Degradation of temporal contrast from post-pedestal interference with a chirped pulse in an optical parametric amplifier

Pre-pedestal generation is observed in a 0.35-PW laser front end coming from a post-pedestal via instantaneous gain and pump depletion in an optical parametric amplifier during chirped-pulse amplification. Generalized simulations show how this effect arises from gain nonlinearity and applies to all optical parametric chirped-pulse-amplification systems with a post-pedestal. An experiment minimizing the effect of B-integral is used to isolate and study the newly observed conversion of a continuous post-pedestal into a continuous pre-pedestal. Matching numerical simulations confirm experimental results and additionally reveal how third-order dispersion largely controls the slope of the generated pre-pedestal.

Global forecasts in reservoir computers

A reservoir computer is a machine learning model that can be used to predict the future state(s) of time-dependent processes, e.g., dynamical systems. In practice, data in the form of an input-signal are fed into the reservoir. The trained reservoir is then used to predict the future state of this signal. We develop a new method for not only predicting the future dynamics of the input-signal but also the future dynamics starting at an arbitrary initial condition of a system. The systems we consider are the Lorenz, Rossler, and Thomas systems restricted to their attractors. This method, which creates a global forecast, still uses only a single input-signal to train the reservoir but breaks the signal into many smaller windowed signals. We examine how well this windowed method is able to forecast the dynamics of a system starting at an arbitrary point on a system's attractor and compare this to the standard method without windows. We find that the standard method has almost no ability to forecast anything but the original input-signal while the windowed method can capture the dynamics starting at most points on an attractor with significant accuracy.

A novel multiplex biomarker panel for profiling human acute and chronic kidney disease

Acute and chronic kidney disease continues to confer significant morbidity and mortality in the clinical setting. Despite high prevalence of these conditions, few validated biomarkers exist to predict kidney dysfunction. In this study, we utilized a novel kidney multiplex panel to measure 21 proteins in plasma and urine to characterize the spectrum of biomarker profiles in kidney disease. Blood and urine samples were obtained from age-/sex-matched healthy control subjects (HC), critically-ill COVID-19 patients with acute kidney injury (AKI), and patients with chronic or end-stage kidney disease (CKD/ESKD). Biomarkers were measured with a kidney multiplex panel, and results analyzed with conventional statistics and machine learning. Correlations were examined between biomarkers and patient clinical and laboratory variables. Median AKI subject age was 65.5 (IQR 58.5-73.0) and median CKD/ESKD age was 65.0 (IQR 50.0-71.5). Of the CKD/ESKD patients, 76.1% were on hemodialysis, 14.3% of patients had kidney transplant, and 9.5% had CKD without kidney replacement therapy. In plasma, 19 proteins were significantly different in titer between the HC versus AKI versus CKD/ESKD groups, while NAG and RBP4 were unchanged. TIMP-1 (PPV 1.0, NPV 1.0), best distinguished AKI from HC, and TFF3 (PPV 0.99, NPV 0.89) best distinguished CKD/ESKD from HC. In urine, 18 proteins were significantly different between groups except Calbindin, Osteopontin and TIMP-1. Osteoactivin (PPV 0.95, NPV 0.95) best distinguished AKI from HC, and β2-microglobulin (PPV 0.96, NPV 0.78) best distinguished CKD/ESKD from HC. A variety of correlations were noted between patient variables and either plasma or urine biomarkers. Using a novel kidney multiplex biomarker panel, together with conventional statistics and machine learning, we identified unique biomarker profiles in the plasma and urine of patients with AKI and CKD/ESKD. We demonstrated correlations between biomarker profiles and patient clinical variables. Our exploratory study provides biomarker data for future hypothesis driven research on kidney disease.

Final amplifier of an ultra-intense all-OPCPA system with 13-J output signal energy and 41% pump-to-signal conversion efficiency

Optical parametric chirped-pulse amplification (OPCPA) using high-energy Nd:glass lasers has the potential to produce ultra-intense pulses (>1023 W/cm2). We report on the performance of the final high-efficiency amplifier in an OPCPA system based on large-aperture (63 × 63-mm2) partially deuterated potassium dihydrogen phosphate (DKDP) crystals. The seed beam (180-nm bandwidth, 110 mJ) was provided by the preceding OPCPA stages. A maximum pump-to-signal conversion efficiency of 41% and signal energy up to 13 J were achieved with a 52-mm-long DKDP crystal due to the flattop super-Gaussian pump beam profile and flat-in-time pulse shape.

Achieving 100 GW idler pulses from an existing petawatt optical parametric chirped pulse amplifier

Optical parametric chirped-pulse-amplification produces two broadband pulses, a signal and an idler, that can both provide peak powers >100 GW. In most cases the signal is used, but compressing the longer-wavelength idler opens up opportunities for experiments where the driving laser wavelength is a key parameter. This paper will describe several subsystems that were added to a petawatt class, Multi-Terawatt optical parametric amplifier line (MTW-OPAL) at the Laboratory for Laser Energetics to address two long-standing issues introduced by the use of the idler, angular dispersion, and spectral phase reversal. To the best of our knowledge, this is the first time that compensation of angular dispersion and phase reversal has been achieved in a single system and results in a 100 GW, 120-fs duration, pulse at 1170 nm.

