Two-dimensional growth of a root system modelled as a diffusion process. I. Analytical solutions

For functioning of a root system, the temporal development of distribution of roots in the soil is important. For example, for computing uptake of water and nutrients the root length density distribution might be required. A way to describe root proliferation is to consider it as a diffusion process with a first-order sink term accounting for decay. In this paper, analytical solutions are derived for two-dimensional diffusion of roots both in a rectangular area, and in a cylindrical volume. The source of root dry matter is located at the surface. Root dry matter enters the soil domain through a part of the soil surface. It is shown that different distribution patterns are obtained, with different ratios of the diffusion coefficients in horizontal and vertical direction. From the solutions obtained it can be shown that for the situation where the dry matter enters through the complete surface eventually a steady-state occurs where root length density decreases exponentially with depth, as often is found in experiments.     

Neuronal polarity: demarcation, growth and commitment

In a biological sense, polarity refers to the extremity of the main axis of an organelle, cell, or organism. In neurons, morphological polarity begins with the appearance of the first neurite from the cell body. In multipolar neurons, a second phase of polarization occurs when a single neurite initiates a phase of rapid growth to become the neuron's axon, while the others later differentiate as dendrites. Finally, during a third phase, axons and dendrites develop an elaborate architecture, acquiring special morphological and molecular features that commit them to their final identities. Mechanistically, each phase must be preceded by spatial restriction of growth activity. We will review recent work on the mechanisms underlying the polarized growth of neurons.     

Type I collagen fibrillogenesis: initiation via reversible linear and lateral growth steps

Type I collagen fibrillogenesis in vitro has been studied by laser light scattering, and the results indicate that initiation of aggregation involves at least two steps. Step I of aggregation involves no change in the intensity of scattered light at an angle of 90° and is accompanied by a decrease in the diffusion coefficient. Step II is characterized by an increased intensity of scattered light and decreased diffusion coefficients. Theoretical calculations using the Stokes-Einstein equation for the translational diffusion coefficient and the Perrin equation for the frictional coefficient of a prolate ellipsoid indicate that the step I aggregates are 4D staggered linear dimers and trimers 570 and 845 nm long, whereas step II aggregates are greater than 950 nm in length. These dimensions are similar to those previously reported based on physicochemical measurements and electron microscopy. It is proposed that the rate and extent of fibrillogenesis in vitro is controlled by the concentration of the linear aggregates and that the effects of temperature and collagen concentration on fibrillogenesis previously observed are qualitatively explained in terms of their effects on the concentration of these aggregates.     

Treatment of saline municipal wastewater using hybrid growth system

Background

In this study, a hybrid treatment system (Fluidized Bed positioned in a biological reactor of an Activated Sludge process) was used to treat saline domestic wastewater. The performance of the mentioned hybrid system was compared with the conventional activated sludge. A pilot study was conducted, and Chemical Oxygen Demand (COD), Electrical Conductivity (EC), Total Dissolved Solids (TDS) and pH were measured to investigate treatment efficiency. Three saline wastewater samples with salt concentrations of 0.5, 1, and 1.5 % and detention times of 2, 4 and 6 h were loaded into both rectors of hybrid system and activated sludge.

Results

The results showed that Chemical Oxygen Demand (COD) removals at salt concentrations of 0.5, 1, 1.5 % were equal to 80, 71, 48.5 for the hybrid system and 62, 47.7, 26.5 for the activated sludge system respectively. Likewise, similar results obtained for other contamination indices indicating the superiority of the hybrid system in comparison to activated sludge system. Moreover, another advantage of the hybrid system was that the activated sludge needed sludge returning while sludge returning was not required in the hybrid system. In addition, by loading fixed rate of air into both systems, dissolved oxygen concentration in the hybrid reactor is higher than the conventional reactor.

Conclusions

Therefore, the hybrid system had a significantly higher efficiency than conventional reactor to treat saline domestic wastewater.

