Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners.

Protein and mRNA levels correlate only moderately. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a system can be predicted from mRNA information. Here we examined the contributions of input features in protein abundance prediction models. Using large proteogenomics data from 8 cancer types within the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data set, we trained models to predict the abundance of over 13,000 proteins using matching transcriptome data from up to 958 tumor or normal adjacent tissue samples each, and compared predictive performances across algorithms, data set sizes, and input features. Over one-third of proteins (4,648) showed relatively poor predictability (elastic net r ≤ 0.3) from their cognate transcripts. Moreover, we found widespread occurrences where the abundance of a protein is considerably less well explained by its own cognate transcript level than that of one or more trans locus transcripts. The incorporation of additional trans-locus transcript abundance data as input features increasingly improved the ability to predict sample protein abundance. Transcripts that contribute to non-cognate protein abundance primarily involve those encoding known or predicted interaction partners of the protein of interest, including not only large multi-protein complexes as previously shown, but also small stable complexes in the proteome with only one or few stable interacting partners. Network analysis further shows a complex proteome-wide interdependency of protein abundance on the transcript levels of multiple interacting partners. The predictive model analysis here therefore supports that protein-protein interaction including in small protein complexes exert post-transcriptional influence on proteome compositions more broadly than previously recognized. Moreover, the results suggest mRNA and protein co-expression analysis may have utility for finding gene interactions and predicting expression changes in biological systems.

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT.

Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H2O2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H2O2-treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H2O2. The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H2O2-consumption assays. Furthermore, an entrance channel for H2O2 was identified and key residues implicated in H2O2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide "redox switch" is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

A novel imaging technique for measuring kinematics of light-weight flexible structures.

A new imaging algorithm is proposed to capture the kinematics of flexible, thin, light structures including frequencies and motion amplitudes for real time analysis. The studied case is a thin flexible beam that is preset at different angles of attack in a wind tunnel. As the angle of attack is increased beyond a critical value, the beam was observed to undergo a static deflection that is ensued by limit cycle oscillations. Imaging analysis of the beam vibrations shows that the motion consists of a superposition of the bending and torsion modes. The proposed algorithm was able to capture the oscillation amplitudes as well as the frequencies of both bending and torsion modes. The analysis results are validated through comparison with measurements from a piezoelectric sensor that is attached to the beam at its root.

Intact HCG, free HCG beta subunit and HCG beta core fragment: longitudinal patterns in urine during early pregnancy.

BACKGROUND: Detecting and monitoring early pregnancy depend on the measurement of HCG. Little is known about how production of various forms of HCG may evolve over the earliest weeks of pregnancy, particularly in naturally conceived pregnancies. METHODS: We describe the daily excretion of three urinary HCG analytes during the first 6 weeks post-conception in 37 naturally conceived pregnancies ending in singleton birth. We assayed daily first morning urine samples for intact HCG, free beta subunit and beta?core fragment, plus the combined measurement of these HCG forms. We calculated doubling times for each analyte and the inter- and intra-subject day-to-day variation. RESULTS: Intact HCG and the free beta subunit were initially the predominant forms of HCG, with the beta core fragment emerging as the predominant form in the fifth week after conception. Intact HCG and the free beta subunit showed the most day-to-day variability, and were transiently undetectable even 10 days after detection of pregnancy. The most stable estimate of doubling time was provided by the combined measurement of all these forms. CONCLUSIONS: Although intact HCG is usually regarded as the main analyte for detection and monitoring of early pregnancy, it can fluctuate markedly during early pregnancy. This variability could affect pregnancy test results based on early pregnancy urine, and may distort estimates of doubling time. Assays that combine several forms of HCG may be more reliable.

Isolation of native human monoclonal autoantibodies to breast cancer.

Using a unique fusion partner cell line, MFP-2, and B-lymphocytes from breast cancer patients, we developed a set of fully human monoclonal antibodies (MAbs) that bind with high specificity and sensitivity to breast cancer cells. Immunofluorescent staining of normal tissues, primary tumors, and metastatic lymph nodes demonstrates that these antibodies are specific for breast cancer of autologous and allogeneic origin. We have also determined that many of the antibodies selected based on specific binding to breast cancer cells and tissue also bind prostate cancer cells and tissue with high specificity and sensitivity. The targets of these antibodies have been localized to the cytoplasm and membrane. Biological assays for internalization and cytotoxicity demonstrated the ability of three antibodies to rapidly internalize. Our study demonstrates that isolation of native human MAbs from the natural antibody repertoire, targeted to cancer cells, is feasible and may provide a source of tools for immunotherapy.

Electrical stimulation of tooth pulp in humans. I. Relationships among physical stimulus intensities, psychological magnitude estimates and cerebral evoked potentials.

Brief electrical pulses were applied to the pulp of individual pre-molar teeth of 14 healthy, adult volunteers via wire electrodes implanted and sealed in dentine. The sensation threshold was estimated in each individual by the Two-Alternative Forced-Choice Staircase (2AFCS) method. Seven, 5 or 4 stimulus intensities were employed which were equally spaced in a logarithmic scale between 10 microA above threshold and 500 microA. Magnitude estimates of the subjective intensity of the sensation produced by individual dental excitations were obtained. Cerebral tooth pulp-evoked potentials were simultaneously recorded in 11 subjects. The growth of psychological sensory magnitude with increasing strength of electrical stimulus conformed to the general psychophysical power law. Individual power function exponents varied from 0.204 to 0.907 with a mean of 0.475 and a standard deviation of 0.190. The amplitude of TPEPs, measured between components N135 and P293, also was a power function of stimulus intensity. The exponents of individual TPEP amplitude-intensity functions ranged from 0.055 to 0.362 with a mean of 0.144 and a standard deviation of 0.100. These last exponents were substantially smaller than those describing the growth of psychological magnitude estimates. Neither magnitude estimation nor TPEP amplitude-intensity functions displayed abrupt changes in slope which might accompany transition from one operating sensory mechanism to another and/or changes in qualities of subjective sensations from 'innocuous' to 'uncomfortable' to 'painful.' The result of our psychophysical and electrophysiologic experiments indicate that: (1) albeit highly specialized both morphologically and functionally, human tooth pulp has certain fundamental properties in common with other sensory systems and (2) late midline TPEP components may provide measures of central events that, within a range of stimulus intensities, are associated with the perception of pain, but should not be looked upon as specific indicators of pain processes.

Electrical stimulation of tooth pulp in humans. II. Qualities of sensations.

Individual premolar teeth of 22 normal volunteers were stimulated via intradentinal electrodes using brief electrical pulses. Questionnaires were used to determine the qualities of sensations produced by this stimulation. Operationally defined 'innocuous' sensations predominated between 1 and 10 dB SL, and were absent above 30 dB SL. Similarly defined 'painful' sensations were observed throughout the range of suprathreshold intensities but were most common above 20 dB SL. These findings demonstrate that non-painful sensations can arise from electrical tooth pulp excitation in circumstances in which spread of the stimulating current to periodontal and gingival structures is most unlikely. Two interpretations of these results are considered: (1) that tooth pulp afferents may have some unspecified sensory function besides mediation of painful sensations and (2) that they may be specialized in the mediation of nociceptive impulses but may give rise to innocuous sensations under special circumstances.