Profiling the Plasma Apolipoproteome of Normo- and Hyperlipidemic Mice by Targeted Mass Spectrometry.

Atherosclerotic cardiovascular disease is the leading cause of death worldwide. For decades, mouse modeling of atherosclerosis has been the mainstay for preclinical testing of genetic and pharmacological intervention. Mouse models of atherosclerosis depend on supraphysiological levels of circulating cholesterol carried in lipoprotein particles. Lipoprotein particles vary in atherogenicity, and it is critical to monitor lipoprotein levels during preclinical interventions in mice. Unfortunately, the small plasma volumes typically harvested during preclinical experiments limit analyses to measuring total cholesterol and triglyceride levels. Here we developed a high-throughput, low-cost targeted multiple reaction monitoring (MRM) stable isotope dilution (SID) mass spectrometry assay for simultaneous relative quantification of nine apolipoproteins using a few microliters of mouse plasma. We applied the MRM assay to investigate the plasma apolipoproteome of two atherosclerosis models: the widely used ApoE knockout model and the emerging recombinant adeno-associated virus-mediated hepatic Pcsk9 overexpression model. By applying the assay on size-exclusion chromatography-separated plasma pools, we provide in-depth characterization of apolipoprotein distribution across lipoprotein species in these models, and finally, we use the assay to quantify apolipoprotein deposition in mouse atherosclerotic plaques. Taken together, we report development and application of an MRM assay that can be adopted by fellow researchers to monitor the mouse plasma apolipoproteome during preclinical investigations.

Contrast-enhanced ultrasound imaging using capacitive micromachined ultrasonic transducers.

Capacitive micromachined ultrasonic transducers (CMUTs) have a nonlinear relationship between the applied voltage and the emitted signal, which is detrimental to conventional contrast enhanced ultrasound (CEUS) techniques. Instead, a three-pulse amplitude modulation (AM) sequence has been proposed, which is not adversely affected by the nonlinearly emitted harmonics. In this paper, this is shown theoretically, and the performance of the sequence is verified using a 4.8 MHz linear capacitive micromachined ultrasonic transducer (CMUT) array, and a comparable lead zirconate titanate (PZT) array, across 6-60 V applied alternating current (AC) voltage. CEUS images of the contrast agent SonoVue flowing through a 3D printed hydrogel phantom showed an average enhancement in contrast-to-tissue ratio (CTR) between B-mode and CEUS images of 49.9 and 37.4 dB for the PZT array and CMUT, respectively. Furthermore, hydrophone recordings of the emitted signals showed that the nonlinear emissions from the CMUT did not significantly degrade the cancellation in the compounded AM signal, leaving an average of 2% of the emitted power between 26 and 60 V of AC. Thus, it is demonstrated that CMUTs are capable of CEUS imaging independent of the applied excitation voltage when using a three-pulse AM sequence.

Life goals as a driving force in traumatic brain injury rehabilitation: a longitudinal dyadic perspective.

BACKGROUND: Traumatic brain injury significantly impacts survivors and their families. Rehabilitation following traumatic brain injury is often complex due to the physical, psychological, and socio-economic problems survivors face. Life goals are considered a motivational factor in rehabilitation. OBJECTIVE: The aim was to explore expectations, problems, and strategies for goal setting in survivors of traumatic brain injury and their family caregivers for one-year during rehabilitation. METHODS: A longitudinal qualitative study using dyadic interviews with survivors and family caregivers was carried out at three time points during the first year following traumatic brain injury. Data was analyzed according to Braun and Clarke's thematic analysis. RESULTS: Eight survivors of traumatic brain injury and their family caregivers completed 24 interviews. Three themes and one sub-theme were identified: 1) life goals as a driving force (subtheme: dyadic discrepancies and conflicts); 2) conflicts between specific, measurable, achievable, realistic, and timed (SMART) goals and life goals; and 3) changing perceptions of the impact of impairments.Life goals are important motivation in the rehabilitation process. Health care professionals must integrate life goals and rehabilitation goals (i.e. SMART goals) to decrease barriers and survivor ambivalence about rehabilitation. Involving both survivors and family caregivers in goal setting increases rehabilitation success.

