Discovery of 505-million-year old chitin in the basal demosponge Vauxia gracilenta.

Sponges are probably the earliest branching animals, and their fossil record dates back to the Precambrian. Identifying their skeletal structure and composition is thus a crucial step in improving our understanding of the early evolution of metazoans. Here, we present the discovery of 505-million-year-old chitin, found in exceptionally well preserved Vauxia gracilenta sponges from the Middle Cambrian Burgess Shale. Our new findings indicate that, given the right fossilization conditions, chitin is stable for much longer than previously suspected. The preservation of chitin in these fossils opens new avenues for research into other ancient fossil groups.

DNA condensation at freestanding cationic lipid bilayers.

We describe a previously unreported coil-globule transition of DNA electrostatically bound to a freestanding fluid cationic lipid membrane. The collapse of a DNA coil into a compact globule takes place after the DNA molecule attaches in an extended conformation to the membrane. DNA condensation is favored at a higher cationic lipid content, while at lower membrane charge densities coexistence of DNA random coils, partially collapsed conformations, and globules is observed.

siRNA modifications and sub-cellular localization: a question of intracellular transport?

RNA interference (RNAi) is an evolutionary conserved post-transcriptional gene silencing mechanism, in which double stranded RNA effector molecules trigger the degradation of complementary mRNA transcripts. The use of RNAi to reduce gene expression with high specificity and ready availability is a powerful tool for reverse genetics and provides great therapeutic potential for targeting diseases caused by the expression of a deleterious gene or mutant allele, e.g. cancer and viral infections. Besides the known preferences of the RNAi technique, there is a need for the development of improved small double stranded silencing triggers with long lasting silencing activity and maximum specificity. The introduction of chemically modified nucleotides into short interfering RNAs (siRNAs) is currently the method of choice. In this review, we summarize the effects of various modifications on siRNA sub-cellular localization and silencing activity, discuss ideal chemical modifications and positions within siRNAs suited for their use in medical therapies and present a new perspective to study siRNA mediated silencing in vivo by fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) to further improve RNAi-based pharmaceuticals.

Immune complexes of auto-antibodies against A beta 1-42 peptides patrol cerebrospinal fluid of non-Alzheimer's patients.

The diagnostic potential of large A beta-peptide binding particles (LAPs) in the cerebrospinal fluid (CSF) of Alzheimer's dementia (AD) patients and non-AD controls (nAD) was evaluated. LAPs were detected by confocal spectroscopy in both groups with high inter-individual variation in number. Molecular imaging by confocal microscopy revealed that LAPs are heterogeneous superaggregates that could be subdivided morphologically into four main types (LAP 1-4). LAP-4 type, resembling a 'large chain of pearls', was detected in 42.1% of all nAD controls but it was virtually absent in AD patients. LAP-4 type could be selectively removed by protein A beads, a clear indication that it contained immunoglobulins in addition to beta-amyloid peptides (A beta 1-42). We observed a close correlation between LAPs and immunoglobulin G (IgG) concentration in CSF in controls but not in AD patients. Double labeling of LAPs with anti-A beta and anti-IgG antibodies confirmed that LAP-4 type consisted of A beta and IgG aggregates. Our results assign a central role to the immune system in regulating A beta1-42 homeostasis by clustering this peptide in immunocomplexes.

Fluorescence lifetime images and correlation spectra obtained by multidimensional time-correlated single photon counting.

Multidimensional time-correlated single photon counting (TCSPC) is based on the excitation of the sample by a high-repetition rate laser and the detection of single photons of the fluorescence signal in several detection channels. Each photon is characterized by its arrival time in the laser period, its detection channel number, and several additional variables such as the coordinates of an image area, or the time from the start of the experiment. Combined with a confocal or two-photon laser scanning microscope and a pulsed laser, multidimensional TCSPC makes a fluorescence lifetime technique with multiwavelength capability, near-ideal counting efficiency, and the capability to resolve multiexponential decay functions. We show that the same technique and the same hardware can be used for precision fluorescence decay analysis and fluorescence correlation spectroscopy (FCS) in selected spots of a sample.

Single molecule fluorescence imaging of the photoinduced conversion and bleaching behavior of the fluorescent protein Kaede.

