Start-up flow in shallow deformable microchannels

Microfluidic systems are usually fabricated with soft materials that deform due to the fluid stresses. Recent experimental and theoretical studies on the steady flow in shallow deformable microchannels have shown that the flow rate is a nonlinear function of the pressure drop due to the deformation of the upper soft wall. Here, we extend the steady theory of Christov et al. (J. Fluid Mech., vol. 841, 2018, pp. 267–286) by considering the start-up flow from rest, both in pressure-controlled and in flow-rate-controlled configurations. The characteristic scales and relevant parameters governing the transient flow are first identified, followed by the development of an unsteady lubrication theory assuming that the inertia of the fluid is negligible, and that the upper wall can be modelled as an elastic plate under pure bending satisfying the Kirchhoff–Love equation. The model is governed by two non-geometrical dimensionless numbers: a compliance parameter β, which compares the characteristic displacement of the upper wall with the undeformed channel height, and a parameter γ that compares the inertia of the solid with its flexural rigidity. In the limit of negligible solid inertia, γ → 0, a quasi-steady model is developed, whereby the fluid pressure satisfies a nonlinear diffusion equation, with β as the only parameter, which admits a self-similar solution under pressure-controlled conditions. This simplified lubrication description is validated with coupled three-dimensional numerical simulations of the Navier equations for the elastic solid and the Navier–Stokes equations for the fluid. The agreement is very good when the hypotheses behind the model are satisfied. Unexpectedly, we find fair agreement even in cases where the solid and liquid inertia cannot be neglected.The authors are grateful to J. Rivero-Rodríguez and B. Scheid for key numerical advice, to I. C. Christov for pointing out a mistake in figure 2 of an earlier version of the manuscript, and to R. Zaera for helpful discussions. A.M.-C. and A.S. thank the Spanish MINECO, Subdirección General de Gestión de Ayudas a la Investigación, for its support through projects DPI2014-59292-C3-1-P and DPI2015-71901-REDT, and the Spanish MCIU-Agencia Estatal de Investigación through project DPI2017-88201- C3-3-R. These research projects have been partly financed through FEDER European funds. A.M.-C. also acknowledges support from the Spanish MECD through the grant FPU16/02562 and to its associated programme Ayudas a la Movilidad 2018 during his stay at the Complex Fluids Group in Princeton. H.A.S. thanks the NSF for support via CMMI-1661672 and through Princeton University’s Material Research Science and Engineering Center DMR-1420541.Publicad

Controlled manipulation of enzyme specificity through immobilization-induced flexibility constraints

It is thought that during immobilization enzymes, as dynamic biomolecules, may become distorted and this may alter their catalytic properties. However, the effects of different immobilization strategies on enzyme rigidity or flexibility and their consequences in specificity and stereochemistry at large scale has not been yet clearly evaluated and understood. This was here investigated by using as model an ester hydrolase, isolated from a bacterium inhabiting a karstic lake, with broad substrate spectrum (72 esters being converted; 61.5 U mg$^{-1}$ for glyceryl tripropionate) but initially non-enantiospecific. We found that the enzyme (7 nm × 4.4 nm × 4.2 nm) could be efficiently ionic exchanged inside the pores (9.3 nm under dry conditions) of amino-functionalized ordered mesoporous material (NH$_{2}$-SBA-15), achieving a protein load of 48 mg g−1, and a specific activity of 4.5 ± 0.1 U mg$^{-1}$. When the enzyme was site-directed immobilized through His interaction with an immobilized cationon the surface of two types of magnetic micro-particles through hexahistidine-tags, protein loads up to 10.2 μg g$^{-1}$ and specific activities of up to 29.9 ± 0.3 U mg$^{-1}$, were obtained. We found that ionically exchanged enzyme inside pores of NH2-SBA-15 drastically narrowed the substrate range (17 esters), to an extent much higher than ionically exchanged enzyme on the surface of magnetic micro-particles (up to 61 esters). This is attributed to differences in surface chemistry, particle size, and substrate accessibility to the active site tunnel. Our results also suggested, for the first time, that immobilization of enzymes in pores of similar size may alter the enzyme structures and produce enzyme active centers with different configuration which promote stereochemical conversions in a manner different to those arising from surface immobilization, where the strength of the ionic exchange also has an influence. This was shown by demonstrating that when the enzyme was introduced inside pores with a diameter (under dry conditions) slightly higher than that of the enzyme crystal structure a biocatalyst enantiospecific for ethyl (R)-4-chloro-3-hydroxybutyrate was produced, a feature not found when using wider pores. By contrast, immobilization on the surface of ferromagnetic microparticles produced selective biocatalysts for methyl (S)-(+)-mandelate or methyl (S)-lactate depending on the functionalization. This study illustrates the benefits of extensive analysis of the substrate spectra to better understand the effects of different immobilization strategies on enzyme flexibility/rigidity, as well as substrate specificity and stereochemistry. Our results will help to design tunable materials and interfaces for a controlled manipulation of specificity and to transform non-enantiospecific enzymes into stereo-chemically substrate promiscuous biocatalysts capable of converting multiple chiral molecules

