GNN-based Concentration Prediction with Variable Input Flow Rates for Microfluidic Mixers

Recent years have witnessed significant advances brought by microfluidic biochips in automating biochemical protocols. Accurate preparation of fluid samples is an essential component of these protocols, where concentration prediction and generation are critical. Equipped with the advantages of convenient fabrication and control, microfluidic mixers demonstrate huge potential in sample preparation. Although finite element analysis (FEA) is the most commonly used simulation method for accurate concentration prediction of a given microfluidic mixer, it is time-consuming with poor scalability for large biochip sizes. Recently, machine learning models have been adopted in concentration prediction, with great potential in enhancing the efficiency over traditional FEA methods. However, the state-of-the-art machine learning-based method can only predict the concentration of mixers with fixed input flow rates and fixed sizes. In this paper, we propose a new concentration prediction method based on graph neural networks (GNNs), which can predict output concentrations for microfluidic mixters with variable input flow rates. Moreover, a transfer learning method is proposed to transfer the trained model to mixers of different sizes with reduced training data. Experimental results show that, for microfluidic mixers with fixed input flow rates, the proposed method obtains an average reduction of 88% in terms of prediction errors compared with the state-of-the-art method. For microfluidic mixers with variable input flow rates, the proposed method reduces the prediction error by 85% on average. Besides, the proposed transfer learning method reduces the training data by 84% for extending the pre-trained model for microfluidic mixers of different sizes with acceptable prediction error.

Automated design of a 3D passive microfluidic particle sorter

Microfluidic chips that can sort mixtures of cells and other particles have important applications in research and healthcare. However, designing a sorter chip for a given application is a slow and difficult process, especially when we extend the design space from 2D into a 3D scenario. Compared to the 2D scenario, we need to explore more geometries to derive the appropriate design due to the extra dimension. To evaluate sorting performance, the simulation of the particle trajectory is needed. The 3D scenario brings particle trajectory simulation more challenges of runtime and collision handling with irregular obstacle shapes. In this paper, we propose a framework to design a 3D microfluidic particle sorter for a given application with an efficient 3D particle trajectory simulator. The efficient simulator enables us to simulate more samples to ensure the robustness of the sorting performance. Our experimental result shows that the sorter designed by our framework successfully separates the particles with the targeted size.

Machine Learning for Two-Phase Flow Separation in a Liquid-Liquid Interface Manipulation Separator

Two-phase flow separation is a key step in various downstream purification processes. The use of a separator with controllable flow behavior is recommended to avoid contamination. In this study, a core-annular separator for biphasic flow separation with four different chemical polarities was developed, and two machine learning-based methods were proposed for answering two emergent questions to meet real industrial needs. (1) Could complete two-phase separation be achieved under these operating conditions? (2) Could the separation process be accelerated by determining the maximum input flow rate of the water? Process prediction for automation, machine learning-based classifiers, and multilayer perceptron were used to address these questions by predicting successful separation and the maximum input flow rates of unknown water-solvent systems with limited experimental data as training samples. The core-annular separator achieved complete two-phase water-solvent separation at a maximum total input flow rate of 4000 μL min^-1. Moreover, the classification accuracy for complete separation reached 92.2%, and the multilayer perceptron network had the best performance for predicting the flow rate. This liquid-liquid interface manipulation separator and machine learning method could decrease the cost of relevant process development.

Conquering the Tyranny of Number With Digital Microfluidics

The development of large-scale integration based on soft lithography has ushered a new revolution in microfluidics. This technology, however, relies inherently on pneumatic control of micromechanical valves that require air pressure to operate, while digital microfluidics uses a purely electrical signal on an electrode for droplet manipulation. In this article, we discuss the prospect and current challenges of digital microfluidics to solve the problem of the tyranny of numbers in arbitrary fluidic manipulation. We distill the fundamental physics governing electrowetting and their implications for specifications of the control electronics. We survey existing control electronics in digital microfluidics and detail the improvements needed to realize a low-power, programmable digital microfluidic system. Such an instrument would attract wide interest in both professional and non-professional (hobbyist) communities.

