Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries. Key features • Mass spectrometry analyzes a range of compounds from E. coli colonies as a proxy for liquid culture testing enzyme mutant libraries. • Colonies are transferred to a MALDI target plate by a simple imprinting method. • The screen compares the ratio among several products or searches for the qualitative presence of specific compounds. • The protocol requires a MALDI mass spectrometer.

MALDI-MS screening of microbial colonies with isomer resolution to select fatty acid desaturase variants

Creating controlled lipid unsaturation locations in oleochemicals can be a key to many bioengineered products. However, evaluating the effects of modifications to the acyl-ACP desaturase on lipid unsaturation is not currently amenable to high-throughput assays, limiting the scale of redesign efforts to <200 variants. Here, we report a rapid MS assay for profiling the positions of double bonds on membrane lipids produced by Escherichia coli colonies after treatment with ozone gas. By MS measurement of the ozonolysis products of Δ6 and Δ8 isomers of membrane lipids from colonies expressing recombinant Thunbergia alata desaturase, we screened a randomly mutagenized library of the desaturase gene at 5 s per sample. Two variants with altered regiospecificity were isolated, indicated by an increase in 16:1 Δ8 proportion. We also demonstrated the ability of these desaturase variants to influence the membrane composition and fatty acid distribution of E. coli strains deficient in the native acyl-ACP desaturase gene, fabA. Finally, we used the fabA deficient chassis to concomitantly express a non-native acyl-ACP desaturase and a medium-chain thioesterase from Umbellularia californica, demonstrating production of only saturated free fatty acids.

macroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Mass spectrometry imaging is well-suited to characterizing sample surfaces for their chemical content in a spatially resolved manner. However, when the surface contains small objects with significant empty spaces between them, more efficient approaches to sample acquisition are possible. Image-guided mass spectrometry (MS) enables high-throughput analysis of a diverse range of sample types, such as microbial colonies, liquid microdroplets, and others, by recognizing and analyzing selected location targets in an image. Here, we describe an imaging protocol and macroMS, an online software suite that can be used to enhance MS measurements of macroscopic samples that are imaged by a camera or a flatbed scanner. The web-based tool enables users to find and filter targets from the optical images, correct optical distortion issues for improved spatial location of selected targets, input the custom geometry files into an MS device to acquire spectra at the selected locations, and finally, perform limited data analysis and use visualization tools to aid locating samples containing compounds of interest. Using the macroMS suite, an enzyme mutant library of Saccharomyces cerevisiae and nL droplet arrays of Escherichia coli and Pseudomonas fluorescens have been assayed at a rate of ∼2 s/sample.

A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids

Microbial cell factories have been extensively engineered to produce free fatty acids (FFAs) as key components of crucial nutrients, soaps, industrial chemicals, and fuels. However, our ability to control the composition of microbially synthesized FFAs is still limited, particularly, for producing medium-chain fatty acids (MCFAs). This is mainly due to the lack of high-throughput approaches for FFA analysis to engineer enzymes with desirable product specificity. Here we report a mass spectrometry (MS)-based method for rapid profiling of MCFAs in Saccharomyces cerevisiae by using membrane lipids as a proxy. In particular, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) MS was used to detect shorter acyl chain phosphatidylcholines from membrane lipids and a higher m/z peak ratio at 730 and 758 was used as an indication for improved MCFA production. This colony-based method can be performed at a rate of ~2 s per sample, representing a substantial improvement over gas chromatography-MS (typically >30 min per sample) as the gold standard method for FFA detection. To demonstrate the power of this method, we performed site-saturation mutagenesis of the yeast fatty acid synthase and identified nine missense mutations that resulted in improved MCFA production relative to the wild-type strain. Colony-based MALDI-ToF MS screening provides an effective approach for engineering microbial fatty acid compositions in a high-throughput manner.

Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis

Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), is known to exhibit host specialization. The virulence of different isolates of the pathogen can be classified into pathotypes based on their compatibility with a differential set composed of specific cucurbit host types. However, the genetic basis of host specialization within P. cubensis is not yet known. Total genomic DNA extracted from nine isolates of P. cubensis collected from 2008 to 2013 from diverse cucurbit host types (Cucumis sativus, C. melo var. reticulatus, Cucurbita maxima, C. moschata, C. pepo, and Citrullus lanatus) in the United States were subjected to whole-genome sequencing. Comparative analysis of these nine genomes confirmed the presence of two distinct evolutionary lineages (lineages I and II) of P. cubensis. Many fixed polymorphisms separated lineage I comprising isolates from Cucurbita pepo, C. moschata, and Citrullus lanatus from lineage II comprising isolates from Cucumis spp. and Cucurbita maxima. Phenotypic characterization showed that lineage II isolates were of the A1 mating type and belonged to pathotypes 1 and 3 that were not known to be present in the United States prior to the resurgence of CDM in 2004. The association of lineage II isolates with the new pathotypes and a lack of genetic diversity among these isolates suggest that lineage II of P. cubensis is associated with the resurgence of CDM on cucumber in the United States.

Clinical features of vivax malaria

Plasmodium vivax malaria reemerged in the Republic of Korea in 1993 near the Demilitarized Zone (DMZ). We reviewed clinical features of 101 symptomatic patients with vivax malaria. Of the patients, 77 patients (76.3%) were veterans who had served near the DMZ; their median age was 23 years. The duration of the minimum latent period was > 6 months in 66.2% (51 of 77) of the patients (median, 278 days). Tertian fever developed in 69 patients (68.3%). Severe thrombocytopenia with platelet counts < 60,000/microL was common (29.6% of patients). The parasite densities ranged 32-52,127 parasites per microliter of blood (geometric mean, 1,287). The only complication was a splenic rupture in one patient. All patients responded promptly to chloroquine therapy. Our data suggest that the clinical features of reemerging vivax malaria may be similar to those of Korean vivax malaria reported in the past.

Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation

Members of HIV-1 group M are responsible for the vast majority of AIDS cases worldwide and have been classified on the basis of their phylogenetic relationships into nine roughly equidistant clades, termed subtypes. Although there are no known phenotypic correlates for these genotypes, the disproportionate spread of certain of these lineages has been taken to indicate that subtype-specific biological differences may exist. The subtype nomenclature thus remains an important molecular epidemiological tool with which to track the course of the group M pandemic. In this study, we have characterized HIV-1 strains described previously as unusual subtype A variants on the basis of partial sequence analysis. Six such strains from Cyprus (CY), South Korea (KR), and the Democratic Republic of Congo (CD) were PCR amplified from infected cell culture or patient PBMC DNA, cloned, and sequences in their entirety (94CY017, 97KR004, 97CDKTB48, and 97CDKP58) or as half genomes (97CDKS10 and 97CDKFE4). Distance and phylogenetic analyses showed that four of these viruses (94CY017, 97CDKTB48, 97CDKFE4, and 97CDKS10) were closely related to each other, but quite divergent from all other HIV-1 strains, except for subtype A viruses, which represented their closest relatives. In phylogenetic trees from gag, pol, env, and nef regions, the four newly characterized HIV-1 strains formed a distinct sister clade to subtype A, which was as closely related to subtype A as subsubtypes F1 and F2 are to each other. According to current nomenclature rules, this defines a subsubtype, which we have tentatively termed A2. The two other viruses, 97KR004 and 97CDKP58, as well as a full-length HIV-1 sequence from the sequence database (ZAM184), were found to represent complex A2/D, A2/G, and A2/C recombinants, respectively. These results indicate that HIV-1 subtype A is composed of two subsubtypes (A1 and A2), both of which appear to have a widespread geographic distribution. The A2 viruses described here represent the first reference reagents for this new group M lineage.

