Zhang J, Winkler JR, Gray HB, Hunter BM. Mechanism of Nickel-Iron Water Oxidation Electrocatalysts [Internet]. ACS energy& fuels 2021; Publisher's VersionAbstract
Hotly debated these days is whether nickel or iron is the active site in nickel–iron water oxidation electrocatalysts. We have previously argued that iron is a likely candidate for highly active materials because it can reach high-oxidation (high-ox) states at potentials relevant to water splitting. Here, we further assert that nickel is likely not an active site for water oxidation electrocatalysis in these materials. Our 3-fold argument is supported by electrochemical measurements on rigorously planar electrodes produced by pulsed laser ablation in liquids: (1) nickel cannot achieve high-ox states in aqueous environments at relevant potentials; (2) large steady-state concentrations of metal sites preclude them from being active, thereby indicating that even more oxidizing moieties are critically important; and (3) unlike nickel sites, high-ox iron sites documented experimentally are neither rare nor unreasonably reactive.
Grognot M, Mittal A, Mah'Moud M, Taute KM. Vibrio cholerae motility in aquatic and mucus-mimicking environments [Internet]. AMS Journals, Applied and Environmental Microbiology 2021; Publisher's VersionAbstract
Cholera disease is caused by Vibrio cholerae infecting the lining of the small intestine and results in severe diarrhea. V. cholerae’s swimming motility is known to play a crucial role in pathogenicity and may aid the bacteria in crossing the intestinal mucus barrier to reach sites of infection, but the exact mechanisms are unknown. The cell can be either pushed or pulled by its single polar flagellum, but there is no consensus on the resulting repertoire of motility behaviors.
We use high-throughput 3D bacterial tracking to observe V. cholerae swimming in buffer, in viscous solutions of the synthetic polymer PVP, and in mucin solutions that may mimic the host environment. We perform a statistical characterization of its motility behavior on the basis of large 3D trajectory datasets. We find that V. cholerae performs asymmetric run-reverse-flick motility, consisting of a sequence of a forward run, reversal, and a shorter backward run, followed by a turn by approximately 90°, called a flick, preceding the next forward run. Unlike many run-reverse-flick swimmers, V. cholerae’s backward runs are much shorter than its forward runs, resulting in an increased effective diffusivity. We also find that the swimming speed is not constant, but subject to frequent decreases. The turning frequency in mucin matches that observed in buffer. Run-reverse-flick motility and speed fluctuations are present in all environments studied, suggesting that these behaviors may also occur in natural aquatic habitats as well as the host environment.
Grognot M, Taute KM. A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms [Internet]. Communications Biology 2021;4 Publisher's VersionAbstract
How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.
Dittmer J, Brucker RM. When your host shuts down: larval diapause impacts host-microbiome interaction in Nasonia vitripennis [Internet]. Microbiome 2021;9 Publisher's VersionAbstract


The life cycles of many insect species include an obligatory or facultative diapause stage with arrested development and low metabolic activity as an overwintering strategy. Diapause is characterised by profound physiological changes in endocrine activity, cell proliferation and nutrient metabolism. However, little is known regarding host-microbiome interactions during diapause, despite the importance of bacterial symbionts for host nutrition and development. In this work, we investigated (i) the role of the microbiome for host nutrient allocation during diapause and (ii) the impact of larval diapause on microbiome dynamics in the parasitoid wasp Nasonia vitripennis, a model organism for host-microbiome interactions.


Our results demonstrate that the microbiome is essential for host nutrient allocation during diapause in N. vitripennis, as axenic diapausing larvae had consistently lower glucose and glycerol levels than conventional diapausing larvae, especially when exposed to cold temperature. In turn, microbiome composition was altered in diapausing larvae, potentially due to changes in the surrounding temperature, host nutrient levels and a downregulation of host immune genes. Importantly, prolonged larval diapause had a transstadial effect on the adult microbiome, with unknown consequences for host fitness. Notably, the most dominant microbiome member, Providencia sp., was drastically reduced in adults after more than 4 months of larval diapause, while potential bacterial pathogens increased in abundance.


