Initial Mapping of the New York City Wastewater Virome.

Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

The plant proteome folding project: structure and positive selection in plant protein families.

Despite its importance, relatively little is known about the relationship between the structure, function, and evolution of proteins, particularly in land plant species. We have developed a database with predicted protein domains for five plant proteomes (http://pfp.bio.nyu.edu) and used both protein structural fold recognition and de novo Rosetta-based protein structure prediction to predict protein structure for Arabidopsis and rice proteins. Based on sequence similarity, we have identified ~15,000 orthologous/paralogous protein family clusters among these species and used codon-based models to predict positive selection in protein evolution within 175 of these sequence clusters. Our results show that codons that display positive selection appear to be less frequent in helical and strand regions and are overrepresented in amino acid residues that are associated with a change in protein secondary structure. Like in other organisms, disordered protein regions also appear to have more selected sites. Structural information provides new functional insights into specific plant proteins and allows us to map positively selected amino acid sites onto protein structures and view these sites in a structural and functional context.

2,5-Dimethyl-2,4-hexadiene induced photodechlorination of 9,10-dichloroanthracene.

Photochemical formation of 9-chloroanthracene (MCA) from 9,10-dichloroanthracene (DCA) is observed in the presence of 2,5-dimethyl-2,4-hexadiene (DMH) in acetonitrile (AN). The mechanism of the reaction was investigated using kinetics, deuterium labeling, and quenching techniques. Contrary to conclusions in a recent publication, our work supports the salient features of the mechanism we had proposed earlier. DCA is photostable in degassed AN in the absence of DMH. When DMH is added, irradiation of DCA at 365 or 404 nm converts it quantitatively to MCA. The photoreaction is strongly inhibited when low concentrations of molecular oxygen or 1,2,4,5-tetracyanobenzene are also present. Results from fluorescence quenching studies along with kinetics parameters from the dependence of DCA loss and MCA formation quantum yields on [DMH] implicate participation of the DCA/DMH singlet exciplex, the DCA/(DMH)(2) triplex and the DCA radical anion (DCA*-) as intermediates in the photodechlorination. Results from experiments using deuterated DMH, deuterated AN, and AN containing D(2)O or H(2)O show that the 10-H of MCA is introduced by protonation of DCA*-. Contrary to a recent report, there is no radical pathway to MCA via dissociation of DCA*- to chloride and MCA radical. Changes in the absorption spectrum of DCA in AN with increasing [DMH] suggest that the static quenching of DCA fluorescence at high [DMH] is due primarily to nearest neighbour quenching instead of DCA/DMH ground state complex formation.

Low-dose remifentanil infusion does not impair natural killer cell function in healthy volunteers.

BACKGROUND: Mu opioid agonists suppress natural killer (NK) cell activity in animal models. Studies in human volunteers, however, have yielded conflicting results, with morphine suppressing and fentanyl increasing NK cell activity. This study evaluated the effect of a constant 8-h infusion of remifentanil on NK cell number and function in human volunteers. METHODS: After IRB approval and informed consent was obtained, 10 healthy volunteers underwent an 11 pm to 7 am infusion of saline, and at least 1 week later an infusion of 0.02-0.04 microg x kg(-1) min(-1) remifentanil. Blood was collected at 7 am for measurement of NK cell cytotoxicity using a (51)Cr release assay and measurement of NK cell number using fluorescent flow cytometry. RESULTS: Median and range of the total NK cell cytotoxicity (KU ml(-1)) was 745.0 (498.3-1483.6) on the control morning and 818.6 (238.5-1454.5) on the morning following the remifentanil infusion. Neither the number of NK cells ml(-1) (2.5 x 10(5) (1.4 x 10(5)-4.2 x 10(5)) vs 2.7 x 10(5) (1.1 x 10(5)-4.4 x 10(5))) nor the cytotoxicity per 1000 NK cells (KU 1000 NK cells(-1)) (3.0 (1.8-5.2) vs 2.9 (0.9-6.7)) changed between the control and remifentanil conditions. CONCLUSIONS: An 8-h infusion of remifentanil did not affect NK cell activity in normal volunteers. This result differs from previous findings of morphine-induced NK cell activity suppression and fentanyl-induced NK cell activity enhancement in normal volunteers.

