Complex nearly immotile behaviour of enzymatically driven cargos.

We report a minimal microtubule-based motile system displaying signatures of unconventional diffusion. The system consists of a single model cargo driven by an ensemble of N340K NCD motors along a single microtubule. Despite the absence of cytosolic or cytoskeleton complexity, the system shows complex behavior, characterized by sub-diffusive motion for short time lag scales and linear mean squared displacement dependence for longer time lags. The latter is also shown to have non-Gaussian character and cannot be ascribed to a canonical diffusion process. We use single particle tracking and analysis at varying temperatures and motor concentrations to identify the origin of these behaviors as enzymatic activity of mutant NCD. Our results show that signatures of non-Gaussian diffusivities can arise as a result of an active process and suggest that some immotility of cargos observed in cells may reflect the ensemble workings of mechanochemical enzymes and need not always reflect the properties of the cytoskeletal network or the cytosol.

Continuous interscalene brachial plexus blockade is associated with reduced length of stay after shoulder arthroplasty.

BACKGROUND: Catheter-delivered continuous interscalene anesthesia has demonstrated improved pain control in randomized clinical trials. The purpose of this study is to determine whether the introduction of continuous catheter anesthesia was associated with a change in length of stay (LOS), readmission, rates of discharge home without home health or nursing services, or opioid administration. We hypothesized that the introduction of continuous catheter anesthesia would be associated with a decrease in LOS, readmission, non-home discharge, and opioid administration. METHODS: During 2012, our center transitioned from ultrasound-guided single-dose interscalene regional anesthesia to combined single-dose anesthesia and additional continuous catheter anesthesia over 48-72hours. This retrospective chart review compared primary shoulder arthroplasties with single-dose anesthesia to those with continuous catheter anesthesia, after excluding the learning curve, with univariate and multivariate analyses. RESULTS: In total, 1697 patients met criteria, 41% with single-dose anesthesia and 59% with continuous catheter anesthesia. On univariate analysis, the continuous catheter group LOS was 2.2±0.7 day and single-dose group LOS was 2.5±0.8 days (P≤0.001). One day LOS's comprised 1% of the single-dose group and 27% of the continuous catheter group (P<0.001). Anesthesia type remained a significant predictor on multivariate analysis (P<0.001) Readmission at 30 and 90 days (P=0.091 and 0.576), and home discharge (P=0.456) were not different. Opioid administration was higher in the continuous catheter group on univariate analysis (P<0.001), but not on multivariate analysis (P=0.607). CONCLUSION: In this retrospective review of 1697 primary shoulder arthroplasties performed at our high-volume, referral center, continuous catheter anesthesia was associated with reduced length of stay when compared to single-dose anesthesia. LEVEL OF EVIDENCE: Therapeutic, level IV.

Bone loss in a new rodent model combining spinal cord injury and cast immobilization.

OBJECTIVES: Characterize bone loss in our newly developed severe contusion spinal cord injury (SCI) plus hindlimb immobilization (IMM) model and determine the influence of muscle contractility on skeletal integrity after SCI. METHODS: Female Sprague-Dawley rats were randomized to: (a) intact controls, (b) severe contusion SCI euthanized at Day 7 (SCI-7) or (c) Day 21 (SCI-21), (d) 14 days IMM-alone, (e) SCI+IMM, or (f) SCI+IMM plus 14 days body weight supported treadmill exercise (SCI+IMM+TM). RESULTS: SCI-7 and SCI-21 exhibited a >20% reduction in cancellous volumetric bone mineral density (vBMD) in the hindlimbs (p⋜0.01), characterized by reductions in cancellous bone volume (cBV/TV%), trabecular number (Tb.N), and trabecular thickness. IMM-alone induced no observable bone loss. SCI+IMM exacerbated cancellous vBMD deficits with values being >45% below Controls (p⋜0.01) resulting from reduced cBV/TV% and Tb.N. SCI+IMM also produced the greatest cortical bone loss with distal femoral cortical area and cortical thickness being 14-28% below Controls (p⋜0.01) and bone strength being 37% below Controls (p⋜0.01). SCI+IMM+TM partially alleviated bone deficits, but values remained below Controls. CONCLUSIONS: Residual and/or facilitated muscle contractility ameliorate bone decrements after severe SCI. Our novel SCI+IMM model represents a clinically-relevant means of assessing strategies to prevent SCI-induced skeletal deficits.