Regulatory Design Governing Progression of Population Growth Phases in Bacteria

It has long been noted that batch cultures inoculated with resting bacteria exhibit a progression of growth phases traditionally labeled lag, exponential, pre-stationary and stationary. However, a detailed molecular description of the mechanisms controlling the transitions between these phases is lacking. A core circuit, formed by a subset of regulatory interactions involving five global transcription factors (FIS, HNS, IHF, RpoS and GadX), has been identified by correlating information from the well- established transcriptional regulatory network of Escherichia coli and genome-wide expression data from cultures in these different growth phases. We propose a functional role for this circuit in controlling progression through these phases. Two alternative hypotheses for controlling the transition between the growth phases are first, a continuous graded adjustment to changing environmental conditions, and second, a discontinuous hysteretic switch at critical thresholds between growth phases. We formulate a simple mathematical model of the core circuit, consisting of differential equations based on the power-law formalism, and show by mathematical and computer-assisted analysis that there are critical conditions among the parameters of the model that can lead to hysteretic switch behavior, which – if validated experimentally – would suggest that the transitions between different growth phases might be analogous to cellular differentiation. Based on these provocative results, we propose experiments to test the alternative hypotheses

Repulsion by Slit and Roundabout prevents Shotgun/E-cadherin–mediated cell adhesion during Drosophila heart tube lumen formation

During Drosophila melanogaster heart development, a lumen forms between apical surfaces of contralateral cardioblasts (CBs). We show that Slit and its receptor Roundabout (Robo) are required at CB apical domains for lumen formation. Mislocalization of Slit outside the apical domain causes ectopic lumen formation and the mislocalization of cell junction proteins, E-cadherin (E-Cad) and Enabled, without disrupting overall CB cell polarity. Ectopic lumen formation is suppressed in robo mutants, which indicates robo's requirement for this process. Genetic evidence suggests that Robo and Shotgun (Shg)/E-Cad function together in modulating CB adhesion. robo and shg/E-Cad transheterozygotes have lumen defects. In robo loss-of-function or shg/E-Cad gain-of-function embryos, lumen formation is blocked because of inappropriate CB adhesion and an accumulation of E-Cad at the apical membrane. In contrast, shg/E-Cad loss-of-function or robo gain-of-function blocks lumen formation due to a loss of CB adhesion. Our data show that Slit and Robo pathways function in lumen formation as a repulsive signal to antagonize E-Cad–mediated cell adhesion

Transcription of Leishmania major U2 small nuclear RNA gene is directed by extragenic sequences located within a tRNA-like and a tRNA-Ala gene

Sequence comparisons of U2 snRNA genes and flanking regions from T. cruzi (CL Brener Non-Esmeraldo-like). Sequences from the genes located on chromosomes 23, 37 and 6 are shown. The U2 snRNA gene from chromosome 23 is presented in blue font. The position of boxes A and B is indicated. Sequence numbers are relative to the TSS (+1) from the U2 snRNA. (PDF 1404 kb