Activity of the farnesyl protein transferase inhibitor SCH66336 against BCR/ABL-induced murine leukemia and primary cells from patients with chronic myeloid leukemia

BCR/ABL, the oncoprotein responsible for chronic myeloid leukemia (CML), transforms hematopoietic cells through both Ras-dependent and -independent mechanisms. Farnesyl protein transferase inhibitors (FTIs) were designed to block mutant Ras signaling, but they also inhibit the growth of transformed cells with wild-type Ras, implying that other farnesylated targets contribute to FTI action. In the current study, the clinical candidate FTI SCH66336 was characterized for its ability to inhibit BCR/ABL transformation. When tested against BCR/ABL-BaF3 cells, a murine cell line that is leukemogenic in mice, SCH66336 potently inhibited soft agar colony formation, slowed proliferation, and sensitized cells to apoptotic stimuli. Quantification of activated guanosine triphosphate (GTP)-bound Ras protein and electrophoretic mobility shift assays for AP-1 DNA binding showed that Ras effector pathways are inhibited by SCH66336. However, SCH66336 was more inhibitory than dominant-negative Ras in assays of soft agar colony formation and cell proliferation, suggesting activity against targets other than Ras. Cell cycle analysis of BCR/ABL-BaF3 cells treated with SCH66336 revealed G2/M blockade, consistent with recent reports that centromeric proteins that regulate the G2/M checkpoint are critical farnesylated targets of FTI action. Mice injected intravenously with BCR/ABL-BaF3 cells developed acute leukemia and died within 4 weeks with massive splenomegaly, elevated white blood cell counts, and anemia. In contrast, nearly all mice treated with SCH66336 survived and have remained disease-free for more than a year. Furthermore, SCH66336 selectively inhibited the hematopoietic colony formation of primary human CML cells. As an oral, nontoxic compound with a mechanism of action distinct from that of ABL tyrosine kinase inhibition, FTI SCH66336 shows promise for the treatment of BCR/ABL-induced leukemia.

Naturally acquired antibody responses to the C-terminal region of merozoite surface protein 1 of Plasmodium vivax in Korea

We expressed a protein in Saccharomyces cerevisiae in order to evaluate the humoral immune responses to the C-terminal region of the merozoite surface protein 1 of Plasmodium vivax. This protein (Pv200(18)) had a molecular mass of 18 kDa and was reactive with the sera of individuals with patent vivax malaria on immunoblotting analysis. The levels of immunoglobulin M (IgM) and IgG antibodies against Pv200(18) were measured in 421 patients with vivax malaria (patient group), 528 healthy individuals from areas of nonendemicity (control group 1), and 470 healthy individuals from areas of endemicity (control group 2), using the indirect enzyme-linked immunosorbent assay (ELISA) method. To study the longevity of the antibodies, 20 subjects from the patient group were also tested for the antibody levels once a month for 1 year. When the cutoff values for seropositivity were determined as the mean + 3 x standard deviation of the antibody levels in control group 1, both IgG and IgM antibody levels were negative in 98.5% (465 of 472) of control group 2. The IgG and IgM antibodies were positive in 88.1% (371 of 421) and 94.5% (398 of 421) of the patient group, respectively. The IgM antibody became negative 2 to 4 months after the onset of symptoms, whereas the IgG antibody usually remained positive for more than 5 months. In conclusion, indirect ELISA using Pv200(18) expressed in S. cerevisiae may be a useful diagnostic method for vivax malaria.

Scrub typhus pneumonitis acquired through the respiratory tract in a laboratory worker

We report a case of scrub typhus pneumonitis in a laboratory worker who apparently acquired it through the respiratory tract. The patient was suffering from fever, cough and dyspnea. He had both cervical and axillary lymphadenopathy, and hepatomegaly. A chest X-ray showed interstitial infiltrates. A diagnosis of scrub typhus was established upon isolation of Orientia tsutsugamushi. 12 days before the patient showed symptoms, he had purified O. tsutsugamushi proteins from infected cells using an ultrasonication method which could generate aerosols containing O. tsutsugamushi.

