Factors Controlling Microbially Induced Desaturation and Precipitation (MIDP) via Denitrification during Continuous Flow

Three continuous-flow column experiments were conducted to investigate the effects of nitrate loading rate and input concentrations of acetate and calcium on the effectiveness of denitrification to promote microbially induced desaturation and precipitation (MIDP). MIDP differs from microbially induced carbonate precipitation (MICP) in that it relies upon desaturation by biogenic gas production, along with carbonate precipitation, to improve the behavior of saturated granular soil. Denitrification is a stepwise process that is susceptible to inhibition and accumulation of intermediates, like nitrite, due to unfavorable chemical conditions (e.g., low pH). Therefore, nitrate reduction, nitrite accumulation, calcite saturation, and formation of carbonate precipitates were monitored in the columns. Factors investigated in these experiments included the effects of nitrate loading rate and input concentrations of calcium and acetate. Low nitrate-loading rates (i.e., ≤0.7?mol/m²-day) generally led to favorable outcomes (i.e., less accumulation of intermediates and more efficient carbonate precipitation). However, faster precipitation rates associated with low nitrate-loading rates led to smaller carbonate crystals and a less uniform precipitation pattern (i.e., precipitation focused near the nutrient source). Input concentrations of calcium and acetate also affected MIDP, but to a lesser extent than nitrate loading rate. The most important stimulated denitrifying bacteria, identified via 16S rDNA sequencing of suspended and dissolved DNA in the soil columns, were Bacillus species, Pseudomonas species, Brevundimonas species, and members of the Rhizobiaceae family. The results support that lower nitrate loading rates can be beneficial for MIDP although higher nitrate loading rates might be useful for some soil improvement applications.     

Perlwapin, an abalone nacre protein with three four-disulfide core (whey acidic protein) domains, inhibits the growth of calcium carbonate crystals

We have isolated a new protein from the nacreous layer of the shell of the sea snail Haliotis laevigata (abalone). Amino acid sequence analysis showed the protein to consist of 134 amino acids and to contain three sequence repeats of approximately 40 amino acids which were very similar to the well-known whey acidic protein domains of other proteins. The new protein was therefore named perlwapin. In addition to the major sequence, we identified several minor variants. Atomic force microscopy was used to explore the interaction of perlwapin with calcite crystals. Monomolecular layers of calcite crystals dissolve very slowly in deionized water and recrystallize in supersaturated calcium carbonate solution. When perlwapin was dissolved in the supersaturated calcium carbonate solution, growth of the crystal was inhibited immediately. Perlwapin molecules bound tightly to distinct step edges, preventing the crystal layers from growing. Using lower concentrations of perlwapin in a saturated calcium carbonate solution, we could distinguish native, active perlwapin molecules from denaturated ones. These observations showed that perlwapin can act as a growth inhibitor for calcium carbonate crystals in saturated calcium carbonate solution. The function of perlwapin in nacre growth may be to inhibit the growth of certain crystallographic planes in the mineral phase of the polymer/mineral composite nacre.     

Pancreatic stone protein, a phosphoprotein which inhibits calcium carbonate precipitation from human pancreatic juice

A soluble protein isolated from human pancreatic stones, and present in pancreatic secretion, strongly inhibits precipitation from supersaturated calcium carbonate solutions. Therefore, we suggest that this new secretory protein may act as an inhibitor of spontaneous calcium carbonate precipitation from supersaturated pancreatic juice.     

Comparison of microbially induced calcium carbonate precipitation eligibility using sporosarcina pasteurii and bacillus licheniformis on two different sands

The use of biological means for ground improvement have become popular, which generally works through the process called microbially-induced calcium carbonate precipitation (MICP). Many studies indicate successful application of MICP based improvement with multiple bacteria and on several soils. Given the proven performance of MICP, this study aims to examine the MICP process by comparing the calcium carbonate precipitation ability of widely studied bacteria, i.e., Sporosarcina pasteurii and relatively under-recognized bacteria, i.e., Bacillus licheniformis to outline the formation success. For this purpose, two different sands were tested for observing precipitation behavior using a series of syringe tests. Furthermore, the effect of concentration and inclusion of calcium chloride for nutrition of bacteria, saturation with water, and hybrid use of two bacteria were investigated in some tests for diversification. X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive x-ray spectroscopy (EDS) were used for the interpretation of results. Results indicated that Sporosarcina pasteurii had performed superior over Bacillus licheniformis when achieving calcium carbonate precipitation in tests for both sands. In addition, many intriguing SEM images contributed to the literature of MICP monitoring, highlighting the effects of the variables investigated.     