3D Printed Hydrogel Multiassay Platforms for Robust Generation of Engineered Contractile Tissues.

We present a method for reproducible manufacture of multiassay platforms with tunable mechanical properties for muscle tissue strip analysis. The platforms result from stereolithographic 3D printing of low protein-binding poly(ethylene glycol) diacrylate (PEGDA) hydrogels. Contractile microtissues have previously been engineered by immobilizing suspended cells in a confined hydrogel matrix with embedded anchoring cantilevers to facilitate muscle tissue strip formation. The 3D shape and mechanical properties of the confinement and the embedded cantilevers are critical for the tissue robustness. High-resolution 3D printing of PEGDA hydrogels offers full design freedom to engineer cantilever stiffness, while minimizing unwanted cell attachment. We demonstrate the applicability by generating suspended muscle tissue strips from C2C12 mouse myoblasts in a compliant fibrin-based hydrogel matrix. The full design freedom allows for new platform geometries that reduce local stress in the matrix and tissue, thus, reducing the risk of tissue fracture.

Self-reported illness behaviour related to chronic obstructive pulmonary disease and rehabilitation: a theory-guided qualitative study.

Illness behaviour effects the quality of life of patients with chronic obstructive pulmonary disease (COPD) but is scarcely described in literature. The aim of this study was to explore self-reported illness behaviour of patients with COPD, who have declined nonpharmacological rehabilitation. The study has a qualitative design using semi-structured interviews. The subsequent analysis is a theory-guided mapping of actions reported by the patients in order to manage symptoms. These actions are understood and categorised according to the styles of coping described by Alonzo. Four categories of illness behaviour are identified: containment of symptoms, coping with symptoms through formal and informal interventions, adjustment of situations through compensating and economising interventions and crisis coping by surrendering. The analysis shows that behaviour that may seem unhelpful from a healthcare perspective may seem rational in the everyday life perspective of the patient. Findings show that reluctance to participation in rehabilitation should not only be interpreted as lack of motivation or health literacy. In the patients' perspective, nonpharmacological interventions might be perceived as a threat that could tip the delicate balance of everyday life with severe COPD.

Unprecedented Arctic ozone loss in 2011.

Chemical ozone destruction occurs over both polar regions in local winter-spring. In the Antarctic, essentially complete removal of lower-stratospheric ozone currently results in an ozone hole every year, whereas in the Arctic, ozone loss is highly variable and has until now been much more limited. Here we demonstrate that chemical ozone destruction over the Arctic in early 2011 was--for the first time in the observational record--comparable to that in the Antarctic ozone hole. Unusually long-lasting cold conditions in the Arctic lower stratosphere led to persistent enhancement in ozone-destroying forms of chlorine and to unprecedented ozone loss, which exceeded 80 per cent over 18-20 kilometres altitude. Our results show that Arctic ozone holes are possible even with temperatures much milder than those in the Antarctic. We cannot at present predict when such severe Arctic ozone depletion may be matched or exceeded.

Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools.

Nucleic acid aptamer selection by systematic evolution of ligands by exponential enrichment (SELEX) has shown great promise for use in the development of research tools, therapeutics and diagnostics. Typically, aptamers are identified from libraries containing up to 10(16) different RNA or DNA sequences by 5-10 rounds of affinity selection towards a target of interest. Such library screenings can result in complex pools of many target-binding aptamers. New high-throughput sequencing techniques may potentially revolutionise aptamer selection by allowing quantitative assessment of the dynamic changes in the pool composition during the SELEX process and by facilitating large-scale post-SELEX characterisation. In the present study, we demonstrate how high-throughput sequencing of SELEX pools, before and after a single round of branched selection for binding to different target variants, can provide detailed information about aptamer binding sites, preferences for specific target conformations, and functional effects of the aptamers. The procedure was applied on a diverse pool of 2'-fluoropyrimidine-modified RNA enriched for aptamers specific for the serpin plasminogen activator inhibitor-1 (PAI-1) through five rounds of standard selection. The results demonstrate that it is possible to perform large-scale detailed characterisation of aptamer sequences directly in the complex pools obtained from library selection methods, thus without the need to produce individual aptamers.

