Half of US population exposed to adverse lead levels in early childhood.

SignificanceConsiderable effort is expended to protect today's children from lead exposure, but there is little evidence on the harms past lead exposures continue to hold for yesterday's children, who are victims of what we term legacy lead exposures. We estimate that over 170 million Americans alive today were exposed to high-lead levels in early childhood, several million of whom were exposed to five-plus times the current reference level. Our estimates allow future work to plan for the health needs of these Americans and to inform estimation of the true contributions of lead exposure to population health. We estimate population-level effects on IQ loss and find that lead is responsible for the loss of 824,097,690 IQ points as of 2015.

Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments.

Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak. IMPORTANCE: Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.

Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer.

Gene fusions are common cancer-causing mutations, but the molecular principles by which fusion protein products affect interaction networks and cause disease are not well understood. Here, we perform an integrative analysis of the structural, interactomic, and regulatory properties of thousands of putative fusion proteins. We demonstrate that genes that form fusions (i.e., parent genes) tend to be highly connected hub genes, whose protein products are enriched in structured and disordered interaction-mediating features. Fusion often results in the loss of these parental features and the depletion of regulatory sites such as post-translational modifications. Fusion products disproportionately connect proteins that did not previously interact in the protein interaction network. In this manner, fusion products can escape cellular regulation and constitutively rewire protein interaction networks. We suggest that the deregulation of central, interaction-prone proteins may represent a widespread mechanism by which fusion proteins alter the topology of cellular signaling pathways and promote cancer.

Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4.

Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.

A "Goldilocks zone" for mind-wandering reports? A secondary data analysis of how few thought probes are enough for reliable and valid measurement.

Mind-wandering assessment relies heavily on the thought probe technique as a reliable and valid method to assess momentary task-unrelated thought (TUT), but there is little guidance available to help researchers decide how many probes to include within a task. Too few probes may lead to unreliable measurement, but too many probes might artificially disrupt normal thought flow and produce reactive effects. Is there a "Goldilocks zone" for how few thought probes can be used to reliably and validly assess individual differences in mind-wandering propensity? We address this question by reanalyzing two published datasets (Study 1, n = 541; Study 2, ns ≈ 260 per condition) in which thought probes were presented in multiple tasks. Our primary analyses randomly sampled probes in increments of two for each subject in each task. A series of confirmatory factor analyses for each probe "bin" size tested whether the latent correlations between TUT rate and theoretically relevant constructs like working memory capacity, attention-control ability, disorganized schizotypy, and retrospective self-reported mind wandering changed as more probes assessed the TUT rate. TUT rates were remarkably similar across increasing probe-bin sizes and zero-order correlations within and between tasks stabilized at 8-10 probes; moreover, TUT-rate correlations with other latent variables stabilized at about 8 thought probes. Our provisional recommendation (with caveats) is that researchers may use as few as 8 thought probes in prototypical cognitive tasks to gain reliable and valid information about individual differences in TUT rate.

Risk of Severe COVID-19 Disease and the Pandemic's Impact on Service Utilization Among a Longitudinal Cohort of Persons with HIV-Washington, DC.

People with HIV (PWH) have a high burden of medical comorbidities, potentially putting them at increased risk for severe COVID-19. Additionally, during the COVID-19 pandemic, HIV care delivery has been restructured and the impact on HIV outcomes is unknown. The objectives of this study were first, to examine the risk of severe COVID-19 among PWH, using a definition incorporating clinical risk factors, and second, to examine the pandemic's impact on HIV care. We used data from the DC Cohort, a large cohort of people receiving HIV care in Washington, DC. We found that a high proportion of participants across all age groups qualified as increased (58%) or high risk (34%) for severe COVID-19. Between 2019 and 2020, encounters increased (17.7%, increasing to 23.5% of active DC Cohort participants had an encounter) while laboratory utilization decreased (14.4%, decreasing to 11.4% of active DC Cohort participants had an HIV RNA test performed). Implications of our work include the importance of protecting vulnerable people with HIV from acquiring COVID-19 and potentially manifesting severe complications through strategies including vaccination. Additionally, acknowledging that HIV service delivery will likely be changed long-term by the pandemic, adaptation is required to ensure continued progress towards 90-90-90 goals.

