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Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications. © 2017 Thermo Fisher Scientific Inc.

Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7-18 different genes per isolate), including the following encoding carbapenemases: blaKPC-2, blaOXA-48, blaOXA-72, blaNDM-1, blaNDM-7 and blaVIM-1. In addition, a novel version of blaSHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance - based on acquired resistance determinants - was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.

Resistance to life-saving antibiotics increases rapidly worldwide, and multiresistant bacteria have become a global threat to human health. Presently, the most serious threat is the increasing spread of Enterobacteriaceae carrying genes coding for extended spectrum β-lactamases (ESBL) and carbapenemases on highly mobile plasmids. We here demonstrate how optical DNA maps of single plasmids can be used as fingerprints to trace plasmids, for example, during resistance outbreaks. We use the assay to demonstrate a potential transmission route of an ESBL-carrying plasmid between bacterial strains/species and between patients, during a polyclonal outbreak at a neonatal ward at Sahlgrenska University Hospital (Gothenburg, Sweden). Our results demonstrate that optical DNA mapping is an easy and rapid method for detecting the spread of plasmids mediating resistance. With the increasing prevalence of multiresistant bacteria, diagnostic tools that can aid in solving ongoing routes of transmission, in particular in hospital settings, will be of paramount importance.

Chromobacterium violaceum is a ß-proteobacterium found widely worldwide with important biotechnological properties and is associated to lethal sepsis in immune-depressed individuals. In this work, we report the discover, complete sequence and annotation of a plasmid detected in C. violaceum that has been unnoticed until now. We used DNA single-molecule analysis to confirm that the episome found was a circular molecule and then proceeded with NGS sequencing. After DNA annotation, we found that this extra-chromosomal DNA is probably a defective bacteriophage of approximately 44 kilobases, with 39 ORFs comprising, mostly hypothetical proteins. We also found DNA sequences that ensure proper plasmid replication and partitioning as well as a toxin addiction system. This report sheds light on the biology of this important species, helping us to understand the mechanisms by which C. violaceum endures to several harsh conditions. This discovery could also be a first step in the development of a DNA manipulation tool in this bacterium.

The rapid spread of antibiotic resistance - currently one of the greatest threats to human health according to WHO - is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.

Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations., 21 pages, 7 figures, 1 table

Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.

The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard "foreign" contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.

Zebrafish are an increasingly popular vertebrate model organism in which to study biological phenomena. It has been widely used, especially in developmental biology and neurobiology, and many aspects of its development and physiology are similar to those of mammals. The popularity of zebrafish relies on its relatively low cost, rapid development and ease of genetic manipulation. Moreover, the optical transparency of the developing fish together with novel imaging techniques enable the direct visualization of complex phenomena at the level of the entire organism. This potential is now also being increasingly appreciated by the lipid research community. In the present review we summarize basic information on the lipid composition and distribution in zebrafish tissues, including lipoprotein metabolism, intestinal lipid absorption, the yolk lipids and their mobilization, as well as lipids in the nervous system. We also discuss studies in which zebrafish have been employed for the visualization of whole-body lipid distribution and trafficking. Finally, recent advances in using zebrafish as a model for lipid-related diseases, including atherosclerosis, obesity, diabetes and hepatic steatosis are highlighted. As the insights into zebrafish lipid metabolism increase, it is likely that zebrafish as a model organism will become an increasingly powerful tool in lipid research.

Objective: To evaluate the impact of an extruded muesli product based on -glucan-rich oat bran on postprandial glycaemia and insulinaemia. Subject/Design: The study is divided in two series. Blood glucose and serum insulin responses were studied after subjects consuming test meals including a serving of muesli with 3 g (series 1) and 4 g (series 2) of -glucans, respectively. The muesli was a component in a single serving packet with muesli and yoghurt. This was served together with white wheat bread in the morning after an overnight fast. The compositions were standardized to contain 50 g available carbohydrates. As a reference meal a serving packet without -glucans was included. The study was performed at Applied Nutrition and Food Chemistry, Lund University, Sweden. Nineteen and thirteen healthy volunteers with normal body mass index were recruited for series 1 and 2, respectively. Results: Muesli with 3 g of -glucans, included in a mixed bread meal, gave no significant differences in glycaemic response compared to a reference meal without muesli and -glucans. In contrast, muesli with 4 g of -glucans significantly (P

The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose we performed new experiments, measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic buffer strength. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths the agreement is less good. We discuss possible reasons. Our approach allows, in principle, to measure the Kuhn length and effective width of a single DNA molecule and more generally of semiflexible polymers in solution., Revised version, 6 pages, 2 figures, 1 table, supplementary material

By simultaneous coherent anti-Stokes Raman scattering (CARS) and 2-photon fluorescence microscopy of Thioflavin-S stained Alzheimer´s diseased human brain tissues, we show evidence of lipid deposits co-localizing with fibrillar β-amyloid (Aβ) plaques. Two lipid morphologies can be observed; lamellar structures and coalescing macro-aggregates of sub-micron sizes to ~25 μm. No significant lipid deposits were observed in non-fibrillar, diffuse plaques identified by Aβ immuno-staining. CARS microscopy of unlabeled samples confirms the lamellar and macro-aggregate lipid morphologies. The composition of the plaques was analyzed by CARS microspectroscopy and Raman microscopy; vibrational signatures of lipids with long acyl chains co-localize with the β-sheet vibrations. The lipid fluidity was evaluated from the CARS spectra, illustrating that the lipid composition/organization varies throughout the plaques. Altogether this indicates close amyloid-lipid interplay in fibrillar Aβ plaques, rendering them more dynamic compositions than previously believed and, hence, potential sources of toxic oligomers.