Why do patients decline participation in offered pulmonary rehabilitation? A qualitative study.

OBJECTIVE: The purpose of this study is to produce insight in the explanations for declining pulmonary rehabilitation given by patients with chronic obstructive pulmonary disease. SETTING: The participants were recruited from a hospital in Denmark, among patients hospitalized due to an exacerbation of chronic obstructive pulmonary disease and among stable patients attending an outpatient clinic. PARTICIPANTS: Patients who decline participation in offered pulmonary rehabilitation, who speak Danish, who are able to give informed consent and to participate in a 1-hour interview. METHOD: The research question was answered through interviews with 19 patients. DATA ANALYSIS: The interviews were recorded and transcribed verbatim. The transcripts were analyzed using inductive content analysis. The transcripts were condensed; categories were developed providing different types of explanations for declining pulmonary rehabilitation. Each category was named using a content characteristic word. RESULTS: This study shows that some patients do not remember or recall that they have been offered pulmonary rehabilitation during hospitalization. Especially the oldest patients perceive themselves to be too frail from chronic obstructive pulmonary disease, comorbidity or multimorbidity. The male patients tend to find pulmonary rehabilitation irrelevant because they do not consider themselves ill. Furthermore, the study shows that pulmonary rehabilitation is perceived to be time-consuming and conflicting with daily activities. CONCLUSIONS: Patients decline pulmonary rehabilitation because the intervention does not fit their perception of health and because they find that participation in the program may collide with priorities and daily activities.

Autocrine CCL19 blocks dendritic cell migration toward weak gradients of CCL21.

BACKGROUND AIMS: Maturation of dendritic cells (DCs) induces their homing from peripheral to lymphatic tissues guided by CCL21. However, in vitro matured human monocyte-derived DC cancer vaccines injected intradermally migrate poorly to lymph nodes (LNs). In vitro maturation protocols generate DCs with high (type 1 DCs) or low (prostaglandin E2 [PGE2]-DCs) autocrine CCL19 levels, which may potentially interfere with LN homing of DCs. METHODS: Employing a three-dimensional (3D) chemotaxis assay, chemokine competition/desensitization studies and short interfering RNA (siRNA) against CCL19, we analyzed the effect of autocrine CCL19 on in vitro migration of human DCs toward CCL21. RESULTS: Using human monocyte-derived DCs in a 3D chemotaxis assay, we are the first to demonstrate that CCL19 more potently induces directed migration of human DCs compared with CCL21. When comparing migration of type 1 DCs and PGE2-DCs, migration of type 1 DCs was strikingly impaired compared with PGE2-DCs, but only toward low concentrations of CCL21. When type 1 DCs were cultured overnight in fresh culture medium (reducing autocrine CCL19 levels), a rescuing effect was observed on migration toward low concentrations of CCL21 in a 3D chemotaxis assay. Finally pre-incubation with CCL19 negatively affected PGE2-DC migration, whereas silencing of CCL19 by siRNA improved type 1 DC migration. Importantly, in both cases, the effect was observed only at low concentrations of CCL21. CONCLUSIONS: Our results demonstrate that autocrine CCL19 negatively affects DC migratory potential toward CCL21, the potency difference between CCL19 and CCL21 being the underlying cause. CCL19 secretion level of in vitro matured DCs is an important indicator of DC vaccine homing potential.

