Improved bounds on entropy production in living systems.

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

Stochastic Dynamics of Eukaryotic Flagellar Growth.

We study the dynamics of flagellar growth in eukaryotes where intraflagellar transporters (IFT) play a crucial role. First we investigate a stochastic version of the original balance point model where a constant number of IFT particles move up and down the flagellum. The detailed model is a discrete event vector-valued Markov process occurring in continuous time. First the detailed stochastic model is compared and contrasted with a simple scalar ordinary differential equation (ODE) model of flagellar growth. Numerical simulations reveal that the steady-state mean value of the stochastic model is well approximated by the ODE model. Then we derive a scalar stochastic differential equation (SDE) as a first approximation and obtain a "small noise" approximation showing flagellar length to be Gaussian with mean and variance governed by simple ODEs. The accuracy of the small noise model is compared favorably with the numerical simulation results of the detailed model. Secondly, we derive a revised SDE for flagellar length following the revised balance point model proposed in 2009 in which IFT particles move in trains instead of in isolation. Small noise approximation of the revised SDE yields the same approximate Gaussian distribution for the flagellar length as the SDE corresponding to the original balance point model.

Assessment of the optimal vitrification protocol for pre-pubertal mice testes leading to successful in vitro production of flagellated spermatozoa.

Testicular tissue cryopreservation offers the hope of preserved future fertility to pre-pubertal boys with cancer before exposition to gonadotoxic treatments. The objective of this study was to compare controlled slow freezing (CSF) with five vitrification techniques for cryopreservation of murine pre-pubertal testicular tissue and to evaluate the best protocol that could provide a successful completion of spermatogenesis after in vitro maturation. Testicular tissue from 24 mice at 6.5 days post-partum (dpp) was used to compare several vitrification protocols with one another, as well as with a CSF protocol. Toxicity test using additional 12 mice was performed for all cryopreservation solutions. Fresh tissue (FT) from six mice was used as a control. Once the optimal vitrification protocol was selected [the modified solid surface vitrification No. 1 (mSSV1 )], testes from 18 mice were cultured in vitro for 30 days with (i) fresh, (ii) slow-frozen/thawed and (iii) vitrified/warmed tissues. Testes from six mice at 36.5 dpp were used as controls. At day 30 of in vitro culture, germ cells of the seminiferous tubules showed a high ability to proliferate and elongated spermatids were observed after both freezing techniques, confirming the successful completion of in vitro spermatogenesis. However, after mSSV1 , the morphological alterations and the percentage of pyknotic seminiferous tubules were lower than CSF (4.67 ± 0.53 vs. 10.1 ± 1.12 and 22.7 ± 2.83% vs. 37.3 ± 4.24% respectively). Moreover, the number of flagellated spermatozoa produced per mg of tissue was higher for mSSV1 than for CSF (35 ± 3 vs. 9 ± 4 cells), with amounts of secreted testosterone during the culture close to those of FT. The mSSV1 protocol resulted in success rates better than CSF in maintaining testicular tissue structure, tubular morphology and tissue functions not solely for immediate frozen/thawed tissues but also after a long-term in vitro culture.

A comparative study on edible Agaricus mushrooms as functional foods.

Agaricus bisporus is a cultivated mushroom; A. bitorquis, A. campestris and A. macrosporus are edible mushrooms growing wild in nature. A chemical characterization was carried out with samples that originated in Serbia. Antioxidant, antimicrobial and anti-quorum sensing properties of their methanolic and ethanolic extracts were assessed. A. campestris had the lowest caloric value and total sugar content and showed the highest concentration in organic and phenolic acids, as also in tocopherols (mainly γ-tocopherol). In general, the methanolic extracts showed higher antioxidant, but lower antibacterial and antifungal potential than ethanolic ones. Sub-inhibitory concentrations of the ethanolic extracts demonstrated reduction of virulence factors, AQ inhibition zones, twitching and swimming motility. The biofilm forming capability of P. aeruginosa PAO1 was also reduced in a concentration-dependent manner at sub-MIC values. The extracts of the tested Agaricus species are a promising source of antioxidant, antimicrobial and antiquorum sensing compounds.