We demonstrate how nanofluidic channels can be used as a tool to rapidly determine the number and sizes of plasmids in bacterial isolates. Each step can be automated at low cost, opening up opportunities for general use in microbiology labs.

In colostrum collected 0-80 h postpartum the contents of immunoglobulins (Igs), transforming growth factor beta-2 (TGF-beta2), insulin-like growth factor-1 (IGF-1) and growth hormone (GH) were analysed. Colostrum initially contained 90 mg mL(-1) IgG1, 2.8 mg mL(-1) IgG2, 1.6 mg mL(-1) IgA, 4.5 mg mL(-1) IgM, and these concentrations declined by 92%, 87%, 93% and 84%, respectively, in the samples collected later. Of the growth factors, colostrum initially contained 289-310 ng mL(-1) TGF-beta2 and the concentration diminished to 66 ng mL(-1). The content of IGF-1 and GH postpartum decreased from 870 to 150 ng mL(-1), and from 0.17 to < 0.03 ng mL(-1), respectively. Heat treatment and freeze-drying of colostral whey decreased the content of Igs to 75%, while the contents of IGF-1 and TGF-beta2 were unaffected. A similar processing, including filtration steps reduced also the IGF-1 and TGF-beta2 by 25%. IgM seems to be the most sensitive of the Igs to processing. (C) 2002 Elsevier Science Ltd. All rights reserved. (Less)

We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50–160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

Alzheimera's disease (AD) is a progressive neurodegenerative disorder currently without cure, characterized by the presence of extracellular plaques surrounded by dystrophic neurites. In an effort to understand the underlying mechanisms, biochemical analysis (protein immunoblot) of plaque extracts reveals that they consist of amyloid-beta (Aβ) peptides assembled as oligomers, protofibrils and aggregates. Their spatial distribution has been confirmed by Thioflavin-S or immuno-staining with fluorescence microscopy. However, it is increasingly understood that the protein aggregation is only one of several mechanism that causes neuronal dysfunction and death. This raises the need for a more complete biochemical analysis. In this study, we have complemented 2-photon fluorescence microscopy of Thioflavin-S and Aβ immuno-stained human AD plaques with CARS microscopy. We show that the chemical build-up of AD plaques is more complex and that Aβ staining does not provide the complete picture of the spatial distribution or the molecular composition of AD plaques. CARS images provide important complementary information to that obtained by fluorescence microscopy, motivating a broader introduction of CARS microscopy in the AD research field.

Several studies have shown that there is a strong physical interaction between cholesterol and sphingomyelin (SM). The critical factor is thought to be the high degree of saturation in the very long acyl chains of SM. In this study we examined the effects of SM on cholesterol absorption in the rat and compared them with those of phosphatidylcholine (PC). Cholesterol absorption was studied by use of the dual-isotope plasma ratio method. We also studied the effect of sterols on the fecal excretion of undigested SM and its metabolites after a single oral meal of (3)H-dihydrosphingosine-labeled SM. When cholesterol was given dissolved in soybean oil, without addition of SM or other phospholipids, absorption was 68 +/- 12% in the rat intestine. As a general feature the absorption was less efficient from the cholesterol/phospholipid dispersions. In dispersions with cholesterol and SM, the lowest cholesterol absorption (9 +/- 2%) was seen with a cholesterol:SM molar ratio of 1:1. With dispersions of cholesterol and different PC substrates the absorption of cholesterol was lower with saturated PC (16 +/- 8%) than with soybean-PC (22 +/- 4%) or dioleoyl PC (23 +/- 8%). Uptake of SM in the rat intestine was reduced by sterols. For example, percentage recovery of (3)H radioactivity in fecal lipids was 38 +/- 8% when SM was given with cholesterol and 16 +/- 3% without any sterol. One third of the radioactivity in feces was present as ceramide. Sitostanol had the same effect on uptake of SM as cholesterol. This study shows that when rats are fed mixtures of SM and cholesterol the intestinal uptake of both lipids is decreased. By feeding mixtures of SM and sterols the exposure of the colon to ceramide can be increased.

