Fluorescence lifetime imaging in an optically sectioning programmable array microscope (PAM).

BACKGROUND: The programmable array microscopes (PAMs) are a family of instruments incorporating arbitrary control of the patterns of illumination and/or detection. The PAM can be used in sectioning and nonsectioning modes, thereby constituting a useful platform for fluorescence lifetime imaging. METHODS AND RESULTS: We used a PAM for acquisition of optically sectioned and widefield fluorescence lifetime images, in which contrast was increased predominantly by suppressing out-of-focus light contributions. We simulate, display, and discuss the effects of blurring and fluorophore heterogeneity on lifetime imaging in widefield and confocal configurations. CONCLUSION: Sectioning improves the quality of lifetime images of samples with multiple fluorophores or spatially varying F?rster resonance energy transfer.     

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

Background  

To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive.     

Chemical lead optimization of a pan Gq mAChR M1, M3, M5 positive allosteric modulator (PAM) lead. Part II: Development of a potent and highly selective M1 PAM

This Letter describes a chemical lead optimization campaign directed at VU0119498, a pan G_q mAChR M₁, M₃, M₅ positive allosteric modulator (PAM) with the goal of developing a selective M₁ PAM. An iterative library synthesis approach delivered a potent (M₁ EC₅₀ = 830 nM) and highly selective M₁ PAM (>30 μM vs M₂–M₅).     

Kinetic chain lengths in highly cross-linked networks formed by the photoinitiated polymerization of divinyl monomers: a gel permeation chromatography investigation

Highly cross-linked networks formed by the photoinitiated polymerization of multifunctional monomers are finding application in the field of biomaterials because of their chemical versatility, reaction control, and ability to polymerize under physiological conditions. Typically, degradation is introduced into these networks via the cross-links and leads to the release of nondegradable but water-soluble kinetic chains formed during the chain polymerization process. In this study, gel permeation chromatography (GPC) was used to characterize kinetic chain length distributions in highly cross-linked systems that are being developed for orthopedic applications. By polymerizing divinyl monomers to various conversions and subsequently degrading them, we investigated the aspects of network structural evolution related to kinetic chain formation. In general, the average kinetic chain length increased with conversion until the onset of autodeceleration, when the kinetic chains decreased in length as the propagation reaction became diffusion-controlled. The distribution of kinetic chains also changed when different initiation conditions (i.e., initiator concentration and incident light intensity) were used, and a decrease in the kinetic chain lengths was observed at higher initiation rates. Finally, kinetic chain lengths were examined as a function of depth in thick samples polymerized with different light intensities and with a photobleaching initiator. Light attenuation through the sample led to different initiation rates as a function of depth and, consequently, spatial heterogeneity in the network structure as measured by the distributions of kinetic chains.     

Developmental expression of peptidylglycine alpha-amidating monooxygenase (PAM) in primary cultures of neonatal rat cardiocytes: a model for studying regulation of PAM expression in the rat heart.

Primary cultures of neonatal rat atrial and ventricular cardiomyocytes were used to investigate the expression of peptidylglycine alpha-amidating monooxygenase (PAM), a bifunctional enzyme required for the production of alpha-amidated neuroendocrine peptides. The use of assays for the individual enzymes, peptidylglycine alpha-amidating monooxygenase (PHM) and peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL), demonstrated that the levels of expression observed in vitro approximated those observed in vivo. Both in vivo and in vitro, atrial and ventricular PAL activity greatly exceeded PHM activity. Atrial and ventricular cardiomyocytes secreted PHM and PAL activity at a constant rate throughout the culture period. Immunofluorescence studies localized PAM proteins to the perinuclear region, with intense punctate staining. Both in vivo and in vitro, PAM mRNAs encoding integral membrane proteins predominated throughout the neonatal period, with PAM-1 mRNA becoming more prevalent after the first week in culture. Although PAM-2 mRNA decreased in prevalence in vivo at the time when PAM-1 expression increased, levels of PAM-2 mRNA remained elevated throughout 2 weeks in vitro. Western blot analysis demonstrated intact PAM-1 and PAM-2 proteins in atrial cultures, with the prevalence of PAM-1 increasing in older cultures. Atrial cardiomyocytes secreted only bifunctional PAM proteins. Many of the features of PAM expression, processing, and storage that are unique to cardiomyocytes as opposed to endocrine cells are faithfully replicated by primary atrial and ventricular cultures.     

