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Our laboratory recently published data that showed that the PAH composition of soot can be exactly determined and spatially resolved by low-fluence laser desorption ionization, coupled with high-resolution mass spectrometry imaging [1] . This analysis revealed that PAHs of 239–838 Da, containing few oxygenated species, comprise the soot observed in an ethylene diffusion flame. In this paper, we demonstrate that the empirical formula of observed species can aid in the enumeration of isomers and places limits on their structures and thermodynamic stability. Specifically, chemical graph theory (CGT) shows that the vast majority of species observed in the sampled particulate matter may be described as benzenoid, consisting of only fused 6-membered rings. We apply CGT to determine the Dias Parameter, dS, for observed, individual PAH peaks and demonstrate that observed PAH species cluster near low dS, indicative of highly condensed structures, with relatively low populations of edge concavity (armchairs, bays, and fjords). Finally, we quantitatively explore the relative stability of PAH isomers using group-additivity estimates (for benzenoid structures) and those containing a single 5-membered rings using density functional theory. For the latter, we show that highly-condensed, benzenoid structures have lower free energy than those containing five-membered rings, with buried 5-membered rings showing the highest free energies.

Laser ablation electrospray ionization (LAESI) driven by mid-infrared laser pulses allows the direct analysis of biological tissues with minimal sample preparation. Dedicated remote ablation chambers have been developed to eliminate the need for close proximity between the sample and the mass spectrometer inlet. This also allows for the analysis of large or irregularly shaped objects, and incorporation of additional optics for microscopic imaging. Here we report on the characterization of a newly designed conical inner volume ablation chamber working in transmission geometry, where a reduced zone of stagnation was achieved by tapering the sample platform and the chamber outlet. As a result, the transmission efficiency of both large (>7.5 μm) and smaller particulates (

Neutral lipids have been implicated in a host of potentially debilitating human diseases, such as heart disease, type-2 diabetes, and metabolic syndrome. Matrix-assisted laser desorption ionization (MALDI), the method-of-choice for mass spectrometry imaging (MSI), has led to remarkable success in imaging several lipid classes from biological tissue sections. However, due to ion suppression by phospholipids, MALDI has limited ability to efficiently ionize and image neutral lipids, such as triglycerides (TGs). To help overcome this obstacle, we have utilized silicon nanopost arrays (NAPA), a matrix-free laser desorption ionization (LDI) platform. Hidradenitis suppurativa (HS) is a chronic, recurrent inflammatory skin disease of the apocrine sweat glands. The ability of NAPA to efficiently ionize lipids is exploited in the analysis of human skin samples from sufferers of HS. Ionization by LDI from NAPA allows for the detection and imaging of a number of neutral lipid species, including TGs comprised of shorter, odd-chain fatty acids, which strongly suggests an increased bacterial load within the host tissue, as well as hexosylceramides (HexCers) and galabiosyl-/lactosylceramides that appear to be correlated with the presence of HS. Our results demonstrate that NAPA-LDI-MSI is capable of imaging and potentially differentiating healthy and diseased human skin tissues based on changes in detected neutral lipid composition.

Mass spectrometry imaging (MSI) is a powerful analytical technique that enables detection, discovery, and identification of multiple classes of biomolecules, while simultaneously mapping their spatial distributions within a sample (e.g., a section of biological tissue). The limitation in molecular coverage afforded by any single MSI platform has led to the development of multimodal approaches that incorporate two or more techniques to obtain greater chemical information. Matrix-assisted laser desorption ionization (MALDI) is a preeminent ionization technique for MSI applications because the wide range of available matrices allows some degree of enhancement with respect to the detection of particular molecular classes. Nonetheless, MALDI has a limited ability to detect and image several classes of molecules, e.g., neutral lipids, in complex samples. Laser desorption ionization from silicon nanopost arrays (NAPA-LDI or NAPA) has been shown to offer complementary coverage with respect to MALDI by providing improved detection of neutral lipids and some small metabolites. Here, we present a multimodal imaging method in which a single tissue section is consecutively imaged at low and high laser fluences, generating spectra that are characteristic of MALDI and NAPA ionization, respectively. The method is demonstrated to map the distributions of species amenable to detection by MALDI (e.g., phospholipids and intermediate-mass metabolites) and NAPA (e.g., neutral lipids such as triglycerides and hexosylceramides, and small metabolites) in mouse brain and lung tissue sections.

Mass spectrometry imaging (MSI) is capable of detection and identification of diverse classes of compounds in brain tissue sections, whereas simultaneously mapping their spatial distributions. Given the vast array of chemical components present in neurological systems, as well as the innate diversity within molecular classes, MSI platforms capable of detecting a wide array of species are useful for achieving a more comprehensive understanding of their biological roles and significance. Currently, matrix-assisted laser desorption ionization (MALDI) is the method of choice for the molecular imaging of brain samples by mass spectrometry. However, nanostructured laser desorption ionization platforms, such as silicon nanopost arrays (NAPA), are emerging as alternative MSI techniques that can provide complementary insight into molecular distributions in the central nervous system. In this work, the molecular coverage of mouse brain lipids afforded by NAPA-MSI is compared to that of MALDI-MSI using two common MALDI matrices. In positive ion mode, MALDI spectra were dominated by phosphatidylcholines and phosphatidic acids. NAPA favored the ionization of phosphatidylethanolamines and glycosylated ceramides, which were poorly detected in MALDI-MSI. In negative ion mode, MALDI favored sulfatides and free fatty acids, whereas NAPA spectra were dominated by signal from phosphatidylethanolamines. The complementarity in lipid coverages between the NAPA- and MALDI-MSI platforms presents the possibility of selective lipid analysis and imaging dependent upon which platform is used. Nanofabrication of the NAPA platform offers better uniformity compared to MALDI, and the wider dynamic range offered by NAPA promises improved quantitation in imaging.

Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize (Zea mays) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone.

Mass spectrometry imaging (MSI) is used increasingly to simultaneously detect a broad range of biomolecules while mapping their spatial distributions within biological tissue sections. Matrix-assisted laser desorption ionization (MALDI) is recognized as the method-of-choice for MSI applications due in part to its broad molecular coverage. In spite of the remarkable advantages offered by MALDI, imaging of neutral lipids, such as triglycerides (TGs), from tissue has remained a significant challenge due to ion suppression of TGs by phospholipids, e.g. phosphatidylcholines (PCs). To help overcome this limitation, silicon nanopost array (NAPA) substrates were introduced to selectively ionize TGs from biological tissue sections. This matrix-free laser desorption ionization (LDI) platform was previously shown to provide enhanced ionization of certain lipid classes, such as hexosylceramides (HexCers) and phosphatidylethanolamines (PEs) from mouse brain tissue. In this work, we present NAPA as an MSI platform offering enhanced ionization efficiency for TGs from biological tissues relative to MALDI, allowing it to serve as a complement to MALDI-MSI. Analysis of a standard lipid mixture containing PC(18:1/18:1) and TG(16:0/16:0/16:0) by LDI from NAPA provided an ~49 and ~227-fold higher signal for TG(16:0/16:0/16:0) relative to MALDI, when analyzed without and with the addition of a sodium acetate, respectively. In contrast, MALDI provided an ~757 and ~295-fold higher signal for PC(18:1/18:1) compared with NAPA, without and with additional Na+ . Averaged signal intensities for TGs from MSI of mouse lung and human skin tissues exhibited an ~105 and ~49-fold increase, respectively, with LDI from NAPA compared with MALDI. With respect to PCs, MALDI provided an ~2 and ~19-fold increase in signal intensity for mouse lung and human skin tissues, respectively, when compared with NAPA. The complementary coverage obtained by the two platforms demonstrates the utility of using both techniques to maximize the information obtained from lipid MS or MSI experiments.

Soot (sometimes referred to as black carbon) is produced when hydrocarbon fuels are burned. Our hypothesis is that polynuclear aromatic hydrocarbon (PAH) molecules are the dominant component of soot, with individual PAH molecules forming ordered stacks that agglomerate into primary particles (PP). Here we show that the PAH composition of soot can be exactly determined and spatially resolved by low-fluence laser desorption ionization, coupled with high-resolution mass spectrometry imaging. This analysis revealed that PAHs of 239-838 Da, containing few oxygenated species, comprise the soot observed in an ethylene diffusion flame. As informed by chemical graph theory (CGT), the vast majority of species observed in the sampled particulate matter may be described as benzenoids, consisting of only fused 6-membered rings. Within that limit, there is clear evidence for the presence of radical PAH in the particulate samples. Further, for benzenoid structures the observed empirical formulae limit the observed isomers to those which are nearly circular with high aromatic conjugation lengths for a given aromatic ring count. These results stand in contrast to recent reports that suggest higher aliphatic composition of primary particles.

Silicon nanopost array (NAPA) structures have been shown to be effective substrates for laser desorption/ionization-mass spectrometry (LDI-MS) and have been used to analyze a variety of samples including peptides, metabolites, drugs, explosives, and intact cells, as well as to image lipids and metabolites in tissue sections. However, no direct comparison has yet been conducted between NAPA-MS and the most commonly used LDI-MS technique, matrix-assisted laser desorption/ionization (MALDI)-MS. In this work, we compare the utility of NAPA-MS to that of MALDI-MS using two common matrices for the analysis of metabolites in cellular extracts and human urine. Considerable complementarity of molecular coverage was observed between the two techniques. Of 178 total metabolites assigned from cellular extracts, 68 were uniquely detected by NAPA-MS and 62 were uniquely detected by MALDI-MS. NAPA-MS was found to provide enhanced coverage of low-molecular weight compounds such as amino acids, whereas MALDI afforded better detection of larger, labile compounds including nucleotides. In the case of urine, a sample largely devoid of higher-mass labile compounds, 88 compounds were uniquely detected by NAPA-MS and 13 by MALDI-MS. NAPA-MS also favored more extensive alkali metal cation adduction relative to MALDI-MS, with the [M + 2Na/K - H]

Transcriptomics response of SK-N-AS cells to methamidophos (an acetylcholine esterase inhibitor) exposure was measured at 10 time points between 0.5 and 48 h. The data was analyzed using a combination of traditional statistical methods, machine learning techniques, and methods to infer causal relations between time profiles. We identified several processes that appeared to be upregulated in cells treated with methamidophos including: unfolded protein response, response to cAMP, calcium ion response, and cell-cell signaling. The data confirmed the expected consequence of acetylcholine buildup. Transcripts with potentially key roles were identified by anomaly detection using convolutional autoencoders and Generative Adversarial Networks, and causal networks relating these transcripts were inferred using Siamese convolutional networks and time warp causal inference.