Automated calibration of 3D-printed microfluidic devices based on computer vision

With the development of 3D printing techniques, the application of it in microfluidic/Lab-on-a-Chip (LoC) fabrication is becoming more and more attractive. However, to achieve a satisfying printing quality of the target devices, researchers usually require quite an amount of work in calibration trials even for high-end 3D printers. To increase the calibration efficiency of the average priced printers and promote the application of 3D printing technology in the microfluidic community, this work has presented a computer vision (CV)-based method for rapid and precise 3D printing calibration with examples on cylindrical hole/post diameters of 0.2-2.4 mm and rectangular hole/post widths of 0.2-1.0 mm by a stereolithography-based 3D printer. Our method is fully automated, which contains five steps and only needs a camera at hand to provide photos for convolutional neural network recognition. The experimental results showed that our CV-based method could provide calibrated dimensions with just one print of the specific calibration ruler to meet user desire. The higher resolution of the photo provides a higher precision in calibration. Subsequently, only one more print for the target device is needed after the calibration process. Overall, this work has provided a quick and precise calibration tool for researchers to apply 3D printing in the fabrication of their microfluidic/LoC devices with average price printers. Besides, with our open source calibration software and calibration ruler design file, researchers can modify the specific setting based on customized needs and conduct calibration on any type of 3D printer.

Predicting the fluid behavior of random microfluidic mixers using convolutional neural networks

With the various applications of microfluidics, numerical simulation is highly recommended to verify its performance and reveal potential defects before fabrication. Among all the simulation parameters and simulation tools, the velocity field and concentration profile are the key parts and are generally simulated using finite element analysis (FEA). In our previous work [Wang et al., Lab Chip, 2016, 21, 4212-4219], automated design of microfluidic mixers by pre-generating a random library with the FEA was proposed. However, the duration of the simulation process is time-consuming, while the matching consistency between limited pre-generated designs and user desire is not stable. To address these issues, we inventively transformed the fluid mechanics problem into an image recognition problem and presented a convolutional neural network (CNN)-based technique to predict the fluid behavior of random microfluidic mixers. The pre-generated 10 513 candidate designs in the random library were used in the training process of the CNN, and then 30 757 brand new microfluidic mixer designs were randomly generated, whose performance was predicted by the CNN. Experimental results showed that the CNN method could complete all the predictions in just 10 seconds, which was around 51 600× faster than the previous FEA method. The CNN library was extended to contain 41 270 candidate designs, which has filled up those empty spaces in the fluid velocity versus solute concentration map of the random library, and able to provide more choices and possibilities for user desire. Besides, the quantitative analysis has confirmed the increased compatibility of the CNN library with user desire. In summary, our CNN method not only presents a much faster way of generating a more complete library with candidate mixer designs but also provides a solution for predicting fluid behavior using a machine learning technique.

Detailed profiling of carbon fixation of in silico synthetic autotrophy with reductive tricarboxylic acid cycle and Calvin-Benson-Bassham cycle in Esherichia coli using hydrogen as an energy source

Carbon fixation is the main route of inorganic carbon in the form of CO₂ into the biosphere. In nature, RuBisCO is the most abundant protein that photosynthetic organisms use to fix CO₂ from the atmosphere through the Calvin-Benson-Bassham (CBB) cycle. However, the CBB cycle is limited by its low catalytic rate and low energy efficiency. In this work, we attempt to integrate the reductive tricarboxylic acid and CBB cycles in silico to further improve carbon fixation capacity. Key heterologous enzymes, mostly carboxylating enzymes, are inserted into the Esherichia coli core metabolic network to assimilate CO₂ into biomass using hydrogen as energy source. Overall, such a strain shows enhanced growth yield with simultaneous running of dual carbon fixation cycles. Our key results include the following. (i) We identified two main growth states: carbon-limited and hydrogen-limited; (ii) we identified a hierarchy of carbon fixation usage when hydrogen supply is limited; and (iii) we identified the alternative sub-optimal growth mode while performing genetic perturbation. The results and modeling approach can guide bioengineering projects toward optimal production using such a strain as a microbial cell factory.