Reality and causality in quantum gravity modified electrodynamics

We present a general description of the propagation properties of quantum gravity modified electrodynamics characterized by constitutive relations up to second order in the correction parameter. The effective description corresponds to an electrodynamics in a dispersive and absorptive non-local medium, where the Green functions and the refraction indices can be explicitly calculated. The reality of the electromagnetic field together with the requirement of causal propagation in a given referrence frame leads to restrictions in the form of such refraction indices. In particular, absorption must be present in all cases and, contrary to the usual assumption, it is the dominant aspect in those effective models which exhibit linear effects in the correction parameter not related to birefringence. In such a situation absorption is linear while propagation is quadratical in the correction parameter.Comment: 15 pages, LaTex, minor changes to clarify some points, version accepted for publicatio

Gene Expression in Trypanosomatid Parasites

The parasites Leishmania spp., Trypanosoma brucei, and Trypanosoma cruzi are the trypanosomatid protozoa that cause the deadly human diseases leishmaniasis, African sleeping sickness, and Chagas disease, respectively. These organisms possess unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes and trans-splicing. Little is known about either the DNA sequences or the proteins that are involved in the initiation and termination of transcription in trypanosomatids. In silico analyses of the genome databases of these parasites led to the identification of a small number of proteins involved in gene expression. However, functional studies have revealed that trypanosomatids have more general transcription factors than originally estimated. Many posttranslational histone modifications, histone variants, and chromatin modifying enzymes have been identified in trypanosomatids, and recent genome-wide studies showed that epigenetic regulation might play a very important role in gene expression in this group of parasites. Here, we review and comment on the most recent findings related to transcription initiation and termination in trypanosomatid protozoa

Peroxidase expression in a cereal cyst nematode (Heterodera avenae) resistant hexaploid wheat line.

The incompatible interaction between plant and pathogen is often determined by the hypersensitive reaction (HR). This response is associated with accumulation of reactive oxygen species (ROS), which results in adverse growth conditions for pathogens. Two major mechanisms involving either NADPH oxidases or peroxidases have been proposed for generation of ROS. Peroxidases (PER, EC 1.11.1.7), present in all land plants, are members of a large multigenic family with high number of isoforms involved in a broad range of physiological processes. PER genes, which are expressed in nematode feeding sites, have been identified in several plant species (Zacheo et al. 1997). A strong correlation between HR and PER activities at four and seven days post nematode infection, was detected in roots of wheat lines carrying Cre2, Cre5 (from Ae. ventricosa) or Cre7 (from Ae. triuncialis) Heterodera avenae resistance genes (Andrés et al. 2001; Montes et al. 2003, 2004). We have studied changes in root of peroxidase mRNAs levels after infection by H. avenae of a wheat/Ae. ven¬tricosa introgression line (H-93-8) carrying Cre2 (Delibes et al. 1993). We also report and classify the predicted protein sequences derived from complete peroxidase transcripts

High pressure effects on the activities of cathepsins B and D of mackerel and horse mackerel muscle

We determined high pressure processing (HPP) effects on the activities of cathepsins B and D in the muscles of mackerel (Scomber scombrus) and horse mackerel (Trachurus trachurus). In mackerel, the cathepsin B activity decrease reached 40% at 450 MPa while in horse mackerel, low and intermediate pressures (150 and 300 MPa) caused an activity increase (30%) but at 450 MPa a decrease of up to 60%. In both species, cathepsin D activity increased after a 300 MPa treatment (up to 2-fold for mackerel and 60% for horse mackerel) and decreased on a 450 MPa treatment. The activity increase is probably due to HPP damage of lysosome releasing enzymes into the fish muscle. Based on the HPP effects on the activities of cathepsins B and D, 450 MPa may be used to reduce the proteolytic activity of cathepsin B prior to chilled or frozen storage of these fish speciesSupported by the Xunta de Galicia, Spain Project 10TAL402001PR, 2010-2012, and FCT (Portugal), European Union, QREN, FEDER and COMPETE thorough QOPNA research unit, Project PEst-C/QUI/UI0062/2013; FCOMP-01-0124-FEDER-037296. Also supported by he USDA National Institute of Food and Agriculture, Grants No. 2011-31200-06041 and 2012-31200-06041S