A fully automated high-throughput plasmid purification workstation for the generation of mammalian cell expression-quality DNA.

Early-stage antibody discovery and engineering typically require the cloning, expression, and screening of large numbers of proteins. Normally, DNA fragments encoding proteins of interest are cloned into extra-chromosomal plasmids that are amplified in Escherichia coli. Following purification from the bacteria, the plasmids are introduced into appropriate cells, and the expressed recombinant proteins screened for desired binding or function in a high-throughput manner. Even in a 96-well plate format, plasmid purification from E. coli is typically a labor intensive and time-consuming process. To further accelerate our existing biotherapeutic discovery workflows we designed, qualified, and enabled a fully integrated high-throughput plasmid purification and quantification workstation which we have termed AMPS (Automated Miniprep Plasmid Station). Using components from a commercially available kit, AMPS can purify plasmid preparations from twenty 96-deep-well plates of E. coli cultures, measure DNA absorbance at 260 nm, calculate plasmid concentrations, and prepare 96-deep-well plates for mammalian expression in an operator-independent manner. Plasmid yields and concentrations are equivalent to those obtained off-line. Furthermore, the quality of the DNA purified on the AMPS is equivalent to that obtained off-line in terms of DNA topology, and absence of contaminating bacterial chromosomal DNA and RNA. Most importantly, plasmids purified on the AMPS provide similar antibody titers following transfection in CHO cells as plasmids purified off-line. The AMPS bridges high-throughput E. coli colony picking capabilities typically available in an automation lab with downstream CHO expression needs and will facilitate screening of large numbers of biotherapeutics in binding and cell assay screens.

A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions.

Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition, and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ∼380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a large and complex network of interactions both within and across biological systems. We identified new PPIs for receptors with well-characterized ligands and binding partners for "orphan" receptors. New PPIs include proteins expressed on multiple cell types and involved in diverse processes including immune and nervous system development and function, differentiation/proliferation, metabolism, vascularization, and reproduction. These PPIs provide a resource for further biological investigation into their functional relevance and may offer new therapeutic drug targets.

A High-Throughput System for Transient and Stable Protein Production in Mammalian Cells.

Recombinant protein expression and purification is an essential component of biomedical research and drug discovery. Advances in automation and laboratory robotics have enabled the development of highly parallel and rapid processes for cell culture and protein expression, purification, and analysis. Human embryonic kidney (HEK) cells and Chinese hamster ovary (CHO) cells have emerged as the standard host cell workhorses for producing recombinant secreted mammalian proteins by using both transient and stable production strategies. In this chapter we describe a fully automated custom platform, Protein Expression and Purification Platform (PEPP), used for transient protein production from HEK cells and stable protein production from CHO cells. Central to PEPP operation is a suite of custom robotic and instrumentation platforms designed and built at GNF, custom cell culture ware, and custom scheduling software referred to as Runtime. The PEPP platform enables cost-effective, facile, consistent production of proteins at quantities and quality useful for early stage drug discovery tasks such as screening, bioassays, protein engineering, and analytics.

Mammalian cell culture density determination using a laser through-beam sensor.

High-throughput protein expression platforms are increasingly used to produce proteins for many applications: to support studies in structure/function, regulation and proteomics, as well as for direct use as potential biotherapeutic agents for medical applications. Here we describe a device that we refer to as the flask density reader (FDR) consisting of a through-beam laser and sensor, and a customized culture flask-receiving nest. The FDR has been integrated onto GNF System™'s automated protein expression platform to enable rapid, noninvasive, fully automated spectrophotometric determination of cell densities in suspension mammalian cell cultures. The FDR reduces the risk of culture contamination from frequent flask sampling and greatly reduces the time and effort needed to count cells using off-line methods.

Speech perception adjusts to stable spectrotemporal properties of the listening environment.

When perceiving speech, listeners compensate for reverberation and stable spectral peaks in the speech signal. Despite natural listening conditions usually adding both reverberation and spectral coloration, these processes have only been studied separately. Reverberation smears spectral peaks across time, which is predicted to increase listeners' compensation for these peaks. This prediction was tested using sentences presented with or without a simulated reverberant sound field. All sentences had a stable spectral peak (added by amplifying frequencies matching the second formant frequency [F2] in the target vowel) before a test vowel varying from /i/ to /u/ in F2 and spectral envelope (tilt). In Experiment 1, listeners demonstrated increased compensation (larger decrease in F2 weights and larger increase in spectral tilt weights for identifying the target vowel) in reverberant speech than in nonreverberant speech. In Experiment 2, increased compensation was shown not to be due to reverberation tails. In Experiment 3, adding a pure tone to nonreverberant speech at the target vowel's F2 frequency increased compensation, revealing that these effects are not specific to reverberation. Results suggest that perceptual adjustment to stable spectral peaks in the listening environment is not affected by their source or cause.

