SciCombinator

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Concept: Phosphate

189

We provide evidence that citrate anions bridge between mineral platelets in bone and hypothesize that their presence acts to maintain separate platelets with disordered regions between them rather than gradual transformations into larger, more ordered blocks of mineral. To assess this hypothesis, we take as a model for a citrate bridging between layers of calcium phosphate mineral a double salt octacalcium phosphate citrate (OCP-citrate). We use a combination of multinuclear solid-state NMR spectroscopy, powder X-ray diffraction, and first principles electronic structure calculations to propose a quantitative structure for this material, in which citrate anions reside in a hydrated layer, bridging between apatitic layers. To assess the relevance of such a structure in native bone mineral, we present for the first time, to our knowledge, (17)O NMR data on bone and compare them with (17)O NMR data for OCP-citrate and other calcium phosphate minerals relevant to bone. The proposed structural model that we deduce from this work for bone mineral is a layered structure with thin apatitic platelets sandwiched between OCP-citrate-like hydrated layers. Such a structure can explain a number of known structural features of bone mineral: the thin, plate-like morphology of mature bone mineral crystals, the presence of significant quantities of strongly bound water molecules, and the relatively high concentration of hydrogen phosphate as well as the maintenance of a disordered region between mineral platelets.

Concepts: DNA, Scientific method, Bone, Apatite, Water, Phosphate, Phosphorus, Salt

168

BACKGROUND: Signal transduction plays a fundamental role in the understanding of cellular physiology. The bacterialphosphotransferase system (PTS) together with the PEP/pyruvate node in central metabolism represents asignaling unit that acts as a sensory element and measures the activity of the central metabolism.Pseudomonas putida possesses two PTS branches, the C-branch (PTSFru) and a second branch (PTSNtr),which communicate with each other by phosphate exchange. Recent experimental results showed a cross talkbetween the two branches. However, the functional role of the crosstalk remains open. RESULTS: A mathematical model was set up to describe the available data of the state of phosphorylation of PtsN, one ofthe PTS proteins, for different environmental conditions and different strain variants. Additionally, data fromflux balance analysis was used to determine some of the kinetic parameters of the involved reactions. Based onthe calculated and estimated parameters, the flux distribution during growth of the wild type strain on fructosecould be determined. CONCLUSION: Our calculations show that during growth of the wild type strain on the PTS substrate fructose, the major partof the phosphoryl groups is provided by the second branch of the PTS. This theoretical finding indicates a newrole of the second branch of the PTS and will serve as a basis for further experimental studies.

Concepts: Signal transduction, Adenosine triphosphate, Enzyme, Mathematics, Phosphate, Cell signaling, Phosphorylation, Pseudomonas putida

168

In the present case of postoperative lumbar spinal stenosis after non-instrumented intertransverse fusion with granules of hydroxyapatite (HA), bone union was not completed and the patient felt the recurrence of his symptoms within two years. We performed re-decompression with fusion, and in hematoxylin and eosin staining of HA granulation harvested during revision surgery, fibrous tissue with hyaline degeneration surrounded the cavity where the HA had existed. Multinuclear giant cells and lymphocytes infiltrated some parts of the marginal layer of the cavity, and no obvious bony bridge had regenerated from autologous bone. No tartrate-resistant acid phosphate (TRAP) -positive osteoclasts could be seen in the new bone, suggesting that the activity of osteoclasts in the new bone decreased during the seven years after the primary surgery.Virtual slidesThe virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/3483360258050263.

Concepts: Present, Bone, Medical terms, Histology, Phosphate, Spinal stenosis

55

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.

Concepts: DNA, Polymerase chain reaction, Metabolism, Adenosine triphosphate, RNA, Phosphate, Nucleic acid, Nucleotide

44

We describe a novel single molecule nanopore-based sequencing by synthesis (Nano-SBS) strategy that can accurately distinguish four bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides. The basic principle is as follows. As each nucleotide is incorporated into the growing DNA strand during the polymerase reaction, its tag is released and enters a nanopore in release order. This produces a unique ionic current blockade signature due to the tag’s distinct chemical structure, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof of principle, we attached four different length PEG-coumarin tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate. We demonstrate efficient, accurate incorporation of the nucleotide analogs during the polymerase reaction, and excellent discrimination among the four tags based on nanopore ionic currents. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

Concepts: DNA, Gene, Genetics, Adenosine triphosphate, RNA, Base pair, Phosphate, Nucleotide

32

High crop yields depend on the continuous input of orthophosphate (PO(4)(−3))-based fertilizers and herbicides. Two major challenges for agriculture are that phosphorus is a nonrenewable resource and that weeds have developed broad herbicide resistance. One strategy to overcome both problems is to engineer plants to outcompete weeds and microorganisms for limiting resources, thereby reducing the requirement for both fertilizers and herbicides. Plants and most microorganisms are unable to metabolize phosphite (PO(3)(−3)), so we developed a dual fertilization and weed control system by generating transgenic plants that can use phosphite as a sole phosphorus source. Under greenhouse conditions, these transgenic plants require 30–50% less phosphorus input when fertilized with phosphite to achieve similar productivity to that obtained by the same plants using orthophosphate fertilizer and, when in competition with weeds, accumulate 2–10 times greater biomass than when fertilized with orthophosphate.

