A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression.

Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype), genomic imprinting [i.e., parent-of-origin (PO)], and maternal [i.e., maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.

In-Line Reactions and Ionizations of Vaporized Diphenylchloroarsine and Diphenylcyanoarsine in Atmospheric Pressure Chemical Ionization Mass Spectrometry.

We propose detecting a fragment ion (Ph2As(+)) using counter-flow introduction atmospheric pressure chemical ionization ion trap mass spectrometry for sensitive air monitoring of chemical warfare vomiting agents diphenylchloroarsine (DA) and diphenylcyanoarsine (DC). The liquid sample containing of DA, DC, and bis(diphenylarsine)oxide (BDPAO) was heated in a dry air line, and the generated vapor was mixed into the humidified air flowing through the sampling line of a mass spectrometer. Humidity effect on the air monitoring was investigated by varying the humidity of the analyzed air sample. Evidence of the in-line conversion of DA and DC to diphenylarsine hydroxide (DPAH) and then BDPAO was obtained by comparing the chronograms of various ions from the beginning of heating. Multiple-stage mass spectrometry revealed that the protonated molecule (MH(+)) of DA, DC, DPAH, and BDPAO could produce Ph2As(+) through their in-source fragmentation. Among the signals of the ions that were investigated, the Ph2As(+) signal was the most intense and increased to reach a plateau with the increased air humidity, whereas the MH(+) signal of DA decreased. It was suggested that DA and DC were converted in-line into BDPAO, which was a major source of Ph2As(+). Graphical Abstract ᅟ.

Real-time air monitoring of mustard gas and Lewisite 1 by detecting their in-line reaction products by atmospheric pressure chemical ionization ion trap tandem mass spectrometry with counterflow ion introduction.

A new method enabling sensitive real-time air monitoring of highly reactive chemical warfare agents, namely, mustard gas (HD) and Lewisite 1 (L1), by detecting ions of their in-line reaction products instead of intact agents, is proposed. The method is based on corona discharge-initiated atmospheric pressure chemical ionization coupled with ion trap tandem mass spectrometry (MS(n)) via counterflow ion introduction. Therefore, it allows for highly sensitive and specific real-time detection of a broad range of airborne compounds. In-line chemical reactions, ionization reactions, and ion fragmentations of these agents were investigated. Mustard gas is oxygenated in small quantity by reactive oxygen species generated in the corona discharge. With increasing air humidity, the MS(2) signal intensity of protonated molecules of mono-oxygenated HD decreases but exceeds that of dominantly existing intact HD. This result can be explained in view of proton affinity. Lewisite 1 is hydrolyzed and oxidized. As the humidity increases from zero, the signal of the final product, namely, didechlorinated, dihydroxylated, and mono-oxygenated L1, quickly increases and reaches a plateau, giving the highest MS(2) and MS(3) signals among those of L1 and its reaction products. The addition of minimal moisture gives the highest signal intensity, even under low humidity. The method was demonstrated to provide sufficient analytical performance to meet the requirements concerning hygienic management and counter-terrorism. It will be the first practical method, in view of sensitivity and specificity, for real-time air monitoring of HD and L1 without sample pretreatment.

Real-time explosive particle detection using a cyclone particle concentrator.

RATIONALE: There is a need for more rapid methods for the detection of explosive particles. We have developed a novel real-time analysis technique for explosive particles that uses a cyclone particle concentrator. This technique can analyze sample surfaces for the presence of particles from explosives such as TNT and RDX within 3 s, which is much faster than is possible by conventional methods. METHODS: Particles are detached from the sample surface with air jet pulses, and then introduced into a cyclone particle concentrator with a high pumping speed of about 80 L/min. A vaporizer placed at the bottom of the cyclone particle concentrator immediately converts the particles into a vapor. The vapor is then ionized in the atmospheric pressure chemical ionization (APCI) source of a linear ion trap mass spectrometer. RESULTS: An online connection between the vaporizer and a mass spectrometer enables high-speed detection within a few seconds, compared with the conventional off-line heating method that takes more than 10 s to raise the temperature of a sample filter unit. Since the configuration enriched the number density of explosive particles by about 80 times compared with that without the concentrator, a sub-ng amount of TNT particles on a surface was detectable. CONCLUSIONS: The detection limit of our technique is comparable with that of an explosives trace detector using ion mobility spectrometry. The technique will be beneficial for trace detection in security applications, because it detects explosive particles on the surface more speedily than conventional methods.

