Direct Biochemical Analyses Research Articles

Comparison of actual and simulated tumoricidal effects induced by photodynamic therapy.

Numerous studies employ mathematical methods, such as Monte Carlo simulation, to predict the tumor killing effects of photodynamic therapy (PDT) by simulating optical propagation, photosensitizer distribution, and oxygen distribution. Whether these models faithfully reflect tumor killing is unknown, and model validation using tumor cross sections in these studies is usually insufficient to answer this question. To fill this gap in our knowledge, we employed a mouse model of breast cancer to determine the spatiotemporal effects of PDT using direct histopathological and biochemical analyses of whole tumors. We prepared approximately 700 5-μm-thick serial sections of breast tumors of syngeneic mice treated with PDT employing the photosensitizer photocarcinorin (PsD-007, a second-generation photosensitizer developed in China). Three adjoining sections were subjected to hematoxylin and eosin staining to assess necrosis, the TUNEL assay to evaluate apoptosis, and CD31 staining to detect angiogenesis, respectively. We then generated a three-dimensional (3D) reconstruction of the tumor to evaluate these processes. We simultaneously used the Monte Carlo method to develop a model of light distribution throughout the tumor to evaluate the actual and simulated tumor killing effects induced by PDT. Tumor necrosis decreased exponentially as a function of distance from the source of illumination, while the distributions of apoptosis and neovascularization were independent of light distribution. Most apoptosis occurred in the lower layers (3000-4000 μm) of the tumor where the light intensity was too low to excite the photosensitizer. Neovascularization occurred at depths ranging from 2500 to 3500 μm. These analyses provided a 3D view of how a tumor is destroyed using PDT. Although the optical distribution model predicted tumor necrosis caused by PDT, it was ineffective in predicting the sites of apoptosis and vascular destruction. Mathematical modeling is limited in its capabilities required to gain a comprehensive understanding of the spatiotemporal events associated with PDT. The mouse model developed here will serve as a platform for detailed direct histopathological, biochemical, and molecular genetic analyses of the effects of PDT, which will facilitate the development of optimized treatment strategies.

Analysis of α-synuclein species enriched from cerebral cortex of humans with sporadic dementia with Lewy bodies.

Since researchers identified α-synuclein as the principal component of Lewy bodies and Lewy neurites, studies have suggested that it plays a causative role in the pathogenesis of dementia with Lewy bodies and other ‘synucleinopathies’. While α-synuclein dyshomeostasis likely contributes to the neurodegeneration associated with the synucleinopathies, few direct biochemical analyses of α-synuclein from diseased human brain tissue currently exist. In this study, we analysed sequential protein extracts from a substantial number of patients with neuropathological diagnoses of dementia with Lewy bodies and corresponding controls, detecting a shift of cytosolic and membrane-bound physiological α-synuclein to highly aggregated forms. We then fractionated aqueous extracts (cytosol) from cerebral cortex using non-denaturing methods to search for soluble, disease-associated high molecular weight species potentially associated with toxicity. We applied these fractions and corresponding insoluble fractions containing Lewy-type aggregates to several reporter assays to determine their bioactivity and cytotoxicity. Ultimately, high molecular weight cytosolic fractions enhances phospholipid membrane permeability, while insoluble, Lewy-associated fractions induced morphological changes in the neurites of human stem cell-derived neurons. While the concentrations of soluble, high molecular weight α-synuclein were only slightly elevated in brains of dementia with Lewy bodies patients compared to healthy, age-matched controls, these observations suggest that a small subset of soluble α-synuclein aggregates in the brain may drive early pathogenic effects, while Lewy body-associated α-synuclein can drive neurotoxicity.

Molecular anatomy of the receptor binding module of a bacteriophage long tail fiber.

