Metabolomic rearrangement controls the intrinsic microbial response to temperature changes

Temperature is one of the key determinants of microbial behavior and survival, whose impact is typically studied under heat- or cold-shock conditions that elicit specific regulation to combat lethal stress. At intermediate temperatures, cellular growth rate varies according to the Arrhenius law of thermodynamics without stress responses, a behavior whose origins have not yet been elucidated. Using single-cell microscopy during temperature perturbations, we show that bacteria exhibit a highly conserved, gradual response to temperature upshifts with a time scale of ~1.5 doublings at the higher temperature, regardless of initial/final temperature or nutrient source. We find that this behavior is coupled to a temperature memory, which we rule out as being neither transcriptional, translational, nor membrane dependent. Instead, we demonstrate that an autocatalytic enzyme network incorporating temperature-sensitive Michaelis-Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, which encodes a temperature memory and successfully predicts alterations in the upshift response observed under simple-sugar, low-nutrient conditions, and in fungi. This model also provides a mechanistic framework for both Arrhenius-dependent growth and the classical Monod Equation through temperature-dependent metabolite flux.

Methyltransferase-like 21C (METTL21C) methylates alanine tRNA synthetase at Lys-943 in muscle tissue

Protein-lysine methylation is a common posttranslational modification (PTM) throughout the human proteome that plays important roles in diverse biological processes. In humans, there are >100 known and candidate protein lysine methyltransferases (PKMTs), many of which are linked to human diseases. Methyltransferase-like protein 21C (METTL21C) is a PKMT implicated in muscle biology that has been reported to methylate valosin-containing protein/p97 (VCP) and heat shock 70-kDa protein 8 (HSPA8). However, a clear in vitro methyltransferase activity for METTL21C remains yet to be demonstrated, and whether it is an active enzyme that directly methylates substrate(s) in vivo is unclear. Here, we used an unbiased biochemistry-based screening assay coupled to MS, which identified alanine tRNA synthetase 1 (AARS1) as a direct substrate of METTL21C. We found that METTL21C catalyzes methylation of Lys-943 of AARS1 (AARS1-K943me) both in vitro and in vivo In vitro METTL21C-mediated AARS1 methylation was independent of ATP or tRNA molecules. Unlike for AARS1, and in conflict with previous reports, we did not detect METTL21C methylation of VCP and HSPA8. AARS1-K943 methylation in HEK293T cells depends upon METTL21C levels. Finally, METTL2C was almost exclusively expressed in muscle tissue, and, accordingly, we detected METTL21C-catalyzed methylation of AARS1 in mouse skeletal muscle tissue. These results reveal that AARS1 is a bona fide in vitro substrate of METTL21C and suggest a role for the METTL21C-AARS1 axis in the regulation of protein synthesis in muscle tissue. Moreover, our study describes a straightforward protocol for elucidating the physiological substrates of poorly characterized or uncharacterized PKMTs.

Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast

The coordination of metabolism and growth with cell division is crucial for proliferation. While it has long been known that cell metabolism regulates the cell division cycle, it is becoming increasingly clear that the cell division cycle also regulates metabolism. In budding yeast, we previously showed that over half of all measured metabolites change concentration through the cell cycle indicating that metabolic fluxes are extensively regulated during cell cycle progression. However, how this regulation is achieved still remains poorly understood. Since both the cell cycle and metabolism are regulated to a large extent by protein phosphorylation, we here decided to measure the phosphoproteome through the budding yeast cell cycle. Specifically, we chose a cell cycle synchronization strategy that avoids stress and nutrient-related perturbations of metabolism, and we grew the yeast on ethanol minimal medium to force cells to utilize their full biosynthetic repertoire. Using a tandem-mass-tagging approach, we found over 200 sites on metabolic enzymes and transporters to be phospho-regulated. These sites were distributed among many pathways including carbohydrate catabolism, lipid metabolism, and amino acid synthesis and therefore likely contribute to changing metabolic fluxes through the cell cycle. Among all one thousand sites whose phosphorylation increases through the cell cycle, the CDK consensus motif and an arginine-directed motif were highly enriched. This arginine-directed R-R-x-S motif is associated with protein-kinase A, which regulates metabolism and promotes growth. Finally, we also found over one thousand sites that are dephosphorylated through the G1/S transition. We speculate that the phosphatase Glc7/PP1, known to regulate both the cell cycle and carbon metabolism, may play an important role because its regulatory subunits are phospho-regulated in our data. In summary, our results identify extensive cell cycle dependent phosphorylation and dephosphorylation of metabolic enzymes and suggest multiple mechanisms through which the cell division cycle regulates metabolic signaling pathways to temporally coordinate biosynthesis with distinct phases of the cell division cycle.