Introduction Cancer pathogenesis and resulting treatment may lead to bone loss and poor skeletal health in survivorship. The purpose of this investigation was to evaluate the influence of 26 weeks of combined aerobic and resistance-training (CART) exercise on bone mineral density (BMD) in a multi-racial sample of female cancer survivors. Methods Twenty-six female cancer survivors volunteered to undergo CART for 1 h/day, 3 days/week, for 26 weeks. The Improving Physical Activity After Cancer Treatment (IMPAACT) Program involves supervised group exercise sessions including 20 min of cardiorespiratory training, 25 min of circuit-style resistance-training, and 15 min of abdominal exercises and stretching. BMD at the spine, hip, and whole body was assessed using dual-energy X-ray absorptiometry (DXA) before and after the intervention. Serum markers of bone metabolism (procollagen-type I N-terminal propeptide, P1NP, and C-terminal telopeptides, CTX) were measured at baseline, 13 weeks, and at study completion. Results Eighteen participants, with the average age of 63.0 ± 10.3 years, completed the program. Mean duration since completion of cancer treatment was 6.2 ± 10.6 years. Paired t-tests revealed significant improvements in BMD of the spine (0.971 ± 0.218 g/cm2 vs. 0.995 ± 0.218 g/cm2, p = 0.012), hip (0.860 ± 0.184 g/cm2 vs. 0.875 ± 0.191 g/cm2, p = 0.048), and whole body (1.002 ± 0.153 g/cm2 vs. 1.022 ± 0.159 g/cm2, p = 0.002). P1NP declined 22% at 13 weeks and 28% at 26 weeks in comparison to baseline (p, Highlights • Combined aerobic and resistance training improves BMD in female cancer survivors. • Participants who had chemotherapy showed significantly greater improvements in BMD. • P1NP and CTX exhibit an inverse relationship with gains in BMD after exercise.

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metal oxide NPs, but chemical interactions are also very important, especially for other NPs. The screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.

Mass spectrometry imaging (MSI) is a comprehensive tool for the analysis of a wide range of biomolecules. The mainstream method for molecular MSI is matrix-assisted laser desorption ionization, however, the presence of a matrix results in spectral interferences and the suppression of some analyte ions. Herein we demonstrate a new matrix-free MSI technique using nanophotonic ionization based on laser desorption ionization (LDI) from a highly uniform silicon nanopost array (NAPA). In mouse brain and kidney tissue sections, the distributions of over 80 putatively annotated molecular species are determined with 40 μm spatial resolution. Furthermore, NAPA-LDI-MS is used to selectively analyze metabolites and lipids from sparsely distributed algal cells and the lamellipodia of human hepatocytes. Our results open the door for matrix-free MSI of tissue sections and small cell populations by nanophotonic ionization.

Identifying the mechanism of action (MoA) of an unknown, possibly novel, substance (chemical, protein, or pathogen) is a significant challenge. Biologists typically spend years working out the MoA for known compounds. MoA determination is especially challenging if there is no prior knowledge and if there is an urgent need to understand the mechanism for rapid treatment and/or prevention of global health emergencies. In this paper, we describe a data analysis approach using Gaussian processes and machine learning techniques to infer components of the MoA of an unknown agent from time series transcriptomics, proteomics, and metabolomics data.

Recent technological advances have pushed the achievable spatial resolution for mass spectrometry imaging (MSI) to cellular and subcellular levels. Direct visualization of maize tissues by this tool has provided key insights into the localization of metabolites and lipids. This chapter outlines methodology for sample preparation, data acquisition, and data analysis of maize tissue sections using high-spatial resolution matrix-assisted laser desorption ionization (MALDI)-MSI, as well as the incorporation of a multi-resolution optical system, which allows for simple inter-conversion between different resolution setups (5, 10, and 50 μm imaging).

Recent technological advances have pushed the achievable spatial resolution for mass spectrometry imaging (MSI) to cellular and subcellular levels. Direct visualization of maize tissues by this tool has provided key insights into the localization of metabolites and lipids. This chapter outlines methodology for sample preparation, data acquisition, and data analysis of maize tissue sections using high-spatial resolution matrix-assisted laser desorption ionization (MALDI)-MSI, as well as the incorporation of a multi-resolution optical system, which allows for simple inter-conversion between different resolution setups (5, 10, and 50 μm imaging).

Laser ablation electrospray ionization-mass spectrometry (LAESI-MS) allows for direct analysis of biological tissues at atmospheric pressure with minimal to no sample preparation. In LAESI, a mid-IR laser beam (λ = 2.94 μm) is focused onto the sample to produce an ablation plume that is intercepted and ionized by an electrospray at the inlet of the mass spectrometer. In the remote LAESI platform, the ablation process is removed from the mass spectrometer inlet and takes place in an ablation chamber, allowing for incorporation of additional optics for microscopic imaging and targeting of specific features of the sample for laser ablation sampling. The ablated material is transported by a carrier gas through a length of tubing, delivering it to the MS inlet where it is intercepted and ionized by an electrospray. Previous proof-of-principle studies used a prolate spheroid ablation chamber with the carrier gas flow perpendicular to the ablation plume. This design resulted in significant losses of MS signal in comparison to conventional LAESI. Here we present a newly designed conical inner volume ablation chamber that radially confines the ablation plume produced in transmission geometry. The carrier gas flow and the expanding ablation plume are aligned in a coaxial configuration to improve the transfer of ablated particles. This new design not only recovered the losses observed with the prolate spheroid chamber design, but was found to provide an ∼12-15% increase in the number of metabolite peaks detected from plant leaves and tissue sections relative to conventional LAESI.

