Interaction of Tumor with Its Micro-environment: A Mathematical Model

This paper is concerned with early development of transformed epithelial cells (TECs) in the presence of fibroblasts in the tumor micro-environment. These two types of cells interact by means of cytokines such as transforming growth factor (TGF-β) and epidermal growth factor (EGF) secreted, respectively, by the TECs and the fibroblasts. As this interaction proceeds, TGF-β induces fibroblasts to differentiate into myofibroblasts which secrete EGF at a larger rate than fibroblasts. We monitor the entire process in silico, in a setup which mimics experiments in a Tumor Chamber Invasion Assay, where a semi-permeable membrane coated by extracellular matrix (ECM) is placed between two chambers, one containing TECs and another containing fibroblasts. We develop a mathematical model, based on a system of PDEs, that includes the interaction between TECs, fibroblasts, myofibroblasts, TGF-β, and EGF, and we show how model parameters affect tumor progression. The model is used to generate several hypotheses on how to slow tumor growth and invasion. In an Appendix, it is proved that the mathematical model has a unique global in-time solution.     

Migration,Diet, or Molt? Interpreting Stable-Hydrogen Isotope Values in Neotropical Bats

Migratory behavior in bats is poorly described, particularly in the Neotropics. Stable-hydrogen isotope (δD) analysis may allow tracking of altitudinal movements of bats but has not been explored. δD values in rainwater (δD_p) deplete linearly with altitude and are reflected in the keratinous tissues of animals through diet. A mismatch between keratin δD (δD_k) and that expected at the capture site based on δD_p can indicate prior migration. We collected rainwater, claws and hair from eight bat species at two lower-montane forest sites in Nicaragua. Claw δD for Carollia brevicauda and hair and claws for Desmodus rotundus (known to be non-migratory) fell within the predicted range based on rainwater (−17 to −60‰) suggesting these tissues were synthesized at the study site. δD tissue values for Artibeus toltecus, Sturnira lilium, Glossophaga soricina, Anoura geoffroyi, and hair for C. brevicauda were more negative than predicted for the capture site (−60‰) suggesting tissue synthesis at higher elevation and migration downslope to the capture site. However, our study area represents the highest elevation in the region; the nearest appropriate higher elevations are 350–500 km away and seasonal migration is expected to be<200 km. Thus we consider that seasonal shifts in δDp (9 to −45‰) may result in differences in species which molt at different times, and that diet may have driven differences in δD. Our results suggest that the effects of molt timing and diet may first need to be understood before δD may be successfully used to track bat movements.     

Coupling Efficiency of Surface Plasmon Polaritons: Far- and Near-Field Analyses

The excitation of surface plasmon polaritons (SPPs) through one-dimentional (1D) metallic (Au) grating on higher refractive index -GaP substrate is investigated. Such grating devices find potential applications in real world, only if the coupling efficiency (η) of a free-space transverse-magnetic plane-wave into a SPPs mode is maximum. A simple and robust technique is used to estimate the η, by simply measuring the transmission through the grating while varying slit width (a) but period (Λ) and the thickness (t) remain fixed. When the wave vector (k ₀ ) of the incident light is matched to that of SPP, highest η is achieved. It is found that Λ/3 < a < Λ/2 yields a maximum η where the intermediate scattering couples more incident energy to SPPs. These gratings are designed in such a way that they support only the fundamental plasmonic mode yielding higher η. Scanning near-field optical measurements also confirm and corroborate the observations of far-field and near-field modeling (COMSOL multiphysics) results.

     

Spatially encoded strategies in the execution of biomolecular-oriented 3D NMR experiments

Three-dimensional nuclear magnetic resonance (3D NMR) provides one of the foremost analytical tools available for the elucidation of biomolecular structure, function and dynamics. Executing a 3D NMR experiment generally involves scanning a series of time-domain signals S(t ₃), as a function of two time variables (t ₁, t ₂) which need to undergo parametric incrementations throughout independent experiments. Recent years have witnessed extensive efforts towards the acceleration of this kind of experiments. Among the different approaches that have been proposed counts an “ultrafast” scheme, which distinguishes itself from other propositions by enabling—at least in principle—the acquisition of the complete multidimensional NMR data set within a single transient. 2D protein NMR implementations of this single-scan method have been demonstrated, yet its potential for 3D acquisitions has only been exemplified on model organic compounds. This publication discusses a number of strategies that could make these spatial encoding protocols compatible with 3D biomolecular NMR applications. These include a merging of 2D ultrafast NMR principles with temporal 2D encoding schemes, which can yield 3D HNCO spectra from peptides and proteins within ≈100 s timescales. New processing issues that facilitate the collection of 3D NMR spectra by relying fully on spatial encoding principles are also assessed, and shown capable of delivering HNCO spectra within 1 s timescales. Limitations and prospects of these various schemes are briefly addressed.     

