Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation.

Directional transport of protons across an energy transducing membrane-proton pumping-is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all-trans retinal chromophore being photoisomerized to a 13-cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.

Deciphering the underlying mechanisms of the pharyngeal pumping motions in Caenorhabditis elegans.

The pharynx of the nematode Caenorhabditis elegans is a neuromuscular organ that exhibits typical pumping motions, which result in the intake of food particles from the environment. In-depth inspection reveals slightly different dynamics at the various pharyngeal areas, rather than synchronous pumping motions of the whole organ, which are important for its effective functioning. While the different pumping dynamics are well characterized, the underlying mechanisms that generate them are not known. In this study, the C. elegans pharynx was modeled in a bottom-up fashion, including all of the underlying biological processes that lead to, and including, its end function, food intake. The mathematical modeling of all processes allowed performing comprehensive, quantitative analyses of the system as a whole. Our analyses provided detailed explanations for the various pumping dynamics generated at the different pharyngeal areas; a fine-resolution description of muscle dynamics, both between and within different pharyngeal areas; a quantitative assessment of the values of many parameters of the system that are unavailable in the literature; and support for a functional role of the marginal cells, which are currently assumed to mainly have a structural role in the pharynx. In addition, our model predicted that in tiny organisms such as C. elegans, the generation of long-lasting action potentials must involve ions other than calcium. Our study exemplifies the power of mathematical models, which allow a more accurate, higher-resolution inspection of the studied system, and an easier and faster execution of in silico experiments than feasible in the lab.

New challenges for photopharmacology and computational modeling.

Mous et al. recently reported the molecular mechanism of chloride transport through a light-activated pumping rhodopsin, a key process involved in a range of cellular functions. Their results open exciting new challenges for photopharmacology and computational modeling that should be addressed in the coming years.

The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase Vo Proton Channel.

The molecular mechanism of transmembrane proton translocation in rotary motor ATPases is not fully understood. Here, we report the 3.5-Å resolution cryoEM structure of the lipid nanodisc-reconstituted Vo proton channel of the yeast vacuolar H+-ATPase, captured in a physiologically relevant, autoinhibited state. The resulting atomic model provides structural detail for the amino acids that constitute the proton pathway at the interface of the proteolipid ring and subunit a. Based on the structure and previous mutagenesis studies, we propose the chemical basis of transmembrane proton transport. Moreover, we discovered that the C terminus of the assembly factor Voa1 is an integral component of mature Vo. Voa1's C-terminal transmembrane α helix is bound inside the proteolipid ring, where it contributes to the stability of the complex. Our structure rationalizes possible mechanisms by which mutations in human Vo can result in disease phenotypes and may thus provide new avenues for therapeutic interventions.

Widespread use of proton-pumping rhodopsin in Antarctic phytoplankton.

Photosynthetic carbon (C) fixation by phytoplankton in the Southern Ocean (SO) plays a critical role in regulating air-sea exchange of carbon dioxide and thus global climate. In the SO, photosynthesis (PS) is often constrained by low iron, low temperatures, and low but highly variable light intensities. Recently, proton-pumping rhodopsins (PPRs) were identified in marine phytoplankton, providing an alternate iron-free, light-driven source of cellular energy. These proteins pump protons across cellular membranes through light absorption by the chromophore retinal, and the resulting pH energy gradient can then be used for active membrane transport or for synthesis of adenosine triphosphate. Here, we show that PPR is pervasive in Antarctic phytoplankton, especially in iron-limited regions. In a model SO diatom, we found that it was localized to the vacuolar membrane, making the vacuole a putative alternative phototrophic organelle for light-driven production of cellular energy. Unlike photosynthetic C fixation, which decreases substantially at colder temperatures, the proton transport activity of PPR was unaffected by decreasing temperature. Cellular PPR levels in cultured SO diatoms increased with decreasing iron concentrations and energy production from PPR photochemistry could substantially augment that of PS, especially under high light intensities, where PS is often photoinhibited. PPR gene expression and high retinal concentrations in phytoplankton in SO waters support its widespread use in polar environments. PPRs are an important adaptation of SO phytoplankton to growth and survival in their cold, iron-limited, and variable light environment.