BACKGROUNDThere is a renewed interest in metabolism of sphingolipids because of their role in signal transduction. Sphingomyelin is the dominating phospholipid in human milk but its metabolism and possible function in the gastrointestinal tract of breast fed infants is unknown. We explored whether bile salt-stimulated milk lipase has a role in sphingolipid metabolism.METHODSIn vitro assays of sphingomyelinase and ceramidase activities, using radiolabeled substrates, human milk samples and purified native and recombinant variants of bile salt-stimulated milk lipase with or without known activators or inhibitors.RESULTSHuman whey and purified lipase catalysed hydrolysis of palmitoyl-labeled ceramide with the highest rate around pH 8.5-9.0. 1 mg of lipase hydrolysed 0.7 micromol ceramide in one hour at pH 8.5 in presence of 4 mM bile salt. The activity of whey was inhibited by antibodies towards human bile salt-stimulated milk lipase, indicating that this lipase accounted for virtually all ceramidase activity in the milk. In contrast, bile salt-stimulated milk lipase showed no activity against sphingomyelin. However we give evidence of a separate, hitherto unknown, acid sphingomyelinase in human milk. Under the used in vitro conditions this sphingomyelinase could account for hydrolysis of half of milk sphingomyelin in one hour.CONCLUSIONSHuman milk bile salt-stimulated milk lipase hydrolyses ceramide and may thus have a role in sphingomyelin digestion, but only after initial hydrolysis to ceramide and phosphorylcholine. Part of the latter could be carried out in the stomach by the acid milk sphingomyelinase now described. We speculate that these two milk enzymes may be of importance for optimal use of human milk sphingolipids. (Less)

Dietary sphingomyelin (SM) undergoes sequential cleavage to ceramide and sphingosine in the intestine. A distinctive intestinal sphingomyelinase (SMase) with alkaline pH-optimum was earlier identified by us. The activity was highest in middle and lower small intestine, but its role in SM digestion has not been clarified. In this study we examined the extension and capacity of SM digestion in vivo. After feeding rats 0.2, 6.6, or 32 μmol SM containing 2 μCi 3H-sphingosine-labeled milk SM (3H-SM), radioactivity was analyzed in intestinal contents and tissues 2, 4, and 8 hr later. The proportion of radioactivity in the contents of small intestine increased with the dose of SM; 9% of given dose with 0.2 μmol, 34% with 6.6 μmol, and 71% with 32 μmol, respectively after 2 hr. Lowest tissue radioactivity was found in duodenum and proximal jejunum and highest in distal jejunum and proximal ileum. Three to twenty one percent of radioactivity in the intestinal tissue was in ceramide, the proportion varying with the dose given, region of the intestine, and time after administration. After administration of 6.6 or 32 μmol SM, significant amounts of intact SM and ceramide was found in intestinal contents, colon, and excreted faeces. Colon was exposed to ceramide derived from exogenous SM in amounts that were rather proportional to the dose of SM fed. SM digestion is thus a process extending over the whole intestine and occurring mainly in the middle and lower parts of the small intestine. The site of digestion coincides with the distribution of the alkaline SMase, indicating that this enzyme catalyzes the first step in the digestion. The extension and limited capacity of the SM digestion leads to an exposure of the lower small intestine and colon to SM and sphingolipid metabolites.

BACKGROUND: The metabolism of sphingomyelin generates important signals regulating cell proliferation and apoptosis. Previous studies found that the administration of colon carcinoma carcinogen was associated with an accumulation of membrane sphingomyelin, and that dietary sphingomyelin inhibited promotion of experimental colon carcinoma in mice, indicating that the abnormal metabolism of sphingomyelin is linked to colon carcinoma development. However, the changes in sphingomyelinase (SMase) activity in colon carcinoma have not been directly studied. The authors identified, specifically in the intestine, a distinctive alkaline SMase that differs from the known acidic and neutral SMases. The functions and clinical implications of the enzyme are unknown. This study examined the changes in all three SMase activities in human colorectal carcinoma. METHODS: Tissue samples were taken from colorectal carcinoma and normal mucosa from 18 patients. After homogenization, the activities of acidic, neutral, and alkaline SMase, as well as ceramidase and alkaline phosphatase, were determined. The enzyme activities in cancer tissue were compared with normal tissue from the same patients. RESULTS: In the normal tissue, there is an activity gradient from the ascending colon to the rectum for neutral and alkaline SMases but not for acidic SMase. In colorectal carcinoma, alkaline SMase activity was preferentially decreased by 75%, whereas acidic and neutral SMase activity decreased by 30% and 50%, respectively. No changes could be found for either ceramidase or alkaline phosphatase activity. CONCLUSIONS: Alkaline SMase activity preferentially decreases in human colorectal carcinoma, suggesting a regulatory role of the enzyme in colon mucosa cell proliferation.

In the monitoring of progression of lung disease in patients with cystic fibrosis (CF), recurrent computed tomography (CT) examinations are often used. The relatively new imaging technique chest tomosynthesis (CTS) may be an interesting alternative in the follow-up of these patients due to its visualization of the chest in slices at radiation doses and costs significantly lower than is the case with CT. A first step towards introducing CTS imaging in the diagnostics of CF patients is to establish a scoring system appropriate for evaluating the severity of CF pulmonary disease based on findings in CTS images. Previously, several such CF scoring systems based on CT imaging have been published. The purpose of the present study was to develop a CF scoring system for CTS, by starting from an existing scoring system dedicated for CT images and making modifications regarded necessary to make it appropriate for use with CTS images. In order to determine any necessary changes, three thoracic radiologists independently used a scoring system dedicated for CT on both CT and CTS images from CF patients. The results of the scoring were jointly evaluated by all the observers, which lead to suggestions for changes to the scoring system. Suggested modifications include excluding the scoring of air trapping and doing the scoring of the findings in quadrants of the image instead of in each lung lobe.