Cyclic Enecarbamates as Precursors of α,ß-Unsaturated Iminium Ions: Reactivity and Synthesis of 6,6-Spirocyclic Ring Systems.

The scalable synthesis of cyclic enecarbamates and their use as convenient precursors of α,ß-unsaturated N-acyl iminium ions is reported. The newly developed route overcomes synthetic and reactivity difficulties in previously reported methods, is readily scaled up, and proceeds through stable intermediates suitable for long-term storage if required. Preliminary investigations probing the reactivity of cyclic α,ß-unsaturated N-acyl iminium ions as dienophiles in Diels-Alder reactions and electrophilic alkylating agents are described. In the presence of Lewis and Brønsted acids, iminium precursor 22a underwent efficient Diels-Alder cycloaddition with a range of simple and complex dienes, culminating in the synthesis of 6,6-spirocyclic ring systems possessing the same relative stereochemistry as the spirocyclic imine present in the marine natural product gymnodimine 1.

Why Do Patients with COPD Decline Rehabilitation.

AIM: This paper aimed to suggest possible answers to the question: Why do patients with COPD decline pulmonary rehabilitation (PR)? METHOD: The study is a metasynthesis inspired by Noblit of the existing qualitative research on the area. The data were collected during 2014. Six studies were found through a systematic literature search in relevant databases. In these six studies, 65 persons were identified as decliners of PR. Four themes were identified from these studies. RESULTS: The themes identified were as follows: the referral process, transport problems, perception of health and other obligations or priorities. The problems with the referral of patients relate to different areas: the referring health professional's conviction and commitment, and the patients' understanding of the referral. It seems that various transport problems cause decline, for example long distance to the PR centre or the expenses of getting back and forth. Perceptions of health cause decline. Decliners feel too sick to join PR or do not identify themselves as a sick person, and do not want undertake the 'patient role'. Other obligations or priorities such as work, family obligations and vacations are prioritised on behalf of PR causing decline. CONCLUSION: The studies included show patients' rational accounts and reflections on declining PR. The included studies tend to describe accounts for deselection of PR in relation to the preferences and beliefs of the patients rather than including the social and economic variables framing the behaviour and choices of the patients.

Confinement dependent chemotaxis in two-photon polymerized linear migration constructs with highly definable concentration gradients.

Dendritic cell chemotaxis is known to follow chemoattractant concentration gradients through tissue of heterogeneous pore sizes, but the dependence of migration velocity on pore size and gradient steepness is not fully understood. We enabled chemotaxis studies for at least 42 hours at confinements relevant to tissue models by two-photon polymerization of linear channel constructs with cross-sections from 10 × 10 µm(2) to 20 × 20 µm(2) inside commercially available chemotaxis analysis chips. Faster directed migration was observed with decreasing channel dimensions despite substantial cell deformation in the narrower channels. Finite element modeling of a cell either partly or fully obstructing chemokine diffusion in the narrow channels revealed strong local accentuation of the chemokine concentration gradients. The modeled concentration differences across a cell correlated well with the observed velocity dependence on channel cross-section. However, added effects due to spatial confinement could not be excluded. The design freedom offered by two-photon polymerization was exploited to minimize the accentuated concentration gradients in cell-blocked channels by introducing "venting slits" to the surrounding medium at a length scale too small (≤500 nm) for the cells to explore, thereby decoupling effects of concentration gradients and spatial confinement. Studies in slitted 10 × 10 µm(2) channels showed significantly reduced migration speeds indistinguishable from speeds observed in unslitted 20 × 20 µm(2) channel. This result agrees with model predictions of very small concentration gradient variations in slitted channels, thus indicating a strong influence of the concentration gradient steepness, not the channel size, on the directed migration velocity.

Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea.

