Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes

The understanding and engineering of complex phenotypes is a critical issue in biotechnology. Conventional approaches for engineering such phenotypes are often resource intensive, marginally effective, and unable to generate the level of biological understanding desired. Here, we report a new approach for rapidly dissecting a complex phenotype that is based upon the combination of genome-scale growth phenotype data, precisely targeted growth selections, and informatic strategies for abstracting and summarizing data onto coherent biological processes. We measured at high resolution (125 NT) and for the entire genome the effect of increased gene copy number on overall biological fitness corresponding to the expression of a complex phenotype (tolerance to 3-hydroxypropionic acid (3-HP) in Escherichia coli). Genetic level fitness data were then mapped according to various definitions of gene-gene interaction in order to generate network-level fitness data. When metabolic pathways were used to define interactions, we observed that genes within the chorismate and threonine super-pathways were disproportionately enriched throughout selections for 3-HP tolerance. Biochemical and genetic studies demonstrated that alleviation of inhibition of either of these super-pathways was sufficient to mitigate 3-HP toxicity. These data enabled the design of combinatorial modifications that almost completely offset 3-HP toxicity in minimal medium resulting in a 20 g/L and 25-fold increase in tolerance and specific growth, respectively.

Direct measurement of the W boson width

We present a direct measurement of the width of the W boson using the shape of the transverse mass distribution of W --> enu candidate events. Data from approximately 1 fb(-1) of integrated luminosity recorded at square root of s = 1.96 TeV by the D0 detector at the Fermilab Tevatron pp collider are analyzed. We use the same methods and data sample that were used for our recently published W boson mass measurement, except for the modeling of the recoil, which is done with a new method based on a recoil library. Our result, 2.028 +/- 0.072 GeV, is in agreement with the predictions of the standard model.

Measurement of dijet angular distributions at square root(s) = 1.96 TeV and searches for quark compositeness and extra spatial dimensions

We present the first measurement of dijet angular distributions in pp collisions at square root(s) = 1.96 TeV at the Fermilab Tevatron Collider. The measurement is based on a dataset corresponding to an integrated luminosity of 0.7 fb(-1) collected with the D0 detector. Dijet angular distributions have been measured over a range of dijet masses, from 0.25 TeV to above 1.1 TeV. The data are in good agreement with the predictions of perturbative QCD and are used to constrain new physics models including quark compositeness, large extra dimensions, and TeV(-1) scale extra dimensions. For all models considered, we set the most stringent direct limits to date.

Measurement of the WW production cross section with dilepton final states in pp collisions at square root(s) = 1.96 TeV and limits on anomalous trilinear gauge couplings

We provide the most precise measurement of the WW production cross section in pp collisions to date at a center of mass energy of 1.96 TeV, and set limits on the associated trilinear gauge couplings. The WW-->lnul'nu (l, l' = e, mu) decay channels are analyzed in 1 fb(-1) of data collected by the D0 detector at the Fermilab Tevatron Collider. The measured cross section is sigma(pp --> WW) = 11.5+/-2.1(stat+syst)+/-0.7(lumi) pb. One- and two-dimensional 95% C.L. limits on trilinear gauge couplings are provided.

Measurement of the W boson mass

We present a measurement of the W boson mass in W-->e(nu) decays using 1 fb-1 of data collected with the D0 detector during Run II of the Fermilab Tevatron collider. With a sample of 499830 W-->e(nu) candidate events, we measure M(W)=80.401+/-0.043 GeV. This is the most precise measurement from a single experiment.

Direct measurement of the mass difference between top and antitop quarks

We present a measurement of the mass difference between t and t[over] quarks in lepton + jets final states of tt[over] events in 1 fb;{-1} of data collected with the D0 detector from Fermilab Tevatron Collider pp[over] collisions at sqrt[s] = 1.96 TeV. The measured mass difference of 3.8 +/- 3.7 GeV is consistent with the equality of t and t[over ] masses. This is the first direct measurement of a mass difference between a quark and its antiquark partner.