The Dutch Encapsulating Peritoneal Sclerosis (EPS) Registry was started in 2009. Cases were identified by contacting all Dutch nephrologists twice yearly. The predefined criteria for EPS allowed for inclusion of patients with diagnosed and suspected EPS. Cases registered between January 2009 and January 2015 were analyzed with follow-up until September 2015. Fifty-three EPS cases were identified, of which 28.3% were post-transplantation EPS cases. Fourteen patients were initially categorized as suspected EPS, of whom 13 developed EPS. A remarkable 6-fold decrease in the yearly incidence of EPS was observed, from 0.85% in 2009 to 0.14% in 2014. This decrease could not be explained by a decrease in the number of PD patients or average duration of PD treatment in this period. Two-year survival of EPS patients was 52%. The use of tamoxifen and surgical interventions increased significantly over the years. Tamoxifen-treated cases showed a trend to better patient survival and post-transplantation EPS had a significantly favorable outcome. In conclusion, the incidence of EPS has declined significantly in the Netherlands from 2009 to 2014.

The nitrophorins (nitro = NO, phorin = carrier) make up a group of NO-carrying heme proteins found in the saliva of at least two species of blood-sucking insects, Rhodnius prolixus, the “kissing bug”, which has four such proteins in the adult insect1−5 and at least three additional nitrophorins in earlier stages of development,6,7 and Cimex lectularius, the bedbug, which has only one.8,9 These interesting heme proteins sequester NO that is produced by a nitric oxide synthase (NOS) that is similar to vertebrate constitutive NOS and is present in the endothelial cells of the salivary glands,10−12 which keeps it stable for long periods of time by binding it as an axial ligand to a ferriheme center.1,3−5 The nitrophorins are at a very high concentration in the salivary glands of R. prolixus (combined NP concentration estimated to be ∼6–10 mMa), thus giving rise to the cherry red color1 of the glands. To function in insect feeding, the nitrophorin proteins must efficiently pack in the gland and stably bind NO, despite its reactive nature. The ferriheme binding site is crucially important in stabilizing the bound NO for long periods of time in the salivary glands. Upon injection into the tissues of the victim, NO dissociates and diffuses through the tissues to the nearby capillaries to cause vasodilation and thereby allow more blood to be transported to the site of the wound. At the same time, histamine, whose role is to cause swelling, itching, and the beginning of the immune response, is released by mast cells and platelets of the victim in the region of the bite. In the case of the Rhodnius proteins, this histamine binds to the heme sites of the nitrophorins, hence preventing the insect’s detection for a period of time.13 These two properties of the nitrophorins of R. prolixus contribute to the transmission of the protozoan Trypanasoma cruzi, the vector of Chagas’ disease,14 to the victim, via the feces of the insect, which are left behind at the site of the bite3 following the extended feeding time. The Rhodnius nitrophorins of the adult insect, which have been named NP1–NP4 in reverse order of their abundance in the saliva,2 occur as two pairs of similar sequence proteins, NP1 and NP4, which are 90% identical, and NP2 and NP3, which are 80% identical;2 the overall level of sequence identity is only 38%. The sequences are shown in Figure S1 of the Supporting Information. These proteins have been investigated by a number of techniques (DOI: 10.1021/bi501305a),1,3,15−41 and the solid state structures of one or more ligand complexes of NP1,15,42 NP2,43,44 and NP445−50 have been determined by X-ray crystallography. The structures are unique for heme proteins, in that the heme is located inside, but at the open end, of a β-barrel,8,51 as shown in Figure ​Figure1,1, rather than in the more commonly observed largely α-helical globin52 or four-helix bundle53 folds. The ferriheme molecule is bound to the protein via a histidine ligand, and the sixth coordination site is available to bind NO or other ligands. In the NO-off form in vitro, either water or ammonia, depending on buffer type, is bound to the sixth site.42,45 Figure 1 Structure of NP4. Shown are the protein backbone (blue for β-strands, red for α-helices, and gray for loops) and the heme (gold). Taken from Protein Data Bank entry 1X8O. Although NP4 and quite a number of its axial ligand complexes have been crystallized and their structures determined to high resolution by single-crystal X-ray diffraction,45−50 NP4 in solution at the low pH of the insect’s saliva (5–6) is an equilibrium mixture of at least two forms, a monomer and a dimer; higher-order oligomers have also been claimed.54 The previous report focused mainly on the gas-phase properties of NP4, which showed up to 14-mers present by mass spectrometry.54 The work presented here focuses on the solution properties that are important to the reaction chemistry of NP4 and its NO complex in the salivary glands and the tissues of the victim. Our work has included the preparation and investigation of site-directed mutants to define which protein side chains are involved in dimerization. We find that NP4 is a dimer at pH 5.0 at ≥1 mM but a monomer at pH 7.3, the approximate pH of the victim’s tissues; the dimer is much more stable when the ferriheme iron is bound to nitric oxide (NO). Because the sequences of NP4 and NP1 are 90% identical, we were surprised that we had not observed a dimeric form for NP1 during our early studies of that protein.15,17,19,21,23,25,28 However, NP1, like NP2 and NP3, has a charged amino acid at its N-terminus (Figure S1 of the Supporting Information), and during expression of any of these three genes, the methionine that results from translation of the start codon of the gene is not cleaved by the methionine aminopeptidase of Escherichia coli, thus leaving M0, with its relatively large side chain, at the N-terminus of these three proteins when they are isolated and purified. In the insect, the nitrophorins are expressed with an N-terminal signal sequence to target the protein for secretion into the salivary gland of the insect; cleavage of the signal sequence after secretion yields the mature N-terminus without methionine. The genes for the recombinant proteins, however, did not include the N-terminal signal sequence but rather began with the start codon, followed by the codon for the first amino acid of the protein. The M0 residue in the recombinant protein was not shown in the crystal structures of NP1 published before 2000,15,42 because of the relatively low resolution of the structures (2.0–2.3 A) and disorder at the N-terminus in the crystals, but mass spectrometry clearly shows the presence of M0 for recombinant NP1, as well as NP224 and NP3, as shown below. In contrast to NP1–NP3, NP4, with its N-terminal amino acid alanine, does not retain M0 when expressed recombinantly. We thus suspected that because NP1 [actually (M0)NP1] did not form a dimer, while NP4 did, the N-terminal region of the NP4 and NP1 proteins might be involved in the observed dimerization of NP4, and we have thus prepared the gene for the K1A mutant of NP1 as well as native N-terminal NP1 in this work. Our precedent for this approach was our earlier work on the D1A mutant of NP2,24 which we found had no M0 present when isolated and had properties markedly different from those of the (M0)NP2 obtained from simple expression of the recombinant gene.24 Later, we also prepared native N-terminal NP2, with D1 as the first amino acid, by combining our NP2 gene with an export sequence provided by the pelB leader sequence from Erwinia carotovora, which is present in the pET-26b expression plasmid (Novagen), to export the protein to the periplasm.29 When the export sequence was naturally cleaved in the E. coli periplasm, we were left with native N-terminal NP2, which could be purified in small quantities. The expression also had to be conducted in small batches, and thus, we have continued to use NP2(D1A) for experiments that require large quantities of protein. We found that these two proteins [NP2(D1A) and native N-terminal NP2] had essentially identical heme 1H NMR spectra and 1H{15N} HSQC spectra and very similar reaction properties, except for the rate constant for NO binding at pH 7.5, which was a factor of 5 smaller, and the equilibrium Kd for NO, which was a factor of 5 larger for the native N-terminal NP2 than for NP2(D1A).29 These findings suggest an important role for D1 in the reactivity of the protein,29 which we have not as yet elucidated. We have likewise recently created N-terminal NP1 in the same manner but find again that NP1(K1A) is easier to prepare in large quantities. We have found that the techniques of size-exclusion chromatography at pH 5.0 and multidimensional NMR spectroscopy over a range of pH values from 4.0 to 8.0 are the most useful for studying the dimer/monomer behavior of NP4 and its mutants, as well as NP1(K1A) and native N-terminal NP1 in solution, and we report our findings below.