Nephrolithiasis and pyelonephritis in two West Indian manatees (Trichechus manatus spp.)

Two West Indian manatees (Trichechus manatus spp.) were reported with severe emaciation. One animal was a Florida manatee from the Everglades; the other was an Antillean manatee from Cuba. On necropsy, both animals had nephrolithiasis, pyelonephritis, and moderate to severe renomegaly. Histopathology revealed multifocal to diffuse pyelonephritis, interstitial nephritis, and nephrocalcinosis. The stones were analyzed and consisted primarily of calcium carbonate. Serum chemistry values for the Florida animal revealed no renal abnormalities. The mechanism of calculus formation remains unclear in manatees. In horses, another hindgut fermenter, the most common urolith is also calcium carbonate. Urinalyses performed on manatees are very similar to those of horses (i.e., alkaline urine, low specific gravity, and calcium carbonate crystals). Formation of uroliths in manatees may have a pathogenesis similar to equine urolithiasis.     

Purification of nonspecific lipid transfer protein (sterol carrier protein 2) from human liver and its deficiency in livers from patients with cerebro-hepato-renal (Zellweger) syndrome

The nonspecific lipid transfer protein (i.e., sterol carrier protein 2) from human liver was purified to homogeneity using ammonium sulfate precipitation, CM-cellulose chromatography, molecular sieve chromatography and fast protein liquid chromatography. Its amino acid composition was determined and found to be very similar to that of the nonspecific lipid transfer protein from bovine and rat liver with, as main feature, the absence of arginine, histidine and tyrosine. By way of a specific enzyme immunoassay using affinity-purified antibodies, the levels of nonspecific lipid transfer protein were determined in human livers. Levels varied from approximately 150 ng nonspecific lipid transfer protein per mg 105,000 X g supernatant protein for juvenile and adult humans to 40 ng per mg supernatant protein for a young infant. Levels of nonspecific lipid transfer protein in livers of infants with cerebro-hepato-renal (Zellweger) syndrome were extremely low (i.e., 2 ng per mg supernatant protein). Immunoblotting revealed the presence of crossreactive proteins of molecular masses of 40,000 and 58,000. The 40 kDa and 58 kDa proteins occurred in control livers, whereas only the 40 kDa protein was present in Zellweger livers. As in rat the 58 kDa protein could be demonstrated in a peroxisomal preparation isolated from an adult liver. A possible link between the occurrence of nonspecific lipid transfer protein and the presence of peroxisomes is discussed.     

Shell repair process in the green ormer Haliotis tuberculata: a histological and microstructural study

In the present paper, juvenile and adult shells of the green ormer Haliotis tuberculata ('Oreille de Saint-Pierre') were perforated in a zone close to the shell edge and the shell repair process was followed at two levels: (1) by observing the histology of the calcifying mantle in the repair zone and (2) by analyzing with SEM the microstructure of the shell repair zone. Histological data clearly show the presence of calcium carbonate granules into the connective tissues, but not in the epithelial cells. This suggests that calcium carbonate granules are synthesized by sub-epithelial cells and actively transported through the epithelium to the repair zone, via a process which may be similar to that described by Mount et al. [Mount, A.S., Wheeler, A.P., Paradkar, R.P., Snider, D., 2004. Hemocyte-mediated shell mineralization in the eastern oyster. Science 304, 297-300]. Furthermore, SEM observations show that the repair zone exhibits different stratified microstructures (spherulitic, thin prismatic, blocklike, sub-nacreous, nacreous, foliated-like), some of which are not continuous (i.e. lenticular) along the repair zone. This suggests a complex secreting regime of the calcifying mantle and an elaborate geometry of the epithelium involved in shell repair.     

Selective medium with nalidixic acid for isolating antibiotic-producing Actinomyces

The majority of actinomycetes belonging to various genera proved to be resistant to nalidixic acid concentrations having an inhibitory effect on bacteria with trailing growth i.e. B. subtilis and B. mycoides. The bacteria prevented isolation of actinomycetes as pure cultures. The use of a selective medium with nalidixic acid for isolation of soil actinomycetes resulted in 20 per cent increase in the number of the actinomycetes isolated as pure cultures. Preliminary treatment of the soil samples with calcium carbonate under moist conditions followed by the inoculation to the medium with nalidixic acid made it possible to increase isolation of actinomycetes at most 100-fold. With this complex method 495 actinomycete cultures were isolated, their antibiotic properties were studied and their taxonomic position at the genus level was determined. The complex method including the preliminary treatment of soil samples with calcium carbonate followed by inoculation to the selective medium with nalidixic acid is efficient and may be recommended for screening organisms producing new antibiotics.     