A mathematical model and quantitative comparison of the small RNA circuit in the Vibrio harveyi and Vibrio cholerae quorum sensing systems.

Quorum sensing is the process by which bacteria regulate their gene expression based on the local cell-population density. The quorum sensing systems of Vibrio harveyi and Vibrio cholerae are comprised of a phosphorelay cascade coupled to a small RNA (sRNA) circuit. The sRNA circuit contains multiple quorum regulated small RNA (Qrr) that regulate expression of the homologous master transcriptional regulators LuxR (in V. harveyi) and HapR (in V. cholerae). Their quorum sensing systems are topologically similar and homologous thereby making it difficult to understand why repression of HapR is more robust than LuxR to changes in Qrr. In this work we formulate and parameterize a novel mathematical model of the V. harveyi and V. cholerae sRNA circuit. We parameterize the model by fitting it to a variety of empirical data from both species. We show that we can distinguish all of the parameters and that the parameterizations (one for each species) are robust to errors in the data. We then use our model to propose some experiments to identify and explain kinetic differences between the species. We find that V. cholerae Qrr are more abundant and more sensitive to changes in LuxO than V. harveyi Qrr and argue that this is why expression of HapR is more robust than LuxR to changes in Qrr.

The effect of divalent vs. monovalent ions on the swelling of mucin-like polyelectrolyte gels: governing equations and equilibrium analysis.

We introduce a comprehensive model of a mucin-like polyelectrolyte gel swelling-deswelling which includes the ion-mediated crosslinking of polymer strands and the exchange of divalent and monovalent ions in the gel. The gel is modeled as a multi-phase mixture which accounts for the polymer and solvent volume fractions and velocities as well as ionic species concentrations. Motion is determined by force balances involving viscous, drag, and chemical forces. The chemical forces are derived from a free energy which includes entropic contributions as well as the chemical and electrostatic interactions among the crosslinked polymer, uncrosslinked polymer, and the ionic solvent. The unified derivation produces all the classical effects (van't Hoff osmotic pressure, Donnan equilibrium potential, Nernst-Planck motion of ions) as well as expressions for Flory interaction parameter and the standard free energy parameters that explicitly depend on the gel chemistry and crosslink structure. For this model, we show how the interplay between ionic bath concentrations, ionic binding, and transient divalent crosslinking leads to a variety of swelled and deswelled phases/phase transitions. In particular, we show how the absorption of divalent ions can lead to a massive deswelling of the gel. We conclude that the unique properties of mucin-like gels can be explained by their ionic binding affinities and transient divalent crosslinking.

A molecular ruler mechanism for length control of extended protein structures in bacteria.

The lengths of the hook structure of flagellar motors and of the needle of the injectosome are both carefully controlled, by apparently similar mechanisms. In this paper we propose a novel mechanism for this length control and develop a mathematical model of this process which shows excellent agreement with published data on hook lengths. The proposed mechanism for length control (described using biochemical nomenclature appropriate for hooks) is as follows: Hook growth is terminated when the C-terminus of the length control molecule FliK interacts with FlhB, the secretion gatekeeper. The probability of this interaction is an increasing function of the length of the hook for two reasons. First, FliK is secreted through the hook intermittently during hook growth. Second, the probability of interaction with FlhB is a function of the amount of time the C-terminus of a secreted FliK spends in the vicinity of FlhB. This time is short when the hook is short because the folding of FliK exiting the distal end of the hook acts to pull the FliK molecule through the hook rapidly. In contrast, this time is much longer when the hook is longer than the unfolded FliK polymer since movement through the tube is not enhanced by folding. Thus, it is much more likely that interaction will occur when the hook is long than when the hook is short.