Photoconversion and photobleaching behavior of the fluorescent protein Kaede immobilized in polyacrylamide gel matrix at room temperature was studied by single molecule wide-field fluorescence microscopy. Photobleaching kinetics of Kaede molecules upon excitation at 488 nm showed slight heterogeneity, suggesting the presence of different protein conformations and/or the distribution of local environments in the gel matrix. Statistical analysis of intensity trajectories of single molecules revealed four major types of fluorescence dynamics behavior upon short illumination by a violet light pulse (405 nm). In particular, two types of photoswitching behavior were observed: the green-to-red photoconversion (4% of Kaede molecules) and the photoactivation of green fluorescence without emission of red fluorescence (13%). Two other major groups show neither photoconversion nor red emission and demonstrate photoinduced partial deactivation (43%) and partial revival (30%) of green fluorescence. The significantly lower green-to-red conversion ratio as compared with bulk measurements in aqueous solution might be induced by the immobilization of the protein molecules within a polyacrylamide gel. Contrary to Ando et al. (Proc Natl Acad Sci 2002;99:12651-12656), we found a significant increase in green fluorescence emission upon illumination with 405-nm light, which is typical for GFP and related proteins.

Diffusion and segmental dynamics of double-stranded DNA.

Diffusion and segmental dynamics of the double-stranded lambda-phage DNA polymer are quantitatively studied over the transition range from stiff to semiflexible chains. Spectroscopy of fluorescence fluctuations of single-end fluorescently labeled monodisperse DNA fragments unambiguously shows that double-stranded DNA in the length range of 10(2) - 2 x 10(4) base pairs behaves as a semiflexible polymer with segmental dynamics controlled by hydrodynamic interactions.

Mobility of Min-proteins in Escherichia coli measured by fluorescence correlation spectroscopy.

In the bacterium Escherichia coli, selection of the division site involves pole-to-pole oscillations of the proteins MinD and MinE. Different oscillation mechanisms based on cooperative effects between Min-proteins and on the exchange of Min-proteins between the cytoplasm and the cytoplasmic membrane have been proposed. The parameters characterizing the dynamics of the Min-proteins in vivo are not known. It has therefore been difficult to compare the models quantitatively with experiments. Here, we present in vivo measurements of the mobility of MinD and MinE using fluorescence correlation spectroscopy. Two distinct timescales are clearly visible in the correlation curves. While the faster timescale can be attributed to cytoplasmic diffusion, the slower timescale could result from diffusion of membrane-bound proteins or from protein exchange between the cytoplasm and the membrane. We determine the diffusion constant of cytoplasmic MinD to be approximately 16 microm(2) s(-1), while for MinE we find about 10 microm(2) s(-1), independently of the processes responsible for the slower time-scale. The implications of the measured values for the oscillation mechanism are discussed.

Characterization of the photoconversion on reaction of the fluorescent protein Kaede on the single-molecule level.

Fluorescent proteins are now widely used in fluorescence microscopy as genetic tags to any protein of interest. Recently, a new fluorescent protein, Kaede, was introduced, which exhibits an irreversible color shift from green to red fluorescence after photoactivation with lambda = 350-410 nm and, thus, allows for specific cellular tracking of proteins before and after exposure to the illumination light. In this work, the dynamics of this photoconversion reaction of Kaede are studied by fluorescence techniques based on single-molecule spectroscopy. By fluorescence correlation spectroscopy, fast flickering dynamics of the chromophore group were revealed. Although these dynamics on a submillisecond timescale were found to be dependent on pH for the green fluorescent Kaede chromophore, the flickering timescale of the photoconverted red chromophore was constant over a large pH range but varied with intensity of the 488-nm excitation light. These findings suggest a comprehensive reorganization of the chromophore and its close environment caused by the photoconversion reaction. To study the photoconversion in more detail, we introduced a novel experimental arrangement to perform continuous flow experiments on a single-molecule scale in a microfluidic channel. Here, the reaction in the flowing sample was induced by the focused light of a diode laser (lambda = 405 nm). Original and photoconverted Kaede protein were differentiated by subsequent excitation at lambda = 488 nm. By variation of flow rate and intensity of the initiating laser we found a reaction rate of 38.6 s(-1) for the complete photoconversion, which is much slower than the internal dynamics of the chromophores. No fluorescent intermediate states could be revealed.