Release of lead-containing particles from a wall enclosure

The 1995 Department of Housing and Urban Development (HUD) Guidelines for the Evaluation and Control of Lead-Based Paint Hazards in Housing discusses using interior and exterior wall enclosures for lead hazard control. Leaded dust may be aerosolized inside enclosures and released through gaps and cracks into a room. The effects of airflow and mechanical disturbances on dust release were studied using a laboratory wall enclosure model with dust collected from homes with lead-based paint hazards. Airflows relevant to residences were blown down the enclosure and out a 4-, 6-, or 8-mm horizontal gap at its bottom, simulating potential enclosure failure. Then, low-frequency mechanical vibrations also were applied to the enclosure. No significant dust release was found when blowing air down the enclosure even at 37 cm/sec (representing extremely high flow); release occurred only with this high flow and 3 Hz mechanical disturbances. Dust was released primarily from the floor area immediately adjacent to the enclosure gap; the release rate fluctuated over time. Most dust initially settled near the enclosure. Dust release for 1 hour at extreme conditions (high airflow with vibration) yields lead loading above the 1995 HUD clearance level of 100 microg/ft2 only within 3-4 cm of the wall; for the HUD standard (1 ft2) sampling area, the lead loading does not exceed 30 microg/ ft2. Redistributing dust over the room's 16 m2 floor space yields average extreme-condition loading rate of 2 microg/ft2/hour. At less-than-extreme conditions, dust would have to be released for years without cleaning to yield a hazard.

The frequency of mutation in CCR5 gene among Koreans

To better understand a role of the delta32 allele of the CCR5 gene in HIV-1 transmission and disease progression, we determined the CCR5 genotypes within several groups of Koreans. Amplification of DNA from each subject was achieved with polymerase chain reaction, using the CCR5 specific primer pair, which flanks the 32 bp deletion. The 1.2 kb coding sequences of CCR5 were examined to see the possible effects of CCR5 polymorphism. All of the 339 healthy, HIV-uninfected individuals had no mutation in the CCR5 gene. All of the 115 HIV-1-infected patients including 11 long-term non-progressors (LTNPs) and 18 discordant spouses were also wild homozygotes. No variation in the 1.2kb CCR5 coding sequence was found in 5 LTNPs and 5 discordant spouses. In conclusion, the 32 bp deletion mutant is rarely present in Koreans. Our data suggest that factors other than the CCR5 coding sequences may also play a role in the resistance to HIV infection.

Spectrum of opportunistic infections and malignancies in patients with human immunodeficiency virus infection in South Korea

To determine the frequency and types of major opportunistic diseases in patients with HIV infection in South Korea, we reviewed the medical records of 173 HIV-infected patients. The patients were seen from 1985 to 1998 at a referral hospital for AIDS in South Korea. Most patients (85%) were male, and 107 (62%) were infected by heterosexual contacts. CD4+ lymphocyte counts at presentation were <200/microL in 27% of the patients. Tuberculosis was the most frequent opportunistic infection (25% of patients), followed by candidiasis (21%), herpes zoster (20%), Pneumocystis carinii pneumonia (10%), cytomegalovirus disease (9.8%). There were no cases of toxoplasmosis. Kaposi's sarcoma developed in 3 patients (1.7%), and non-Hodgkin's lymphoma, in 2 (1.2%). Eleven patients (6.4%) developed peripheral neuropathy, and 8 (4.6%) had HIV encephalopathy. Tuberculosis was the single most important HIV-related infection in South Korean patients.

Epidemiology of HIV infection in the Republic of Korea

Since the first case of human immunodeficiency virus (HIV) infection in the Republic of Korea (ROK) was detected in 1985, 876 HIV-infected patients have been reported, as of December 1998. The male to female ratio was 6.8:1, and 87% of the patients were between 20 and 49 years of age. The major modes of transmission were sexual contacts, accounting for 86% of the cases (65% heterosexuals and 21% homosexuals). Transmission through blood and blood products accounted for 28 cases (3.2%), and vertical transmission for one case. No cases among intravenous drug abusers were reported. The seroprevalence among the blood donors was approximately one in 100,000. Subtypes A, B, C, D, E, and G of HIV-1 have been introduced into the ROK, and subtype B is the most predominant subtype. The frequency of the a deletion in the CCR5 gene, a coreceptor of HIV-1, was less than 1% among Koreans.

Direct photoaffinity labeling of cysteine-295 of alpha-tubulin by guanosine 5'-triphosphate bound in the nonexchangeable site

The alphabeta-tubulin heterodimer has two high affinity guanosine 5'-triphosphate binding sites, so that purified tubulin usually contains two molecules of bound guanosine nucleotide. Half this nucleotide is freely exchangeable with exogenous guanine nucleotide, and its binding site has been readily localized to the beta-subunit. The remaining nonexchangeable guanosine 5'-triphosphate can only be released from tubulin by denaturing the protein. We replaced the exchangeable site nucleotide of tubulin with 2'-deoxyguanosine 5'-diphosphate, exposed the resulting tubulin to ultraviolet light, degraded the protein, and isolated ribose-containing peptide derived from the nonexchangeable site. A large cyanogen bromide peptide was recovered, and its further degradation with endoproteinase Glu-C established that cysteine-295 of alpha-tubulin was the major reactive amino acid cross-linked to guanosine by ultraviolet irradiation.