Inhibition of autophagy by benzyl alcohol

Benzyl alcohol caused a rather complete and selective inhibition of the methylamine sensitive (i.e., the putative lysosomal) pathway of protein degradation in isolated rat hepatocytes. The effect was found to be entirely reversible within 30 min of removing the agent. A morphometric examination of electron micrographs revealed that the inhibition of lysosomal protein degradation coincided with a block in the formation of autophagic vacuoles. The number of acidic vacuoles (i.e., vacuoles induced to swell by adding methylamine) was not drastically reduced.     

Identification of myosin-like proteins included in chromatin

A myosin-like protein was purified 40-fold from rat liver chromatin (as determined by the K+-EDTA-ATPase activity equal to 0.013 and 0.442 M PPi/mg.min for chromatin and purified protein, respectively). Electrophoresis performed under non-denaturating conditions revealed that the overall ATPase activity of the sample is associated with one component whose migration is very similar to that of skeletal muscle myosin. The myosin components isolated from the nuclei and cytoplasm of rat cardiac muscle differ by their electrophoretic mobilities; those from nuclei of different tissues, i.e., liver and heart, have similar mobilities.     

Perlinhibin, a cysteine-, histidine-, and arginine-rich miniprotein from abalone (Haliotis laevigata) nacre, inhibits in vitro calcium carbonate crystallization

We have isolated a 4.785 Da protein from the nacreous layer of the sea snail Haliotis laevigata (greenlip abalone) shell after demineralization with acetic acid. The sequence of 41 amino acids was determined by Edman degradation supported by mass spectrometry. The most abundant amino acids were cysteine (19.5%), histidine (17%), and arginine (14.6%). The positively charged amino acids were almost counterbalanced by negatively charged ones resulting in a calculated isoelectric point of 7.86. Atomic-force microscopy studies of the interaction of the protein with calcite surfaces in supersaturated calcium carbonate solution or calcium chloride solution showed that the protein bound specifically to calcite steps, inhibiting further crystal growth at these sites in carbonate solution and preventing crystal dissolution when carbonate was substituted with chloride. Therefore this protein was named perlinhibin. X-ray diffraction investigation of the crystal after atomic-force microscopy growth experiments showed that the formation of aragonite was induced on the calcite substrate around holes caused by perlinhibin crystal-growth inhibition. The strong interaction of the protein with calcium carbonate was also shown by vapor diffusion crystallization. In the presence of the protein, the crystal surfaces were covered with holes due to protein binding and local inhibition of crystal growth. In addition to perlinhibin, we isolated and sequenced a perlinhibin-related protein, indicating that perlinhibin may be a member of a family of closely related proteins.     

Regulation of Ca2+ influx in myocardial cells by beta adrenergic receptors,cyclic nucleotides,and phosphorylation

Calcium channels in the heart play a major role in cardiac function. These channels are modulated in a variety of ways, including protein phosphorylation. Cyclic AMP-mediated phosphorylation is the best understood phosphorylation mechanism which regulates calcium influx into cardiac cells. Binding of an agonist (e.g., a catecholamine) to the appropriate receptor stimulates production of cyclic AMP by adenylate cyclase. The cyclic AMP may subsequently bind to and activate a cyclic AMP-dependent protein kinase, which then can phosphorylate a number of substrates, including the calcium channel (or a closely-associated regulatory protein). This results in stimulation of the calcium channels, greater calcium influx, and increased contractility. The cyclic AMP system is not the only protein kinase system in the heart. Thus, the possibility exists that other protein kinases may also regulate the calcium channels and, hence, cardiac function. Recent evidence suggests that cyclic GMP-mediated phosphorylation may play a role opposite to cyclic AMP-mediated phosphorylation, i.e., inhibition of the calcium current rather than stimulation. Other recent evidence also suggests that a calcium/calmodulin-dependent protein kinase and calcium/phospholipid-dependent protein kinase (protein kinase C) may also regulate the myocardial calcium channels. Thus, protein phosphorylation may be a general mechanism whereby calcium channels and cardiac function are modulated under a variety of conditions.     

Isolated fibrils rescue cohesion and development in the Dsp mutant of Myxococcus xanthus.