Enzyme assays for confocal single molecule spectroscopy.

During the last years confocal techniques have become increasingly popular for probing biological enzymatic reactions. In this paper we will summarize some of these methods, mainly focusing on measurement techniques suitable for analysis of freely diffusing molecules, where either the substrates or the enzymes are fluorescently labeled. The different approaches are classified according to their basic principles and algorithms. Several examples of enzymatic studies involving correlation strategies for data processing, like auto- and cross correlation analysis, will be presented. In addition, other evaluation schemes like coincidence analysis and fluorescence intensity distribution analysis are introduced and discussed. With respect to assay development, the fluorescence energy transfer principle is addressed as far as it is has been applied for investigating biocatalysis in solution. Finally, one part of this review addresses the aspects of bioconjugation and the basic requirements for proper labeling dyes in order to be compatible with single molecule fluorescent spectroscopy.

Media calcification, low erythrocyte magnesium, altered plasma magnesium, and calcium homeostasis following grafting of the thoracic aorta to the infrarenal aorta in the rat--differential preventive effects of long-term oral magnesium supplementation alone and in combination with alkali.

Calcifications in arterial media are clinically well documented, but the role played by magnesium in pathophysiology and therapy is uncertain. To clarify this, an animal model in which the juxtacardial aorta was grafted to the infrarenal aorta, and the subsequent calcifications in the media of the graft and their response to oral supplementation with three magnesium-containing and alkalinizing preparations was investigated. Groups of highly inbred rats were formed as follows: sham-operation (Sham, n = 12), aorta transplantation (ATx, n = 12), ATx + magnesium citrate (MgC, n = 12), ATx + MgC + potassium citrate (MgCPC, n = 12), ATx + MgC + MgCPC (MgCPCSB, n = 12). At 84 (+/-2) days after ATx with or without treatment the following observations were made: (1) weight gain and general status were normal; (2) ATx rats developed massive media calcification, mineral accumulation in the graft, decreased erythrocyte magnesium and plasma parathyroid hormone, and increased plasma ionized magnesium and calcium, and uric acid; (3) Mg-treated rats developed variable degrees of metabolic alkalosis, but only MgCPCSB supplementation prevented calcifications. Additional findings after ATx alone were: imbalance in endothelin and nitric oxide production, the mineral deposited in media was poorly crystallized calcium phosphate, calcium exchange between plasma and graft, and bone resorption were unchanged. The superior anti-calcification effect of MgCPCSB was characterized by complete restoration of normal extracellular mineral homeostasis and uric acid, but sub-optimal normalization of erythrocyte magnesium. It was concluded that in the rat: (1) ATx causes loss of cellular magnesium, excess of extracellular magnesium and calcium in the presence of apparently unchanged bone resorption, and increased uricemia; (2) ATx facilitates enhanced influx of calcium into vascular tissue, leading to calcium phosphate deposition in the media; (3) ATx-induced calcification is prevented by dietary supplementation with a combination of magnesium, alkali citrate and bases. Although the described circulatory model of media calcification in the rat requires further investigation, the data allow ascribing a fundamental role to magnesium and acid-base metabolism.

Regional bone loss after orthotopic liver transplantation in inbred rats: the role of hepatic denervation.

Bone loss and long-term persistence of osteoporosis with increased fracture risk are common after liver transplantation. It is unknown whether transplantation-induced disruption of hepatic nerves, serving numerous regulatory metabolic and sensory functions, is herein involved. To test this possibility, we measured bone mineral density (BMD) by peripheral quantitative computed tomography (pQCT) and studied dynamic histomorphometry, radiocalcium kinetics, and biochemical parameters in 7 liver-transplanted and 7 sham-operated inbred rats. Although liver function was normal in TX rats, trabecular BMD of the first lumbar vertebra and total BMD of the femoral diaphysis were decreased by 13% and 6%, respectively, 9 months postsurgery. The breaking force of the femur was significantly lower by 21%. However, bone mass in the femoral and tibial metaphysis was preserved as evidenced by pQCT measurements and histomorphometry. Trabecular width and wall thickness were significantly decreased in vertebral cancellous bone, whereas indices of bone formation and resorption were normal or slightly reduced. Serum minerals, mineral balance, fractional and net absorption of Ca and Mg, serum calciotropic hormones, IGF-I, leptin, specific activity of 45Ca in bone, 45Ca excretion, and biochemical indices of bone formation and bone resorption remained unchanged. We conclude that liver transplantation-related denervation causes cancellous and cortical bone loss in well-innervated bone sites such as the lumbar spine and the long bone diaphysis. Cancellous bone loss in TX rats is due to an impairment of osteoblast team performance and subsequent trabecular thinning. The mechanism uncovered by our study may contribute to long-term bone loss after liver transplantation.

