Hunting Novel Viruses in a Lab Course

Last Fall the Biology department mounted a new course (BIOL 152B),  the Virus Hunter Lab. This course combines practical experience in the lab with computer based approaches in bioinformatics. Students in the class isolated a type of virus that infects bacteria called a bacteriophage. In the wet lab, they learned basic microbiology techniques for isolating the viruses and basic molecular biology techniques for extracting the DNA of the viral genomes. With the biological material in hand the class prepared next generation sequencing libraries. The students assembled and annotated the complete genome of two previously unknown bacteriophage using next generation sequencing data from the samples they prepared. To find out more about it you can read their paper. Grad students Meghan Harris (MCB), their TA, and Tereasa Ho (Biotechnology) along with the inaugural group of undergraduate students are all authors on a paper recently published in the journal Microbiology Resource Announcements (MRA).

Harris MT, Ho TC, Fruchtman H, Garin ME, Kubatin V, Lu T, Xue L, Marr MT. Complete Genome Sequences of Two Vibrio natriegens Bacteriophages. Microbiology Resource Announcements. 2020;9(45).

Electron microscope image of the novel bacteriophage (VH2), photo by Jesse Cochrane

A new twist on interfacial tension

In a mixture of two molecular components, the surface tension is defined as the energetic cost per unit area of moving molecules from the bulk and bringing them to the interface. The higher the magnitude of the surface tension, the greater the tendency of two components to demix. Surface tension allows trees to carry nutrients from the roots out to the branches, and water striders to walk on the surface of water.

The interface between hydrophobic and hydrophilic components has very high interfacial tension. A common way to adjust the magnitude of surface tension is to add amphiphilic molecules (like soaps), which contain both hydrophilic and hydrophobic components. These amphiphilic molecules prefer to be at the interface between the two components, and effectively lower the interfacial tension, allowing the components to mix more easily. This is how detergent causes oily stains to dissolve in water.

In a recently published article in Nature, an interdisciplinary team of researchers at Brandeis headed by Zvonimir Dogic, and consisting of experimental, theoretical, and computational physicists as well as biologists, has demonstrated a new way of controlling interfacial tension using a molecular property called chirality, or lack of mirror symmetry. The study was performed on a model system of two-dimensional colloidal membranes composed of the rod-like bacteriophage virus fd, which are about one micrometer in length and 7 nanometers in diameter. The electrostatically repulsive virus particles are condensed into membranes through the depletion mechanism by adding non-adsorbing polymer to a virus suspension. Because the fd rods are chiral, they tend to twist by a small angle with respect to neighboring rods. However, the geometry of the membrane prevents twisting in the structure’s interior; only along the perimeter can the rods twist. Thus, increasing the strength of chirality of the rods both lowers the energy of the rods along the membrane’s edge and increases the frustration of untwisted rods in the bulk, lowering the interfacial tension. This contrasts the standard method of controlling interfacial tension using amphiphilic molecules, since the rod-like particles are completely homogenous, and do not contain any hydrophilic components.

The strength of chiral interactions in fd is temperature sensitive; the rods are achiral at 60o C, and the strength of chirality increases with decreasing temperature. By increasing the strength of chiral interactions in-situ, the team of researchers was able to dynamically vary the membrane’s interfacial tension in order to drive a dramatic transition from a membrane to several twisted ribbon structures (Movie 1). The twisted ribbons have much more interfacial area than the membranes, but are much “twistier” structures, and are therefore favored when the strength of chirality is relatively high. Additionally, the team was able to drive the same membrane-to-ribbon transition using optical tweezers, as shown in Movie 2. Membranes and ribbons are only two of a myriad of structures that were observed in the fd system. This work presents a powerful new method to control the assembly of materials by tuning interfacial tension with chirality.

Barry and Dogic receive 2010 Cozzarelli Prize

Physics graduate student Edward Barry and Professor Zvonimir Dogic have been selected to receive the 2010 Cozzarelli Prize in Engineering and Applied Sciences from the Proceedings of the National Academy of Sciences (PNAS) for their work entitled “Entropy driven self-assembly of non-amphiphilic colloidal membranes.”

The work of Barry and Dogic was selected for exploring a novel pathway for the self-assembly of 2D fluid-like surfaces or monolayer membranes from non-amphiphilic molecules. Amphiphilic molecules consist of immiscible components, such as a hydrophobic tail and a hydrophilic head, which are irreversibly linked to each other, thus frustrating their bulk separation. When added to water, these molecules self-assemble into a variety of structures in order to satisfy competing affinities for the solvent. One particular structure, a bilayer membrane, which is a thin flexible sheet with remarkable mechanical and chemical properties, plays an essential role in biology, physics, and material science. Over the past decade the paramount example of conventional amphiphilic self-assembly has inspired the synthesis of numerous amphiphilic-type building blocks for studies of membrane self-assembly including various block-copolymers, heterogeneous nanorods, and hybrid protein-polymer complexes. Underlying all of these studies is the belief that amphiphilic molecules are an essential requirement for membrane assembly.

Barry and Dogic, using a combination of theory and experiments, describe for the first time a set of design principles required for the assembly of non-amphiphilic membranes in which the constituent rod-like molecules are chemically homogeneous.  Using a simple mixture of filamentous bacteriophages and non-adsorbing polymer, they were able to assemble macroscopic membranes roughly 4-5 orders of magnitude larger than the constituent molecules themselves. Due to unique properties of their system, Barry and Dogic were able to characterize the physical behavior of the resulting non-amphiphilic membranes at all relevant length scales and provide an entropic mechanism that explains their stability. The importance of these results lies in their potential to establish a fundamentally different route toward solution based self-assembly of 2D materials.

Papers selected for the Cozzarelli Prize were chosen from more than 3,700 research articles published by PNAS in 2010 and represent the six broadly defined classes under which the National Academy of Sciences is organized. The award was established in 2005 and named the Cozzarelli Prize in 2007 to honor late PNAS Editor-in-Chief Nicholas R. Cozzarelli. The annual award acknowledges recently published papers that reflect scientific excellence and originality. The 2010 awards will be presented at the PNAS Editorial Board Meeting, and awardees are recognized at the awards ceremony, during the National Academy of Sciences Annual Meeting on May 1, 2011, in National Harbor, Maryland.

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