Effects of hypoxic compound exercise to promote HIF-1α expression on cardiac pumping function, sleep activity behavior, and exercise capacity in Drosophila.

Alteration of HIF-1α expression levels under hypoxic conditions affects the sequence of its downstream target genes thereby producing different effects. In order to investigate whether the effect of hypoxic compound exercise (HE) on HIF-1α expression alters cardiac pumping function, myocardial structure, and exercise capacity, we developed a suitable model of hypoxic exercise using Drosophila, a model organism, and additionally investigated the effect of hypoxic compound exercise on nocturnal sleep and activity behavior. The results showed that hypoxic compound exercise at 6% oxygen concentration for five consecutive days, lasting 1 h per day, significantly improved the cardiac stress resistance of Drosophila. The hypoxic complex exercise promoted the whole-body HIF-1α expression in Drosophila, and improved the jumping ability, climbing ability, moving speed, and moving distance. The expression of HIF-1α in the heart was increased after hypoxic exercise, which made a closer arrangement of myofilaments, an increase in the diameter of cardiac tubules, and an increase in the pumping function of the heart. The hypoxic compound exercise improved the sleep quality of Drosophila by increasing its nocturnal sleep time, the number of deep sleeps, and decreasing its nocturnal awakenings and activities. Therefore, we conclude that hypoxic compound exercise promoted the expression of HIF-1α to enhance the exercise capacity and heart pumping function of Drosophila, and improved the quality of sleep.

Spontaneous phase coordination and fluid pumping in model ciliary carpets.

Ciliated tissues, such as in the mammalian lungs, brains, and reproductive tracts, are specialized to pump fluid. They generate flows by the collective activity of hundreds of thousands of individual cilia that beat in a striking metachronal wave pattern. Despite progress in analyzing cilia coordination, a general theory that links coordination and fluid pumping in the limit of large arrays of cilia remains lacking. Here, we conduct in silico experiments with thousands of hydrodynamically interacting cilia, and we develop a continuum theory in the limit of infinitely many independently beating cilia by combining tools from active matter and classical Stokes flow. We find, in both simulations and theory, that isotropic and synchronized ciliary states are unstable. Traveling waves emerge regardless of initial conditions, but the characteristics of the wave and net flows depend on cilia and tissue properties. That is, metachronal phase coordination is a stable global attractor in large ciliary carpets, even under finite perturbations to cilia and tissue properties. These results support the notion that functional specificity of ciliated tissues is interlaced with the tissue architecture and cilia beat kinematics and open up the prospect of establishing structure to function maps from cilium-level beat to tissue-level coordination and fluid pumping.

An Electrically Pumped Topological Polariton Laser.

With a seminal work of Raghu and Haldane in 2008, concepts of topology have been introduced into optical systems, where some of the most promising routes to an application are efficient and highly coherent topological lasers. While some attempts have been made to excite such structures electrically, the majority of published experiments use a form of laser excitation. In this paper, we use a lattice of vertical resonator polariton micropillars to form an exponentially localized topological Su-Schrieffer-Heeger defect. Upon electrical excitation, the system unequivocally shows polariton lasing from the topological defect using a carefully placed gold contact. Despite the presence of doping and electrical contacts, the polariton band structure clearly preserves its topological properties. At high excitation power the Mott density is exceeded, leading to highly efficient lasing in the weak coupling regime. This work is an important step toward applied topological lasers using vertical resonator microcavity structures.

Flow-dependent regulation of rat mesenteric lymphatic vessel contractile response requires activation of endothelial TRPV4 channels.

