The influence of light attenuation on the biogeomorphology of a marine karst cave: a case study of Puerto Princesa Underground River, Palawan, the Philippines

Karst caves are unique biogeomorphological systems. Cave walls offer habitat for microorganisms which in-turn have a geomorphological role via their involvement in rock weathering, erosion and mineralisation. The attenuation of light with distance into caves is known to affect ecology, but the implications of this for biogeomorphological processes and forms have seldom been examined. Here we describe a semi-quantitative microscopy study comparing the extent, structure, and thickness of biocover and depth of endolithic penetration for samples of rock from the Puerto Princesa Underground River system in Palawan, the Philippines, which is a natural UNESCO World Heritage Site. Organic growth at the entrance of the cave was abundant (100% occurrence) and complex, dominated by phototrophic organisms (green microalgae, diatoms, cyanobacteria, mosses and lichens). Thickness of this layer was 0.28 ± 0.18 mm with active endolith penetration into the limestone (mean depth = 0.13 ± 0.03 mm). In contrast, phototrophs were rare 50 m into the cave and biofilm cover was significantly thinner (0.01 ± 0.01 mm, p < 0.000) and spatially patchy (33% occurrence). Endolithic penetration here was also shallower (< 0.01 mm, p < 0.000) and non-uniform. Biofilm was found 250 m into the cave, but with a complete absence of phototrophs and no evidence of endolithic bioerosion. We attribute these findings to light-induced stress gradients, showing that the influence of light on phototroph abundance has knock-on consequences for the development of limestone morphological features. In marine caves this includes notches, which were most well-developed at the sheltered cave entrance of our study site, and for which variability in formation rates between locations is currently poorly understood

Variability of three-dimensional forces increase during experimental knee pain

Knee pain is a common symptom of different knee pathologies, affecting muscle strength and force generation. Although the control of precise three-dimensional forces is essential for the performance of functional tasks, current evidence of pain effects in force variability is limited to single-directional assessments of contractions at moderate force levels. This study assessed the effects of experimental knee joint pain in the three-dimensional force variability during isometric knee extensions at a wide range of target forces (2.5-80 % of maximal voluntary contraction, MVC). Fifteen healthy subjects performed contractions before, immediately following, and after injections of hypertonic (painful) or isotonic (control) saline into the infrapatellar fat pad. Pain intensity was measured on a 10-cm visual analogue scale. Force magnitude, direction, and variability were assessed using a six-axis force sensor while activity of quadriceps and hamstring muscles was recorded by surface electromyography. Significant correlation was found between tangential force displacements and variability of quadriceps muscle activity. Experimental knee pain increased the variability of the task-related force component at all force levels, while variability of tangential force components increased at low forces (≤5 % of MVC). The mean quadriceps activity decreased during painful contractions only at 80 % of MVC. Pain adaptations underlying increased force variability at low contraction levels probably involve heterogeneous reorganization of muscle activity, which could not be detected by surface electrodes. These findings indicate a less efficient motor strategy during knee joint pain, suggesting that pain relief may enhance training for the control of smooth forces by knee pain patients

Michaelis-Menten dynamics in protein subnetworks

To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly, and is also more efficient computationally

Designing and engineering evolutionary robust genetic circuits

<p>Abstract</p> <p>Background</p> <p>One problem with engineered genetic circuits in synthetic microbes is their stability over evolutionary time in the absence of selective pressure. Since design of a selective environment for maintaining function of a circuit will be unique to every circuit, general design principles are needed for engineering evolutionary robust circuits that permit the long-term study or applied use of synthetic circuits.</p> <p>Results</p> <p>We first measured the stability of two BioBrick-assembled genetic circuits propagated in <it>Escherichia coli </it>over multiple generations and the mutations that caused their loss-of-function. The first circuit, T9002, loses function in less than 20 generations and the mutation that repeatedly causes its loss-of-function is a deletion between two homologous transcriptional terminators. To measure the effect between transcriptional terminator homology levels and evolutionary stability, we re-engineered six versions of T9002 with a different transcriptional terminator at the end of the circuit. When there is no homology between terminators, the evolutionary half-life of this circuit is significantly improved over 2-fold and is independent of the expression level. Removing homology between terminators and decreasing expression level 4-fold increases the evolutionary half-life over 17-fold. The second circuit, I7101, loses function in less than 50 generations due to a deletion between repeated operator sequences in the promoter. This circuit was re-engineered with different promoters from a promoter library and using a kanamycin resistance gene (<it>kanR</it>) within the circuit to put a selective pressure on the promoter. The evolutionary stability dynamics and loss-of-function mutations in all these circuits are described. We also found that on average, evolutionary half-life exponentially decreases with increasing expression levels.</p> <p>Conclusions</p> <p>A wide variety of loss-of-function mutations are observed in BioBrick-assembled genetic circuits including point mutations, small insertions and deletions, large deletions, and insertion sequence (IS) element insertions that often occur in the scar sequence between parts. Promoter mutations are selected for more than any other biological part. Genetic circuits can be re-engineered to be more evolutionary robust with a few simple design principles: high expression of genetic circuits comes with the cost of low evolutionary stability, avoid repeated sequences, and the use of inducible promoters increases stability. Inclusion of an antibiotic resistance gene within the circuit does not ensure evolutionary stability.</p