There is convincing evidence that consumption of fish and fish oil rich in long-chain (LC)n-3 PUFA (n-3 LCPUFA), EPA (20 : 5n-3) and DHA (22 : 6n-3) reduce the risk of CHD. The aim of the present study was to investigate whethern-3 LCPUFA-enriched food products provide similar beneficial effects as fish oil with regard to incorporation into plasma lipids and effects on cardiovascular risk markers. A parallel 7-week intervention trial was performed where 159 healthy men and women were randomised to consume either 34 g fish pâté (n44), 500 ml fruit juice (n38) or three capsules of concentrated fish oil (n40), all contributing to a daily intake of approximately 1 g EPA and DHA. A fourth group did not receive any supplementation or food product and served as controls (n37). Plasma fatty acid composition, serum lipids, and markers of inflammation and oxidative stress were measured. Compared with the control group, plasman-3 LCPUFA and EPA:arachidonic acid ratio increased equally in all intervention groups. However, no significant changes in blood lipids and markers of inflammation and oxidative stress were observed. In conclusion, enriched fish pâté and fruit juice represent suitable delivery systems forn-3 LCPUFA. However, although the dose given is known to reduce the risk of CVD, no significant changes were observed on cardiovascular risk markers in this healthy population.

The properties of sphingomyelin obtained from bovine milk were investigated. In particular, the properties of liposomes and emulsions prepared from the spingomyelin, as well as the liquid crystalline behavior, were investigated and compared to those of related phosphatidylcholine systems. Like sphingomyelins from other sources, sphingomyelin from milk contains a large fraction of long and saturated acyl groups, which results in a high gel-to-liquid crystal transition temperature (Tc 35–82°C, depending on the lipid concentration). At high sphingomyelin concentrations, a lamellar phase forms above Tc, while a swollen gel phase is obtained below Tc. The gel phase swells to about 20 wt% water, whereas the swelling continues to about 40 wt% water above Tc. The limiting areas per molecule are 51 and 68 A2 below and above Tc, respectively. Sphingomyelin from milk forms liposomes readily in the presence of cholesterol. The liposomes formed have a diameter of about 100 nm and are stable, even at 0.1 M NaCl or HCl. Materials entrapped in the liposomes are released rather slowly (typically 40% over 5 h). A comparison shows that the sphingomyelin liposomes behave similarly to those formed by phosphatidylcholine systems. Furthermore, sphingomyelin from milk forms stable oil-in-water emulsions with soybean oil. The size of the emulsion droplets obtained was about 200 nm. Both the size of the emulsion droplets and its dependence on electrolyte addition correlate closely with those of emulsions formed by the corresponding phosphatidylcholine system. Therefore, it is possible to use sphingomyelin as an alternative for saturated phosphatidylcholines, which may be advantageous for oral and dermal pharmaceutical applications, as well as in cosmetics.

Eight crossbred, ovariectomized gilts (Swedish Landrace x Swedish Yorkshire x Hampshire), with a mean age of 7.5 mo, were studied during anesthesia and surgery, control-sampling, relocation, and grouping during a period of 3 wk. Acute treatment with a hydrocortisone injection (5 mg, i.v.) was also given. Blood samples were taken frequently (every 10 min) during the intensive part of the experimental days. The blood samples were analyzed for catecholamines (CA), adrenaline (A) and noradrenaline (NA), cortisol, and corticosteroid-binding globulin (CBG). The surgical period with anesthesia and surgery showed significant effects on CA, cortisol, and CBG. The A level increased immediately after the surgery. A biphasic increase in the cortisol level was observed on the day of surgery; the greatest increase was seen when the animals had regained consciousness after surgery but still were drowsy and staggering. The CBG level decreased on the day after the surgery. The study showed that the levels of the analyzed substances were back to normal 2 d after surgery. During relocation and grouping there was a short, significant increase in CA and cortisol levels, whereas the CBG level was not affected. Treatment with hydrocortisone significantly increased the cortisol level, but no change was seen in plasma CA or CBG levels. In conclusion, anesthesia and surgery induced significant effects on the levels of CA, cortisol, and CBG in gilts and the animals needed 2 d to recover before regaining their normal condition. During relocation and a limited grouping period, the significant increases in CA and cortisol levels were of short duration and CBG did not change.(ABSTRACT TRUNCATED AT 250 WORDS)

