Katharine Jensen

Global Analysis of Gene Expression: Methods, Interpretation, and Pitfalls

Over the past 15 years, global analysis of mRNA expression has emerged as a powerful strategy for biological discovery. Using the power of parallel processing, robotics, and computer-based informatics, a number of high-throughput methods have been devised. These include DNA microarrays, serial analysis of gene expression, quantitative RT-PCR, differential-display RT-PCR, and massively parallel signature sequencing. Each of these methods has inherent advantages and disadvantages, often related to expense, technical difficulty, specificity, and reliability. Further, the ability to generate large data sets of gene expression has led to new challenges in bioinformatics. Nonetheless, this technological revolution is transforming disease classification, gene discovery, and our understanding of regulatory gene networks.

Rapid growth of large, defect-free colloidal crystals

We demonstrate controlled growth of face-centered cubic (FCC), monodisperse hard-sphere colloidal crystals by centrifugation at up to 3000g onto FCC (100) templates. Such rapid deposition rates often result in an amorphous sediment. Surprisingly, however, growth onto (100) templates results only in single crystals with few or no extended defects. By contrast, deposition onto flat, (111), or (110) templates causes rapid disordering to an amorphous sediment if the dimensionless flux (particle volume fraction × Peclet number) exceeds a critical value. This crystalline-to-amorphous crossover results from the degeneracy of possible stacking positions for these orientations. No such degeneracy exists for growth onto (100). After growth, extended defects can nucleate and grow only if the crystal exceeds a critical thickness that depends on the lattice misfit with the template spacing. The experimental observations of the density of misfit dislocations are accounted for by the Frank–van der Merwe theory, adapted for the depth-dependent variation of lattice spacing and elastic constants that results from the gravitational pressure.

Note: A three-dimensional calibration device for the confocal microscope

Modern confocal microscopes enable high-precision measurement in three dimensions by collecting stacks of 2D (x-y) images that can be assembled digitally into a 3D image. It is difficult, however, to ensure position accuracy, particularly along the optical (z) axis where scanning is performed by a different physical mechanism than in x-y. We describe a simple device to calibrate simultaneously the x, y, and z pixel-to-micrometer conversion factors for a confocal microscope. By taking a known 2D pattern and positioning it at a precise angle with respect to the microscope axes, we created a 3D reference standard. The device is straightforward to construct and easy to use.

Erratum: Stiffening solids with liquid inclusions

Nature Physics 11, 82–87 (2015); published online 15 December 2014; corrected after print 8 January 2015. In the text following equation 7, the expression describing the limit where stiffening occurs was incorrect and should have read: surface tension dominates over elasticity (R ≪ ϒ/E). This has now been corrected in the online versions of the Article.

Three Dimensional Confocal Microscopy Study of Boundaries between Colloidal Crystals

Colloidal crystals were grown on flat or patterned glass slides. The structure of the grains and their defects was first visualized by 3D confocal microscopy and then characterized using simple geometric measurements. Crystals grown on a flat surface maintained a layered structure induced by the closed-packed planes. In the case of the [110] •5 grain boundary, the presence of particles in interlayer position was established.