Sensitive and comprehensive detection of chemical warfare agents in air by atmospheric pressure chemical ionization ion trap tandem mass spectrometry with counterflow introduction.

A highly sensitive and specific real-time field-deployable detection technology, based on counterflow air introduction atmospheric pressure chemical ionization, has been developed for a wide range of chemical warfare agents (CWAs) comprising gaseous (two blood agents, three choking agents), volatile (six nerve gases and one precursor agent, five blister agents), and nonvolatile (three lachrymators, three vomiting agents) agents in air. The approach can afford effective chemical ionization, in both positive and negative ion modes, for ion trap multiple-stage mass spectrometry (MS(n)). The volatile and nonvolatile CWAs tested provided characteristic ions, which were fragmented into MS(3) product ions in positive and negative ion modes. Portions of the fragment ions were assigned by laboratory hybrid mass spectrometry (MS) composed of linear ion trap and high-resolution mass spectrometers. Gaseous agents were detected by MS or MS(2) in negative ion mode. The limits of detection for a 1 s measurement were typically at or below the microgram per cubic meter level except for chloropicrin (submilligram per cubic meter). Matrix effects by gasoline vapor resulted in minimal false-positive signals for all the CWAs and some signal suppression in the case of mustard gas. The moisture level did influence the measurement of the CWAs.

Sensitive monitoring of volatile chemical warfare agents in air by atmospheric pressure chemical ionization mass spectrometry with counter-flow introduction.

A new method for sensitively and selectively detecting chemical warfare agents (CWAs) in air was developed using counter-flow introduction atmospheric pressure chemical ionization mass spectrometry (MS). Four volatile and highly toxic CWAs were examined, including the nerve gases sarin and tabun, and the blister agents mustard gas (HD) and Lewisite 1 (L1). Soft ionization was performed using corona discharge to form reactant ions, and the ions were sent in the direction opposite to the airflow by an electric field to eliminate the interfering neutral molecules such as ozone and nitrogen oxide. This resulted in efficient ionization of the target CWAs, especially in the negative ionization mode. Quadrupole MS (QMS) and ion trap tandem MS (ITMS) instruments were developed and investigated, which were movable on the building floor. For sarin, tabun, and HD, the protonated molecular ions and their fragment ions were observed in the positive ion mode. For L1, the chloride adduct ions of L1 hydrolysis products were observed in negative ion mode. The limit of detection (LOD) values in real-time or for a 1 s measurement monitoring the characteristic ions were between 1 and 8 µg/m(3) in QMS instrument. Collision-induced fragmentation patterns for the CWAs were observed in an ITMS instrument, and optimized combinations of the parent and daughter ion pairs were selected to achieve real-time detection with LOD values of around 1 µg/m(3). This is a first demonstration of sensitive and specific real-time detection of both positively and negatively ionizable CWAs by MS instruments used for field monitoring.

High-throughput walkthrough detection portal for counter terrorism: detection of triacetone triperoxide (TATP) vapor by atmospheric-pressure chemical ionization ion trap mass spectrometry.

With the aim of improving security, a high-throughput portal system for detecting triacetone triperoxide (TATP) vapor emitted from passengers and luggage was developed. The portal system consists of a push-pull air sampler, an atmospheric-pressure chemical ionization (APCI) ion source, and an explosives detector based on mass spectrometry. To improve the sensitivity of the explosives detector, a novel linear ion trap mass spectrometer with wire electrodes (wire-LIT) is installed in the portal system. TATP signals were clearly obtained 2 s after the subject under detection passed through the portal system. Preliminary results on sensitivity and throughput show that the portal system is a useful tool for preventing the use of TATP-based improvised explosive devices by screening persons in places where many people are coming and going.