1,5-diaminonaphthalene (DAN) has previously been reported as an effective matrix for matrix-assisted laser desorption ionization-mass spectrometry of phospholipids. In the current work, we investigate the use of DAN as a matrix for small metabolite analysis in negative ion mode. DAN was found to provide superior ionization to the compared matrices for MW < ~400 Da; however, 9-aminoacridine (9-AA) was found to be superior for a uridine diphosphate standard (MW 566 Da). DAN was also found to provide a more representative profile of a natural phospholipid mixture than 9-AA. Finally, DAN and 9-AA were applied for imaging of metabolites directly from corn leaf sections. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Background Encapsulating peritoneal sclerosis (EPS) is a rare complication of peritoneal dialysis (PD). It is characterized by encapsulation of the bowel, causing symptoms of intestinal obstruction. Exclusive involvement of parts of the bowel may occur and may be more common than previously thought. Our main objective was to investigate and report on patients with localized EPS. Methods Between July 2002 and December 2011, 9 of 17 EPS patients were referred to our department of surgery for a diagnostic laparotomy. Three of the 9 cases showed localized encapsulation of the small bowel and were selected for the purpose of this study. Results All 3 patients presented with an acute inflammatory state and symptoms of bowel obstruction. In 2 patients, EPS became clinically overt after kidney transplantation; the third patient was diagnosed while on hemodialysis. All shared a history of PD ranging from 31 to 101 months. In none of the patients was radiologic examination conclusive, although 2 showed peritoneal thickening and ascites. Each patient underwent laparotomy, confirming EPS. In all cases, a thickened peritoneal membrane became apparent, predominantly covering the ileocecal region of the intestine. In addition, a constrictive membrane at the level of the terminal ileum was noted. In 2 cases, the patients underwent enterolysis and dissection of the constricting fibrotic peritoneal membrane (peritonectomy) without bowel resection. The 3rd patient was managed with parenteral nutrition and tamoxifen. The postoperative course in 1 patient was complicated by infected ascites that resolved with antibiotic treatment. Eventually, all patients were doing well, with adequate oral intake and without the need for repeat surgery. Conclusions Localized EPS may be more common than previously thought. It has a predilection for the level of the terminal ileum. We believe that an elective diagnostic laparotomy should be considered early, because this procedure offers both diagnostic opportunities and therapeutic options. Localized EPS cases may benefit most from enterolysis and peritonectomy.