Photochemistry of methoxyhydroquinone and methoxy-p-benzoquinone in solution related to the photoyellowing of the lignocellulosics.

The photoreactivity of methoxy-p-benzoquinone (MQ) and methoxyhydroquinone (MHQ) in dilute solution (10(-4)-10(-3) M) was studied using continuous irradiation and laser flash photolysis (LFP). The quinone irradiated in degassed tetrahydrofuran (THF) gives MHQ and an adduct with the solvent. Only the formation of hydroquinone is observed in ethanol, and hydroxylation is evidenced in water, whereas the compound is stable in CCl4. The bis-quinone, 4,4'-dimethoxybiphenyl-2,5,2',5'-bisquinone, and the dibenzofurane-quinone, 8-hydroxy-3,7-dimethoxydibenzofuran-1,4-quinone, are formed in the presence of MHQ, whereas the reactivity is low with ethylconiferyl alcohol. When MHQ is irradiated selectively in degassed THF, the formation of MQ and of the bis-hydroquinone, 4,4'-dimethoxy-2,5,2',5'-tetrahydroxy-biphenyl, are observed. The dimer is oxidized photochemically or thermally into the mono- or bis-quinones, the process being accelerated in alkaline medium. The formation of the dimers is strongly favored by the contiguous presence of quinone and hydroquinone. When MHQ is selectively irradiated in the presence of transethylconiferaldehyde (EtC), quinone formation and isomerization of EtC are observed. LFP experiments, performed with a selective excitation of MQ, indicate that the triplet state of the quinone is strongly quenched by MHQ to conduce to a semiquinone radical. The interaction between 3MQ* and MQ is mainly driven by an electron transfer process according to the similar value of the quenching rate constant found with another electron donor compound such as 1,4-dimethoxybenzene. By contrast, no strong quenching of 3EtC* by MHQ was observed. It is proposed that the photochemistry of the couple MQ/MHQ is governed by the formation of encounter complex between either 3MQ* and MHQ or 3MHQ* and MQ. Consequently, the fast part of the photoyellowing of lignocellulosics does not appear to involve the couple MHQ/MQ or MHQ/etherified coniferaldehyde, but more likely a combination of oxidation of the hydroquinone by ground-state oxygen and photohydration of the formed quinone from its triplet state, giving inter-alia more colored o-quinonoid type molecules.

Functional inferences from blind ab initio protein structure predictions.

Ab initio protein structure prediction methods have improved dramatically in the past several years. Because these methods require only the sequence of the protein of interest, they are potentially applicable to the open reading frames in the many organisms whose sequences have been and will be determined. Ab initio methods cannot currently produce models of high enough resolution for use in rational drug design, but there is an exciting potential for using the methods for functional annotation of protein sequences on a genomic scale. Here we illustrate how functional insights can be obtained from low-resolution predicted structures using examples from blind ab initio structure predictions from the third and fourth critical assessment of structure prediction (CASP3, CASP4) experiments.

Ab initio protein structure prediction: progress and prospects.

Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.

Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.

This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA and then identifying the free energy minima common to all folded sequences via simultaneous clustering of the independent folding runs. Global measures of hydrophobic core formation, using ellipsoidal rather than spherical representations of the hydrophobic core, are found to be useful in removing non-native conformations before cluster analysis. Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set. Proteins 2001;43:1-11.

Rosetta in CASP4: progress in ab initio protein structure prediction.

Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 A) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fold largely correct were produced for several targets with new folds, and for several difficult fold recognition targets, the Rosetta models were more accurate than those produced with traditional fold recognition models. These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information.

Mechanisms underlying chemical sympathectomy-induced suppression of herpes simplex virus-specific cytotoxic T lymphocyte activation and function.

