Micro- and nanofluidic technologies for epigenetic profiling

This short review provides an overview of the impact micro- and nanotechnologies can make in studying epigenetic structures. The importance of mapping histone modifications on chromatin prompts us to highlight the complexities and challenges associated with histone mapping, as compared to DNA sequencing. First, the histone code comprised over 30 variations, compared to 4 nucleotides for DNA. Second, whereas DNA can be amplified using polymerase chain reaction, chromatin cannot be amplified, creating challenges in obtaining sufficient material for analysis. Third, while every person has only a single genome, there exist multiple epigenomes in cells of different types and origins. Finally, we summarize existing technologies for performing these types of analyses. Although there are still relatively few examples of micro- and nanofluidic technologies for chromatin analysis, the unique advantages of using such technologies to address inherent challenges in epigenetic studies, such as limited sample material, complex readouts, and the need for high-content screens, make this an area of significant growth and opportunity.     

Responses of endothelial cells to extremely slow flows

The process of blood vessel formation is accompanied by very minimal flow in the beginning, followed by increased flow rates once the vessel develops sufficiently. Many studies have been performed for endothelial cells at shear stress levels of 0.1-60 dyn∕cm(2); however, little is known about the effect of extremely slow flows (shear stress levels of 10(-4)-10(-2) dyn∕cm(2)) that endothelial cells may experience during early blood vessel formation where flow-sensing by indirect mass transport sensing rather than through mechanoreceptor sensing mechanisms would become more important. Here, we show that extremely low flows enhance proliferation, adherens junction protein localization, and nitric oxide secretion of endothelial cells, but do not induce actin filament reorganization. The responses of endothelial cells in different flow microenvironments need more attention because increasing evidence shows that endothelial cell behaviors at the extremely slow flow regimes cannot be linearly extrapolated from observations at faster flow rates. The devices and methods described here provide a useful platform for such studies.     

A microfluidic model to study fluid dynamics of mucus plug rupture in small lung airways

Fluid dynamics of mucus plug rupture is important to understand mucus clearance in lung airways and potential effects of mucus plug rupture on epithelial cells at lung airway walls. We established a microfluidic model to study mucus plug rupture in a collapsed airway of the 12th generation. Mucus plugs were simulated using Carbopol 940 (C940) gels at concentrations of 0.15%, 0.2%, 0.25%, and 0.3%, which have non-Newtonian properties close to healthy and diseased lung mucus. The airway was modeled with a polydimethylsiloxane microfluidic channel. Plug motion was driven by pressurized air. Global strain rates and shear stress were defined to quantitatively describe plug deformation and rupture. Results show that a plug needs to overcome yield stress before deformation and rupture. The plug takes relatively long time to yield at the high Bingham number. Plug length shortening is the more significant deformation than shearing at gel concentration higher than 0.15%. Although strain rates increase dramatically at rupture, the transient shear stress drops due to the shear-thinning effect of the C940 gels. Dimensionless time-averaged shear stress, T_xy, linearly increases from 3.7 to 5.6 times the Bingham number as the Bingham number varies from 0.018 to 0.1. The dimensionless time-averaged shear rate simply equals to T_xy/2. In dimension, shear stress magnitude is about one order lower than the pressure drop, and one order higher than yield stress. Mucus with high yield stress leads to high shear stress, and therefore would be more likely to cause epithelial cell damage. Crackling sounds produced with plug rupture might be more detectable for gels with higher concentration.     

High-throughput single-cell manipulation system for a large number of target cells

A sequential and high-throughput single-cell manipulation system for a large volume of cells was developed and the successive manipulation for single cell involving single-cell isolation, individual labeling, and individual rupture was realized in a microhydrodynamic flow channel fabricated by using two-dimensional simple flow channels. This microfluidic system consisted of the successive single-cell handlings of single-cell isolation from a large number of cells in cell suspension, labeling each isolated single cell and the lysate extraction from each labeled single cell. This microfluidic system was composed of main channels, cell-trapping pockets, drain channels, and single-cell content collection channels which were fabricated by polydimethylsiloxane. We demonstrated two kinds of prototypes for sequential single-cell manipulations, one was equipped with 16 single-cell isolation pockets in microchannel and the other was constructed of 512 single-cell isolation pockets. In this study, we demonstrated high-throughput and high-volume single-cell isolation with 512 pocket type device. The total number of isolated single cells in each isolation pocket from the cell suspension at a time was 426 for the cell line of African green monkey kidney, COS-1, and 360 for the rat primary brown preadipocytes, BAT. All isolated cells were stained with fluorescence dye injected into the same microchannel successfully. In addition, the extraction and collection of the cell contents was demonstrated using isolated stained COS-1 cells. The cell contents extracted from each captured cell were individually collected within each collection channel by local hydrodynamic flow. The sequential trapping, labeling, and content extraction with 512 pocket type devices realized high-throughput single-cell manipulations for innovative single-cell handling, feasible staining, and accurate cell rupture.     

Individual differences and course attendance: why do students skip class?

Individual differences are theorised as being key predictors of students’ lecture attendance. Understanding students’ (lack of) motivation for studying is an essential first step in supporting these individual differences and potentially increasing class/lecture attendance. The current study explored the role of students’ deficits in motivations (ability/effort/task value) for studying and their predictive relationship with course attendance, while controlling for prior competence and academic self-concept. Second-year students (n = 219; Female = 40) undertaking three semester-long courses in English as a foreign language participated in the year-long study. The structural model tested included prior achievement and self-concept (Time-1; 15 weeks prior), the motivational deficits for studying in the course (Time-2; ability, effort and task value), and class attendance across the two semesters of study. Self-concept negatively predicted all motivational deficits (moderate-large effects), and positively predicted attendance. Two of the motivational deficits (ability and effort) also had strongly contrasting effects (positive and negative respectively) on attendance. The implications and practical suggestions for intervention are discussed.     

Electronic journals and their unbundled functions in scholarly communication: Views and utilization by scientific,technological and medical researchers in Japan

In recent years, electronic journals are in common use in scholarly communication and we can interpret this situation in various ways. On the one hand, we can say that scholarly communication is now much dependent on electronic resources. On the other hand, it would be too simplistic to say that scholarly communication is now greatly dependent on electronic resources because researchers seldom use other electronic resources. The purpose of this article is to show the position of electronic journals in scholarly communication based on Japanese researchers’ information behavior and estimation. The main focus is on distinguishing the function of scholarly journal and the electronic form. A questionnaire was sent to 1427 physicists, 1026 chemists and 1276 pathologists in universities and other research institutes all over Japan, of whom 775 (54.3%), 494 (48.1%) and 541 (42.4%), respectively, supplied answers. The main results are as follows. Japanese researchers in STM fields use electronic journals as a matter of course, and other electronic resources to some extent, for accessing information; but this shift to electronic resources seemed to be not a transformation but a modification of traditional patterns of use. Researchers still rely on traditional scholarly journals for accessing information and publication, although their recognition has begun to change.