Genetic requirements for cell division in a genomically minimal cell.

Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. Although this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics that result in irregular morphologies. A genome with 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents morphology similar to that of JCVI-syn1.0. We further identified seven of these 19 genes, including two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, which are required together to restore a phenotype similar to that of JCVI-syn1.0. This result emphasizes the polygenic nature of cell division and morphology in a genomically minimal cell.

Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer.

Prostate cancer is the second leading cause of cancer death in men in the developed world. A more sensitive and specific detection strategy for lethal prostate cancer beyond serum prostate specific antigen (PSA) population screening is urgently needed. Diagnosis by canine olfaction, using dogs trained to detect cancer by smell, has been shown to be both specific and sensitive. While dogs themselves are impractical as scalable diagnostic sensors, machine olfaction for cancer detection is testable. However, studies bridging the divide between clinical diagnostic techniques, artificial intelligence, and molecular analysis remains difficult due to the significant divide between these disciplines. We tested the clinical feasibility of a cross-disciplinary, integrative approach to early prostate cancer biosensing in urine using trained canine olfaction, volatile organic compound (VOC) analysis by gas chromatography-mass spectroscopy (GC-MS) artificial neural network (ANN)-assisted examination, and microbial profiling in a double-blinded pilot study. Two dogs were trained to detect Gleason 9 prostate cancer in urine collected from biopsy-confirmed patients. Biopsy-negative controls were used to assess canine specificity as prostate cancer biodetectors. Urine samples were simultaneously analyzed for their VOC content in headspace via GC-MS and urinary microbiota content via 16S rDNA Illumina sequencing. In addition, the dogs' diagnoses were used to train an ANN to detect significant peaks in the GC-MS data. The canine olfaction system was 71% sensitive and between 70-76% specific at detecting Gleason 9 prostate cancer. We have also confirmed VOC differences by GC-MS and microbiota differences by 16S rDNA sequencing between cancer positive and biopsy-negative controls. Furthermore, the trained ANN identified regions of interest in the GC-MS data, informed by the canine diagnoses. Methodology and feasibility are established to inform larger-scale studies using canine olfaction, urinary VOCs, and urinary microbiota profiling to develop machine olfaction diagnostic tools. Scalable multi-disciplinary tools may then be compared to PSA screening for earlier, non-invasive, more specific and sensitive detection of clinically aggressive prostate cancers in urine samples.

Machine learning metrology of cell confinement in melt electrowritten three-dimensional biomaterial substrates.

Tuning cell shape by altering the biophysical properties of biomaterial substrates on which cells operate would provide a potential shape-driven pathway to control cell phenotype. However, there is an unexplored dimensional scale window of three-dimensional (3D) substrates with precisely tunable porous microarchitectures and geometrical feature sizes at the cell's operating length scales (10-100 µm). This paper demonstrates the fabrication of such high-fidelity fibrous substrates using a melt electrowriting (MEW) technique. This advanced manufacturing approach is biologically qualified with a metrology framework that models and classifies cell confinement states under various substrate dimensionalities and architectures. Using fibroblasts as a model cell system, the mechanosensing response of adherent cells is investigated as a function of variable substrate dimensionality (2D vs. 3D) and porous microarchitecture (randomly oriented, "non-woven" vs. precision-stacked, "woven"). Single-cell confinement states are modeled using confocal fluorescence microscopy in conjunction with an automated single-cell bioimage data analysis workflow that extracts quantitative metrics of the whole cell and sub-cellular focal adhesion protein features measured. The extracted multidimensional dataset is employed to train a machine learning algorithm to classify cell shape phenotypes. The results show that cells assume distinct confinement states that are enforced by the prescribed substrate dimensionalities and porous microarchitectures with the woven MEW substrates promoting the highest cell shape homogeneity compared to non-woven fibrous substrates. The technology platform established here constitutes a significant step towards the development of integrated additive manufacturing-metrology platforms for a wide range of applications including fundamental mechanobiology studies and 3D bioprinting of tissue constructs to yield specific biological designs qualified at the single-cell level.

Evolthon: A community endeavor to evolve lab evolution.

In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stress-low temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation.

Self-assembled photosystem-I biophotovoltaics on nanostructured TiO(2 )and ZnO.

The abundant pigment-protein membrane complex photosystem-I (PS-I) is at the heart of the Earth's energy cycle. It is the central molecule in the "Z-scheme" of photosynthesis, converting sunlight into the chemical energy of life. Commandeering this intricately organized photosynthetic nanocircuitry and re-wiring it to produce electricity carries the promise of inexpensive and environmentally friendly solar power. We here report that dry PS-I stabilized by surfactant peptides functioned as both the light-harvester and charge separator in solar cells self-assembled on nanostructured semiconductors. Contrary to previous attempts at biophotovoltaics requiring elaborate surface chemistries, thin film deposition, and illumination concentrated into narrow wavelength ranges the devices described here are straightforward and inexpensive to fabricate and perform well under standard sunlight yielding open circuit photovoltage of 0.5 V, fill factor of 71%, electrical power density of 81 µW/cm(2) and photocurrent density of 362 µA/cm(2), over four orders of magnitude higher than any photosystem-based biophotovoltaic to date.