Predicting contrast effects following reliable spectral properties in speech perception.

Vowel perception is influenced by precursor sounds that are resynthesized to shift frequency regions [Ladefoged and Broadbent (1957). J. Acoust. Soc. Am. 29(1), 98-104] or filtered to emphasize narrow [Kiefte and Kluender (2008). J. Acoust. Soc. Am. 123(1), 366-376] or broad frequency regions [Watkins (1991). J. Acoust. Soc. Am. 90(6), 2942-2955]. Spectral differences between filtered precursors and vowel targets are perceptually enhanced, producing spectral contrast effects (e.g., emphasizing spectral properties of /ɪ/ in the precursor elicited more /ɛ/ responses to an /ɪ/-/ɛ/ vowel continuum, and vice versa). Historically, precursors have been processed by high-gain filters, resulting in prominent stable long-term spectral properties. Perceptual sensitivity to subtler but equally reliable spectral properties is unknown. Here, precursor sentences were processed by filters of variable bandwidths and different gains, then followed by vowel sounds varying from /ɪ/-/ɛ/. Contrast effects were widely observed, including when filters had only 100-Hz bandwidth or +5 dB gain. Average filter power was a good predictor of the magnitudes of contrast effects, revealing a close linear correspondence between the prominence of a reliable spectral property and the size of shifts in perceptual responses. High sensitivity to subtle spectral regularities suggests contrast effects are not limited to high-power filters, and thus may be more pervasive in speech perception than previously thought.

Modest, reliable spectral peaks in preceding sounds influence vowel perception.

When a spectral property is reliable across an acoustic context and subsequent vowel target, perception deemphasizes this cue and shifts toward less predictable, more informative cues. This phenomenon (auditory perceptual calibration) has been demonstrated for reliable spectral peaks +20 dB or larger, but psychoacoustic findings predict sensitivity to more modest spectral peaks. Listeners identified vowel targets following a sentence with a reliable +2 to +15 dB spectral peak centered at F2 of the vowel. Vowel identifications weighted F2 significantly less when reliable peaks were at least +5 dB. Results demonstrate high sensitivity to reliable acoustic properties in the sensory environment.

Auditory/visual distance estimation: accuracy and variability.

Past research has shown that auditory distance estimation improves when listeners are given the opportunity to see all possible sound sources when compared to no visual input. It has also been established that distance estimation is more accurate in vision than in audition. The present study investigates the degree to which auditory distance estimation is improved when matched with a congruent visual stimulus. Virtual sound sources based on binaural room impulse response (BRIR) measurements made from distances ranging from approximately 0.3 to 9.8 m in a concert hall were used as auditory stimuli. Visual stimuli were photographs taken from the participant's perspective at each distance in the impulse response measurement setup presented on a large HDTV monitor. Participants were asked to estimate egocentric distance to the sound source in each of three conditions: auditory only (A), visual only (V), and congruent auditory/visual stimuli (A+V). Each condition was presented within its own block. Sixty-two participants were tested in order to quantify the response variability inherent in auditory distance perception. Distance estimates from both the V and A+V conditions were found to be considerably more accurate and less variable than estimates from the A condition.

Amplitude modulation detection by human listeners in reverberant sound fields: Effects of prior listening exposure.

Previous work [Zahorik et al., POMA, 15, 050002 (2012)] has reported that for both broadband and narrowband noise carrier signals in a simulated reverberant sound field, human sensitivity to amplitude modulation (AM) is higher than would be predicted based on the acoustical modulation transfer function (MTF) of the listening environment. These results may be suggestive of mechanisms that functionally enhance modulation in reverberant listening, although many details of this enhancement effect are unknown. Given recent findings that demonstrate improvements in speech understanding with prior exposure to reverberant listening environments, it is of interest to determine whether listening exposure to a reverberant room might also influence AM detection in the room, and perhaps contribute to the AM enhancement effect. Here, AM detection thresholds were estimated (using an adaptive 2-alternative forced-choice procedure) in each of two listening conditions: one in which consistent listening exposure to a particular room was provided, and a second that intentionally disrupted listening exposure by varying the room from trial-to-trial. Results suggest that consistent prior listening exposure contributes to enhanced AM sensitivity in rooms. [Work supported by the NIH/NIDCD.].