How Salmonella Typhimurium measures the length of flagellar filaments.

We present a mathematical model for the growth and length regulation of the filament of the flagellar motor of Salmonella Typhimurium. Under the assumption that the molecular constituents are translocated into the nascent filament by an ATPase and then move by molecular diffusion to the growing end, we find a monotonically decreasing relationship between the speed and the velocity of growth that is inversely proportional to length for a large length. This gives qualitative but not quantitative agreement with data of the velocity of growth. We also propose that the length of filaments is "measured" by the rate of secretion of the sigma(28)-antifactor FlgM, using negative feedback, and present a mathematical model of this regulatory network. The combination of this regulatory network with the length-dependent rate of growth enable the bacterium to detect length shortening and regrow severed flagellar filaments.

A model for length control of flagellar hooks of Salmonella typhimurium.

We present a mathematical model for the growth and length regulation of the hook component of the flagellar motor of Salmonella typhimurium. Under the assumption that the molecular constituents are translocated into the nascent filament by an ATP-ase and then move by molecular diffusion to the growing end, where they polymerize into the growing tube, we find that there is a detectable transition from secretion limited growth to diffusion limited growth. We propose that this transition can be detected by the secretant FliK, allowing FliK to interact with FlhB thereby changing the secretion target of the type III secretion machinery and terminating the growth of the hook.

Intrinsic H(+) ion mobility in the rabbit ventricular myocyte.

The intrinsic mobility of intracellular H(+) ions was investigated by confocally imaging the longitudinal movement of acid inside rabbit ventricular myocytes loaded with the acetoxymethyl ester (AM) form of carboxy-seminaphthorhodafluor-1 (carboxy-SNARF-1). Acid was diffused into one end of the cell through a patch pipette filled with an isotonic KCl solution of pH 3.0. Intracellular H(+) mobility was low, acid taking 20-30 s to move 40 microm down the cell. Inhibiting sarcolemmal Na(+)-H(+) exchange with 1 mM amiloride had no effect on this time delay. Net H(+)(i) movement was associated with a longitudinal intracellular pH (pH(i)) gradient of up to 0.4 pH units. H(+)(i) movement could be modelled using the equations for diffusion, assuming an apparent diffusion coefficient for H(+) ions (D(H)(app)) of 3.78 x 10(-7) cm(2) s(-1), a value more than 300-fold lower than the H(+) diffusion coefficient in a dilute, unbuffered solution. Measurement of the intracellular concentration of SNARF (approximately 400 microM) and its intracellular diffusion coefficient (0.9 x 10(-7) cm(2) s(-1)) indicated that the fluorophore itself exerted an insignificant effect (between 0.6 and 3.3 %) on the longitudinal movement of H(+) equivalents inside the cell. The longitudinal movement of intracellular H(+) is discussed in terms of a diffusive shuttling of H(+) equivalents on high capacity mobile buffers which comprise about half (approximately 11 mM) of the total intrinsic buffering capacity within the myocyte (the other half being fixed buffer sites on low mobility, intracellular proteins). Intrinsic H(+)(i) mobility is consistent with an average diffusion coefficient for the intracellular mobile buffers (D(mob)) of ~9 x 10(-7) cm(2) s(-1).

Facilitation of intracellular H(+) ion mobility by CO(2)/HCO(3)(-) in rabbit ventricular myocytes is regulated by carbonic anhydrase.