Micro-Electrode-Dot-Array Digital Microfluidic Biochips: Technology, Design Automation, and Test Techniques

Digital microfluidic biochips (DMFBs) are being increasingly used for DNA sequencing, point-of-care clinical diagnostics, and immunoassays. DMFBs based on a micro-electrode-dot-array (MEDA) architecture have recently been proposed, and fundamental droplet manipulations, e.g., droplet mixing and splitting, have also been experimentally demonstrated on MEDA biochips. There can be thousands of microelectrodes on a single MEDA biochip, and the fine-grained control of nanoliter volumes of biochemical samples and reagents is also enabled by this technology. MEDA biochips offer the benefits of real-time sensitivity, lower cost, easy system integration with CMOS modules, and full automation. This review paper first describes recent design tools for high-level synthesis and optimization of map bioassay protocols on a MEDA biochip. It then presents recent advances in scheduling of fluidic operations, placement of fluidic modules, droplet-size-aware routing, adaptive error recovery, sample preparation, and various testing techniques. With the help of these tools, biochip users can concentrate on the development of nanoscale bioassays, leaving details of chip optimization and implementation to software tools.

Pressure-Aware Control Layer Optimization for Flow-Based Microfluidic Biochips

Flow-based microfluidic biochips are attracting increasing attention with successful biomedical applications. One critical issue with flow-based microfluidic biochips is the large number of microvalves that require peripheral control pins. Even using the broadcasting addressing scheme, i.e., one control pin controls multiple microvalves simultaneously, thousands of microvalves would still require hundreds of control prins, which is unrealistic. To address this critical challenge in control scalability, the control-layer multiplexer is introduced to effectively reduce the number of control pins into log scale of the number of microvalves. There are two practical design issues with the control-layer multiplexer: (1) the reliability issue caused by the frequent control-valve switching, and (2) the pressure degradation problem caused by the control-valve switching without pressure refreshing from the pressure source. This paper addresses these two design issues by the proposed Hamming-distance-based switching sequence optimization method and the XOR-based pressure refreshing method. Simulation results demonstrate the effectiveness and efficiency of the proposed methods with an average 77.2% (maximum 89.6%) improvement in total pressure refreshing cost, and an average 88.5% (maximum 90.0%) improvement in pressure deviation.

Droplet Size-Aware and Error-Correcting Sample Preparation Using Micro-Electrode-Dot-Array Digital Microfluidic Biochips

Sample preparation in digital microfluidics refers to the generation of droplets with target concentrations for on-chip biochemical applications. In recent years, digital microfluidic biochips (DMFBs) have been adopted as a platform for sample preparation. However, there remain two major problems associated with sample preparation on a conventional DMFB. First, only a (1:1) mixing/splitting model can be used, leading to an increase in the number of fluidic operations required for sample preparation. Second, only a limited number of sensors can be integrated on a conventional DMFB; as a result, the latency for error detection during sample preparation is significant. To overcome these drawbacks, we adopt a next generation DMFB platform, referred to as micro-electrode-dot-array (MEDA), for sample preparation. We propose the first sample-preparation method that exploits the MEDA-specific advantages of fine-grained control of droplet sizes and real-time droplet sensing. Experimental demonstration using a fabricated MEDA biochip and simulation results highlight the effectiveness of the proposed sample-preparation method.

Droplet Size-Aware High-Level Synthesis for Micro-Electrode-Dot-Array Digital Microfluidic Biochips

A digital microfluidic biochip (DMFB) is an attractive technology platform for automating laboratory procedures in biochemistry. In recent years, DMFBs based on a microelectrode-dot-array (MEDA) architecture have been demonstrated. However, due to the inherent differences between today's DMFBs and MEDA, existing synthesis solutions for biochemistry mapping cannot be utilized for MEDA biochips. We present the first synthesis approach that can be used for MEDA biochips. We first present a general analytical model for droplet velocity and validate it experimentally using a fabricated MEDA biochip. We then present the proposed synthesis method targeting reservoir placement, operation scheduling, module placement, routing of droplets of various sizes, and diagonal movement of droplets in a two-dimensional array. Simulation results using benchmarks and experimental results using a fabricated MEDA biochip demonstrate the effectiveness of the proposed synthesis technique.