Cross-immunity against SARS-COV-2 variants of concern in naturally infected critically ill COVID-19 patients

Critically ill patients infected with SARS-CoV-2 display adaptive immunity, but it is unknown if they develop cross-reactivity to variants of concern (VOCs). We profiled cross-immunity against SARS-CoV-2 VOCs in naturally infected, non-vaccinated, critically ill COVID-19 patients. Wave-1 patients (wild-type infection) were similar in demographics to Wave-3 patients (wild-type/alpha infection), but Wave-3 patients had higher illness severity. Wave-1 patients developed increasing neutralizing antibodies to all variants, as did patients during Wave-3. Wave-3 patients, when compared to Wave-1, developed more robust antibody responses, particularly for wild-type, alpha, beta and delta variants. Within Wave-3, neutralizing antibodies were significantly less to beta and gamma VOCs, as compared to wild-type, alpha and delta. Patients previously diagnosed with cancer or chronic obstructive pulmonary disease had significantly fewer neutralizing antibodies. Naturally infected ICU patients developed adaptive responses to all VOCs, with greater responses in those patients more likely to be infected with the alpha variant, versus wild-type.

Short-term risk prediction after major lower limb amputation: PERCEIVE study

BACKGROUND

The accuracy with which healthcare professionals (HCPs) and risk prediction tools predict outcomes after major lower limb amputation (MLLA) is uncertain. The aim of this study was to evaluate the accuracy of predicting short-term (30 days after MLLA) mortality, morbidity, and revisional surgery.

METHODS

The PERCEIVE (PrEdiction of Risk and Communication of outcomE following major lower limb amputation: a collaboratIVE) study was launched on 1 October 2020. It was an international multicentre study, including adults undergoing MLLA for complications of peripheral arterial disease and/or diabetes. Preoperative predictions of 30-day mortality, morbidity, and MLLA revision by surgeons and anaesthetists were recorded. Probabilities from relevant risk prediction tools were calculated. Evaluation of accuracy included measures of discrimination, calibration, and overall performance.

RESULTS

Some 537 patients were included. HCPs had acceptable discrimination in predicting mortality (931 predictions; C-statistic 0.758) and MLLA revision (565 predictions; C-statistic 0.756), but were poor at predicting morbidity (980 predictions; C-statistic 0.616). They overpredicted the risk of all outcomes. All except three risk prediction tools had worse discrimination than HCPs for predicting mortality (C-statistics 0.789, 0.774, and 0.773); two of these significantly overestimated the risk compared with HCPs. SORT version 2 (the only tool incorporating HCP predictions) demonstrated better calibration and overall performance (Brier score 0.082) than HCPs. Tools predicting morbidity and MLLA revision had poor discrimination (C-statistics 0.520 and 0.679).

CONCLUSION

Clinicians predicted mortality and MLLA revision well, but predicted morbidity poorly. They overestimated the risk of mortality, morbidity, and MLLA revision. Most short-term risk prediction tools had poorer discrimination or calibration than HCPs. The best method of predicting mortality was a statistical tool that incorporated HCP estimation.

Elevated vascular transformation blood biomarkers in Long-COVID indicate angiogenesis as a key pathophysiological mechanism

BACKGROUND

Long-COVID is characterized by prolonged, diffuse symptoms months after acute COVID-19. Accurate diagnosis and targeted therapies for Long-COVID are lacking. We investigated vascular transformation biomarkers in Long-COVID patients.

METHODS

A case-control study utilizing Long-COVID patients, one to six months (median 98.5 days) post-infection, with multiplex immunoassay measurement of sixteen blood biomarkers of vascular transformation, including ANG-1, P-SEL, MMP-1, VE-Cad, Syn-1, Endoglin, PECAM-1, VEGF-A, ICAM-1, VLA-4, E-SEL, thrombomodulin, VEGF-R2, VEGF-R3, VCAM-1 and VEGF-D.

RESULTS

Fourteen vasculature transformation blood biomarkers were significantly elevated in Long-COVID outpatients, versus acutely ill COVID-19 inpatients and healthy controls subjects (P < 0.05). A unique two biomarker profile consisting of ANG-1/P-SEL was developed with machine learning, providing a classification accuracy for Long-COVID status of 96%. Individually, ANG-1 and P-SEL had excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, P < 0.0001; validated in a secondary cohort). Specific to Long-COVID, ANG-1 levels were associated with female sex and a lack of disease interventions at follow-up (P < 0.05).

CONCLUSIONS

Long-COVID patients suffer prolonged, diffuse symptoms and poorer health. Vascular transformation blood biomarkers were significantly elevated in Long-COVID, with angiogenesis markers (ANG-1/P-SEL) providing classification accuracy of 96%. Vascular transformation blood biomarkers hold potential for diagnostics, and modulators of angiogenesis may have therapeutic efficacy.

Implementation of a Preoperative Huddle at a Level 1 Trauma Center

OBJECTIVE

Medical errors resulting in patient harm still occur at an alarmingly high rate. Surgery is a high-risk area that can frequently result in patient harm if errors occur. There is a need for standardization of communication and processes to decrease errors. We sought to determine whether the implementation of a preoperative huddle at our hospital could standardize communication and decrease medical errors.