BACKGROUND: Sphingomyelin occurs in modest amounts in the diet, in sloughed mucosal cells, and in bile. It is digested by the mucosal enzymes alkaline sphingomyelinase and ceramidase. In humans, alkaline sphingomyelinase is also secreted in bile. The digestion of sphingomyelin is slow and incomplete, which has been linked to the inhibition of cholesterol absorption and colonic carcinogenesis. OBJECTIVE: We evaluated whether the supply of moderate amounts of milk sphingomyelin increases the exposure of the colon to sphingomyelin and its metabolites. DESIGN: Two experimental series were performed. In experiment A, we measured the content of sphingomyelin and ceramide in human ileostomy content by HPLC during 8 h after consumption of a test meal containing 250 mg milk sphingomyelin. In experiment B, we measured the molecular species of sphingomyelin and ceramide by HPLC-tandem mass spectrometry after doses of 50, 100, or 200 mg sphingomyelin. RESULTS: In experiment A, the average increase in ileostomy content of ceramide plus sphingomyelin amounted to 19% of the fed dose of sphingomyelin. In experiment B, the output of C-22:0-sphingomyelin, C-23:0-sphingomyelin, C-24:0-sphingomyelin, and sphingosine increased significantly and palmitoyl-sphingomyelin increased proportionally less. Outputs and concentrations of palmitoyl-ceramide and sphingosine showed great individual variation, and stearoyl-sphingomyelin and stearoyl-ceramide did not increase after the meals. Although the output of long-chain sphingomyelin species increased significantly, the data indicated that >81% of all measured sphingomyelin species had been digested. CONCLUSIONS: Humans digest and absorb most of the sphingomyelin in normal diets. The level of sphingolipid metabolites to which the colon is exposed can, however, be influenced by realistic amounts of dietary sphingomyelin. (Less)

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder without cure, characterized by the presence of extracellular plaques surrounded by dystrophic neuritis . Fundamental understanding of the molecular processes involved is urgently needed in order to develop strategies to inhibit steps in the AD pathogenesis. Current understanding is that the senile plaques are composed of peptide fragments (Amyloid- β peptides) formed after the cleavage of the transmembrane protein amyloid protein precursor (APP) . This knowledge relies primarily on biochemical analysis of the plaques in cell extracts together with fluorescence microscopy of tissue samples exposed to harsh preparation procedures and labeling. Thus, it is disputed to which extent the observations reported reflect the true biochemistry and morphology of AD brain tissue. By the powerful combination of Raman microspectroscopy, Coherent Anti-Stokes Raman Scattering (CARS) and 2-photon fluorescence microscopy, we show that the molecular composition of AD plaques is more complex and consequently the mechanisms behind their formation.

Stem cell growth and migration on nanofibrous scaffolds and micro-fluidic channels on Silicon-Chip were studied by using neural stem cells isolated from adult rats' brain. Electrospinning and lithographic technique were used for developing nanofibrous-polylactic acid (PLA) and polyurethane (PU) based-scaffolds and micro-fluidic channels on Si-Chips respectively. Immunocytochemical and morphological analysis showed better cell-matrix interaction with profound adhesion, proliferation and migration on the developed scaffolds. Cell culture assay with microfluidic channel revealed the ability of developed channel system in guiding neuronal stem cell growth towards specified directions. These studies extend the possibility of using developed nanofibrous scaffolds and micro-fluidic channel system for future electrical signal transmission based on living neural stem cells.

The interactions of the bile salt sodium taurocholate (TC) in 50 mM Trizma-HCl buffer and 150 mM NaCl (pH 9) at 37 degrees C with membranes composed of sphingomyelin (SM) were studied by dynamic light scattering, cryogenic transmission electron microscopy (cryo-TEM) and turbidity measurements. Small unilamellar SM vesicles were prepared by extrusion. Below the CMC of TC, taurocholate addition leads to vesicle growth due to incorporation of the taurocholate molecules into the vesicle bilayer. At around half the CMC of the bile salt, the SM vesicles are transformed into SM/TC mixed worm-like micelles, which are visualized by cryo-TEM for the first time. Further increase in the taurocholate concentration leads to the rupture of these structures into small spherical micelles. Interestingly, large non-spherical micelles were also identified for pure taurocholate solutions. Similar threadlike structures have been reported earlier for the bile salt sodium taurodeoxycholate [Rich, A., Blow, D., 1958. Nature 182, 1777; Blow, D.M., Rich, A., 1960. J. Am. Chem. Soc. 82, 3566-3571; Galantini, L., Giglio, E., La Mesa, C., Viorel-Pavel, N., Punzo, F., 2002. Langmuir 18, 2812] and for mixtures of taurocholate and phosphatidylcholate [Ulmius, J., Lindblom, G., Wennerstrom, H., Johansson, L.B.-A., Fontel, K., Soderman, O., Ardvisson, G., 1982. Biochemistry 21, 1553; Hjelm, R.P., Thiyagarajan, P., Alkan-Onyuksel, H., 1992. J. Phys. Chem. 96, 8653] as determined by various scattering methods.

Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.