Chemical lead optimization of a pan Gq mAChR M1, M3, M5 positive allosteric modulator (PAM) lead. Part I: Development of the first highly selective M5 PAM

This Letter describes a chemical lead optimization campaign directed at VU0238429, the first M₅-preferring positive allosteric modulator (PAM), discovered through analog work around VU0119498, a pan G_q mAChR M₁, M₃, M₅ PAM. An iterative library synthesis approach delivered the first selective M₅ PAM (no activity at M₁–M₄ @ 30 μM), and an important tool compound to study the role of M₅ in the CNS.     

Peptide array X-linking (PAX): a new peptide-protein identification approach

Many protein interaction domains bind short peptides based on canonical sequence consensus motifs. Here we report the development of a peptide array-based proteomics tool to identify proteins directly interacting with ligand peptides from cell lysates. Array-formatted bait peptides containing an amino acid-derived cross-linker are photo-induced to crosslink with interacting proteins from lysates of interest. Indirect associations are removed by high stringency washes under denaturing conditions. Covalently trapped proteins are subsequently identified by LC-MS/MS and screened by cluster analysis and domain scanning. We apply this methodology to peptides with different proline-containing consensus sequences and show successful identifications from brain lysates of known and novel proteins containing polyproline motif-binding domains such as EH, EVH1, SH3, WW domains. These results suggest the capacity of arrayed peptide ligands to capture and subsequently identify proteins by mass spectrometry is relatively broad and robust. Additionally, the approach is rapid and applicable to cell or tissue fractions from any source, making the approach a flexible tool for initial protein-protein interaction discovery.     

Thiorphan, tiopronin, and related analogs as substrates and inhibitors of peptidylglycine alpha-amidating monooxygenase (PAM)

Peptidyglycine alpha-amidating monooxygenase is a copper- and zinc-dependent, bifunctional enzyme that catalyzes the cleavage of glycine-extended peptides or N-acylglycines to the corresponding amides and glyoxylate. This reaction is a key step in the biosynthesis of bioactive alpha-amidated peptides and, perhaps, the primary fatty acids amides also. Two clinically useful N-acylglycines are thiorphan and tiopronin, each with a thiol moiety attached to the acyl group. We report here that thiorphan and tiopronin are substrates for PAM, exhibiting relatively low K(M,app) and V(MAX,app) values. The low V(MAX,app) values result, most likely, from a decrease in active PAM.2Cu(II) as the enzyme competes ineffectively with thiorphan and tiopronin for free copper.     

Copper (II) induced polymerization of human albumin, and its depolymerization by diglycyl-L-histidine: a pH static and ultracentrifugation study.

Copper (II) ions successively induce dimers and tetramers of human serum albumin (L) when the Cu (II) concentration is extended beyond that of 200 muM. This is shown by emf titrations and by ultracentrifugation experiments. The emf titrations, which involve a new pH static method, were performed at 25 degrees, in a 0.5 M NaCIO4 medium at pH 6.59, using glass and copper amalgam electrodes. The total concentration of Cu(II) varied from 0.14 to 2.2 mM and the albumin concentration from 0.05 to 0.7 mM. In order to evaluate the formula of the main complexes, without using any a priori assumptions regarding their compositions, a detailed graphic procedure was used. The results, in the form of equilibrium constants for the main species, were refined by the use of a general least squares computer program. The experimental data are found to be consistent with the formation of the monomeric CuL, Cu5L, and Cu6L species and the dimeric Cu3L2, Cu4L, Cu6L, and Cu8L2 species. In addition, there is some indication for a minor species, most probably the Cu12L4 tetramer. The pH static results qualitatively agree with the findings obtained by ultracentrifugation. As indicated by distinct bands and their S-values, ultracentrifugation experiments show not only monomeric and dimeric species of albumin, but also tetrameric species. The polymerization of the albumin is reversible, since diglycyl-L-histidine, a peptide designed to mimic the Cu (II) transport site of albumin, depolymerizes the Cu (II)-albumin polymers.     

A(1) adenosine receptors in human neutrophils: direct binding and electron microscope visualization.

By occupying specific surface receptors, adenosine and adenosine analogues modulate neutrophil functions; in particular, functional and biochemical studies have shown that A(1) adenosine receptors modulate chemotaxis in response to chemotactic peptides. Until now, the characteristics of the specific agonist binding and the visualization of A(1) receptors in human neutrophils have not been investigated. In the present study, we used the agonist [(3)H] CHA for radioligand binding studies and a CHA-biotin XX probe in order to visualize the A(1) binding sites in human neutrophils, ultrastructurally, by conjugation with colloidal gold-streptavidin. [(3)H] CHA bound A(1) adenosine receptors with selectivity and specificity, although with a low binding capacity. Scatchard analysis showed a Kd value of 1.4 +/- 0.08 nM and a maximum density of binding sites of 7.1 +/- 0.37 fmol/mg of proteins. The good affinity and selectivity of the CHA-biotin XX probe for A(1) adenosine receptors allowed us to visualize them, after conjugation with colloidal gold-streptavidin, as electron-dense gold particles on the neutrophil surface and inside the cell. The internalization of the ligand-receptor complex was followed in a controlled temperature system, and occurred through a receptor-mediated pathway. The kinetics of the intracellular trafficking was fast, taking less than 5 min. These data suggest that the CHA-biotin XX-streptavidin-gold complex is a useful marker for the specific labelling of A(1) binding sites and to follow the intracellular trafficking of these receptors.     