Toxicity analysis of busulfan pharmacokinetic therapeutic dose monitoring.

Busulfan-based conditioning regimens are associated with serious toxicities and literature reports increased risk of toxicities when daily area under the curve concentrations exceed 6000 µM-minute. We implemented real time pharmacokinetic-guided therapeutic drug monitoring of busulfan for myeloablative conditioning regimens. The objective was to compare toxicity of intravenous busulfan before and after therapeutic drug monitoring implementation. The primary endpoint was incidence of hepatotoxicity. Medical records were retrospectively reviewed with weight-based dose Busulfan/Cyclophosphamide (BuCy) conditioning from August 2017 through March 2018 (N = 14) and therapeutic drug monitoring from April 2018 through December 2018 (N = 22). Recipients of busulfan therapeutic drug monitoring were younger than those receiving weight-based dose (median: 45 vs. 58 years, p = 0.008). No other baseline differences were observed. There was no difference in hepatotoxicity between therapeutic drug monitoring and weight-based dose (median 1 vs. 0 days, p = 0.40). In the therapeutic drug monitoring group, 45% of patients had increases and 41% had decreases in busulfan dose after Bu1. Repeat pharmacokinetic after Bu2 were required in 32% of patients. A pharmacokinetic dose monitoring program for myeloablative conditioning intravenous busulfan regimens may be considered a safe practice in stem cell transplant recipients. The majority of patients receiving pharmacokinetic-guided therapeutic drug monitoring required dose changes and therapeutic drug monitoring patients had no significant difference in toxicity compared to those receiving weight-based dose.

COVID-19 mRNA Vaccination Generates Greater Immunoglobulin G Levels in Women Compared to Men.

We investigated whether the antibody response to coronavirus disease 2019 (COVID-19) mRNA vaccination is similar in women and men. In a community cohort without prior COVID-19, first vaccine dose produced higher immunoglobulin G (IgG) levels and percent inhibition of spike-ACE2 receptor binding, a surrogate measure of virus neutralization, in women compared to men (7.0 µg/mL, 51.6% vs 3.3 µg/mL, 36.4%). After 2 doses, IgG levels remained significantly higher for women (30.4 µg/mL) compared to men (20.6 µg/mL), while percent inhibition was similar (98.4% vs 97.7%). Sex-specific antibody response to mRNA vaccination informs future efforts to understand vaccine protection and side effects.

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

Here, we present a major update to the SUPERFAMILY database and the webserver. We describe the addition of new SUPERFAMILY 2.0 profile HMM library containing a total of 27 623 HMMs. The database now includes Superfamily domain annotations for millions of protein sequences taken from the Universal Protein Recourse Knowledgebase (UniProtKB) and the National Center for Biotechnology Information (NCBI). This addition constitutes about 51 and 45 million distinct protein sequences obtained from UniProtKB and NCBI respectively. Currently, the database contains annotations for 63 244 and 102 151 complete genomes taken from UniProtKB and NCBI respectively. The current sequence collection and genome update is the biggest so far in the history of SUPERFAMILY updates. In order to the deal with the massive wealth of information, here we introduce a new SUPERFAMILY 2.0 webserver (http://supfam.org). Currently, the webserver mainly focuses on the search, retrieval and display of Superfamily annotation for the entire sequence and genome collection in the database.

Testing the attention-distractibility trait.