A Simple Total Synthesis of (±)-(δ-Cadinene

This paper reports on a total synthesis of racemic δ-cadinene (2), which had been obtained previously in optically active form by acid-catalyzed cyclization of (–)-germacrene D. The Robinson annelation using cyclohexenone enamine (12) proceeded stereoselectively to form δ-cadinenone (3), whose oxygen was removed by the thioketal–Raney Ni method to produce δ-cadinene.     

Mathematical modeling of ventricular disturbances following atrial fibrillation

The present study presents the results of mathematical and computer modeling of atrial fibrillation and ventricular disturbances following atrial fibrillation. The model is based on the assumption that electric impulsation arriving on the atrioventricular node during atrial fibrillation is sum of N independent pulse streams with various amplitude-frequency and phase characteristics. With this model it becomes possible to investigate the dependence of nonlinear dynamics of PP and RR intervals on amplitude-frequency and phase characteristics pulse streams. Results of computer experiments are compared with real physiological experiments on rabbits. Identification of model was carried out by means of least-squares procedure.     

TGF-Mediated Dynamics in a System of Many Coupled Nephrons

This paper presents a mathematical model of a system of many coupled nephrons branching from a common cortical radial artery, and accompanying analysis of that system. This modeling effort is a first step in understanding how coupling magnifies the tendency of nephrons to oscillate owing to tubuloglomerular feedback. Central to the present work is the single nephron integral model (as in Pitman et al., The IMA Volumes in Mathematics and Its Applications, vol. 129, pp. 345–364, 2002 and in Zaritski, Ph.D. Dissertation, 1999) which is a simplification of the single nephron PDE model of Layton et al. (Am. J. Physiol. 261, F904–F919, 1991). A second principal idea used in the present model is a coupling of model nephrons, generalizing the work of Pitman et al. (Bull. Math. Biol. 66, 1463–1492, 2004) who proposed a model of two coupled nephrons. In this study, we couple nephrons through a nearest neighbor interaction. Speaking generally, our results suggest that a series of similar nephrons coupled to their nearest neighbors are more prone to be found in an oscillatory mode, relative to a single nephron with the same properties. More specifically, we show analytically that, for N coupled identical nephrons, the region supporting oscillatory solutions in the time delay–gain parameter plane increases with N. Numerical simulations suggest that, if N nephrons have gains and time delays that do not differ by much, the system is, again, more prone to oscillate, relative to a single nephron, and the oscillations tend to be approximately synchronous and in-phase. We examine the effect of parameters on bifurcation. We also examine alternative models of coupling; this analysis allows us to conclude that the increased propensity of coupled nephrons to oscillate is a robust finding, true for several models of nephron interaction.     

Light scattering and viscosity study of heat aggregation of insulin

Aggregation behavior and hydrodynamic parameters of insulin have been determined from static and dynamic light scattering experiments and intrinsic viscosity measurements carried out at pH 4.0, 7.5, and 9.0 in the temperature range 20–40°C in aqueous solutions. The protein aggregated extensively at elevated temperatures in the acidic solutions. Intermolecular interactions were found to be attractive and to increase with temperature. The measured intrinsic viscosity [η], diffusion coefficient D₀, molecular weight M, and radius of gyration R_g exhibited the universal behavior: M[η] = (2.4 ± 02) × 10⁻²⁷ (R_e,η/R_e,D)³(D_0η/T)⁻³ and (D₀√n)₋₁ ≃ (√6 πη₀ζβ/k_BT) [1 + 0.201)(v/β³)√n], where n is the number of segments in the polypeptide. The effective hydrodynamic radii deduced from [η], (R_e, η) and the same deduced from D₀, (R_e,D) showed a constant ratio, (R_e,η/R_e,D = 1.1 ± 0.1). R_e,D/R_g = ξ was found to be (0.76 ± 0.07). From the known solvent viscosity η₀, the segment length β was deduced to be (10 ± 1) Å. The excluded volume was deduced to be (5 Å)³ regardless of pH. The Flory-Huggins interaction parameter was found to be χ = 0.45 ± 0.04, independent of pH and temperature. © 1998 John Wiley & Sons, Inc. Biopoly 45: 1–8, 1998     