Intracellular H(+) mobility was estimated in the rabbit isolated ventricular myocyte by diffusing HCl into the cell from a patch pipette, while imaging pH(i) confocally using intracellular ratiometric SNARF fluorescence. The delay for acid diffusion between two downstream regions approximately 40 microm apart was reduced from approximately 25 s to approximately 6 s by replacing Hepes buffer in the extracellular superfusate with a 5 % CO(2)/HCO(3)(-) buffer system (at constant pH(o) of 7.40). Thus CO(2)/HCO(3)(-) (carbonic) buffer facilitates apparent H(+)(i) mobility. The delay with carbonic buffer was increased again by adding acetazolamide (ATZ), a membrane permeant carbonic anhydrase (CA) inhibitor. Thus facilitation of apparent H(+)(i) mobility by CO(2)/HCO(3)(-) relies on the activity of intracellular CA. By using a mathematical model of diffusion, the apparent intracellular H(+) equivalent diffusion coefficient (D(H)(app)) in CO(2)/HCO(3)(-)-buffered conditions was estimated to be 21.9 x 10(-7) cm(2) s(-1), 5.8 times faster than in the absence of carbonic buffer. Facilitation of H(+)(i) mobility is discussed in terms of an intracellular carbonic buffer shuttle, catalysed by intracellular CA. Turnover of this shuttle is postulated to be faster than that of the intrinsic buffer shuttle. By regulating the carbonic shuttle, CA regulates effective H(+)(i) mobility which, in turn, regulates the spatiotemporal uniformity of pH(i). This is postulated to be a major function of CA in heart.

Diffusion induced oscillatory insulin secretion.

Oscillatory secretion of insulin has been observed in many different experimental preparations. Here we examine a mathematical model for in vitro insulin secretion from pancreatic beta cells in a flow-through reactor. The analysis shows that oscillations result because of an important interplay between flow rate of the reactor and insulin diffusion. In particular, if the ratio of flow rate to volume of the reaction bed is too large, oscillations are eliminated, in contradiction to the conclusions of Maki and Keizer (L. W. Maki and Keizer J. Mathematical analysis of a proposed mechanism for oscillatory insulin secretion in perifused HIT-15 cells. Bull. Math. Biol., 57(1995), 569-591). Furthermore, with reasonable numbers for the experimental parameters and the diffusion of insulin, the model equations do not exhibit oscillations.

Transcription of chromosomal rRNA genes by both RNA polymerase I and II in yeast uaf30 mutants lacking the 30 kDa subunit of transcription factor UAF.

UAF, a yeast RNA polymerase I transcription factor, contains Rrn5p, Rrn9p, Rrn10p, histones H3 and H4, and uncharacterized protein p30. Mutants defective in RRN5, RRN9 or RRN10 are unable to transcribe rDNA by polymerase I and grow extremely slowly, but give rise to variants able to grow by transcribing chromosomal rDNA by polymerase II. Thus, UAF functions as both an activator of polymerase I and a silencer of polymerase II for rDNA transcription. We have now identified the gene for subunit p30. This gene, UAF30, is not essential for growth, but its deletion decreases the cellular growth rate. Remarkably, the deletion mutants use both polymerase I and II for rDNA transcription, indicating that the silencer function of UAF is impaired, even though rDNA transcription by polymerase I is still occurring. A UAF complex isolated from the uaf30 deletion mutant was found to retain the in vitro polymerase I activator function to a large extent. Thus, Uaf30p plays only a minor role in its activator function. Possible reasons for slow growth caused by uaf30 mutations are discussed.

Net1 stimulates RNA polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit.

The budding yeast RENT complex, consisting of at least three proteins (Net1, Cdc14, Sir2), is anchored to the nucleolus by Net1. RENT controls mitotic exit, nucleolar silencing, and nucleolar localization of Nop1. Here, we report two new functions of Net1. First, Net1 directly binds Pol I and stimulates rRNA synthesis both in vitro and in vivo. Second, Net1 modulates nucleolar structure by regulating rDNA morphology and proper localization of multiple nucleolar antigens, including Pol I. Importantly, we show that the nucleolar and previously described cell cycle functions of the RENT complex can be uncoupled by a dominant mutant allele of CDC14. The independent functions of Net1 link a key event in the cell cycle to nucleolar processes that are fundamental to cell growth.