Forster and Lavie (Journal of Experimental Psychology: Learning, Memory, and Cognition, 40[1], 251-260, 2014; Psychological Science, 27[2], 203-212, 2016) found that task-irrelevant distraction correlated positively with a measure of mind-wandering and a report of attention-deficit/hyperactivity disorder (ADHD) symptomology. Based primarily on these results, Forster and Lavie claimed to establish an attention-distractibility trait. Here, I tested whether these associations could be distinguished from associations with working memory capacity and task-relevant distraction (measured with an antisaccade task). With data collected from 226 subjects (ns differ among analyses), the results from the current study suggest that the measures of task-irrelevant distraction and working memory capacity were not (or only very weakly) associated with measures of mind wandering (measured both with a stand-alone questionnaire and in-task thought probes) and ADHD symptomology. Task-relevant interference (i.e., antisaccade accuracy) was associated with mind-wandering reports from in-task thought probes (presented in a separate task), but not the stand-alone mind wandering questionnaire or ADHD symptomology. Additionally, the measure of irrelevant-distraction exhibited low internal consistency suggesting that (as measured) it may not be a suitable individual difference measure. [Preregistration, data, analysis scripts and output are available via the Open Science Framework: https://osf.io/bhs24/ ].

Testing the construct validity of competing measurement approaches to probed mind-wandering reports.

Psychology faces a measurement crisis, and mind-wandering research is not immune. The present study explored the construct validity of probed mind-wandering reports (i.e., reports of task-unrelated thought [TUT]) with a combined experimental and individual-differences approach. We examined laboratory data from over 1000 undergraduates at two U.S. institutions, who responded to one of four different thought-probe types across two cognitive tasks. We asked a fundamental measurement question: Do different probe types yield different results, either in terms of average reports (average TUT rates, TUT-report confidence ratings), or in terms of TUT-report associations, such as TUT rate or confidence stability across tasks, or between TUT reports and other consciousness-related constructs (retrospective mind-wandering ratings, executive-control performance, and broad questionnaire trait assessments of distractibility-restlessness and positive-constructive daydreaming)? Our primary analyses compared probes that asked subjects to report on different dimensions of experience: TUT-content probes asked about what they'd been mind-wandering about, TUT-intentionality probes asked about why they were mind-wandering, and TUT-depth probes asked about the extent (on a rating scale) of their mind-wandering. Our secondary analyses compared thought-content probes that did versus didn't offer an option to report performance-evaluative thoughts. Our findings provide some "good news"-that some mind-wandering findings are robust across probing methods-and some "bad news"-that some findings are not robust across methods and that some commonly used probing methods may not tell us what we think they do. Our results lead us to provisionally recommend content-report probes rather than intentionality- or depth-report probes for most mind-wandering research.

Therapeutic Dose Monitoring of Busulfan Is Associated with Reduced Risk of Relapse in Non-Hodgkin Lymphoma Patients Undergoing Autologous Stem Cell Transplantation.

Optimal administration of busulfan (Bu) is hampered by variable and unpredictable drug metabolism in individual patients. At our institution, Bu was previously administered with fixed weight-based dosing (WBD) in combination with cyclophosphamide (Cy) and etoposide (E) for patients with non-Hodgkin lymphoma (NHL) undergoing autologous stem cell transplantation (ASCT). In 2014, we adopted real-time pharmacokinetic (PK)-guided therapeutic drug monitoring (TDM) of Bu for all NHL patients undergoing Bu-containing ASCT. Here we compare outcomes of NHL patients who underwent ASCT with Bu/Cy/E using WBD and those who did so using TDM of Bu. We studied 336 consecutive adult NHL patients who underwent ASCT with Bu/Cy/E using WBD from January 2007 to December 2013 (n = 258) or TDM from May 2014 to December 2017 (n = 78), excluding patients with mantle cell lymphoma. Clinical outcomes, including relapse, nonrelapse mortality (NRM), progression-free survival (PFS), and overall survival (OS), hepatotoxicity and pulmonary toxicity were compared in the 2 groups. To adjust for differences in baseline characteristics between the groups, propensity-matched cohorts of WBD and TDM patients were also studied. After the first dose of Bu, the dose was increased in 36% of the patients and decreased in 41%. Changes in pulmonary and liver function from baseline to transplantation were not different between the 2 groups, although these changes showed significantly less variability with TDM than with WBD. Relapse was significantly lower and PFS was improved with TDM; 2-year estimates were 19% for TDM and 38% for WBD for relapse (P = .004) and 69% and 55%, respectively, for PFS (P = .038). No significant between-group differences in NRM or OS were seen. In multivariable analysis, TDM remained prognostic for lower risk of relapse (hazard ratio [HR], .52; 95% confidence interval [CI], .30 to .89; P = .018), but did not remain prognostic for PFS (HR, .74; 95% CI, .48 to 1.16; P = .19). Propensity-matched cohorts displayed similar patterns of outcomes. In subset analysis based on disease status at ASCT, TDM was associated with less relapse and better PFS than WBD for patients who underwent transplantation in less than complete remission (CR) compared with those who underwent transplantation in CR. Compared with WBD, PK-directed TDM of Bu reduces the incidence of relapse when used in combination with Cy and E for patients with NHL undergoing ASCT, particularly for patients in less than CR. These data support the continued use of personalized PK-guided dosing for all NHL patients undergoing ASCT with Bu-containing preparative regimens.