     

FastStor: improving the performance of a large scale hybrid storage system via caching and prefetching

Storing enormous amount of data on hybrid storage systems has become a widely accepted solution for today’s production level applications in order to trade off the performance and cost. However, how to improve the performance of large scale storage systems with hybrid components (e.g. solid state disks, hard drives and tapes) and complicated user behaviors is not fully explored. In this paper, we conduct an in-depth case study (we call it FastStor) on designing a high performance hybrid storage system to support one of the world’s largest satellite images distribution systems operated by the U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) center. We demonstrate how to combine conventional caching policies with innovative current popularity oriented and user-specific prefetching algorithms to improve the performance of the EROS system. We evaluate the effectiveness of our proposed solution using over 5 million real world user download requests provided by EROS. Our experimental results show that using the Least Recently Used (LRU) caching policy alone, we are able to achieve an overall 64 % or 70 % hit ratio on a 100 TB or 200 TB FTP server farm composed of Solid State Disks (SSDs) respectively. The hit ratio can be further improved to 70 % (for 100 TB SSDs) and 76 % (for 200 TB SSDs) if intelligent prefetching algorithms are used together with LRU.     

Neuronal compartments and axonal transport of synapsin I

Studies on the transport kinetics and the posttranslational modification of synapsin I in mouse retinal ganglion cells were performed to obtain an insight into the possible factors involved in forming the structural and functional differences between the axon and its terminals. Synapsin I, a neuronal phosphoprotein associated with small synaptic vesicles and cytoskeletal elements at the presynaptic terminals, is thought to be involved in modulating neurotransmitter release. The state of phosphorylation of synapsin I in vitro regulates its interaction with both synaptic vesicles and cytoskeletal components, including microtubules and microfilaments. Here we present the first evidence that in the mouse retinal ganglion cells most synapsin I is transported down the axon, together with the cytomatrix proteins, at the same rate as the slow component b of axonal transport, and is phosphorylated at both the head and tail regions. In addition, our data suggest that, after synapsin I has reached the nerve endings, the relative proportions of variously phosphorylated synapsin I molecules change, and that these changes lead to a decrease in the overall content of phosphorus. These results are consistent with the hypothesis that, in vivo, the phosphorylation of synapsin I along the axon prevents the formation of a dense network that could impair organelle movement. On the other hand, the dephosphorylation of synapsin I at the nerve endings may regulate the clustering of small synaptic vesicles and modulate neurotransmitter release by controlling the availability of small synaptic vesicles for exocytosis.     

Peptide crystal growth via vapor diffusion. Crystal structure of glycyl-L-tyrosyl-L-alanine dihydrate.

The structure of a dihydrated form of glycyl-L-tyrosyl-L-alanine (GYA) has been determined as part of a series of peptide structural investigations and development of microscale vapor diffusion experiments for peptide crystal growth. Crystals were grown by the hanging-drop method against sodium acetate. The tripeptide is a zwitterion in the crystal, adopting an extended conformation through glycine, a nearly perpendicular bend at tyrosine and a reverse turn for the C-terminal carboxylate. Principal backbone torsion angles are psi 1 175(1) degrees, omega 2 173(1) degrees, phi 2 -119(1) degrees, psi 2 120(1) degrees, omega 3 172(1) degrees, phi 3 -73(1) degrees, psi 31 -9(1) degrees, psi 32 171(1) degrees. The tyrosyl side chain adopts an unusual orientation (chi 1/2 = -86(1) degrees). The relationship of the GYA.2H2O structure to GYA sequences in proteins is examined, particularly as regards its helix-forming potential. Crystal data: C14H19N3O4.2H2O, M(r) = 345.36, orthorhombic, P2(1)2(1)2(1), a = 4.810 (4), b = 11.400(7), c = 30.162(23)A, V = 1653.8(24)A-3, Z = 4, Dx = 1.387 Mgm-3, lambda(CuK- alpha) = 1.540 A, mu = 9.053 mm-1, F(000) = 736, T = 199 K, R = 0.041 for 1458 observations with I greater than or equal to 3 sigma(I).     