Observation of single top-quark production

We report observation of the electroweak production of single top quarks in pp[over ] collisions at sqrt[s]=1.96 TeV based on 2.3 fb(-1) of data collected by the D0 detector at the Fermilab Tevatron Collider. Using events containing an isolated electron or muon and missing transverse energy, together with jets originating from the fragmentation of b quarks, we measure a cross section of sigma(pp[over ]--> tb + X, tqb + X) = 3.94 + or - 0.88 pb. The probability to measure a cross section at this value or higher in the absence of signal is 2.5 x 10(-7), corresponding to a 5.0 standard deviation significance for the observation.

Search for dark photons from supersymmetric hidden valleys

We search for a new light gauge boson, a dark photon, with the D0 experiment. In the model we consider, supersymmetric partners are pair produced and cascade to the lightest neutralinos that can decay into the hidden sector state plus either a photon or a dark photon. The dark photon decays through its mixing with a photon into fermion pairs. We therefore investigate a previously unexplored final state that contains a photon, two spatially close leptons, and large missing transverse energy. We do not observe any evidence for dark photons and set a limit on their production.

Search for resonant pair production of neutral long-lived particles decaying to bb in pp collisions at square root(S)=1.96 TeV

We report on a first search for resonant pair production of neutral long-lived particles (NLLP) which each decay to a bb pair, using 3.6 fb(-1) of data recorded with the D0 detector at the Fermilab Tevatron collider. We search for pairs of displaced vertices in the tracking detector at radii in the range 1.6-20 cm from the beam axis. No significant excess is observed above background, and upper limits are set on the production rate in a hidden-valley benchmark model for a range of Higgs boson masses and NLLP masses and lifetimes.

Search for next-to-minimal supersymmetric Higgs bosons in the h --> aa --> micromicromicromicro, micromicrotautau channels using pp[over] collisions at sqrt[s] = 1.96 TeV

We report on a first search for production of the lightest neutral CP-even Higgs boson (h) in the next-to-minimal supersymmetric standard model, where h decays to a pair of neutral pseudoscalar Higgs bosons (a), using 4.2 fb;{-1} of data recorded with the D0 detector at Fermilab. The a bosons are required to either both decay to micro;{+}micro;{-} or one to micro;{+}micro;{-} and the other to tau;{+}tau;{-}. No significant signal is observed, and we set limits on its production as functions of M_{a} and M_{h}.

Search for the standard model Higgs boson in tau final states

We present a search for the standard model Higgs boson using hadronically decaying tau leptons, in 1 fb(-1) of data collected with the D0 detector at the Fermilab Tevatron pp collider. We select two final states: tau+/- plus missing transverse energy and b jets, and tau+ tau- plus jets. These final states are sensitive to a combination of associated W/Z boson plus Higgs boson, vector boson fusion, and gluon-gluon fusion production processes. The observed ratio of the combined limit on the Higgs production cross section at the 95% C.L. to the standard model expectation is 29 for a Higgs boson mass of 115 GeV.

Search for resonant diphoton production with the D0 detector

We present a search for a narrow resonance in the inclusive diphoton final state using approximately 2.7 fb(-1) of data collected with the D0 detector at the Fermilab Tevatron pp Collider. We observe good agreement between the data and the background prediction, and set the first 95% C.L. upper limits on the production cross section times the branching ratio for decay into a pair of photons for resonance masses between 100 and 150 GeV. This search is also interpreted in the context of several models of electroweak symmetry breaking with a Higgs boson decaying into two photons.