An individual differences investigation of the relations among life event stress, working memory capacity, and mind wandering: A preregistered replication-extension study.

Klein and Boals (2001a, Applied Cognitive Psychology, 15[5], 565-579, Experiments 1 and 2) found that working memory capacity correlated negatively with perceived negative life event stress and speculated the relation may be driven by thoughts produced from these experiences. Here, we sought to replicate the association between working memory capacity and perceived negative life experience and to assess potential mediators of this association such as mind wandering propensity, rumination propensity, and the sum of negatively valenced mind wandering reports. In this preregistered replication and extension study, with data collected from 356 subjects (ns differ among analyses), we found no evidence suggesting that perceived negative life stress is associated with working memory capacity. Additionally, we found evidence consistent with the claim that negatively valenced mind wandering is uniquely detrimental to cognitive task performance, but we highlight a potential confound that may account for this association that should be addressed in future work.

Is There a Positive Association Between Working Memory Capacity and Mind Wandering in a Low-Demand Breathing Task? A Preregistered Replication of a Study by Levinson, Smallwood, and Davidson (2012).

Levinson, Smallwood, and Davidson (2012, Experiment 2) found that working memory capacity (WMC) correlated positively with mind-wandering rates measured by thought probes in a breath-awareness task but was unassociated with the tendency to self-catch mind wandering. Here, I sought to replicate the associations between mind wandering and WMC in Levinson et al.'s breath-awareness task. The data from the current study, collected from 315 subjects ( ns differed among analyses) and two measures of WMC, suggest that if WMC correlates with probe-caught mind wandering, the association is most likely negative. In addition, the evidence regarding self-caught mind wandering is consistent with that found by Levinson et al. for the sum of self-caught responses, but when self-caught responses were considered in proportion to probe-caught mind wandering, modest evidence was found for a positive association with WMC.

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity.

Of the three classes of enzymes involved in ubiquitination, ubiquitin-conjugating enzymes (E2) have been often incorrectly considered to play merely an auxiliary role in the process, and few E2 enzymes have been investigated in plants. To reveal the role of E2 in plant innate immunity, we identified and cloned 40 tomato genes encoding ubiquitin E2 proteins. Thioester assays indicated that the majority of the genes encode enzymatically active E2. Phylogenetic analysis classified the 40 tomato E2 enzymes into 13 groups, of which members of group III were found to interact and act specifically with AvrPtoB, a Pseudomonas syringae pv tomato effector that uses its ubiquitin ligase (E3) activity to suppress host immunity. Knocking down the expression of group III E2 genes in Nicotiana benthamiana diminished the AvrPtoB-promoted degradation of the Fen kinase and the AvrPtoB suppression of host immunity-associated programmed cell death. Importantly, silencing group III E2 genes also resulted in reduced pattern-triggered immunity (PTI). By contrast, programmed cell death induced by several effector-triggered immunity elicitors was not affected on group III-silenced plants. Functional characterization suggested redundancy among group III members for their role in the suppression of plant immunity by AvrPtoB and in PTI and identified UBIQUITIN-CONJUGATING11 (UBC11), UBC28, UBC29, UBC39, and UBC40 as playing a more significant role in PTI than other group III members. Our work builds a foundation for the further characterization of E2s in plant immunity and reveals that AvrPtoB has evolved a strategy for suppressing host immunity that is difficult for the plant to thwart.