Insulin-like growth factor I receptor beta-subunit heterogeneity. Evidence for hybrid tetramers composed of insulin-like growth factor I and insulin receptor heterodimers

In both NIH3T3 cells and HepG2 cells, insulin-like growth factor I (IGF-I) receptors possess two beta-subunits that display different electrophoretic mobilities. Increasing concentrations of IGF-I stimulated the phosphorylation of both beta-subunits to a similar extent, whereas insulin stimulated the phosphorylation of both subunits only at elevated concentrations. Both beta-subunits were immunoprecipitated with p5, an insulin receptor-specific anti-peptide antibody, or with A410, a polyclonal anti-insulin receptor antisera. However, if the tetrameric IGF-I receptor was first dissociated into alpha-beta heterodimers with 1 mM dithiothreitol, only the lower molecular weight beta-subunit was immunoprecipitated. These results suggested that p5 and A410 specifically recognized the lower molecular weight beta-subunit but immunoprecipitated the higher molecular weight beta-subunit because it was present in the same disulfide linked tetramer. Similarly, alpha-IR-3, an antibody specific for the alpha-subunit of the IGF-I receptor, immunoprecipitated both types of beta-subunit from the intact tetramer but only the higher molecular weight beta-subunit from the dissociated heterodimers, suggesting that there are two types of alpha-subunits in the same tetramer and that the alpha-subunit recognized by alpha-IR-3 is only associated with the higher molecular weight beta-subunit. Tryptic phosphopeptide maps of the lower molecular weight beta-subunit of IGF-I receptor were different from the higher molecular weight beta-subunit, but were similar to those of the insulin receptor beta-subunit. Thus, by immunochemical cross-reactivity and structural criteria, the lower molecular weight beta-subunit of the IGF-I receptor was similar to the beta-subunit of insulin receptor. These data suggest that there exists a species of IGF-I receptor that is a hybrid composed of an insulin receptor alpha-beta heterodimer and an IGF-I receptor alpha-beta heterodimer. The existence of such a hybrid receptor could have important functional consequences.     

Neuronal regulation of otolith growth and kinetotic behaviour

Inner ear stones (otoliths) of larval cichlid fish were labelled with the calcium-tracer alizarin-complexone (AC) before animals were subjected to hypergravity (hg; 3 g). After the experiment, the otoliths' area between the two AC-labellings was measured. Growth of hg-otoliths was significantly slowed down as compared to 1 g-control specimens. In the course of a second experiment, the vestibular nerve was unilaterally transacted in neonate swordtail fish which were subsequently incubated in AC. Incorporation of AC was considerably lower in the otoliths of the transacted side. The results strongly suggest that otolith growth is continuously regulated in dependence of the environmental gravity vector. Since the otolithic calcium incorporation ceased on the transected head sides, it is concluded that the regulation of otolith growth is based on the central nervous efferent vestibular system.     

Mirtazapine inhibits tumor growth via immune response and serotonergic system

To study the tumor inhibition effect of mirtazapine, a drug for patients with depression, CT26/luc colon carcinoma-bearing animal model was used. BALB/c mice were randomly divided into six groups: two groups without tumors, i.e. wild-type (no drug) and drug (mirtazapine), and four groups with tumors, i.e. never (no drug), always (pre-drug, i.e. drug treatment before tumor inoculation and throughout the experiment), concurrent (simultaneously tumor inoculation and drug treatment throughout the experiment), and after (post-drug, i.e. drug treatment after tumor inoculation and throughout the experiment). The "psychiatric" conditions of mice were observed from the immobility time with tail suspension and spontaneous motor activity post tumor inoculation. Significant increase of serum interleukin-12 (sIL-12) and the inhibition of tumor growth were found in mirtazapine-treated mice (always, concurrent, and after) as compared with that of never. In addition, interferon-γ level and immunocompetent infiltrating CD4+/CD8+ T cells in the tumors of mirtazapine-treated, tumor-bearing mice were significantly higher as compared with that of never. Tumor necrosis factor-α (TNF-α) expressions, on the contrary, are decreased in the mirtazapine-treated, tumor-bearing mice as compared with that of never. Ex vivo autoradiography with [(123)I]ADAM, a radiopharmaceutical for serotonin transporter, also confirms the similar results. Notably, better survival rates and intervals were also found in mirtazapine-treated mice. These findings, however, were not observed in the immunodeficient mice. Our results suggest that tumor growth inhibition by mirtazapine in CT26/luc colon carcinoma-bearing mice may be due to the alteration of the tumor microenvironment, which involves the activation of the immune response and the recovery of serotonin level.     