This work investigates host-microbiome interactions during a crucial developmental stage, which challenges both the insect host and its microbial associates. The impact of diapause on the microbiome is likely due to several factors, including altered host regulatory mechanisms and changes in the host environment.

Grognot M, Taute KM. More than propellers: how flagella shape bacterial motility behaviors [Internet]. Current Opinion in Microbiology 2021;61(June 2021):73-81. Publisher's VersionAbstract
Bacteria use a wide variety of flagellar architectures to navigate their environment. While the iconic run-tumble motility strategy of the peritrichously flagellated Escherichia coli has been well studied, recent work has revealed a variety of new motility behaviors that can be achieved with different flagellar architectures, such as single, bundled, or opposing polar flagella. The recent discovery of various flagellar gymnastics such as flicking and flagellar wrapping is increasingly shifting the view from flagella as passive propellers to versatile appendages that can be used in a wide range of conformations. Here, we review recent observations of how flagella shape motility behaviors and summarize the nascent structure-function map linking flagellation and behavior.
Tao Y. Forging Aspirant Undergraduate Scientists and Engineers into Steller Researchers [Internet]. Matter 2020;3(5):1383-1386. Publisher's Version tao_matter_op-ed.pdf
Trepka K, Hauert R, Cancellieri C, Tao Y. A Robust Metal Oxide Thin Film with Saturation Magnetization Exceeding 2 Telsa [Internet]. SSRN 2020; Publisher's VersionAbstract
High saturation magnetization, hysteresis-less long linear response range, and resistance to devicefabrication conditions are figures of merit for magnetic materials in science and technology.Despite advances in materials research, many high-saturating micro- and nanomagnetic materialsare hysteresis-prone, have short linear ranges, and are sensitive to oxidation, resulting in deviceinefficiencies in high-frequency electronics and unpredictable responses in magnetic sensing applications.Holmium oxide is a promising material because of its high magnetic susceptibility,but synthetic options are limited, with low-temperature magnetism incompletely characterized.Here, we present physical vapor deposition synthesis and material characterization of polycrystallineholmium oxide thin films. The product has saturation magnetization exceeding 2 Tesla,linear range (μ0H) also exceeding 2 Tesla, zero magnetic remanence and coercivity, and resistanceto harsh processing conditions including oxygen plasma and concentrated hydrofluoricacid etching, making these thin films ideal for fabricating next-generation nanoscale magneticdevices in advanced scientific and engineering applications.
Trepka K, Tao Y. Magnetic characterization of rare-earth oxide nanoparticles [Internet]. Applied Physics Letters 2020;117(12) Publisher's VersionAbstract
High saturation magnetization and hysteresis-less magnetic responses are desirable for nanoparticles in scientific and technological applications. Rare-earth oxides are potentially promising materials because of their paramagnetism and high magnetic susceptibility in the bulk, but the magnetic properties of their nanoparticles remain incompletely characterized. Here, we present full M–H loops for commercial RE2O3 nanoparticles (RE = Er, Gd, Dy, Ho) with radii from 10–25 nm at room temperature and 4 K. The magnetic responses are consistent with two distinct populations of atoms, one displaying the ideal Re3+ magnetic moment and the other displaying a sub-ideal magnetic moment. If all sub-ideal ions are taken to be on the surface, the data are consistent with ≈2−10" id="MathJax-Element-1-Frame" role="presentation" style="border-bottom-color:currentColor;border-bottom-style:none;border-bottom-width:0px;border-image-outset:0;border-image-repeat:stretch;border-image-slice:100%;border-image-source:none;border-image-width:1;border-left-color:currentColor;border-left-style:none;border-left-width:0px;border-right-color:currentColor;border-right-style:none;border-right-width:0px;border-top-color:currentColor;border-top-style:none;border-top-width:0px;direction:ltr;display:inline;float:none;100%;none;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;margin-bottom:0px;margin-left:0px;margin-right:0px;margin-top:0px;max-height:none;max-width:none;min-height:0px;min-width:0px;overflow-wrap:normal;padding-bottom:0px;padding-left:0px;padding-right:2px;padding-top:0px;position:relative;text-align:left;text-indent:0px;text-transform:none;white-space:nowrap;word-spacing:normal;" tabindex="0">210≈2−10 nm surface layers of reduced magnetization. The magnetization of the rare-earth oxide nanoparticles at low temperatures (1.3–1.9 T) exceeds that of the best iron-based nanoparticles, making rare-earth oxides candidates for use in next-generation cryogenic magnetic devices that demand a combination of hysteresis-less response and high magnetization.