Role of TATA binding protein (TBP) in yeast ribosomal dna transcription by RNA polymerase I: defects in the dual functions of transcription factor UAF cannot be suppressed by TBP.

Initiation of ribosomal DNA (rDNA) transcription by RNA polymerase I (Pol I) in the yeast Saccharomyces cerevisiae involves upstream activation factor (UAF), core factor, the TATA binding protein (TBP), and Rrn3p in addition to Pol I. We found previously that yeast strains carrying deletions in the UAF component RRN9 switch completely to the use of Pol II for rRNA transcription, with no residual Pol I transcription. These polymerase-switched strains initially grow very slowly, but subsequent expansion in the number of rDNA repeats on chromosome XII leads to better growth. Recently, it was reported that TBP overexpression could bypass the requirement of UAF for Pol I transcription in vivo, producing nearly wild-type levels of growth in UAF mutant strains (P. Aprikian, B. Moorefield, and R. H. Reeder, Mol. Cell. Biol. 20:5269-5275, 2000). Here, we demonstrate that deletions in the UAF component RRN5, RRN9, or RRN10 lead to Pol II transcription of rDNA. TBP overexpression does not suppress UAF mutation, and these strains continue to use Pol II for rRNA transcription. We do not find evidence for even low levels of Pol I transcription in UAF mutant strains carrying overexpressed TBP. In diploid strains lacking both copies of the UAF component RRN9, Pol II transcription of rDNA is more strongly repressed than in haploid strains but TBP overexpression still fails to activate Pol I. These results emphasize that UAF plays an essential role in activation of Pol I transcription and silencing of Pol II transcription of rDNA and that TBP functions to recruit the Pol I machinery in a manner completely dependent on UAF.

A mathematical model for quorum sensing in Pseudomonas aeruginosa.

The bacteria Pseudomonas aeruginosa use the size and density of their colonies to regulate the production of a large variety of substances, including toxins. This phenomenon, called quorum sensing, apparently enables colonies to grow to sufficient size undetected by the immune system of the host organism. In this paper, we present a mathematical model of quorum sensing in P. aeruginosa that is based on the known biochemistry of regulation of the autoinducer that is crucial to this signalling mechanism. Using this model we show that quorum sensing works because of a biochemical switch between two stable steady solutions, one with low levels of autoinducer and one with high levels of autoinducer.

Elimination of spiral waves in cardiac tissue by multiple electrical shocks.

We study numerically the elimination of a spiral wave in cardiac tissue by application of multiple shocks of external current. To account for the effect of shocks we apply a recently developed theory for the interaction of the external current with cardiac tissue. We compare two possible feedback algorithms for timing of the shocks: a "local" feedback algorithm 11 (using an external electrode placed directly on the tissue) and a "global" feedback algorithm 22 (using the electrocardiogram). Our main results are: application of the external current causes a parametric resonant drift similar to that reported in previous model computations; the ratio of the threshold of elimination of the spiral wave by multiple shocks to the threshold of conventional single shock defibrillation in our model for cardiac tissue is about 0.5, while earlier, less realistic models predicted the value about 0.2; we show that an important factor for successful defibrillation is the location of the feedback electrode and the best results are achieved if the feedback electrode or the ECG lead is located at the boundary (or edge) of the cardiac tissue; the "local" and the "global" feedback algorithms show similar efficiency.

Common apolipoprotein A-IV variants are associated with differences in body mass index levels and percentage body fat.