METHODS

A unique preoperative huddle was developed and implemented at a level 1 trauma center. We reviewed data before and after the implementation of the preoperative huddle including patient surveys and comments, the percentage of on-time operating room (OR) starts, OR turnover times, and the number of sentinel events.

RESULTS

After huddle implementation, we observed a trend of improvement in our patient survey results on patient's perception that the doctors/nurses explained the procedure understandably after huddle implementation. There was a statistically yet limited clinically significant increase in OR turnover time from 37 to 40 minutes (P < 0.001). There was also an increase in on-time OR starts from 37% to 45% (P < 0.001). We observed a decrease in the number of sentinel events, with only 1 occurring each year since implementation.

CONCLUSIONS

A preoperative huddle was successfully implemented at a level 1 trauma hospital and helped standardize communication without significantly disrupting workflow. To our knowledge, this method of preoperative huddling has not been previously described in the literature.

Analysis of pump-to-signal noise transfer in two-stage ultra-broadband optical parametric chirped-pulse amplification

In optical parametric chirped-pulse amplification (OPCPA), pump temporal intensity modulation is transferred to the chirped-signal spectrum via instantaneous parametric gain and results in contrast degradation of the recompressed signal. We investigate, for the first time to our knowledge, the pump-to-signal noise transfer in a two-stage ultra-broadband OPCPA pumped by a single laser and show the dependence of pump-induced signal noise, characterized both before and after pulse compression, on the difference in pump-seed delay in the two stages. We demonstrate an up-to-15-dB reduction of the pump-induced contrast degradation via pump-seed delay optimization. Experiments and simulations show that, even when parametric amplifiers are operated in saturation, the pump-seed delay can be used to minimize the pump-induced contrast degradation that is attributed largely to the noises from the unsaturated edges of the pulse and that of the beam.

Comparison of photoactivatable crosslinkers for in-gel immunoassays

While fluorescence readout is a key detection modality for hydrogel-based immunoassays, background fluorescence due to autofluorescence or non-specific antibody interactions impairs the lower limit of detection of fluorescence immunoassays. Chemical modifications to the hydrogel structure impact autofluorescence and non-specific interactions. Benzophenone is a common photoactivatable molecule, and benzophenone methacrylamide (BPMA) has been used for cross-linking protein in polyacrylamide (PA) hydrogels. However, previous studies have suggested that the aromatic structure of benzophenone can contribute to increased autofluorescence and non-specific hydrophobic interactions with unbound fluorescent probes. Here, we synthesize diazirine methacrylamide (DZMA) as an alternative photoactivatable molecule to crosslink into PA hydrogels for in-gel protein capture for in-gel immunoassays. We hypothesize that the less hydrophobic structure of diazirine (based on previously reported predicted and experimental log P values) exhibits both reduced autofluorescence and non-specific hydrophobic interactions. We find that while equal concentrations of DZMA and BPMA result in lower protein target photocapture in the diazirine configuration, increasing the DZMA concentration up to 12 mM improves in-gel protein capture to be on par with previously reported and characterized 3 mM BPMA hydrogels. Furthermore, despite the higher concentration of diazirine, we observe negligible autofluorescence signal and a 50% reduction in immunoassay fluorescence background signal in diazirine gels compared to BPMA gels resulting in comparable signal-to-noise ratios (SNR) of the probed protein target. Finally, we test the utility of DZMA for single-cell immunoblotting in an open microfluidic device and find that protein migrates ∼1.3× faster in DZMA hydrogels than in BPMA hydrogels. However, in DZMA hydrogels we detect only 15% of the protein signal compared to BPMA hydrogels suggesting that the diazirine chemistry results in greater protein losses following electrophoretic separations. We establish that while diazirine has lower background fluorescence signal, which may potentially improve immunoassay performance, the lower capture efficiency of diazirine reduces its utility in open microfluidic systems susceptible to sample losses.

Looking down: a model for visual route following in flying insects

Insect visual navigation is often assumed to depend on panoramic views of the horizon, and how these change as the animal moves. However, it is known that honey bees can visually navigate in flat, open meadows where visual information at the horizon is minimal, or would remain relatively constant across a wide range of positions. In this paper we hypothesise that these animals can navigate using view memories of the ground. We find that in natural scenes, low resolution views from an aerial perspective of ostensibly self-similar terrain (e.g. within a field of grass) provide surprisingly robust descriptors of precise spatial locations. We propose a new visual route following approach that makes use of transverse oscillations to centre a flight path along a sequence of learned views of the ground. We deploy this model on an autonomous quadcopter and demonstrate that it provides robust performance in the real world on journeys of up to 30 m. The success of our method is contingent on a robust view matching process which can evaluate the familiarity of a view with a degree of translational invariance. We show that a previously developed wavelet based bandpass orientated filter approach fits these requirements well, exhibiting double the catchment area of standard approaches. Using a realistic simulation package, we evaluate the robustness of our approach to variations in heading direction and aircraft height between inbound and outbound journeys. We also demonstrate that our approach can operate using a vision system with a biologically relevant visual acuity and viewing direction.