Immuno-proteomic interrogation of antigen presentation during Dengue infection reveals novel and HLA haplotype-specific MHC-I antigens

Dengue (DEN) virus infection is a leading cause of hospitalization and death in the developing world and broadly effective vaccines and therapies remain elusive. Identifying infection-specific peptide antigens would open new avenues for developing T cell based interventions. Past efforts towards mapping viral antigens used computational predictions that only partially reflect actual antigens presented by the major histocompatibility complex (MHC). To identify DEN-specific antigens without relying on error prone predictions, we developed an immuno-proteomics approach for interrogating antigen presentation in DEN infected B-lymphocytes. This approach enabled three fundamental findings; First, we identified 86 viral MHC-I antigens (59 novel), and mapped them to presentation hotspots in the DEN genome. Second, we discovered post-translationally modified viral and host antigens and antigens derived from alternate reading frames. Predicting these antigens using computational methods alone would be infeasible. Third, we found antigens responsible for HLA-haplotype dependent immune responses against DEN infection: we genetically engineered B-lymphocytes to express HLA alleles associated with either strong or weak DEN-immune responses and identified corresponding allele specific antigens. Together these discoveries let us assay the immunogenic potentials of an unprecedented range of DEN-specific antigens. Ex-vivo assays including ELISPOT and HLA tetramer staining supported our identification of immunogenic antigens in DEN-specific CD8+ T cells. These antigens have potential as both diagnostic tools to characterize DEN-specific T cell immunity, and serve as candidates for designing effective DEN vaccines.

A role for the MRN complex in ATR activation via TOPBP1 recruitment

The MRN (MRE11-RAD50-NBS1) complex has been implicated in many aspects of the DNA damage response. It has key roles in sensing and processing DNA double-strand breaks, as well as in activation of ATM (ataxia telangiectasia mutated). We reveal a function for MRN in ATR (ATM- and RAD3-related) activation by using defined ATR-activating DNA structures in Xenopus egg extracts. Strikingly, we demonstrate that MRN is required for recruitment of TOPBP1 to an ATR-activating structure that contains a single-stranded DNA (ssDNA) and a double-stranded DNA (dsDNA) junction and that this recruitment is necessary for phosphorylation of CHK1. We also show that the 911 (RAD9-RAD1-HUS1) complex is not required for TOPBP1 recruitment but is essential for TOPBP1 function. Thus, whereas MRN is required for TOPBP1 recruitment at an ssDNA-to-dsDNA junction, 911 is required for TOPBP1 "activation." These findings provide molecular insights into how ATR is activated.

Search for new physics in photon-lepton events in pp collisions at sqrt[s] = 1.8 TeV

We present the results of a search in pp collisions at sqrt[s] = 1.8 TeV for anomalous production of events containing a photon and a lepton (e or mu), both with large transverse energy, using 86 pb(-1) of data collected with the Collider Detector at Fermilab during the 1994-1995 collider run at the Fermilab Tevatron. The presence of large missing transverse energy (E(T)), additional photons, or additional leptons in these events is also analyzed. The results are consistent with standard model expectations, with the possible exception of photon-lepton events with large E(T), for which the observed total is 16 events and the expected mean total is 7.6+/-0.7 events.

Upsilon production and polarization in p p macro collisions at square root of s = 1.8 TeV

We report on measurements of the Upsilon(1S), Upsilon(2S), and Upsilon(3S) differential cross sections (d(2)sigma/dp(T)dy)(/y/<0.4), as well as on the Upsilon(1S) polarization in p p macro collisions at square root of s = 1.8 TeV using a sample of 77+/-3 pb(-1) collected by the collider detector at Fermilab. The three resonances were reconstructed through the decay Upsilon-->mu(+)mu(-). The measured angular distribution of the muons in the Upsilon(1S) rest frame is consistent with unpolarized meson production.