Tailed bacteriophages (phages) are one of the most abundant life forms on Earth. They encode highly efficient molecular machines to infect bacteria, but the initial interactions between a phage and a bacterium that then lead to irreversible virus attachment and infection are poorly understood. This information is critically needed to engineer machines with novel host specificities in order to combat antibiotic resistance, a major threat to global health today. The tailed phage T4 encodes a specialized device for this purpose, the long tail fiber (LTF), which allows the virus to move on the bacterial surface and find a suitable site for infection. Consequently, the infection efficiency of phage T4 is one of the highest, reaching the theoretical value of 1. Although the atomic structure of the tip of the LTF has been determined, its functional architecture and how interactions with two structurally very different Escherichia coli receptor molecules, lipopolysaccharide (LPS) and outer membrane protein C (OmpC), contribute to virus movement remained unknown. Here, by developing direct receptor binding assays, extensive mutational and biochemical analyses, and structural modeling, we discovered that the ball-shaped tip of the LTF, a trimer of gene product 37, consists of three sets of symmetrically alternating binding sites for LPS and/or OmpC. Our studies implicate reversible and dynamic interactions between these sites and the receptors. We speculate that the LTF might function as a “molecular pivot” allowing the virus to “walk” on the bacterium by adjusting the angle or position of interaction of the six LTFs attached to the six-fold symmetric baseplate.

Type IX Collagen Neo-Deposition in Degenerative Discs of Surgical Patients Whether Genotyped Plus or Minus for COL9 Risk Alleles

Immunohistochemical analysis of type IX collagen in disc tissue from spinal fusion patients. To determine if collagen IX can be detected in adult disc tissue removed at spinal fusion surgery from patients either with or without degeneration-associated tryptophan single nucleotide polymorphisms (SNPs) and whether the distribution is associated either with severity of degeneration or incidence of a collagen IX SNP genotype. Genetic factors are strongly associated with risk of development and/or progression of disc degeneration. Two SNPs that introduce tryptophan polymorphisms in COL9A2 and COL9A3 are independently linked to an increased risk of lumbar disc disease. Although tryptophan variants are associated with accelerated degeneration, it is not known if collagen IX can be detected in adult disc tissue. We selected age-matched disc samples from five clinical groups: fracture with Trp(-) (six cases), herniation (six cases), degeneration (five cases), spondylolisthesis with Trp(-) (eight cases), and spondylolisthesis/herniation/fracture with Trp(+) (six cases of Trp3 allele and one case of Trp2 allele). Using hematoxylin and eosin staining and immunohistochemical staining (collagens IX and IIA), 78 sections from 32 patients were analyzed. Selected disc tissues were assayed biochemically for collagen IX. Focal deposition of collagen IX was observed in regions of adult human disc tissue from spines showing degenerative changes in patients whether or not they were positive for a tryptophan SNP. However, in nondegenerative control disc tissue from fracture cases, little or no collagen IX was detected. The latter finding was confirmed by direct biochemical analyses for collagen IX in pooled samples of normal adult human annulus fibrosus or nucleus pulposus. During growth and maturation of the disc, collagen IX is presumably removed completely during matrix remodeling so that the protein is absent from normal adult annulus and nucleus but can reappear at sites of degeneration presumably as part of a repair response to mechanical injury.

Ethylene Interacts with Abscisic Acid to Regulate Endosperm Rupture during Germination: A Comparative Approach UsingLepidium sativumandArabidopsis thaliana