BACKGROUND: In recent years, new neonatal porcine diarrhoea (NNPD) of unknown aetiology has emerged in Denmark. NNPD affects piglets during the first week of life and results in impaired welfare, decreased weight gain, and in the worst-case scenario death. Commonly used preventative interventions such as vaccination or treatment with antibiotics, have a limited effect on NNPD. Previous studies have investigated the clinical manifestations, histopathology, and to some extent, microbiological findings; however, these studies were either inconclusive or suggested that Enterococci, possibly in interaction with Escherichia coli, contribute to the aetiology of NNPD. This study examined ileal and colonic luminal contents of 50 control piglets and 52 NNPD piglets by means of the qPCR-based Gut Microbiotassay and 16 samples by 454 sequencing to study the composition of the bacterial gut microbiota in relation to NNPD. RESULTS: NNPD was associated with a diminished quantity of bacteria from the phyla Actinobacteria and Firmicutes while genus Enterococcus was more than 24 times more abundant in diarrhoeic piglets. The number of bacteria from the phylum Fusobacteria was also doubled in piglets suffering from diarrhoea. With increasing age, the gut microbiota of NNPD affected piglet and control piglets became more diverse. Independent of diarrhoeic status, piglets from first parity sows (gilts) possessed significantly more bacteria from family Enterobacteriaceae and species E. coli, and fewer bacteria from phylum Firmicutes. Piglets born to gilts had 25 times higher odds of having NNPD compared with piglets born to multiparous sows. Finally, the co-occurrence of genus Enterococcus and species E. coli contributed to the risk of having NNPD. CONCLUSION: The results of this study support previous findings that points towards genus Enterococcus and species E. coli to be involved in the pathogenesis of NNPD. Moreover, the results indicate that NNPD is associated with a disturbed bacterial composition and larger variation between the diarrhoeic piglets.

Facile photoimmobilization of proteins onto low-binding PEG-coated polymer surfaces.

Immobilization of proteins onto polymer surfaces usually requires specific reactive functional groups. Here, we show an easy one-step method to conjugate protein covalently onto almost any polymer surface, including low protein-binding poly(ethylene glycol) (PEG), without the requirement for the presence of specific functional groups. Several types of proteins, including alkaline phosphatase, bovine serum albumin, and polyclonal antibodies, were photoimmobilized onto a PEG-coated polymer surface using a water-soluble benzophenone as photosensitizer. Protein functionality after immobilization was verified for both enzymes and antibodies, and their presence on the surface was confirmed by X-ray photoelectron spectroscopy (XPS) and confocal fluorescence microscopy. Conjugation of capture antibody onto the PEG coating was employed for a simplified ELISA protocol without the need for blocking uncoated surface areas, showing ng/mL sensitivity to a cytokine antigen target. Moreover, spatially patterned attachment of fluorescently labeled protein onto the low-binding PEG-coated surface was achieved with a projection lithography system that enabled the creation of micrometer-sized protein features.

Underestimation of Flow Velocity in 2-D Super-Resolution Ultrasound Imaging.

Velocity estimation in ultrasound imaging is a technique to measure the speed and direction of blood flow. The flow velocity in small blood vessels, i.e., arterioles, venules, and capillaries, can be estimated using super-resolution ultrasound imaging (SRUS). However, the vessel width in SRUS is relatively small compared with the full-width-half-maximum of the ultrasound beam in the elevation direction (FWHMy), which directly impacts the velocity estimation. By taking into consideration the small vessel widths in SRUS, it is hypothesized that the velocity is underestimated in 2-D super-resolution ultrasound imaging when the vessel diameter is smaller than the FWHMy. A theoretical model is introduced to show that the velocity of a 3-D parabolic velocity profile is underestimated by up to 33% in 2-D SRUS, if the width of the vessel is smaller than the FWHMy. This model was tested using Field II simulations and 3-D printed micro-flow hydrogel phantom measurements. A Verasonics Vantage 256™ scanner and a GE L8-18i-D linear array transducer with FWHMy of approximately 770 µm at the elevation focus were used in the simulations and measurements. Simulations of different parabolic velocity profiles showed that the velocity underestimation was 36.8%±1.5% (mean±standard deviation). The measurements showed that the velocity was underestimated by 30%±6.9%. Moreover, the results of vessel diameters, ranging from 0.125×FWHMy to 3×FWHMy, indicate that velocities are estimated according to the theoretical model. The theoretical model can, therefore, be used for the compensation of velocity estimates under these circumstances.