Controlling plant growth via the gibberellin biosynthesis system – I. Growth parameter alterations in apple seedlings

'York Imperial' apple seedlings ( Malus domestica Borkh.) were continuously supplied via the roots with paclobutrazol [(2RS, 3RS)-1-(4-chlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pentan-3-ol)], a triazole GA biosynthesis inhibitor, at 0.68 μ M in a nutrient solution. In comparison to controls, seedlings treated with paclobutrazol for 66 days showed a 91% reduction in shoot length, a 66% reduction in leaf area but only a 17% reduction in leaf number. This effect could be reversed by GA₃ applied to the foliage at 71.4 μ M 0, 19 or 35 days after paclobutrazol was initially supplied and leaf area values for paclobutrazol-treated seedlings given both treatments did not differ significantly from controls. Plots of growth data indicate linearity of shoot longitudinal growth of GA₃-treated seedlings. Leaf area increase was non-linear after GA₃ treatment up to approximately 30 days, when the rate dropped. On a per shoot basis, leaf weight closely followed leaf area but on a per unit area basis, paclobutrazol-treated leaves were heavier than controls; GA₃ applications temporarily reversed this trend.     

Molecular genetics of growth and development in Populus. I. Triploidy in hybrid poplars

Summary While constructing a genetic linkage map of a hybrid poplar genome (Populus trichocarpa x P. deltoides), we identified several restriction fragment length polymorphismus (RFLPs) for which the parental trees are heterozygous. Although 8 of the 11 F₁ hybrid offspring inherited, as expected, single RFLP alleles from each parent, 3 F₁ trees in the mapping pedigree inherited both maternal alleles along with a single paternal allele at some loci. Aneuploidy or polyploidy in these 3 F₁ trees due to partial or complete nondisj unction during female gametogenesis is the simplest explanation for this finding. Of the 3 f₁ offspring with supernumerary RFLP alleles 2 have triploid nuclear DNA contents as measured by fluorescence flow cytometry; the 3rd F₁ with supernumerary alleles has a sub-triploid nuclear DNA content and is probably aneuploid. Among the tri/aneuploid hybrids, leaf quantitative traits either are skewed toward those values characteristic of the P. trichocarpa female parent (adaxial stomate density, petiole length: blade length ratio; abaxial color) or show transgressive variation (epidermal cell size). Abaxial leaf color was used to screen a large population of P. trichocarpa x P. deltoides hybrids for further evidence of tri/aneuploidy. In each case where a white abaxial leaf surface was observed and the nuclear DNA content measured, the hybrid proved to be tri/aneuploid. All sexually mature female triploids examined were sterile, although the inflorescences completed their development in the absence of embryo formation. The (probably) aneuploid F₁ hybrid is a fertile female. Of 15 female P. trichocarpa parents used in crosses to P. deltoides, 10 produced one or more tri/aneuploid hybrid offspring. In an intraspecific cross using a P. trichocarpa female that had produced triploid hybrids with five different P. deltoides males, no tri/aneuploid offpsring were found.     

Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery

Background  

Expert knowledge in journal articles is an important source of data for reconstructing biological pathways and creating new hypotheses. An important need for medical research is to integrate this data with high throughput sources to build useful models that span several scales. Researchers traditionally use mental models of pathways to integrate information and development new hypotheses. Unfortunately, the amount of information is often overwhelming and these are inadequate for predicting the dynamic response of complex pathways. Hierarchical computational models that allow exploration of semi-quantitative dynamics are useful systems biology tools for theoreticians, experimentalists and clinicians and may provide a means for cross-communication.     

Interactions between growth factor receptors and adhesion molecules: breaking the rules

Adhesion molecules, although catalytically inactive, are able to translate environmental cues into complex intracellular signals. They can do this by associating with tyrosine kinase receptors for growth factors, which can prime, integrate or feedback adhesion-based signals. Recent results show that reciprocal crosstalk between the two systems is only one facet of such a collaboration, and that unconventional and alternative hierarchies can be established in which, on the one hand, cell adhesion can trigger ligand-independent activation of growth factor receptors, and, on the other, growth factors can induce adhesion molecules to propagate adhesion-independent signals.     