The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology

Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization. In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Our goal is to create a simple, open-source software infrastructure which is effective, easy to implement and easy to understand. SBW uses a broker-based architecture and enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe the SBW architecture and the current set of modules, as well as alternative implementation technologies

Differential contribution of the MTOR and MNK pathways to the regulation of mRNA translation in meiotic and postmeiotic mouse male germ cells

Translation of stored mRNAs accounts for protein synthesis during the transcriptionally inactive stages of spermatogenesis. A key step in mRNA translation is the assembly of the initiation complex EIF4F, which is regulated by the MTOR (mammalian target of rapamycin) and MNK1/2 (MAP kinase-interacting kinase 1 and 2) pathways. We investigated the expression and activity of regulatory proteins of these pathways in male germ cells at different stages of differentiation. All translation factors analyzed were expressed in germ cells throughout spermatogenesis. However, while EIF4G and PABP1 (poly[A]-binding protein 1) were more abundant in postmeiotic cells, MTOR and its target EIF4EBP1 (4E-BP1) decreased steadily during spermatogenesis. In vivo labeling showed that pachytene spermatocytes display higher rates of protein synthesis, which are partially dependent on MTOR and MNK activity. By contrast, haploid spermatids are characterized by lower levels of protein synthesis, which are independent of the activity of these pathways. Accordingly, MTOR and MNK activity enhanced formation of the EIF4F complex in pachytene spermatocytes but not in round spermatids. Moreover, external cues differentially modulated the activity of these pathways in meiotic and haploid cells. Heat shock decreased MTOR and MNK activity in pachytene spermatocytes, whereas round spermatids were much less sensitive. On the other hand, treatment with the phosphatase inhibitor okadaic acid activated MTOR and MNK in both cell types. These results indicate that translational regulation is differentially dependent on the MTOR and MNK pathways in mouse spermatocytes and spermatids and suggest that the late stages of germ cell differentiation display constitutive assembly of the translation initiation complex

Di-Calcium Phosphate and Phytosphingosine as an Innovative Acid-Resistant Treatment to Occlude Dentine Tubules

The present investigation evaluated the ability of an experimental di-calcium phosphate (DCP) desensitising agent used alone or combined with phytosphingosine (PHS) to occlude dentine tubules and resist a citric acid (CA) or artificial saliva (AS) challenge. Three groups of human dentine specimens (DS) were treated with the following: (1) PHS alone, (2) DCP or (3) a combination of PHS and DCP. Dentine hydraulic conductance of DS was evaluated using a digital flow sensor at 6.9 kPa. The average fluid volume for each of the treated DS was used to calculate the total dentine permeability reduction (%P) prior to and following CA immersion for 1 min or AS immersion for 4 weeks. The treated DS were subjected to both scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy analysis. Statistically significant differences (%P) were identified between the groups by ANOVA and Fisher's multiple comparison test (p 0.05) or show any evidence of occlusion of the dentine tubules. DCP can be used alone or combined with PHS to decrease the dentine permeability as well as to resist a CA and AS challenge. These results would, therefore, suggest that DCP may be a suitable treatment option for dentine hypersensitivity

Risultato di valorizzazione applicativa: progettazione e realizzazione di un prototipo di sensore wireless per il monitoraggio di carichi elettrici in ambiente Smart Building

Oggetto del presente lavoro è stata la progettazione e realizzazione di un prototipo di sensore wireless a basso costo per il monitoraggio di carichi elettrici in ambiente Smart Building, capace di inviare dati ad un sistema remoto (ad esempio un EMS) mediante una comune connessione WiFi. L’attività si inquadra nell’ambito di una collaborazione scientifica tra l’Istituto di Studi sui Sistemi Intelligenti per l’Automazione (ISSIA) del Consiglio Nazionale delle Ricerche (CNR) e il Dipartimento di Matematica e Informatica (DMI) dell’Università degli Studi di Palermo (UNIPA). Il prototipo è stato realizzato interfacciando opportunamente alcuni dispositivi hardware commerciali, aggiungendo gli opportuni circuiti per il condizionamento dei segnali da acquisire e scrivendo il codice per l’implementazione del firmware del sensore wireless (per l’invio dei dati) e del client remoto (per la ricezione dei dati)

Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations

We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power law dependence of the translocation time on the polymer length with an exponent $\alpha$ $\approx 1.2$. The actual value of the exponent from the simulations is $\alpha = 1.28 \pm 0.01$, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.Comment: 7 pages, 5 figures. to appear in Phys. Rev.