Interactions of oral permeation enhancers with lipid membranes in simulated intestinal environments.

The oral bioavailability of therapeutic peptides is generally low. To increase peptide transport across the gastrointestinal barrier, permeation enhancers are often used. Despite their widespread use, mechanistic knowledge of permeation enhancers is limited. To address this, we here investigate the interactions of six commonly used permeation enhancers with lipid membranes in simulated intestinal environments. Specifically, we study the interactions of the permeation enhancers sodium caprate, dodecyl maltoside, sodium cholate, sodium dodecyl sulfate, melittin, and penetratin with epithelial cell-like model membranes. To mimic the molecular composition of the real intestinal environment, the experiments are performed with two peptide drugs, salmon calcitonin and desB30 insulin, in fasted-state simulated intestinal fluid. Besides providing a comparison of the membrane interactions of the studied permeation enhancers, our results demonstrate that peptide drugs as well as intestinal-fluid components may substantially change the membrane activity of permeation enhancers. This highlights the importance of testing permeation enhancement in realistic physiological environments and carefully choosing a permeation enhancer for each individual peptide drug.

Super Resolution Ultrasound Imaging Using the Erythrocytes: II: Velocity Images.

Super resolution ultrasound imaging using the erythrocytes (SURE) has recently been introduced. The method uses erythrocytes as targets instead of fragile microbubbles (MBs). The abundance of erythrocyte scatterers makes it possible to acquire SURE data in just a few seconds compared to several minutes in ultrasound localization microscopy (ULM) using MBs. A high number of scatterers can reduce the acquisition time, however, the tracking of uncorrelated and high-density scatterers is quite challenging. This paper hypothesizes that it is possible to detect and track erythrocytes as targets to obtain vascular flow images. A SURE tracking pipeline is used with modules for beamforming, recursive synthetic aperture imaging, motion estimation, echo canceling, peak detection, and recursive nearest neighbor tracker. The SURE tracking pipeline is capable of distinguishing the flow direction and separating tubes of a simulated Field II phantom with 125 to 25 µm wall-to-wall tube distances, as well as a 3D-printed hydrogel micro-flow phantom with 100 to 60 µm wall-to-wall channel distances. The comparison of an in-vivo SURE scan of a Sprague-Dawley rat kidney with ULM and micro-CT scans with voxel sizes of 26.5µm and 5µm demonstrated consistent findings. A microvascular structure composed of 16 vessels exhibited similarities across all imaging modalities. The flow direction and velocity profiles in the SURE scan were found to be concordant with those from ULM.

Super Resolution Ultrasound Imaging using the Erythrocytes: I: Density Images.

A new approach for vascular super resolution imaging using the erythrocytes as targets (SURE imaging) is described and investigated. SURE imaging does not require fragile contrast agent bubbles, making it possible to use the maximum allowable mechanical index for ultrasound scanning for an increased penetration depth. A synthetic aperture ultrasound sequence was employed with 12 virtual sources using a 10 MHz GE L8-18i-D linear array hockey stick probe. The axial resolution was 1.20λ,(185.0µm) and the lateral resolution was 1.50λ,(231.3µm). Field IIpro simulations were conducted on 12.5 µm radius vessel pairs with varying separations. A vessel pair with a separation of 70 µm could be resolved, indicating a SURE image resolution below half a wavelength. A Verasonics research scanner was used for the in vivo experiments to scan the kidneys of Sprague-Dawley rats for up to 46 s to visualize their microvasculature by processing from 0.1 up to 45 s of data for SURE imaging, and for 46.8 s for super resolution (SR) imaging with a SonoVue contrast agent. Afterward, the renal vasculature was filled with the ex vivo micro-CT contrast agent Microfil, excised, and scanned in a micro-CT scanner at both a 22.6 µm voxel size for 11 hours, and for 20 hours in a 5 µm voxel size for validating the SURE images. Comparing the SURE and micro-CT images revealed that vessels with a diameter of 28 µm, five times smaller than the ultrasound wavelength, could be detected, and the dense grid of microvessels in the full kidney was shown for scan times between 1 to 10 s. The vessel structure in the cortex was also similar for the SURE and SR images. Fourier ring correlation indicated a resolution capability of 29 µm. SURE images are acquired in seconds rather than minutes without any patient preparation or contrast injection, making the method translatable to clinical use.