The role of contrast enhanced computed tomography in the diagnosis of low density pulmonary nodules

Contrast enhanced CT manifestations of 141 pulmonary nodules having internal density less than 40 HU were evaluated to study the prevalence of causative disease and their differential points. Tuberculosis (n = 79) was most common, active in 96%. There were 22 cancers, 10 abscesses, 9 paragonimiases, 8 cysts, 7 metastases, 4 aspergillomas without air meniscus sign, and so on. 35% of the benign lesions were greater than 3 cm in diameter and 67% of benign lesions did not show a smooth outer margin. Lung cysts and aspergillomas showed relatively thin peripheral enhanced rim (PER), sharp transitional zone (TZ), a smooth inner border (IB), and homogeneous low densities (LD). Tuberculous nodules tended to be smaller in size with thin PER and most had smooth IB and homogeneous LD. Paragonimiasis, abscess, and cancer tended to present with thick PER and lobulated IB. Lung abscess and paragonimiasis both showed homogeneous LD and narrow TZ. However, in paragonimiasis, multiple locules were seen. Lung cancer showed wider TZ and heterogeneous LD. The size and outer margin of pulmonary nodules as a diagnostic criteria is less useful in LD pulmonary nodule. Therefore, CT can be more useful in differentiating the benign from the malignant lesions by observing a more specific and characteristic pattern of peripheral enhanced rim, transitional zone, inner border, and homogeneity of low density area.

Spinal epidural granulocytic sarcoma preceding acute myelogenous leukemia

A rare case of spinal epidural granulocytic sarcoma (GS) preceding acute myelogenous leukemia is described. A 10-year-old boy presented with lower leg weakness. The initial diagnosis was a histiocytic lymphoma, and he was treated accordingly. No evidence of bone marrow involvement was found at that time. The correct diagnosis of epidural GS was made possible in retrospect by using immunoperoxidase staining for lysozyme fourteen months later when the patient showed the full-blown features of leukemia. This rare tumor should be considered in the differential diagnosis of an epidural mass with cord compression in patients with or even without acute leukemia, because early diagnosis followed by appropriate combined chemotherapy and radiation may obviate surgical intervention and eventually prevent leukemic transformation.

Strip extensiometry for comparison of the mechanical response of bovine, rabbit, and human corneas

Specimens of bovine, rabbit, and human corneas were systematically tested in uniaxial tension to experimentally determine their effective nonlinear stress-strain relations, and hysteresis. Cyclic tensile tests were performed over the physiologic load range of the cornea, up to a maximum of 10 percent strain beyond slack strain. Dimensional changes to corneal test specimens, due to varying laboratory environmental conditions, were also assessed. The measured stress-strain data was found to closely fit exponential power function relations typical of collagenous tissues when appropriate account was taken of specimen slack strain. These constitutive relations are very similar for rabbit, human and bovine corneas; there was no significant difference between the species after preconditioning by one cycle. The uniaxial stress strain curves for all species behave similarly in that their tangent moduli increase at high loads and decrease at low loads as a function of cycling. In the bovine and rabbit data, there is a general trend towards more elastic behavior from the first to second cycles, but there is little variation in these parameters from the second to third cycles. In comparison, the human data demonstrates relatively little change between cycles. Increases in width of corneal test specimens, up to a maximum of 2 percent were found to occur under 95 percent relative humidity test conditions over 10 minutes elapsed time test periods, while specimens which were exposed to normal laboratory conditions (45 percent RH) were found to shrink in width up to a maximum of 9.5 percent over the same elapsed time period. The thickness of the test specimens were observed to decrease by 3 percent in 95 percent relative humidity and by 12 percent in 45 percent relative humidity over the same elapsed time period.