Ral GTPase interacts with the N-terminal in addition to the C-terminal region of PLC-δ1

Previously, we have shown that RalA, a calmodulin (CaM)-binding protein, binds to the C2 region in the C-terminal of PLC-δ1, and increases its enzymatic activity. Since PLC-δ1 contains a CaM-like region in its N-terminus, we have investigated if RalA can also bind to the N-terminus of PLC-δ1. Therefore, we created a GST-PLC-δ1 construct consisting of the first 294 amino acids of PLC-δ1 (GST-PLC-δ1_1-294). In vitro binding experiments confirmed that PLC-δ1_1-294 was capable of binding directly to RalA. W-7 coupled to polyacrylamide beads bound pure PLC-δ1, demonstrating that PLC-δ1 contains a CaM-like region. Competition assays with W-7, peptides representing RalA and the newly identified RalB CaM-binding regions, or the IQ peptide from PLC-δ1 were able to inhibit RalA binding to PLC-δ1_1-294. This study demonstrates that there are two binding sites for RalA in PLC-δ1 and provides further insight into the role of Ral GTPase in the regulation of PLC-δ1 function.     

Analysis of functions in plasmid pHZ1358 influencing its genetic and structural stability in <Emphasis Type="Italic">Streptomyces lividans</Emphasis> 1326

The complete DNA sequence of plasmid pHZ1358, a widely used vector for targeted gene disruption and replacement experiments in many Streptomyces hosts, has been determined. This has allowed a detailed analysis of the basis of its structural and segregational instability, compared to the high copy number plasmid pIJ101 of Streptomyces lividans 1326 from which it was derived. A 574-bp DNA region containing sti (strong incompatibility locus) was found to be a determinant for segregational instability in its original S. lividans 1326 host, while the structural instability was found to be related to the facile deletion of the entire Escherichia coli-derived part of pHZ1358, mediated by recombination between 36-bp direct repeats. A point mutation removing the BamHI site inside the rep gene encoding a replication protein (rep*) and/or a spontaneous deletion of the 694-bp region located between rep and sti including the uncharacterized ORF85 (orf85 ⁻) produced little or no effect on stability. A pHZ1358 derivative (pJTU412, sti ⁻ , rep*, orf85 ⁻) was then constructed which additionally lacked one of the 36-bp direct repeats. pJTU412 was demonstrated to be structurally stable but segregationally unstable and, in contrast to sti ⁺ pHZ1358, allowed efficient targeted gene replacement in S. lividans 1326.     

Hydrogen sulphide suppresses human atrial fibroblast proliferation and transformation to myofibroblasts

Cardiac fibroblasts are crucial in pathophysiology of the myocardium whereby their aberrant proliferation has significant impact on cardiac function. Hydrogen sulphide (H₂S) is a gaseous modulator of potassium channels on cardiomyocytes and has been reported to attenuate cardiac fibrosis. Yet, the mechanism of H₂S in modulating proliferation of cardiac fibroblasts remains poorly understood. We hypothesized that H₂S inhibits proliferative response of atrial fibroblasts through modulation of potassium channels. Biophysical property of potassium channels in human atrial fibroblasts was examined by whole‐cell patch clamp technique and their cellular proliferation in response to H₂S was assessed by BrdU assay. Large conductance Ca²⁺‐activated K⁺ current (BK_Ca), transient outward K⁺ current (I_to) and inwardly rectifying K⁺ current (IK_ir) were found in human atrial fibroblasts. Current density of BK_Ca (IC₅₀ = 69.4 μM; n = 6), I_to (IC₅₀ = 55.1 μM; n = 6) and IK_ir (IC₅₀ = 78.9 μM; n = 6) was significantly decreased (P < 0.05) by acute exposure to NaHS (a H₂S donor) in atrial fibroblasts. Furthermore, NaHS (100–500 μM) inhibited fibroblast proliferation induced by transforming growth factor‐β1 (TGF‐β1; 1 ng/ml), Ang II (100 nM) or 20% FBS. Pre‐conditioning of fibroblasts with NaHS decreased basal expression of Kv4.3 (encode I_to), but not KCa1.1 (encode BK_Ca) and Kir2.1 (encode IK_ir). Furthermore, H₂S significantly attenuated TGF‐β1–stimulated Kv4.3 and α‐smooth muscle actin expression, which coincided with its inhibition of TGF‐β–induced myofibroblast transformation. Our results show that H₂S attenuates atrial fibroblast proliferation via suppression of K⁺ channel activity and moderates their differentiation towards myofibroblasts.     

