Jessica Polka

Harvard Medical School | HMS · Department of Systems Biology

Movement of molecules across membranes in response to a stimulus is a key component of cellular programming. Here, we characterize and manipulate the response of a protein-based piston capable of puncturing membranes in a pH-dependent manner. Our protein actuator consists of modified R bodies found in a bacterial endosymbiont of paramecium. We expr...

The landscape of scientific research and funding is in flux as a result of tight budgets, evolving models of both publishing and evaluation, and questions about training and workforce stability. As future leaders, junior scientists are uniquely poised to shape the culture and practice of science in response to these challenges. A group of postdocs...

Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such a...

Significance Many bacteria contain large, circular DNA molecules, called plasmids, that encode physiologically, medically, and commercially important genes, including genes conferring virulence and drug resistance. The largest plasmids use active segregation systems to maintain themselves in the host bacterium. Such segregation systems provide rema...

Cyanobacteria play a significant role in the global carbon cycle. In Synechococcuselongatus, the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is concentrated into polyhedral, proteinaceous compartments called carboxysomes. Using live cell fluorescence microscopy, we show that carboxysomes are first detected as smal...

Significance Actin filaments are dynamic cytoskeletal elements that assemble upon ATP binding. Actin homologs are present in all domains of life, and all share a similar 3D structure of the assembling subunit, but evolutionary changes to the subunit have generated many different actin filament structures. The filament structure of the bacterial act...

Bacterial actins are an evolutionarily diverse family of ATP-dependent filaments built from protomers with a conserved structural fold. Actin-based segregation systems are encoded on many bacterial plasmids and function to partition plasmids into daughter cells. The bacterial actin AlfA segregates plasmids by a mechanism distinct from other partiti...

Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme RuBisCO in a paracrystalline lattice, making it possible for these organisms to fix CO2 from the atmosphere. The protein responsible for th...

Bacteria of the genus Prosthecobacter express homologs of eukaryotic α-and β-tubulin, called BtubA and BtubB, that have been observed to assemble into bacterial microtubules (bMTs). The btubAB genes likely entered the Prosthecobacter lineage via horizontal gene transfer and may derive from an early ancestor of the modern eukaryotic microtubule (MT)...

Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme RuBisCO in a paracrystalline lattice, making it possible for these organisms to fix CO 2 from the atmosphere. The protein responsible for t...

Subcellular organization is critical for isolating, concentrating, and protecting biological activities. Natural subcellular organization is often achieved using colocalization of proteins on scaffold molecules, thereby enhancing metabolic fluxes and enabling coregulation. Synthetic scaffolds extend these benefits to new biological processes and ar...

Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biolo...

Subcellular organization is critical for isolating, concentrating, and protecting biological activities. Natural subcellular organization is often achieved using co-localization of proteins on scaffold molecules, thereby enhancing metabolic fluxes and enabling co-regulation. Synthetic scaffolds extend these benefits to new biological processes, and...

The refractile (R) bodies found in Caedibacter taeniospiralis, a bacterial endosymbiont of Paramecium tetraurelia, are large, polymeric protein structures that can switch between two conformations. At cytoplasmic pH, they resemble coiled ribbons of protein 500nm in diameter. At low pH, they extend to form hollow needles up to 20 microns long. They...

There is a common misconception that the United States is suffering from a "STEM shortage," a dearth of graduates with scientific, technological, engineering, and mathematical backgrounds. In biomedical science, however, we are likely suffering from the opposite problem and could certainly better tailor training to actual career outcomes. At the Fu...

Taking as a statement of fact that academic research requires rescue (Alberts et al. 2014), the question is now how change can be effected. Alberts et al. made the call for early career researchers (ECRs), such as graduate students and postdoctoral researchers, to make their voices heard. We have previously advocated for ECRs contributing to the co...

This section dedicated to makers brings together a wide range of people who give their own tour through the world of making. In "Why Scientists Should Make," by Jun Axup, "What Do I Make?," by AnnMarie Thomas, "Adults Are the Future," by Ariel Waldman, "Women Who Make: Undercounted as Makers and Underwhelmed by Maker Spaces," by Susan Faulkner, "A...

The landscape of scientific research and funding is in flux as a result of tight budgets, evolving models of both publishing and evaluation, and questions about training and workforce stability. As future leaders, junior scientists are uniquely poised to shape the culture and practice of science in response to these challenges. A group of postdocs...

scientific enterprise is facing a series of challenges that are directly impacting the careers of young researchers. In response to concerns expressed by senior researchers and policy-makers, and to begin the involvement of young researchers in the discussion, the Future of Research Symposium was held in Boston in October 2014. Through a series of...