Timing and duration of nursing from birth affect neonatal porcine uterine matrix metalloproteinase 9 and tissue inhibitor of metalloproteinase 1

Nursing for 2 d from birth supports neonatal porcine uterine and cervical development. However, it is not clear how timing or duration of lactocrine signaling from birth (postnatal day = PND 0) affects development of neonatal female reproductive tract tissues. Therefore, studies were conducted to determine effects of age at first nursing and duration of nursing from birth on specific elements of the matrix metalloproteinase (MMP)/tissue inhibitor of metalloproteinase (TIMP) system in uterine and cervical tissues at PND 2. When nursing was initiated at 0 h or 30 min of age, targeted proteins, including proMMP9 and MMP9, were detected in uterine and cervical tissues on PND 2, as was uterine TIMP1. However, these proteins were undetectable when nursing was delayed for 12 h and when gilts were fed milk replacer for 48 h from birth. Increasing the duration of nursing from 30 min to 12 h from birth increased uterine (P < 0.05) and cervical (P < 0.001) MMP9 levels to those observed in gilts nursed for 48 h. Similarly, uterine TIMP1 levels increased with duration of nursing. Uterine MMP2 levels were detectable but unaffected by age at first nursing or duration of nursing from birth. Uterine MMP2 and MMP9 activities, monitored by zymography, reflected immunoblotting data. Results provide evidence for the utility of MMP9 and TIMP1 as markers of age- and lactocrine-sensitive porcine female reproductive tract development.

Inhibitory effect of anti-pyretic and anti-inflammatory herbs on herpes simplex virus replication

The increasing clinical use of acyclovir, ganciclovir, and foscarnet against herpes simplex virus (HSV), varicella-zoster virus, and cytomegalovirus has been associated with the emergence of drug-resistant herpesvirus strains. To develop anti-HSV compounds from plants, 31 herbs used as antipyretic and anti-inflammatory agents in Chinese medicine were screened. Five different preparations (cold aqueous, hot aqueous, ethanolic, acid ethanolic, and methanolic) from 31 herbs were analyzed by plaque reduction assay, and 7 extracts. which showed significant antiviral activities, were further elucidated for their antiviral mechanisms. Our results showed that ethanolic extract of Rheum officinale and methanolic extract of Paeonia suffruticosa prevented the process of virus attachment and penetration. Aqueous extract of P. suffruticosa and ethanolic extract of Melia toosendan inhibited virus attachment to cell surface. Aqueous extract of Sophora flavescens and methanolic extract of M. toosendan showed no effect on virus attachment and penetration. These data indicated that these 4 herbs have a potential value as a source of new powerful anti-HSV compounds.

The effectiveness of Tsu-San-Li (St-36) and Tai-Chung (Li-3) acupoints for treatment of acute liver damage in rats

This study investigated the effects of acupuncture on carbon tetrachloride (CCl4) induced acute liver injury in male rats (n=36). The experimental groups were injected with CCl4 before, during, or after acupuncture therapy. Acupoints similar to the human Tsu-San-Li (St-36) and Tai-Chung (Li-3) were needled bilaterally. Rats treated with CCl4 had higher levels of serum glutamate-oxalate-transaminase (sGOT) and serum glutamate-pyruvate-transaminase (sGPT). Comparing the experimental groups, biochemical and pathological parameters of liver injury were significantly reduced when rats were acupunctured after, not before, CCl4-induced hepatotoxicity. Acupuncture at the Tsu-San-Li and Tai-Chung acupoints cannot prevent acute liver injury but may be effective in treating liver injury induced by carbon tetrachloride in rats.

Biotyping of Penicillium marneffei reveals concentration-dependent growth inhibition by galactose

Thirty-two isolates of the dimorphic fungus Penicillium marneffei were studied for their biochemical properties. All isolates possessed the enzyme urease and were inhibited by 500 mg of cycloheximide per liter. No strain fermented glucose, and thus no strain fermented any of the other five sugars tested. All assimilated glucose, maltose, and cellobiose; only one of the isolates did not assimilate salicin. Totals of 65.6, 84.4, and 71.9% of the isolates assimilated trehalose, xylose, and nitrate, respectively. Twelve strains possessed the enzyme beta-galactosidase. Overall, 17 different biotypes were recognized, but no association was found between the human immunodeficiency virus status of the patients and the biotype. A novel finding of concentration-dependent growth inhibition of P. marneffei by galactose is described. Inhibition of growth occurred at a low concentration of galactose (0.015 to 0.25%) when galactose was the sole carbon source in the medium. Morphological changes of the fungal cells were observed in the presence of galactose.