Measurement of the Zgamma --> nunu[over ]gamma production cross section and limits on anomalous ZZgamma and Zgammagamma couplings in pp[over] collisions at sqrt[s] = 1.96 TeV

We present the first observation of the Zgamma --> nunu[over ]gamma process at the Fermilab Tevatron at 5.1 standard deviations significance, based on 3.6 fb;{-1} of integrated luminosity collected with the D0 detector at the Fermilab Tevatron pp[over ] Collider at sqrt[s] = 1.96 TeV. The measured Zgamma production cross section multiplied by the branching fraction of Z --> nunu[over] is 32 +/- 9(stat + syst) +/-2 (lumi) fb for the photon E_{T} > 90 GeV. It is in agreement with the standard model prediction of 39 +/- 4 fb. We set limits on anomalous trilinear Zgammagamma and ZZgamma gauge boson couplings, most of which are the most restrictive to date.

Randomized phase III trials of standard chemotherapy with or without targeted agents as first-line therapy in non-small cell lung cancer

e19092

Purpose: To characterize the pattern and outcome of randomized phase III trials involving standard chemotherapy with/without novel agents as first-line treatment in advanced NSCLC patients (pts). Methods: The trials included in this analysis were identified through a search of MEDLINE as well as websites (ASCO, IASLC) and meeting proceedings. Studies comparing novel agents alone to standard regimens were excluded. Results: Of 20 identified trials (16,050 pts), 11 (8,647 pts) were published between 2004–2008, and 9 (7,403 pts) were reported at scientific meetings (mostly between 2005–2008), but have not been published yet. All studies were conducted within the last 10 years. Majority were industry-sponsored studies; 4 (20%) were conducted by cooperative or non-profit groups. Chemotherapy chosen as the standard regimens involved cisplatin or carboplatin in combination with a third-generation drug with paclitaxel (10 trials) and gemcitabine (6 trials) being the most common drugs. The experimental drugs included agents with different molecular targets (EGFR, VEGF, MMP, PKC, FTI, TLR-9¼). Overall survival was primary endpoint in all 11 published studies. PFS was chosen as primary in 2 non-published studies. When comparing the standard arms (chemotherapy alone) across the 11 published trials, there was a large difference in term of response rate RR (15% to 47%), while survival endpoints showed a smaller difference (median overall survival OS 9–10.9 months; progression free survival PFS 4.5–5.5 months; and time to progression TTP 4.9–6 months). Among 11 published studies, only one showed positive result with a consistency in all endpoints (OS, PFS and RR). Of 9 non-published studies, 2 studies were reported as positive by the investigators, although preliminary results of primary and secondary endpoints were somewhat inconsistent. Conclusions: Within the last decade, 20 randomized phase III trials involving a large number of chemo-naïve NSCLC patients were conducted. There was a variation in eligibility and patient characteristics, study design (primary endpoints) as well as results among the studies.

No significant financial relationships to disclose.

Phase I/II study of MKC-1 and pemetrexed (PEM) as second-line therapy in patients (pts) with advanced non-small cell lung cancer (NSCLC)

e19005

Background: MKC-1 is a novel oral cell cycle inhibitor with preclinical activity against NSCLC cell lines including multi-drug resistant lines, and single agent activity in NSCLC pts. Binding targets of MKC-1 include microtubules, members of the importin-β family and AKT-mTOR. This phase 1/2 study evaluated MKC-1 in combination with PEM as second-line therapy in pts with advanced NSCLC. Methods: Eligible pts had NSCLC previously treated with one regimen for metastatic disease or disease progression within one year following adjuvant and neoadjuvant therapy. Phase 1 dose escalation used 3+3 design. Phase 2 pts were treated with MKC-1 at 75 mg/m2 given p.o. BID for 14 days along with PEM at 500 mg/m2 given i.v. on day 1 of each 21 day cycle. Following 4 cycles of combined treatment, single agent MKC-1 was continued as maintenance therapy. An interim analysis after 17 pts in phase 2 would allow accrual to continue provided one response was confirmed. Results: 27 pts were enrolled (8 in phase 1 and 19 in phase 2). Median age/PS for phase 2 is 64/1 and 89% had adenocarcinoma. Total # of treatment cycles to date for phase 2 pts is 95, with a median of 4 cycles. Of the 19 phase 2 pts, 18 were evaluable for tumor response. The best response was confirmed PR, noted in 3 pts. 5 additional pts (4 confirmed) had minor responses (>10% but <30% shrinkage). One additional pt continues on study with stable disease for >18 months. In phase 2 (n=19), all grade toxicities were anorexia (59%), fatigue (63%), nausea (58%), and dyspnea (48%). Grade 3/4 toxicities included fatigue (26%); neutropenia (22%); dyspnea, anorexia, AST and ALT elevation (11% each); nausea and constipation (5% each). 7 pts had at least one dose reduction of both PEM and MKC-1 and 3 additional pts had only MKC-1 reduced. Median PFS was 86 days with two pts continuing on study (treated for 530+ days and 140+ days, respectively). Conclusions: The phase 2 dose of MKC-1 (75 mg/m2 BID) and PEM (500 mg/m2) has been defined. The combination is well tolerated with 17% of patients achieving a confirmed PR thus far. A decision to proceed with additional accrual in this single arm study versus initiating a randomized phase 2 study of this combination is pending.