The alkaline sphingomyelinase (SMase) was first found in rat intestinal brush border. The important roles of this enzyme in digestion of sphingomyelin and in mucosal cell proliferation have been suggested. In the present work, the distribution of the alkaline SMase in the tissues of human beings and animals have been studied. By assaying the enzyme activity in human biopsy samples, we found that the alkaline SMase activity was absent in the stomach, increased in the duodenum, present at high levels in the small intestine, and slightly declined in the colon and rectum. High activities were found similarly in the intestinal contents of the healthy adults and infants. The activities were also found in the intestinal mucosa of rats, normal and germ-free mice, and hamsters with the same distribution pattern as in humans, but not in the intestinal mucosa of guinea pigs. Apart from the intestinal tract, a SMase activity preferring alkaline pH was identified in human and guinea pig bile, but not in the bile of rat, pig, sheep, and cow. No activity was found in either pancreatic tissue or pancreatic juice in all species tested, and none was detected in human urine and milk. In conclusion, alkaline SMase exists predominantly in the digestive system with considerable tissue and species differences.

The hydrolysis of sphingomyelin has been found to generate important signals regulating cell proliferation, differentiation and apoptosis. However, the enzymes responsible for digestion of dietary sphingomyelin have not been well documented. This study demonstrates the occurrence of a sphingomyelinase (SMase) in both human hepatic bile and gallbladder bile. The enzyme was equally found in both bacteria negative and positive bile samples and in samples obtained from patients with or without gallbladder diseases. A bacteria-free gallbladder bile was used for characterization. It was found that bile SMase hydrolyzed sphingomyelin to phosphorylcholine and ceramide with negligible activity against either phosphatidylcholine or p-nitrophenyl phosphate. The enzyme preferred an alkaline condition and the optimal pH was 9. The activity of this alkaline SMase was bile salt dependent and was fully activated by 4–6 mM bile salts. Triton X-100, the non-ionic detergent did not activate bile SMase. Ca2+ and Mg2+ ions had no significant effect at optimal bile salt concentration. The molecular mass of this enzyme was about 85 kDa as measured by Sephadex G200 gel chromatography. In conclusion, we demonstrated a SMase in bile which differs markedly from the known acid and neutral SMase. Its potential important roles in sphingomyelin digestion and gallbladder diseases require further investigation.

Previous studies indicated that there was an alkaline sphingomyelinase (SMase) activity in small intestine, but its properties have not been studied in detail. In the present work, we studied the distribution of this enzyme activity in rat gastrointestinal tract and characterized it in intestinal mucosal homogenates. Little alkaline SMase activity was detected in the stomach and the duodenum. The activity in both mucosa and intestinal content increased in the small intestine and reached the maximum at the distal jejunum, then declined in the ileum and slightly increased again in the colon. The activity distribution pattern differed markedly from those of acid SMase and alkaline phosphatase. Little alkaline SMase activity could be found in bile, liver and pancreas before or after treatment with trypsin. The optimum pH of the alkaline SMase was 9. It specifically hydrolyzed sphingomyelin (SM), not phosphatidylcholine, to ceramide and phosphocholine. The alkaline SMase was bile salt dependent and was optionally activated by 3 mM bile salts. Triton X-100 could not mimic the effect of bile salt, rather dose-dependently inhibited the enzyme activity. Ca2+, Mg2+ did not change the alkaline SMase activity in the presence of bile salts, and reduced the activity in the absence of bile salt. Trypsin inactivated acid SMase in pancreas, liver and duodenum but had no influence on intestinal alkaline SMase activity. In conclusion, the intestinal alkaline SMase has a specific distribution pattern and the characters of it differ in several respects from the known acid and neutral SMases.

Various markers for stress were evaluated in the plasma of pigs. Treadmill exercise was chosen as a well defined and quantifiable stressor. One group of non-stress-susceptible pigs had to carry out two intense exercise bouts at a one-week interval, and another group remained in their pens and served as controls. Large interindividual differences in the performance and in the hormonal and metabolic responses to exercise were observed. The exercise stress resulted in an immediate increase in the plasma concentrations of cortisol, lactate and hypoxanthine, with a return to the pre-exercise levels within one hour. No direct effect of physical stress on CBG binding capacity or on the concentrations of xanthine and uric acid was observed. In two very nervous pigs, even mild stress in connection with the first blood sampling resulted in an elevated concentration of lactate, but the cortisol and hypoxanthine values remained at the basal level. It is concluded that plasma concentrations of cortisol, lactate and hypoxanthine are valuable markers for physical stress.

Corticosteroid binding globulin (CGB) from term-pregnant mouse serum was isolated and characterized by peptide analysis after treatment with CNBr and Lys-specific protease, respectively. Amino acid sequence analysis of six segments, covering 189 of 383 positions in different regions of the protein, showed unexpectedly low overall homology (60%) to the indirectly deduced human amino acid sequence previously reported. However, some segments displayed a greater resemblance to their human counterparts. Differences were observed in at least two of six potential glycosylation sites. The nature of electrophoretic CBG variants and their immunological properties are described.