Concepts: Photosynthesis, Ammonia, Fertilizer, Phosphate, Nitrogen, Phosphorus, Weed, Glyphosate

31

It has been hypothesized that before the emergence of modern DNA-RNA-protein life, biology evolved from an “RNA world.” However, synthesizing RNA and other organophosphates under plausible early Earth conditions has proved difficult, with the incorporation of phosphorus (P) causing a particular problem because phosphate, where most environmental P resides, is relatively insoluble and unreactive. Recently, it has been proposed that during the Hadean-Archean heavy bombardment by extraterrestrial impactors, meteorites would have provided reactive P in the form of the iron-nickel phosphide mineral schreibersite. This reacts in water, releasing soluble and reactive reduced P species, such as phosphite, that could then be readily incorporated into prebiotic molecules. Here, we report the occurrence of phosphite in early Archean marine carbonates at levels indicating that this was an abundant dissolved species in the ocean before 3.5 Ga. Additionally, we show that schreibersite readily reacts with an aqueous solution of glycerol to generate phosphite and the membrane biomolecule glycerol-phosphate under mild thermal conditions, with this synthesis using a mineral source of P. Phosphite derived from schreibersite was, hence, a plausible reagent in the prebiotic synthesis of phosphorylated biomolecules and was also present on the early Earth in quantities large enough to have affected the redox state of P in the ocean. Phosphorylated biomolecules like RNA may, thus, have first formed from the reaction of reduced P species with the prebiotic organic milieu on the early Earth.

Concepts: DNA, Molecular biology, Organism, Life, Chemistry, Phosphate, Solubility, Phosphorus

29

Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiamine-dependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.

Concepts: Metabolism, Adenosine triphosphate, Enzyme, Vitamin, Phosphate, Cofactor, Thiamine, Thiamine pyrophosphate

28

Although case reports link proton-pump inhibitor (PPI) use and hypomagnesemia, no large-scale studies have been conducted. Here we examined the serum magnesium concentration and the likelihood of hypomagnesemia (<1.6 mg/dl) with a history of PPI or histamine-2 receptor antagonist used to reduce gastric acid, or use of neither among 11,490 consecutive adult admissions to an intensive care unit of a tertiary medical center. Of these, 2632 patients reported PPI use prior to admission, while 657 patients were using a histamine-2 receptor antagonist. PPI use was associated with 0.012 mg/dl lower adjusted serum magnesium concentration compared to users of no acid-suppressive medications, but this effect was restricted to those patients taking diuretics. Among the 3286 patients concurrently on diuretics, PPI use was associated with a significant increase of hypomagnesemia (odds ratio 1.54) and 0.028 mg/dl lower serum magnesium concentration. Among those not using diuretics, PPI use was not associated with serum magnesium levels. Histamine-2 receptor antagonist use was not significantly associated with magnesium concentration without or with diuretic use. The use of PPI was not associated with serum phosphate concentration regardless of diuretic use. Thus, we verify case reports of the association between PPI use and hypomagnesemia in those concurrently taking diuretics. Hence, serum magnesium concentrations should be followed in susceptible individuals on chronic PPI therapy.Kidney International advance online publication, 16 January 2013; doi:10.1038/ki.2012.452.

Concepts: Receptor, Phosphate, Receptor antagonist, Diuretic, Hypomagnesemia

28

Waste streams offer a compelling opportunity to recover phosphorus (P). 15-20% of world demand for phosphate rock could theoretically be satisfied by recovering phosphorus from domestic waste streams alone. For very dilute streams (<10mgPL(-1)), including domestic wastewater, it is necessary to concentrate phosphorus in order to make recovery and reuse feasible. This review discusses enhanced biological phosphorus removal (EBPR) as a key technology to achieve this. EBPR relies on polyphosphate accumulating organisms (PAOs) to take up phosphorus from waste streams, so concentrating phosphorus in biomass. The P-rich biosolids can be either directly applied to land, or solubilized and phosphorus recovered as a mineral product. Direct application is effective, but the product is bulky and carries contaminant risks that need to be managed. Phosphorus release can be achieved using either thermochemical or biochemical methods, while recovery is generally by precipitation as struvite. We conclude that while EBPR technology is mature, the subsequent phosphorus release and recovery technologies need additional development.

Concepts: DNA, Biology, Organism, Water, Phosphate, Phosphorus, Enhanced biological phosphorus removal, Recovery