Identification of the copper-zinc superoxide dismutase activity in Mycoplasma hyopneumoniae

Copper-zinc superoxide dismutase (Cu/ZnSOD), a key enzyme in defense against toxic oxygen-free radicals, is widespread in eukaryotes and several species of gram-negative bacteria. The presence of this enzyme in Mycoplasma hyopneumoniae (M. hyopneumoniae), the primary pathogen of mycoplasmal pneumonia in pigs, was examined since the polyclonal antibody against bovine Cu/ZnSOD was dominantly cross-reactive with the M. hyopneumoniae Cu/ZnSOD from whole cellular proteins. In situ activity staining on SDS-PAGE showed that the molecular mass of M. hyopneumoniae Cu/ZnSOD in reducing form was approximately 17kDa. The presence of Cu and Zn ions at the active site of the enzyme was confirmed on the basis of inhibition by KCN and by H(2)O(2). The activity of M. hyopneumoniae Cu/ZnSOD on both SDS- and native-polyacrylamide gels was completely inhibited by 2mM KCN and the gels showed no iron-containing SOD (FeSOD) or manganese-containing SOD (MnSOD) in the crude extracts. The activity of M. hyopneumoniae Cu/ZnSOD in crude extract was 70units/mg protein and was 55% inhibited by 5mM KCN and 56% inactivated by 40mM H(2)O(2). This enzyme was growth-stage dependent and evidenced markedly higher production during the early log phase. Different expression levels of Cu/ZnSOD activity in field isolates were also detected. Taken together, the presence of Cu/ZnSOD in M. hyopneumoniae was identified for the first time.

Identification of a DNA-binding domain and an active-site residue of pseudorabies virus DNase

The pseudorabies virus (PRV) DNase gene has an open reading frame of 1476 nt, capable of coding a 492-residue protein. A previous study showed that PRV DNase is an alkaline exonuclease and endonuclease, exhibiting an Escherichia coli RecBCD-like catalytic function. To analyse its catalytic mechanism further, we constructed a set of clones truncated at the N-terminus or C-terminus of PRV DNase. The deleted mutants were expressed in E. coli with the use of pET expression vectors, then purified to homogeneity. Our results indicate that (1) the region spanning residues 274-492 exhibits a DNA-binding ability 7-fold that of the intact DNase; (2) the N-terminal 62 residues and the C-terminal 39 residues have important roles in 3'-exonuclease activity, and (3) residues 63-453 are responsible for 5'- and 3'-exonuclease activities. Further chemical modification of PRV DNase revealed that the inactivation of DNase by diethyl pyrocarbonate, which was reversible on treatment with hydroxylamine, seemed to be attributable solely to the modification of histidyl residues. Because the herpesviral DNases contained only one well-conserved histidine residue, site-directed mutagenesis was performed to replace His(371) with Ala. The mutant lost most of its nuclease activity; however, it still exhibited a wild-type level of DNA-binding ability. In summary, these results indicate that PRV DNase contains an independent DNA-binding domain and that His(371) is the active-site residue that has an essential role in PRV DNase activity.

Pseudorabies virus early protein 0 trans-activates the TATA-associated promoter by stimulating the transcription initiation

Pseudorabies virus (PRV) early protein 0 (EP0) is a transactivator containing a RING finger domain. To assess the transactivation mechanism of PRV EP0, we performed the in vitro transcription by combining HeLa nuclear extract, purified recombinant EP0 and simple promoter constructs, and evaluated the results by primer extension. The data showed that EP0 could significantly activate the TATA-containing synthetic promoters. Moreover, EP0 activated transcription by stabilizing the formation of transcription initiation complex instead of enhancing the elongation rate. To further understand the role of EP0 on assembling the transcription initiation complex, we performed the pull-down assay using affinity precipitation of proteins from HeLa nuclear extracts and bacterially expressed glutathione-S-transferase EP0 RING finger fusion. The data showed that at least six nuclear proteins physically interacted with the EP0 RING finger. Overall, the transactivation of PRV EP0 is accomplished by enhancing the transcription initiation and is associated with at least six nuclear proteins.