Urokinase-type plasminogen activator-like proteases in teleosts lack genuine receptor-binding epidermal growth factor-like domains.

Plasminogen activation catalyzed by urokinase-type plasminogen activator (uPA) plays an important role in normal and pathological tissue remodeling processes. Since its discovery in the mid-1980s, the cell membrane-anchored urokinase-type plasminogen activator receptor (uPAR) has been believed to be central to the functions of uPA, as uPA-catalyzed plasminogen activation activity appeared to be confined to cell surfaces through the binding of uPA to uPAR. However, a functional uPAR has so far only been identified in mammals. We have now cloned, recombinantly produced, and characterized two zebrafish proteases, zfuPA-a and zfuPA-b, which by several criteria are the fish orthologs of mammalian uPA. Thus, both proteases catalyze the activation of fish plasminogen efficiently and both proteases are inhibited rapidly by plasminogen activator inhibitor-1 (PAI-1). But zfuPA-a differs from mammalian uPA by lacking the exon encoding the uPAR-binding epidermal growth factor-like domain; zfuPA-b differs from mammalian uPA by lacking two cysteines of the epidermal growth factor-like domain and a uPAR-binding sequence comparable with that found in mammalian uPA. Accordingly, no zfuPA-b binding activity could be found in fish white blood cells or fish cell lines. We therefore propose that the current consensus of uPA-catalyzed plasminogen activation taking place on cell surfaces, derived from observations with mammals, is too narrow. Fish uPAs appear incapable of receptor binding in the manner known from mammals and uPA-catalyzed plasminogen activation in fish may occur mainly in solution. Studies with nonmammalian vertebrate species are needed to obtain a comprehensive understanding of the mechanism of plasminogen activation.

The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity.

BACKGROUND: The intestinal microbiota is a complex and diverse ecosystem that plays a significant role in maintaining the health and well-being of the mammalian host. During the last decade focus has increased on the importance of intestinal bacteria. Several molecular methods can be applied to describe the composition of the microbiota. This study used a new approach, the Gut Microbiotassay: an assembly of 24 primer sets targeting the main phyla and taxonomically related subgroups of the intestinal microbiota, to be used with the high-throughput qPCR chip 'Access Array 48.48', AA48.48, (Fluidigm®) followed by next generation sequencing. Primers were designed if necessary and all primer sets were screened against DNA extracted from pure cultures of 15 representative bacterial species. Subsequently the setup was tested on DNA extracted from small and large intestinal content from piglets with and without diarrhoea. The PCR amplicons from the 2304 reaction chambers were harvested from the AA48.48, purified, and sequenced using 454-technology. RESULTS: The Gut Microbiotassay was able to detect significant differences in the quantity and composition of the microbiota according to gut sections and diarrhoeic status. 454-sequencing confirmed the specificity of the primer sets. Diarrhoea was associated with a reduced number of members from the genus Streptococcus, and in particular S. alactolyticus. CONCLUSION: The Gut Microbiotassay provides fast and affordable high-throughput quantification of the bacterial composition in many samples and enables further descriptive taxonomic information if combined with 454-sequencing.