Diffractive dijet production at sqrt[s] = 630 and 1800 GeV at the Fermilab Tevatron

We report a measurement of the diffractive structure function F(D)(jj) of the antiproton obtained from a study of dijet events produced in association with a leading antiproton in pp collisions at sqrt[s] = 630 GeV at the Fermilab Tevatron. The ratio of F(D)(jj) at sqrt[s] = 630 GeV to F(D)(jj) obtained from a similar measurement at sqrt[s] = 1800 GeV is compared with expectations from QCD factorization and other theoretical predictions. We also report a measurement of the xi ( x-Pomeron) and beta ( x of parton in Pomeron) dependence of F(D)(jj) at sqrt[s] = 1800 GeV. In the region 0.035<xi<0.095, /t/<1 GeV2, and beta<0.5, F(D)(jj)(beta,xi) is found to be of the form beta(-1.0+/-0.1)xi(-0.9+/-0.1), which obeys beta-xi factorization.

Search for new heavy particles in the WZ0 final state in pp collisions at square root[s] = 1.8 TeV

We present the first general search for new heavy particles, X, which decay via X --> WZ0 --> e(nu)+jj as a function of M(X) and Gamma(X) in pp collisions at square root[s] = 1.8 TeV. No evidence is found for production of X in 110 pb(-1) of data collected by the Collider Detector at Fermilab. General cross section limits are set at the 95% C.L. as a function of mass and width of the new particle. The results are further interpreted as mass limits on the production of new heavy charged vector bosons which decay via W' --> WZ0 in an extended gauge model as a function of the width, Gamma(W'), and mixing factor between the W' and the standard model W bosons.

Study of B0 --> J/psiK(*)0pi(+)pi(-) decays with the collider detector at Fermilab

We report a study of the decays B0 --> J/psiK(*)0pi(+)pi(-), which involve the creation of a uu or dd quark pair in addition to a b -->c(cs) decay. The data sample consists of 110 pb(-1) of pp collisions at square root[s] = 1.8 TeV collected by the CDF detector at the Fermilab Tevatron collider during 1992-1995. We measure the branching fractions to be B(B0 --> J/psiK(*0)pi(+)pi(-)) = (6.6 +/- 1.9 +/- 1.1)x10(-4) and B(B0 --> J/psiK0pi(+)pi(-)) = (10.3 +/- 3.3 +/- 1.5)x10(-4). Evidence is seen for contributions from psi(2S)K(*)0, J/psiK0rho(0), J/psiK(*+)pi(-), and J/psiK1(1270).

Search for gluinos and scalar quarks in pp collisions at square root[s] = 1.8 TeV using the missing energy plus multijets signature

We have performed a search for gluinos (g) and scalar quarks (q) in a data sample of 84 pb(-1) of pp collisions at square root[s] = 1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and three or more jets, a characteristic signature in R-parity-conserving supersymmetric models. The analysis has been performed "blind," in that the inspection of the signal region is made only after the predictions from standard model backgrounds have been calculated. Comparing the data with predictions of constrained supersymmetric models, we exclude gluino masses below 195 GeV/c2 (95% C.L.), independent of the squark mass. For the case m(q) approximately m(g), gluino masses below 300 GeV/c2 are excluded.

Measurement of the strong coupling constant from inclusive jet production at the Tevatron pp collider

We report a measurement of the strong coupling constant, alpha(s)(MZ), extracted from inclusive jet production in pp collisions at square root[s] = 1800 GeV. The QCD prediction for the evolution of alpha(s) with jet transverse energy ET is tested over the range 40<ET<450 GeV using ET for the renormalization scale. The data show good agreement with QCD in the region below 250 GeV. The value of alpha(s) at the mass of the Z0 boson averaged over the range 40<ET<250 GeV is found to be alpha(s)(MZ) = 0.1178+/-0.0001(stat)+0.0081(-0.0095)(expt. syst). The associated theoretical uncertainties are mainly due to the choice of renormalization scale ((+6%)(-4%)) and input parton distribution functions (5%).

Search for gluinos and squarks using like-sign dileptons in pp macro collisions at square root of s = 1.8 TeV

We present results of the first search for like-sign dilepton ( e(+/-)e(+/-), e(+/-)mu(+/-), mu(+/-)mu(+/-)) events associated with multijets and large missing energy using 106 pb(-1) of data in pp macro collisions at square root of s = 1.8 TeV collected during 1992-1995 by the CDF experiment. Finding no events that pass our selection, we examine pair production of gluinos (tilde g) and squarks (tilde q) in a constrained framework of the minimal supersymmetric standard model. At tan beta = 2 and mu = -800 GeV/c(2), we set 95% confidence level limits of M(tilde g)>221 GeV/c(2) for M(tilde g) approximately M(tilde q), and M(tilde q)>168 GeV/c(2) for M(tilde q)>>M(tilde g), both with small variation as a function of mu.

