related genes nearby in the genome?) to determine the posterior belief that a candidate has the required function. The method can be applied across an entire metabolic pathway network and is generally applicable to any pathway database. The program uses a set of sequences encoding the required activity in other genomes to identify candidate proteins in the genome of interest, and then evaluates each candidate by using a simple Bayes classifier to determine the probability that the candidate has the desired function. We achieved 71% precision at a probability threshold of 0.9 during cross-validation using known reactions in computationally-predicted pathway databases. After applying our method to 513 pathway holes in 333 pathways from three Pathway/Genome databases, we increased the number of complete pathways by 42%. We made putative assignments to 46% of the holes, including annotation of 17 sequences of previously unknown function. CONCLUSIONS: Our pathway hole filler can be used not only to increase the utility of Pathway/Genome databases to both experimental and computational researchers, but also to improve predictions of protein function.

The importance of localized culling in stabilizing chronic wasting disease prevalence in white-tailed deer populations.

Strategies to contain the spread of disease often are developed with incomplete knowledge of the possible outcomes but are intended to minimize the risks associated with delaying control. Culling of game species by government agencies is one approach to control disease in wild populations but is unpopular with hunters and wildlife enthusiasts, politically unpalatable, and erodes public support for agencies responsible for wildlife management. We addressed the functional differences between hunting and government culling programs for managing chronic wasting disease (CWD) in white-tailed deer by comparing prevalence over a 10-year period in Illinois and Wisconsin. When both Illinois and Wisconsin were actively culling from 2003 - 2007, there were no statistical differences between state CWD prevalence estimates. Wisconsin government culling concluded in 2007 and average prevalence over the next five years was 3.09 ± 1.13% with an average annual increase of 0.63%. During that same time period, Illinois continued government culling and there was no change in prevalence throughout Illinois. Despite its unpopularity among hunters, localized culling is a disease management strategy that can maintain low disease prevalence while minimizing impacts on recreational deer harvest.

Computational prediction of human metabolic pathways from the complete human genome.

BACKGROUND: We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary first step toward quantitative modeling of metabolism. RESULTS: Our analysis assigns 2,709 human enzymes to 896 bioreactions; 622 of the enzymes are assigned roles in 135 predicted metabolic pathways. The predicted pathways closely match the known nutritional requirements of humans. This analysis identifies probable omissions in the human genome annotation in the form of 203 pathway holes (missing enzymes within the predicted pathways). We have identified putative genes to fill 25 of these holes. The predicted human metabolic map is described by a Pathway/Genome Database called HumanCyc, which is available at http://HumanCyc.org/. We describe the generation of HumanCyc, and present an analysis of the human metabolic map. For example, we compare the predicted human metabolic pathway complement to the pathways of Escherichia coli and Arabidopsis thaliana and identify 35 pathways that are shared among all three organisms. CONCLUSIONS: Our analysis elucidates a significant portion of the human metabolic map, and also indicates probable unidentified genes in the genome. HumanCyc provides a genome-based view of human nutrition that associates the essential dietary requirements of humans with a set of metabolic pathways whose existence is supported by the human genome. The database places many human genes in a pathway context, thereby facilitating analysis of gene expression, proteomics, and metabolomics datasets through a publicly available online tool called the Omics Viewer.

A multidomain TIGR/olfactomedin protein family with conserved structural similarity in the N-terminal region and conserved motifs in the C-terminal region.

Based on the similarity between the TIGR (trabecular-meshwork inducible glucocorticoid response) (also known as myocilin) and olfactomedin protein families identified throughout the length of the TIGR protein, we have identified more distantly related proteins to determine the elements essential to the function/structure of the TIGR and olfactomedin proteins. Using a sequence walk method and the Shotgun program, we have identified a family including 31 olfactomedin domain-containing sequences. Multiple sequence alignments and secondary structure analyses were used to identify conserved sequence elements. Pairwise identity in the olfactomedin domain ranges from 8 to 64%, with an average pairwise identity of 24%. The N-terminal regions of the proteins fall into two subgroups, one including the TIGR and olfactomedin families and another group of apparently unrelated domains. The TIGR and olfactomedin sequences display conserved motifs including a residual leucine zipper region and maintain a similar secondary structure throughout the N-terminal region. The correlation between conserved elements and disease-associated mutations and apparent polymorphisms in human TIGR was also examined to evaluate the apparent importance of conserved residues to the function/structure of TIGR. Several residues have been identified as essential to the function and/or structure of the human TIGR protein based on their degree of conservation across the family and their implication in the pathogenesis of primary open-angle glaucoma. Additionally, we have identified a group of chitinase sequences containing several of the highly conserved motifs present in the C-terminal region of the olfactomedin domain-containing sequences.