We have recently developed a multiplex mass spectrometry imaging (MSI) method which incorporates high mass resolution imaging and MS/MS and MS(3) imaging of several compounds in a single data acquisition utilizing a hybrid linear ion trap-Orbitrap mass spectrometer (Perdian and Lee, Anal. Chem. 82, 9393-9400, 2010). Here we extend this capability to obtain positive and negative ion MS and MS/MS spectra in a single MS imaging experiment through polarity switching within spiral steps of each raster step. This methodology was demonstrated for the analysis of various lipid class compounds in a section of mouse brain. This allows for simultaneous imaging of compounds that are readily ionized in positive mode (e.g., phosphatidylcholines and sphingomyelins) and those that are readily ionized in negative mode (e.g., sulfatides, phosphatidylinositols and phosphatidylserines). MS/MS imaging was also performed for a few compounds in both positive and negative ion mode within the same experimental set-up. Insufficient stabilization time for the Orbitrap high voltage leads to slight deviations in observed masses, but these deviations are systematic and were easily corrected with a two-point calibration to background ions.

We have previously developed in-parallel data acquisition of orbitrap mass spectrometry (MS) and ion trap MS and/or MS/MS scans for matrix-assisted laser desorption/ionization MS imaging (MSI) to obtain rich chemical information in less data acquisition time. In the present study, we demonstrate a novel application of this multiplex MSI methodology for latent fingerprints. In a single imaging experiment, we could obtain chemical images of various endogenous and exogenous compounds, along with simultaneous MS/MS images of a few selected compounds. This work confirms the usefulness of multiplex MSI to explore chemical markers when the sample specimen is very limited. Copyright © 2013 John Wiley & Sons, Ltd.

Fluoroquinolone (FQ) antibacterial compounds are frequently detected in the aquatic environment, and photodegradation is expected to play an important role in FQ fate in some sunlit surface waters. This study investigated the direct aquatic photochemistry of three FQs: norfloxacin, ofloxacin, and enrofloxacin. The direct photolysis rate of each drug exhibited strong pH dependence when exposed to simulated sunlight. For each FQ, direct photolysis rates and total light absorbance were used to calculate quantum yields for each of three environmentally relevant protonation states: a cationic, a zwitterionic, and an anionic form. In each case, quantum yields of the species varied significantly. The quantum yield for the zwitterionic form was 2-3 times higher than that of the anionic form and over an order of magnitude higher than that of the cationic form. Antibacterial activity assays were used to determine whether the loss of parent FQ due to photolysis led to loss of activity. Norfloxacin and ofloxacin photoproducts were found to be inactive, whereas enrofloxacin photoproducts were found to retain significant activity. These results are important for aiding in predictions of the potential impacts of FQs in surface waters.

Background: Encapsulating peritoneal sclerosis (EPS) may occur after kidney transplantation (post-transplantation EPS) or may be diagnosed during or after peritoneal dialysis treatment (classical EPS). The aim of the present study was to investigate to what extent both EPS entities differ in clinical presentation, radiological findings, outcome, and the systemic inflammatory response, as measured by plasma C-reactive protein (CRP) levels both prior to and after EPS diagnosis. Methods: We performed a retrospective analysis of 15 post-transplantation EPS and 19 classical EPS patients who were diagnosed at seven hospitals in the Netherlands between January 1, 2000, and January 1, 2011. Results: There were no inter-group differences in age, duration of peritoneal dialysis, clinical presentation, or radiology findings at diagnosis. Post-transplantation patients had experienced a lower number of peritonitis episodes per patient-year (0.2 (0.0-0.4) vs. 0.7 (0.3-1.2), p = 0.01) with a longer interval between the last peritonitis and EPS diagnosis (18.1 (4.6-34.3) vs. 4.4 (0.89-13.78) months, p = 0.01). Post-transplantation EPS patients showed a remarkably lower mortality rate (40.0 vs. 84.2%, p < 0.05). In both groups a pattern of elevated CRP values was observed, increasing within the year before EPS diagnosis. In the post-transplantation group the median CRP level at diagnosis was lower (56.0 vs. 144.50 mg/l, p < 0.05) than in the classical EPS group. Conclusion: Post-transplantation EPS has a similar clinical presentation as classical EPS but with a lower systemic inflammatory response and better outcome.

Advances in mass spectrometry (MS) have made comprehensive lipidomics analysis of complex tissues relatively commonplace. These compositional analyses, although able to resolve hundreds of molecular species of lipids in single extracts, lose the original cellular context from which these lipids are derived. Recently, high-resolution MS of individual lipid droplets from seed tissues indicated organelle-to-organelle variation in lipid composition, suggesting that heterogeneity of lipid distributions at the cellular level may be prevalent. Here, we employed matrix-assisted laser desorption/ ionization–MS imaging (MALDI-MSI) approaches to visualize lipid species directly in seed tissues of upland cotton (Gossypium hirsutum). MS imaging of cryosections of mature cotton embryos revealed a distinct, heterogeneous distribution of molecular species of triacylglycerols and phosphatidylcholines, the major storage and membrane lipid classes in cotton embryos. Other lipids were imaged, including phosphatidylethanolamines, phosphatidic acids, sterols, and gossypol, indicating the broad range of metabolites and applications for this chemical visualization approach. We conclude that comprehensive lipidomics images generated by MALDI-MSI report accurate, relative amounts of lipid species in plant tissues and reveal previously unseen differences in spatial distributions providing for a new level of understanding in cellular biochemistry.