Small bowel resection in the rat: the effect upon bone and mineral metabolism.

BACKGROUND AND AIMS: We analyzed bone and mineral metabolism after long-segment small bowel resection in the rat to detect functional and morphological alterations and to determine the development of osteopathy. METHODS: Twelve-week-old male Lewis rats were randomized into short (8-week) or long (16-week) follow-up groups. Sham operation, resection of the proximal third of the small bowel, resection of the distal third of the bowel and resection of the entire jejunum and ileum were carried out. Nineteen days before the end of the experiment the animals were transferred into a metabolic cage to analyze weight gain/loss, food intake, and fecal excretion/24 h. At the end of the experiment the animals were killed; blood samples and bowel and bone specimens were collected, length, weight, volume, density, mineral content, and fracturing energy were determined, and bone histology was examined. The calcium/phosphorus ratio, nonmineralized tissue content and the ratio fracturing energy/mean bone density were calculated. RESULTS: After 8 weeks there were significant differences to the control group in body weight, weight gain, food efficiency, femur length, weight, volume, mineral content, mineral density, fracturing energy per bone volume, and bone density but not in bone calcium or magnesium. After 16 weeks there were differences in body weight, weight gain, food efficiency, femur length, weight, volume, bone mineral content and density, bone minerals, and nonmineralized tissue but not in fracturing energy; the average values of all these parameters were lower in the resected groups, and lowest in the group after resection of the entire jejunum and ileum. Bone histology showed a reduction in trabecular bone mass after long-segment small bowel resection. CONCLUSIONS: Long-segment small bowel resection causes a significant loss of body weight despite of a comparable mean chow ingestion resulting in a significant decreased food efficiency. We conclude that there is no inverse relationship of bone calcium content and the fracture risk, and that there is no severe mineralization defect after long-segment small bowel resection.

Calcium oxalate crystallization in undiluted postprandial urine of healthy male volunteers as influenced by citrate.

The crystallization of calcium oxalate (CaOx) in undiluted urine of healthy male volunteers, collected 3 h after intake of a test meal, was evaluated. In two experiments in vitro either the urinary total citrate concentration was increased (urine A) or the urinary pH was elevated (urine B). In one clinical trial the bioequivalence of orally taken potassium citrate (PC) or potassium-sodium citrate (PSC) (n = 9) was studied, in two other trials the dose-response effects of oral PC (n = 8) and oral calcium-sodium citrate (CSC; n = 8). Elevation of urinary citrate (urine A) decreased CaOx crystallization (nucleation, growth, agglomeration time), the crystal content of calcium and oxalate was low and the one of citrate was high. Elevation of urinary pH (urine B) also inhibited CaOx crystallization, the calculated molar ratio free (ionised) citrate/free (ionised) calcium at pH 7.0 was about twice the value observed at pH 5.5, and the ratio complexed citrate/complexed calcium was low. PC and PSC, leading to high urinary citrate and pH, inhibited CaOx crystallization, the former at the stages nucleation, growth and agglomeration, the latter largely beyond nucleation. CSC increased calciuria and crystal growth, but left crystal agglomeration time unchanged. The urinary molar ratio total calcium/total citrate appeared to indicate the state of crystallization, as influenced by alkali containing citrate. It was concluded that 1) application of a technically simple test allows to study CaOx crystallization in undiluted urine; 2) changes in urinary pH and citrate manifest as altered CaOx crystallization, presumably inhibiting this process, the stage of nucleation included, via the action of free citrate and the formation of a calcium citrate complex (stoichiometry < 3:2); 3) oral intake of PC, PSC or CSC modulate differently CaOx crystallization. The significance of these findings, especially with CSC, for renal stone risk is uncertain, but awaits clarification by long-term studies using the described techniques and the calcium/citrate ratio in postprandial urine.