Associations between carbon isotope ratios of ecosystem respiration, water availability and canopy conductance

We tested the hypothesis that the stable carbon isotope signature of ecosystem respiration (δ¹³C_R) was regulated by canopy conductance (G_c) using weekly Keeling plots (n=51) from a semiarid old‐growth ponderosa pine (Pinus ponderosa) forest in Oregon, USA. For a comparison of forests in two contrasting climates we also evaluated trends in δ¹³C_R from a wet 20‐year‐old Douglas‐fir (Pseudotsuga menziesii) plantation located near the Pacific Ocean. Intraannual variability in δ¹³C_R was greater than 8.0‰ at both sites, was highest during autumn, winter, and spring when rainfall was abundant, and lowest during summer drought. The δ¹³C_R of the dry pine forest was consistently more positive than the wetter Douglas‐fir forest (mean annual δ¹³C_R: ?25.41‰ vs. ?26.23‰, respectively, P=0.07). At the Douglas‐fir forest, δ¹³C_R–climate relationships were consistent with predictions based on stomatal regulation of carbon isotope discrimination (Δ). Soil water content (SWC) and vapor pressure deficit (vpd) were the most important factors governing δ¹³C_R in this forest throughout the year. In contrast, δ¹³C_R at the pine forest was relatively insensitive to SWC or vpd, and exhibited a smaller drought‐related enrichment (～2‰) than the enrichment observed during drought at the Douglas‐fir forest (～5‰). Groundwater access at the pine forest may buffer canopy–gas exchange from drought. Despite this potential buffering, δ¹³C_R at the pine forest was significantly but weakly related to canopy conductance (G_c), suggesting that δ¹³C_R remains coupled to canopy–gas exchange despite groundwater access. During drought, δ¹³C_R was strongly correlated with soil temperature at both forests. The hypothesis that canopy‐level physiology is a critical regulator of δ¹³C_R was supported; however, belowground respiration may become more important during rain‐free periods.     

Contribution of BKCa-Channel Activity in Human Cardiac Fibroblasts to Electrical Coupling of Cardiomyocytes-Fibroblasts

Cardiac fibroblasts are involved in the maintenance of myocardial tissue structure. However, little is known about ion currents in human cardiac fibroblasts. It has been recently reported that cardiac fibroblasts can interact electrically with cardiomyocytes through gap junctions. Ca²⁺-activated K⁺ currents (I _K[Ca]) of cultured human cardiac fibroblasts were characterized in this study. In whole-cell configuration, depolarizing pulses evoked I _K(Ca) in an outward rectification in these cells, the amplitude of which was suppressed by paxilline (1 μM) or iberiotoxin (200 nM). A large-conductance, Ca²⁺-activated K⁺ (BK_Ca) channel with single-channel conductance of 162 ± 8 pS was also observed in human cardiac fibroblasts. Western blot analysis revealed the presence of α-subunit of BK_Ca channels. The dynamic Luo-Rudy model was applied to predict cell behavior during direct electrical coupling of cardiomyocytes and cardiac fibroblasts. In the simulation, electrically coupled cardiac fibroblasts also exhibited action potential; however, they were electrically inert with no gap-junctional coupling. The simulation predicts that changes in gap junction coupling conductance can influence the configuration of cardiac action potential and cardiomyocyte excitability. I _k(Ca) can be elicited by simulated action potential waveforms of cardiac fibroblasts when they are electrically coupled to cardiomyocytes. This study demonstrates that a BK_Ca channel is functionally expressed in human cardiac fibroblasts. The activity of these BK_Ca channels present in human cardiac fibroblasts may contribute to the functional activities of heart cells through transfer of electrical signals between these two cell types.     