Collagen type I and hyaluronic acid based hybrid scaffolds for heart valve tissue engineering

Tissue engineers have achieved limited success so far in designing an ideal scaffold for aortic valve; scaffolds lack in mechanical compatibility, appropriate degradation rate, and microstructural similarity. This paper, therefore, has demonstrated a carbodiimide-based sequential crosslinking technique to prepare aortic valve extracellular matrix mimicking (ECM) hybrid scaffolds from collagen type I and hyaluronic acid (HA), the building blocks of heart valve ECM, with tailorable crosslinking densities. Swelling studies revealed that crosslinking densities of parent networks increased with increasing the concentration of the crosslinking agents whereas crosslinking densities of hybrid scaffolds averaged from those of parent collagen and HA networks. Hybrid scaffolds also offered a wide range of pore size (66-126 μm) which fulfilled the criteria for valvular tissue regeneration. Scanning electron microscopy and images of Alcian blue-Periodic acid Schiff stained samples suggested that our crosslinking technique yielded an ECM mimicking microstructure with interlaced bands of collagen and HA in the hybrid scaffolds. The mutually reinforcing networks of collagen and HA also resulted in increased bending moduli up to 1660 kPa which spanned the range of natural aortic valves. Cardio sphere-derived cells (CDCs) from rat hearts showed that crosslinking density affected the available cell attachment sites on the surface of the scaffold. Increased bending moduli of CDCs seeded scaffolds up to two folds (2-6 kPa) as compared to the non-seeded scaffolds (1 kPa) suggested that an increase in crosslinking density of the scaffolds could not only increase the in vitro bending modulus but also prevented its disintegration in the cell culture medium.     

Reconstitution of fibroblast growth factor receptor interactions in the yeast two hybrid system

Fibroblast growth factors (FGF) activate their receptors through the formation of trimolecular complexes, composed of a ligand, a receptor, and a heparan sulfate oligosaccharide, all of which are members of particularly large families capable of multiple interactions in a combinatorial fashion. Understanding this large network of interactions not only presents a great challenge, but is practically beyond the capacity of most classical techniques routinely used to study ligand receptor interactions. We have used the yeast two hybrid system to study protein-protein interaction in the FGF family. Both ligand and receptor ectodomains are properly folded and functional in the yeast. Basic FGF (bFGF) expressed in the yeast dimerizes spontaneously. This self-assembly occurs at low affinity, which can be greatly enhanced by the introduction of heparin, supporting a defined role for heparin in bFGF dimerization. Screening a rat embryo cDNA library with bFGF in the yeast two hybrid system identified a short variant of FGF receptor 1, found most frequently in embryonal and tumor cells and which possesses affinity toward bFGF that is significantly greater than that of the more abundant, full-length receptor. We find the yeast two hybrid system, a most suitable alternative method for the analysis of growth factor-receptor interactions as well as for screening for novel interacting proteins and modulators of FGF and its receptors.     

An insulin-like growth factor I/insulin hybrid exhibiting high potency for interaction with the type I insulin-like growth factor and insulin receptors of placental plasma membranes

We have prepared by semisynthetic methods a two-chain insulin/insulin-like growth factor I hybrid that contains a synthetic peptide related to residues 22-41 of insulin-like growth factor I linked via peptide bond to ArgB22 of des-octapeptide-(B23-B30)-insulin and have applied the analog to the analysis of ligand interactions with the type I insulin-like growth factor and insulin receptors of placental plasma membranes. Relative potencies for the inhibition of 125I-labeled insulin-like growth factor I binding to type I insulin-like growth factor receptors were 1.0:0.20:0.003 for insulin-like growth factor I, the hybrid analog, and insulin, respectively. Corresponding relative potencies for the inhibition of 125I-labeled insulin binding to insulin receptors were 0.007:0.28:1 for the three respective peptides. Additional studies identified that the hybrid analog interacts with only one of two populations of insulin-like growth factor I binding sites on placental plasma membranes and permitted the analysis of insulin-like growth factor I interactions with the separate populations of binding sites. We conclude that (a) des-octapeptide-(B23-B30)-insulin can serve well as a scaffold to support structural elements of insulin-like growth factor I and insulin necessary for high affinity binding to their receptors, (b) major aspects of structure relevant to the conferral of receptor binding affinity lie in the COOH-terminal region of the insulin B chain and in the COOH-terminal region of the insulin-like growth factor I B domain and in its C domain, and (c) the evolution of ligand-receptor specificity in these systems has relied as much on restricting interactions (through the selective introduction of negative structural elements) as it has on enhancing interactions (through the introduction of affinity conferring elements of structure).