Amplitude modulation detection by human listeners in reverberant sound fields: Carrier bandwidth effects and binaural versus monaural comparison.

Previous work [Zahorik et al., POMA, 12, 050005 (2011)] has reported that for a broadband noise carrier signal in a simulated reverberant sound field, human sensitivity to amplitude modulation (AM) is higher than would be predicted based on the broadband acoustical modulation transfer function (MTF) of the listening environment. Interpretation of this result was complicated by the fact that acoustical MTFs of rooms are often quite different for different carrier frequency regions, and listeners may have selectively responded to advantageous carrier frequency regions where the effective acoustic modulation loss due to the room was less than indicated by a broadband acoustic MTF analysis. Here, AM sensitivity testing and acoustic MTF analyses were expanded to include narrowband noise carriers (1-octave and 1/3-octave bands centered at 4 kHz), as well as monaural and binaural listening conditions. Narrowband results were found to be consistent with broadband results: In a reverberant sound field, human AM sensitivity is higher than indicated by the acoustical MTFs. The effect was greatest for modulation frequencies above 32 Hz and was present whether the stimulation was monaural or binaural. These results are suggestive of mechanisms that functionally enhance modulation in reverberant listening.

Amplitude modulation detection by human listeners in sound fields.

The temporal modulation transfer function (TMTF) approach allows techniques from linear systems analysis to be used to predict how the auditory system will respond to arbitrary patterns of amplitude modulation (AM). Although this approach forms the basis for a standard method of predicting speech intelligibility based on estimates of the acoustical modulation transfer function (MTF) between source and receiver, human sensitivity to AM as characterized by the TMTF has not been extensively studied under realistic listening conditions, such as in reverberant sound fields. Here, TMTFs (octave bands from 2 - 512 Hz) were obtained in 3 listening conditions simulated using virtual auditory space techniques: diotic, anechoic sound field, reverberant room sound field. TMTFs were then related to acoustical MTFs estimated using two different methods in each of the listening conditions. Both diotic and anechoic data were found to be in good agreement with classic results, but AM thresholds in the reverberant room were lower than predictions based on acoustical MTFs. This result suggests that simple linear systems techniques may not be appropriate for predicting TMTFs from acoustical MTFs in reverberant sound fields, and may be suggestive of mechanisms that functionally enhance modulation during reverberant listening.

Cross-species hybridization of woodchuck hepatitis viral infection-induced woodchuck hepatocellular carcinoma using human, rat and mouse oligonucleotide microarrays.

BACKGROUND AND AIM: We aimed to evaluate the transcriptional characteristics of viral infection-induced woodchuck hepatocellular carcinoma (HCC), to compare the use of human, rat and mouse gene arrays for cross-species hybridization, and to look into gene expression profiles in woodchuck HCC by the combined use of these arrays. METHODS: Commercially available human, rat and mouse oligonucleotide microarrays were used to determine the gene expression profiles on the same woodchuck liver samples. Differentially expressed genes between HCC and the surrounding hepatic tissues found in the arrays were selected for quantitative reverse transcription polymerase chain reaction. RESULTS: Despite the difference in the number of the probes from each array, the percentage of genes that were detectable was similar. Stringent microarray data analysis using both supervised and unsupervised methods identified 281 differentially expressed genes via the human array with a false discovery rate (FDR) of 0.99%, 107 genes via the rat array with an FDR of 1.85% and 78 genes via the mouse array with an FDR of 7.41%. Eleven genes were differentially changed in all three arrays that include the upregulation of NPM1, H2AFZ, EEF1G, HNRPAB, RPS18, EIF5, CKS2, ARIH1, RPS12 and RPS10, and the downregulation of EGR1. The quantitative reverse transcription polymerase chain reaction with woodchuck-specific primers confirmed the reliability of the microarray results. CONCLUSION: This study further demonstrated the utility of cross-species hybridization of microarrays on woodchuck HCC. A combined use of three types of arrays identified more differential genes in HCC than individual arrays with the human array providing the richest information among the three arrays used.