This work was supported by a Rowland Fellowship to Y.T. K.T. acknowledges support from the Rowland Institute and the Harvard Office of Undergraduate Research and Fellowships. The authors would like to thank Shaw Huang for assistance with SQUID and all group members for helpful discussions. SEM sample characterization studies were carried out at the Center for Nanoscale Systems (CNS) at Harvard University.
Kurtz DA, Rossman GR, Hunter BM. The Nature of the Mn(III) Color Centers in Elbaite Tourmalines [Internet]. Inorganic Chemistry 2020;59(14):9618-9626. Publisher's VersionAbstract
The characteristic red color of many natural tourmalines is due to the presence of Mn(III) cations substituting for aluminum and lithium. These sites originate as Mn(II) and are oxidized by natural γ-irradiation over geologic time as they sit in the Earth’s crust. Presented here is a thorough analysis of the spin-allowed and spin-forbidden transitions which give rise to the color of these gemstones. Ligand field analysis, supplemented by time-dependent density functional theory, was used to correct the historical assignments of the symmetry-allowed transitions in the polarized UV–visible absorption spectrum. Heat-induced reduction of the oxidized manganese sites provided a probe of the relationship between the spin-allowed and spin-forbidden bands. Notably, the intensity of the spin-forbidden transition was highly dependent on the neighboring ions in the Y-site. Simulations and modeling showed that increased intensity was observed only when two Mn(III) ions occupied adjacent substitutions in the Y-site via a proposed exchange-coupling mechanism.
Gude S, Pinçe E, Taute KM, Seinen A-B, Shimizu TS, Tans SJ. Bacterial coexistence driven by motility and spatial competition [Internet]. Nature 2020;(578):588-592. Publisher's VersionAbstract
Elucidating elementary mechanisms that underlie bacterial diversity is central to ecology1,2 and microbiome research3. Bacteria are known to coexist by metabolic specialization4, cooperation5 and cyclic warfare6,7,8. Many species are also motile9, which is studied in terms of mechanism10,11, benefit12,13, strategy14,15, evolution16,17 and ecology18,19. Indeed, bacteria often compete for nutrient patches that become available periodically or by random disturbances2,20,21. However, the role of bacterial motility in coexistence remains unexplored experimentally. Here we show that—for mixed bacterial populations that colonize nutrient patches—either population outcompetes the other when low in relative abundance. This inversion of the competitive hierarchy is caused by active segregation and spatial exclusion within the patch: a small fast-moving population can outcompete a large fast-growing population by impeding its migration into the patch, while a small fast-growing population can outcompete a large fast-moving population by expelling it from the initial contact area. The resulting spatial segregation is lost for weak growth–migration trade-offs and a lack of virgin space, but is robust to population ratio, density and chemotactic ability, and is observed in both laboratory and wild strains. These findings show that motility differences and their trade-offs with growth are sufficient to promote diversity, and suggest previously undescribed roles for motility in niche formation and collective expulsion–containment strategies beyond individual search and survival.