Molecular vibration-sensing component in Drosophila melanogaster olfaction.

A common explanation of molecular recognition by the olfactory system posits that receptors recognize the structure or shape of the odorant molecule. We performed a rigorous test of shape recognition by replacing hydrogen with deuterium in odorants and asking whether Drosophila melanogaster can distinguish these identically shaped isotopes. We report that flies not only differentiate between isotopic odorants, but can be conditioned to selectively avoid the common or the deuterated isotope. Furthermore, flies trained to discriminate against the normal or deuterated isotopes of a compound, selectively avoid the corresponding isotope of a different odorant. Finally, flies trained to avoid a deuterated compound exhibit selective aversion to an unrelated molecule with a vibrational mode in the energy range of the carbon-deuterium stretch. These findings are inconsistent with a shape-only model for smell, and instead support the existence of a molecular vibration-sensing component to olfactory reception.

Source of sustained voltage difference between the xylem of a potted Ficus benjamina tree and its soil.

It has long been known that there is a sustained electrical potential (voltage) difference between the xylem of many plants and their surrounding soil, but the mechanism behind this voltage has remained controversial. After eliminating any extraneous capacitive or inductive couplings and ground-mediated electric current flows, we have measured sustained differences of 50-200 mV between the xylem region of a Faraday-caged, intact, potted Ficus benjamina tree and its soil, as well as between its cut branches and soils and ionic solutions standardized to various pH values. Using identical platinum electrodes, no correlation between the voltage and time of day, illumination, sap flow, electrode elevation, or ionic composition of soil was found, suggesting no direct connection to simple dissimilar-metal redox reactions or transpirational activity. Instead, a clear relationship between the voltage polarity and magnitude and the pH difference between xylem and soil was observed. We attribute these sustained voltages to a biological concentration cell likely set up by the homeostatic mechanisms of the tree. Potential applications of this finding are briefly explored.

Impedance spectroscopy of alpha-beta tubulin heterodimer suspensions.

Impedance spectroscopy is a technique that reveals information, such as macromolecular charges and related properties about protein suspensions and other materials. Here we report on impedance measurements over the frequency range of 1 Hz to 1 MHz of alpha-beta tubulin heterodimers suspended in a buffer. These and other polyelectrolyte suspensions show enormous dielectric responses at low frequencies, due both to the motion of charges suspended in the medium and to an electrical double layer that forms at each electrode-medium interface. We propose an equivalent circuit model to minimize electrode polarization effects and extract the intrinsic response of the bulk medium. At megaHertz frequencies, the conductivity increases with concentration below the critical concentration of approximately 1 mg/ml for microtubule polymerization, above which the conductivity decreases. This suggests that such measurements can be used to monitor the dynamics of microtubule polymerization. Finally, we obtain the net charge number per tubulin dimer of /Z/ = 306 in the saline buffer, which, if maintained as the dimers polymerized, would yield a linear charge density of 3.8 e/angstroms for the assembled microtubules. These results are potentially important for fundamental electrostatic processes in biomolecules and suggest the possibility of developing future bioelectronic applications.

Effect of varying electric potential on surface-plasmon resonance sensing.

The high sensitivity of surface-plasmon resonance (SPR) sensors allows measurements of small variations in surface potentials to be made. We studied the changes of the SPR angle when an oscillating electric potential was applied to a gold film on which surface plasmons were excited. The shifts of the SPR resonance angle were observed for various aqueous solutions as an adjacent medium. A model that takes into account the redistribution of charges at the double layer near the metal-liquid interface as well as the oxidation of the gold film was developed. It was found that a change in the electronic density at voltages below the oxidation potential and, in addition, the oxidation of the gold surface above this potential are the main mechanisms that account for the observed dependences. It was shown that relatively slow oxidation-reduction processes can explain the observed hysteresis effect. Application of these techniques to studies of dielectric properties and conformational changes of polar biomolecules, such as tubulin, are discussed.

Learning and memory deficits upon TAU accumulation in Drosophila mushroom body neurons.

Mutations in the neuronal-specific microtubule-binding protein TAU are associated with several dementias and neurodegenerative diseases. However, the effects of elevated TAU accumulation on behavioral plasticity are unknown. We report that directed expression of wild-type vertebrate and Drosophila TAU in adult mushroom body neurons, centers for olfactory learning and memory in Drosophila, strongly compromised associative olfactory learning and memory, but olfactory conditioning-relevant osmotactic and mechanosensory responses remained intact. In addition, TAU accumulation in mushroom body neurons did not result in detectable neurodegeneration or premature death. Therefore, TAU-mediated structural or functional perturbation of the microtubular cytoskeleton in mushroom body neurons is likely causal of the behavioral deficit. These results indicate that behavioral plasticity decrements may be the earliest detectable manifestations of tauopathies.