Detection and Profiling of Human Coronavirus Immunoglobulins in Critically Ill Coronavirus Disease 2019 Patients

OBJECTIVES

Coronavirus disease 2019 continues to spread worldwide with high levels of morbidity and mortality. We performed anticoronavirus immunoglobulin G profiling of critically ill coronavirus disease 2019 patients to better define their underlying humoral response.

DESIGN

Blood was collected at predetermined ICU days to measure immunoglobulin G with a research multiplex assay against four severe acute respiratory syndrome coronavirus 2 proteins/subunits and against all six additionally known human coronaviruses.

SETTING

Tertiary care ICU and academic laboratory.

SUBJECTS

ICU patients suspected of being infected with severe acute respiratory syndrome coronavirus 2 had blood collected until either polymerase chain reaction testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative) or until death or discharge if the patient tested polymerase chain reaction positive (coronavirus disease 2019 positive).

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Age- and sex-matched healthy controls and ICU patients who were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well-balanced with the exception that coronavirus disease 2019 positive patients had greater body mass indexes, presented with bilateral pneumonias more frequently, and suffered lower Pao2:Fio2 ratios, when compared with coronavirus disease 2019 negative patients (p < 0.05). Mortality rate for coronavirus disease 2019 positive patients was 50%. On ICU days 1-3, anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G was significantly elevated in coronavirus disease 2019 positive patients, as compared to both healthy control subjects and coronavirus disease 2019 negative patients (p < 0.001). Weak severe acute respiratory syndrome coronavirus immunoglobulin G serologic responses were also detected, but not other coronavirus subtypes. The four anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G were maximal by ICU day 3, with all four anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G providing excellent diagnostic potential (severe acute respiratory syndrome coronavirus 2 Spike 1 protein immunoglobulin G, area under the curve 1.0, p < 0.0005; severe acute respiratory syndrome coronavirus receptor binding domain immunoglobulin G, area under the curve, 0.93-1.0; p ≤ 0.0001; severe acute respiratory syndrome coronavirus 2 Spike proteins immunoglobulin G, area under the curve, 1.0; p < 0.0001; severe acute respiratory syndrome coronavirus 2 Nucleocapsid protein immunoglobulin G area under the curve, 0.90-0.95; p ≤ 0.0003). Anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G increased and/or plateaued over 10 ICU days.

CONCLUSIONS

Critically ill coronavirus disease 2019 patients exhibited anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G, whereas serologic responses to non-severe acute respiratory syndrome coronavirus 2 antigens were weak or absent. Detection of human coronavirus immunoglobulin G against the different immunogenic structural proteins/subunits with multiplex assays may be useful for pathogen identification, patient cohorting, and guiding convalescent plasma therapy.

From Electronic Sequence to Purified Protein Using Automated Gene Synthesis and In Vitro Transcription/Translation

De novo gene synthesis is the state-of-the-art method used to obtain genetic material adapted to the requirements of the host organism and a cornerstone for modern synthetic biology. Yet, little progress has been made regarding downstream processes of protein production from synthetic genetic material. The production of recombinant proteins traditionally requires extensive preparatory work including gene amplification, cloning, sequencing, transformation or transfection of the expression host, cultivation of living cells, and purification of the overexpressed protein. In this work we describe a fast and automated workflow for cell-free production of proteins starting from an electronic protein sequence or accession number. PRESTO (protein expression starting from oligonucleotides) seamlessly combines a tailored in silico sequence optimization with the assembly of short oligonucleotides into synthetic linear DNA expression cassettes, mammalian in vitro transcription/translation, and protein purification thereof. Integrated on a small liquid handling system it provides a hands-free high throughput source for functional synthetic proteins within 1 day.

Simulation of grating compressor misalignment tolerances and mitigation strategies for chirped-pulse-amplification systems of varying bandwidths and beam sizes

The effects of pulse compressor grating misalignment on pulse duration and focusability are simulated for chirped-pulse-amplification systems of varying bandwidths, beam sizes, groove densities, and incident angles. Tilt-alignment tolerances are specified based on a 2 drop in focused intensity, illustrating how tolerances scale with bandwidth and compressor beam size, which scales with energy when transformed via known grating damage thresholds. Grating-alignment tolerance scaling with grating groove density and incident/diffracted angles is investigated and applied to compressor design. A correlation between grating tip and in-plane rotation error sensitivity is defined and used to compensate residual out-of-plane angular dispersion, even for ultra-broadband pulses. Simulation of dispersion compensation methods after grating misalignment is shown to mitigate pulse lengthening, limited by temporal contrast degradation and higher-order effects for ultrabroad bandwidths.

Mapping the interview transcript: Identifying spatial policy areas from daily working practices

An interview transcript can be a rich source of geographical references whose potential are not always fully realised in their conventional analysis. Geo-referencing techniques can be used to assign a spatial footprint to place names, adding value to these data and allowing the geographic information within them to be exploited when coupled with GIS technology. This paper discusses a method of analysing and visualising interview transcripts in order to understand the spatial extent of public policy practitioners' activities. Through aggregation and statistical mapping it is possible to gain insight into the importance of space across a range of public policy themes and to understand the relationship between practitioner-defined policy themes and the formal administrative boundaries within which they typically work. The research demonstrates that spatial working practices rarely conform to formal administrative boundaries and that there are varying degrees of spatial focus between different policy themes within localities. It also reveals that spatial working practices can continue to be influenced by historic geographies and can be pulled in different directions, reflecting both the devolved nature of the sector and the particular geographical context of the setting. It concludes that mapping the interview transcript can add value and provide additional insights to more conventional analysis.