Observation of diffractive J/psi production at the Fermilab Tevatron

We report the first observation of diffractive J/psi(--> mu+mu-) production in pp collisions at root square[s] = 1.8 TeV. Diffractive events are identified by their rapidity gap signature. In a sample of events with two muons of transverse momentum p(mu)T>2 GeV/c within the pseudorapidity region /eta/ < 1.0, the ratio of diffractive to total J/psi production rates is found to be R(J/psi) = [1.45 +/- 0.25]%. The ratio R(J/psi)(x) is presented as a function of x-Bjorken. By combining it with our previously measured corresponding ratio R(jj)(x) for diffractive dijet production, we extract a value of 0.59 +/- 0.15 for the gluon fraction of the diffractive structure function of the proton.

Search for quark-lepton compositeness and a heavy W' Boson using the enu channel in p p macro collisions at square root of [s] = 1.8 TeV

We present searches for quark-lepton compositeness and a heavy W' boson at high electron-neutrino transverse mass. We use approximately 110 pb(-1) of data collected in p p macro collisions at square root of [s] = 1.8 TeV by the CDF Collaboration during 1992-1995. The data are consistent with standard model expectations. Limits are set on the quark-lepton compositeness scale Lambda, the ratio of partial cross sections sigma(W'-->enu)/sigma(W-->enu), and the mass of a W' boson with standard model couplings. We exclude Lambda<2.81 TeV and a W' boson with mass below 754 GeV/c(2) at the 95% confidence level. Combining with our previously published limit obtained using the muon channel, we exclude a W' boson with mass below 786 GeV/c(2) at the 95% confidence level.

Charged-particle multiplicity pp collisions at square root of (s) = 1.8 TeV

We report on a measurement of the mean charged-particle multiplicity of jets in dijet events with dijet masses in the range 80-630 GeV/c(2), produced at the Tevatron in pp collisions with square root (s) = 1.8 TeV and recorded by the Collider Detector at Fermilab. The data are fit to perturbative-QCD calculations carried out in the framework of the modified leading log approximation and the hypothesis of local parton-hadron duality. The fit yields values for two parameters in that framework: the ratio of parton multiplicities in gluon and quark jets, r identical withN(g-jet)(partons)/N(q-jet)(partons) = 1.7+/-0.3, and the ratio of the number of charged hadrons to the number of partons in a jet, K(charged)(LPHD) identical with N(charged)(hadrons)/N(partons) = 0.57+/-0.11.

Double diffraction dissociation at the Fermilab Tevatron collider

We present results from a measurement of double diffraction dissociation in pp collisions at the Fermilab Tevatron collider. The production cross section for events with a central pseudorapidity gap of width Deltaeta(0)>3 (overlapping eta = 0) is found to be 4.43+/-0.02(stat)+/-1.18(syst) mb [ 3.42+/-0.01(stat)+/-1.09(syst) mb] at square root of (s) = 1800[630] GeV. Our results are compared with previous measurements and with predictions based on Regge theory and factorization.

Measurement of d sigma/dM and forward-backward charge asymmetry for high-mass Drell-Yan e(+)e(-) pairs from pp macro collisions at square root of s = 1.8 TeV

We report on a measurement of the mass dependence of the forward-backward charge asymmetry, A(FB), and production cross section d sigma/dM for e(+)e(-) pairs with mass M(ee)>40 GeV/c(2). The data sample consists of 108 pb(-1) of pp macro collisions at square root of s = 1.8 TeV taken by the Collider Detector at Fermilab during 1992-1995. The measured asymmetry and d sigma/dM are compared with the predictions of the standard model and a model with an extra Z' gauge boson.

Measurement of the top quark p(T) distribution

We have measured the p(T) distribution of top quarks that are pair produced in pp collisions at sqrt[s] = 1.8 TeV using a sample of tt decays in which we observe a single high- p(T) charged lepton, a neutrino, and four or more jets. We use a likelihood technique that corrects for the experimental bias introduced due to event reconstruction and detector resolution effects. The observed distribution is consistent with the standard model prediction. We use these data to place limits on the production of high- p(T) top quarks suggested in some models of anomalous top quark pair production.