Laser desorption/ionization (LDI) mass spectrometry imaging (MSI) was used to acquire chemical images of flavonoid metabolites on the surface of wild-type and mutant (tt7) Arabidopsis thaliana flowers. Flavonoids were localized to the petals and carpels of flowers, with tissue heterogeneity in the petals. Specifically, kaempferol and/or its glycosides were abundant in the distal region of petals and quercetin and its downstream flavonoids were highly enriched in the more proximal region of petals. As a result of a mutation in the TT7 gene which blocks the conversion of dihydrokaempferol to dihydroquercetin, the downstream metabolites, quercetin, isohamnetin, and their glycosides, were not observed in the mutant flowers. Instead, the metabolites in an alternative pathway, kaempferol and/or its glycosides, were as highly abundant on the proximal region of the petals as in the distal region. In addition, the combined flavonoid amounts on the proximal region of petals in the wild-type are almost equivalent to the amounts of kaempferol and/or its glycosides in the mutant. This strongly suggests that the expression of the TT7 gene is localized on the proximal part of the petal while the other genes in the upper stream pathway are evenly expressed throughout the petal. Most importantly, this work demonstrates MSI of metabolites can be utilized for the localization of gene expression.

Encapsulating peritoneal sclerosis (EPS) is a severe complication of peritoneal dialysis (PD) and may present after kidney transplantation, a condition known as posttransplantation EPS. The prevalence and impact of posttransplantation EPS on survival after kidney transplantation is unknown. From January 1, 1996 until July 1, 2007, 1241 PD patients were transplanted. Thirty-eight cases of posttransplantation EPS (3%) were identified from the Dutch multicenter EPS study. In EPS patients the mean pretransplant dialysis duration was longer than in the controls (71.4 ± 37.5 months vs. 34.7 ± 25.5, p < 0.0001). The majority of EPS cases were observed within the first 2 years after transplantation, but some cases appeared many years after transplantation. Two hundred and one (16.2%) patients died after transplantation, of which 17 were EPS patients. After infection (23.9%), cardiovascular disease (21.9%) and malignancy (10.9%), EPS (8.5%) was the fourth known cause of death after transplantation. Kaplan-Meier analysis showed a significant decreased survival for transplanted patients with posttransplantation EPS compared to transplanted patients without EPS. In conclusion, posttransplantation EPS is rare but carries a high mortality. A prolonged clinical vigilance and a high index of suspicion for the diagnosis are warranted, specifically in PD patients with a relatively long cumulative pretransplant duration of PD.

Background. Encapsulating peritoneal sclerosis (EPS) is a serious complication of peritoneal dialysis (PD) with an increasing incidence. There is no clear consensus on the treatment of EPS, but anecdotal reports indicate improvement in EPS patients treated with tamoxifen. At present, there is no evidence for the effect of tamoxifen treatment in EPS patients. This study investigates the effect of treatment with tamoxifen on survival in EPS patients. Methods. This study is a retrospective analysis of survival in EPS patients as part of the Dutch multicentre EPS study in the period January 1996 to July 2007. Sixty-three patients with severe EPS were followed up until August 2008. Demographic, patient and PD-related variables of EPS patients were investigated. Patients treated with tamoxifen were compared to patients not treated with tamoxifen. Survival was analysed with multivariate Cox regression analysis. Results. Twenty-four patients were treated with tamoxifen, and 39 were not treated with tamoxifen. The clinical and demographic characteristics were similar for the tamoxifen-treated and non-treated groups. The mortality rate was significantly lower in tamoxifen-treated patients compared to EPS patients not treated with tamoxifen (45.8% vs 74.4%, P = 0.03). Survival in tamoxifen-treated patients, adjusted for calendar time, age, use of corticosteroids, presence of functioning transplantation, use of parental nutrition and centre influences was longer in comparison to not-treated patients (HR 0.39, P = 0.056). Conclusions. Tamoxifen treatment in EPS patients is associated with lower mortality and shows a trend to an increased multivariate-adjusted survival. This supports additional use of tamoxifen to treat patients with severe EPS.

Encapsulating peritoneal sclerosis (EPS) is a rare but serious complication in patients on peritoneal dialysis (PD). We describe a cluster of 13 EPS cases occurring in 2 university hospitals in The Netherlands. Most of these cases were diagnosed after recent kidney transplantation, when the patients developed severe symptoms of bowel obstruction. This accumulation raised the question as to whether other than known risk factors, such as duration of PD treatment, could be involved in the development or course of EPS after transplantation. According to various publications, EPS has been diagnosed often after withdrawal from PD, suggesting that cessation in itself may be a risk factor. In addition, transplantation-related management should be considered to play a role, including the use of the profibrotic calcineurin inhibitors and the trend to reduce the load of corticosteroids in treatment regimes. To identify risk factors, further multicenter studies are required, paying special attention to alterations in immunosuppressive treatment regimens as well as PD prescriptions, including PD fluid characteristics. Transfer from PD to hemodialysis should be under serious consideration in patients eligible for kidney transplantation as soon as there are indications of ultrafiltration failure.

Chronic peritoneal dialysis (PD) can be complicated by encapsulating peritoneal sclerosis (EPS), a rare but the most severe complication associated with long-term PD. Morbidity and mortality are still high (range from 25% to 55%) especially in the first year after diagnosis. The international Society for Peritoneal Dialysis (ISPD) defined EPS by clinical signs of abdominal pain, bowel obstruction or weight loss in late stages of the disease. Clinical symptoms, radiologic findings and histologic criteria are the three diagnostic pillars.