Characterization and Use of TurboLuc Luciferase as a Reporter for High-Throughput Assays

Luciferase-based reporter assays are powerful tools for monitoring gene expression in cells because of their ultrasensitive detection capacity and wide dynamic range. Here we describe the characterization and use of a luciferase reporter enzyme derived from the marine copepod Metridia luciferase family, referred to as TurboLuc luciferase (TurboLuc). To develop TurboLuc, the wild-type luciferase was modified to decrease its size, increase brightness, slow luminescent signal decay, and provide for efficient intracellular expression. To determine the enzyme susceptibility to compound inhibition and judge the suitability of using of TurboLuc as a reporter in screening assays, purified TurboLuc enzyme was screened for inhibitors using two different compound libraries. No inhibitors of this enzyme were identified in a library representative of typical diverse low molecular weight (LMW) compounds using a purified TurboLuc enzyme assay supporting that such libraries will show very low interference with this enzyme. We were able to identify a few inhibitors from a purified natural product library which can serve as useful tools to validate assays using TurboLuc. In addition to the inhibitor profile for TurboLuc we describe the use of this reporter in cells employing miniaturized assay volumes within 1536-well plates. TurboLuc luciferase is the smallest luciferase reporter enzyme described to date (16 kDa), shows bright luminescence and low interference by LMW compounds, and therefore should provide an ideal reporter in assays applied to high-throughput screening.

Abstract 1599: Epithelial mesenchymal transition and its role in TKI resistant NSCLC cell lines

NSCLC cells acquire resistance to EGFR and c-Met TKIs after prolonged use. Our studies indicate that resistance maybe due to upregulation of alternative signaling pathways such as Wnt and mTOR. We have found that activation of Wnt/β-Catenin is also associated with EMT which results in loss of cell adhesion properties and gain of motility and invasiveness. To understand the mechanism of TKI resistance in NSCLC cells with wild type EGFR, we have developed and used H2170-P (parental) cells and the TKI resistant H2170-ER (erlotinib resistant) and H2170-SR (SU11274 resistant) cells. We aim to study EMT and determine if inhibition of β-Catenin, a key regulator of transcription by siRNA or inhibition of ZEB-1 a transcriptional repressor of cell adhesion proteins by inducing mir-200a will help overcome the TKI resistance in NSCLC cells.

Using immunoblotting, we observed modulations in key EMT-related proteins in H2170-ER cells which showed upregulation of ZEB-1, N-cadherin, active beta-catenin, Vimentin, PRMT1 and ZO1 by 1.8, 2.4, 2, 1.8, 2.6 and 2 fold, respectively, and downregulation of E-cadherin (1.8 fold) as compared to H2170-P cells. Similar results were observed for H2170-SR cells. These results were verified using qPCR where we show that β-catenin (3.4-3.2 fold) and N-cadherin (2-1.9 fold) have increased gene expression while E-cadherin (1.7-2.4 fold) has a decreased gene expression in TKI resistant H2170-ER and SR cells when compared to H2170-P cells. miR-200a induction in H2170-ER cells showed significant downregulation of ZEB-1 (3 fold) at 72 hr and an upregulation of E-cadherin (2 fold) when compared to the mock transfected cells. Morphological changes indicative of EMT were detected using immunofluorescence with Vimentin and E-Cadherin antibodies, which displayed upregulation of Vimentin filaments (2 fold) and downregulation of E-Cadherin (3 fold) in H2170-ER and H2170-SR cells when compared to H2170-P cells. We then conducted experiments where we suppressed ZEB-1 by inducing miR-200a in TKI resistant cells. The immunoblotting results suggested recovery of E-Cadherin, and downregulation of ZEB-1 and N-Cadherin in TKI resistant cells. We also observed increased sensitivity towards erlotinib and SU11274 by 20-25%. Additionally, we observed decrease in levels of β-Catenin and upon siRNA knockdown of β-Catenin, suppression of levels of ZEB-1. This indicates a direct correlation between nuclear accumulation of β-Catenin and occurrence of EMT in TKI resistant cells by increase in expression of ZEB-1.

Our results indicate that increased activation of Wnt/β-Catenin pathway in the TKI resistant NSCLC cells is due to the EMT. In NSCLC patients, L858R and T790M mutations are associated with TKI resistance which could be responsible for inducing EMT. We are further studying cell lines with EGFR mutations to determine their role in induction of EMT this may provide clinicians with novel targets to overcome TKI resistance in NSCLC patients.

Citation Format: Ichwaku Rastogi, Tsatsral Iderzorig, Gagan Chhabra, Gregory M. Botting, Andrew Webb, Brad Foster, Brian Webb, Marie Nlend, Neelu Puri. Epithelial mesenchymal transition and its role in TKI resistant NSCLC cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1599.