OBJECTIVES: The objective of our study is to evaluate the involvement of the transient receptor potential vanilloid 4 (TRPV4) in the alteration of lymphatic pumping in response to flow and determine the signaling pathways involved. METHODS: We used immunofluorescence imaging and western blotting to assess TRPV4 expression in rat mesenteric lymphatic vessels. We examined inhibition of TRPV4 with HC067047, nitric oxide synthase (NOS) with L-NNA and cyclooxygenases (COXs) with indomethacin on the contractile response of pressurized lymphatic vessels to flow changes induced by a stepwise increase in pressure gradients, and the functionality of endothelial TRPV4 channels by measuring the intracellular Ca2+ response of primary lymphatic endothelial cell cultures to the selective agonist GSK1016790A. RESULTS: TRPV4 protein was expressed in both the endothelial and the smooth muscle layer of rat mesenteric lymphatics with high endothelial expression around the valve sites. When maintained under constant transmural pressure, most lymphatic vessels displayed a decrease in contraction frequency under conditions of flow and this effect was ablated through inhibition of NOS, COX or TRPV4. CONCLUSIONS: Our findings demonstrate a critical role for TRPV4 in the decrease in contraction frequency induced in lymphatic vessels by increases in flow rate via the production and action of nitric oxide and dilatory prostanoids.

Directed Dual Charge Pumping Tunes the d-Orbital Configuration of Pt Cluster Boosting Hydrogen Evolution Kinetic.

Achieving high catalytic activity with a minimum amount of platinum (Pt) is crucial for accelerating the cathodic hydrogen evolution reaction (HER) in proton exchange membrane (PEM) water electrolysis, yet it remains a significant challenge. Herein, a directed dual-charge pumping strategy to tune the d-orbital electronic distribution of Pt nanoclusters for efficient HER catalysis is proposed. Theoretical analysis reveals that the ligand effect and electronic metal-support interactions (EMSI) create an effective directional electron transfer channel for the d-orbital electrons of Pt, which in turn optimizes the binding strength to H*, thereby significantly enhancing HER efficiency of the Pt site. Experimentally, this directed dual-charge pumping strategy is validated by elaborating Sb-doped SnO2 (ATO) supported Fe-doped PtSn heterostructure catalysts (Fe-PtSn/ATO). The synthesized 3%Fe-PtSn/ATO catalysts exhibit lower overpotential (requiring only 10.5 mV to reach a current density of 10 mA cm- 2), higher mass activity (28.6 times higher than commercial 20 wt.% Pt/C), and stability in the HER process in acidic media. This innovative strategy presents a promising pathway for the development of highly efficient HER catalysts with low Pt loading.

An Ion-Pumping Quasi-Solid Electrolyte Enabled by Electrokinetic Effects for Stable Aqueous Zinc Metal Batteries.

The practical application of aqueous zinc (Zn) metal batteries (ZMBs) is hindered by the complicated hydrogen evolution, passivation reactions, and dendrite growth of Zn metal anodes. Here, an ion-pumping quasi-solid electrolyte (IPQSE) with high Zn2+ transport kinetics enabled by the electrokinetic phenomena to realize high-performance quasi-solid state Zn metal batteries (QSSZMBs) is reported. The IPQSE is prepared through the in situ ring-opening polymerization of tetramethylolmethane-tri-ß-aziridinylpropionate in the aqueous electrolyte. The porous polymer framework with high zeta potential provides the IPQSE with an electrokinetic ion-pumping feature enabled by the electrokinetic effects (electro-osmosis and electrokinetic surface conduction), which significantly accelerates the Zn2+ transport, reduces the concentration polarization and overcomes the diffusion-limited current. Moreover, the Zn2+ affinity of the polymer and hydrogen bonding interactions in the IPQSE changes the Zn2+ coordination environment and reduces the amount of free H2O, which lowers the H2O activity and inhibits H2O-induced side reactions. Consequently, the highly reversible and stable Zn metal anodes are achieved. The assembled QSSZMBs based on the IPQSE display excellent cycling stability with high capacity retention and Coulombic efficiency. The high-performance quasi-solid state Zn metal pouch cells are demonstrated, showing great promise for the practical application of the IPQSE.

VUV absorption spectra of water and nitrous oxide by a double-duty differentially pumped gas filter.