The micropylar endosperm cap covering the radicle in the mature seeds of most angiosperms acts as a constraint that regulates seed germination. Here, we report on a comparative seed biology study with the close Brassicaceae relatives Lepidium sativum and Arabidopsis thaliana showing that ethylene biosynthesis and signaling regulate seed germination by a mechanism that requires the coordinated action of the radicle and the endosperm cap. The larger seed size of Lepidium allows direct tissue-specific biomechanical, biochemical, and transcriptome analyses. We show that ethylene promotes endosperm cap weakening of Lepidium and endosperm rupture of both species and that it counteracts the inhibitory action of abscisic acid (ABA) on these two processes. Cross-species microarrays of the Lepidium micropylar endosperm cap and the radicle show that the ethylene-ABA antagonism involves both tissues and has the micropylar endosperm cap as a major target. Ethylene counteracts the ABA-induced inhibition without affecting seed ABA levels. The Arabidopsis loss-of-function mutants ACC oxidase2 (aco2; ethylene biosynthesis) and constitutive triple response1 (ethylene signaling) are impaired in the 1-aminocyclopropane-1-carboxylic acid (ACC)-mediated reversion of the ABA-induced inhibition of seed germination. Ethylene production by the ACC oxidase orthologs Lepidium ACO2 and Arabidopsis ACO2 appears to be a key regulatory step. Endosperm cap weakening and rupture are promoted by ethylene and inhibited by ABA to regulate germination in a process conserved across the Brassicaceae.

Towards a better understanding of the substrate specificity of the UDP-N-acetylglucosamine C4 epimerase WbpP

WbpP is the only genuine UDP-GlcNAc (UDP-N-acetylglucosamine) C4 epimerase for which both biochemical and structural data are available. This represents a golden opportunity to elucidate the molecular basis for its specificity for N-acetylated substrates. Based on the comparison of the substrate binding site of WbpP with that of other C4 epimerases that convert preferentially non-acetylated substrates, or that are able to convert both acetylated and non-acetylated substrates equally well, specific residues of WbpP were mutated, and the substrate specificity of the mutants was determined by direct biochemical assays and kinetic analyses. Most of the mutations tested were anticipated to trigger a significant switch in substrate specificity, mostly towards a preference for non-acetylated substrates. However, only one of the mutations (A209H) had the expected effect, and most others resulted in enhanced specificity of WbpP for N-acetylated substrates (Q201E, G102K, Q201E/G102K, A209N and S143A). One mutation (S144K) totally abolished enzyme activity. These data indicate that, although all residues targeted in the present study turned out to be important for catalysis, determinants of substrate specificity are not confined to the substrate-binding pocket and that longer range interactions are essential in allowing proper positioning of various ligands in the binding pocket. Hence prediction or engineering of substrate specificity solely based on sequence analysis, or even on modelling of the binding pocket, might lead to incorrect functional assignments.

Simple flow cytometric method used to assess lipid accumulation in fat cells

Adipogenesis of preadipocytes in culture has been frequently used to study the molecular basis and effect of drugs on fat cell conversion. However, after adipogenic induction, cells respond to the inducing agent with various speeds of conversion and fat accumulation, which complicates direct molecular and biochemical analyses. Here we present a simple and sensitive method to detect and quantify fat accumulation inside cells by flow cytometry. Using this method, we detected elevated levels of cytoplasmic granularity that correlated well with an increased level of fat accumulated inside cells after adipogenic conversion. We further demonstrated the ability of this method to monitor and quantify fat cell maturation within a complex population of cells and to identify and collect the fat cells with similar fat storage for further analysis. Flow cytometry offers distinct advantages over existing detection systems for cytoplasmic lipid staining and lipid extraction and could represent a powerful analytical tool to monitor the effect of chemicals and biological molecules on fat cell conversion and maturation. Moreover, in combination with a cell sorting facility, our method offers a simple and efficient means of collecting fat cells of specific status for further analysis.