Quantitative evaluation of 2-deoxy-2[F-18]fluoro-D-glucose-positron emission tomography imaging on the woodchuck model of hepatocellular carcinoma with histological correlation.

PURPOSE: The Eastern woodchuck (Marmota monax) is considered as a naturally occurring animal model of hepatocellular carcinoma (HCC). The performance of 2-deoxy-2-[F-18]fluoro-D-glucose (FDG) for imaging HCC on the woodchuck using Positron emission tomography (PET) was investigated in this study. PROCEDURES: Dynamic FDG-PET scans were performed on five woodchucks with HCC and one healthy woodchuck before removal and processing of the liver tissues for histology. The parameters of a two-tissue compartment model with dual input were estimated using weighted least squares (WLS). RESULTS: Ten HCCs were confirmed histologically. Six HCCs had a tumor-to-liver standardized uptake value (SUV) ratio < or =1.15, a k (4) / k (3) ratio similar to that in hepatic tissues and were well-differentiated. Four HCCs had a tumor-to-liver SUV ratio >1.15, a lower k (4) / k (3) ratio than the hepatic tissues and were moderately differentiated. CONCLUSIONS: Increased FDG uptake was observed in HCCs that were the least differentiated and correlated with a lower k (4) / k (3) ratio.

Gene expression studies of hepatitis virus-induced woodchuck hepatocellular carcinoma in correlation with human results.

The lack of good molecular markers for diagnosis as well as treatment assessment has rendered the hepatocellular carcinoma (HCC) a major challenge in health care. In this study, woodchucks were used as an animal model for hepatitis virus-induced HCC, and gene expression studies were performed using a human oligonucleotide microarray. An analysis approach combing supervised significant analysis of microarray (SAM), prediction analysis of microarray (PAM), and unsupervised hierarchical cluster methodologies statistically determined 211 upregulated and 78 downregulated genes between liver cancer and non-cancer liver tissues, and demonstrated > or = 93% accuracy in classifying the tissue samples. RT-PCR results confirmed the differential expression of selected sequenced woodchuck genes (SAT, IDH3B, SCD) in the microarray. Our study showed that differentially expressed genes were involved in transcription, RNA splicing, translation, cell cycle, metabolism, protein folding and degradation, apoptosis, immune response, metal binding, etc. Interestingly, some genes were involved with signaling pathways such as Ras/MAPK (MAPKAP1), Src-dependent pathways (CSK), hedgehog signaling pathway (HHIP), while Wnt signaling pathway may not be dominant in woodchuck HCC as shown by the downregulation of beta-catenin (TNNB1) and the upregulation of CXXC4 and CSNK2B. Numerous genes found in this study were also differentially expressed in human HCC and many other human cancers including breast, prostate and lung cancers, etc., serving as tumor suppressors, promoters, prognostic markers or chemotherapy targets. In conclusion, this study has demonstrated the robustness of the data analysis and the potential of using human microarrays on woodchuck samples. In particular, some of the differentially expressed genes in the woodchuck HCC can be further explored for possible molecular imaging targets or biological markers in human HCC.

Cross-species hybridization of woodchuck hepatitis virus-induced hepatocellular carcinoma using human oligonucleotide microarrays.

AIM: To demonstrate the feasibility of using woodchuck samples on human microarrays, to provide insight into pathways involving positron emission tomography (PET) imaging tracers and to identify genes that could be potential molecular imaging targets for woodchuck hepatocellular carcinoma. METHODS: Labeled cRNA from woodchuck tissue samples were hybridized to Affymetrix U133 plus 2.0 GeneChips. Ten genes were selected for validation using quantitative RT-PCR and literature review was made. RESULTS: Testis enhanced gene transcript (BAX Inhibitor 1), alpha-fetoprotein, isocitrate dehydrogenase 3 (NAD+) beta, acetyl-CoA synthetase 2, carnitine palmitoyltransferase 2, and N-myc2 were up-regulated and spermidine/spermine N1-acetyltransferase was down-regulated in the woodchuck HCC. We also found previously published results supporting 8 of the 10 most up-regulated genes and all 10 of the 10 most down-regulated genes. CONCLUSION: Many of our microarray results were validated using RT-PCR or literature search. Hence, we believe that woodchuck HCC and non-cancerous liver samples can be used on human microarrays to yield meaningful results.