The differentially pumped rare-gas filter at the end of the VUV beamline of the Swiss Light Source has been adapted to house a windowless absorption cell for gases. Absorption spectra can be recorded from 7 eV to up to 21 eV photon energies routinely, as shown by a new water and nitrous oxide absorption spectrum. By and large, the spectra agree with previously published ones both in terms of resonance energies and absorption cross sections, but that of N2O exhibits a small shift in the {\tilde{\bf D}} band and tentative fine structures that have not yet been fully described. This setup will facilitate the measurement of absorption spectra in the VUV above the absorption edge of LiF and MgF2 windows. It will also allow us to carry out condensed-phase measurements on thin liquid sheets and solid films. Further development options are discussed, including the recording of temperature-dependent absorption spectra, a stationary gas cell for calibration measurements, and the improvement of the photon energy resolution.

Molecular Dynamics Study of Protein Aggregation at Moving Interfaces.

Repeated compression and dilation of a protein film adsorbed to an interface lead to aggregation and entry of film fragments into the bulk. This is a major mechanism for protein aggregate formation in drug products upon mechanical stress, such as shaking or pumping. To gain a better understanding of these events, we developed a molecular dynamics (MD) setup, which would, in a later stage, allow for in silico formulation optimization. In contrast to previous approaches, the molecules of our model protein human growth hormone displayed realistic shapes, surfaces, and interactions with each other and the interface. This enabled quantitative assessment of protein cluster formation. Simulation outcomes aligned with experimental data on subvisible particles and turbidity, thereby validating the model. Computational and experimental results indicated that compression speed does not affect the aggregation behavior of preformed protein films but rather their regeneration. Protein clusters that formed during compression disassembled upon relaxation, suggesting that the particles originate from a partly compressed state. Desorption studies via steered MD revealed that proteins from compressed systems are more likely to detach as clusters, implying that compression effects at the interface translate into aggregates present in the bulk solution. With the possibility of studying the impact of different variables upon compression and dilation at the interface on a molecular level, our model contributes to the understanding of the mechanisms of protein aggregation at moving interfaces. It also enables further studies to change formulation parameters, interfaces, or proteins.

Understanding lactation policies and resources across a university system: survey and document review.

BACKGROUND: In the U.S., employees often return to work within 8-12 weeks of giving birth, therefore, it is critical that workplaces provide support for employees combining breastfeeding and work. The Affordable Care Act requires any organization with more than 50 employees to provide a space other than a restroom to express breastmilk and a reasonable amount of time during the workday to do so. States and worksites differ in the implementation of ACA requirements and may or may not provide additional support for employees combining breastfeeding and work. The purpose of this study was to conduct an analysis of the policies and resources available at 26 institutions within a state university system to support breastfeeding when employees return to work after giving birth. METHODS: Survey data was collected from Well-being Liaisons in the human resources departments at each institution. In addition, we conducted a document review of policies and online materials at each institution. We used univariate statistics to summarize survey results and an inductive and deductive thematic analysis to analyze institutional resources available on websites and in policies provided by the liaisons. RESULTS: A total of 18 (65.3%) liaisons participated in the study and revealed an overall lack of familiarity with the policies in place and inconsistencies in the resources offered to breastfeeding employees across the university system. Only half of the participating liaisons reported a formal breastfeeding policy was in place on their campus. From the document review, six major themes were identified: placing the burden on employees, describing pregnancy or postpartum as a "disability," having a university-specific policy, inclusion of break times for breastfeeding, supervisor responsibility, and information on lactation policies. CONCLUSION: The review of each institution's online resources confirmed the survey findings and highlighted the burden placed on employees to discover the available resources and advocate for their needs. This paper provides insight into how institutions support breastfeeding employees and provides implications on strategies to develop policies at universities to improve breastfeeding access for working parents.

Mixed uncertainty analysis on pumping by peristaltic hearts using Dempster-Shafer theory.

In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster-Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief functions. With three representative probability distributions consistent with the belief structure, global sensitivity analysis has also been implemented to identify important uncertain factors and the results have been compared between different peristalsis models. To reduce the computational cost, physics constrained generalized polynomial chaos method is adopted to construct cheaper surrogates as approximations for the full simulation.

Characterization of organic fouling on thermal bubble-driven micro-pumps.