A fast and reproducible two-step method with high resolution was developed for purification of murine corticosteroid-binding globulin (CBG). The first step was liquid chromatography on a Sephacryl-S-200 column, and the CBG-containing residual was subsequently chromatographed by fast protein liquid chromatography (FPLC). This enabled us to quickly obtain a highly purified protein and the apparently isolated CBG was tested for its purity by sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis (SDS-PAGE) and sedimentation equilibrium centrifugation. The CBG concentration in pregnant mouse serum was estimated to 0.78 g/l (1.5% of the total protein). The monomeric organization of the protein was demonstrated by mercaptoethanol treatment. No NH 2 -terminal amino acid could be detected, probably owing to a blocked amino acid. The mol. wt (M r ) of murine CBG was determined to be 52,000 and the sedimentation constant S 20°,w to 3.9 S by analytical ultracentrifugation. The protein showed 5 bands when subjected to isoelectric focusing: 3 bands with apparent isoelectric points (pI) between pH 3.15–3.25 and two between pH 3.40–3.50.

Treatment of mice with ACTH not only increased plasma corticosterone levels, but also reduced the ligand-binding capacity of the glucocorticoid receptor in skeletal muscle cytosol. Non-linear Scatchard plots were obtained for the glucocorticoid receptor following ACTH treatment. This upward concave curvilinearity could not be reproduced by simply adding to the cytosol an amount of corticosterone corresponding to the increase, even though this treatment resulted in reduced binding capacity. The addition of corticosterone resulted in a slower formation of ligand-receptor complexes (lower association rate constant), which offered a partial explanation for the low binding. In addition, ACTH treatment was also found to reduce the binding capacity in adrenalectomized mice that did not respond with corticosterone elevation. However, in this case Scatchard plots were linear.

5-hydroxytryptamine (5-HT, serotonin)- and opsin-immunoreactive sites were studied in the developing pineal complex of the stickleback, Gasterosteus aculeatus L., by use of light-microscopic indirect immunoperoxidase techniques. 5-HT immunoreactivity first occurs in the pineal organ at the age of 80 h after fertilization and appears to be localized in cells of the photoreceptor type. The outer segments of a few pineal photosensory cells exhibit opsin immunoreactivity at the age of 84 h after fertilization. The number of cells seems to increase until the pineal organ is completely developed. The increase in the number of 5-HT immunoreactive perikarya runs parallel in time to that of the opsin-immunoreactive outer segments. The cells of the parapineal organ show neither opsin nor 5-HT immunoreactivity. The retina of the embryonic stickleback does not display opsin immunoreactivity until after hatching, which takes place about 144 h after fertilization. These results suggest, in the three-spined stickleback, an earlier light-perception capacity for the developing pineal organ than for the retina.

Effects of stress on concentrations of cortisol and corticosteroid-binding globulin (CBG) in blood plasma and on glucocorticoid receptor concentrations in muscle cytosol were studied in pigs representing three Halothane (Hal) genotypes (NN, Nn, nn). At 12 wk of age, animals were divided into four groups: pigs subjected to transport (5 h in a truck), pigs treated with amperozide prior to transport, pigs not transported but treated with amperozide and pigs neither transported nor given amperozide. Animals were slaughtered the week they reached 100 kg live weight (3 mo later). The Hal gene showed no major influence on the variables studied except for cortisol concentrations (P = .06) measured directly after transport at 12 wk of age (NN = 66.8 nM, Nn = 61.4 nM, nn = 69.4 nM). However, the response in each Hal genotype differed, depending on whether or not the pigs had been exposed to transport. Two weeks after transport, NN pigs developed higher cortisol concentrations than untransported animals, whereas the response was reversed in nn animals; Nn pigs showed no difference in this regard. At slaughter, the effect of transport (12 wk of age) on cortisol and CBG was still apparent. In NN pigs cortisol and CBG concentrations were elevated (P less than or equal to .05, P = .08, respectively), whereas concentrations tended to be lower in nn pigs (P = .17, P = .07, respectively) when compared with untransported pigs. Transported pigs had lower receptor concentrations at slaughter (P less than or equal to .01) than untransported pigs. However, pigs given amperozide in connection with transport had a receptor concentration comparable to that in untransported pigs. Our study shows conclusively that transport stress had long-term effects on cortisol, CBG and glucocorticoid receptor concentrations. In addition, amperozide had long-term effects on cortisol and receptor concentrations.

The ontogenetic development of serotoninergic neurons in the brain of the stickleback was investigated with the indirect immunocytochemical peroxidase-antiperoxidase technique, using a specific antibody to serotonin (5-hydroxytryptamine, 5-HT). Formation of neuronal populations takes place during embryonic development. By 80 h after fertilization, the first 5-HT perikarya have appeared in the ventricular zone of the hypothalamus (nucleus recessus lateralis) and the raphe region. At 108 h the first 5-HT perikarya can be observed in area praetectalis. At 118 h a transient group of 5-HT neurons appears rostral to the nucleus recessus lateralis, and at this same age the first 5-HT perikarya may be visualized in nucleus recessus posterioris. A group of 5-HT neurons appears in the dorsolateral tegmentum at 166 h (one day after hatching, which occurs at 120-144 h after fertilization). Differentiation of the neuronal populations, in terms of migration and formation of subdivisions, starts between 80 h and 94 h, and seems to be completed between 1 and 5 days after hatching. Raphe nuclei form an anterior group comprising nuclei raphe dorsalis, raphe medialis and a ventrolateral group, and a posterior group comprising a nucleus raphe pallidus/obscurus complex, a lateral nucleus reticularis paragigantocellularis and a ventromedial nucleus raphe magnus. The posterior and ventral raphe nuclei, which are well developed at the time of hatching, have not been visualized in the adult stickleback. While formation of 5-HT neuronal systems, as well as their primary efferent pathways, takes place during early ontogenetic development, the establishment of terminal areas and their subsequent differentiation apparently takes place during later ontogenetic stages. Most presumptive target areas are penetrated by 5-HT axons at hatching, although terminal formation does not seem to start until later. A considerable number of 5-HT neuronal groups present in the embryonic and newly hatched stickleback have not been visualized in the adult stickleback. This may be due to selective cell death, changes in transmitter phenotype or maturation of axonal transport processes during development.

