Hydrodynamic dispersion in long microchannels under conditions of electroosmotic circulation: II. Electrolytes

This work describes the steady-state transport of an electrolyte due to a stationary concentration difference in straight long channels under conditions of electroosmotic circulation. The electroosmotic flow is induced due to the slip produced at the charged channel walls. This flow is assumed to be compensated by a pressure-driven counterflow so that the net volume flow through the channel is exactly zero. Owing to the concentration dependence of electroosmotic slip, there is an involved coupling between the solute transfer, hydrodynamic flow and charge conservation. Nevertheless, for such a system the Taylor–Aris dispersion (TAD) theory is shown to be approximately applicable locally within an inner part of the channel for a wide range of Péclet numbers (Pe) irrespective of the concentration difference. Numerical simulations reveal only small deviations from analytical solutions for the inner part of the channel. The breakdown of TAD theory occurs within boundary regions near the channel ends and is related to the variation of the dispersion mechanism from the purely molecular diffusion at the channel ends to the hydrodynamic dispersion within the inner part of the channel. This boundary region is larger at the lower-concentration channel edge and its size increases nearly linearly with Pe number. It is possible to derive a simple analytical approximation for the inner profile of cross-section-averaged electrolyte concentration in terms of only few parameters, determined numerically. Such analytical approximations can be useful for experimental studies of concentration polarization phenomena in long microchannels.Peer ReviewedPostprint (author's final draft

Asymmetric electroosmotic pumping across porous media sandwiched with perforated ion-exchange membranes

To have non-zero net flow in AC electroosmotic pumps, the electroosmosis (EO) has to be non-linear and asymmetric. This can be achieved due to ionic concentration polarization. This is known to occur close to micro-/nano-interfaces provided that the sizes of the nanopores are not too large compared to the Debye screening length. However, operation of the corresponding EO pumps can be quite sensitive to the solution concentration and, thus, unstable in practical applications. Concentration polarization of ion-exchange membranes is much more robust. However, the hydraulic permeability of the membrane is very low, which makes EO flows through them extremely small. This communication shows theoretically how this problem can be resolved via making scarce microscopic perforations in an ion-exchange membrane and putting it in series with an EO-active nano-porous medium. The problem of coupled flow, concentration and electrostatic-potential distributions is solved numerically by using finite-element methods. This analysis reveals that even quite scarce perforations of micron-scale diameters are sufficient to observe practically-interesting EO flows in the system. If the average distance between the perforations is smaller than the thickness of the EO-active layer, there is an effective homogenization of the electrolyte concentration and hydrostatic pressure in the lateral direction at some distance from the interface. The simulations show this distance to be somewhat lower than the half-distance between the perforations. On the other hand, when the surface fraction of perforations is sufficiently small (below a fraction of a percent) this “homogeneous” concentration is considerably reduced (or increased, depending on the current direction), which makes the EO strongly non-linear and asymmetric. This analysis provides initial guidance for the design of high-productivity and inexpensive AC electroosmotic pumps.Peer ReviewedPostprint (published version

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer

MHC class II-alpha chain knockout mice support increased viral replication that is independent of their lack of MHC class II cell surface expression and associated immune function deficiencies

MHCII molecules are heterodimeric cell surface proteins composed of an α and β chain. These molecules are almost exclusively expressed on thymic epithelium and antigen presenting cells (APCs) and play a central role in the development and function of CD4 T cells. Various MHC-II knockout mice have been generated including MHC-IIAα-/- (I-Aα-/-), MHC-IIAβ-/- (I-β-/-) and the double knockout (I-Aαxβ-/-). Here we report a very striking observation, namely that alphaviruses including the avirulent strain of Semliki Forest virus (aSFV), which causes asymptomatic infection in wild-type C57BL6/J (B6) mice, causes a very acute and lethal infection in I-Aα-/-, but not in I-β-/- or I-Aαxβ-/-, mice. This susceptibility to aSFV is associated with high virus titres in muscle, spleen, liver, and brain compared to B6 mice. In addition, I-Aα-/- mice show intact IFN-I responses in terms of IFN-I serum levels and IFN-I receptor expression and function. Radiation bone marrow chimeras of B6 mice reconstituted with I-Aα-/- bone marrow expressed B6 phenotype, whereas radiation chimeras of I-Aα-/- mice reconstituted with B6 bone marrow expressed the phenotype of high viral susceptibility. Virus replication experiments both in vivo and in vitro showed enhanced virus growth in tissues and cell cultures derived form I-Aα-/- compared to B6 mice. This enhanced virus replication is evident for other alpha-, flavi- and poxviruses and may be of great benefit to producers of viral vaccines. In conclusion, I-Aα-/- mice exhibit a striking susceptibility to virus infections independent of their defective MHC-II expression. Detailed genetic analysis will be carried out to characterise the underlining genetic defects responsible for the observed phenomenon.Mohammed Alsharifi, Aulikki Koskinen, Danushka K. Wijesundara, Jayaram Bettadapura, Arno Müllbache

Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA

Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy1. The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study2. A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy

Hydrodynamic dispersion in long microchannels under conditions of electroosmotic circulation: II. Electrolytes

This work describes the steady-state transport of an electrolyte due to a stationary concentration difference in straight long channels under conditions of electroosmotic circulation. The electroosmotic flow is induced due to the slip produced at the charged channel walls. This flow is assumed to be compensated by a pressure-driven counterflow so that the net volume flow through the channel is exactly zero. Owing to the concentration dependence of electroosmotic slip, there is an involved coupling between the solute transfer, hydrodynamic flow and charge conservation. Nevertheless, for such a system the Taylor–Aris dispersion (TAD) theory is shown to be approximately applicable locally within an inner part of the channel for a wide range of Péclet numbers (Pe) irrespective of the concentration difference. Numerical simulations reveal only small deviations from analytical solutions for the inner part of the channel. The breakdown of TAD theory occurs within boundary regions near the channel ends and is related to the variation of the dispersion mechanism from the purely molecular diffusion at the channel ends to the hydrodynamic dispersion within the inner part of the channel. This boundary region is larger at the lower-concentration channel edge and its size increases nearly linearly with Pe number. It is possible to derive a simple analytical approximation for the inner profile of cross-section-averaged electrolyte concentration in terms of only few parameters, determined numerically. Such analytical approximations can be useful for experimental studies of concentration polarization phenomena in long microchannels.Peer Reviewe

Asymmetric electroosmotic pumping across porous media sandwiched with perforated ion-exchange membranes

To have non-zero net flow in AC electroosmotic pumps, the electroosmosis (EO) has to be non-linear and asymmetric. This can be achieved due to ionic concentration polarization. This is known to occur close to micro-/nano-interfaces provided that the sizes of the nanopores are not too large compared to the Debye screening length. However, operation of the corresponding EO pumps can be quite sensitive to the solution concentration and, thus, unstable in practical applications. Concentration polarization of ion-exchange membranes is much more robust. However, the hydraulic permeability of the membrane is very low, which makes EO flows through them extremely small. This communication shows theoretically how this problem can be resolved via making scarce microscopic perforations in an ion-exchange membrane and putting it in series with an EO-active nano-porous medium. The problem of coupled flow, concentration and electrostatic-potential distributions is solved numerically by using finite-element methods. This analysis reveals that even quite scarce perforations of micron-scale diameters are sufficient to observe practically-interesting EO flows in the system. If the average distance between the perforations is smaller than the thickness of the EO-active layer, there is an effective homogenization of the electrolyte concentration and hydrostatic pressure in the lateral direction at some distance from the interface. The simulations show this distance to be somewhat lower than the half-distance between the perforations. On the other hand, when the surface fraction of perforations is sufficiently small (below a fraction of a percent) this “homogeneous” concentration is considerably reduced (or increased, depending on the current direction), which makes the EO strongly non-linear and asymmetric. This analysis provides initial guidance for the design of high-productivity and inexpensive AC electroosmotic pumps.Peer Reviewe

Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression

The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous. Several prognostic factors have been identified that can stratify patients into groups that differ in their relative tendency for disease progression and/or survival. Here, we pursued a subnetwork-based analysis of gene expression profiles to discriminate between groups of patients with disparate risks for CLL progression. From an initial cohort of 130 patients, we identified 38 prognostic subnetworks that could predict the relative risk for disease progression requiring therapy from the time of sample collection, more accurately than established markers. The prognostic power of these subnetworks then was validated on 2 other cohorts of patients. We noted reduced divergence in gene expression between leukemia cells of CLL patients classified at diagnosis with aggressive versus indolent disease over time. The predictive subnetworks vary in levels of expression over time but exhibit increased similarity at later time points before therapy, suggesting that degenerate pathways apparently converge into common pathways that are associated with disease progression. As such, these results have implications for understanding cancer evolution and for the development of novel treatment strategies for patients with CLL. (Blood. 2012; 120(13):2639-2649