Wang G-H, Berdy BM, Velasquez O, Jovanovic N, Alkhalifa S, Minibiole KPC, Brucker R. Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticides Exposure [Internet]. Cell Host & Microbe 2020;(27):213-224. Publisher's VersionAbstract

The gut is a first point of contact with ingested xeno- biotics, where chemicals are metabolized directly by the host or microbiota. Atrazine is a widely used pesticide, but the role of the microbiome metabolism of this xenobiotic and the impact on host responses is unclear. We exposed successive generations of the wasp Nasonia vitripennis to subtoxic levels of atrazine and observed changes in the structure and function of the gut microbiome that conveyed atra- zine resistance. This microbiome-mediated resis- tance was maternally inherited and increased over successive generations, while also heightening the rate of host genome selection. The rare gut bacteria Serratia marcescens and Pseudomonas protegens contributed to atrazine metabolism. Both of these bacteria contain genes that are linked to atrazine degradation and were sufficient to confer resistance in experimental wasp populations. Thus, pesticide exposure causes functional, inherited changes in the microbiome that should be considered when as- sessing xenobiotic exposure and as potential coun- termeasures to toxicity. 

Mathis MW, Mathis A. Deep learning tools for the measurement of animal behavior in neuroscience [Internet]. Current Opinion in Neurobiology 2020;60:1-11. Publisher's VersionAbstract
Recent advances in computer vision have made accurate, fast and robust measurement of animal behavior a reality. In the past years powerful tools specifically designed to aid the measurement of behavior have come to fruition. Here we discuss how capturing the postures of animals — pose estimation - has been rapidly advancing with new deep learning methods. While challenges still remain, we envision that the fast-paced development of new deep learning tools will rapidly change the landscape of realizable real-world neuroscience.
Sayler RI, Hunter BM, Fu W, Gray HB, Britt RD. EPR spectroscopy of iron- and nickel-doped [ZnAI]-layered double hydroxides: modeling active sites in heterogenous water oxidation catalysts [Internet]. Journal of the American Chemical Society 2019; Publisher's VersionAbstract
Iron-doped nickel layered double hydroxides (LDHs) are among the most active heterogeneous water oxidation catalysts. Due to inter-spin interactions, however, the high density of magnetic centers results in line-broadening in magnetic resonance spectra. As a result, gaining atomic-level insight into the catalytic mechanism via electron paramagnetic resonance (EPR) is not generally possible. To circumvent spin-spin broadening, iron and nickel atoms were doped into non-magnetic [ZnAl]-LDH materials and the coordination environments of the isolated Fe(III) and Ni(II) sites were characterized. Multifrequency EPR spectroscopy identified two distinct Fe(III) sites (S = 5/2) in [Fe:ZnAl]-LDH. Changes in zero field splitting (ZFS) were induced by dehydration of the material, revealing that one of the Fe(III) sites is solvent-exposed (i.e. at an edge, corner, or defect site). These solvent-exposed sites feature an axial ZFS of 0.21 cm-1 when hydrated. The ZFS increases dramatically upon dehydration (to -1.5 cm-1), owing to lower symmetry and a decrease in the coordination number of iron. The ZFS of the other (“inert”) Fe(III) site maintains an axial ZFS of 0.19-0.20 cm-1 under both hydrated and dehydrated conditions. We observed a similar effect in [Ni:ZnAl]-LDH materials; notably, Ni(II) (S = 1) atoms displayed a single, small ZFS (±0.30 cm-1) in hydrated material, whereas two distinct Ni(II) ZFS values (±0.30 and ±1.1 cm-1) were observed in the dehydrated samples. Although the magnetically-dilute materials were not active catalysts, the identification of model sites in which the coordination environments of iron and nickel were particularly labile (e.g. by simple vacuum drying) is an important step towards identifying sites in which the coordination number may drop spontaneously in water, a probable mechanism of water oxidation in functional materials.