The programmable implantable medication system (PIMS): design features and pre-clinical trials

This report describes the clinically significant design features of a variable rate implantable insulin infusion pump, the Programmable Implantable Medication System (PIMS), and its function in pre-clinical trials. PIMS has a number of unique features, including a solenoid, pulsatile pump design requiring minimal power (less than 15 microwatts) and a less-than-atmospheric pressure reservoir. Two-way communication is accomplished by radiotelemetry. The implanted device stores programs, and records its own hourly history of insulin delivery. Limits are set on total insulin delivery over time. Basal rates are adjustable, and patterned prandial insulin delivery curves can be programmed. Initial trials (3.1 dog-years) identified four problems which were corrected prior to final pre-clinical trials: microcracks in the diaphragm, a valve-seating leak, electronic failure of prototype microchips, and insulin aggregation. Sixteen dog-years of final pre-clinical trials with a single system design demonstrated that 5 pumps were still working continuously after up to 3.75 years (mean 3.3 years) without mechanical or electronic pump failure. The longest interval between reservoir refills was 5 months. Remaining potential causes of flow stoppage, however, include blockage of the peritoneal catheter by omentum (which occurred once), and air lock (which occurred two times).     

Solids,organic load and nutrient concentration reductions in swine waste slurry using a polyacrylamide (PAM)-aided solids flocculation treatment

Increased swine production results in concentration of wastes generated within a limited geographical area, which may lead to land application rates exceeding the local or regional assimilatory capacity. This may result in pollutant transfer through surface water or soil-groundwater systems, environmental degradation, and/or odor concerns. Existing swine waste pit storage and lagoon treatment technologies may be inadequate to store or treat waste prior to land application without these concerns resulting. Efficient swine waste solids separation may reduce environmental health concerns and generate a value-added bioresource (solids). This study evaluated the efficiency of a polyacrylamide (PAM) flocculant-aided solids separation treatment to reduce pollution indicator concentrations in raw (untreated) swine waste slurry. Swine waste slurry solids separation efficiency through gravity settling (sedimentation) was evaluated before and after the addition of a proprietary polymeric (PAM) flocculant. Results indicated that polymer amendments at concentrations of 62.5-750 mg/l improved slurry solids separation efficiency and significantly reduced concentrations of other associated aquatic pollution indicators in a majority of analyses conducted (33 of 50 total analyses conducted). Results also suggested that PAM-aided solids separation from swine waste slurry might facilitate further treatment and/or disposal and therefore reduce associated environmental degradation potential.     

Acrylate end-capped poly(ester-carbonate) and poly(ether-ester)s for polymer-on-multielectrode array devices: synthesis, photocuring, and biocompatibility

Polymeric materials based on epsilon-caprolactone (CL), 1,5-dioxepan-2-one (DXO), and trimethylene carbonate (TMC) were prepared and evaluated as possible candidates for polymer-on-multielectrode (PoM) applications. CL was copolymerized with either DXO or TMC in the presence of the diol initiator 1,4-benzenedimethanol (BDM). The ring-opening polymerization experiments, carried out in bulk and using tin(II) catalysis, yielded the desired low molecular weight random copolymer diols, as evidenced by NMR, IR, MALDI-ToF MS, and DSC techniques. Upon reaction with acryloyl chloride, the corresponding diacrylate end-capped copolymers were obtained. The latter were characterized by NMR and IR spectroscopy, and their photocross-linking (in the presence of a UV initiator) was followed by ATR-FTIR spectroscopy. Transparent and soft thin films of the copoly(ether-ester) and copoly(ester-carbonate) diacrylates were prepared and cured under UV irradiation. The resulting polymeric films showed good biocompatibility properties as far as in vitro neural stem cells proliferation and differentiation to neurons and astrocytes are concerned. Noteworthy are the beneficial effects obtained upon preconditioning the copolymers by means of the cell-culture medium and the excellent properties shown particularly by the CL-TMC copolymer. Moreover, preliminary results show that microchannel formation by photocuring is possible with the synthesized polymers.     