Adenosine nucleotides in rat bone measured by ion-pair reversed-phase high-performance liquid chromatography: effect of hemorrhagic shock, with and without retransfusion of blood.

The measurement of bone adenosine nucleotides (ATP. ADP. AMP) using a simple HPLC procedure is described for rat tibia; the response to hemorrhagic shock with and without blood retransfusion is also described. With respect to the measurement of nucleotides, a number of validation criteria are met. In the anesthetized intact rat (Normal) there was a declining gradient of the three nucleotides, expressed as nmol per g dry matter, from proximal over middle to distal diaphysis, with the mean ratio ATP/ADP (0.21, 0.20, 0.20) and the mean energy charge (0.34, 0.31, 0.30) being low. Irrespective of the anatomic site, hemorrhagic shock of 30-min duration evoked a further decrease versus Normal of ATP, ATP/ADP and energy charge. Blood retransfusion after shock kept nucleotides and other variables in the proximal and distal, but not the middle, diaphysis within normal limits. It was concluded that: (i) bone nucleotides are reliably measurable by HPLC, allowing the described method to be recommended for wider use in bone research and related areas; (ii) in contrast to more parenchymatous tissues, low ATP, ATP/ADP and energy charge may be characteristic for long bones, pointing towards different energy metabolism; and (iii) bone is a "shock organ", reflecting blood hypoperfusion, O2 deficiency and decreased ATP in this situation.

Renal cortical calcification in syngeneic intact rats and those receiving an infrarenal thoracic aortic graft: possible etiological roles of endothelin, nitrate and minerals, and different preventive effects of long-term oral treatment with magnesium, citrate and alkali-containing preparations.

Renal cortical nephrocalcinosis (C-NC) is a rare disorder of uncertain etiology. Using highly inbred (syngeneic) male Lewis rats, we describe the spontaneous occurrence of histologically detectable C-NC in sham operated control rats (Sham; n=12), its aggravation following grafting of the ascending thoracic aorta from a donor rat to the infrarenal aorta of a recipient (ATx; n=12), and differences in C-NC inhibition after 12 weeks of oral administration of magnesium (Mg), citrate and alkali. C-NC is characterized by Kossa-positive areas located in cells of the proximal tubule close to blood vessels and also, to a lesser extent, within glomeruli. After ATx there was vascular overproduction of endothelin (ET-1) but decreased production of nitrate; in renal cortical tissue there was an excess of calcium over Mg and phosphorus and oxalate over citrate. In plasma there was an increase in calcium and creatinine within the normal range. Calcification of tubular cells was eliminated by a preparation containing potassium, sodium and bases (from citrate degradation and bicarbonate) in addition to Mg. Less effective than the latter was Mg-potassium citrate and least effective, Mg citrate. The former treatment also normalized calcemia and urinary nitrate, but only incompletely suppressed ET-1 and had no significant effect on glomerular calcification or tissue and urinary oxalate. Urinary ET-1 excess appeared directly related to the cortical tissue calcium/Mg ratio, and urinary excretion of Mg, citrate and total protein appeared to be inversely related to the severity of C-NC. It was concluded that (1) the highly inbred rat is prone to precipitation of calcium phosphate in the renal cortex; (2) this type of C-NC occurs in close proximity to and within renal vascular tissue and is associated with an imbalance of vasoconstrictors and vasodilators of endothelial origin; (3) effective inhibition of C-NC can be achieved by an alkalinizing combination of Mg, potassium, sodium and citrate, underscoring its utility in the prophylaxis of pathological calcium phosphate deposition. The significance of these findings for the etiology and treatment of clinical disorders with renal and vascular calcification is uncertain and requires further investigation.

Analyzing single protein molecules using optical methods.

Studies on single protein molecules have advanced from mere proofs of principle to insightful investigations of otherwise inaccessible biological phenomena. Recent studies predict a tremendous number of possible future applications. The long-term vision of biologists to watch single molecular processes in real time by peering into a cell with three-dimensional resolution might finally be realized. Another fascinating perspective is the identification and selection of single favorable variants from complex libraries of diverse biomolecules.