Chapter 3 Myogenesis in Xenopus Embryos

This chapter discusses myogenesis in Xenopus embryos. Axial Muscle derives from the somites, which in turn come from mesoderm tissue that is invaginated during gastrulation. The location of the mesoderm as seen during gastrulation is more complicated in Xenopus than in other amphibians. Lineage labeling studies have shown that two blastomeres of the 32-cell stage contribute to the embryonic heart. During gastrulation, the regions of mesoderm destined to form the heart tube are found on either side of the dorsal lip and are distinct from the somitic mesoderm. By the end of gastrulation, these are arranged bilaterally, at the anterior edge of the newly forming neural plate. After gastrulation, it is sometimes useful to be able to dissect embryos into different tissues. Xenopus embryos are large enough that direct biochemical analyses can be carried out on tissues from only a few embryos. Interestingly, tissues among which an induction is taking place tend to be tightly adherent to each other and difficult to separate. A 0.3% solution of commercial collagenase in 1 X modified Barth's saline (MBS) is very helpful in enabling tissues to be separated by gentle action with needles. However, it is essential first to break the very impermeable surface coat of embryos by removing the endoderm.

Oligomerization of Endothelial Nitric Oxide Synthase: EVIDENCE FOR A DOMINANT NEGATIVE EFFECT OF TRUNCATION MUTANTS

Nitric oxide produced by the endothelial isoform of nitric oxide synthase (ecNOS) is a key determinant of vascular tone. In contrast to other nitric oxide synthase (NOS) isoforms, which have been characterized as soluble homodimeric enzymes, ecNOS is predominantly membrane-associated, a feature that has hindered direct biochemical analyses of its oligomeric structure. We investigated ecNOS oligomerization using co-immunoprecipitation experiments in transiently transfected COS-7 cells. When COS-7 cells co-transfected with constructs encoding wild-type ecNOS and an epitope-tagged myristoylation-deficient mutant were biosynthetically labeled with [3H]myristate, the antibody to the epitope tag specifically immunoprecipitated 3H-labeled ecNOS, reflecting enzyme oligomerization. In COS-7 cells transfected with cDNAs encoding epitope-tagged truncation mutants and untagged full-length ec-NOS, the wild-type enzyme could be immunoprecipitated by the antibody to the epitope tag. Co-immunoprecipitation of ecNOS with truncation mutants documented that both N- and C-terminal domains are involved in ecNOS oligomerization. When these truncation mutants are co-expressed with wild-type ecNOS, they exert a marked dominant negative effect on enzyme activity. Since NOS oligomerization itself may be subject to dynamic modulation, the regulation of ecNOS assembly may have implications for NO signaling in the vascular wall.

Gene sequence, overproduction, purification and determination of the wild-type level of the Escherichia coli flagellar switch protein FliG

The flagellar motor switch in Escherichia coli and Salmonella typhimurium controls swimming behavior by regulating the direction of flagellar rotation. The switch is a complex apparatus composed of at least three proteins — FliG, FliM and FliN. During chemotactic behavior, the switch responds to signals transduced by the chemotaxis sensory signaling system. CheY, the chemotaxis response regulator, is thought to act directly on the switch to induce tumbles in the swimming pattern, but physical interaction of CheY and switch proteins has not been shown. We have undertaken this work to develop the molecular tools to investigate CheY binding to switch proteins, as well as to understand more about the structure and function of the switch. We present here the sequences of the fliG gene and its protein product, the engineering and amplification of fliG by the polymerase chain reaction (PCR) and its subcloning, and the overproduction, purification and determination of the wild-type (wt) level of the FliG protein. The sequence data revealed a 91.8% amino acid (aa) identity between E. coli and S. typhimurium FliG. Engineering and amplifying fliG by PCR allowed convenient cloning into an efficient expression vector. FliG was successfully overproduced and purified to > 98% purity. Polyclonal antibodies (Ab) were generated against purified FliG and used in quantitative Western blots to determine that the wt expression level of fliG results in about 3700 FliG copies per cell. Purified FliG and anti-FliG Ab will be useful for direct biochemical analyses of CheY-switch protein interaction.