Diurnal variation in the stable isotope composition of water and dry matter in fruiting Lupinus angustifolius under field conditions

In this paper, we present an integrated account of the diurnal variation in the stable isotopes of water (δD and δ¹⁸O) and dry matter (δ¹⁵N, δ¹³C, and δ¹⁸O) in the long‐distance transport fluids (xylem sap and phloem sap), leaves, pod walls, and seeds of Lupinus angustifolius under field conditions in Western Australia. The δD and δ¹⁸O of leaf water showed a pronounced diurnal variation, ranging from early morning minima near 0‰ for both δD and δ¹⁸O to early afternoon maxima of 62 and 23‰, respectively. Xylem sap water showed no diurnal variation in isotopic composition and had mean values of ?13·2 and ?2·3‰ for δD and δ¹⁸O. Phloem sap water collected from pod tips was intermediate in isotopic composition between xylem sap and leaf water and exhibited only a moderate diurnal fluctuation. Isotopic compositions of pod wall and seed water were intermediate between those of phloem and xylem sap water. A model of average leaf water enrichment in the steady state (Craig & Gordon, pp. 9–130 in Proceedings of a Conference on Stable Isotopes in Oceanographic Studies and Palaeotemperatures, Lischi and Figli, Pisa, Italy, 1965; Dongmann et al., Radiation and Environmental Biophysics 11, 41–52, 1974; Farquhar & Lloyd, pp. 47–70 in Stable Isotopes and Plant Carbon–Water Relations, Academic Press, San Diego, CA, USA, 1993) agreed closely with observed leaf water enrichment in the morning and early afternoon, but poorly during the night. A modified model taking into account non‐steady‐state effects (Farquhar and Cernusak, unpublished) gave better predictions of observed leaf water enrichments over a full diurnal cycle. The δ¹⁵N, δ¹³C, and δ¹⁸O of dry matter varied appreciably among components. Dry matter δ¹⁵N was highest in xylem sap and lowest in leaves, whereas dry matter δ¹³C was lowest in leaves and highest in phloem sap and seeds, and dry matter δ¹⁸O was lowest in leaves and highest in pod walls. Phloem sap, leaf, and fruit dry matter δ¹⁸O varied diurnally, as did phloem sap dry matter δ¹³C. These results demonstrate the importance of considering the non‐steady‐state when modelling biological fractionation of stable isotopes in the natural environment.     

A High-Resolution Genetic Map of Mouse Chromosome 5 Encompassing the Reeler (rl) Locus

Using interspecific crosses between BALB/c and Mus spretus (SEG) mice, the murine reeler (rl) gene was mapped to the proximal region of chromosome 5 between the hepatocyte growth factor gene (Hgf) and the D5Mit66 microsatellite. The following order was defined: (centromere)-Cchl2a/Hgf-D5Mit1-D5Nam1/D5Nam2 - rl/D5Mit61 - D5Mit72 - Xmv45 - Htr5a - Peplb - D5Nam3-D5Mit66. Estimated distances between reeler and the nearest flanking markers D5Nam1 and D5Mit72 are 1.5 and 1.0 cM, respectively (95% confidence level), suggesting that the region could be physically mapped using a manageable number of YAC clones.     

Purification and Characterization of a DNA Topoisomerase I from Bifidobacterium breve

The monoacylation of (η⁶-1,2-benzenedimethanol)tricarbonylchromium (2) by vinyl acetate, palmitate and benzoate, alcoholysis of the corresponding diesters of 2 in n-butanol, and acylation of (η⁶-benzyl alcohol) tricarbonylchromium by (±)-vinyl 2-phenoxypropanoate and 2-phenylpropanoate were accomplished with lipase P (from P. fluorescens) and lipase CC (from C. cylindracea) to give optically active organometallic esters. Their configurations indicated that the stereoselectivity of each of these two lipases was in marked contrast. An active site model for them is proposed.     