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A significant limiting factor in achieving high spatial resolution for matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) imaging is the size of the laser spot at the sample surface. Here, we present modifications to the beam-delivery optics of a commercial MALDI-linear ion trap-Orbitrap instrument, incorporating an external Nd:YAG laser, beam-shaping optics, and an aspheric focusing lens, to reduce the minimum laser spot size from ~50 μm for the commercial configuration down to ~9 μm for the modified configuration. This improved system was applied for MALDI-MS imaging of cross sections of juvenile maize leaves at 5-μm spatial resolution using an oversampling method. A variety of different metabolites including amino acids, glycerolipids, and defense-related compounds were imaged at a spatial resolution well below the size of a single cell. Such images provide unprecedented insights into the metabolism associated with the different tissue types of the maize leaf, which is known to asymmetrically distribute the reactions of C4 photosynthesis among the mesophyll and bundle sheath cell types. The metabolite ion images correlate with the optical images that reveal the structures of the different tissues, and previously known and newly revealed asymmetric metabolic features are observed.

Plant tissues present intriguing systems for study by mass spectrometry imaging, as they exhibit a complex metabolism and a high degree of spatial localization. This chapter presents a methodology for preparation of plant tissue sections for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) analysis and the use of a hybrid mass spectrometer for "multiplex" imaging. The multiplex method described here provides a wide range of analytical information, including high-resolution, accurate mass imaging and tandem MS scans for structural information, all within a single experiment. While this procedure was developed for plant tissues, it can be readily adapted for analysis of other sample types.

Plant tissues present intriguing systems for study by mass spectrometry imaging, as they exhibit a complex metabolism and a high degree of spatial localization. This chapter presents a methodology for preparation of plant tissue sections for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) analysis and the use of a hybrid mass spectrometer for "multiplex" imaging. The multiplex method described here provides a wide range of analytical information, including high-resolution, accurate mass imaging and tandem MS scans for structural information, all within a single experiment. While this procedure was developed for plant tissues, it can be readily adapted for analysis of other sample types.

1,5-Diaminonaphthalene (DAN) has previously been reported as an effective matrix for matrix-assisted laser desorption ionization-mass spectrometry of phospholipids. In the current work, we investigate the use of DAN as a matrix for small metabolite analysis in negative ion mode. DAN was found to provide superior ionization to the compared matrices for MW ~400 Da; however, 9-aminoacridine (9-AA) was found to be superior for a uridine diphosphate standard (MW 566 Da). DAN was also found to provide a more representative profile of a natural phospholipid mixture than 9-AA. Finally, DAN and 9-AA were applied for imaging of metabolites directly from corn leaf sections. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

To assess the interrater reproducibility of malaria microscopy in epidemiological studies, 711 thick blood films from population-based surveys were randomly selected and reread by 4 experienced microscopists. Sample estimates of the prevalence of P. falciparum infection, geometric mean parasite density and the proportion of samples above various parasite density cut-off levels were almost identical in the routine and quality control readings. Differences were, however, encountered in the sample estimates for gametocyte ratio, proportion of mixed infection and average density index. In all three cases the quality control result was significantly higher than the routine evaluation. On the level of the individual slide there was good interrater agreement for the presence of P. falciparum infections (Kappa index kappa = 0.79) which was even better when parasite densities between 4 and 100/microl were excluded (kappa = 0.94). With respect to the assessment of parasite density, a high level of disagreement was found. While the mean difference between the two readings was not different from 0, the second reading was between 0.12 and 10 times that of the first. However, the level of disagreement significantly fell with increasing parasite densities. Thus malaria microscopy is very reliable for the estimation of parasite ratios and geometric mean parasite densities within and between studies as long as the same methodology is used, but tends to underestimate the gametocyte ratio and proportion of mixed infections. Care must be taken, however, when individual parasite density is related to other explanatory variables, due to the high degree of variability in the parasite enumeration.

To further define teratogenicity associated with 13-cis-retinoic acid (13-cis-RA) in the cynomolgus monkey, the drug was orally administered on three different treatment regimens. Experiment (Exp.) 1 (2.5 mg/kg/day, gestational day [GD] 12–27, n = 11) investigated the teratogenicity of a single daily dose of 13-cis-RA administered shortly after embryo implantation. Pharmacokinetic sampling was done to determine retinoid profiles on the first (GD12) and last (GD27) days of treatment. Exposure to 13-cis-RA during early organogenesis in Exp. 2 (2.5 mg/kg/day, GD20–27, and 2 × 2.5 mg/kg/day, GD28–30, n = 5) investigated the potential adverse effects of 13-cis-RA on the developing limb. The use of multiple doses of 13-cis-RA in Exp. 3 (2 × 2.5 mg/kg/day, GD26–27, n = 5) investigated the necessity of double dosing on the induction of retinoid embryopathy in the macaque. Malformations of retinoid target organs as well as embryolethality were most prevalent when single daily doses of 13-cis-RA were administered during pre- and early organogenesis in Exp. 1. Moreover, multiple doses on GD26–27 failed to induce any manifestation of abnormal development in Exp. 3. These results confirm that the lowest observed adverse effect level (LOAEL) in macaques is 2.5 rather than 5.0 times greater than that observed in human pregnancies. Exposure during forelimb development (GD20–30) in Exp. 2 was unsuccessful in inducing defects of this skeletal region, although defects in several retinoid target organs (i.e., cerebellum and internal ear) were present, indicating that a teratogenic threshold was achieved. Pharmacokinetic analysis of 13-cis-RA and its metabolites on GD12 and 27 in Exp. 1 showed considerable exposure to the administered drug and its 4-oxo-metabolite. In contrast, the exposure to all-trans-RA was negligible. The results support the use of a specific treatment schedule in early gestation in the macaque as the most appropriate model for characterizing the teratogenic potential of retinoids in humans.