Paradoxical DSP-4 effects: protection against gastric erosions and depletion of musocal glycoproteins

We have previously reported that rats pretreated with the central noradrenergic neurotoxin DSP-4 are protected against 23 h restraint-induced gastric erosions. To elucidate the peripheral mechanisms of this protection, we undertook direct biochemical analyses of the gastric mucosa in terms of glycoproteins and proteins. A simple method for preparation of gastric mucosa devoide of the muscular stomach wall tissue is described. A restrain-induced decrease in gastric wet weight and mucosal glycoprotein content was revealed. Restraint had no effect no mucosal protein content, and no changes were found in gastric wall glycoprotein or protein content. Despite showing protection against restrain-induced gastric erosions, unrestrained DSP-4-treated animals exhibited reduced mucosal wet weight mucosal glycoprotein content when compared to unrestrained controls. After the stress period, no significant differences on mucosal weight or glycoproteins could be detected between control and DSP-4 treated animals. The results indicate that the protective effect of DSP-4 in this paradign is not due to enhanced gastric mucosal protection against erosive factors. We suggest that an additional effect of central nervous NA depletion by DSP-4 may be elimination of aggresive factors which precipitate overt ulcers.

Direct Biochemical Analyses of Human Muscle Tissue

Direct Biochemical Analyses of Human Muscle Tissue

Most Synaptic Vesicles Isolated from Rat Brain Carry Three Membrane Proteins, SV2, Synaptophysin, and p65

We have prepared highly purified synaptic vesicles from rat brain by subjecting vesicles purified by our previous method to a further fractionation step, i.e., equilibrium centrifugation on a Ficoll gradient. Monoclonal antibodies to three membrane proteins enriched in synaptic vesicles--SV2, synaptophysin, and p65--each were able to immunoprecipitate specifically approximately 90% of the total membrane protein from Ficoll-purified synaptic vesicle preparations. Anti-SV2 precipitated 96% of protein, anti-synaptophysin 92%, and anti-p65 83%. These results demonstrate two points: (1) Ficoll-purified synaptic vesicles appear to be greater than 90% pure, i.e., less than 10% of membranes in the preparation do not carry synaptic vesicle-associated proteins. These very pure synaptic vesicles may be useful for direct biochemical analyses of mammalian synaptic vesicle composition and function. (2) SV2, synaptophysin, and p65 coexist on most rat brain synaptic vesicles. This result suggests that the functions of these proteins are common to most brain synaptic vesicles. However, if SV2, synaptophysin, or p65 is involved in synaptic vesicle dynamics, e.g., in vesicle trafficking or exocytosis, separate cellular systems are very likely required to modulate the activity of such proteins in a temporally or spatially specific manner.

Identification of the neutral glycosphingolipids of murine mast cells: expression of Forssman glycolipid by the serosal but not the bone marrow-derived subclass.

The expression of neutral glycosphingolipids by mouse T cell-dependent, bone marrow-derived mast cells (BMMC) obtained in vitro was determined by chromatographic and immunochemical criteria. Neutral glycosphingolipids were isolated from BMMC by extraction of 3 to 5 X 10(8) cells in chloroform/methanol (1/1, v/v) and chromatography on DEAE-Sephadex, and were analyzed by thin layer chromatography with orcinol staining. The predominant neutral glycosphingolipids of BMMC were glucosylceramide (CMH), lactosylceramide (CDH), globotriosylceramide (CTH), globotetraosylceramide (globoside), and a molecule migrating slightly faster than gangliotetraosylceramide (asialo GM1) and slower than globopentaosylceramide (Forssman glycolipid). The profiles on thin layer chromatograms of the neutral glycosphingolipids were the same for BMMC derived from BALB/c, C57BL/6, WBBF1-W/Wv, and WBBF1-+/+ mice, and for cells differentiated in either WEHI-3 conditioned medium or concanavalin A-splenocyte conditioned medium. High performance liquid chromatography of benzoylated neutral glycosphingolipids of BMMC on a Zipax column confirmed the identity of the four neutral glycosphingolipids identified by thin layer chromatography. The fifth major glycosphingolipid had an elution time greater than that of globotetraosylceramide and did not co-elute with any of the standards tested. Direct biochemical analyses of the neutral glycosphingolipids of mouse serosal mast cells (SMC) were not feasible because only 2 X 10(6) SMC could be isolated per 100 mice. However, mouse SMC bound a rat monoclonal anti-globopentaosylceramide antibody (M1/87.27.7) and rat monoclonal B1.1 antibody, as assessed by indirect immunofluorescence and flow cytometry, whereas mouse BMMC did not. The binding of B1.1 antibody to SMC could be blocked by the anti-globopentaosylceramide antibody, and the specificity of B1.1 antibody for globopentaosylceramide was confirmed immunochemically with the use of a solid phase radioimmunoassay. As estimated immunochemically, the amount of globopentaosylceramide in mouse SMC was 62 ng/10(6) cells, whereas BMMC contained less than 8 ng/10(6) cells. Thus, the expression of globopentaosylceramide is a characteristic of the mouse SMC that is lacking in the T cell-dependent BMMC.