Chemical Composition of the Essential Oil and Diethyl Ether Extract of Trinia glauca (L.) Dumort. (Apiaceae) and the Chemotaxonomic Significance of 5‐O‐Methylvisamminol

Analyses by GC, GC/MS, and NMR spectroscopy (1D‐ and 2D‐experiments) of the essential oil and Et₂O extract of Trinia glauca (L .) Dumort . (Apiaceae) aerial parts allowed a successful identification of 220 constituents, in total. The major identified compounds of the essential oil were (Z)‐falcarinol (10.6%), bicyclogermacrene (8.0%), germacrene D (7.4%), δ‐cadinene (4.3%), and β‐caryophyllene (3.2%), whereas (Z)‐falcarinol (47.2%), nonacosane (7.4%), and 5‐O‐methylvisamminol (4.0%) were the dominant constituents of the extract of T. glauca. One significant difference between the compositions of the herein and the previously analyzed T. glauca essential oils (only two reports) was noted. (Z)‐Falcarinol was the major constituent in our case, whereas germacrene D (14.4 and 19.6%) was the major component of the previously studied oils. Possible explanations for this discrepancy were discussed. 5‐O‐Methylvisamminol, a (furo)chromone identified in the extract of T. glauca, has a limited occurrence in the plant kingdom and is a possible excellent chemotaxonomic marker (family and/or subfamily level) for Apiaceae.     

A novel role for fanconi anemia (FA) pathway effector protein FANCD2 in cell cycle progression of untransformed primary human cells

Fanconi Anemia (FA) is a cancer-susceptibility syndrome characterized by cellular sensitivity to DNA inter-strand cross-link (ICL)-inducing agents. The Fanconia Anemia D2 (FANCD2) protein is implicated in repair of various forms of DNA damage including ICLs. Studies with replicating extracts from Xenopus eggs indicate a role for FANCD2 in processing and repair of DNA replication-associated double stranded breaks (DSB). We have investigated the role of FANCD2 in cell cycle progression of cultured human cells. Similar to Xenopus cell-free extracts, we show that chromatin association of FANCD2 in human cells is coupled to ongoing DNA replication. siRNA depletion experiments demonstrate that FANCD2 is necessary for efficient DNA synthesis. However, in contrast with Xenopus extracts, FANCD2-deficiency does not elicit a DNA damage response, and does not affect the elongation phase of DNA synthesis, suggesting that FANCD2 is dispensable for repair of replication-associated DNA damage. Using synchronized cultures of primary untransformed human dermal fibroblasts we demonstrate that FANCD2 is necessary for efficient initiation of DNA synthesis. Taken together, our results suggest a novel role for the FA pathway in regulation of DNA synthesis and cell cycle progression. Inefficient DNA replication may contribute to the genome instability and cancer-propensity of FA patients.     

Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats

Background  

Variability of the VRN1 promoter region of the unique collection of spring polyploid and wild diploid wheat species together with diploid goatgrasses (donor of B and D genomes of polyploid wheats) were investigated. Accessions of wild diploid (T. boeoticum, T. urartu) and tetraploid (T. araraticum, T. timopheevii) species were studied for the first time.     

Transpiration rate relates to within‐ and across‐species variations in effective path length in a leaf water model of oxygen isotope enrichment

Stable oxygen isotope ratio of leaf water (δ¹⁸O_L) yields valuable information on many aspects of plant–environment interactions. However, current understanding of the mechanistic controls on δ¹⁸O_L does not provide complete characterization of effective path length (L) of the Péclet effect, – a key component of the leaf water model. In this study, we collected diurnal and seasonal series of leaf water enrichment and estimated L in six field‐grown angiosperm and gymnosperm tree species. Our results suggest a pivotal role of leaf transpiration rate (E) in driving both within‐ and across‐species variations in L. Our observation of the common presence of an inverse scaling of L with E in the different species therefore cautions against (1) the conventional treatment of L as a species‐specific constant in leaf water or cellulose isotope (δ¹⁸O_p) modelling; and (2) the use of δ¹⁸O_p as a proxy for g_s or E under low E conditions. Further, we show that incorporation of a multi‐species L‐E scaling into the leaf water model has the potential to both improve the prediction accuracy and simplify parameterization of the model when compared with the conventional approach. This has important implications for future modelling of oxygen isotope ratios.