Search for neutral supersymmetric Higgs bosons in pp collisions at sqrt[s] = 1.8TeV

We present the results of a search for neutral Higgs bosons produced in association with b quarks in pp-->bb(phi)-->bbb final states with 91+/-7 pb(-1) of pp collisions at sqrt[s] = 1.8 TeV recorded by the Collider Detector at Fermilab. We find no evidence of such a signal and the data are interpreted in the context of the neutral Higgs sector of the minimal supersymmetric extension of the standard model. With basic parameter choices for the supersymmetric scale and the stop-quark mixing, we derive 95% C.L. lower mass limits for neutral Higgs bosons for tan(beta) values in excess of 35.

Production of chi(c1) and chi(c2) in pp collisions at sqrt[S] = 1.8 TeV

We have measured the ratio of prompt production rates of the charmonium states chi(c1) and chi(c2) in 110 pb(-1) of pp collisions at sqrt[s] = 1.8 TeV. The photon from their decay into J/psi(gamma) is reconstructed through conversion into e+e- pairs. The energy resolution this technique provides makes the resolution of the two states possible. We find the ratio of production cross sections sigma(chi(c2))/sigma(chi(c1)) = 0.96+/-0.27(stat)+/-0.11(syst) for events with pT(J/psi) > 4.0 GeV/c, /eta(J/psi)/ < 0.6, and pT(gamma) > 1.0 GeV/c.

First measurement of the ratio B(t --> Wb)/B(t --> Wq) and associated limit on the Cabibbo-Kobayashi-Maskawa element /V(tb)/

We present the first measurement of the ratio of branching fractions R identical withB(t-->Wb)/B(t-->Wq) from p_p collisions at sqrt[s] = 1.8 TeV. The data set corresponds to 109 pb(-1) of data recorded by the Collider Detector at Fermilab during the 1992-95 Tevatron run. We measure R = 0.94(+0.31)(-0.24)(stat+syst) or R>0.61 (0.56) at 90% (95)% C.L., in agreement with the standard model predictions. This measurement yields a limit on the Cabibbo-Kobayashi-Maskawa quark mixing matrix element /V(tb)/ under the assumption of three generations and unitarity.

Measurement of J/psi and psi(2S) polarization in pp collisions at sqrt[s] = 1.8 TeV

We have measured the polarization of J/psi and psi(2S) mesons produced in pp collisions at sqrt[s] = 1.8 TeV, using data collected at the Collider Detector at Fermilab during 1992-1995. The polarization of promptly produced J/psi [psi(2S)] mesons is isolated from those produced in B-hadron decay, and measured over the kinematic range 4 [5.5]<P(T)<20 GeV/c and |y|<0.6. For P(T) greater than or approximately equal 12 GeV/c we do not observe significant polarization in the prompt component.

Search for scalar top and scalar bottom quarks in pp collisions at square root s=1.8 TeV

We have searched for direct pair production of scalar top and scalar bottom quarks in 88 pb-1 of pp collisions at sqrt[s]=1.8 TeV with the CDF detector. We looked for events with a pair of heavy flavor jets and missing energy, consistent with scalar top (bottom) quark decays to a charm (bottom) quark and a neutralino. The numbers of events that pass our selections show no significant deviation from standard model expectations. We compare our results to the next-to-leading order scalar quark production cross sections to exclude regions in scalar quark-neutralino mass parameter space.

Search for a W' boson via the decay mode W'-->munumu in 1.8 TeV pp collisions

We report the results of a search for a W' boson produced in pp collisions at a center-of-mass energy of 1.8 TeV using a 107 pb-1 data sample recorded by the Collider Detector at Fermilab. We consider the decay channel W'-->&munumu and search for anomalous production of high transverse mass munumu lepton pairs. We observe no excess of events above background and set limits on the rate of W' boson production and decay relative to standard model W boson production and decay using a fit of the transverse mass distribution observed. If we assume standard model strength couplings of the W' boson to quark and lepton pairs, we exclude a W' boson with invariant mass less than 660 GeV/c2 at 95% confidence level.

Gender differences in sexual fantasy and behavior in a college population: a ten-year replication

This report is a replication of a study conducted 10 years ago by Person et al., investigating gender differences in sexual behaviors and fantasies in a college population. We found that men continue to fantasize more than women, but the gender differences have narrowed. Recent sexual experiences of our population show a trend toward an increase in gender differences, and there is a greater correlation between sexual fantasy and experiences in women than in men. As in Person's study, we did not find that men had more aggressive/sadistic fantasies than women.