The scientific enterprise is facing a series of challenges that will directly impact the careers of postdocs both presently and in the future. A growing body of literature and correspondence highlights the concerns that are felt by many senior researchers and policy-makers in the academic and wider research community. However, the involvement of...

Bacteria from several taxa, including Kurthia zopfii , Myxococcus xanthus , and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such...

Bacteria from several taxa, including Kurthia zopfii , Myxococcus xanthus , and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such...

Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such a...

Bacterial from several taxa, including Kurthia zopfii , Myxococcus xanthus , and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, suc...

Bacterial from several taxa, including Kurthia zopfii , Myxococcus xanthus , and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, suc...

Graduate students must educate themselves and others about academia's dim job prospects, says Jessica Polka.

Organizing this symposium was a tremendous learning process for all of us. Here, we record the process we used, and the guidelines we'd follow (or not!) if we were to do it all over again. We hope they're helpful to junior scientists looking to organize meetings of any kind, but especially those dealing with systemic issues affecting the research e...

The elaborate spatial organization of cells enhances, restricts, and regulates protein-protein interactions. However, the biological significance of this organization has been difficult to study without ways of directly perturbing it. We highlight synthetic biology tools for engineering novel cellular organization, describing how they have been, an...

Bar carboxysomes colocalize with shell but are not oxidized. (A) Bar carboxysomes contain both RuBisCO and shell protein. Red, CcmK4-GFP. Green, RbcL-mOrange. Scale bar, 1µm. (B) Bar carboxysomes are relatively reduced compared to punctate carboxysomes. Still frame composite images of 488nm (reducing, green) and 408nm (oxidizing, purple) RbcL-roGFP...

Additional shell protein assembly data. (A–C) Individual traces of the fluorescence intensity of CcmK4 foci. Each panel represents a different cell, and only shell foci in the process of assembling are represented. Time interval: 5 minutes. (TIF)

Nascent, reduced carboxysomes oxidize as they mature. Oxidation events occur 2 seconds after the appearance of a white asterisk ~1µm above the relevant carboxysome. Imaging was initiated ~24 hours after induction. Green: 488Ex RbcL-roGFP1. Magenta: 410Ex RbcL-roGFP1. Scale bar, 2µm. Frame rate, 7 frames (10 minute)/second. (AVI)

Additional bar carboxysome FRAP data. Bleaching events are indicated by grey lines. Unbleached portions of the bar were used to correct for photobleaching. (TIFF)

Normal and bar carboxysomes are born from replicative events. Division events occur 2 seconds after the appearance of a white asterisk ~2µm above the relevant carboxysome. Imaging was initiated ~1 hour after induction. Green: RbcL-GFP. Red: phase contrast. Scale bar, 2µm. Frame rate, 12 frames (5 minute)/second. (AVI)

Shell protein is late to localize to RuBisCO assemblies. Shell localization events occur 2 seconds after the appearance of a white asterisk ~1µm above the relevant carboxysome. The top-most highlighted carboxysome also nucleates a daughter at the 12 hour mark. Imaging was initiated ~3 hours after induction. Green: RbcL-mOrange. Red: CcmK4-GFP. Scal...

Mean and maximum velocities of carboxysome motion. 126 carboxysomes were tracked over a minimum of 85 frames, and the mean and maximum velocity of each track quantified. (A) The tracks overlaid on one frame of the movie. Different colors represent different tracks. (B) The mean of the mean carboxysome velocity is 11.5nm/minute. (C) The mean of the...

Eubacteria and archaea contain a variety of actin-like proteins (ALPs) that form filaments with surprisingly diverse architectures, assembly dynamics, and cellular functions. Although there is much data supporting differences between ALP families, there is little data regarding conservation of structure and function within these families. We asked...

Microtubules are nucleated in vivo by gamma-tubulin complexes. The 300-kDa gamma-tubulin small complex (gamma-TuSC), consisting of two molecules of gamma-tubulin and one copy each of the accessory proteins Spc97 and Spc98, is the conserved, essential core of the microtubule nucleating machinery. In metazoa multiple gamma-TuSCs assemble with other p...

Bacterial cytoskeletal proteins participate in a variety of processes, including cell division and DNA segregation. Polymerization of one plasmid-encoded, actin-like protein, ParM, segregates DNA by pushing two plasmids in opposite directions and forms the current paradigm for understanding active plasmid segregation. An essential feature of ParM a...

Kinetochores are proteinaceous assemblies that mediate the interaction of chromosomes with the mitotic spindle. The 180 kDa Ndc80 complex is a direct point of contact between kinetochores and microtubules. Its four subunits contain coiled coils and form an elongated rod structure with functional globular domains at either end. We crystallized an en...