Metabolomics spectral formatting, alignment and conversion tools (MSFACTs)

MOTIVATION: The amplified interest in metabolic profiling has generated the need for additional tools to assist in the rapid analysis of complex data sets. RESULTS: A new program; metabolomics spectral formatting, alignment and conversion tools, (MSFACTs) is described here for the automated import, reformatting, alignment, and export of large chromatographic data sets to allow more rapid visualization and interrogation of metabolomic data. MSFACTs incorporates two tools: one for the alignment of integrated chromatographic peak lists and another for extracting information from raw chromatographic ASCII formatted data files. MSFACTs is illustrated in the processing of GC/MS metabolomic data from different tissues of the model legume plant, Medicago truncatula. The results document that various tissues such as roots, stems, and leaves from the same plant can be easily differentiated based on metabolite profiles. Further, similar types of tissues within the same plant, such as the first to eleventh internodes of stems, could also be differentiated based on metabolite profiles. AVAILABILITY: Freely available upon request for academic and non-commercial use. Commercial use is available through licensing agreement http://www.noble.org/PlantBio/MS/MSFACTs/MSFACTs.html.     

Light and electron microscope studies on Helicosporidium sp. parasitizing oribatid mites (Oribatei,Acarina) and collembola (Apterygota,Insecta) in forest soils

The life cycle of Helicosporidium sp. parasitizing natural populations of oribatid mites and collembolans in forest soils, is described by means of light, Nomarski interference, and electron microscopy. The ultrastructure of some early sporogonic stages (cysts), the young (maturing) spore, and the mature spore is discussed. Some data on the host-parasite relationships and prevalence of infection are presented.     

Polyadenylation-specific complexes undergo a transition early in the polymerization of a poly(A) tail.

We have analyzed several properties of the complex that forms between RNAs that end at the poly(A) site of simian virus 40 late mRNA and factors present in a HeLa cell nuclear extract. Formation of this polyadenylation-specific complex requires the sequence AAUAAA and a proximal 3' end. We have observed three changes in the polyadenylation complex early in the addition of the poly(A) tail. First, the complex becomes heparin sensitive after the addition of approximately 10 adenosines. Second, a 68-kilodalton protein present in the complex, which can be cross-linked by UV light to the RNA before polyadenylation has begun, no longer can be cross-linked after approximately 10 adenosines have been added. Third, after 30 adenosines have been added, the AAUAAA sequence becomes accessible to a complementary oligonucleotide and RNase H. This accessibility gradually increases with longer poly(A) tail lengths until, with the addition of 60 A's, all substrates are accessible at AAUAAA. Sheets and Wickens (Genes Dev. 3:1401-1412, 1989) have recently demonstrated two phases in the addition of a poly(A) tail: the first requires AAUAAA, whereas the second is independent of AAUAAA but requires a short oligo(A) primer. The data reported here further support a biphasic model for poly(A) addition and may indicate disengagement of specific factors from AAUAAA after the initiation phase.     

Development of a novel, CNS-penetrant, metabotropic glutamate receptor 3 (mGlu3) NAM probe (ML289) derived from a closely related mGlu5 PAM

Herein we report the discovery and SAR of a novel metabotropic glutamate receptor 3 (mGlu(3)) NAM probe (ML289) with 15-fold selectivity versus mGlu(2). The mGlu(3) NAM was discovered via a 'molecular switch' from a closely related, potent mGlu(5) positive allosteric modulator (PAM), VU0092273. This NAM (VU0463597, ML289) displays an IC(50) value of 0.66 μM and is inactive against mGlu(5).     

BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)

The array CGH technique (Array Comparative Genome Hybridization) has been developed to detect chromosomal copy number changes on a genome-wide and/or high-resolution scale. It is used in human genetics and oncology, with great promise for clinical application. Until recently primarily PCR amplified bacterial artificial chromosomes (BACs) or cDNAs have been spotted as elements on the array. The large-scale DNA isolations or PCR amplifications of the large-insert clones necessary for manufacturing the arrays are elaborate and time-consuming. Lack of a high-resolution highly sensitive (commercial) alternative has undoubtedly hindered the implementation of array CGH in research and diagnostics. Recently, synthetic oligonucleotides as arrayed elements have been introduced as an alternative substrate for array CGH, both by academic institutions as well as by commercial providers. Oligonucleotide libraries or ready-made arrays can be bought off-the-shelf saving considerable time and efforts. For RNA expression profiling, we have seen a gradual transition from in-house printed cDNA-based expression arrays to oligonucleotide arrays and we expect a similar transition for array CGH. This review compares the different platforms and will attempt to shine a light on the ‘BAC to the future’ of the array CGH technique.