Lymphoid tissues are extensively innervated by noradrenergic fibers of the sympathetic nervous system. 6-hydroxydopamine (6-OHDA)-induced chemical sympathectomy is commonly used to assess the impact of this innervation on immune function. Using the glucocorticoid receptor antagonist RU486, the mineralocorticoid receptor antagonist spironolactone, and the beta-adrenergic receptor antagonist nadolol, the roles of corticosterone and norepinephrine in sympathectomy-mediated modulation of both the primary and memory cellular immune responses to herpes simplex virus type 1 (HSV-1) infection was investigated. We demonstrated that both of these immunomodulators play a role in mediating sympathectomy-induced suppression of the generation of HSV-specific primary cytotoxic T lymphocytes (CTL) and the activation of HSV-specific memory CTL (CTLm). Furthermore, we demonstrated a role for both Type I and Type II corticosteroid receptors in the regulation of HSV-specific immunity. Overall, these findings not only further support a role for neuroendocrine-mediated modulation of immune function, but also a need to exercise caution in attributing the effects of chemical sympathectomy to solely the absence of sympathetic innervation of lymphoid tissues.

In vivo effects of chronic treatment with [MET5]-enkephalin on hematological values and natural killer cell activity in athymic mice.

The role of endogenous opioids in immunological mechanisms was examined by subjecting athymic (nu/nu) mice to chronic injections of the opioid agonist [Met5]-enkephalin (MET) or continuous opioid receptor blockade with naltrexone (NTX). After 8 days of treatment, neither excess peptide nor deprivation of opioids from receptors had any effect on body weight, spleen index (spleen to body weight ratio), total and differential white blood cell counts, and natural killer (NK) cell activity in peripheral blood or splenic lymphocytes. At 28 days, chronic treatment with MET or NTX had no effect on any of these parameters with the exception of an elevation from controls in NK cell activity in peripheral blood in mice receiving NTX, and subnormal NK cell activity related to splenic lymphocytes in the MET group. These results suggest that chronic exposure to an opioid agonist, or persistent opioid receptor blockade, have little influence on a variety of immunological properties in athymic mice, suggesting that native opioids such as MET do not play a marked role in defense mechanisms in the athymic mouse.

Chemical sympathectomy alters cytotoxic T lymphocyte responses to herpes simplex virus infection.

Numerous studies have sought to delineate the impact of neuroendocrine function on overall immune responsiveness. Using various murine models, we and others have previously shown that both adrenal-dependent and adrenal-independent mechanisms regulate components of the primary and memory cellular immune responses to herpes simplex virus type 1 (HSV-1) infection. We have extended these studies by determining the impact of 6-hydroxydopamine (6-OHDA)-induced peripheral sympathetic denervation on these responses. C57BL/6 mice treated with 6-OHDA (200 mg/kg) were inhibited in their ability to generate primary, HSV-specific cytotoxic T lymphocytes (CTL) in response to HSV infection. Sympathectomy also suppressed the activation and function of HSV-specific memory CTL (CTLm). In addition, administration of 6-OHDA resulted in a transient but substantial increase in levels of circulating corticosterone and hypothalamic Fos expression. Together, these findings suggest that peripheral sympathetic denervation may modulate immune function via activation of the hypothalamic-pituitary-adrenal (HPA) axis.

Ab initio protein structure prediction of CASP III targets using ROSETTA.

To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence-independent terms representing hard sphere packing, alpha-helix and beta-strand packing, and the collection of beta-strands in beta-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 A to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 A, a 75-residue segment of DNAB helicase with an rmsd of 4.7 A, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 A. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.

Immunogenicity of herpes simplex virus type 1 mutants containing deletions in one or more alpha-genes: ICP4, ICP27, ICP22, and ICP0.