The genome of Aiptasia, a sea anemone model for coral symbiosis.

The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal-algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal-algal pair also with its prokaryotic microbiome.

Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures.

The proper development of neuronal circuits during neuromorphogenesis and neuronal-network formation is critically dependent on a coordinated and intricate series of molecular and cellular cues and responses. Although the cortical actin cytoskeleton is known to play a key role in neuromorphogenesis, relatively little is known about the specific molecules important for this process. Using linkage analysis and whole-exome sequencing on samples from families from the Amish community of Ohio, we have demonstrated that mutations in KPTN, encoding kaptin, cause a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures. Our immunofluorescence analyses in primary neuronal cell cultures showed that endogenous and GFP-tagged kaptin associates with dynamic actin cytoskeletal structures and that this association is lost upon introduction of the identified mutations. Taken together, our studies have identified kaptin alterations responsible for macrocephaly and neurodevelopmental delay and define kaptin as a molecule crucial for normal human neuromorphogenesis.

For Whom the Mind Wanders, and When, Varies Across Laboratory and Daily-Life Settings.

Undergraduates ( N = 274) participated in a weeklong daily-life experience-sampling study of mind wandering after being assessed in the lab for executive-control abilities (working memory capacity; attention-restraint ability; attention-constraint ability; and propensity for task-unrelated thoughts, or TUTs) and personality traits. Eight times a day, electronic devices prompted subjects to report on their current thoughts and context. Working memory capacity and attention abilities predicted subjects' TUT rates in the lab, but predicted the frequency of daily-life mind wandering only as a function of subjects' momentary attempts to concentrate. This pattern replicates prior daily-life findings but conflicts with laboratory findings. Results for personality factors also revealed different associations in the lab and daily life: Only neuroticism predicted TUT rate in the lab, but only openness predicted mind-wandering rate in daily life (both predicted the content of daily-life mind wandering). Cognitive and personality factors also predicted dimensions of everyday thought other than mind wandering, such as subjective judgments of controllability of thought. Mind wandering in people's daily environments and TUTs during controlled and artificial laboratory tasks have different correlates (and perhaps causes). Thus, mind-wandering theories based solely on lab phenomena may be incomplete.

Splice junctions are constrained by protein disorder.

We have discovered that positions of splice junctions in genes are constrained by the tolerance for disorder-promoting amino acids in the translated protein region. It is known that efficient splicing requires nucleotide bias at the splice junction; the preferred usage produces a distribution of amino acids that is disorder-promoting. We observe that efficiency of splicing, as seen in the amino-acid distribution, is not compromised to accommodate globular structure. Thus we infer that it is the positions of splice junctions in the gene that must be under constraint by the local protein environment. Examining exonic splicing enhancers found near the splice junction in the gene, reveals that these (short DNA motifs) are more prevalent in exons that encode disordered protein regions than exons encoding structured regions. Thus we also conclude that local protein features constrain efficient splicing more in structure than in disorder.

The SUPERFAMILY 1.75 database in 2014: a doubling of data.

We present updates to the SUPERFAMILY 1.75 (http://supfam.org) online resource and protein sequence collection. The hidden Markov model library that provides sequence homology to SCOP structural domains remains unchanged at version 1.75. In the last 4 years SUPERFAMILY has more than doubled its holding of curated complete proteomes over all cellular life, from 1400 proteomes reported previously in 2010 up to 3258 at present. Outside of the main sequence collection, SUPERFAMILY continues to provide domain annotation for sequences provided by other resources such as: UniProt, Ensembl, PDB, much of JGI Phytozome and selected subcollections of NCBI RefSeq. Despite this growth in data volume, SUPERFAMILY now provides users with an expanded and daily updated phylogenetic tree of life (sTOL). This tree is built with genomic-scale domain annotation data as before, but constantly updated when new species are introduced to the sequence library. Our Gene Ontology and other functional and phenotypic annotations previously reported have stood up to critical assessment by the function prediction community. We have now introduced these data in an integrated manner online at the level of an individual sequence, and--in the case of whole genomes--with enrichment analysis against a taxonomically defined background.