Mechanism of c-Met and EGFR tyrosine kinase inhibitor resistance through epithelial mesenchymal transition in non-small cell lung cancer

According to currently available estimates from Cancer Research UK, 14.1 million new lung cancer cases were diagnosed and a staggering 8.2 million people worldwide died from lung cancer in 2012. EGFR and c-Met are two tyrosine kinase receptors most commonly overexpressed or mutated in Non-small Cell Lung Cancer (NSCLC) resulting in increased proliferation and survival of lung cancer cells. Tyrosine kinase inhibitors (TKIs), such as erlotinib, approved by the FDA as first/second line therapy for NSCLC patients have limited clinical efficacy due to acquired resistance. In this manuscript, we investigate and discuss the role of epithelial mesenchymal transition (EMT) in the development of resistance against EGFR and c-Met TKIs in NSCLC. Our findings show that Zeb-1, a transcriptional repressor of E-Cadherin, is upregulated in TKI-resistant cells causing EMT. We observed that TKI-resistant cells have increased gene and protein expression of EMT related proteins such as Vimentin, N-Cadherin, β-Catenin and Zeb-1, while expression of E-Cadherin, an important cell adhesion molecule, was suppressed. We also confirmed that TKI-resistant cells display mesenchymal cell type morphology, and have upregulation of β-Catenin which may regulate expression of Zeb-1, a transcriptional repressor of E-Cadherin in TKI-resistant NSCLC cells. Finally, we show that down-regulating Zeb-1 by inducing miR-200a or β-Catenin siRNA can increase drug sensitivity of TKI-resistant cells.

Human severe sepsis cytokine mixture increases β2-integrin-dependent polymorphonuclear leukocyte adhesion to cerebral microvascular endothelial cells in vitro

Introduction

Sepsis-associated encephalopathy (SAE) is a state of acute brain dysfunction in response to a systemic infection. We propose that systemic inflammation during sepsis causes increased adhesion of leukocytes to the brain microvasculature, resulting in blood-brain barrier dysfunction. Thus, our objectives were to measure inflammatory analytes in plasma of severe sepsis patients to create an experimental cytokine mixture (CM), and to use this CM to investigate the activation and interactions of polymorphonuclear leukocytes (PMN) and human cerebrovascular endothelial cells (hCMEC/D3) in vitro.

Methods

The concentrations of 41 inflammatory analytes were quantified in plasma obtained from 20 severe sepsis patients and 20 age- and sex-matched healthy controls employing an antibody microarray. Two CMs were prepared to mimic severe sepsis (SSCM) and control (CCM), and these CMs were then used for PMN and hCMEC/D3 stimulation in vitro. PMN adhesion to hCMEC/D3 was assessed under conditions of flow (shear stress 0.7 dyn/cm²).

Results

Eight inflammatory analytes elevated in plasma obtained from severe sepsis patients were used to prepare SSCM and CCM. Stimulation of PMN with SSCM led to a marked increase in PMN adhesion to hCMEC/D3, as compared to CCM. PMN adhesion was abolished with neutralizing antibodies to either β2 (CD18), α_L/β₂ (CD11α/CD18; LFA-1) or α_M/β₂ (CD11β/CD18; Mac-1) integrins. In addition, immune-neutralization of the endothelial (hCMEC/D3) cell adhesion molecule, ICAM-1 (CD54) also suppressed PMN adhesion.

Conclusions

Human SSCM up-regulates PMN pro-adhesive phenotype and promotes PMN adhesion to cerebrovascular endothelial cells through a β2-integrin-ICAM-1-dependent mechanism. PMN adhesion to the brain microvasculature may contribute to SAE.

Comparative Modeling of Drug Target Proteins☆

In this perspective, we begin by describing the comparative protein structure modeling technique and the accuracy of the corresponding models. We then discuss the significant role that comparative prediction plays in drug discovery. We focus on virtual ligand screening against comparative models and illustrate the state-of-the-art by a number of specific examples.

Compartmentalized oxidative stress in dopaminergic cell death induced by pesticides and complex I inhibitors: distinct roles of superoxide anion and superoxide dismutases

The loss of dopaminergic neurons induced by the parkinsonian toxins paraquat, rotenone, and 1-methyl-4-phenylpyridinium (MPP(+)) is associated with oxidative stress. However, controversial reports exist regarding the source/compartmentalization of reactive oxygen species (ROS) generation and its exact role in cell death. We aimed to determine in detail the role of superoxide anion (O2(•-)), oxidative stress, and their subcellular compartmentalization in dopaminergic cell death induced by parkinsonian toxins. Oxidative stress and ROS formation were determined in the cytosol, intermembrane (IMS), and mitochondrial matrix compartments, using dihydroethidine derivatives and the redox sensor roGFP, as well as electron paramagnetic resonance spectroscopy. Paraquat induced an increase in ROS and oxidative stress in both the cytosol and the mitochondrial matrix prior to cell death. MPP(+) and rotenone primarily induced an increase in ROS and oxidative stress in the mitochondrial matrix. No oxidative stress was detected at the level of the IMS. In contrast to previous studies, overexpression of manganese superoxide dismutase (MnSOD) or copper/zinc SOD (CuZnSOD) had no effect on alterations in ROS steady-state levels, lipid peroxidation, loss of mitochondrial membrane potential (ΔΨm), and dopaminergic cell death induced by MPP(+) or rotenone. In contrast, paraquat-induced oxidative stress and cell death were selectively reduced by MnSOD overexpression, but not by CuZnSOD or manganese-porphyrins. However, MnSOD also failed to prevent ΔΨm loss. Finally, paraquat, but not MPP(+) or rotenone, induced the transcriptional activation of the redox-sensitive antioxidant response elements (ARE) and nuclear factor kappa-B (NF-κB). These results demonstrate a selective role of mitochondrial O2(•-) in dopaminergic cell death induced by paraquat, and show that toxicity induced by the complex I inhibitors rotenone and MPP(+) does not depend directly on mitochondrial O2(•-) formation.