Replication defective mutants of HSV have been proposed both as vaccine candidates and as vehicles for gene therapy because of their inability to produce infectious progeny. The immunogenicity of these HSV replication mutants, at both qualitative and quantitative levels, will directly determine their effectiveness for either of these applications. We have previously reported (Brehm et al., J. Virol., 71, 3534, 1997) that a replication defective mutant of HSV-1, which expresses a substantial level of viral genes without producing virus particles, is as efficient as wild-type HSV-1 in eliciting an HSV-specific cytotoxic T-lymphocyte (CTL) response. In this report, we have further evaluated the immunogenic potential of HSV-1-derived replication defective mutants by examining the generation of HSV-specific CTL following immunization with viruses that are severely restricted in viral gene expression due to mutations in one or more HSV alpha genes (ICP4, ICP27, ICP22, and ICP0). To measure the CTL responses induced by the HSV alpha-mutants, we have targeted two H-2Kb-restricted CTL epitopes: an epitope in a virion protein, gB (498-505), and an epitope in a nonvirion protein, ribonucleotide reductase (RR1 822-829). The HSV mutants used in this study are impaired in their ability to express gB while a majority of them still express RR1. Our findings demonstrate that a single immunization with these mutants is able to generate a strong CTL response not only to RR1 822-829, but also to gB498-505 despite their inability to express wild-type levels of gB. Furthermore, a single immunization with any individual mutant can also provide immune protection against HSV challenge. These results suggest that mutants which are restricted in gene expression may be used as effective immunogens in vivo.

Immunization with a single major histocompatibility complex class I-restricted cytotoxic T-lymphocyte recognition epitope of herpes simplex virus type 2 confers protective immunity.

We have evaluated the potential of conferring protective immunity to herpes simplex virus type 2 (HSV-2) by selectively inducing an HSV-specific CD8(+) cytotoxic T-lymphocyte (CTL) response directed against a single major histocompatibility complex class I-restricted CTL recognition epitope. We generated a recombinant vaccinia virus (rVV-ES-gB498-505) which expresses the H-2Kb-restricted, HSV-1/2-cross-reactive CTL recognition epitope, HSV glycoprotein B residues 498 to 505 (SSIEFARL) (gB498-505), fused to the adenovirus type 5 E3/19K endoplasmic reticulum insertion sequence (ES). Mucosal immunization of C57BL/6 mice with this recombinant vaccinia virus induced both a primary CTL response in the draining lymph nodes and a splenic memory CTL response directed against HSV gB498-505. To determine the ability of the gB498-505-specific memory CTL response to provide protection from HSV infection, immunized mice were challenged with a lethal dose of HSV-2 strain 186 by the intranasal (i.n.) route. Development of the gB498-505-specific CTL response conferred resistance in 60 to 75% of mice challenged with a lethal dose of HSV-2 and significantly reduced the levels of infectious virus in the brains and trigeminal ganglia of challenged mice. Finally, i.n. immunization of C57BL/6 mice with either a recombinant influenza virus or a recombinant vaccinia virus expressing HSV gB498-505 without the ES was also demonstrated to induce an HSV-specific CTL response and provide protection from HSV infection. This finding confirms that the induction of an HSV-specific CTL response directed against a single epitope is sufficient for conferring protective immunity to HSV. Our findings support the role of CD8(+) T cells in the control of HSV infection of the central nervous system and suggest the potential importance of eliciting HSV-specific mucosal CD8(+) CTL in HSV vaccine design.

Peripheral sympathetic denervation alters both the primary and memory cellular immune responses to herpes simplex virus infection.

Numerous studies have sought to delineate the impact of neuroendocrine function on overall immune responsiveness. Using various murine models, we and others have previously shown that both adrenal-dependent and adrenal-independent mechanisms associated with psychological stress modulate components of both the primary and memory cellular immune responses to herpes simplex virus type 1 (HSV-1) infection. We have extended these studies by determining the impact of 6-hydroxydopamine (6-OHDA)-mediated peripheral sympathetic denervation on both responses. C57BL/6 mice treated with 6-OHDA (200 mg/kg) exhibited reduced generation of both primary lymph node- and splenic-derived cytotoxic T lymphocytes (CTL) following a local (footpad) and systemic HSV infection, respectively. 6-OHDA also suppressed activation of HSV-specific memory CTL (CTLm). In both models, alterations in cytokine production and lymphocyte subset distribution were also observed. Administration of 6-OHDA also resulted in substantial but transient activation of the hypothalamic-pituitary-adrenal (HPA) axis as was indicated by a dramatic elevation of serum corticosterone and hypothalamic Fos expression. Moreover, the corticosterone levels were directly correlated with the extent of CTLm activation. Together, these findings suggest that peripheral sympathetic denervation alters immune function through activation of the HPA axis.