Flagellar filament bio-templated inorganic oxide materials - towards an efficient lithium battery anode.

Designing a new generation of energy-intensive and sustainable electrode materials for batteries to power a variety of applications is an imperative task. The use of biomaterials as a nanosized structural template for these materials has the potential to produce hitherto unachievable structures. In this report, we have used genetically modified flagellar filaments of the extremely halophilic archaea species Halobacterium salinarum to synthesize nanostructured iron oxide composites for use as a lithium-ion battery anode. The electrode demonstrated a superior electrochemical performance compared to existing literature results, with good capacity retention of 1032 mAh g(-1) after 50 cycles and with high rate capability, delivering 770 mAh g(-1) at 5 A g(-1) (~5 C) discharge rate. This unique flagellar filament based template has the potential to provide access to other highly structured advanced energy materials in the future.

Quantitative high-throughput assays for flagella-based motility in chlamydomonas using plate-well image analysis and transmission correlation spectroscopy.

Cilia are motile and sensory organelles with important roles in human development, physiology, and disease. Genetic defects in cilia produce a host of disease symptoms, including polycystic kidney disease, hydrocephalus, retinal degeneration, chronic bronchiectasis, infertility, and polydactyly. Currently, there are no known drugs for pharmacological remediation of ciliary defects. Small-molecule modulators of ciliary assembly or function would provide potential lead compounds for drug discovery efforts and would immediately be invaluable tools for a chemical biology approach to studying cilia. Here the author describes 2 assays for ciliary motility that are quantitative, automatable, cost-effective, and simple to implement. Both assays exploit cell-based strategies using the model organism Chlamydomonas reinhardtii. The first assay scores cilia-dependent gravitaxis by analyzing the cell distribution in wells of U-bottom microplates, using a simple and robust image analysis algorithm. The second assay measures motility directly by estimating the time required for cells to swim across a small illuminated aperture using a method equivalent to fluorescence correlation spectroscopy adapted to transmitted-light microscopy. The 2 assays have different advantages in terms of speed and sensitivity to small reductions in motility and may be most efficiently used in combination.

The flagellum of Trypanosoma brucei: new tricks from an old dog.

African trypanosomes, i.e. Trypanosoma brucei and related sub-species, are devastating human and animal pathogens that cause significant human mortality and limit sustained economic development in sub-Saharan Africa. T. brucei is a highly motile protozoan parasite and coordinated motility is central to both disease pathogenesis in the mammalian host and parasite development in the tsetse fly vector. Therefore, understanding unique aspects of the T. brucei flagellum may uncover novel targets for therapeutic intervention in African sleeping sickness. Moreover, studies of conserved features of the T. brucei flagellum are directly relevant to understanding fundamental aspects of flagellum and cilium function in other eukaryotes, making T. brucei an important model system. The T. brucei flagellum contains a canonical 9+2 axoneme, together with additional features that are unique to kinetoplastids and a few closely-related organisms. Until recently, much of our knowledge of the structure and function of the trypanosome flagellum was based on analogy and inference from other organisms. There has been an explosion in functional studies in T. brucei in recent years, revealing conserved as well as novel and unexpected structural and functional features of the flagellum. Most notably, the flagellum has been found to be an essential organelle, with critical roles in parasite motility, morphogenesis, cell division and immune evasion. This review highlights recent discoveries on the T. brucei flagellum.

Hidden stochastic nature of a single bacterial motor.

The rotary flagellar motor of Escherichia coli bacterium switches stochastically between the clockwise (CW) and counterclockwise (CCW) direction. We found that the CW and CCW intervals could be described by a gamma distribution, suggesting the existence of hidden Markov steps preceding each motor switch. Power spectra of time series of switching events exhibited a peaking frequency instead of the Lorentzian profile expected from standard kinetic two-state models. Our analysis indicates that the number of hidden steps may be a key dynamical parameter underlying the switching process in a single bacterial motor as well as in large cooperative molecular systems.

Amperometric biosensing systems based on motility and gravitaxis of flagellate algae for aquatic risk assessment.