Thermal bubble-driven micro-pumps are an upcoming micro-actuator technology that can be directly integrated into micro/mesofluidic channels, have no moving parts, and leverage existing mass production fabrication approaches. These micro-pumps consist of a high-power micro-resistor that boils fluid in microseconds to create a high-pressure vapor bubble which performs mechanical work. As such, these micro-pumps hold great promise for micro/mesofluidic systems such as lab-on-a-chip technologies. However, to date, no current work has studied the interaction of these micro-pumps with biofluids such as blood and protein-rich fluids. In this study, the effects of organic fouling due to egg albumin and bovine whole blood are characterized using stroboscopic high-speed imaging and a custom deep learning neural network based on transfer learning of RESNET-18. It was found that the growth of a fouling film inhibited vapor bubble formation. A new metric to quantify the extent of fouling was proposed using the decrease in vapor bubble area as a function of the number of micro-pump firing events. Fouling due to egg albumin and bovine whole blood was found to significantly degrade pump performance as well as the lifetime of thermal bubble-driven micro-pumps to less than 104 firings, which may necessitate the use of protective thin film coatings to prevent the buildup of a fouling layer.

From the 'black box' to 'domino effect' mechanism: what have we learned from the structures of respiratory complex I.

My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant 'black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm ('domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.

Time intervals between pumping did not affect breastmilk protein produced by mothers of preterm infants.

AIM: Few studies investigate factors that might influence the content of expressed breastmilk. This study aims to investigate the influence of the intervals between breastmilk pumping and the time of the day on protein and fat concentration in breastmilk. METHODS: Mothers of very preterm infants in a neonatal ward who expressed more than 400 mL per day were included. Expressed breastmilk was obtained from each mother over 30 h who were pumping at strictly planned and varying intervals: 2, 3, 4 and 6 h. All samples were analysed using infrared transmission spectroscopy. RESULTS: Ten mothers participated at a median of 22 days postpartum. A total of 176 milk samples were analysed, and the average protein and fat concentrations in g/100 mL were 1.1 ± 0.23 and 4.2 ± 1.3, respectively. The time intervals between breast pumping sessions did not impact protein content, but fat content decreased by longer intervals (p < 0.01). The time of the day for milk pumping did not influence the protein or fat content. CONCLUSION: A single milk sample collected after any 2-6 h interval, at any time during the day, represents the protein content in the breastmilk, but not the fat content which decreased with longer intervals.

Maternal Work and Infant Feeding Practices in the First 6 Months.

OBJECTIVES: The purpose of this study was to examine the relationship between maternal work and infant feeding practices and explore the moderating impact of parental stress. METHODS: Prospective data on categorical hours worked and infant feeding practices were collected at 3 and 6 months postpartum in a prospective prenatal cohort of 95 women. Chi-square tests were used to compare change in proportion of exclusive breastfeeding from birth to 6 months and maternal work status. RESULTS: Rates of exclusive breastfeeding significantly decreased from birth to 6 months, while the percent of mothers working outside of the home significantly increased from 3 to 6 months. At 6 months, mothers who worked full time pumped significantly more than their non-working counterparts. Multivariate logistic regression models were used to test the prediction of exclusive breastfeeding by maternal work, including sociodemographic covariates, and the moderating impact of parental stress. Results indicated that maternal education, paternal education, and maternal work significantly predicted exclusive breastfeeding at 6 months. Full time work (OR = 0.09, 95% CI = 0.01, 0.62) was associated with a decreased odds of exclusive breastfeeding. Additionally, higher maternal (OR = 1.44, 95% CI = 1.05, 1.97) and paternal (OR = 1.28, 95% CI = 1.00, 1.66) education was associated with an increased odds of exclusive breastfeeding. Maternal stress did not predict exclusive breastfeeding, nor did it have a moderating effect on the relationship between maternal work and breastfeeding. CONCLUSIONS FOR PRACTICE: Future studies should investigate maternal work in more diverse birthing populations to better understand how families can incorporate breastfeeding as a primary infant feeding practice.

O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism.

Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-µs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.