Identification, expression, and characterization of the pseudorabies virus DNA-binding protein gene and gene product

The pseudorabies virus (PRV) gene encoding a DNA-binding protein (DBP) was first identified in this study. The DBP gene has an open reading frame of 3531 nucleotides, capable of coding a 1177-amino-acid polypeptide of 125 kDa. The deduced DBP exhibits a conserved zinc-binding motif and a conserved DNA-binding region, suggesting the similar DNA-binding mechanism occurs among alphaherpesviral DBP homologs. To further identify the biochemical properties of PRV DBP, this protein was expressed in Escherichia coli by using a pET expression vector and purified to homogeneity. The PRV DBP binds cooperatively and preferentially to single-stranded DNA with no significant base preference, judged by agarose gel electrophoresis and competitive nitrocellulose filter binding assays. Taken together, these results suggest that PRV DBP may play an important role in PRV DNA replication by binding cooperatively and nonspecifically to single-stranded DNA that is formed during the replication origin unwinding and replication fork movement.

DNA vaccination induces a long-term antibody response and protective immunity against pseudorabies virus in mice

In order to investigate the mechanism of long-term immunity and the effect of protective immunity induced by DNA vaccination, we constructed the expression plasmid containing a pseudorabies virus (PRV) gD gene encoding an envelope glycoprotein. Intramuscular vaccination of mice with the plasmid DNA induced a strong antibody response which lasted for one year after final vaccination. An IgM to IgG class switch occurred, indicating helper T-lymphocyte activity. We further analyzed the persistence and expression of gD gene by polymerase chain reaction and reverse transcriptase polymerase chain reaction. The results showed that gD gene was present and expressed in the muscle cell up to one year after final booster injection. Furthermore, mice vaccinated with the plasmid DNA were protected against a subsequent lethal challenge with PRV. Therefore, the DNA vaccination does induce a protective immunity and long-term antibody response against PRV, which could be maintained by persistent expression of gD gene in muscle cells.

Recombinant pseudorabies virus DNase exhibits a RecBCD-like catalytic function

The pseudorabies virus (PRV) DNase gene has previously been mapped within the PRV genome. To characterize further the enzymic properties of PRV DNase, this enzyme was expressed in Escherichia coli with the use of a pET expression vector. The protein was purified to homogeneity and assayed for nuclease activity in vitro. Recombinant PRV DNase exhibited an alkaline pH preference and an absolute requirement for Mg2+ ions that could not be replaced by Ca2+ and Na+ ions. Further studies showed that PRV DNase exhibited endonuclease, 5'-exonuclease and 3'-exonuclease activities in both single-stranded and double-stranded DNA. This activity occurred randomly and no significant base preference was demonstrated. The multiple biochemical activities of PRV DNase are similar to the activities of Neurospora crassa endo-exonuclease and E. coli RecBCD, two additional enzymes that are involved in recombination. Taken together, the similarity of action between N. crassa endo-exonuclease, E. coli RecBCD, and PRV DNase suggests that PRV DNase might have a role in the process of recombination that occurs during PRV infection.

Stimulation of type I DNA topoisomerase gene expression by pseudorabies virus

Previous results from our laboratory have demonstrated that type I DNA topoisomerase activity is required for the replication and gene expression of pseudorabies virus (PRV). In the present report, we further analyzed the expression of topoisomerase I in PRV-infected cells, and the western blot result showed that the expression of topoisomerase I was increased after virus infection. The increase sustained to late time of infection when the cytopathic effect was obvious and the synthesis of most host proteins was shut off by PRV. From transient expression assay, it was also found that the promoter of cellular topoisomerase I gene could be stimulated by immediate-early protein (IE180) and viral early protein 0 (EP0), and these two regulatory proteins appeared to work synergistically. Collectively, these findings provide evidence that PRV can stimulate the expression of topoisomerase I and that the stimulation is mediated at least by IE180 and EP0 proteins of PRV at the transcriptional level.