[Table: see text]

Measurement of gamma+b+X and gamma+c+X Production Cross Sections in pp[over ] Collisions at sqrt[s]=1.96 TeV

First measurements of the differential cross sections d;{3}sigma/(dp_{T};{gamma}dy;{gamma}dy;{jet}) for the inclusive production of a photon in association with a heavy quark (b, c) jet are presented, covering photon transverse momenta 30<p_{T};{gamma}<150 GeV, photon rapidities |y;{gamma}|<1.0, jet rapidities |y;{jet}|<0.8, and jet transverse momenta p_{T};{jet}>15 GeV. The results are based on an integrated luminosity of 1 fb;{-1} in pp[over ] collisions at sqrt[s]=1.96 TeV recorded with the D0 detector at the Fermilab Tevatron Collider. The results are compared with next-to-leading order perturbative QCD predictions.

Evidence of WW and WZ production with lepton + jets final states in pp collisions at square root s=1.96 TeV

We present first evidence for WW+WZ production in lepton + jets final states at a hadron collider. The data correspond to 1.07 fb-1 of integrated luminosity collected with the D0 detector at the Fermilab Tevatron in pp collisions at square root s=1.96 TeV. The observed cross section for WW+WZ production is 20.2+/-4.5 pb, consistent with the standard model and more precise than previous measurements in fully leptonic final states. The probability that background fluctuations alone produce this excess is <5.4 x 10-6, which corresponds to a significance of 4.4 standard deviations.

Search for anomalous top-quark couplings with the D0 detector

Anomalous Wtb couplings modify the angular correlations of the top-quark decay products and change the single top-quark production cross section. We present limits on anomalous top-quark couplings by combining information from W boson helicity measurements in top-quark decays and anomalous coupling searches in the single top-quark final state. We set limits on right-handed vector couplings as well as left-handed and right-handed tensor couplings based on about 1 fb(-1) of data collected by the D0 experiment.

Evidence for the decay Bs0-->Ds(*)Ds(*) and a measurement of DeltaGammasCP/Gammas

We search for the semi-inclusive process Bs0-->Ds(*)Ds(*) using 2.8 fb(-1) of pp collisions at sqrt[s]=1.96 TeV recorded by the D0 detector operating at the Fermilab Tevatron Collider. We observe 26.6+/-8.4 signal events with a significance above background of 3.2 standard deviations yielding a branching ratio of B(Bs0-->Ds(*)Ds(*))=0.035+/-0.010(stat.)+/-0.011(syst.). Under certain theoretical assumptions, these double-charm final states saturate CP-even eigenstates in the Bs0 decays resulting in a width difference of DeltaGammasCP/Gammas=0.072+/-0.021(stat.)+/-0.022(syst.).