A genetic basis for neuroendocrine-immune interactions.

Psychoneuroimmunology is an exciting, complex field that elucidates interactions among the nervous, endocrine, and immune systems. The contribution of psychosocial factors and behavioral processes to these interactions has been the focus of numerous studies designed to investigate the intricate pathways that are involved in the "mind-body connection." In addition, the effects of this connection on the development and progression of various disease conditions are of considerable interest. Although efforts have been made to identify the cellular and molecular mechanisms underlying these relationships, the impact of genetic makeup on the communication among these systems has yet to be fully realized. The development of sophisticated genetic analytical methods and gene mapping techniques now provide the "tools" to determine the influence of genetics on behavior-neuroendocrine-immune interactions--an area of study that may represent the next frontier in psychoneuroimmunology.

Differential effects of stress-induced adrenal function on components of the herpes simplex virus-specific memory cytotoxic T-lymphocyte response.

We have previously demonstrated in a murine model system that psychological stress, applied in the form of physical restraint, suppresses both the activation of splenic-derived, herpes simplex virus (HSV)-specific memory cytotoxic T-lymphocytes (CTLm) to the lytic phenotype and the production of cytokines associated with CTL activation and function. In the studies described herein, we investigated the hypothesis that an adrenal-dependent event is responsible, either in whole or in part, for these observations. While adrenalectomy was shown to abrogate stress-induced suppression of both HSV-specific CTLm activation and the production of IL-6 and IFN-gamma, the reduction in splenic cellularity associated with restraint stress remained, In addition, a role for adrenal function in the regulation of splenic cellularity and IFN-gamma production in non-stressed mice was observed. Together, these results indicate that both adrenal-dependent and adrenal-independent events, operative under both baseline and stress conditions, mediate control of the memory component of the cellular immune response to HSV infection. Overall, these studies provide insight into the mechanisms by which psychological stress modulates immune responsiveness to viral pathogens.

A simian virus 40 large T-antigen segment containing amino acids 1 to 127 and expressed under the control of the rat elastase-1 promoter produces pancreatic acinar carcinomas in transgenic mice.

The simian virus 40 large T antigen induces tumors in a wide variety of tissues in transgenic mice, the precise tissues depending on the tissue specificity of the upstream region controlling T-antigen expression. Expression of mutant T antigens that contain a subset of the protein's activities restricts the spectrum of tumors induced. Others showed previously that expression of a mutant large T antigen containing the N-terminal 121 amino acids (T1-121) under control of the lymphotropic papovavirus promoter resulted in slow-growing choroid plexus tumors, whereas full-length T antigen under the same promoter induced rapidly growing CPR tumors, T-cell lymphomas, and B-cell lymphomas. In those instances, the alteration in tumor induction or progression correlated with inability of the mutant large T antigen to bind the tumor suppressor p53. In the study reported here, we investigated the capacity of an N-terminal T antigen segment (T1-127) expressed in conjunction with small t antigen under control of the rat elastase-1 (E1) promoter to induce pancreatic tumors. The results show that pancreases of transgenic mice expressing T1-127 and small t antigen display acinar cell dysplasia at birth that progresses to neoplasia. The average age to death in these mice is within the range reported for transgenic mice expressing full-length T antigen under control of the E1 promoter. These results indicate that sequestering p53 by binding is not required for the development of rapidly growing acinar cell carcinomas. In addition, we provide evidence that small t antigen is unlikely to be required. Finally, we show that the p53 protein in acinar cell carcinomas is wild type in conformation.