Increased gene expression in human promyeloid leukemia cells exposed to trans,trans-muconaldehyde, a hematotoxic benzene metabolite

The hematotoxicity of benzene, a human leukemogen, has been postulated to be mediated by reactive metabolites and involve cell damage caused by reactive oxygen species. Because expression of the transcription factors AP-1 and NF-kappaB is sensitive to the redox state in eukaryotic cells, the DNA binding activity of AP-1 and NF-kappaB was examined in HL-60 promyeloid leukemia cells exposed to trans,trans-muconaldehyde, a microsomal hematotoxic metabolite of benzene. There was little AP-1 binding activity in nuclear extracts from control HL-60 cells based on electrophoretic mobility shift assays. Exposure to 0.1 microM MUC for 4 h resulted in significantly increased levels of nuclear protein with high sequence specificity for the consensus AP-1 sequence. In addition, electrophoretic mobility shift assays showed a strong increase in the binding of a factor to the NF-kappaB site. The latter was highest in nuclear extracts from HL-60 cells treated with 1.0 microM muconaldehyde and cultured for 4 h. Exposure of HL-60 cells to muconaldehyde resulted in an increase in c-fos and c-jun mRNA levels. Western blot analysis showed that the protein levels of c-jun increased in HL-60 cells treated with 1 microM muconaldehyde and cultured for 4-6 h and subsequently decreased gradually. Increased AP-1 binding was observed in bone marrow cells from B6C3F1 mice 2 h after administration of 440 mg/kg benzene. We suggest that increased gene expression of NF-kappaB and AP-1 binding activity and up-regulation of c-fos and c-jun may play a role in the mechanism of benzene leukemogenesis.

Identification of a pseudorabies virus UL12 (deoxyribonuclease) gene

We characterized the gene encoding the pseudorabies virus (PrV) homologue of the herpes simplex virus 1 UL12 open reading frame that encodes the alkaline nuclease. The deduced PrV UL12 product was 492 amino acid residues and exhibited three conserved regions among herpesviruses. Northern blot analysis indicated that three transcripts (3.2, 1.6 and 1 kb) were encoded in this region and the UL12 corresponds to the 1.6-kb transcript. Primer extension and UL12-specific cDNA cloning were performed to verify the precise location of the UL12 transcript. These data indicated that the transcription start site of UL12 was located at 47-62 nucleotides upstream of the UL12 translation start site and the polyadenylation cleavage site was located at 15 or 16 nucleotides downstream the typical polyadenylation signal. Furthermore, the 53-kDa UL12 product, which indeed has deoxyribonuclease activity, was evidenced by in vitro expression.

Analysis of pseudorabies virus genes by cDNA sequencing

Cloning and sequencing of cDNA could provide a complementary approach to functional analysis of the pseudorabies virus (PrV) genome. Using colony hybridization, Southern hybridization, and DNA sequencing, four species of PrV-specific cDNA were identified. Among these four species of PrV-specific cDNA, three unidentified genes, UL26, UL29, and UL31, were mapped and a novel gI-11K bicistronic cDNA was confirmed. Thus, analysis of PrV-specific transcripts provided a way for identifying genes and a foundation to further study the roles of these transcripts in PrV infection.

Analysis of upregulated cellular genes in pseudorabies virus infection: use of mRNA differential display

Virus infection usually alters the host cell and shuts off the synthesis of cellular macromolecules. In order to screen the upregulated cellular transcripts during pseudorabies virus (PRV) infection, we employed the mRNA differential display technique. The screen is based on positive selection at the mRNA level for genes expressed in normal cells but increased in corresponding PRV-infected cells. Over 14000 species of mRNA, isolated from mock-infected and PRV-infected Madin-Darby bovine kidney cell at 1 h post infection, were screened, and 40 candidate clones were recovered. Southern blot analysis revealed that 17 out of 40 candidate clones, were enhanced in PRV-infected cells. Partial DNA sequences demonstrated that 17 clones were distinct cellular genes, including those encoding the modulators of signal transduction (saposin, 14-3-3, adenylate kinase, adenylyl cyclase, protein kinase C-alpha), those encoding the components of translation (fau, ribosomal proteins S11, L31, L36), other cellular genes (peptidase, cyclin E, rch1, oligo-C-rich single-stranded nucleic acid binding protein, rap, arginyl-tRNA synthetase), and two unknown genes. Thus, this study identifies successfully the transcriptionally regulated cellular genes which are associated with PRV infection. Furthermore, this study provides support for the use of mRNA differential display as a method to rapidly isolate differentially expressed genes in virus infection.