Marques JC, Li M, Schaak D, Robson DN, Li JM. Internal state dynamics shape brained activity and foraging behavior [Internet]. Nature 2019;(577):239-243. Publisher's VersionAbstract
The brain has persistent internal states that can modulate every aspect of an animal’s mental experience1,2,3,4. In complex tasks such as foraging, the internal state is dynamic5,6,7,8Caenorhabditis elegans alternate between local search and global dispersal5. Rodents and primates exhibit trade-offs between exploitation and exploration6,7. However, fundamental questions remain about how persistent states are maintained in the brain, which upstream networks drive state transitions and how state-encoding neurons exert neuromodulatory effects on sensory perception and decision-making to govern appropriate behaviour. Here, using tracking microscopy to monitor whole-brain neuronal activity at cellular resolution in freely moving zebrafish larvae9, we show that zebrafish spontaneously alternate between two persistent internal states during foraging for live prey (Paramecia). In the exploitation state, the animal inhibits locomotion and promotes hunting, generating small, localized trajectories. In the exploration state, the animal promotes locomotion and suppresses hunting, generating long-ranging trajectories that enhance spatial dispersion. We uncover a dorsal raphe subpopulation with persistent activity that robustly encodes the exploitation state. The exploitation-state-encoding neurons, together with a multimodal trigger network that is associated with state transitions, form a stochastically activated nonlinear dynamical system. The activity of this oscillatory network correlates with a global retuning of sensorimotor transformations during foraging that leads to marked changes in both the motivation to hunt for prey and the accuracy of motor sequences during hunting. This work reveals an important hidden variable that shapes the temporal structure of motivation and decision-making.
Pun AB, Sanders SN, Sfeir MY, Campos LM, Congreve DN. Annihilator dimers enhance triplet fusion upconversion [Internet]. Chemical Science 2019;10(14):3969-3975. Publisher's VersionAbstract
Optical upconversion is a net process by which two low energy photons are converted into one higher energy photon. There is vast potential to exploit upconversion in applications ranging from solar energy and biological imaging to data storage and photocatalysis. Here, we link two upconverting chromophores together to synthesize a series of novel tetracene dimers for use as annihilators. When compared with the monomer annihilator, TIPS–tetracene, the dimers yield a strong enhancement in the triplet fusion process, also known as triplet–triplet annihilation, as demonstrated via a large increase in upconversion efficiency and an order of magnitude reduction of the threshold power for maximum yield. Along with the ongoing rapid improvements to sensitizer materials, the dimerization improvements demonstrated here open the way to a wide variety of emerging upconversion applications.
Sanders SN, Gangishetty MK, Sfeir MY, Congreve DN. Photon Upconversion in Aqueous Nanodroplets [Internet]. Journal of the American Chemical Society 2019;141(23):9180-9184. Publisher's VersionAbstract
Triplet fusion upconversion, the conversion of two low-energy photons into one higher-energy photon via excitonic intermediates, has the potential to revolutionize fields as diverse as biological imaging, photovoltaics, and optogenetics. However, important hurdles to widespread application still exist; for example, the vast majority of demonstrations are in nonpolar solvents, limiting applications. Furthermore, the necessary high concentrations of dyes limit optical penetration depth. Efforts toward aqueous solutions utilizing micelles and other nanoencapsulants have been limited by poor efficiencies or scatter from the nanoparticles. Here, we demonstrate a facile micellular fabrication method that drives a high boiling point solvent into the core of a block copolymer micelle, greatly reducing molecular aggregation. We show that this simple preparation is scalable and provides benefits across five different colors of photon upconversion. We expect this simple, user-friendly, and high-performance system to aid a multitude of photon upconversion applications, in particular, for optogenetics, photodynamic therapy, and photochemistry.
Nath T, Mathis A, Chen AC, Bethge M, Mathis MW. Using DeepLabCut for 3D markerless pose estimation across species and behaviors [Internet]. Nature Protocols 2019; Publisher's VersionAbstract
Noninvasive behavioral tracking of animals during experiments is critical to many scientific pursuits. Extracting the poses of animals without using markers is often essential to measuring behavioral effects in biomechanics, genetics, ethology, and neuroscience. However, extracting detailed poses without markers in dynamically changing backgrounds has been challenging. We recently introduced an open-source toolbox called DeepLabCut that builds on a state-of-the-art human pose-estimation algorithm to allow a user to train a deep neural network with limited training data to precisely track user-defined features that match human labeling accuracy. Here, we provide an updated toolbox, developed as a Python package, that includes new features such as graphical user interfaces (GUIs), performance improvements, and active-learning-based network refinement. We provide a step-by-step procedure for using DeepLabCut that guides the user in creating a tailored, reusable analysis pipeline with a graphical processing unit (GPU) in 1–12 h (depending on frame size). Additionally, we provide Docker environments and Jupyter Notebooks that can be run on cloud resources such as Google Colaboratory.