Extracellular fibrils are involved in cell cohesion and cell development in Myxococcus xanthus. One group of social motility mutants, Dsp, is unable to produce extracellular fibrils; these mutants also lose the abilities to cohere and to develop. Extracellular fibrils isolated from vegetative wild-type cells and added to Dsp cells fully restored the abilities of these cells to cohere and to undergo normal morphological development. The fibrils thus mimic the ability of intact, wild-type cells to carry out the same rescue. Optimal cohesion rescue by fibrils required calcium and magnesium ions, did not require protein synthesis, but was energy dependent, i.e., sodium azide and sodium cyanide blocked rescue. Cohesion rescue was also blocked by the diazo dye Congo red. Cohesion rescue is genus specific, i.e., isolated fibrils did not cause the cohesion of Pseudomonas aeruginosa, Bacillus subtilis, Proteus mirabilis, Escherichia coli, or the related myxobacterium Stigmatella aurantiaca. Developmental rescue of Dsp by isolated fibrils included aggregation, fruiting body formation, and myxospore morphogenesis. Developmental gene expression in the Dsp mutant was only partially rescued by the isolated fibrils.     

Phosphorylation of P0 Glycoprotein in Peripheral Nerve Myelin

The P0 protein in mammalian PNS myelin is known to undergo several posttranslational modifications, such as glycosylation, acylation, sulfation, and phosphorylation. Phosphorylation of purified P0 protein in vitro was studied comparatively using three enzymes, i.e., calcium/phospholipid-dependent protein kinase (protein kinase C), calcium/calmodulin-dependent protein kinase II (CaM kinase II), and the catalytic subunit of cyclic AMP-dependent protein kinase (A kinase). The phosphorylation of P0 protein by CaM kinase II was the greatest, followed by that by protein kinase C; phosphorylation by A kinase, however, was much lower. In order to identify phosphorylation sites, P0 protein was phosphorylated with [32P]ATP and each kinase and then digested with lysylendopeptidase. The resulting phosphopeptides were isolated by HPLC. Subsequent amino acid sequence analysis and comparison with the known sequence of P0 protein revealed that Ser181 and Ser204 were strongly phosphorylated by both protein kinase C and CaM kinase II. In addition, Ser214 was also phosphorylated by protein kinase C, but not by CaM kinase II. Because all of these sites are located in the cytoplasmic domain of P0 protein, phosphorylation may be important for maintenance of the major dense line of PNS myelin.     

Morphine and anandamide stimulate intracellular calcium transients in human arterial endothelial cells: coupling to nitric oxide release.

Both morphine and anandamide significantly stimulated cultured endothelial intracellular calcium level increases in a concentration-dependent manner in cells pre-loaded with fura 2/AM. Morphine is more potent than anandamide (approximately 275 vs. 135 nM [Ca]i), and the [Ca]i for both ligands was blocked by prior exposure of the cells to their respective receptor antagonist, i.e., naloxone and SR 171416A. Various opioid peptides did not exhibit this ability, indicating a morphine-mu3-mediated process. In comparing the sequence of events concerning morphine's and anandamide's action in stimulating both [Ca]i and nitric oxide production in endothelial cells, we found that the first event precedes the second by 40+/-8 sec. The opiate and cannabinoid stimulation of [Ca]i was attenuated in cells leeched of calcium, strongly suggesting that intracellular calcium levels regulate cNOS activity.     

Phospholipid fatty acyl chain asymmetry in the membrane bilayer of isolated skeletal muscle sarcoplasmic reticulum

We previously showed [Herbette, L. G., Blasie, J. K., DeFoor, P., Fleischer, S., Bick, R. J., Van Winkle, W. B., Tate, C. A., & Entman, M. L. (1984) Arch. Biochem. Biophys. 234, 235-242; Herbette, L. G., DeFoor, P., Fleischer, S., Pascolini, D., Scarpa, A., & Blasie, J. K. (1985) Biochim. Biophys. Acta 817, 103-122] that the phospholipid head-group distribution in the membrane bilayer of isolated sarcoplasmic reticulum is asymmetric. From these studies, both the total number of phospholipid head groups and the total lipid, as well as the head-group species for these lipids, were found to be different for each monolayer of the membrane bilayer. In this paper, we demonstrate for the first time that there is significant asymmetry in the distribution of unsaturated fatty acids between the two monolayers; i.e., the outer monolayer of the sarcoplasmic reticulum contained more unsaturated and polyunsaturated chains when compared to the inner monolayer. X-ray diffraction measurements demonstrated that the time-averaged fatty acyl chain extension for the outer monolayer was approximately 20% less than for the inner monolayer. This is consistent with the concept that the greater degree of unsaturation in the outer monolayer may provide for a decreased average fatty acyl chain extension for that layer. This architecture for the bilayer may be related to both the "resting" state mass distribution of the calcium pump protein within the membrane bilayer and possible "conformational" states of the calcium pump protein during calcium transport by the sarcoplasmic reticulum.     