Reporter enzyme inhibitor study to aid assembly of orthogonal reporter gene assays

Reporter gene assays (RGAs) are commonly used to measure biological pathway modulation by small molecules. Understanding how such compounds interact with the reporter enzyme is critical to accurately interpret RGA results. To improve our understanding of reporter enzymes and to develop optimal RGA systems, we investigated eight reporter enzymes differing in brightness, emission spectrum, stability, and substrate requirements. These included common reporter enzymes such as firefly luciferase (Photinus pyralis), Renilla reniformis luciferase, and β-lactamase, as well as mutated forms of R. reniformis luciferase emitting either blue- or green-shifted luminescence, a red-light emitting form of Luciola cruciata firefly luciferase, a mutated form of Gaussia princeps luciferase, and a proprietary luciferase termed "NanoLuc" derived from the luminescent sea shrimp Oplophorus gracilirostris. To determine hit rates and structure-activity relationships, we screened a collection of 42,460 PubChem compounds at 10 μM using purified enzyme preparations. We then compared hit rates and chemotypes of actives for each enzyme. The hit rates ranged from <0.1% for β-lactamase to as high as 10% for mutated forms of Renilla luciferase. Related luciferases such as Renilla luciferase mutants showed high degrees of inhibitor overlap (40-70%), while unrelated luciferases such as firefly luciferases, Gaussia luciferase, and NanoLuc showed <10% overlap. Examination of representative inhibitors in cell-based assays revealed that inhibitor-based enzyme stabilization can lead to increases in bioluminescent signal for firefly luciferase, Renilla luciferase, and NanoLuc, with shorter half-life reporters showing increased activation responses. From this study we suggest strategies to improve the construction and interpretation of assays employing these reporter enzymes.

Robust microarray production of freshly expressed proteins in a human milieu

PURPOSE

In vitro transcription/translation (IVTT) systems are widely used in proteomics. For clinical applications, mammalian systems are preferred for protein folding and activity; however, the level of protein obtained is low. A new system extracted from human cells (1-Step Human Coupled IVT (HCIVT)) has the potential to overcome this problem and deliver high yields of protein expressed in a human milieu.

EXPERIMENTAL DESIGN

Western blots and self-assembled protein microarrays were used to test the efficiency of protein synthesis by HCIVT compared to rabbit reticulocyte lysate (RRL). The arrays were also used to measure the immune response obtained from serum of patients exposed to pathogens or vaccine.

RESULTS

HCIVT performed better than RRL in all experiments. The yield of protein synthesized in HCIVT is more than ten times higher than RRL, in both Western blot and protein microarrays. Moreover, HCIVT showed a robust lot-to-lot reproducibility. In immune assays, the signals of many antigens were detected only in HCIVT-expressed arrays, mainly due to the reduction in the background signal and the increased levels of protein on the array.

CONCLUSION AND CLINICAL RELEVANCE

HCIVT is a robust in vitro transcription and translation system that yields high levels of protein produced in a human milieu. It can be used in applications where protein expression in a mammalian system and high yields are needed. The increased immunogenic response of HCIVT-expressed proteins will be critical for biomarker discovery in many diseases, including cancer.

Elemental and non-elemental olfactory learning in Drosophila

Brain complexity varies across many orders of magnitude between animals, and it is often assumed that complexity underpins cognition. It is thus important to explore the cognitive capacity of widely used model organisms such as Drosophila. We systematically investigated the fly's ability to learn discriminations involving compound olfactory stimuli associated with shock. Flies could distinguish binary mixtures (AB+ CD-), including overlapping mixtures (AB+ BC-). They could learn positive patterning (AB+A- B-) but could not learn negative patterning (A+ B+ AB-) or solve a biconditional discrimination task (AB+ CD+ AC- BD-). Learning about the elements of a compound (AB+) was not affected by prior conditioning of one of the elements (A+ AB+): flies do not exhibit blocking in this task. We compare these results with the predictions from simulation of several well-known theoretical models of learning, and find none are fully consistent with the overall pattern of observed behaviour.

Elevated plasma matrix metalloproteinases and their tissue inhibitors in patients with severe sepsis

PURPOSE

Matrix metalloproteinases (MMPs) are essential for tissue remodeling. Our objectives were to determine (1) the concentrations of MMPs and their tissue inhibitors (TIMPs) in plasma obtained from patients with severe sepsis, (2) to correlate changes in MMP and TIMP levels with disease severity, and (3) to investigate recombinant activated protein C (rAPC) actions on plasma MMP2, 9 activities from severe sepsis patients.