Electrochemical biosensing systems for toxic substances were developed on the basis of motility and negative gravitaxis of the unicellular flagellate Chlamydomonas reinhardtii. Changes in the flagellar movement of the flagellates in response to three toxic chemicals, toluene, copper(II) sulfate, and nickel(II) chloride, were monitored as changes in the redox currents for a coexisiting redox marker. The gravitaxis-based flagellate biosensing system was more sensitive to toluene than the motility-based system. A thin-layer flagellate biosensor was also developed. In comparison with the conventional algal biosensors monitoring the photosynthetic activity, the gravitaxis-based thin-layer sensor was more sensitive by more than 1 order of magnitude.

Assessment of inner dynein arm structure and possible function in ciliary and flagellar axonemes.

The construction and assessment of a three-dimensional computer-generated model of inner dynein arms on a 96-nm repeat unit of an axonemal doublet is described. The model is based on published electron micrographs of axonemes from Tetrahymena cilia and eel sperm, which were prepared using several different techniques: negative stain, freeze etch, and thin section. The inner arm structure is represented as three inner dynein arm complexes containing four inner dynein arms (IDAs), three dyads, and one single-headed arm, each capable of bridging the interdoublet gap. The IDA structures in the model have been correlated with the domains containing dynein heavy-chain isoforms mapped by several authors using genetic analyses of Chlamydomonas mutants. The model is consistent with micrographic evidence from axonemes of cilia and flagella from other organisms that led previously to conflicting structural interpretations. In this reconciling interpretation, the different alignments of the IDAs relative to the corresponding outer dynein arms observed in micrographs of differently prepared samples, result from the IDAs being arrested at different stages of their cycles of activity in each preparation. By interpolating between these positions of arrest, cycles of activity are proposed for each of the IDAs during which the arms attach to the neighbouring doublet microtubule and drive it tipwards.

Protein turbines. I: The bacterial flagellar motor.

The bacterial flagellar motor is driven by a flux of ions between the cytoplasm and the periplasmic lumen. Here we show how an electrostatic mechanism can convert this ion flux into a rotary torque. We demonstrate that, with reasonable parameters, the model can reproduce many of the experimental measurements.

A model of flagellar movement based on cooperative dynamics of dynein-tubulin cross-bridges.

A theoretical model based on molecular mechanisms of both dynein cross-bridges and radial spokes is used to study bend propagation by eukaryotic flagella. Though nine outer doublets are arranged within an axoneme, a simplified model with four doublets is constructed on the assumption that cross-bridges between two of the four doublets are opposed to those between the other two, corresponding to the geometric array of cross-bridges on the 6-9 and the 1-4 doublets in the axoneme. We also assume that external viscosity is zero, whereas internal viscosity is non-zero in order to reduce numerical complexity. For demonstrating flagellar movement, computer simulations are available by dividing a long flagellum into many straight segments. Considering the fact that dynein cross-bridge spacing is almost equal to attachment site spacing, we may use a localized cross-bridge distribution along attachment sites in each straight segment. Dynamics of cross-bridges are determined by a three-state model, and effects of radial spokes are represented by a periodic mechanical potential whose periodicity is considered to be a stroke distance of the radial spoke. First of all, we examine the model of a short segment to know basic properties of the system. Changing parameters relating to "activation" of cross-bridges, our model demonstrates various phenomena; for example "excitable properties with threshold phenomena" and "limit cycle oscillation". Here, "activation" and "inactivation" (i.e. switching mechanisms) between a pair of oppositely-directed cross-bridges are essential for generation of excitable or oscillatory properties. Next, the model for a flagellar segment is incorporated into a flagellum with a whole length to show bending movement. When excitable properties of cross-bridges, not oscillatory properties, are provided along the length of the flagellum and elastic links between filaments are presented at the base, then our model can demonstrate self-organization of bending waves as well as wave propagation without special feedback control by the curvature of the flagellum. Here, "cooperative interaction" between adjacent short segments, based on "cooperative dynamics" of cross-bridges, is important for wave propagation.