Are opioid peptides co-transmitters in noradrenergic vesicles of sympathetic nerves?

Biogenic amines and peptide hormones co-exist in paraneurones1 or amine precursor uptake and decarboxylation (APUD) cells2. Opioid peptide immunohistofluorescence occurs in the gland cells and nerve endings of the adrenal medulla3, and both dopamine β-hydroxylase (EC 1.14.17.1) and enkephalin-like immunohistofluorescence occurs in some small intensely fluorescent and sympathetic ganglion cells4. Direct biochemical assays demonstrate opiate-like peptides (OLPs) including Met- and Leu-enkephalin in the adrenal medulla, and the highest specific activity is attained in the purified adrenomedullary chromaffin granule fraction5. Chromaffin cells also synthesize enkephalins de novo6. Adrenal medullae from larger species, including ox and man, contain much more OLP material than those from smaller species such as rodents5,7; fortunately so, because only from ox is it practical to purify both chromaffin granules and splenic nerve vesicles at particle purity and yield suitable for chemical composition studies. In ox and man the large dense-cored vesicles (LDVs) comprise 30–50% of the vesicle population in terminals of blood vessels, spleen and vas deferens, equivalent to 80–90% of the total terminal vesicle capacity. For these reasons, we chose bovine splenic nerve in which to investigate the localization of OLPs in the peripheral sympathetic system. Our results, reported here and based on direct biochemical analyses, indicate that OLPs, putative transmitters and noradrenaline probably coexist in sympathetic C-fibres, which constitute 98% of the bovine splenic nerve. Further, the OLPs and noradrenaline can probably co-exist in the large dense-cored noradrenergic vesicles of this nerve. We believe the obtained 1:60 molar ratio of opioid peptides:noradrenaline to be the highest yet demonstrated for enkephalins in any neurotransmitter organelle or tissue.

Accelerated Cytopathology in HeLa Cells Induced by Reovirus and Cycloheximide

The addition of the protein inhibitor cycloheximide, at concentrations which suppress virus replication, to HeLa cell monolayers infected with reovirus type 2 results in the appearance of accelerated cytopathic effects (CPE). At high multiplicity of infection, CPE appeared after a lag period of 2 to 3 hr and increased progressively, until by 12 hr the entire monolayer had rounded and sloughed off. During this same period, both the uninfected cycloheximide-treated and untreated virus-infected controls exhibited no CPE. The phenomenon is affected by the kind of cell species employed and can be reversed if the antibiotic is removed within 1 hr after exposure. The evidence obtained through studies in which specific metabolic inhibitors and direct biochemical analyses were used suggests that the accelerated CPE observed in cycloheximide-treated reovirus-infected cells is the consequence of the combined inhibition of the synthesis of both cellular protein and ribonucleic acid. The accelerated CPE is also induced in the antibiotic-treated cells by reovirus serotypes 1 and 3.