Light-induced flickering of DsRed provides evidence for distinct and interconvertible fluorescent states.

Green fluorescent protein (GFP) from jellyfish Aequorea victoria, the powerful genetically encoded tag presently available in a variety of mutants featuring blue to yellow emission, has found a red-emitting counterpart. The recently cloned red fluorescent protein DsRed, isolated from Discosoma corals (), with its emission maximum at 583 nm, appears to be the long awaited tool for multi-color applications in fluorescence-based biological research. Studying the emission dynamics of DsRed by fluorescence correlation spectroscopy (FCS), it can be verified that this protein exhibits strong light-dependent flickering similar to what is observed in several yellow-shifted mutants of GFP. FCS data recorded at different intensities and excitation wavelengths suggest that DsRed appears under equilibrated conditions in at minimum three interconvertible states, apparently fluorescent with different excitation and emission properties. Light absorption induces transitions and/or cycling between these states on time scales of several tens to several hundreds of microseconds, dependent on excitation intensity. With increasing intensity, the emission maximum of the static fluorescence continuously shifts to the red, implying that at least one state emitting at longer wavelength is preferably populated at higher light levels. In close resemblance to GFP, this light-induced dynamic behavior implies that the chromophore is subject to conformational rearrangements upon population of the excited state.

Accessing molecular dynamics in cells by fluorescence correlation spectroscopy.

Fluorescence correlation spectroscopy (FCS) analyzes spontaneous fluctuations in the fluorescence emission of small molecular ensembles, thus providing information about a multitude of parameters, such as concentrations, molecular mobility and dynamics of fluorescently labeled molecules. Performed within diffraction-limited confocal volume elements, FCS provides an attractive alternative to photobleaching recovery methods for determining intracellular mobility parameters of very low quantities of fluorophores. Due to its high sensitivity sufficient for single molecule detection, the method is subject to certain artifact hazards that must be carefully controlled, such as photobleaching and intramolecular dynamics, which introduce fluorescence flickering. Furthermore, if molecular mobility is to be probed, nonspecific interactions of the labeling dye with cellular structures can introduce systematic errors. In cytosolic measurements, lipophilic dyes, such as certain rhodamines that bind to intracellular membranes, should be avoided. To study free diffusion, genetically encoded fluorescent labels such as green fluorescent protein (GFP) or DsRed are preferable since they are less likely to nonspecifically interact with cellular substructures.

The solution to hyperglucagonemia after pancreas transplantation in inbred rats.

BACKGROUND: We studied the possible role of the diseased host pancreas and site of venous graft drainage in the development of hyperglucagonemia after pancreas transplantation, to identify the crucial steps of the technique capable of eliminating hyperglucagonemia and its possible diabetogenic effect. METHODS: Therefore, we compared 4 groups of inbred rats: (1) heterotopic pancreas transplantation with either systemic (n = 9); or (2) portal (n = 5) venous drainage after prior induction of diabetes with streptozotocin; (3) orthotopic pancreaticoduodenal transplantation with portal venous drainage after prior pancreaticoduodenectomy (n = 7), and (4) sham-operation (Sham; n = 10). The postoperative period was 6 months. RESULTS: Only heterotopic transplantation with systemic venous drainage and loss of glucagon's first pass hepatic extraction, resulted in arterial hyperglucagonemia, whereas the arterial plasma insulin level was only slightly higher in comparison with the other groups. After either type of heterotopic transplantation the glucagon content of host pancreata remained unchanged, whereas the insulin content was approximately 5% of that in the pancreas of Sham rats. The insulin and glucagon contents of all grafts were similar to those of the control pancreas in Sham rats, and the insulin release was sufficient to normalize fasting plasma glucose and lipids after either type of transplantation. CONCLUSION: To remove the diseased host pancreas appears unnecessary, as the hyperglucagonemia and the concomitant slight hyperinsulinemia, capable of preventing glucagon's diabetogenic effects, are due to loss of the first pass hepatic extraction by systemic venous drainage alone. This disadvantage can be eliminated by portal venous graft drainage.