Search for neutral Higgs Bosons at high tanbeta in the b(h/H/A)-->btau;{+}tau;{-} channel

The first search in pp[over ] collisions at sqrt[s]=1.96 TeV for the production of neutral Higgs bosons in association with bottom quarks and decaying in two tau leptons is presented. The cross section for this process is enhanced in many extensions of the standard model, such as its minimal supersymmetric extension (MSSM) at large tanbeta. The data, corresponding to an integrated luminosity of 328 pb;{-1}, were collected with the D0 detector at the Fermilab Tevatron Collider. An upper limit is set on the production cross section of neutral Higgs bosons in the mass range of 90 to 150 GeV, and this limit is used to exclude part of the MSSM parameter space.

Is ribosome synthesis controlled by pol I transcription?

Regulation of growth ultimately depends on the control of synthesis of new ribosomes. Ribosome biogenesis is thus a key element of cell biology, which is tightly regulated in response to environmental conditions. In eukaryotic cells, the supply of ribosomal components involves the activities of the three forms of nuclear RNA polymerase (Pol I, Pol II and Pol III). Recently, we demonstrated that upon rapamycin treatment, a partial derepression of Pol I transcription led to a concomitant derepression of Pol II transcription restricted to a small subset of class II genes encompassing the genes encoding all ribosomal proteins, and 19 additional genes. The products of 14 of these 19 genes are principally involved in rDNA structure, ribosome biogenesis or translation, whereas the five remaining genes code for hypothetical proteins. We demonstrate that the proteins encoded by these five genes are required for optimal pre-rRNA processing. In addition, we show that cells in which regulation of Pol I transcription was specifically impaired are either resistant or hypersensitive to different stresses compared to wild-type cells. These results highlight the critical role of the regulation of Pol I activity for the physiology of the cells.

Psychophysiological correlates of the inter-individual variability of head movement control in seated humans

We recently conducted experiments where 24 seated participants were subjected (with eyes closed) to small amplitude, high-jerk impulses of linear acceleration. Responses were distributed as a continuum between two extremes. The "stiff" participants showed little movement of the head relative to the trunk, whereas the "floppy" participants showed a large head rotation in the direction opposite the sled movement. We hypothesized that the stiff behavior resulted from the spontaneous use of an imagined visual frame of reference and undertook this larger-scale study to test that idea. The distribution along the "stiff-floppy" continuum was compared with the scores on psychophysiological tests measuring vividness of imagery, visual field-dependence and motion sickness susceptibility. Multivariate regression analysis revealed that the "stiffness" of individuals was loosely, but significantly related to the vividness of their imagery. However, "stiffness" was not linked to visual field-dependence or motion sickness susceptibility. Even if it explains only 20% of the variance of the data, the increase of "stiffness" with vividness of imagery fits our hypothesis. With eyes closed, stiff people may use imagined external visual cues to stabilize their head and trunk. Floppy people, who are poorer imagers, may rely more on "egocentric", proprioceptive and vestibular inputs.

Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction

Esf2p is the Saccharomyces cerevisiae homolog of mouse ABT1, a protein previously identified as a putative partner of the TATA-element binding protein. However, large-scale studies have indicated that Esf2p is primarily localized to the nucleolus and that it physically associates with pre-rRNA processing factors. Here, we show that Esf2p-depleted cells are defective for pre-rRNA processing at the early nucleolar cleavage sites A0 through A2 and consequently are inhibited for 18S rRNA synthesis. Esf2p was stably associated with the 5' external transcribed spacer (ETS) and the box C+D snoRNA U3, as well as additional box C+D snoRNAs and proteins enriched within the small-subunit (SSU) processome/90S preribosomes. Esf2p colocalized on glycerol gradients with 90S preribosomes and slower migrating particles containing 5' ETS fragments. Strikingly, upon Esf2p depletion, chromatin spreads revealed that SSU processome assembly and compaction are inhibited and glycerol gradient analysis showed that U3 remains associated within 90S preribosomes. This suggests that in the absence of proper SSU processome assembly, early pre-rRNA processing is inhibited and U3 is not properly released from the 35S pre-rRNAs. The identification of ABT1 in a large-scale analysis of the human nucleolar proteome indicates that its role may also be conserved in mammals.