OBJECTIVE: To determine the relationship between two common apoA-IV variants (Thr347-->Ser; Gln360-->His), and body mass index (BMI) and percentage body fat. DESIGN: Cross-sectional study. SUBJECTS: Eight-hundred and forty-eight subjects screened for participation in ongoing clinical studies. MEASUREMENTS: ApoA-IV genotype, body mass index, waist-to-hip ratio and percentage body fat by bioelectric impedance. RESULTS: Participants had an average age of 41+/-12 y and an average BMI of 28.2+/-5.5 kg/m2. Individuals homozygous for the Ser347 allele had higher BMI (32.3+/-6.6 vs 28.6+/-5.3 kg/m2; P<0.01) and percentage body fat (36.9+/-7.8 vs 31.0+/-9.6%; P<0.05) compared with individuals homozygous for Thr347. In contrast, the presence of at least one copy of the His360 allele was associated with lower BMI (27.2+/-5.0 vs 28.4+/-5.6 kg/m2; P<0.05) and percentage body fat (28.6+/-8.2 vs 30.7+/-9.1%; P<0.05). The genotype effects persisted after normalization of the data for the potential confounding effects of gender, age and race. When grouped by BMI percentile, the frequency of the Ser347/Ser347 genotype increased while the frequency of the His360 allele decreased with increasing BMI. CONCLUSIONS: These data suggest a role for apoA-IV in fat storage or mobilization and that genetic variations in the apoA-IV gene may play a role in the development of obesity.

The biphasic mystery: why a biphasic shock is more effective than a monophasic shock for defibrillation.

We demonstrate that a biphasic shock is more effective than a monophasic shock at eliminating reentrant electrical activity in an ionic model of cardiac ventricular electrical activity. This effectiveness results from early hyperpolarization that enhances the recovery of sodium inactivation, thereby enabling earlier activation of recovering cells. The effect can be seen easily in a model of a single cell and also in a cable model with a ring of excitable cells. Finally, we demonstrate the phenomenon in a two-dimensional model of cardiac tissue.

Isoaspartate in ribosomal protein S11 of Escherichia coli.

Isoaspartyl sites, in which an aspartic acid residue is linked to its C-flanking neighbor via its beta-carboxyl side chain, are generally assumed to be an abnormal modification arising as proteins age. The enzyme protein L-isoaspartate methyltransferase (PIMT), present in many bacteria, plants, and animals, catalyzes the conversion of isoaspartate to normal alpha-linked aspartyl bonds and is thought to serve an important repair function in cells. Having introduced a plasmid into Escherichia coli that allows high-level expression of rat PIMT, we explored the possibility that the rat enzyme reduces isoaspartate levels in E. coli proteins, a result predicted by the repair hypothesis. The present study demonstrates that this is indeed the case; E. coli cells expressing rat PIMT had significantly lower isoaspartate levels than control cells, especially in stationary phase. Moreover, the distribution of isoaspartate-containing proteins in E. coli differed dramatically between logarithmic- and stationary-phase cultures. In stationary-phase cells, a number of proteins in the molecular mass range of 66 to 14 kDa contained isoaspartate, whereas in logarithmic-phase cells, nearly all of the detectable isoaspartate resided in a single 14-kDa protein which we identified as ribosomal protein S11. The near stoichiometric levels of isoaspartate in S11, estimated at 0.5 mol of isoaspartate per mol of S11, suggests that this unusual modification may be important for S11 function.

Reconstitution of yeast RNA polymerase I transcription in vitro from purified components. TATA-binding protein is not required for basal transcription.

Five purified protein components, RNA polymerase I, Rrn3p, core factor, TBP (TATA-binding protein), and upstream activation factor, are sufficient for high level transcription in vitro from the Saccharomyces cerevisiae rDNA promoter. Rrn3p and pol I form a complex in solution that is active in specific initiation. Three protein components, pol I, Rrn3p, and core factor, and promoter sequence to -38, suffice for basal transcription. Unlike pol II and pol III, yeast pol I basal transcription does not require TBP. Instead, TBP, upstream activation factor, and the upstream element of the promoter together stimulate pol I basal transcription to a fully activated level. The role of TBP in pol I transcription is fundamentally different from its role in pol II or pol III transcription.