Environmental Factors Affecting the Compressive Strength of Microbiologically Induced Calcite Precipitation-Treated Soil

Some microorganisms such as Sporoscarcina pasteurii precipitate calcium carbonate and are suitable for biocementation. This study aimed to investigate the effects of several factors including concentration of bacteria, chemical reactants, temperature, and pH on precipitation of calcium carbonate. The results showed that after 7 and 14 days of curing, the compressive strength of silty clay soil samples increased steadily as pH increased from 5 to 9. It was observed that pH plays an important role in biocementation. The highest compressive strength (i.e. 92 kPa) was observed when the soil was treated with 50 ml of bacterial solution after 14 days of curing. In addition, it was observed that the highest compressive strength of samples was achieved when the temperature was 40°C.     

Quantitative ichnology of modern pelagic deposits in the abyssal Atlantic

Quantitative sedimentologic aspects of bioturbation were investigated in a series of deep-sea box cores, which were collected over a broad latitudinal range (35°N to 30°S) and bathymetric range (1.4 to 5.7 km) in the central Atlantic Ocean. All cores were thoroughly bioturbated, and numerous generations of burrowing could be discerned in many instances. Preservation of individually distinct burrows ranged from poor to excellent, and eight ichnogenera plus several unnamed biogenic structures were recognized.The distribution of calcium carbonate, organic carbon, selected species of planktic foraminifera and sediment grain size were examined in several cores. These measurements indicated that the surficial Mixed Layer, which ranged from 3 to 10 cm thick, was statistically more homogeneous than the underlying Transition Layer. This relationship is seen most clearly with respect to lateral and vertical variations in the calcium carbonate content of the cores. Bioturbation of abyssal pelagic deposits appears to be a two-phase process consisting of (a) homogenization of the upper few centimeters (i.e., the Mixed Layer) by shallow-burrowing meiofauna, and (b) heterogeneous mixing of the underlying strata (i.e., the Transition Layer) by relatively deep burrowers. The heterogeneously mixed Transition Layer becomes the preserved trace fossil record; under normal circumstances the homogenized Mixed Layer is not preserved.     

Effect of magnesium on the contractile behavior of actomyosin aggregates isolated from Physarum plasmodia

The dependence on calcium concentration of the contractile behavior of actomyosin isolated from Physarum plasmodia according to Kohama & Kendrick-Jones (1986) was investigated under different magnesium conditions. The inhibitory calcium sensitivity is reduced at magnesium concentrations above or below 1 mM, i.e., contraction of actomyosin aggregates is most effectively inhibited in the presence of 1 mM calcium in combination with physiological magnesium concentrations. In the absence of calcium reactivation optimum is obtained at 8.5 mM Mg2+.     

Mechanism of inhibition of polypeptide chain initiation in calcium- depleted Ehrlich ascites tumor cells

Protein synthesis in Ehrlich ascites tumor cells is inhibited when cellular calcium is depleted by the addition of EGTA to the growth medium. This inhibition is at the level of polypeptide chain initiation as evidenced by a disaggregation of polyribosomes accompanied by a significant elevation in 80-S monomers. To identify direct effects of calcium on the protein synthesis apparatus we have developed a calcium-dependent, cell-free protein-synthesizing system from the Ehrlich cells by using 1,2-bis(O-aminophenoxy)-ethane-N,N,N',N'-tetraacetic acid (BAPTA), a recently developed chelator with a high (greater than 10(5)) selectivity for calcium (pKa = 6.97) over magnesium (pKa = 1.77). BAPTA inhibits protein synthesis by 70% at 1 mM and 90% at 2 mM. This effect was reversed by calcium but not by other cations tested. The levels of 43-S complexes (i.e., 40-S subunits containing bound methionyl-tRNAf.eIF-2.GTP) were significantly lower in the calcium-deprived incubations, indicating either inhibition of the rate of formation or decreased stability of 43-S complexes. Analysis of 43-S complexes on CsCl gradients showed that in BAPTA-treated lysates, 40-S subunits containing eIF-3, completely disappeared and the residual methionyl-tRNA-containing complexes were bound to 40-S subunits lacking eIF-3. Our results demonstrate a direct involvement of Ca2+ in protein synthesis and we have localized the effect of calcium deprivation to decreased binding of eIF-2 and eIF-3 to 40-S subunits.