The antibody response to two Escherichia coli antigens (0149 and K88) and the in vitro reactivity of peripheral blood lymphocytes (PBLs) to pokeweed mitogen was studied in growing pigs after exposure to varying degrees of stress. Three experimental groups were used; transportation by lorry, transportation by lorry after a previous injection of a tranquillizing drug (amperozide), no transportation but an amperozide injection. Another group was used as a control group. This group was not transported and received no amperozide injection. The animals were the offspring of boars and sows heterozygous (Nn) for the Hal gene, and all 3 Hal genotypes (NN, Nn, nn) were identified and could thus be compared within litters. Immediately after the experimental treatment, the highest PBL reactivity was found for the amperozide-treated animals and for the non-transported animals, with no differences in reactivity between Hal genotypes. Two weeks later, the treatments caused different effects on pigs of the 3 Hal genotypes, both with regard to the PBL reactivity and the IgG response to 0149. The NN pigs had a higher PBL reactivity than the nn pigs for all treatments except the ‘drug + transport’ class where the reverse rank order was found. The NN pigs also had a higher IgG response to 0149 than the nn pigs in the ‘drug + no transport’ class. The amperozide treatment was followed by a higher PBL reactivity in non-transported NN pigs and in transported nn pigs. The amperozide-treated non-transported NN pigs also had a higher IgG response to 0149. The highest PBL reactivity and IgG response to 0149 were found mainly in pigs with the lowest cortisol levels. Pronounced differences between litters were found for both the antibody response and the PBL reactivity.

Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as wel ...

Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.Circular DNA is of interest since it is found in many biologically relevant contexts, such as bacterial plasmids, viruses and eukaryotic mitochondrial DNA. Furthermore, the circular topology forces two strands in close proximity to each other in nanochannel, which changes the polymer physics compared to linear DNA. Circular DNA is difficult to study with traditional single molecule techniques because such techniques generally require the attachment of handles to the, but is readily accessed using nanofluidics.Circular DNA has less entropy and higher conformational free energy than in its unfolded configuration. Therefore, as a double-strand break occurs and circular DNA opens up, it unfolds to its linear configuration inside the nanochannel. This study compares the static properties of confined linear and circular DNA as well as investigates the dynamics of the transition from circular to linear DNA as a double-strand break occurs.We observe that the difference in extension between the circular and linear configurations depends on the degree of confinement, which we confirm with theoretical predictions. Our data for unfolding of the circular DNA to the linear configuration suggests that hydrodynamic friction between the DNA and the solvent is the main rate-determining factor but that DNA-DNA contacts are also important. Finally, by staining the DNA inhomogeneously, we can follow the local dynamics of the DNA as the folding occurs and conclude, for example, how the two different strands move relative to each other during the unfolding process. We are thus able to study the dynamics of confined DNA with unprecedented resolution and obtain completely new information about confined polymers.

It has long been known that the commonly used fluorescent dye YOYO-1 (YOYO) stains DNA unevenly at sub-stoichiometric concentrations, and that equilibration is slow. We use this uneven staining to increase the resolution in measurements on how YOYO affects the properties of DNA confined in nanofluidic channels. The emission intensity from each DNA-YOYO complex correlates directly with the amount of YOYO bound. We can thus, in one single experiment, study DNA-YOYO molecules ranging from fully saturated to molecules with a low degree of YOYO bound. Interestingly we find that the extension of the DNA does not increase linearly with increasing amount of YOYO bound. Our data instead suggests that there are two different phases with different behavior. We explain this as being due to a transition from a region where intramolecular electrostatics dominates to where also the charges on the channel walls become important.Our observations are of importance not only for YOYO but are general for cationic ligands that bind to DNA by intercalation and the nanochannels are excellently suited for probing such subtle changes in the physics of the DNA-ligand complex.Finally we show how a mix of YOYO and netropsin, a DNA-binding molecule with extreme selectivity for AT-DNA, can be used to map DNA sequences. When adding the two molecules to DNA simultaneously and stretching it in the nanochannel we obtain an emission intensity variation along the DNA that corresponds to the underlying AT/GC ratio. The intensity variation correlates well with the known sequence and we believe that such maps can be useful for example for fast identification of bacterial infections from extremely small sample volumes.