Gangishetty MK, Sanders SN, Congreve DN. Mn2+ Doping Enhances the Brightness, Efficiency, and Stability of Bulk Perovskite Light-Emitting Diodes [Internet]. ACS Photonics 2019;6(5):1111-1117. Publisher's VersionAbstract
Interest in organic–inorganic hybrid perovskite (ABX3) LEDs has exploded over the past several years, yet significant gains in stability, efficiency, and brightness are required before commercialization is possible, particularly for blue devices. The perovskite composition has been shown to play a crucial role in its performance, yet to date nearly all existing reports focus on tuning the A-site composition. Here, we find that doping the B-site with manganese allows us to achieve bright, efficient, and stable LEDs regardless of A or X composition. By doping with Mn, we demonstrate ultrabright sky-blue, green, and red perovskite LEDs with a maximum brightness of 11800, 97000, and 1470 cd/m2 and quantum efficiencies of 0.58%, 3.2%, and 5.1%, respectively. Crucially, these devices show excellent operational stability, with the sky-blue devices lasting for 20 min and red devices over 5 h with strong spectral stability. Moreover, the green devices showed over 1% efficiency even at higher current densities, ∼2000 mA/cm2. Mn doping allows for universal improvement in perovskite performance and stability, opening the door to a huge number of applications.
Pun AB, Campos LM, Congreve DN. Tunable Emission from Triplet Fusion Upconversion in Diketopyrrolopyrroles [Internet]. Journal of the American Chemical Society 2019; Publisher's VersionAbstract
Optical upconversion based on triplet fusion (TF), also known as triplet–triplet annihilation, is a process by which two or more low-energy photons are converted to one higher energy photon. This process requires two components, a sensitizer which absorbs the incident low-energy photons and an annihilator which emits the higher energy photons. While much attention has been given to the investigation of new types of sensitizers, very little work has been done on the exploration of new annihilators. In this work, we show that the singlet energy of diketopyrrolopyrroles (DPPs) can be altered by modifying the pendant aryl substituents to the core. This allows us to meet the energetic requirements necessary for TF upconversion and demonstrates DPPs as a new class of annihilator molecules. Using this new DPP platform, the output wavelength from upconversion can easily be tuned, which will greatly diversify the number of applications of DPPs in upconversion technologies.
Ravetz BD, Pun AB, Churchill EM, Congreve DN, Rovis T, Campos LM. Photoredox catalysis using infrared light via triplet fusion up conversion [Internet]. Nature 2019;565:343-346. Publisher's VersionAbstract
Recent advances in photoredox catalysis have made it possible to achieve various challenging synthetic transformations, polymerizations and surface modifications1,2,3. All of these reactions require ultraviolet- or visible-light stimuli; however, the use of visible-light irradiation has intrinsic challenges. For example, the penetration of visible light through most reaction media is very low, leading to problems in large-scale reactions. Moreover, reactants can compete with photocatalysts for the absorption of incident light, limiting the scope of the reactions. These problems can be overcome by the use of near-infrared light, which has a much higher penetration depth through various media, notably biological tissue4. Here we demonstrate various photoredox transformations under infrared radiation by utilizing the photophysical process of triplet fusion upconversion, a mechanism by which two low-energy photons are converted into a higher-energy photon. We show that this is a general strategy applicable to a wide range of photoredox reactions. We tune the upconversion components to adjust the output light, accessing both orange light and blue light from low-energy infrared light, by pairwise manipulation of the sensitizer and annihilator. We further demonstrate that the annihilator itself can be used as a photocatalyst, thus simplifying the reaction. This approach enables catalysis of high-energy transformations through several opaque barriers using low-energy infrared light.