Rapid screening of pseudorabies virus-specific cDNAs from a cDNA library

In order to reduce the time and cost for screening of pseudorabies virus (PRV)-specific cDNAs, a rapid and inexpensive method was developed that involved subtractive hybridization of the plasmid, which contained cDNA fragment, to PRV genomic DNA which was bound to nylon membranes. Ninety percent of DNA background was subtracted successfully by this method and the eluted DNA in the form of plasmid could be used to transform bacteria directly. Applying this technique, 200 colonies were screened from a cDNA library containing 30000 colonies. Furthermore, 17 colonies containing PRV-specific cDNAs, including PRV43, UL42, gII, DNase, EP0, 11K, gX, and RSP40, were identified from the 200 colonies by colony hybridization, Southern hybridization, and DNA sequencing. Thus, the subtractive hybridization can be used to construct and successfully establish the PRV cDNA library from PRV-infected cells.

Polypeptide pattern of human breast epithelial cells following human chorionic gonadotropin (hCG) treatment

Numerous attempts have made to describe the particular protein pattern of malignant cells by using high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The placental hormone human chorionic gonadotropin (hCG) inhibits tumor initiation and progression in experimental animals and has an inhibitory effect on the proliferation of human breast epithelial cells (HBEC) in vitro. The inhibitory effect on the immortalized HBEC MCF-10F is accompanied by the immunocytochemical expression of inhibin alpha and beta subunits by treated cells. With the purpose of clarifying the molecular mechanisms involved in this effect, the pattern of protein synthesis and mRNA were studied by 2-D PAGE in the immortalized HBEC MCF-10F cells treated in vitro 1001U for 24 h. The effect of hCG treatment on the synthesis of MCF-10F cells was monitored by labeling both control and treated cells with [S35]methionine and separation by 2-D PAGE. At least 11 proteins were preferentially synthesized and five specific polypeptides were decreased in hCG treated cells in comparison with controls. The hCG induced at least four new mRNAs which encoded protein in the molecular mass range of 24-72 kDa. It also increased the expression of at least six mRNAs and reduced the expression of least four mRNAs in comparison with control cells. The hCG-treated cells actively synthesized a 33-kDa polypeptide which was not present in control cells. The nature of this hCG-inducible 33 kDa protein elucidated by immunoprecipating [S35]methionine-labeled proteins with antisera directed against rat inhibin subunit alpha and beta b.(ABSTRACT TRUNCATED AT 250 WORDS)

Residual analgesic effects of morphine in 55 four-period crossover analgesic studies

Subjective response data from 55 postoperative pain studies were examined for the residual analgesic effects of morphine. The studies were planned as four-period crossover designs for four treatments. Each patient received 5 and 10 mg of morphine and two doses of a test preparation. Two measures of analgesia were used: Sum of the Pain Intensity Difference (SPID) and Total Pain Relief (TOTPAR). To facilitate analysis, two two-period groups were defined. Morphine data for periods 1 and 2 were designated as group A, and morphine data for periods 3 and 4 were designated as group B. Residual analgesic effects were 0.12 for both SPID and TOTPAR in group A and were 0.65 and 0.17 for SPID and TOTPAR, respectively, in group B. In these 55 studies, there was no evidence of significant residual analgesic effects. Thus the crossover design is an appropriate method for the evaluation of selected parenteral analgesics in the postoperative pain model.

Radiocarbon dating of petroleum-impregnated bone from tar pits at Rancho La Brea, California

A liquid-chromatography method has been developed for the separation of amino acids with the same specific activity in radiocarbon from bones impregnated with isotopically dead petroleum compounds found in the La Brea tar pits. This technique permits the application of radiocarbon dating to such bone assemblages.