MATERIALS AND METHODS

Matrix metalloproteinase and TIMP levels were quantified in plasma from patients with severe sepsis using antibody microarrays and gelatin zymography.

RESULTS

Plasma MMPs (3, 7, 8, 9) and TIMPs (1, 2, 4) on microarray were increased in severe sepsis on intensive care unit (ICU) day 1, with more than 3-fold increases in MMP3, MMP7, MMP8, MMP9, and TIMP4. Latent forms of MMP2, 9 on zymography were increased in plasma from patients with severe sepsis, whereas only half of severe sepsis patients showed active MMP9. Elevated MMP7 and MMP9 on ICU days 1 and 3 negatively correlated with multiple organ dysfunctions. The temporal activity patterns of MMP2, 9 during 21 ICU days were not altered in patients treated with rAPC or by the addition of exogenous rAPC to plasma.

CONCLUSION

Most plasma MMPs and TIMPS were elevated in patients with severe sepsis, but only a limited subset of MMPs (7, 9) negatively correlated with disease severity. Recombinant activated protein C does not appear to directly alter MMP2, 9 activities.

Abstract 4958: Analysis of the AKT signaling pathway in prostate cancer using a streamlined Western blot workflow

Relative protein levels in the Akt pathway were analyzed in metastasized and normal prostate cancer cell lines using a new streamlined Western blot workflow and compared to a traditional Western blot method. Protein expression levels in the Akt pathway are commonly studied using Western blotting; however, current Western blot techniques involve multiple time-consuming steps taking more than 5 hours or even days. We used a streamlined Western blot workflow that combines a rapid 10-minute protein transfer and a one-hour immunoblotting protocol. When using an overnight primary antibody incubation, the protocol requires less than 30 minutes. Importantly, this method does not require the use of additional equipment or consumables and does not limit throughput. These data illustrate that current Western blot techniques involving multiple time-consuming steps can be streamlined to yield comparable results for phospho-specific and total protein targets. Results obtained in the analysis of the Akt pathway yielded comparable sensitivity to traditional Western blotting methods for both low- and high-abundance target proteins.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4958.

Antibody microarray analysis of inflammatory mediator release by human leukemia T-cells and human non small cell lung cancer cells

Cytokines and chemokines are responsible for regulating inflammation and the immune response. Cytokine and chemokine release is typically measured by quantitative enzyme-linked immunosorbant assay (ELISA) or Western blot analysis. To expedite the analysis of samples for multiple cytokines/chemokines, we have developed slide-based Thermo Scientific ExcelArray Antibody Sandwich Microarrays. Each slide consists of 16 subarrays (wells), each printed with 12 specific antibodies in triplicate and positive and negative control elements. This 16-well format allows for the analysis of 10 test samples using a six-point standard curve. The array architecture is based on the "sandwich" ELISA, in which an analyte protein is sandwiched between an immobilized capture antibody and a biotinylated detection antibody, using streptavidin-linked Thermo Scientific DyLight 649 Dye for quantitation. The observed sensitivity of this assay was <10 pg/mL. In our experiments, the Jurkat cell line was used as a model for human T-cell leukemia, and the A549 cell line was used as a model for human non-small cell lung cancer. To evoke a cytokine/chemokine response, cells were stimulated with tumor necrosis factor alpha (TNFalpha), phorbol-12-myristate-13-acetate (PMA, TPA), and phytohemagglutinin (PHA). Cell supernatants derived from both untreated and stimulated cells were analyzed on four different arrays (Inflammation I, Inflammation II, Angiogenesis, and Chemotaxis), enabling the quantitation of 41 unique analytes. Stimulated cells showed an increase in the expression level of many of the test analytes, including IL-8, TNF-alpha, and MIP-1alpha, compared to the non-treated controls. Our experiments clearly demonstrate the utility of antibody microarray analysis of cell-culture supernatants for the profiling of cellular inflammatory mediator release.

Multiplexing G protein-coupled receptors in microarrays: A radioligand-binding assay

Multiplexing of G protein-coupled receptors (GPCRs) in microarrays promises to increase the efficiency, reduce the costs, and improve the quality of high-throughput assays. However, this technology is still nascent and has not yet achieved the status of "high throughput" or laid claim to handling a large set of receptors. In addition, the technology has been demonstrated only when using fluorescent ligands to detect binding, limiting its application to a subset of GPCRs. To expand the impact of multiplexing on this receptor class, we have developed a radiometric approach to the microarray assay. In these studies, we considered two receptors in the alpha-adrenergic receptor family, alpha2A and alpha2C, and the 125I-labeled agonist clonidine. We demonstrate that microarrays of these receptors can be readily detected (signal/noise ratio approximately 160) using a Typhoon 9210 PhosphorImager. In addition, biochemical characterization shows that ligand-binding profiles and selectivity are preserved with the selective antagonists BRL44408 and ARC239. Importantly, these microarrays use approximately 200- to 400-fold less membrane preparation required by conventional assay methods and allow two or more receptors to be assayed in an area equivalent to a standard well of a microtiter plate. The impact of this approach on screening in drug discovery is discussed.